Items where Subject is "gene expression"

Paper

Abeshouse, A., Ahn, J., Akbani, R., Ally, A., Amin, S., Andry, C. D., Annala, M., Aprikian, A., Armenia, J., Arora, A., Auman, J. T., Balasundaram, M., Balu, S., Barbieri, C. E., Bauer, T., Benz, C. C., Bergeron, A., Beroukhim, R., Berrios, M., Bivol, A., Bodenheimer, T., Boice, L., Bootwalla, M. S., Borges Dos Reis, R., Boutros, P. C., Bowen, J., Bowlby, R., Boyd, J., Bradley, R. K., Breggia, A., Brimo, F., Bristow, C. A., Brooks, D., Broom, B. M., Bryce, A. H., Bubley, G., Burks, E., Butterfield, Y. S. N., Button, M., Canes, D., Carlotti, C. G., Carlsen, R., Carmel, M., Carroll, P. R., Carter, S. L., Cartun, R., Carver, B. S., Chan, J. M., Chang, M. T., Chen, Y., Cherniack, A. D., Chevalier, S., Chin, L., Cho, J., Chu, A., Chuah, E., Chudamani, S., Cibulskis, K., Ciriello, G., Clarke, A., Cooperberg, M. R., Corcoran, N. M., Costello, A. J., Cowan, J., Crain, D., Curley, E., David, K., Demchok, J. A., Demichelis, F., Dhalla, N., Dhir, R., Doueik, A., Drake, B., Dvinge, H., Dyakova, N., Felau, I., Ferguson, M. L., Frazer, S., Freedland, S., Fu, Y., Gabriel, S. B., Gao, J., Gardner, J., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Gerstein, M. B., Getz, G., Godwin, A. K., Gopalan, A., Graefen, M., Graim, K., Gribbin, T., Guin, R., Gupta, M., Hadjipanayis, A., Haider, S., Hamel, L., Hayes, D. N., Heiman, D. I., Hess, J., Hoadley, K. A., Holbrook, A. H., Holt, R. A., Holway, A., Hovens, C. M., Hoyle, A. P., Huang, M., Hutter, C. M., Ittmann, M., Iype, L., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Juhl, H., Kahles, A., Kane, C. J., Kasaian, K., Kerger, M., Khurana, E., Kim, J., Klein, R. J., Kucherlapati, R., Lacombe, L., Ladanyi, M., Lai, P. H., Laird, P. W., Lander, E. S., Latour, M., Lawrence, M. S., Lau, K., Lebien, T., Lee, D., Lee, S., Lehmann, K. V., Leraas, K. M., Leshchiner, I., Leung, R., Libertino, J. A., Lichtenberg, T. M., Lin, P., Linehan, W. M., Ling, S., Lippman, S. M., Liu, J., Liu, W., Lochovsky, L., Loda, M., Logothetis, C., Lolla, L., Longacre, T., Lu, Y., Luo, J., Ma, Y., Mahadeshwar, H. S., Mallery, D., Mariamidze, A., Marra, M. A., Mayo, M., McCall, S., McKercher, G., Meng, S., Mes-Masson, A. M., Merino, M. J., Meyerson, M., Mieczkowski, P. A., Mills, G. B., Shaw, K. R. M., Minner, S., Moinzadeh, A., Moore, R. A., Morris, S., Morrison, C., Mose, L. E., Mungall, A. J., Murray, B. A., Myers, J. B., Naresh, R., Nelson, J., Nelson, M. A., Nelson, P. S., Newton, Y., Noble, M. S., Noushmehr, H., Nykter, M., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Paulauskis, J., Penny, R., Perou, C. M., Piché, A., Pihl, T., Pinto, P. A., Prandi, D., Protopopov, A., Ramirez, N. C., Rao, A., Rathmell, W. K., Rätsch, G., Ren, X., Reuter, V. E., Reynolds, S. M., Rhie, S. K., Rieger-Christ, K., Roach, J., Robertson, A. G., Robinson, B., Rubin, M. A., Saad, F., Sadeghi, S., Saksena, G., Saller, C., Salner, A., Sanchez-Vega, F., Sander, C., Sandusky, G., Sauter, G., Sboner, A., Scardino, P. T., Scarlata, E., Schein, J. E., Schlomm, T., Schmidt, L. S., Schultz, N., Schumacher, S. E., Seidman, J., Neder, L., Seth, S., Sharp, A., Shelton, C., Shelton, T., Shen, H., Shen, R., Sherman, M., Sheth, M., Shi, Y., Shih, J., Shmulevich, I., Simko, J., Simon, R., Simons, J. V., Sipahimalani, P., Skelly, T., Sofia, H. J., Soloway, M. G., Song, X., Sorcini, A., Sougnez, C., Stepa, S., Stewart, C., Stewart, J., Stuart, J. M., Sullivan, T. B., Sun, C., Sun, H., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Tarvin, K., Taylor, B. S., Teebagy, P., Tenggara, I., Têtu, B., Tewari, A., Thiessen, N., Thompson, T., Thorne, L. B., Tirapelli, D. P., Tomlins, S. A., Trevisan, F. A., Troncoso, P., True, L. D., Tsourlakis, M. C., Tyekucheva, S., Van Allen, E., Van Den Berg, D. J., Veluvolu, U., Verhaak, R., Vocke, C. D., Voet, D., Wan, Y., Wang, Q., Wang, W., Wang, Z., Weinhold, N., Weinstein, J. N., Weisenberger, D. J., Wilkerson, M. D., Wise, L., Witte, J., Wu, C. C., Wu, J., Wu, Y., Xu, A. W., Yadav, S. S., Yang, L., Yang, L., Yau, C., Ye, H., Yena, P., Zeng, T., Zenklusen, J. C., Zhang, H., Zhang, J., Zhang, J., Zhang, W., Zhong, Y., Zhu, K., Zmuda, E. (2015) The Molecular Taxonomy of Primary Prostate Cancer. Cell, 163 (4). pp. 1011-1025. ISSN 0092-8674

Agaram, N. P., Laquaglia, M. P., Ustun, B., Guo, T., Wong, G. C., Socci, N. D., Maki, R. G., DeMatteo, R. P., Besmer, P., Antonescu, C. R. (May 2008) Molecular characterization of pediatric gastrointestinal stromal tumors. Clin Cancer Res, 14 (10). pp. 3204-15. ISSN 1078-0432 (Print)1078-0432 (Linking)

Aguirre, A. J., Nowak, J. A., Camarda, N. D., Moffitt, R. A., Ghazani, A. A., Hazar-Rethinam, M., Raghavan, S., Kim, J., Brais, L. K., Ragon, D., Welch, M. W., Reilly, E., McCabe, D., Marini, L., Anderka, K., Helvie, K., Oliver, N., Babic, A., Da Silva, A., Nadres, B., Van Seventer, E. E., Shahzade, H. A., St Pierre, J. P., Burke, K. P., Clancy, T. E., Cleary, J. M., Doyle, L. A., Jajoo, K., McCleary, N. J., Meyerhardt, J. A., Murphy, J. E., Ng, K., Patel, A. K., Perez, K., Rosenthal, M. H., Rubinson, D. A., Ryou, M., Shapiro, G. I., Sicinska, E., Silverman, S. G., Nagy, R. J., Lanman, R. B., Knoerzer, D., Welsch, D. J., Yurgelun, M. B., Fuchs, C. S., Garraway, L. A., Getz, G., Hornick, J. L., Johnson, B. E., Kulke, M. H., Mayer, R. J., Miller, J. W., Shyn, P. B., Tuveson, D. A., Wagle, N., Yeh, J. J., Hahn, W. C., Corcoran, R. B., Carter, S. L., Wolpin, B. M. (June 2018) Real-time genomic characterization of advanced pancreatic cancer to enable precision medicine. Cancer Discov, 8 (9). pp. 1096-1111. ISSN 2159-8274

Ahola, H., Stenlund, A., Moreno-Lopez, J., Pettersson, U. (May 1983) Sequences of bovine papillomavirus type 1 DNA--functional and evolutionary implications. Nucleic Acids Res, 11 (9). pp. 2639-50. ISSN 0305-1048 (Print)0305-1048 (Linking)

Alexander, Katherine A, García-García, María J (January 2019) Imprinted gene expression at the Dlk1-Dio3 cluster is controlled by both maternal and paternal IG-DMRs in a tissue-specific fashion. bioRxiv. (Submitted)

Andersen, L., Ballester, R., Marchuk, D., Saulino, A., Wigler, M. H., Collins, F. (October 1991) Alternative Splicing in the Proposed Catalytic Domain of the Type-1 Neurofibromatosis Gene. American Journal of Human Genetics, 49 (4). p. 21. ISSN 0002-9297

Andersen, L. B., Ballester, R., Marchuk, D. A., Chang, E., Gutmann, D. H., Saulino, A. M., Camonis, J., Wigler, M. H., Collins, F. S. (January 1993) A conserved alternative splice in the von Recklinghausen neurofibromatosis (NF1) gene produces two neurofibromin isoforms, both of which have GTPase-activating protein activity. Molecular and Cellular Biology, 13 (1). pp. 487-495. ISSN 0270-7306

Antonescu, C. R., Viale, A., Sarran, L., Tschernyavsky, S. J., Gonen, M., Segal, N. H., Maki, R. G., Socci, N. D., DeMatteo, R. P., Besmer, P. (May 2004) Gene expression in gastrointestinal stromal tumors is distinguished by KIT genotype and anatomic site. Clin Cancer Res, 10 (10). pp. 3282-90. ISSN 1078-0432 (Print)1078-0432 (Linking)

Asp, M., Giacomello, S., Larsson, L., Wu, C., Furth, D., Qian, X., Wardell, E., Custodio, J., Reimegard, J., Salmen, F., Osterholm, C., Stahl, P. L., Sundstrom, E., Akesson, E., Bergmann, O., Bienko, M., Mansson-Broberg, A., Nilsson, M., Sylven, C., Lundeberg, J. (December 2019) A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell, 179 (7). 1647-1660.e19. ISSN 0092-8674

Athma, P., Grotewold, E., Peterson, T. (May 1992) Insertional mutagenesis of the maize P gene by intragenic transposition of Ac. Genetics, 131 (1). pp. 199-209. ISSN 0016-6731 (Print)0016-6731 (Linking)

Aurora, R., Herr, W. (1991) Oct-1 Binds to Diverse Target Sequences through Interactions with Multiple Regions of the Pou-Domain. Journal of Cellular Biochemistry, 47 (Suppl ). p. 170.

Balasooriya, Gayan I, Spector, David L (October 2022) Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. Nature Communications, 13 (1). p. 5984. ISSN 2041-1723

Ballester, R., Marchuk, D., Boguski, M., Saulino, A., Letcher, R., Wigler, M. H., Collins, F. (November 1990) The NF1 locus encodes a protein functionally related to mammalian GAP and yeast IRA proteins. Cell, 63 (4). pp. 851-9. ISSN 0092-8674

Ballester, R., Wigler, M. H. (1990) Isolation and Characterization of Genes That Regulate Ras Function in the Yeast Saccharomyces-Cerevisiae. Yeast, 6 (SPEC. ). S212.

Ballesteros, M. L., Bolle, C., Lois, L. M., Moore, J. M., Vielle-Calzada, J. P., Grossniklaus, U., Chua, N. H. (October 2001) LAF1, a MYB transcription activator for phytochrome A signaling. Genes & Development, 15 (19). pp. 2613-2625. ISSN 0890-9369

Ballouz, S., Gillis, J. (April 2016) AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PLoS Comput Biol, 12 (4). e1004868. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Ballouz, S., Pavlidis, P., Gillis, J. (October 2016) Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Res. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Ballouz, Sara, Mangala, Melissa M, Perry, Matthew D, Heitmann, Stewart, Gillis, Jesse A, Hill, Adam P, Vandenberg, Jamie I (October 2020) Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events. Cardiovascular Research. ISSN 0008-6363

Barr, M. M., Tu, H., Van Aelst, L., Wigler, M. H. (October 1996) Identification of Ste4 as a potential regulator of Byr2 in the sexual response pathway of Schizosaccharomyces pombe. Mol Cell Biol, 16 (10). pp. 5597-603. ISSN 0270-7306 (Print)

Batut, P. J., Dobin, A., Plessy, C., Carninci, P., Gingeras, T. R. (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res, 23 (1). pp. 169-180. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Baulcombe, D., Huttly, A., Martienssen, R. (1987) Hormonal and development control of gene expression in wheat. Biochem Soc Trans, 15 (1). pp. 9-11. ISSN 0300-5127

Belleau, Pascal, Deschênes, Astrid, Chambwe, Nyasha, Tuveson, David A, Krasnitz, Alexander (December 2022) Genetic ancestry inference from cancer-derived molecular data across genomic and transcriptomic platforms. Cancer Research. CAN-22. ISSN 0008-5472

Benoit, Matthias (January 2022) Hot 'n cold: Applying the cis-regulatory code to predict heat and cold stress response in maize. The Plant cell, 34 (1). pp. 497-498. ISSN 1532-298X

Bessho, Y., Nawa, H., Nakanishi, S. (January 1994) Selective up-Regulation of an Nmda Receptor Subunit Messenger-Rna in Cultured Cerebellar Granule Cells by K+-Induced Depolarization and Nmda Treatment. Neuron, 12 (1). pp. 87-95. ISSN 0896-6273

Beyaz, S., Kim, J. H., Pinello, L., Xifaras, M. E., Hu, Y., Huang, J., Kerenyi, M. A., Das, P. P., Barnitz, R. A., Herault, A., Dogum, R., Haining, W. N., Yilmaz, O. H., Passegue, E., Yuan, G. C., Orkin, S. H., Winau, F. (February 2017) The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nat Immunol, 18 (2). pp. 184-195. ISSN 1529-2916 (Electronic)1529-2908 (Linking)

Beyaz, Semir, Mana, Miyeko D, Yilmaz, Ömer H (April 2021) High-fat diet activates a PPAR-δ program to enhance intestinal stem cell function. Cell Stem Cell, 28 (4). pp. 598-599. ISSN 1934-5909

Bhagwat, A. S., Vakoc, C. R. (September 2015) Targeting Transcription Factors in Cancer. Trends Cancer, 1 (1). pp. 53-65. ISSN 2405-8033 (Print)

Birchmeier, C., Birnbaum, D., Waitches, G., Fasano, O., Wigler, M. H. (1986) Characterization of an activated human ros gene. Molecular & Cellular Biology, 6 (9). pp. 3109-3116.

Birchmeier, C., O'Neill, K., Riggs, M., Wigler, M. H. (1990) Characterization of Ros1 cDNA from a Human Glioblastoma Cell Line. Proceedings of the National Academy of Sciences of the United States of America, 87 (12). pp. 4799-4803.

Birchmeier, C., Sharma, S., Wigler, M. H. (December 1987) Expression and rearrangement of the ROS1 gene in human glioblastoma cells. Proc Natl Acad Sci U S A, 84 (24). pp. 9270-4. ISSN 0027-8424

Birchmeier, C., Young, D., Wigler, M. H. (June 1986) Characterization of two new human oncogenes. Cold Spring Harbor Symposia on Quantitative Biology, 51 (2). pp. 993-1000. ISSN 00917451 (ISSN)

Blasco, M. A., Funk, W., Villeponteau, B., Greider, C. W. (September 1995) Functional characterization and developmental regulation of mouse telomerase RNA. Science, 269 (5228). pp. 1267-70. ISSN 0036-8075 (Print)

Boguski, M. S., Murray, A. W., Powers, S. (April 1992) Novel repetitive sequence motifs in the alpha and beta subunits of prenyl-protein transferases and homology of the alpha subunit to the MAD2 gene product of yeast. The New Biologist, 4 (4). pp. 408-11. ISSN 1043-4674 (Print)1043-4674

Bolger, G., Michaeli, T., Martins, T., St John, T., Steiner, B., Rodgers, L., Riggs, M., Wigler, M. H., Ferguson, K. (October 1993) A family of human phosphodiesterases homologous to the dunce learning and memory gene product of Drosophila melanogaster are potential targets for antidepressant drugs. Mol Cell Biol, 13 (10). pp. 6558-71. ISSN 0270-7306 (Print)

Bolger, G. B., Rodgers, L., Riggs, M. (November 1994) Differential CNS expression of alternative mRNA isoforms of the mammalian genes encoding cAMP-specific phosphodiesterases. Gene, 149 (2). pp. 237-44. ISSN 0378-1119 (Print)

Bolwig, G., Chromey, C., Crittenden, J., Dauwalder, B., Dezazzo, J., Han, K. A., Han, P. L., Nighorn, A., Qiu, Y. H., Skoulakis, E., West, R., Wu, K., Davis, R. L. (March 1993) Gene-Expression and Learning in Drosphila. Journal of Cellular Biochemistry, 53 (S17D). p. 246. ISSN 0730-2312

Bortiri, E., Jackson, D. P., Hake, S. (April 2006) Advances in maize genomics: The emergence of positional cloning. Current Opinion in Plant Biology, 9 (2). pp. 164-171. ISSN 13695266

Bott, A. J., Shen, J., Tonelli, C., Zhan, L., Sivaram, N., Jiang, Y. P., Yu, X., Bhatt, V., Chiles, E., Zhong, H., Maimouni, S., Dai, W., Velasquez, S., Pan, J. A., Muthalagu, N., Morton, J., Anthony, T. G., Feng, H., Lamers, W. H., Murphy, D. J., Guo, J. Y., Jin, J., Crawford, H. C., Zhang, L., White, E., Lin, R. Z., Su, X., Tuveson, D. A., Zong, W. X. (October 2019) Glutamine Anabolism Plays a Critical Role in Pancreatic Cancer by Coupling Carbon and Nitrogen Metabolism. Cell Rep, 29 (5). 1287-1298.e6.

Breschi, A., Djebali, S., Gillis, J., Pervouchine, D. D., Dobin, A., Davis, C. A., Gingeras, T. R., Guigo, R. (2016) Gene-specific patterns of expression variation across organs and species. Genome Biol, 17 (1). p. 151. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Broek, D., Samily, N., Fasano, O., Fujiyama, A., Tamanoi, F., Northup, J., Wigler, M. H. (1985) Differential activation of yeast adenylate cyclase by wild type and mutant RAS proteins. Cell, 41 (3). pp. 763-770.

Broek, D., Toda, T., Michaeli, T., Levin, L., Birchmeier, C., Zoller, M., Powers, S., Wigler, M. H. (March 1987) The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway. Cell, 48 (5). pp. 789-800.

Brooks, J. E., Gingeras, T. R. (1983) The control of expression of a type-ll restriction modification system from Pseudomonas Aeroginosa. Federation Proceedings, 42 (7). p. 2038. ISSN 0014-9446

Brown, J., Sundaresan, V. (April 1992) Genetic study of the loss and restoration of Mutator transposon activity in maize: evidence against dominant-negative regulator associated with loss of activity. Genetics, 130 (4). pp. 889-98. ISSN 0016-6731 (Print)0016-6731 (Linking)

Byrd, C., Turner, G. C., Varshavsky, A. (1998) The N-end rule pathway controls the import of peptides through degradation of a transcriptional repressor. Embo Journal, 17 (1). pp. 269-277. ISSN 02614189 (ISSN)

Byrne, M. E., Barley, R., Curtis, M., Arroyo, J. M., Dunham, M., Hudson, A., Martienssen, R. A. (December 2000) Asymmetric leaves1 mediates leaf patterning and stem cell function in Arabidopsis. Nature, 408 (6815). pp. 967-971. ISSN 0028-0836

Byrne, M. E., Simorowski, J., Martienssen, R. A. (April 2002) ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis. Development, 129 (8). pp. 1957-1965. ISSN 0950-1991

Caligiuri, M., Beach, D. (February 1993) Sct1 functions in partnership with Cdc10 in a transcription complex that activates cell cycle START and inhibits differentiation. Cell, 72 (4). pp. 607-19. ISSN 0092-8674 (Print)

Cameron, S., Levin, L., Zoller, M., Wigler, M. H. (May 1988) cAMP-independent control of sporulation, glycogen metabolism, and heat shock resistance in S. cerevisiae. Cell, 53 (4). pp. 555-66. ISSN 0092-8674

Capellini, T. D., Dunn, M. P., Passamaneck, Y. J., Selleri, L., Di Gregorio, A. (November 2008) Conservation of notochord gene expression across chordates: insights from the Leprecan gene family. Genesis, 46 (11). pp. 683-96. ISSN 1526-954x

Carl, S., Daniels, R., Iafrate, A. J., Easterbrook, P., Greenough, T. C., Skowronski, J., Kirchhoff, F. (January 2000) Partial "repair" of defective NEF genes in a long-term nonprogressor with human immunodeficiency virus type 1 infection. Journal of Infectious Diseases, 181 (1). pp. 132-140. ISSN 0022-1899

Carmel, G., Kuret, J. (June 1992) A solid-phase screen for protein kinase substrate selectivity. Anal Biochem, 203 (2). pp. 274-80. ISSN 0003-2697 (Print)0003-2697 (Linking)

Carvalho, F. I., Johns, C., Gillespie, M. E. (May 2012) Gene expression analysis: Teaching Students to do 30,000 Experiments at once with Microarray. Biochemistry and Molecular Biology Education, 40 (3). pp. 181-190. ISSN 1470-8175

Caspari, Ernst W. (1949) On the action of genes in development. Portugaliae acta biologica, Series (R.B. G). pp. 147-160.

Castellano, S., Macchi, F., Scali, M., Huang, Z. J., Bozzi, Y. (September 2006) Cytosolic branched chain aminotransferase (BCATc) mRNA is up-regulated in restricted brain areas of BDNF transgenic mice. Brain Research, 1108 (1). pp. 12-18. ISSN 00068993

Cecchini, Katharine, Biasini, Adriano, Yu, Tianxiong, Säflund, Martin, Mou, Haiwei, Arif, Amena, Eghbali, Atiyeh, Colpan, Cansu, Gainetdinov, Ildar, de Rooij, Dirk G, Weng, Zhiping, Zamore, Phillip, Ozata, Deniz M (November 2022) The transcription factor TCFL5 responds to A MYB to elaborate the male meiotic program in mice. Reproduction. REP-22. ISSN 1470-1626

Chan-Seng-Yue, M., Kim, J. C., Wilson, G. W., Ng, K., Figueroa, E. F., O'Kane, G. M., Connor, A. A., Denroche, R. E., Grant, R. C., McLeod, J., Wilson, J. M., Jang, G. H., Zhang, A., Liang, S. B., Borgida, A., Chadwick, D., Kalimuthu, S., Lungu, I., Bartlett, J. M. S., Krzyzanowski, P. M., Sandhu, V., Tiriac, H., Froeling, F. E. M., Karasinska, J. M., Topham, J. T., Renouf, D. J., Schaeffer, D. F., Jones, S. J. M., Marra, M. A., Laskin, J., Chetty, R., Stein, L. D., Zogopoulos, G., Haibe-Kains, B., Campbell, P. J., Tuveson, D. A., Knox, J. J., Fischer, S. E., Gallinger, S., Notta, F. (January 2020) Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat Genet. ISSN 1061-4036 (Public Dataset)

Chang, E. C., Barr, M., Wang, Y., Jung, V., Xu, H. P., Wigler, M. H. (October 1994) Cooperative interaction of S. pombe proteins required for mating and morphogenesis. Cell, 79 (1). pp. 131-41. ISSN 0092-8674 (Print)

Chang, K., Marran, K., Valentine, A., Hannon, G. J. (2013) Creating an miR30-based shRNA vector. Cold Spring Harbor Protocols, 8 (7). pp. 631-635. ISSN 19403402

Chang, K., Marran, K., Valentine, A., Hannon, G. J. (2014) Generation of transgenic drosophila expressing shRNAs in the miR-1 backbone. Cold Spring Harbor Protocols, 2014 (5). pp. 501-509. ISSN 19403402

Chardin, P., Camonis, J. H., Gale, N. W., van Aelst, L., Schlessinger, J., Wigler, M. H., Bar-Sagi, D. (May 1993) Human Sos1: a guanine nucleotide exchange factor for Ras that binds to GRB2. Science, 260 (5112). pp. 1338-1343.

Chattopadhyaya, B., Di Cristo, G., Higashiyama, H., Knott, G. W., Kuhlman, S. J., Welker, E., Huang, Z. J. (October 2004) Experience and activity-dependent maturation of perisomatic GABAergic innervation in primary visual cortex during a postnatal critical period. Journal of Neuroscience, 24 (43). pp. 9598-611. ISSN 0270-6474

Cheadle, L., Tzeng, C. P., Kalish, B. T., Harmin, D. A., Rivera, S., Ling, E., Nagy, M. A., Hrvatin, S., Hu, L., Stroud, H., Burkly, L. C., Chen, C., Greenberg, M. E. (August 2018) Visual Experience-Dependent Expression of Fn14 Is Required for Retinogeniculate Refinement. Neuron, 99 (3). 525-539.e10. ISSN 0896-6273 (Print)0896-6273

Chen, Qian, Wang, Saisai, Zhang, Juqing, Xie, Min, Lu, Bin, He, Jie, Zhen, Zhuoran, Li, Jing, Zhu, Jiajun, Li, Rong, Li, Pilong, Wang, Haifeng, Vakoc, Christopher, Roeder, Robert G, Chen, Mo (October 2024) JMJD1C forms condensates to facilitate a RUNX1-dependent gene expression program shared by multiple types of AML cells. Protein and Cell. pwae059. ISSN 1674-800X (Public Dataset)

Chen, C. D., Helfman, D. M. (February 1999) Donor site competition is involved in the regulation of alternative splicing of the rat beta-tropomyosin pre-mRNA. Rna, 5 (2). pp. 290-301. ISSN 1355-8382 (Print)

Chen, C. D., Kobayashi, R., Helfman, D. M. (March 1999) Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene. Genes and Development, 13 (5). pp. 593-606. ISSN 0890-9369 (Print)

Chen, G. X., Jaradat, S. A., Banerjee, N., Tanaka, T. S., Ko, M. S. H., Zhang, M. Q. (January 2002) Evaluation and comparison of clustering algorithms in analyzing es cell gene expression data. Statistica Sinica, 12 (1). pp. 241-262. ISSN 1017-0405

Chen, J., Guo, T., Zhang, L., Qin, L. X., Singer, S., Maki, R. G., Taguchi, T., Dematteo, R., Besmer, P., Antonescu, C. R. (February 2012) CD133 and CD44 are universally overexpressed in GIST and do not represent cancer stem cell markers. Genes Chromosomes Cancer, 51 (2). pp. 186-95. ISSN 1098-2264 (Electronic)1045-2257 (Linking)

Chen, J. P., Jiao, Y. P., Laza, H., Payton, P., Ware, D., Xin, Z. G. (November 2019) Identification of the First Nuclear Male Sterility Gene (Male-sterile 9) in Sorghum. Plant Genome, 12 (3). Article No 190020. ISSN 1940-3372

Chen, X., Sun, Y. C., Zhan, H., Kebschull, J. M., Fischer, S., Matho, K., Huang, Z. J., Gillis, J., Zador, A. M. (October 2019) High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. Cell, 179 (3). 772-786.e19. ISSN 0092-8674 (Public Dataset)

Chen, Shuonan, Loper, Jackson, Chen, Xiaoyin, Vaughan, Alex, Zador, Anthony M, Paninski, Liam (March 2021) BARcode DEmixing through Non-negative Spatial Regression (BarDensr). PLoS Computational Biology, 17 (3). e1008256. ISSN 1553-734X

Cheng, J., Sedlazek, F., Altmuller, J., Nolte, A. W. (September 2015) Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus). Proc Biol Sci, 282 (1815). ISSN 1471-2954 (Electronic)0962-8452 (Linking)

Cherepinsky, V., Feng, J. W., Rejali, M., Mishra, B. (August 2003) Shrinkage-based similarity metric for cluster analysis of microarray data. Proceedings of the National Academy of Sciences of the United States of America, 100 (17). pp. 9668-9673. ISSN 0027-8424

Chi, P., Chen, Y., Zhang, L., Guo, X., Wongvipat, J., Shamu, T., Fletcher, J. A., Dewell, S., Maki, R. G., Zheng, D., Antonescu, C. R., Allis, C. D., Sawyers, C. L. (October 2010) ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature, 467 (7317). pp. 849-53. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Choi, Charlotte P, Tay, Rebecca J, Starostik, Margaret R, Feng, Suhua, Moresco, James J, Montgomery, Brooke E, Xu, Emily, Hammonds, Maya A, Schatz, Michael C, Montgomery, Taiowa A, Yates, John R, Jacobsen, Steven E, Kim, John K (February 2021) SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. eLife, 10. pp. 1-35. ISSN 2050-084X

Chou, S. T., Khandros, E., Bailey, L. C., Nichols, K. E., Vakoc, C. R., Yao, Y., Huang, Z., Crispino, J. D., Hardison, R. C., Blobel, G. A., Weiss, M. J. (July 2009) Graded repression of PU.1/Sfpi1 gene transcription by GATA factors regulates hematopoietic cell fate. Blood, 114 (5). pp. 983-994.

Cisse, Y. M., Borniger, J. C., Lemanski, E., Walker, W. H., Nelson, R. J. (January 2018) Time-Restricted Feeding Alters the Innate Immune Response to Bacterial Endotoxin. J Immunol, 200 (2). pp. 681-687. ISSN 1550-6606 (Electronic)0022-1767 (Linking)

Cleary, M. A., Stern, S., Tanaka, M., Herr, W. (January 1993) Differential positive control by Oct-1 and Oct-2: activation of a transcriptionally silent motif through Oct-1 and VP16 corecruitment. Genes Dev, 7 (1). pp. 72-83. ISSN 0890-9369 (Print)

Cline, H. (December 2003) Sperry and Hebb: oil and vinegar? Trends in Neurosciences, 26 (12). pp. 655-661. ISSN 0166-2236

Clouston, W. M. (November 1990) The angiotensinogen gene of Swiss mice is closely linked to a retrovirus-like element. DNA and Cell Biology, 9 (9). pp. 623-630. ISSN 1044-5498

Colicelli, J., Birchmeier, C., Michaeli, T., O'Neill, K., Riggs, M., Wigler, M. H. (May 1989) Isolation and characterization of a mammalian gene encoding a high-affinity cAMP phosphodiesterase. Proc Natl Acad Sci U S A, 86 (10). pp. 3599-603. ISSN 0027-8424

Colicelli, J., Nicolette, C., Birchmeier, C., Rodgers, L., Riggs, M., Wigler, M. H. (April 1991) Expression of three mammalian cDNAs that interfere with RAS function in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A, 88 (7). pp. 2913-7. ISSN 0027-8424

Cone, R. D., Platzer, M., Piccinini, L. A., Jaramillo, M., Davies, T. F. (October 1988) Hla-Dr Gene-Expression in a Proliferating Human Thyroid Cell Clone (12s). Endocrinology, 123 (4). pp. 2067-2074. ISSN 0013-7227

Conklin, D. S. (October 2003) RNA-interference-based silencing of mammalian gene expression. Chembiochem, 4 (10). pp. 1033-1039. ISSN 1439-4227

Connolly, T., Caligiuri, M., Beach, D. (June 1997) The Cdc2 protein kinase controls Cdc10/Sct1 complex formation. Molecular Biology of the Cell, 8 (6). pp. 1105-15. ISSN 1059-1524 (Print)

Cranston, K. A., Hurwitz, B. L., Ware, D. H., Stein, L. D., Wing, R. A. (October 2009) Species Trees from Highly Incongruent Gene Trees in Rice. Systematic Biology, 58 (5). pp. 489-500. ISSN 1063-5157

Crews, L., Gates, P. B., Brown, R., Joliot, A., Foley, C., Brockes, J. P., Gann, A. A. (February 1995) Expression and activity of the newt Msx-1 gene in relation to limb regeneration. Proceedings of the Royal Society B: Biological Sciences, 259 (1355). pp. 161-71. ISSN 0962-8452 (Print)0962-8452

Crow, M., Gillis, J. (August 2018) Co-expression in Single-Cell Analysis: Saving Grace or Original Sin? Trends Genet, 34 (11). pp. 823-831. ISSN 0168-9525 (Print)0168-9525

Crow, M., Lim, N., Ballouz, S., Pavlidis, P., Gillis, J. (March 2019) Predictability of human differential gene expression. Proc Natl Acad Sci U S A. ISSN 0027-8424

Crow, Megan, Suresh, Hamsini, Lee, John, Gillis, Jesse (November 2020) Coexpression reveals conserved mechanisms of transcriptional cell identity. BioRxiv. (Unpublished)

Daar, I., Nebreda, A. R., Yew, N., Sass, P., Paules, R., Santos, E., Wigler, M. H., Vandewoude, G. F. (July 1991) The Ras Oncoprotein and M-Phase Activity. Science, 253 (5015). pp. 74-76. ISSN 0036-8075

Dachet, Fabien, Brown, James B, Valyi-Nagy, Tibor, Narayan, Kunwar D, Serafini, Anna, Boley, Nathan, Gingeras, Thomas R, Celniker, Susan E, Mohapatra, Gayatry, Loeb, Jeffrey A (March 2021) Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Scientific Reports, 11 (1). p. 6078. ISSN 2045-2322

Dalton, J. E., Kacheria, T. S., Knott, S. R., Lebo, M. S., Nishitani, A., Sanders, L. E., Stirling, E. J., Winbush, A., Arbeitman, M. N. (2010) Dynamic, mating-induced gene expression changes in female head and brain tissues of Drosophila melanogaster. BMC Genomics, 11. p. 541. ISSN 1471-2164

Dancsok, A. R., Setsu, N., Gao, D., Blay, J. Y., Thomas, D., Maki, R. G., Nielsen, T. O., Demicco, E. G. (July 2019) Expression of lymphocyte immunoregulatory biomarkers in bone and soft-tissue sarcomas. Mod Pathol, 32 (12). pp. 1662-1785. ISSN 0893-3952

Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., Cheung, V. G., Kraus, W. L., Lis, J. T., Siepel, A. (May 2015) Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods, 12 (5). pp. 433-8. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

DeZazzo, J., Xia, S., Christensen, J., Velinzon, K., Tully, T. (October 1999) Developmental expression of an amn(+) transgene rescues the mutant memory defect of amnesiac adults. Journal of Neuroscience, 19 (20). pp. 8740-6. ISSN 1529-2401 (Electronic)

Degroat, Thomas J, Wiersielis, Kimberly, Denney, Katherine, Kodali, Sowmya, Daisey, Sierra, Tollkuhn, Jessica, Samuels, Benjamin A, Roepke, Troy A (December 2023) Chronic stress and its effects on behavior, RNA expression of the bed nucleus of the stria terminalis, and the M-current of NPY neurons. Psychoneuroendocrinology, 161. p. 106920. ISSN 0306-4530

Demetrick, D. J., Zhang, H., Beach, D. H. (1994) Chromosomal mapping of human CDK2, CDK4, and CDK5 cell cycle kinase genes. Cytogenet Cell Genet, 66 (1). pp. 72-4. ISSN 0301-0171 (Print)

Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., Lagarde, J., Veeravalli, L., Ruan, X. A., Ruan, Y. J., Lassmann, T., Carninci, P., Brown, J. B., Lipovich, L., Gonzalez, J. M., Thomas, M., Davis, C. A., Shiekhattar, R., Gingeras, T. R., Hubbard, T. J., Notredame, C., Harrow, J., Guigo, R. (September 2012) The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research, 22 (9 Spe). pp. 1775-1789. ISSN 1088-9051

Di Como, C. J., Bose, R., Arndt, K. T. (January 1995) Overexpression of SIS2, which contains an extremely acidic region, increases the expression of SWI4, CLN1 and CLN2 in sit4 mutants. Genetics, 139 (1). pp. 95-107. ISSN 0016-6731 (Print)

Di Como, C. J., Chang, H., Arndt, K. T. (April 1995) Activation of CLN1 and CLN2 G1 cyclin gene expression by BCK2. Mol Cell Biol, 15 (4). pp. 1835-46. ISSN 0270-7306 (Print)

Diaz-Nido, J., Mizuno, K., Nawa, H., Marshak, D. R. (1994) Regulation of protein kinase CK2 isoform expression during rat brain development. Cell Mol Biol Res, 40 (5-6). pp. 581-5. ISSN 0968-8773 (Print)

Diniz, A. L., da Silva, D. I. R., Lembke, C. G., Costa, M. D. L., Ten-Caten, F., Li, F., Vilela, R. D., Menossi, M., Ware, D., Endres, L., Souza, G. M. (November 2020) Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. Int J Mol Sci, 21 (23). p. 9124. ISSN 1422-0067

Dong, X., Greven, M. C., Kundaje, A., Djebali, S., Brown, J. B., Cheng, C., Gingeras, T. R., Gerstein, M., Guigó, R., Birney, E., Weng, Z. (September 2012) Modeling gene expression using chromatin features in various cellular contexts. Genome Biology, 13 (9).

Dowen, Jill M., Bilodeau, Steve, Orlando, David A., Hübner, Michael R., Abraham, Brian J., Spector, David L., Young, Richard A. (October 2013) Multiple Structural Maintenance of Chromosome Complexes at Transcriptional Regulatory Elements. Stem Cell Reports, 1 (5). pp. 371-378. ISSN 2213-6711

Downs, G. S., Liseron-Monfils, C., Lukens, L. N. (March 2014) Regulatory motifs identified from a maize developmental coexpression network. Genome, 57 (3). pp. 181-184. ISSN 0831-2796

Du, Yanfang, Lunde, China, Li, Yunfu, Jackson, David, Hake, Sarah, Zhang, Zuxin (February 2021) Gene duplication at the Fascicled ear1 locus controls the fate of inflorescence meristem cells in maize. Proceedings of the National Academy of Sciences of USA, 118 (7). e2019218118-e2019218118. ISSN 0027-8424

Dubnau, J. T., Chiang, A. S., Grady, L., Barditch, J., Gossweiler, S., McNeil, J., Smith, P., Buldoc, F. V., Scott, R., Certa, U., Broger, C., Tully, T. (February 2003) The staufen/pumilio pathway is involved in Drosophila long-term memory. Current Biology, 13 (4). pp. 286-296. ISSN 0960-9822

Ducommun, B., Draetta, G., Young, P., Beach, D. (February 1990) Fission yeast cdc25 is a cell-cycle regulated protein. Biochem Biophys Res Commun, 167 (1). pp. 301-9. ISSN 0006-291X (Print)0006-291X (Linking)

Dugourd, Aurelien, Kuppe, Christoph, Sciacovelli, Marco, Gjerga, Enio, Gabor, Attila, Emdal, Kristina B, Vieira, Vitor, Bekker-Jensen, Dorte B, Kranz, Jennifer, Bindels, Eric MJ, Costa, Ana SH, Sousa, Abel, Beltrao, Pedro, Rocha, Miguel, Olsen, Jesper V, Frezza, Christian, Kramann, Rafael, Saez-Rodriguez, Julio (January 2021) Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses. Molecular Systems Biology, 17 (1). e9730. ISSN 1744-4292

Dukler, N., Gulko, B., Huang, Y. F., Siepel, A. (December 2016) Is a super-enhancer greater than the sum of its parts? Nat Genet, 49 (1). pp. 2-3. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Dukler, N., Huang, Y-F., Siepel, A. (March 2020) Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data. Mol Biol Evol, 37 (7). pp. 2137-2152. ISSN 0737-4038

Dunn, M. P., Di Gregorio, A. (April 2009) The evolutionarily conserved leprecan gene: its regulation by Brachyury and its role in the developing Ciona notochord. Dev Biol, 328 (2). pp. 561-74. ISSN 0012-1606

Dura, J. M., Preat, T., Tully, T. (1993) Identification of Linotte, a New Gene Affecting Learning and Memory in Drosophila-Melanogaster. Journal of Neurogenetics, 9 (1). pp. 1-14. ISSN 0167-7063

Eckersley-Maslin, M. A., Spector, D. L. (June 2014) Random monoallelic expression: Regulating gene expression one allele at a time. Trends in Genetics, 30 (6). pp. 237-244. ISSN 13624555

Eckersley-Maslin, M. A., Thybert, D., Bergmann, J. H., Marioni, J. C., Flicek, P., Spector, D. L. (February 2014) Random Monoallelic Gene Expression Increases upon Embryonic Stem Cell Differentiation. Developmental Cell, 28 (4). pp. 351-65. ISSN 1534-5807

Efrat, S., Linde, S., Kofod, H., Spector, D., Delannoy, M., Grant, S., Hanahan, D., Baekkeskov, S. (December 1988) Beta-cell lines derived from transgenic mice expressing a hybrid insulin gene-oncogene. Proceedings of the National Academy of Sciences of the United States of America, 85 (23). pp. 9037-41. ISSN 0027-8424 (Print)0027-8424

Eggan, S. M., Lazarus, M. S., Stoyak, S. R., Volk, D. W., Glausier, J. R., Huang, Z. J., Lewis, D. A. (2012) Cortical glutamic acid decarboxylase 67 deficiency results in lower cannabinoid 1 receptor messenger RNA expression: Implications for schizophrenia. Biological Psychiatry, 71 (2). pp. 114-119. ISSN 00063223 (ISSN)

Ehrenhofer-Wolfer, K., Puchner, T., Schwarz, C., Rippka, J., Blaha-Ostermann, S., Strobl, U., Hormann, A., Bader, G., Kornigg, S., Zahn, S., Sommergruber, W., Schweifer, N., Zichner, T., Schlattl, A., Neumuller, R. A., Shi, J., Vakoc, C. R., Kogl, M., Petronczki, M., Kraut, N., Pearson, M. A., Wohrle, S. (August 2019) SMARCA2-deficiency confers sensitivity to targeted inhibition of SMARCA4 in esophageal squamous cell carcinoma cell lines. Sci Rep, 9 (1). p. 11661. ISSN 2045-2322

Ehrt, S., Schnappinger, D., Bekiranov, S., Drenkow, J., Shi, S., Gingeras, T. R., Gaasterland, T., Schoolnik, G., Nathan, C. (2001) Reprogramming of the macrophage transcriptome in response to interferon-γ and mycobacterium tuberculosis: Signaling roles of nitric oxide synthase-2 and phagocyte oxidase. Journal of Experimental Medicine, 194 (8). pp. 1123-1139. ISSN 00221007 (ISSN)

Elkin, Rena, Oh, Jung Hun, Dela Cruz, Filemon, Norton, Larry, Deasy, Joseph O, Kung, Andrew L, Tannenbaum, Allen R (January 2024) Dynamic network curvature analysis of gene expression reveals novel potential therapeutic targets in sarcoma. Scientific Reports, 14 (1). p. 488. ISSN 2045-2322 (Public Dataset)

Ellegood, J., Anagnostou, E., Babineau, B. A., Crawley, J. N., Lin, L., Genestine, M., DiCicco-Bloom, E., Lai, J. K., Foster, J. A., Penagarikano, O., Geschwind, D. H., Pacey, L. K., Hampson, D. R., Laliberte, C. L., Mills, A. A., Tam, E., Osborne, L. R., Kouser, M., Espinosa-Becerra, F., Xuan, Z., Powell, C. M., Raznahan, A., Robins, D. M., Nakai, N., Nakatani, J., Takumi, T., van Eede, M. C., Kerr, T. M., Muller, C., Blakely, R. D., Veenstra-VanderWeele, J., Henkelman, R. M., Lerch, J. P. (February 2015) Clustering autism: using neuroanatomical differences in 26 mouse models to gain insight into the heterogeneity. Mol Psychiatry, 20 (1). pp. 118-125. ISSN 1359-4184

Ellis, S. B., Brust, P. F., Koutz, P. J., Waters, A. F., Harpold, M. M., Gingeras, T. R. (May 1985) Isolation of alcohol oxidase and two other methanol regulatable genes from the yeast Pichia pastoris. Mol Cell Biol, 5 (5). pp. 1111-21. ISSN 0270-7306 (Print)0270-7306 (Linking)

Ellisen, L. W., Palmer, R. E., Maki, R. G., Truong, V. B., Tamayo, P., Oliner, J. D., Haber, D. A. (May 2001) Cascades of transcriptional induction during human lymphocyte activation. Eur J Cell Biol, 80 (5). pp. 321-8. ISSN 0171-9335 (Print)0171-9335 (Linking)

Ezhkova, E., Pasolli, H. A., Parker, J. S., Stokes, N., Su, I. H., Hannon, G. J., Tarakhovsky, A., Fuchs, E. (March 2009) Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells. Cell, 136 (6). pp. 1122-1135. ISSN 0092-8674

Falcone Ferreyra, M. L., Casas, M. I., Questa, J. I., Herrera, A. L., Deblasio, S., Wang, J., Jackson, D., Grotewold, E., Casati, P. (2012) Evolution and expression of tandem duplicated maize flavonol synthase genes. Frontiers in Plant Science, 3. p. 101. ISSN 1664-462x

Fasano, O., Birnbaum, D., Edlund, L., Fogh, J., Wigler, M. H. (September 1984) New human transforming genes detected by a tumorigenicity assay. Molecular & Cellular Biology, 4 (9). pp. 1695-1705.

Fernald, G. H., Knott, S., Pachner, A., Caillier, S. J., Narayan, K., Oksenberg, J. R., Mousavi, P., Baranzini, S. E. (April 2007) Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humans. J Immunol, 178 (8). pp. 5076-85. ISSN 0022-1767 (Print)0022-1767

Ferrandiz, C., Gu, Q., Martienssen, R., Yanofsky, M. F. (February 2000) Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development, 127 (4). pp. 725-734. ISSN 0950-1991

Field, J., Vojtek, A., Ballester, R., Bolger, G., Colicelli, J., Ferguson, K., Gerst, J., Kataoka, T., Michaeli, T., Powers, S., Riggs, M., Rodgers, L., Wieland, I., Wheland, B., Wigler, M. H. (April 1990) Cloning and characterization of CAP, the S. cerevisiae gene encoding the 70 kd adenylyl cyclase-associated protein. Cell, 61 (2). pp. 319-327. ISSN 0092-8674

Filipkowski, R. K. (2000) Inducing gene expression in barrel cortex - focus on immediate early genes. Acta Neurobiologiae Experimentalis, 60 (3). pp. 411-418. ISSN 0065-1400

Filipkowski, R. K., Rydz, M., Berdel, B., Morys, J., Kaczmarek, L. (March 2000) Tactile experience induces c-fos expression in rat barrel cortex. Learning & Memory, 7 (2). pp. 116-122. ISSN 1072-0502

Filipkowski, R. K., Rydz, M., Kaczmarek, L. (2001) Expression of c-Fos, Fos B, Jun B, and Zif268 transcription factor proteins in rat barrel cortex following apomorphine-evoked whisking behavior. Neuroscience, 106 (4). pp. 679-688. ISSN 0306-4522

Fitch, I., Dahmann, C., Surana, U., Amon, A., Nasmyth, K., Goetsch, L., Byers, B., Futcher, B. (July 1992) Characterization of four B-type cyclin genes of the budding yeast Saccharomyces cerevisiae. Mol Biol Cell, 3 (7). pp. 805-18. ISSN 1059-1524 (Print)1059-1524 (Linking)

Flanagan, C. A., Ma, H. (January 1993) Agl1 and Agl2, 2 Agamous-Related Mads-Box Genes, Are Differentially Expressed During Flower Development. Journal of Cellular Biochemistry, 53 (S17B). p. 14. ISSN 0730-2312

Flanagan, C. A., Ma, H. (October 1994) Spatially and temporally regulated expression of the MADS-box gene AGL2 in wild-type and mutant arabidopsis flowers. Plant Mol Biol, 26 (2). pp. 581-95. ISSN 0167-4412 (Print)

Forest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., De Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U., Medvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Altschuler, I. A., Albanese, D., Altschule, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Rennie, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A. M., Califano, A., Cannistraci, C. V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H. C., Dalla, E., Davis, C. A., Detmar, M., Diehl, A. D., Dohi, T., Drabløs, F., Edge, A. S. B., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G. J., Favorov, A. V., Fisher, M. E., Frith, M. C., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J. I., Geijtenbeek, T. B., Gibson, A. P., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K. J., Sui, S. J. H., Hofmann, O. M., Hoof, I., Hori, F., Huminiecki, L. (March 2014) A promoter-level mammalian expression atlas. Nature, 507 (7493). pp. 462-470. ISSN 14764687

Frangeul, Laura, Pouchelon, Gabrielle, Telley, Ludovic, Lefort, Sandrine, Luscher, Christian, Jabaudon, Denis (October 2016) A cross-modal genetic framework for the development and plasticity of sensory pathways. Nature, 538 (7623). pp. 96-98. ISSN 0028-0836

Franza, B. R., Rauscher, F. J., Josephs, S. F., Curran, T. (March 1988) The Fos complex and Fos-related antigens recognize sequence elements that contain AP-1 binding sites. Science, 239 (4844). pp. 1150-3. ISSN 0036-8075

Fraser, A. G., James, C., Evan, G. I., Hengartner, M. O. (March 1999) Caenorhabditis elegans inhibitor of apoptosis protein (IAP) homologue BIR-1 plays a conserved role in cytokinesis. Current Biology, 9 (6). pp. 292-301. ISSN 0960-9822 (Print)

Fraser, C. M., Arakawa, S., McCombie, W. R., Venter, J. C. (1989) Cloning, sequence analysis, and permanent expression of a human α2-adrenergic receptor in Chinese hamster ovary cells. Evidence for independent pathways of receptor coupling to adenylate cyclase attenuation and activation. Journal of Biological Chemistry, 264 (20). pp. 11754-11761. ISSN 00219258 (ISSN)

Fuller, S. J., Davies, E. L., Gillespie Brown, J., Sun, H., Tonks, N. K. (April 1997) Mitogen-activated protein kinase phosphatase 1 inhibits the stimulation of gene expression by hypertrophic agonists in cardiac myocytes. Biochemical Journal, 323. pp. 313-319. ISSN 0264-6021

Futcher, B. (December 2000) Microarrays and cell cycle transcription in yeast. Current Opinion in Cell Biology, 12 (6). pp. 710-715. ISSN 0955-0674

Galaktionov, K., Lee, A. K., Eckstein, J., Draetta, G., Meckler, J., Loda, M., Beach, D. (September 1995) CDC25 phosphatases as potential human oncogenes. Science, 269 (5230). pp. 1575-7. ISSN 0036-8075 (Print)

Gegenhuber, B., Tollkuhn, J. (January 2020) Signatures of Sex: Sex Differences in Gene Expression in the Vertebrate Brain. Wiley Interdiscip Rev Dev Biol, 9 (1). e348.

Gelti Douka, H., Gingeras, T. R., Kambysellis, M. P. (1973) Site of the yolk protein synthesis in D. silvestris. Drosophila Information Service, 50. pp. 161-162.

Gershon, E. S., Kelsoe, J. R., Kendler, K. S., Watson, J. D. (November 2001) A scientific opportunity. Science, 294 (5544). p. 957. ISSN 0036-8075

Getz, G., Levine, E., Domany, E., Zhang, M. Q. (May 2000) Super-paramagnetic clustering of yeast gene expression profiles. Physica A: Statistical Mechanics and its Applications, 279 (1-4). pp. 457-464. ISSN 03784371 (ISSN)

Gianfranceschi, L., Siciliano, R., Walls, J., Morales, B., Kirkwood, A., Huang, Z. J., Tonegawa, S., Maffei, L. (October 2003) Visual cortex is rescued from the effects of dark rearing by overexpression of BDNF. Proceedings of the National Academy of Sciences of the United States of America, 100 (21). pp. 12486-12491. ISSN 0027-8424

Gillis, J., Mistry, M., Pavlidis, P. (2010) Gene function analysis in complex data sets using ErmineJ. Nature Protocols, 5 (6). pp. 1148-1159. ISSN 17502799 (ISSN)

Gingeras, T. R., Gelti Douka, H., Kambysellis, M. P. (1973) Yolk proteins in Drosophila. Drosophila Information Service, 50. p. 58.

Giuliano, C. J., Lin, A., Smith, J. C., Palladino, A. C., Sheltzer, J. M. (February 2018) MELK expression correlates with tumor mitotic activity but is not required for cancer growth. Elife, 7. ISSN 2050-084x

Giuliano, G., Pollock, D., Stapp, H., Scolnik, P. A. (July 1988) A Genetic-Physical Map of the Rhodobacter-Capsulatus Carotenoid Biosynthesis Gene Cluster. Molecular & General Genetics, 213 (1). pp. 78-83. ISSN 0026-8925

Gladman, N., Jiao, Y., Lee, Y. K., Zhang, L., Chopra, R., Regulski, M., Burow, G., Hayes, C., Christensen, S. A., Dampanaboina, L., Chen, J., Burke, J., Ware, D., Xin, Z. (October 2019) Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module. Int J Mol Sci, 20 (19). ISSN 1422-0067

Goldfarb, M., Shimizu, K., Perucho, M., Wigler, M. H. (1982) Isolation and Preliminary Characterization of a Human Transforming Gene from T24 Bladder-Carcinoma Cells. Nature, 296 (5856). pp. 404-409. ISSN 0028-0836

Goodwin, S., McCombie, W. R. (December 2019) Sequencing Complex Genomes with PromethION Technology in a Core Setting. J Biomol Tech, 30 (Suppl). S36-s37. ISSN 1524-0215

Grange, Pascal, Mitra, Partha P (May 2012) Computational neuroanatomy and gene expression: optimal sets of marker genes for brain regions. (Submitted)

Grange, Pascal, Mitra, Partha P (May 2011) Marker Genes for Anatomical Regions in the Brain: Insights from the Allen Gene Expression Atlas. (Submitted)

Grange, Pascal, Mitra, Partha P (November 2011) Statistical analysis of co-expression properties of sets of genes in the mouse brain. (Submitted)

Grange, P., Bohland, J. W., Hawrylycz, M., Mitra, P. P. (November 2012) Brain Gene Expression Analysis: a MATLAB toolbox for the analysis of brain-wide gene-expression data. arXiv. (Unpublished)

Grange, P., Mitra, Partha P. (March 2012) Computational neuroanatomy and gene expression: Optimal sets of marker genes for brain regions. 46th Annual Conference on Information Sciences and Systems (CISS).

Grange, P., Bohland, J. W., Okaty, B. W., Sugino, K., Bokil, H., Nelson, S. B., Ng, L., Hawrylycz, M., Mitra, P. P. (April 2014) Cell-type-based model explaining coexpression patterns of genes in the brain. Proceedings of the National Academy of Sciences of the United States of America, 111 (14). pp. 5397-5402. ISSN 0027-8424

Greenberg, M. E., Iafrate, A. J., Skowronski, J. (May 1998) The SH3 domain-binding surface and an acidic motif in HIV-1 Nef regulate trafficking of class I MHC complexes. Embo Journal, 17 (10). pp. 2777-89. ISSN 0261-4189

Greenberg, M. E., Mathews, M. B. (December 1997) Effects of heterologous downstream sequences on the activity of the HIV-1 promoter and its response to Tat. Nucleic Acids Research, 25 (24). pp. 5017-24. ISSN 0305-1048

Greider, C. W. (February 1992) Telomere chromatin and gene expression. Curr Biol, 2 (2). pp. 62-4. ISSN 0960-9822 (Print)0960-9822 (Linking)

Grossniklaus, U., Vielle-Calzada, J. P., Hoeppner, M. A., Gagliano, W. B. (April 1998) Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science, 280 (5362). pp. 446-50. ISSN 0036-8075 (Print)

Grubor, V., Krasnitz, A., Troge, J. E., Meth, J. L., Lakshmi, B., Kendall, J. T., Yamrom, B., Alex, G., Pai, D., Navin, N. E., Hufnagel, L. A., Lee, Y. H., Cook, K., Allen, S. L., Rai, K. R., Damle, R. N., Calissano, C., Chiorazzi, N., Wigler, M. H., Esposito, D. (February 2009) Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood, 113 (6). pp. 1294-1303. ISSN 0006-4971

Guatelli, J. C., Gingeras, T. R., Richman, D. D. (1990) Alternative splice acceptor utilization during human immunodeficiency virus type 1 infection of cultured cells. Journal of Virology, 64 (9). pp. 4093-4098. ISSN 0022538X (ISSN)

Guillotin, Bruno, Rahni, Ramin, Passalacqua, Michael, Mohammed, Mohammed Ateequr, Xu, Xiaosa, Raju, Sunil Kenchanmane, Ramírez, Carlos Ortiz, Jackson, David, Groen, Simon C, Gillis, Jesse, Birnbaum, Kenneth D (May 2023) A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature, 617 (7962). pp. 785-791. ISSN 0028-0836

Guo, Yu, Alexander, Katherine, Clark, Andrew G, Grimson, Andrew, Yu, Haiyuan (November 2016) Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs. RNA: A publication of the RNA Society, 22 (11). pp. 1663-1672. ISSN 1355-8382

Gutiérrez, R. A., Stokes, T. L., Thum, K., Xu, X., Obertello, M., Katari, M. S., Tanurdzic, M., Dean, A., Nero, D. C., McClung, C. R., Coruzzi, G. M. (March 2008) Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A, 105 (12). pp. 4939-4944. ISSN 0027-8424

Gutmann, D. H., Boguski, M., Marchuk, D., Wigler, M. H., Collins, F. S., Ballester, R. (March 1993) Analysis of the neurofibromatosis type-1 (NF1) GAP-related domain by site-directed mutagenesis. Oncogene, 8 (3). pp. 761-769. ISSN 0950-9232

Gutschner, T., Hammerle, M., Eißmann, M., Hsu, J., Kim, Y., Hung, G., Revenko, A., Arun, G., Stentrup, M., Groß, M., Zörnig, M., MacLeod, A. R., Spector, D. L., Diederichs, S. (February 2013) The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Research, 73 (3). pp. 1180-1189. ISSN 00085472 (ISSN)

Hachiya, T., Ueda, N., Kitagawa, M., Hanke, G., Suzuki, A., Hase, T., Sakakibara, H. (September 2016) Arabidopsis Root-Type Ferredoxin:NADP(H) Oxidoreductase 2 Is Involved in Detoxification of Nitrite in Roots. Plant Cell Physiol, 57 (11). pp. 2440-2450. ISSN 1471-9053 (Electronic)0032-0781 (Linking)

Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T., Kraus, W. L. (May 2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 145 (4). pp. 622-34. ISSN 0092-8674

Hajdu, M., Singer, S., Maki, R. G., Schwartz, G. K., Keohan, M. L., Antonescu, C. R. (July 2010) IGF2 over-expression in solitary fibrous tumours is independent of anatomical location and is related to loss of imprinting. J Pathol, 221 (3). pp. 300-7. ISSN 1096-9896 (Electronic)0022-3417 (Linking)

Hamaguchi, M., Meth, J. L., von Klitzing, C., Wei, W., Esposito, D., Rodgers, L., Walsh, T., Welcsh, P., King, M. C., Wigler, M. H. (October 2002) DBC2, a candidate for a tumor suppressor gene involved in breast cancer. Proceedings of the National Academy of Sciences of the United States of America, 99 (21). pp. 13647-13652. ISSN 0027-8424

Han, C. D., Coe, E. H., Martienssen, R. A. (1992) Molecular cloning and characterization of iojap (ij), a pattern striping gene of maize. EMBO J, 11 (11). pp. 4037-4046. ISSN 0261-4189

Hannon, G. J., Rivas, F. V., Murchison, E. P., Steitz, J. A. (2006) The Expanding Universe of Noncoding RNAs. Cold Spring Harb Symp Quant Biol, 71. pp. 551-564. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

Hannon, G. J., Sun, P., Carnero, A., Xie, L. Y., Maestro, R., Conklin, D. S., Beach, D. (February 1999) MaRX: an approach to genetics in mammalian cells. Science, 283 (5405). pp. 1129-30. ISSN 0036-8075

Harris, L. N., Parker, J., Broadwater, G., Schulz, V., Halligan, K., Geyda, K., Seidman, A., Berry, D., Winer, E., Hudis, C., Krasnitz, A., Hicks, J., Tuck, D. P., Perou, C. (December 2009) Genome-Wide Profiling of Archived Material from CALGB 9840 and 9342 for Paclitaxel (P) and Trastuzumab (T) Response Biomarkers Using Gene Expression and Copy Number Analysis. Cancer Research, 69 (24 (S3). 716S-717S. ISSN 0008-5472

Harris, Benjamin D, Crow, Megan, Fischer, Stephan, Gillis, Jesse (May 2021) Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. Cell Systems. ISSN 2405-4712

Harshey, R. M., Bukhari, A. I. (1980) Flip-Flop Control of Gene Expression. Abstracts of the Annual Meeting of the American Society for Microbiology.

Hasegawa, Y., Tang, D., Takahashi, N., Hayashizaki, Y., Forrest, A. R., Suzuki, H., FANTOM Consortium (2014) CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Sci Rep, 4. p. 5228. ISSN 2045-2322

Hay, A., Jackson, D. P., Ori, N., Hake, S. (2003) Analysis of the competence to respond to KNOTTED1 activity in Arabidopsis leaves using a steroid induction system. Plant Physiology, 131 (4). pp. 1671-1680. ISSN 00320889 (ISSN)

Hazra, Rasmani, Utama, Raditya, Naik, Payal, Dobin, Alexander, Spector, David L (October 2023) Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA sequencing datasets. Stem Cell Reports. ISSN 2213-6711

He, Shuning, Krens, Sf Gabby, Zhan, Huiqing, Gong, Zhiyuan, Hogendoorn, Pancras Cw, Spaink, Herman P, Snaar-Jagalska, B Ewa (September 2011) A ΔRaf1-ER-inducible oncogenic zebrafish liver cell model identifies hepatocellular carcinoma signatures. Journal of Pathology, 225 (1). pp. 19-28. ISSN 0022-3417

Helfman, D. M., Guo, W., Lees-Miller, J. P., Mulligan, G. J., Tsukahara, T., Wormsley, S. (October 1991) Alternative Rna Splicing in the Control of Cytoskeletal Protein Gene-Expression. Journal of Muscle Research and Cell Motility, 12 (5). p. 487. ISSN 0142-4319

Helfman, D. M., Guo, W., Mulligan, G. J., Tsukahara, T., Wormsley, S. (1991) Alternative Rna Splicing in the Control of Gene Expression. Journal of Cellular Biochemistry, 47 (Suppl ). p. 15.

Helfman, D. M., Levy, E. T., Berthier, C., Shtutman, M., Riveline, D., Grosheva, I., Lachish-Zalait, A., Elbaum, M., Bershadsky, A. D. (October 1999) Caldesmon inhibits nonmuscle cell contractility and interferes with the formation of focal adhesions. Molecular Biology of the Cell , 10 (10). pp. 3097-112. ISSN 1059-1524 (Print)

Hemann, M. T., Fridman, J. S., Zilfou, J. T., Hernando, E., Paddison, P. J., Cordon-Cardo, C., Hannon, G. J., Lowe, S. W. (March 2003) An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nature Genetics, 33 (3). pp. 396-400. ISSN 1061-4036

Henderson, B. R., Tansey, W. P., Phillips, S. M., Ramshaw, I. A., Kefford, R. F. (May 1992) Transcriptional and posttranscriptional activation of urokinase plasminogen activator gene expression in metastatic tumor cells. Cancer Res, 52 (9). pp. 2489-96. ISSN 0008-5472 (Print)0008-5472 (Linking)

Henry, Samantha, Trousdell, Marygrace C, Cyrill, Samantha L, Zhao, Yixin, Feigman, Mary J, Bouhuis, Julia M, Aylard, Dominik A, Siepel, Adam, Dos Santos, Camila O (May 2021) Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland. Journal of Mammary Gland Biology and Neoplasia. ISSN 1083-3021

Herrmann, C. H., Mathews, M. B. (December 1989) The adenovirus E1B 19-kilodalton protein stimulates gene expression by increasing DNA levels. Molecular & Cellular Biology, 9 (12). pp. 5412-23. ISSN 0270-7306

Hicks, J. B., Herskowitz, I. (March 1977) Interconversion of Yeast Mating Types II. Restoration of Mating Ability to Sterile Mutants in Homothallic and Heterothallic Strains. Genetics, 85 (3). pp. 373-93. ISSN 0016-6731 (Print)0016-6731 (Linking)

Hicks, J. B., Strathern, J. N., Herskowitz, I. (March 1977) Interconversion of Yeast Mating Types III. Action of the Homothallism (HO) Gene in Cells Homozygous for the Mating Type Locus. Genetics, 85 (3). pp. 395-405. ISSN 0016-6731 (Print)0016-6731 (Linking)

Hodges, E., Smith, A. D., Kendall, J. T., Xuan, Z., Ravi, K., Rooks, M., Zhang, M. Q., Ye, K., Bhattacharjee, A., Brizuela, L., McCombie, W. R., Wigler, M. H., Hannon, G. J., Hicks, J. B. (September 2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research, 19 (9). pp. 1593-1605. ISSN 1088-9051

Hoeppner, D. J., Hengartner, M. O., Schnabel, R. (July 2001) Engulfment genes cooperate with ced-3 to promote cell death in Caenorhabditis elegans. Nature, 412 (6843). pp. 202-206. ISSN 0028-0836

Holt, T. G., Chang, C., Laurent-Winter, C., Murakami, T., Garrels, J. I., Davies, J. E., Thompson, C. J. (April 1992) Global changes in gene expression related to antibiotic synthesis in Streptomyces hygroscopicus. Mol Microbiol, 6 (8). pp. 969-80. ISSN 0950-382X (Print)0950-382X (Linking)

Hopper, J. E., Broach, J. R., Rowe, L. B. (June 1978) Regulation of the galactose pathway in Saccharomyces cerevisiae: induction of uridyl transferase mRNA and dependency on GAL4 gene function. Proc Natl Acad Sci U S A, 75 (6). pp. 2878-82. ISSN 0027-8424 (Print)0027-8424 (Linking)

Hrvatin, S., Hochbaum, D. R., Nagy, M. A., Cicconet, M., Robertson, K., Cheadle, L., Zilionis, R., Ratner, A., Borges-Monroy, R., Klein, A. M., Sabatini, B. L., Greenberg, M. E. (January 2018) Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat Neurosci, 21 (1). pp. 120-129. ISSN 1097-6256 (Print)1097-6256

Hu, J. S., Durst, M., Kerb, R., Truong, V., Ma, J. T., Khurgin, E., Balaban, D., Gingeras, T. R., Hoffman, B. B. (2000) Analysis of drug pharmacology towards predicting drug behavior by expression profiling using high-density oligonucleotide arrays. Annals of the New York Academy of Sciences, 919. pp. 9-15. ISSN 00778923 (ISSN)

Huang, Z. J., Curtin, K. D., Rosbash, M. (1995) PER protein interactions and temperature compensation of a circadian clock in Drosophila. Science, 267 (5201). pp. 1169-1172. ISSN 00368075 (ISSN)

Huang, Z. J., Yu, W., Lovett, C., Tonegawa, S. (2002) Cre/loxP recombination-activated neuronal markers in mouse neocortex and hippocampus. Genesis, 32 (3). pp. 209-217. ISSN 1526954X (ISSN)

Huang, Longwen, Kebschull, Justus M, Fürth, Daniel, Musall, Simon, Kaufman, Matthew T, Churchland, Anne K, Zador, Anthony M (July 2020) BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals. Cell, 182 (1). 177-188.e27. ISSN 0092-8674

Hubisz, Melissa, Williams, Amy, Siepel, Adam (June 2019) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. BioRxiv. (Unpublished)

Hurst, Laurence D, Ghanbarian, Avazeh T, Forrest, Alistair RR, FANTOM consortium, Huminiecki, Lukasz (December 2015) The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biology, 13 (12). e1002315. ISSN 1544-9173

Huttly, A. K., Martienssen, R. A., Baulcombe, D. C. (1988) Sequence heterogeneity and differential expression of the alpha-Amy2 gene family in wheat. Mol Gen Genet, 214 (2). pp. 232-240. ISSN 0026-8925

Hwang, G., Zhu, J. Y., Lee, Y. K., Kim, S., Nguyen, T. T., Kim, J., Oh, E. (July 2017) PIF4 promotes expression of LNG1 and LNG2 to induce thermomorphogenic growth in arabidopsis. Frontiers in Plant Science, 8.

Iijima-Ando, K., Hearn, S. A., Granger, L., Shenton, C., Gatt, A., Chiang, H. C., Hakker, I., Zhong, Y., Iijima, K. (July 2008) Overexpression of neprilysin reduces Alzheimer amyloid-beta 42 (A beta 42)-induced neuron loss and intraneuronal A beta 42 deposits but causes a reduction in cAMP-responsive element-binding protein-mediated transcription, age-dependent axon pathology, and premature death in Drosophila. Journal of Biological Chemistry, 283 (27). pp. 19066-19076. ISSN 0021-9258

Iossifov, I., Levy, D., Allen, J., Ye, K., Ronemus, M., Lee, Y. H., Yamrom, B., Wigler, M. (September 2015) Low load for disruptive mutations in autism genes and their biased transmission. Proc Natl Acad Sci U S A. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Italiano, A., Thomas, R., Breen, M., Zhang, L., Crago, A. M., Singer, S., Khanin, R., Maki, R. G., Mihailovic, A., Hafner, M., Tuschl, T., Antonescu, C. R. (June 2012) The miR-17-92 cluster and its target THBS1 are differentially expressed in angiosarcomas dependent on MYC amplification. Genes Chromosomes Cancer, 51 (6). pp. 569-78. ISSN 1098-2264 (Electronic)1045-2257 (Linking)

Ivanov, S. V., Miller, J., Lucito, R., Tang, C. L., Ivanova, A. V., Pei, J. M., Carbone, M., Cruz, C., Beck, A., Webb, C., Nonaka, D., Testa, J. R., Pass, H. I. (February 2009) Genomic events associated with progression of pleural malignant mesothelioma. International Journal of Cancer, 124 (3). pp. 589-599. ISSN 0020-7136

Jackson, D. P., Roberts, K., Martin, C. (July 1992) Temporal And Spatial Control Of Expression Of Anthocyanin Biosynthetic Genes In Developing Flowers Of Antirrhinum majus. Plant Journal, 2 (4). pp. 425-434. ISSN 0960-7412

Janas, M. L., Hodson, D., Stamataki, Z., Hill, S., Welch, K., Gambardella, L., Trotman, L. C., Pandolfi, P. P., Vigorito, E., Turner, M. (January 2008) The Effect of Deleting p110{delta} on the Phenotype and Function of PTEN-Deficient B Cells. Journal of Immunology, 180 (2). pp. 739-46. ISSN 0022-1767

Je, B. I., Xu, F., Wu, Q., Liu, L., Meeley, R., Gallagher, J. P., Corcilius, L., Payne, R. J., Bartlett, M. E., Jackson, D. (March 2018) The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors. Elife, 7. ISSN 2050-084x

Jia, H., Li, M., Li, W., Liu, L., Jian, Y., Yang, Z., Shen, X., Ning, Q., Du, Y., Zhao, R., Jackson, D., Yang, X., Zhang, Z. (February 2020) A Serine/Threonine Protein Kinase Encoding Gene KERNEL NUMBER PER ROW6 Regulates Maize Grain Yield. Nature Communications, 11 (988). pp. 1-11. ISSN 2041-1723 (Public Dataset)

Jiang, W., Sordella, R., Chen, G. C., Hakre, S., Roy, A. L., Settleman, J. (January 2005) An FF domain-dependent protein interaction mediates a signaling pathway for growth factor-induced gene expression. Molecular Cell, 17 (1). pp. 23-35. ISSN 1097-2765

Johnson, K. E., Cameron, S., Toda, T., Wigler, M. H., Zoller, M. J. (1987) Expression in Escherichia coli of BCY1, the regulatory subunit of cyclic AMP-dependent protein kinase from Saccharomyces cerevisiae. Journal of Biological Chemistry, 262 (18). pp. 8636-8642.

Joneson, T., White, M. A., Wigler, M. H., Bar-Sagi, D. (February 1996) Stimulation of membrane ruffling and MAP kinase activation by distinct effectors of RAS. Science, 271 (5250). pp. 810-812. ISSN 0036-8075

Jordan, Shawn (2016) David Spector: Coordinating gene expression in space and time. The Journal of Cell Biology, 214 (7). pp. 786-787.

Jung, V., Chen, L., Hofmann, S. L., Wigler, M. H., Powers, S. (March 1995) Mutations in the SHR5 gene of Saccharomyces cerevisiae suppress Ras function and block membrane attachment and palmitoylation of Ras proteins. Mol Cell Biol, 15 (3). pp. 1333-42. ISSN 0270-7306 (Print)

Jung, V., Wei, W., Ballester, R., Camonis, J., Mi, S., Van Aelst, L., Wigler, M. H., Broek, D. (June 1994) Two types of RAS mutants that dominantly interfere with activators of RAS. Mol Cell Biol, 14 (6). pp. 3707-18. ISSN 0270-7306 (Print)

Kaaij, L. T. J., van de Wetering, M., Fang, F., Decato, B., Molaro, A., van de Werken, H. J. G., van Es, J. H., Schuijers, J., de Wit, E., de Laat, W., Hannon, G. J., Clevers, H. C., Smith, A. D., Ketting, R. F. (2013) DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus. Genome Biology, 14 (5). ISSN 1465-6906

Kang, Y. J., Lee, Y. K., Kim, I. J. (October 2019) Identification of Differentially Up-regulated Genes in Apple with White Rot Disease. Plant Pathol J, 35 (5). pp. 530-537. ISSN 1598-2254 (Print)1598-2254

Kapranov, P., Sementchenko, V. I., Gingeras, T. R. (April 2003) Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Briefings in Functional Genomics & Proteomics, 2 (1). pp. 47-56. ISSN 1473-9550 (Print)1473-9550

Kataoka, T., Broek, D., Wigler, M. H. (December 1985) DNA sequence and characterization of the S. cerevisiae gene encoding adenylate cyclase. Cell, 43 (2). pp. 493-505. ISSN 0092-8674

Kataoka, T., Powers, S., Cameron, S., Fasano, O., Goldfarb, M., Broach, J., Wigler, M. H. (1985) Functional homology of mammalian and yeast RAS genes. Cell, 40 (1). pp. 19-26.

Kataoka, T., Powers, S., McGill, C., Fasano, O., Strathern, J., Broach, J., Wigler, M. H. (June 1984) Genetic analysis of yeast RAS1 and RAS2 genes. Cell, 37 (2). pp. 437-445. ISSN 0092-8674

Katz, E. B., Steinhelper, M. E., Delcarpio, J. B., Daud, A. I., Claycomb, W. C., Field, L. J. (June 1992) Cardiomyocyte proliferation in mice expressing alpha-cardiac myosin heavy chain-SV40 T-antigen transgenes. Am J Physiol, 262 (6 Pt 2). H1867-76. ISSN 0002-9513 (Print)0002-9513 (Linking)

Kaufmann, Berwind Petersen, Gay, Helen (1958) The nuclear membrane as an intermediary in gene-controlled reactions. The Nucleus, 1. pp. 57-74.

Kel, A. E., Kel-Margoulis, O. V., Farnham, P. J., Bartley, S. M., Wingender, E., Zhang, M. Q. (May 2001) Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. Journal of Molecular Biology, 309 (1). pp. 99-120. ISSN 0022-2836

Keller, M. M., Jaillais, Y., Pedmale, U. V., Moreno, J. E., Chory, J., Ballare, C. L. (July 2011) Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades. Plant J, 67 (2). pp. 195-207. ISSN 0960-7412

Kelley, K. A., Stamm, S., Kozak, C. A. (June 1992) Expression and chromosome localization of the murine cystic fibrosis transmembrane conductance regulator. Genomics, 13 (2). pp. 381-8. ISSN 0888-7543 (Print)0888-7543 (Linking)

Ketting, R. F., Fischer, S. E. J., Bernstein, E., Sijen, T., Hannon, G. J., Plasterk, R. H. A. (October 2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes and Development, 15 (20). pp. 2654-2659. ISSN 0890-9369

Khosravi-Far, R., White, M. A., Westwick, J. K., Solski, P. A., Chrzanowska-Wodnicka, M., Van Aelst, L., Wigler, M. H., Der, C. J. (July 1996) Oncogenic Ras activation of Raf/mitogen-activated protein kinase-independent pathways is sufficient to cause tumorigenic transformation. Mol Cell Biol, 16 (7). pp. 3923-33. ISSN 0270-7306 (Print)

Khouider, Souraya, Borges, Filipe, LeBlanc, Chantal, Ungru, Alexander, Schnittger, Arp, Martienssen, Robert, Colot, Vincent, Bouyer, Daniel (January 2021) Male fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function. Nature Communications, 12 (1). p. 410. ISSN 2041-1723

Kininis, M., Chen, B. S., Diehl, A. G., Isaacs, G. D., Zhang, T., Siepel, A. C., Clark, A. G., Kraus, W. L. (July 2007) Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol, 27 (14). pp. 5090-104. ISSN 0270-7306 (Print)0270-7306

Kinney, Brian, Sahu, Shubham, Stec, Natalia, Hills-Muckey, Kelly, Adams, Dexter W, Wang, Jing, Jaremko, Matt, Joshua-Tor, Leemor, Keil, Wolfgang, Hammell, Christopher M (August 2023) A circadian-like gene network programs the timing and dosage of heterochronic miRNA transcription during C. elegans development. Developmental Cell. S1534-5807(23)00402. ISSN 1534-5807

Klein, Harry, Gallagher, Joseph, Demesa-Arevalo, Edgar, Abraham-Juárez, María Jazmín, Heeney, Michelle, Feil, Regina, Lunn, John E, Xiao, Yuguo, Chuck, George, Whipple, Clinton, Jackson, David, Bartlett, Madelaine (January 2022) Recruitment of an ancient branching program to suppress carpel development in maize flowers. Proceedings of the National Academy of Sciences of USA, 119 (2). e2115871119-e2115871119. ISSN 0027-8424

Kline, A. D., Krantz, I. D., Bando, M., Shirahige, K., Chea, S., Sakata, T., Rao, S., Dorsett, D., Singh, V. P., Gerton, J. L., Horsfield, J. A., Calof, A. L., Katz, O., Grados, M., Raible, S., Baranano, K., Lyon, G., Musio, A., Carrico, C. S., Clemens, D. K., Caudill, P., Massa, V., McGill, B. E., Dommestrup, A., O'Connor, J., Haaland, R. E. (March 2019) Cornelia de Lange syndrome, related disorders, and the Cohesin complex: Abstracts from the 8th biennial scientific and educational symposium 2018. Am J Med Genet A, 179 (6). pp. 1080-1090. ISSN 1552-4825

Kosiol, C., Vinar, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., Siepel, A. (2008) Patterns of positive selection in six Mammalian genomes. Plos Genetics, 4 (8). e1000144. ISSN 1553-7390

Kozal, M. J., Shah, N., Yang, R., Shen, N., Fucini, R., Merigan, T. C., Richman, D. D., Chee, M. S., Gingeras, T. R. (1995) Natural polymorphism of HIV-1 clade B protease gene and implications for therapy. Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology, 10 (S3). p. 76. ISSN 1077-9450

Krainer, A. R., Mayeda, A., Kozak, D., Binns, G. (July 1991) Functional expression of cloned human splicing factor SF2: homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators. Cell, 66 (2). pp. 383-394. ISSN 0092-8674

Kraus, V. B., Inostroza, J. A., Reinberg, D., Moran, E., Nevins, J. R. (January 1993) The Activation of the Hsp70-Promoter by E1a Coincides with a Release of Tbp from an Interaction with the Inhibitory Factor Dr1. Journal of Cellular Biochemistry, 53 (17B). p. 226. ISSN 0730-2312

Krishnakumar, V., Choi, Y., Beck, E., Wu, Q., Luo, A., Sylvester, A., Jackson, D., Chan, A. P. (November 2015) A Maize Database Resource that Captures Tissue-Specific and Subcellular-Localized Gene Expression, via Fluorescent Tags and Confocal Imaging. (Maize Cell Genomics Database). Plant & cell physiology, 56 (1). e12. ISSN 0032-0781

Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Marques-Bonet, T., Andres, A. M., Viola, B., Paabo, S., Meyer, M., Siepel, A., Castellano, S. (February 2016) Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530 (7591). pp. 429-433. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Kusenda, M., Vacic, V., Malhotra, D., Rodgers, L., Pavon, K., Meth, J., Kumar, R. A., Christian, S. L., Peeters, H., Cho, S. S., Addington, A., Rapoport, J. L., Sebat, J. (December 2015) The Influence of Microdeletions and Microduplications of 16p11.2 on Global Transcription Profiles. J Child Neurol, 30 (14). pp. 1947-1953. ISSN 1708-8283 (Electronic)0883-0738 (Linking)

Kwoh, T. J., Kwoh, D. Y., McCue, A. W., Davis, G. R., Patrick, D., Gingeras, T. R. (October 1986) Introduction and expression of the bacterial PaeR7 methylase gene in mammalian cells. Proc Natl Acad Sci U S A, 83 (20). pp. 7713-7. ISSN 0027-8424 (Print)0027-8424 (Linking)

Kwoh, T. J., Zipser, D., Wigler, M. H. (1983) Mutational analysis of the cloned chicken thymidine kinase gene. J Mol Appl Genet, 2 (2). pp. 191-200. ISSN 0271-6801 (Print)

Lachke, S. A., Alkuraya, F. S., Kneeland, S. C., Ohn, T., Aboukhalil, A., Howell, G. R., Saadi, I., Cavallesco, R., Yue, Y. Z., Tsai, A. C. H., Nair, K. S., Cosma, M. I., Smith, R. S., Hodges, E., AlFadhli, S. M., Al-Hajeri, A., Shamseldin, H. E., Behbehani, A., Hannon, G. J., Bulyk, M. L., Drack, A. V., Anderson, P. J., John, S. W. M., Maas, R. L. (March 2011) Mutations in the RNA Granule Component TDRD7 Cause Cataract and Glaucoma. Science, 331 (6024). pp. 1571-1576. ISSN 0036-8075

Lai, J. S., Cleary, M. A., Herr, W. (January 1993) A Single Amino-Acid Exchange Transfers Vp16-Induced Positive Control from the Oct-1 to the Oct-2 Homeodomain. Journal of Cellular Biochemistry, 53 (17B). p. 81. ISSN 0730-2312

Lam, Siew Hong, Wu, Yi Lian, Vega, Vinsensius B, Miller, Lance D, Spitsbergen, Jan, Tong, Yan, Zhan, Huiqing, Govindarajan, Kunde R, Lee, Serene, Mathavan, Sinnakarupan, Murthy, Karuturi R Krishna, Buhler, Donald R, Liu, Edison T, Gong, Zhiyuan (January 2006) Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression. Nature Biotechnology, 24 (1). pp. 73-75. ISSN 1087-0156

Lanctot, Amy (January 2024) On the cutting edge of development: Laser-assisted microdissection of the Arabidopsis gynoecium reveals tissue-specific gene expression patterns. Plant Physiology. ISSN 0032-0889

Laspia, M. F., Rice, A. P., Mathews, M. B. (December 1990) Synergy between HIV-1 Tat and adenovirus E1A is principally due to stabilization of transcriptional elongation. Genes Dev, 4 (12B). pp. 2397-408. ISSN 0890-9369 (Print)0890-9369 (Linking)

Laspia, M. F., Rice, A. P., Mathews, M. B. (1991) Transactivation Hiv-1 Gene Expression by Tat Is Due to Stimulation of Both Transcriptional Initiation and Elongation. AIDS Research & Human Retroviruses, 7 (2). pp. 173-174.

Latham, K. E., Garrels, J. I., Solter, D. (January 1993) Two-dimensional gel analysis of protein synthesis. Methods Enzymol, 225. pp. 473-89. ISSN 0076-6879

Lee, B. H., Liu, M., Mathews, M. B. (February 1998) Regulation of the human proliferating cell nuclear antigen promoter by the adenovirus E1A-associated protein p107. Journal of Virology, 72 (2). pp. 1138-45. ISSN 0022-538X

Lee, I. S., Carvalho, C. M., Douvaras, P., Ho, S. M., Hartley, B. J., Zuccherato, L. W., Ladran, I. G., Siegel, A. J., McCarthy, S., Malhotra, D., Sebat, J., Rapoport, J., Fossati, V., Lupski, J. R., Levy, D. L., Brennand, K. J. (June 2015) Characterization of molecular and cellular phenotypes associated with a heterozygous deletion using patient-derived hiPSC neural cells. NPJ Schizophr, 1. ISSN 2334-265X (Print)2334-265X (Linking)

Lee, J. H. (March 2017) Quantitative approaches for investigating the spatial context of gene expression. Wiley Interdiscip Rev Syst Biol Med, 9 (2). ISSN 1939-005X (Electronic)1939-005X (Linking)

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Ferrante, T. C., Terry, R., Turczyk, B. M., Yang, J. L., Lee, H. S., Aach, J., Zhang, K., Church, G. M. (March 2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc, 10 (3). pp. 442-58. ISSN 1750-2799

Lee, J. H., Park, I. H., Gao, Y., Li, J. B., Li, Z., Daley, G. Q., Zhang, K., Church, G. M. (November 2009) A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet, 5 (11). e1000718. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Lee, Je H. (July 2017) De Novo Gene Expression Reconstruction in Space. Trends in Molecular Medicine, 23 (7). pp. 583-593. ISSN 1471-4914

Lee, J., Shah, M., Ballouz, S., Crow, M., Gillis, J. (May 2020) CoCoCoNet: conserved and comparative co-expression across a diverse set of species. Nucleic Acids Research. ISSN 0305-1048

Lee, John, Shah, Manthan, Ballouz, Sara, Crow, Megan, Gillis, Jesse (April 2020) CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species. BioRxiv. (Unpublished)

Lee, Seung Cho, Martienssen, Robert A (September 2021) Regulation of retrotransposition in Arabidopsis. Biochemical Society Transactions. ISSN 0300-5127

Lees-Miller, J. P., Helfman, D. M. (September 1991) The molecular basis for tropomyosin isoform diversity. Bioessays, 13 (9). pp. 429-37. ISSN 0265-9247 (Print)0265-9247 (Linking)

Lei, K. J., Gluzman, Y., Pan, C. J., Chou, J. Y. (May 1992) Immortalization of Virus-Free Human Placental Cells That Express Tissue-Specific Functions. Molecular Endocrinology, 6 (5). pp. 703-712. ISSN 0888-8809

Li, Zhen, Huang, Xiaoqian, Zhan, Huiqing, Zeng, Zhiqiang, Li, Caixia, Spitsbergen, Jan M, Meierjohann, Svenja, Schartl, Manfred, Gong, Zhiyuan (February 2012) Inducible and repressable oncogene-addicted hepatocellular carcinoma in Tet-on xmrk transgenic zebrafish. Journal of Hepatology, 56 (2). pp. 419-425. ISSN 0168-8278

Li, Zhen, Zheng, Weiling, Wang, Zhengyuan, Zeng, Zhiqiang, Zhan, Huiqing, Li, Caixia, Zhou, Li, Yan, Chuan, Spitsbergen, Jan M, Gong, Zhiyuan (March 2013) A transgenic zebrafish liver tumor model with inducible Myc expression reveals conserved Myc signatures with mammalian liver tumors. DMM Disease Models and Mechanisms, 6 (2). pp. 414-423. ISSN 1754-8403

Li, H., Wu, G., Ware, D., Davis, K. R., Yang, Z. (October 1998) Arabidopsis Rho-related GTPases: differential gene expression in pollen and polar localization in fission yeast. Plant Physiology, 118 (2). pp. 407-17. ISSN 0032-0889 (Print)

Li, L., Ljung, K., Breton, G., Schmitz, R. J., Pruneda-Paz, J., Cowing-Zitron, C., Cole, B. J., Ivans, L. J., Pedmale, U. V., Jung, H. S., Ecker, J. R., Kay, S. A., Chory, J. (April 2012) Linking photoreceptor excitation to changes in plant architecture. Genes Dev, 26 (8). pp. 785-90. ISSN 0890-9369

Li, L., Petsch, K., Shimizu, R., Liu, S., Xu, W. W., Ying, K., Yu, J., Scanlon, M. J., Schnable, P. S., Timmermans, M. C. P., Springer, N. M., Muehlbauer, G. J. (January 2013) Mendelian and Non-Mendelian Regulation of Gene Expression in Maize. PLoS Genetics, 9 (1). Article number e1003202. ISSN 15537390 (ISSN)

Li, L., Zhang, Q., Pedmale, U. V., Nito, K., Fu, W., Lin, L., Hazen, S. P., Chory, J. (October 2014) PIL1 participates in a negative feedback loop that regulates its own gene expression in response to shade. Mol Plant, 7 (10). pp. 1582-5. ISSN 1674-2052

Li, T., Huang, J., Jiang, Y., Zeng, Y., He, F., Zhang, M. Q., Han, Z., Zhang, X. (March 2009) Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics, 93 (3). pp. 235-242.

Li, Y., Brooks, M., Yeoh-Wang, J., McCoy, R. M., Rock, T. M., Pasquino, A., Moon, C. I., Patrick, R. M., Tanurdzic, M., Ruffel, S., Widhalm, J. R., McCombie, W. R., Coruzzi, G. M. (October 2019) SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling. Plant Physiol. ISSN 0032-0889

Liao, S. C., Hsu, H. W., Chuang, K. L., Huang, Z. Y., Lin, K. T., Hsu, W. H., Chang, K. H., Huang, C. F., Su, C. L. (June 2019) Using the Pleiotropic Characteristics of Curcumin to Validate the Potential Application of a Novel Gene Expression Screening Platform. Nutrients, 11 (6). ISSN 2072-6643

Lin, C. I., Livi, G. P., Ivy, J. M., Klar, A. J. (June 1990) Extragenic suppressors of mar2(sir3) mutations in Saccharomyces cerevisiae. Genetics, 125 (2). pp. 321-31. ISSN 0016-6731 (Print)0016-6731 (Linking)

Little, Clarence Cook (May 1920) Is there linkage between the genes for yellow and for black in mice? The American Naturalist, 54 (632). pp. 267-270.

Liu, H. C., Enikolopov, G., Chen, Y. Z. (September 2012) Cul4B regulates neural progenitor cell growth. BMC Neuroscience, 13. p. 13. ISSN 1471-2202

Liu, H. X., Cartegni, L., Zhang, M. Q., Krainer, A. R. (January 2001) A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nature Genetics, 27 (1). pp. 55-58. ISSN 1061-4036

Liu, J. D., Rivas, F. V., Wohlschlegel, J., Yates, J. R., Parker, R., Hannon, G. J. (December 2005) A role for the P-body component GW182 in microRNA function. Nature Cell Biology, 7 (12). pp. 1261-1266. ISSN 1465-7392

Liu, M., Lee, B. H., Mathews, M. B. (May 1999) Involvement of RFX1 protein in the regulation of the human proliferating cell nuclear antigen promoter. Journal of Biological Chemistry, 274 (22). pp. 15433-9. ISSN 0021-9258 (Print)

Liu, X., Yu, Q., Huang, Z., Zwiebel, L. J., Hall, J. C., Rosbash, M. (1991) The strength and periodicity of D. melanogaster circadian rhythms are differentially affected by alterations in period gene expression. Neuron, 6 (5). pp. 753-766. ISSN 08966273 (ISSN)

Liu, Y., Gong, W., Huang, C. C., Herr, W., Cheng, X. (July 1999) Crystal structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16. Genes and Development, 13 (13). pp. 1692-703. ISSN 0890-9369 (Print)

Liu, Y., Hengartner, M. O., Herr, W. (January 1999) Selected elements of herpes simplex virus accessory factor HCF are highly conserved in Caenorhabditis elegans. Molecular and Cellular Biology, 19 (1). pp. 909-15. ISSN 0270-7306 (Print)

Lo Iacono, N., Mantero, S., Chiarelli, A., Garcia, E. L., Mills, A. A., Morasso, M. I., Costanzo, A., Levi, G., Guerrini, L., Merlo, G. R. (April 2008) Regulation of Dlx5 and Dlx6 gene expression by p63 is involved in EEC and SHFM congenital limb defects. Development, 135 (7). pp. 1377-1388. ISSN 0950-1991

Lodha, M., Marco, C. F., Timmermans, M. C. (March 2013) The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes & Development, 27 (6). pp. 596-601. ISSN 0890-9369

Lohia, Ruchi, Fox, Nathan, Gillis, Jesse (November 2022) A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships. Genome Biology, 23 (1). p. 238. ISSN 1474-760X

Lovell, P. V., Wirthlin, M., Kaser, T., Buckner, A. A., Carleton, J. B., Snider, B. R., McHugh, A. K., Tolpygo, A., Mitra, P. P., Mello, C. V. (February 2020) ZEBrA - Zebra finch Expression Brain Atlas: a resource for comparative molecular neuroanatomy and brain evolution studies. J Comp Neurol. ISSN 0021-9967 (Public Dataset)

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D. (August 2011) Three periods of regulatory innovation during vertebrate evolution. Science, 333 (6045). pp. 1019-24. ISSN 0036-8075

Lu, Shaina, Ortiz, Cantin, Fürth, Daniel, Fischer, Stephan, Meletis, Konstantinos, Zador, Anthony, Gillis, Jesse (July 2021) Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain. PLoS Biology, 19 (7). e3001341. ISSN 1545-7885

Lu, Shaina, Ortiz, Cantin, Fürth, Daniel, Fischer, Stephan, Meletis, Konstantinos, Zador, Anthony, Gillis, Jesse (October 2020) Replicability of spatial gene expression atlas data from the adult mouse brain. bioRxiv. (Unpublished)

Luke, M. M., Della Seta, F., Di Como, C. J., Sugimoto, H., Kobayashi, R., Arndt, K. T. (June 1996) The SAP, a new family of proteins, associate and function positively with the SIT4 phosphatase. Molecular and Cellular Biology, 16 (6). pp. 2744-55. ISSN 0270-7306

Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D., Woolf, P. J. (May 2009) GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 10. p. 161.

Luo, W., Hankenson, K. D., Woolf, P. J. (November 2008) Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinformatics, 9. p. 467.

Luo, W. J., Friedman, M. S., Hankenson, K. D., Woolf, P. J. (May 2011) Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization. BMC Systems Biology, 5 (82). ISSN 1752-0509

Ma, H. (May 1997) Polycomb in plants. Trends in Genetics, 13 (5). p. 167. ISSN 0168-9525

Ma, H. (June 1997) The on and off of floral regulatory genes. Cell, 89 (6). pp. 821-4. ISSN 0092-8674 (Print)

Ma, H. (April 1994) The unfolding drama of flower development: recent results from genetic and molecular analyses. Genes Dev, 8 (7). pp. 745-56. ISSN 0890-9369 (Print)

Macleod, K. F., Sherry, N., Hannon, G., Beach, D., Tokino, T., Kinzler, K., Vogelstein, B., Jacks, T. (1995) p53-Dependent and independent expression of p21 during cell growth, differentiation, and DNA damage. Genes and Development, 9 (8). pp. 935-944. ISSN 08909369

Maestro, R., Dei Tos, A. P., Hamamori, Y., Krasnokutsky, S., Sartorelli, V., Kedes, L., Doglioni, C., Beach, D. H., Hannon, G. J. (September 1999) Twist is a potential oncogene that inhibits apoptosis. Genes and Development, 13 (17). pp. 2207-17. ISSN 0890-9369

Marcus, S., Polverino, A., Barr, M., Wigler, M. H. (August 1994) Complexes between STE5 and components of the pheromone-responsive mitogen-activated protein kinase module. Proc Natl Acad Sci U S A, 91 (16). pp. 7762-6. ISSN 0027-8424 (Print)

Marcus, S., Polverino, A., Chang, E., Robbins, D., Cobb, M. H., Wigler, M. H. (June 1995) Shk1, a homolog of the Saccharomyces cerevisiae Ste20 and mammalian p65PAK protein kinases, is a component of a Ras/Cdc42 signaling module in the fission yeast Schizosaccharomyces pombe. Proc Natl Acad Sci U S A, 92 (13). pp. 6180-4. ISSN 0027-8424 (Print)

Marcus, S., Polverino, A., Robbins, D., Cobb, M., Wigler, M. H. (April 1994) Conservation of Ste20-Related Protein-Kinases in Eukaryotes. Faseb Journal, 8 (7). A1431-A1431. ISSN 0892-6638

Martienssen, R. A. (March 1998) Functional genomics: Probing plant gene function and expression with transposons. Proceedings of the National Academy of Sciences of the United States of America, 95 (5). pp. 2021-2026. ISSN 0027-8424

Martinez, M. A. Q., Kinney, B. A., Medwig-Kinney, T. N., Ashley, G., Ragle, J. M., Johnson, L., Aguilera, J., Hammell, C. M., Ward, J. D., Matus, D. Q. (January 2020) Rapid Degradation of Caenorhabditis elegans Proteins at Single-Cell Resolution with a Synthetic Auxin. G3 (Bethesda, Md.), 10 (1). pp. 267-280. ISSN 21601836 (ISSN) (Public Dataset)

Maturana, Carola J, Verpeut, Jessica L, Kooshkbaghi, Mahdi, Engel, Esteban A (June 2021) Novel tool to quantify with single-cell resolution the number of incoming AAV genomes co-expressed in the mouse nervous system. Gene Therapy (Basingstoke). ISSN 0969-7128

Matushansky, I., Hernando, E., Socci, N. D., Matos, T., Mills, J., Edgar, M. A., Schwartz, G. K., Singer, S., Cordon-Cardo, C., Maki, R. G. (April 2008) A developmental model of sarcomagenesis defines a differentiation-based classification for liposarcomas. Am J Pathol, 172 (4). pp. 1069-80. ISSN 0002-9440 (Print)0002-9440 (Linking)

Matushansky, I., Hernando, E., Socci, N. D., Mills, J. E., Matos, T. A., Edgar, M. A., Singer, S., Maki, R. G., Cordon-Cardo, C. (November 2007) Derivation of sarcomas from mesenchymal stem cells via inactivation of the Wnt pathway. J Clin Invest, 117 (11). pp. 3248-57. ISSN 0021-9738 (Print)0021-9738 (Linking)

McArthur, H. L., Tan, L. K., Patil, S., Wigler, M. H., Hudis, C. A., Hicks, J. B., Norton, L. (January 2009) High resolution representational oligonucleotide microarray analysis (ROMA) suggests that TOPO2 and HER2 co-amplification is uncommon in human breast cancer. Cancer Res, 69 (2, Sup). 163S-163S. ISSN 0008-5472

McClintock, B. (1951) Chromosome organization and genic expression. Cold Spring Harb Symp Quant Biol, 16. pp. 13-47. ISSN 0091-7451 (Print)0091-7451 (Linking)

McClintock, B. (1983) Trauma as a Means of Initiating Change in Genome Organization and Expression. In Vitro-Journal of the Tissue Culture Association, 19 (3). pp. 283-284. ISSN 0073-5655

McCombie, W. R., De la Bastide, M., Habermann, K., Parnell, L., Dedhia, N., Gnoj, L., Schutz, K., Huang, E., Spiegel, L., Yordan, C., Sehkon, M., Murray, J., Sheet, P., Cordes, M., Threideh, J., Stoneking, T., Kalicki, J., Graves, T., Harmon, G., Edwards, J., Latreille, P., Courtney, L., Cloud, J., Abbott, A., Scott, K., Johnson, D., Minx, P., Bentley, D., Fulton, B., Miller, N., Greco, T., Kemp, K., Kramer, J., Fulton, L., Mardis, E., Dante, M., Pepin, K., Hillier, L., Nelson, J., Spieth, J., Simorowski, J., May, B., Ma, P., Preston, R., Vil, D., Lei, H. S., Shekher, M., Matero, A., Shah, R., Swaby, I., O'Shaughnessy, A., Rodriguez, M., Hoffman, J., Till, S., Granat, S., Shohdy, N., Hasegawa, A., Hameed, A., Lodhi, M., Johnson, A., Chen, E., Marra, M., Wilson, R. K., Martienssen, R. (2000) The complete sequence of a heterochromatic island from a higher eukaryote. Cell, 100 (3). pp. 377-386. ISSN 00928674 (ISSN)

McKay, R. (December 1979) Probing eukaryotic gene control. Nature, 282 (5739). pp. 556-7. ISSN 0028-0836 (Print)0028-0836 (Linking)

McVey, D., Ray, S., Gluzman, Y., Berger, L., Wildeman, A. G., Marshak, D. R., Tegtmeyer, P. (September 1993) Cdc2 Phosphorylation of Threonine 124 Activates the Origin-Unwinding Functions of Simian-Virus 40-T Antigen. Journal of Virology, 67 (9). pp. 5206-5215. ISSN 0022-538X

Meyers, D. A., Antonarakis, S. E., Fearon, E. R., Mallonee, R. L., Waber, P. G., Phillips, J. A., Kazazian, H. H., Levine, M., Kronenberg, H. M., Wigler, M. H., Ullrich, A. (1984) Use of DNA Polymorphisms to Establish the Linkage Map of the Pth, Beta-Globin, C-Ha-Ras-1, and Insulin Loci on 11p. Cytogenetics and Cell Genetics, 37 (1-4). pp. 540-541. ISSN 0301-0171

Michaeli, T., Bloom, T. J., Martins, T., Loughney, K., Ferguson, K., Riggs, M., Rodgers, L., Beavo, J. A., Wigler, M. H. (June 1993) Isolation and characterization of a previously undetected human cAMP phosphodiesterase by complementation of cAMP phosphodiesterase- deficient Saccharomyces cerevisiae. Journal of Biological Chemistry, 268 (17). pp. 12925-12932. ISSN 0021-9258

Michaeli, T., Field, J., Ballester, R., O'Neill, K., Wigler, M. H. (October 1989) Mutants of H-ras that interfere with RAS effector function in Saccharomyces cerevisiae. Embo J, 8 (10). pp. 3039-44. ISSN 0261-4189

Mills, A. A. (June 2001) Changing colors in mice: an inducible system that delivers. Genes & Development, 15 (12). pp. 1461-1467. ISSN 0890-9369

Mirbahai, Leda, Williams, Timothy D, Zhan, Huiqing, Gong, Zhiyuan, Chipman, J Kevin (January 2011) Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis. BMC Genomics, 12 (1). p. 3. ISSN 1471-2164

Misteli, T., Spector, D. L. (1998) The cellular organization of gene expression. Current Opinion in Cell Biology, 10. pp. 323-331. ISSN 0955-0674

Mistry, M., Gillis, J., Pavlidis, P. (2013) Genome-wide expression profiling of schizophrenia using a large combined cohort. Molecular Psychiatry, 18 (2). pp. 215-225. ISSN 13594184 (ISSN)

Mistry, M., Gillis, J., Pavlidis, P. (September 2013) Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls. BMC Neuroscience, 14 (1). p. 105. ISSN 1471-2202

Mital, R., Kobayashi, R., Hernandez, N. (December 1996) RNA polymerase III transcription from the human U6 and adenovirus type 2 VAI promoters has different requirements for human BRF, a subunit of human TFIIIB. Molecular and Cellular Biology, 16 (12). pp. 7031-42. ISSN 0270-7306

Miyabayashi, Koji, Baker, Lindsey A, Deschênes, Astrid, Traub, Benno, Caligiuri, Giuseppina, Plenker, Dennis, Alagesan, Brinda, Belleau, Pascal, Li, Siran, Kendall, Jude, Jang, Gun Ho, Kawaguchi, Risa Karakida, Somerville, Tim DD, Tiriac, Hervé, Hwang, Chang-Il, Burkhart, Richard A, Roberts, Nicholas J, Wood, Laura D, Hruban, Ralph H, Gillis, Jesse, Krasnitz, Alexander, Vakoc, Christopher R, Wigler, Michael, Notta, Faiyaz, Gallinger, Steven, Park, Youngkyu, Tuveson, David A (October 2020) Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes. Cancer Discovery, 10 (10). pp. 1566-1589. ISSN 2159-8274

Mizukami, Y., Ma, H. (March 1997) Determination of Arabidopsis floral meristem identity by AGAMOUS. Plant Cell, 9 (3). pp. 393-408. ISSN 1040-4651 (Print)

Mizukami, Y., Ma, H. (October 1992) Ectopic expression of the floral homeotic gene AGAMOUS in transgenic Arabidopsis plants alters floral organ identity. Cell, 71 (1). pp. 119-31. ISSN 0092-8674 (Print)0092-8674 (Linking)

Mizukami, Y., Ma, H. (January 1993) Functional-Analysis of the Arabidopsis Floral Homeotic Gene Agamous in Transgenic Plants. Journal of Cellular Biochemistry, 53 (17B). p. 15. ISSN 0730-2312

Mo, Yan, Duan, Shoufu, Zhang, Xu, Hua, Xu, Zhou, Hui, Wei, Hong-Jian, Watanabe, Jun, McQuillan, Nicholas, Su, Zhenyi, Gu, Wei, Wu, Cheng-Chia, Vakoc, Christopher R, Hashizume, Rintaro, Chang, Kenneth, Zhang, Zhiguo (October 2022) Epigenome programing by H3.3K27M mutation creates a dependence of pediatric glioma on SMARCA4. Cancer Discovery. CD-21. ISSN 2159-8274

Mohammed, J., Bortolamiol-Becet, D., Flynt, A. S., Gronau, I., Siepel, A., Lai, E. C. (August 2014) Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila. RNA, 20 (8). pp. 1195-209. ISSN 1355-8382

Moreno, Pablo, Fexova, Silvie, George, Nancy, Manning, Jonathan R, Miao, Zhichiao, Mohammed, Suhaib, Muñoz-Pomer, Alfonso, Fullgrabe, Anja, Bi, Yalan, Bush, Natassja, Iqbal, Haider, Kumbham, Upendra, Solovyev, Andrey, Zhao, Lingyun, Prakash, Ananth, García-Seisdedos, David, Kundu, Deepti J, Wang, Shengbo, Walzer, Mathias, Clarke, Laura, Osumi-Sutherland, David, Tello-Ruiz, Marcela Karey, Kumari, Sunita, Ware, Doreen, Eliasova, Jana, Arends, Mark J, Nawijn, Martijn C, Meyer, Kerstin, Burdett, Tony, Marioni, John, Teichmann, Sarah, Vizcaíno, Juan Antonio, Brazma, Alvis, Papatheodorou, Irene (November 2021) Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Research. ISSN 0305-1048

Morris, G. F., Bischoff, J. R., Mathews, M. B. (January 1996) Transcriptional activation of the human proliferating-cell nuclear antigen promoter by p53. Proceedings of the National Academy of Sciences, 93 (2). pp. 895-9. ISSN 0027-8424 (Print)

Morris, G. F., Mathews, M. B. (December 1991) The adenovirus E1A transforming protein activates the proliferating cell nuclear antigen promoter via an activating transcription factor site. J Virol, 65 (12). pp. 6397-406. ISSN 0022-538X (Print)0022-538X (Linking)

Moukarzel, Lea A, Ferrando, Lorenzo, Da Cruz Paula, Arnaud, Brown, David N, Geyer, Felipe C, Pareja, Fresia, Piscuoglio, Salvatore, Papanastasiou, Anastasios D, Fusco, Nicola, Marchiò, Caterina, Abu-Rustum, Nadeem R, Murali, Rajmohan, Brogi, Edi, Wen, Hannah Y, Norton, Larry, Soslow, Robert A, Vincent-Salomon, Anne, Reis-Filho, Jorge S, Weigelt, Britta (April 2021) The genetic landscape of metaplastic breast cancers and uterine carcinosarcomas. Molecular Oncology, 15 (4). pp. 1024-1039. ISSN 1574-7891

Mu, D., Chen, L. Y., Zhang, X. P., See, L. H., Koch, C. M., Yen, C., Tong, J. J., Spiegel, L., Nguyen, K. C. Q., Servoss, A., Peng, Y., Pei, L., Marks, J. R., Lowe, S. W., Hoey, T., Jan, L. Y., McCombie, W. R., Wigler, M. H., Powers, S. (March 2003) Genomic amplification and oncogenic properties of the KCNK9 potassium channel gene. Cancer Cell, 3 (3). pp. 297-302. ISSN 1535-6108

Murchison, E. P., Kheradpour, P., Sachidanandam, R., Smith, C., Hodges, E., Xuan, Z., Kellis, M., Grutzner, F., Stark, A., Hannon, G. J. (June 2008) Conservation of small RNA pathways in platypus. Genome Research, 18 (6). pp. 995-1004. ISSN 1088-9051

Myers, M. P., Pass, I., Batty, I. H., Van der Kaay, J., Stolarov, J. P., Hemmings, B. A., Wigler, M. H., Downes, C. P., Tonks, N. K. (November 1998) The lipid phosphatase activity of PTEN is critical for its tumor supressor function. Proc Natl Acad Sci U S A, 95 (23). pp. 13513-8. ISSN 0027-8424 (Print)

Nahreini, P., Mathews, M. B. (February 1995) Effects of the simian virus 40 origin of replication on transcription from the human immunodeficiency virus type 1 promoter. J Virol, 69 (2). pp. 1296-301. ISSN 0022-538X (Print)

Narita, M., Nunez, S., Heard, E., Narita, M., Lin, A. W., Hearn, S. A., Spector, D. L., Hannon, G. J., Lowe, S. W. (June 2003) Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell, 113 (6). pp. 703-716. ISSN 0092-8674

Natesan, S., Gilman, M. (November 1995) YY1 facilitates the association of serum response factor with the c-fos serum response element. Mol Cell Biol, 15 (11). pp. 5975-82. ISSN 0270-7306 (Print)

Navlakha, S., Kingsford, C. (April 2010) The power of protein interaction networks for associating genes with diseases. Bioinformatics, 26 (8). pp. 1057-63. ISSN 1367-4803 (Public Dataset)

Neumann, M., Wilisch, A., Diddens, H., Probst, H., Gekeler, V. (November 1992) Mdr Hamster-Cells Exhibiting Multiple Altered Gene-Expression - Effects of Dexniguldipine-Hcl (B859-35), Cyclosporine-a and Buthionine Sulfoximine. Anticancer Research, 12 (6B). pp. 2297-2302. ISSN 0250-7005

Ng, L., Bernard, A., Lau, C., Overly, C. C., Dong, H.-W., Kuan, C., Pathak, S., Sunkin, S. M., Dang, C., Bohland, J. W., Bokil, H. S., Mitra, P. P., Puelles, L., Hohmann, J., Anderson, D. J., Lein, E. S., Jones, A. R., Hawrylycz, M. (March 2009) An anatomic gene expression atlas of the adult mouse brain. Nat Neurosci, 12 (3). pp. 356-362. ISSN 1097-6256

Niida, A., Smith, A. D., Imoto, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (February 2009) Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinformatics, 10. p. 71. ISSN 1471-2105

Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., Kawashima, T., Kojima, M., Kubosaki, A., Manabe, R. I., Murata, M., Nagao-Sato, S., Nakazato, K., Ninomiya, N., Nishiyori-Sueki, H., Noma, S., Saijyo, E., Saka, A., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R. A., Babina, M., Baillie, J. K., Barnett, T. C., Beckhouse, A. G., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A. J., Clevers, H. C., Davis, C. A., Detmar, M., Dohi, T., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach-Carson, M. C., Faulkner, G. J., Ferrai, C., Fisher, M. E., Forrester, L. M., Fujita, R., Furusawa, J. I., Geijtenbeek, T. B., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P., Hitchens, K. J., Hume, D. A., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y. I., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Klein, S., Klinken, S. P., Knox, A. J., Kojima, S., Koseki, H., Koyasu, S., Lee, W., Lennartsson, A., Mackay-Sim, A., Mejhert, N., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Morris, K. J., Motohashi, H. (August 2017) FANTOM5 CAGE profiles of human and mouse samples. Sci Data, 4. p. 170112. ISSN 2052-4463

O'Donnell, W. T., Zito, K., Burbach, B., Svoboda, K., Warren, S. T. (October 2001) Identification of genes differentially expressed in wildtype and Fmr1 knockout mouse barrel cortex. American Journal of Human Genetics, 69 (4). p. 577. ISSN 0002-9297

O'Gara, M., Adams, G. M., Gong, W., Kobayashi, R., Blumenthal, R. M., Cheng, X. (August 1997) Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific). European Journal of Biochemistry , 247 (3). pp. 1009-18. ISSN 0014-2956 (Print)

Olive, V., Bennett, M. J., Walker, J. C., Ma, C., Jiang, I., Cordon-Cardo, C., Li, Q. J., Lowe, S. W., Hannon, G. J., He, L. (December 2009) miR-19 is a key oncogenic component of mir-17-92. Genes & Development, 23 (24). pp. 2839-2849. ISSN 0890-9369

Oran, A. R., Adams, C. M., Zhang, X. Y., Gennaro, V. J., Pfeiffer, H. K., Mellert, H. S., Seidel, H. E., Mascioli, K., Kaplan, J., Gaballa, M. R., Shen, C., Rigoutsos, I., King, M. P., Cotney, J. L., Arnold, J. J., Sharma, S. D., Martinez-Outschoorn, U. E., Vakoc, C. R., Chodosh, L. A., Thompson, J. E., Bradner, J. E., Cameron, C. E., Shadel, G. S., Eischen, C. M., McMahon, S. B. (November 2016) Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget, 7 (45). pp. 72395-72414. ISSN 1949-2553 (Electronic)1949-2553 (Linking)

Osborn, T. C., Pires, J. C., Birchler, J. A., Auger, D. L., Chen, Z. J., Lee, H. S., Comai, L., Madlung, A., Doerge, R. W., Colot, V., Martienssen, R. A. (March 2003) Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics, 19 (3). pp. 141-7. ISSN 0168-9525

Paddison, P. J., Caudy, A. A., Hannon, G. J. (2002) Stable suppression of gene expression by RNAi in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 99 (3). pp. 1443-1448. ISSN 00278424 (ISSN)

Pan, Xiufang, Zhan, Huiqing, Gong, Zhiyuan (2008) Ornamental expression of red fluorescent protein in transgenic founders of white skirt tetra (Gymnocorymbus ternetzi). Marine Biotechnology, 10 (5). pp. 497-501. ISSN 1436-2228

Passamaneck, Y. J., Katikala, L., Perrone, L., Dunn, M. P., Oda-Ishii, I., Di Gregorio, A. (November 2009) Direct activation of a notochord cis-regulatory module by Brachyury and FoxA in the ascidian Ciona intestinalis. Development, 136 (21). pp. 3679-89. ISSN 0950-1991

Paul, Thomas A, Rovnak, Joel, Quackenbush, Sandra L, Whitlock, Kathleen, Zhan, Huiqing, Gong, Zhiyuan, Spitsbergen, Jan, Bowser, Paul R, Casey, James W (April 2011) Transgenic expression of walleye dermal sarcoma virus rv-cyclin (orfA) in zebrafish does not result in tissue proliferation. Marine Biotechnology, 13 (2). pp. 142-150. ISSN 1436-2228

Paxton, W. A., Liu, R., Kang, S., Wu, L., Gingeras, T. R., Landau, N. R., MacKay, C. R., Koup, R. A. (1998) Reduced HIV-1 infectability of CDd4+ lymphocytes from exposed- uninfected individuals: Association with low expression of CCR5 and high production of β-chemokines. Virology, 244 (1). pp. 66-73. ISSN 00426822 (ISSN)

Pedmale, U. V., Huang, S. S., Zander, M., Cole, B. J., Hetzel, J., Ljung, K., Reis, P. A., Sridevi, P., Nito, K., Nery, J. R., Ecker, J. R., Chory, J. (January 2016) Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light. Cell, 164 (1-2). pp. 233-45. ISSN 0092-8674

Pellicer, A., Wigler, M. H., Axel, R., Silverstein, S. (1978) The transfer and stable integration of HSV thymidine kinase gene into mouse cells. Cell, 14 (1). pp. 133-141. ISSN 0092-8674

Pena, L. A., Marshak, D. R. (December 1993) Beta-Amyloid Regulates S100-Beta Gene-Expression in C6 Glioma-Cells and Primary Astrocyte Cultures. Journal of Neurochemistry, 61 (S). S200-S200. ISSN 0022-3042

Pendergrast, P. S., Hernandez, N. (February 1997) RNA-targeted activators, but not DNA-targeted activators, repress the synthesis of short transcripts at the human immunodeficiency virus type 1 long terminal repeat. Journal of Virology, 71 (2). pp. 910-7. ISSN 0022-538X

Pereira, L, Sapkota, M, Alonge, M, Zheng, Y, Zhang, Y, Razifard, H, Taitano, NK, Schatz, MC, Fernie, AR, Wang, Y, Fei, Z, Caicedo, AL, Tieman, DM, van der Knaap, E (June 2021) Natural Genetic Diversity in Tomato Flavor Genes. Frontiers in Plant Science, 12. ISSN 1664-462X

Perucho, M., Hanahan, D., Lipsich, L., Wigler, M. H. (May 1980) Isolation of the chicken thymidine kinase gene by plasmid rescue. Nature, 285 (5762). pp. 207-210.

Pervouchine, D. D., Djebali, S., Breschi, A., Davis, C. A., Barja, P. P., Dobin, A., Tanzer, A., Lagarde, J., Zaleski, C., See, L. H., Fastuca, M., Drenkow, J., Wang, H., Bussotti, G., Pei, B., Balasubramanian, S., Monlong, J., Harmanci, A., Gerstein, M., Beer, M. A., Notredame, C., Guigo, R., Gingeras, T. R. (January 2015) Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun, 6. p. 5903. ISSN 2041-1723

Pervouchine, Dmitri, Djebali, Sarah, Breschi, Alessandra, Davis, Carrie, Prieto Barja, Pablo, Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Zaleski, Chris, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Wang, Huaien, Bussotti, Giovanni, Pei, Baikang, Balasubramanian, Suganthi, Monlong, Jean, Harmanci, Arif, Gerstein, Mark, Beer, Michael, Notredame, Cedric, Guigo, Roderic, Gingeras, Thomas (October 2014) Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes. BioRxiv. (Unpublished)

Pessler, F., Pendergrast, P. S., Hernandez, N. (July 1997) Purification and characterization of FBI-1, a cellular factor that binds to the human immunodeficiency virus type 1 inducer of short transcripts. Molecular and Cellular Biology, 17 (7). pp. 3786-98. ISSN 0270-7306 (Print)

Petersen, M., Brodersen, P., Naested, H., Andreasson, E., Lindhart, U., Johansen, B., Nielsen, H. B., Lacy, M., Austin, M. J., Parker, J. E., Sharma, S. B., Klessig, D. F., Martienssen, R., Mattsson, O., Jensen, A. B., Mundy, J. (December 2000) Arabidopsis MAP kinase 4 negatively regulates systemic acquired resistance. Cell, 103 (7). pp. 1111-1120. ISSN 0092-8674

Piano, F., Schetter, A. J., Mangone, M., Stein, L., Kemphues, K. J. (December 2000) RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Current Biology, 10 (24). pp. 1619-1622. ISSN 0960-9822

Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M. A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., Kern, A. D., Dehay, C., Igel, H., Ares, M., Vanderhaeghen, P., Haussler, D. (September 2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature, 443 (7108). pp. 167-72. ISSN 0028-0836

Poremba, C., Scheel, C., Hero, B., Christiansen, H., Schaefer, K. L., Nakayama, J., Berthold, F., Juergens, H., Boecker, W., Dockhorn-Dworniczak, B. (July 2000) Telomerase activity and telomerase subunits gene expression patterns in neuroblastoma: A molecular and immunohistochemical study establishing prognostic tools for fresh-frozen and paraffin-embedded tissues. Journal of Clinical Oncology, 18 (13). pp. 2582-2592. ISSN 0732-183X

Porteous, D. J., Thomson, P. A., Millar, J. K., Evans, K. L., Hennah, W., Soares, D. C., McCarthy, S., McCombie, W. R., Clapcote, S. J., Korth, C., Brandon, N. J., Sawa, A., Kamiya, A., Roder, J. C., Lawrie, S. M., McIntosh, A. M., St Clair, D., Blackwood, D. H. (February 2014) DISC1 as a genetic risk factor for schizophrenia and related major mental illness: response to Sullivan. Mol Psychiatry, 19 (2). pp. 141-3. ISSN 1359-4184

Powers, S., Kataoka, T., Toda, T., Fasano, O., Wigler, M. H. (1985) Control of Yeast Adenyl-Cyclase by Ras Proteins. Federation Proceedings, 44 (3). R8-R8. ISSN 0014-9446

Powers, S., Michaelis, S., Broek, D., Ann-A, S. S., Field, J., Herskowitz, I., Wigler, M. H. (1986) RAM, a gene of yeast required for a functional modification of RAS proteins and for production of mating pheromone a-factor. Cell, 47 (3). pp. 413-422.

Powers, S., O'Neill, K., Wigler, M. H. (February 1989) Dominant yeast and mammalian RAS mutants that interfere with the CDC25-dependent activation of wild-type RAS in Saccharomyces cerevisiae. Molecular & Cellular Biology, 9 (2). pp. 390-5. ISSN 0270-7306

Prakash, S., Sarran, L., Socci, N., DeMatteo, R. P., Eisenstat, J., Greco, A. M., Maki, R. G., Wexler, L. H., LaQuaglia, M. P., Besmer, P., Antonescu, C. R. (April 2005) Gastrointestinal stromal tumors in children and young adults: a clinicopathologic, molecular, and genomic study of 15 cases and review of the literature. J Pediatr Hematol Oncol, 27 (4). pp. 179-87. ISSN 1077-4114 (Print)1077-4114 (Linking)

Prasanth, K. V. , Sacco-Bubulya, P. A., Prasanth, S. G., Spector, D. L. (2003) Sequential entry of components of the gene expression machinery into daughter nuclei. Molecular Biology of the Cell, 14 (3). pp. 1043-1057. ISSN 1059-1524

Ptashne, M., Gann, A. (November 1998) Imposing specificity by localization: mechanism and evolvability. Current Biology, 8 (22). R812-22. ISSN 0960-9822

Ptashne, M., Gann, A. A. (July 1990) Activators and targets. Nature, 346 (6282). pp. 329-31. ISSN 0028-0836 (Print)0028-0836

Quelle, D. E., Ashmun, R. A., Shurtleff, S. A., Kato, J. Y., Barsagi, D., Roussel, M. F., Sherr, C. J. (August 1993) Overexpression of Mouse D-Type Cyclins Accelerates G(1) Phase in Rodent Fibroblasts. Genes Dev, 7 (8). pp. 1559-1571. ISSN 0890-9369

Ragno, S., Romano, M., Howell, S., Pappin, D. J., Jenner, P. J., Colston, M. J. (September 2001) Changes in gene expression in macrophages infected with Mycobacterium tuberculosis: a combined transcriptomic and proteomic approach. Immunology, 104 (1). pp. 99-108. ISSN 0019-2805 (Print)0019-2805 (Linking)

Rahmanian, S., Murad, R., Breschi, A., Zeng, W., Mackiewicz, M., Williams, B., Davis, C. A., Roberts, B., Meadows, S., Moore, D., Trout, D., Zaleski, C., Dobin, A., Sei, L. H., Drenkow, J., Scavelli, A., Gingeras, T. R., Wold, B. J., Myers, R. M., Guigo, R., Mortazavi, A. (November 2019) Dynamics of microRNA expression during mouse prenatal development. Genome Res, 29 (11). pp. 1900-1909. ISSN 1088-9051

Ramani, R., Megason, G., Schallheim, J., Karlson, C., Vijayakumar, V., Vijayakumar, S., Hicks, C. (April 2017) Integrative Analysis of MicroRNA-Mediated Gene Signatures and Pathways Modulating White Blood Cell Count in Childhood Acute Lymphoblastic Leukemia. Biomarker Insights, 12. p. 1177271917702895. ISSN 1177-2719

Rattay, K., Meyer, H. V., Herrmann, C., Brors, B., Kyewski, B. (February 2016) Evolutionary conserved gene co-expression drives generation of self-antigen diversity in medullary thymic epithelial cells. J Autoimmun, 67. pp. 65-75. ISSN 0896-8411

Riabowol, K. T., Fink, J. S., Gilman, M. Z., Walsh, D. A., Goodman, R. H., Feramisco, J. R. (November 1988) The catalytic subunit of cAMP-dependent protein kinase induces expression of genes containing cAMP-responsive enhancer elements. Nature, 336 (6194). pp. 83-6. ISSN 0028-0836

Rigo, F., Hua, Y. M., Chun, S. J., Krainer, A. R., Bennett, C. F. (October 2011) Modulation of Gene Expression By Oligonucleotide Chemistry-Dependent Recruitment of Proteins to RNA Transcripts. Nucleic Acid Therapeutics, 21 (5). A53-A54. ISSN 2159-3337

Rothstein, J. L., Johnson, D., DeLoia, J. A., Skowronski, J., Solter, D., Knowles, B. (July 1992) Gene expression during preimplantation mouse development. Genes Dev, 6 (7). pp. 1190-201. ISSN 0890-9369 (Print)0890-9369 (Linking)

Rozowsky, J., Wu, J., Lian, Z., Nagalakshmi, U., Korbel, J. O., Kapranov, P., Zheng, D., Dyke, S., Newburger, P., Miller, P., Gingeras, T. R., Weissman, S., Gerstein, M., Snyder, M. (2006) Novel transcribed regions in the human genome. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 111-116. ISSN 00917451 (ISSN)

Russnes, H. G., Sorlie, T., Krasnitz, A., Zetterberg, A., Naume, B., Borgen, E., Nesland, J. M., Wigler, M. H., Borresen-Dale, A. L., Hicks, J. B. (July 2008) Molecular subclassification of breast carcinomas based on aCGH, gene expression, IHC and ploidy - relevance for clinical outcome. European Journal of Cancer Supplements, 6 (9). p. 9. ISSN 1359-6349

Sabin, L. R., Delas, M. J., Hannon, G. J. (March 2013) Dogma derailed: the many influences of RNA on the genome. Molecular Cell, 49 (5). pp. 783-94. ISSN 1097-2765

Sass, P., Field, J., Nikawa, J., Toda, T., Wigler, M. H. (1986) Cloning and characterization of the high-affinity cAMP phosphodiesterase of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America, 83 (24). pp. 9303-9307.

Scheffzek, K., Grunewald, P., Wohlgemuth, S., Kabsch, W., Tu, H., Wigler, M. H., Wittinghofer, A., Herrmann, C. (November 2001) The Ras-Byr2RBD complex: Structural basis for Ras effector recognition in yeast. Structure, 9 (11). pp. 1043-1050. ISSN 0969-2126

Schmitt, A., Koschel, J., Zink, M., Bauer, M., Sommer, C., Frank, J., Treutlein, J., Schulze, T., Schneider-Axmann, T., Parlapani, E., Rietschel, M., Falkai, P., Henn, F. A. (March 2010) Gene expression of NMDA receptor subunits in the cerebellum of elderly patients with schizophrenia. European Archives of Psychiatry and Clinical Neuroscience, 260 (2). pp. 101-11. ISSN 0940-1334 (Print)0940-1334 (Linking)

Schmitt, A., Zink, M., Muller, B., May, B., Herb, A., Jatzko, A., Braus, D. F., Henn, F. A. (February 2003) Effects of long-term antipsychotic treatment on NMDA receptor binding and gene expression of subunits. Neurochemical Research, 28 (2). pp. 235-41. ISSN 0364-3190

Schmitt, A., Zink, M., Petroianu, G., May, B., Braus, D. F., Henn, F. A. (August 2003) Decreased gene expression of glial and neuronal glutamate transporters after chronic antipsychotic treatment in rat brain. Neuroscience Letters, 347 (2). pp. 81-4. ISSN 03043940 (ISSN)

Schmitz, A. A., Lucito, R., Van Aelst, L. (2002) Using cDNA-representational difference analysis (cDNA-RDA) in combination with microarrays to identify Rac regulated genes. Methods Mol Biol, 189. pp. 25-43. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Scorer, C. A., Clare, J. J., McCombie, W. R., Romanos, M. A., Sreekrishna, K. (1994) Rapid selection using G418 of high copy number transformants of Pichia pastoris for high-level foreign gene expression. Nature Biotechnology, 12 (2). pp. 181-184. ISSN 10870156 (ISSN)

Senturk, S., Shirole, N. H., Nowak, D. G., Corbo, V., Pal, D., Vaughan, A., Tuveson, D. A., Trotman, L. C., Kinney, J. B., Sordella, R. (February 2017) Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun, 8. p. 14370. ISSN 2041-1723 (Public Dataset)

Serrano, M., Lin, A. W., McCurrach, M. E., Beach, D., Lowe, S. W. (March 1997) Oncogenic ras provokes premature cell senescence associated with accumulation of p53 and p16INK4a. Cell, 88 (5). pp. 593-602. ISSN 0092-8674 (Print)

Shao, L., Shuai, Y., Wang, J., Feng, S., Lu, B., Li, Z., Zhao, Y., Wang, L., Zhong, Y. (2011) Schizophrenia susceptibility gene dysbindin regulates glutamatergic and dopaminergic functions via distinctive mechanisms in Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 108 (46). pp. 18831-18836. ISSN 00278424 (ISSN)

Sharma, S., Birchmeier, C., Nikawa, J., O'Neill, K., Rodgers, L., Wigler, M. H. (1989) Characterization of the ros1-gene products expressed in human glioblastoma cell lines. Oncogene Res, 5 (2). pp. 91-100. ISSN 0890-6467

Sheltzer, J. M. (November 2013) A transcriptional and metabolic signature of primary aneuploidy is present in chromosomally unstable cancer cells and informs clinical prognosis. Cancer Res, 73 (21). pp. 6401-12. ISSN 1538-7445 (Electronic)0008-5472 (Linking)

Sheltzer, J. M., Torres, E. M., Dunham, M. J., Amon, A. (July 2012) Transcriptional consequences of aneuploidy. Proc Natl Acad Sci U S A, 109 (31). pp. 12644-9. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Shi, Xi, Lu, Congyi, Corman, Alba, Nikish, Alexandra, Zhou, Yang, Platt, Randy J, Iossifov, Ivan, Zhang, Feng, Pan, Jen Q, Sanjana, Neville E (October 2023) Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction. American Journal of Human Genetics, 110 (10). pp. 1750-1768. ISSN 0002-9297 (Public Dataset)

Shimizu, K., Goldfarb, M., Suard, Y., Perucho, M., Li, Y., Kamata, T., Feramisco, J., Stavnezer, E., Fogh, J., Wigler, M. H. (April 1983) Three human transforming genes are related to the viral ras oncogenes. Proceedings of the National Academy of Sciences of the United States of America, 80 (8). pp. 2112-2116. ISSN 0027-8424

Siddiqi, I., Ganesh, G., Grossniklaus, U., Subbiah, V. (January 2000) The dyad gene is required for progression through female meiosis in Arabidopsis. Development, 127 (1). pp. 197-207. ISSN 0950-1991

Singer, S., Socci, N. D., Ambrosini, G., Sambol, E., Decarolis, P., Wu, Y., O'Connor, R., Maki, R., Viale, A., Sander, C., Schwartz, G. K., Antonescu, C. R. (July 2007) Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. Cancer Res, 67 (14). pp. 6626-36. ISSN 0008-5472 (Print)0008-5472 (Linking)

Singh, R., Low, E. T. L., Ooi, L. C. L., Ong-Abdullah, M., Ting, N. C., Nagappan, J., Nookiah, R., Amiruddin, M. D., Rosli, R., Manaf, M. A. A., Chan, K. L., Halim, M. A., Azizi, N., Lakey, N., Smith, S. W., Budiman, M. A., Hogan, M., Bacher, B., Van Brunt, A., Wang, C., Ordway, J. M., Sambanthamurthi, R., Martienssen, R. A. (August 2013) The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. Nature, 500 (7462). pp. 340-344. ISSN 00280836

Skoulakis, E. M., Kalderon, D., Davis, R. L. (August 1993) Preferential expression in mushroom bodies of the catalytic subunit of protein kinase A and its role in learning and memory. Neuron, 11 (2). pp. 197-208. ISSN 0896-6273 (Print)

Skowronski, J., Parks, D., Mariani, R. (February 1993) Altered T-Cell Activation and Development in Transgenic Mice Expressing the Hiv-1 Nef Gene. Embo J, 12 (2). pp. 703-713. ISSN 0261-4189

Soyk, Sebastian, Lemmon, Zachary H., Oved, Matan, Fisher, Josef, Liberatore, Katie L., Park, Soon Ju, Goren, Anna, Jiang, Ke, Ramos, Alexis, van der Knaap, Esther, Van Eck, Joyce, Zamir, Dani, Eshed, Yuval, Lippman, Zachary B. (June 2017) Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell, 169 (6). pp. 1142-1155. ISSN 0092-8674

Spector, D. L. (1996) Nuclear organization and gene expression. Experimental Cell Research, 229 (2). pp. 189-197. ISSN 0014-4827

Spector, D. L., Misteli, T. (December 1999) 8 dynamics of gene expression. Journal of Histochemistry and Cytochemistry, 47 (12). 1644C-1644. ISSN 0022-1554

Spector, D. L., Tsukamota, T., Bertrand, E., Fusco, D., Singer, R., Janicki, S. M. (November 2002) Visualizing the dynamics of gene expression in living cells. Molecular Biology of the Cell, 13. 2A-2A. ISSN 1059-1524

Sroka, Martyna W, Vakoc, Christopher R (February 2021) An epigenetic tipping point in cancer comes under the microscope. Nature, 590 (7846). pp. 399-400. ISSN 0028-0836

Stamm, S., Casper, D., Dinsmore, J., Kaufmann, C. A., Brosius, J., Helfman, D. M. (October 1992) Clathrin light chain B: gene structure and neuron-specific splicing. Nucleic Acids Res, 20 (19). pp. 5097-103. ISSN 0305-1048 (Print)0305-1048 (Linking)

Stamm, S., Casper, D., Lees-Miller, J. P., Helfman, D. M. (November 1993) Brain-specific tropomyosins TMBr-1 and TMBr-3 have distinct patterns of expression during development and in adult brain. Proc Natl Acad Sci U S A, 90 (21). pp. 9857-61. ISSN 0027-8424 (Print)

Staropoli, John F., Li, Huo, Chun, Seung J., Allaire, Norm, Cullen, Patrick, Thai, Alice, Fleet, Christina M., Hua, Yimin, Bennett, C. Frank, Krainer, Adrian R., Kerr, Doug, McCampbell, Alexander, Rigo, Frank, Carulli, John P. (January 2015) Rescue of gene-expression changes in an induced mouse model of spinal muscular atrophy by an antisense oligonucleotide that promotes inclusion of SMN2 exon 7. Genomics, 105 (4). pp. 220-228. ISSN 0888-7543

Stasiv, Y., Regulski, M., Kuzin, B., Tully, T., Enikolopov, G. (November 2001) The Drosophila nitric-oxide synthase gene (dNOS) encodes a family of proteins that can modulate NOS activity by acting as dominant negative regulators. Journal of Biological Chemistry, 276 (45). pp. 42241-42251. ISSN 0021-9258

Stebbins, M. J., Yin, J. C. P. (May 2001) Adaptable doxycycline-regulated gene expression systems for Drosophila. Gene, 270 (1-2). pp. 103-111. ISSN 0378-1119

Stec, Natalia, Doerfel, Katja, Hills-Muckey, Kelly, Ettorre, Victoria M, Ercan, Sevinc, Keil, Wolfgang, Hammell, CM (September 2020) An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output. BioRxiv. (Unpublished)

Steffan, J. S., Agrawal, N., Pallos, J., Rockabrand, E., Trotman, L. C., Slepko, N., Illes, K., Lukacsovich, T., Zhu, Y. Z., Cattaneo, E., Pandolfi, P. P., Thompson, L. M., Marsh, J. L. (April 2004) SUMO Modification of Huntingtin and Huntington's Disease Pathology. Science, 304 (5667). pp. 100-104. ISSN 00368075 (ISSN)

Steinhelper, M. E., Cochrane, K. L., Field, L. J. (December 1991) Engineering the cardiovascular system. Blood pressure regulation. Ann N Y Acad Sci, 646. pp. 248-53. ISSN 0077-8923 (Print)0077-8923 (Linking)

Steinhelper, M. E., Cochrane, K. L., Field, L. J. (September 1990) Hypotension in transgenic mice expressing atrial natriuretic factor fusion genes. Hypertension, 16 (3). pp. 301-7. ISSN 0194-911X (Print)0194-911X (Linking)

Stern, S., Powers, T., Changchien, L. M., Noller, H. F. (May 1989) Rna-Protein Interactions in 30s Ribosomal Subunits Folding and Function of 16s Ribosomal Rna. Science (Washington D C), 244 (4906). pp. 783-790. ISSN :0036-8075

Sturm, R. A., Cassady, J. L., Das, G., Romo, A., Evans, G. A. (May 1993) Chromosomal Structure and Expression of the Human Otf1 Locus Encoding the Oct-1 Protein. Genomics, 16 (2). pp. 333-341. ISSN 0888-7543

Su, H. P., Brugnera, E., Van Criekinge, W., Smits, E., Hengartner, M., Bogaert, T., Ravichandran, K. S. (March 2000) Identification and characterization of a dimerization domain in CED-6, an adapter protein involved in engulfment of apoptotic cells. Journal of Biological Chemistry, 275 (13). pp. 9542-9549. ISSN 0021-9258

Sugrue, M. M., Brugge, J. S., Marshak, D. R., Greengard, P., Gustafson, E. L. (August 1990) Immunocytochemical localization of the neuron-specific form of the c-src gene product, pp60c-src(+), in rat brain. J Neurosci, 10 (8). pp. 2513-27. ISSN 0270-6474 (Print)0270-6474 (Linking)

Sun, P., Dong, P., Dai, K., Hannon, G. J., Beach, D. (December 1998) p53-independent role of MDM2 in TGF-beta1 resistance. Science, 282 (5397). pp. 2270-2. ISSN 0036-8075 (Print)

Sun, Yonghao, Dong, Liang, Zhang, Ying, Lin, Da, Xu, Weize, Ke, Changxiong, Han, Linqian, Deng, Lulu, Li, Guoliang, Jackson, David, Li, Xingwang, Yang, Fang (June 2020) 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize. Genome Biology, 21 (1). p. 143. ISSN 1474-760X

Sun, Yu-Chi, Chen, Xiaoyin, Fischer, Stephan, Lu, Shaina, Gillis, Jesse, Zador, Anthony (August 2020) Integrating barcoded neuroanatomy with spatial transcriptional profiling reveals cadherin correlates of projections shared across the cortex. bioRxiv. (Unpublished)

Sun, Yu-Chi, Chen, Xiaoyin, Fischer, Stephan, Lu, Shaina, Zhan, Huiqing, Gillis, Jesse, Zador, Anthony M (May 2021) Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. Nature Neuroscience. ISSN 1097-6256

Suresh, Hamsini, Crow, Megan, Jorstad, Nikolas, Hodge, Rebecca, Lein, Ed, Dobin, Alexander, Bakken, Trygve, Gillis, Jesse (September 2023) Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution. Nature Ecology and Evolution. ISSN 2397-334X

Taguchi-Shiobara, F., Yuan, Z., Hake, S., Jackson, D. (October 2001) The fasciated ear2 gene encodes a leucine-rich repeat receptor-like protein that regulates shoot meristem proliferation in maize. Genes & Development, 15 (20). pp. 2755-2766. ISSN 0890-9369

Takao, Sumiko, Forbes, Lauren, Uni, Masahiro, Cheng, Shuyuan, Pineda, Jose Mario Bello, Tarumoto, Yusuke, Cifani, Paolo, Minuesa, Gerard, Chen, Celine, Kharas, Michael G, Bradley, Robert K, Vakoc, Christopher R, Koche, Richard P, Kentsis, Alex (February 2021) Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. eLife, 10. pp. 1-46. ISSN 2050-084X

Tam, O. H., Aravin, A. A., Stein, P., Girard, A., Murchison, E. P., Cheloufi, S., Hodges, E., Anger, M., Sachidanandam, R., Schultz, R. M., Hannon, G. J. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature, 453 (7194). pp. 534-538. ISSN 00280836 (ISSN)

Tamanoi, F., Walsh, M., Kataoka, T., Wigler, M. H. (1984) A product of yeast RAS-2 gene is a guanine nucleotide binding protein. Proceedings of the National Academy of Sciences of the United States of America, 81 (22). pp. 6924-6928.

Tanaka, E. M., Gann, A. A., Gates, P. B., Brockes, J. P. (January 1997) Newt myotubes reenter the cell cycle by phosphorylation of the retinoblastoma protein. Journal of Cell Biology, 136 (1). pp. 155-65. ISSN 0021-9525 (Print)0021-9525

Tanaka, M. (April 1996) Modulation of promoter occupancy by cooperative DNA binding and activation-domain function is a major determinant of transcriptional regulation by activators in vivo. Proceedings of the National Academy of Sciences of the United States of America, 93 (9). pp. 4311-5. ISSN 0027-8424

Tansey, W. P., Catanzaro, D. F. (May 1991) Sp1 and thyroid hormone receptor differentially activate expression of human growth hormone and chorionic somatomammotropin genes. J Biol Chem, 266 (15). pp. 9805-13. ISSN 0021-9258 (Print)0021-9258 (Linking)

Tansey, William P., Ruppert, Siegfried, Tjian, Robert, Herr, Winship (November 1994) Multiple regions of TBP participate in the response to transcriptional activators in vivo. Genes Dev, 8 (22). pp. 2756-69. ISSN 0890-9369 (Print)

Taparowsky, E., Shimizu, K., Goldfarb, M., Wigler, M. H. (1983) Structure and Activation of the Human N-Ras Gene. Cell, 34 (2). pp. 581-586.

Taparowsky, E., Suard, Y., Fasano, O., Shimizu, K., Goldfarb, M., Wigler, M. H. (1982) Activation of the T24 Bladder-Carcinoma Transforming Gene Is Linked to a Single Amino-Acid Change. Nature, 300 (5894). pp. 762-765. ISSN 0028-0836

Tareen, Ammar, Posfai, Anna, Ireland, William, McCandlish, David, Kinney, Justin (July 2020) MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. BioRxiv. (Unpublished)

Thiagalingam, S., Lisitsyn, N. A., Hamaguchi, M., Wigler, M. H., Willson, J. K., Markowitz, S. D., Leach, F. S., Kinzler, K. W., Vogelstein, B. (July 1996) Evaluation of the FHIT gene in colorectal cancers. Cancer Res, 56 (13). pp. 2936-9. ISSN 0008-5472 (Print)

Thiebaut, F., Rojas, C. A., Grativol, C., Motta, M. R., Vieira, T., Regulski, M., Martienssen, R. A., Farinelli, L., Hemerly, A. S., Ferreira, P. C. G. (September 2014) Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize. BMC Genomics, 15. p. 766. ISSN 1471-2164

Thome, J., Duman, R. S., Henn, F. A. (July 2002) Molecular aspects of antidepressive therapy. Transsynaptic effects on signal transduction, gene expression and neuronal plasticity. Nervenarzt, 73 (7). pp. 595-9. ISSN 0028-2804 (Print)0028-2804 (Linking)

Thomson, P. A., Parla, J. S., McRae, A. F., Kramer, M., Ramakrishnan, K., Yao, J., Soares, D. C., McCarthy, S., Morris, S. W., Cardone, L., Cass, S., Ghiban, E., Hennah, W., Evans, K. L., Rebolini, D., Millar, J. K., Harris, S. E., Starr, J. M., MacIntyre, D. J., McIntosh, A. M., Watson, J. D., Deary, I. J., Visscher, P. M., Blackwood, D. H., McCombie, W. R., Porteous, D. J. (June 2014) 708 Common and 2010 rare DISC1 locus variants identified in 1542 subjects: Analysis for association with psychiatric disorder and cognitive traits. Molecular Psychiatry, 19 (6). pp. 668-675. ISSN 14765578

Toda, T., Cameron, S., Sass, P., Wigler, M. H. (May 1988) SCH9, a gene of Saccharomyces cerevisiae that encodes a protein distinct from, but functionally and structurally related to, cAMP-dependent protein kinase catalytic subunits. Genes Dev, 2 (5). pp. 517-27. ISSN 0890-9369

Toda, T., Cameron, S., Sass, P., Zoller, M., Scott, J. D., McMullen, B., Hurwitz, M., Krebs, E. G., Wigler, M. H. (April 1987) Cloning and characterization of BCY1, a locus encoding a regulatory subunit of the cyclic AMP-dependent protein kinase in Saccharomyces cerevisiae. Molecular & Cellular Biology, 7 (4). pp. 1371-1377.

Toda, T., Cameron, S., Sass, P., Zoller, M., Wigler, M. H. (1987) Three different genes in Saccharomyces cerevisiae encode the catalytic subunits of the cAMP-dependent protein kinase. Cell, 50 (2). pp. 277-288.

Tollkuhn, J., Xu, X., Shah, N. M. (August 2010) A custody battle for the mind: evidence for extensive imprinting in the brain. Neuron, 67 (3). pp. 359-62. ISSN 1097-4199 (Electronic)0896-6273 (Linking)

Tolonen, A. C., Albeanu, D. F., Corbett, J. F., Handley, H., Henson, C., Malik, P. (October 2002) Optimized in situ construction of oligomers on an array surface. Nucleic Acids Research, 30 (20). e107. ISSN 0305-1048

Tschopp, J. F., Brust, P. F., Cregg, J. M., Stillman, C. A., Gingeras, T. R. (1987) Expression of the lacZ gene from two methanol-regulated promoters in Pichia pastoris. Nucleic Acids Research, 15 (9). pp. 3859-3876. ISSN 03051048 (ISSN)

Tsukamoto, T., Hashiguchi, N., Janicki, S. M., Tumbar, T., Belmont, A. S., Spector, D. L. (December 2000) Visualization of gene activity in living cells. Nature Cell Biology, 2. pp. 871-878. ISSN 1465-7392

Tu, H., Barr, M., Dong, D. L., Wigler, M. H. (October 1997) Multiple regulatory domains on the Byr2 protein kinase. Mol Cell Biol, 17 (10). pp. 5876-87. ISSN 0270-7306 (Print)

Tu, H., Wigler, M. H. (January 1999) Genetic evidence for Pak1 autoinhibition and its release by Cdc42. Mol Cell Biol, 19 (1). pp. 602-11. ISSN 0270-7306 (Print)

Tully, T. (April 1997) Regulation of gene expression and its role in long-term memory and synaptic plasticity. Proc Natl Acad Sci U S A, 94 (9). pp. 4239-41. ISSN 0027-8424 (Print)

Turco, G. M., Kajala, K., Kunde-Ramamoorthy, G., Ngan, C. Y., Olson, A., Deshphande, S., Tolkunov, D., Waring, B., Stelpflug, S., Klein, P., Schmutz, J., Kaeppler, S., Ware, D., Wei, C. L., Etchells, J. P., Brady, S. M. (May 2017) DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. New Phytol, 214 (3). pp. 1213-1229. ISSN 0028-646x (Public Dataset)

Turner, B. C., Tonks, N. K., Rapp, U. R., Reed, J. C. (June 1993) Interleukin-2 Regulates Raf-1 Kinase-Activity through a Tyrosine Phosphorylation-Dependent Mechanism in a T-Cell Line. Proceedings of the National Academy of Sciences of the United States of America, 90 (12). pp. 5544-5548. ISSN 0027-8424

Turner, G. C., Du, F., Varshavsky, A. (2000) Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature, 405 (6786). pp. 579-583. ISSN 00280836 (ISSN)

Tuveson, D., Clevers, H. (June 2019) Cancer modeling meets human organoid technology. Science, 364 (6444). pp. 952-955. ISSN 0036-8075

Tyers, M., Tokiwa, G., Futcher, B. (May 1993) Comparison of the Saccharomyces cerevisiae G1 cyclins: Cln3 may be an upstream activator of Cln1, Cln2 and other cyclins. Embo J, 12 (5). pp. 1955-68. ISSN 0261-4189 (Print)

Vakoc, C. R., Blobel, G. A., Wen, Y.-Y., Gibbs, R. A., Johnstone, C. N., Rustgi, A. K. (March 2009) Low frequency of MLL3 mutations in colorectal carcinoma. Cancer Genetics and Cytogenetics, 189 (2). pp. 140-141. ISSN 0165-4608

Vakoc, C. R., Letting, D. L., Gheldof, N., Sawado, T., Bender, M. A., Groudine, M., Weiss, M. J., Dekker, J., Blobel, G. A. (2005) Proximity among distant regulatory elements at the β-globin locus requires GATA-1 and FOG-1. Molecular Cell, 17 (3). pp. 453-462. ISSN 10972765 (ISSN)

Van Aelst, L., Barr, M., Marcus, S., Polverino, A., Wigler, M. H. (July 1993) Complex formation between RAS and RAF and other protein kinases. Proc Natl Acad Sci U S A, 90 (13). pp. 6213-7. ISSN 0027-8424 (Print)

Van Aelst, L., Hohmann, S., Bulaya, B., Dekoning, W., Sierkstr, L., Neves, M. J., Luyten, K., Alijo, R., Ramos, J., Coccetti, P., Martegani, E., Demagalhaesrocha, N. M., Brandao, R. L., Vandijck, P., Vanhalewyn, M., Durnez, P., Jans, A. W. H., Thevelein, J. M. (May 1993) Molecular-Cloning of a Gene Involved in Glucose Sensing in the Yeast Saccharomyces-Cerevisiae. Molecular Microbiology, 8 (5). pp. 927-943. ISSN 0950-382X

Vojtek, A., Field, J., Gerst, J., Wigler, M. H. (1991) The Ras Signalling Pathway in Yeast. Journal of Cellular Biochemistry - Supplement.(15 PART B). p. 84.

Vojtek, A., Haarer, B., Field, J., Gerst, J., Pollard, T. D., Brown, S., Wigler, M. H. (August 1991) Evidence for a functional link between profilin and CAP in the yeast S. cerevisiae. Cell, 66 (3). pp. 497-505. ISSN 0092-8674

Wang, D. G., Fan, J. B., Siao, C. J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson, E., Mittmann, M., Morris, M. S., Shen, N. P., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T. J., Lipshutz, R., Chee, M., Lander, E. S. (May 1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280 (5366). pp. 1077-1082. ISSN 0036-8075

Wang, X., Trotman, L. C., Koppie, T., Alimonti, A., Chen, Z., Gao, Z., Wang, J., Erdjument-Bromage, H., Tempst, P., Cordon-Cardo, C., Pandolfi, P. P., Jiang, X. (January 2007) NEDD4-1 Is a Proto-Oncogenic Ubiquitin Ligase for PTEN. Cell, 128 (1). pp. 129-139. ISSN 00928674 (ISSN)

Wang, Y., Boguski, M., Riggs, M., Rodgers, L., Wigler, M. (1991) sar1, a gene from Schizosaccharomyces pombe encoding a protein that regulates ras1. Cell Regulation, 2 (6). pp. 453-465. ISSN 10442030 (ISSN)

Wang, Y. L., Zheng, H. W., Liu, X. L., Zhang, Y. Z. (July 1998) High efficient expression in Escherichia coli of chitinase gene cloned from Bacillus circulans C-2. Acta Biochimica Et Biophysica Sinica, 30 (4). pp. 352-356. ISSN 0582-9879

Wang, B., Tseng, E., Baybayan, P., Eng, K., Regulski, M., Jiao, Y., Wang, L., Olson, A., Chougule, K., Buren, P. V., Ware, D. (February 2020) Variant phasing and haplotypic expression from long-read sequencing in maize. Commun Biol, 3 (1). p. 78. ISSN 2399-3642 (Public Dataset)

Wanner, L. A., Li, G., Ware, D., Somssich, I. E., Davis, K. R. (January 1995) The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana. Plant Mol Biol, 27 (2). pp. 327-38. ISSN 0167-4412 (Print)

Webb, C. P., Van Aelst, L., Wigler, M. H., Woude, G. F. (July 1998) Signaling pathways in Ras-mediated tumorigenicity and metastasis. Proc Natl Acad Sci U S A, 95 (15). pp. 8773-8. ISSN 0027-8424 (Print)

Wei, Y., Gokhale, R. H., Sonnenschein, A., Montgomery, K. M., Ingersoll, A., Arnosti, D. N. (October 2016) Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator. Development, 143 (19). pp. 3591-3603. ISSN 0950-1991

Weiss, C., Huang, H., Ma, H. (January 1993) Characterization of Agl3, a Mads-Box Gene with Non-Flower-Specific Expression. Journal of Cellular Biochemistry. p. 37. ISSN 0730-2312

Welch, J. J., Watts, J. A., Vakoc, C. R., Yao, Y., Wang, H., Hardison, R. C., Blobel, G. A., Chodosh, L. A., Weiss, M. J. (2004) Global regulation of erythroid gene expression by transcription factor GATA-1. Blood, 104 (10). pp. 3136-3147. ISSN 00064971 (ISSN)

White, E., Cipriani, R., Sabbatini, P., Denton, A. (June 1991) Adenovirus E1B 19-kilodalton protein overcomes the cytotoxicity of E1A proteins. J Virol, 65 (6). pp. 2968-78. ISSN 0022-538X (Print)0022-538X (Linking)

White, M. A., Nicolette, C., Minden, A., Polverino, A., Van Aelst, L., Karin, M., Wigler, M. H. (February 1995) Multiple Ras functions can contribute to mammalian cell transformation. Cell, 80 (4). pp. 533-41. ISSN 0092-8674 (Print)

Wigler, M. H., Cameron, S., Powers, S., Field, J., Toda, T., Broek, D., Nikawa, J., Michaelis, T., Colicelli, J. (1988) Integration of Ras and Adenylate Cyclase Pathways in Yeast. Journal of Cell Biology, 107 (6 PART). 4A.

Wigler, M. H., Fasano, O., Taparowsky, E., Birnbaum, D., Goldfarb, M., Fogh, J. (1984) Human Transforming Genes. DNA-a Journal of Molecular & Cellular Biology, 3 (1). p. 65. ISSN 0198-0238

Wigler, M. H., Sweet, R., Sim, G. K., Wold, B., Pellicer, A., Lacy, E., Maniatis, T., Silverstein, S., Axel, R. (1979) Transformation of mammalian cells with genes from procaryotes and eucaryotes. Cell, 16 (4). pp. 777-785. ISSN 0092-8674

Wilson, A. C., Freiman, R. N., Goto, H., Nishimoto, T., Herr, W. (October 1997) VP16 targets an amino-terminal domain of HCF involved in cell cycle progression. Molecular and Cellular Biology, 17 (10). pp. 6139-46. ISSN 0270-7306

Wilusz, J. E., Spector, D. L. (2010) An unexpected ending: Noncanonical 3′ end processing mechanisms. RNA, 16 (2). pp. 259-266. ISSN 13558382 (ISSN)

Wold, B., Wigler, M. H., Lacy, E., Maniatis, T., Silverstein, S., Axel, R. (November 1979) Introduction and expression of a rabbit Beta-globin gene in mouse fibroblasts. Proceedings of the National Academy of Sciences of the United States of America, 76 (11). pp. 5684-5688. ISSN 0027-8424

Won, K. A., Xiong, Y., Beach, D., Gilman, M. Z. (October 1992) Growth-regulated expression of D-type cyclin genes in human diploid fibroblasts. Proc Natl Acad Sci U S A, 89 (20). pp. 9910-4. ISSN 0027-8424 (Print)0027-8424 (Linking)

Xia, Z., Turner, G. C., Hwang, C. S., Byrd, C., Varshavsky, A. (October 2008) Amino acids induce peptide uptake via accelerated degradation of CUP9, the transcriptional repressor of the PTR2 peptide transporter. Journal of Biological Chemistry, 283 (43). pp. 28958-68. ISSN 0021-9258

Xu, H. P., Rajavashisth, T., Grewal, N., Jung, V., Riggs, M., Rodgers, L., Wigler, M. H. (July 1992) A gene encoding a protein with seven zinc finger domains acts on the sexual differentiation pathways of Schizosaccharomyces pombe. Mol Biol Cell, 3 (7). pp. 721-34. ISSN 1059-1524 (Print)

Xu, H. P., Riggs, M., Rodgers, L., Wigler, M. H. (1990) A gene from Schizosaccharomyces-Pombe with homology to Escherichia-Coli RNAse III blocks conjugation and sporulation when overexpressed in wild type cells. Nucleic Acids Research, 18 (17). p. 5304.

Xu, H. P., Wang, Y., Riggs, M., Rodgers, L., Wigler, M. H. (September 1990) Biological activity of the mammalian RAP genes in yeast. Cell Regulation, 1 (10). pp. 763-769. ISSN 1044-2030

Xu, R. M. (June 2003) A pivotal role of the coiled coil of Sir4. Structure, 11 (6). pp. 608-609. ISSN 0969-2126

Xu, X., Crow, M., Rice, B. R., Li, F., Harris, B., Liu, L., Demesa-Arevalo, E., Lu, Z., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S. N., Yang, B., Sylvester, A. W., Gingeras, T. R., Schmitz, R. J., Ware, D., Lipka, A. E., Gillis, J., Jackson, D. (December 2020) Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell, S1534- (20). pp. 31021-31022. ISSN 1534-5807

Xu, Xiaosa, Jackson, David (December 2022) Single-cell analysis opens a goldmine for plant functional studies. Current Opinion in Biotechnology, 79. p. 102858. ISSN 0958-1669

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., Revill, K., Weissmueller, S., Rappaport, A. R., Simon, J., Zhang, J., Luo, W. J., Hicks, J., Zender, L., Wang, X. W., Powers, S., Wigler, M., Lowe, S. W. (May 2012) A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109 (21). pp. 8212-8217. ISSN 0027-8424

Xue, W., Krasnitz, A., Lucito, R., Sordella, R., Van Aelst, L., Cordon-Cardo, C., Singer, S., Kuehnel, F., Wigler, M. H., Powers, S., Zender, L., Lowe, S. W. (June 2008) DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma. Genes & Development, 22 (11). pp. 1439-44. ISSN 0890-9369

Yaciuk, P., Carter, M. C., Pipas, J. M., Moran, E. (April 1991) Simian virus 40 large-T antigen expresses a biological activity complementary to the p300-associated transforming function of the adenovirus E1A gene products. Mol Cell Biol, 11 (4). pp. 2116-24. ISSN 0270-7306 (Print)0270-7306 (Linking)

Yajnik, V., Paulding, C., Sordella, R., McClatchey, A. I., Saito, M., Wahrer, D. C., Reynolds, P., Bell, D. W., Lake, R., van den Heuvel, S., Settleman, J., Haber, D. A. (March 2003) DOCK4, a GTPase activator, is disrupted during tumorigenesis. Cell, 112 (5). pp. 673-84. ISSN 0092-8674 (Print)

Yan, X., Hu, Z., Feng, Y., Hu, X., Yuan, J., Zhao, S. D., Zhang, Y., Yang, L., Shan, W., He, Q., Fan, L., Kandalaft, L. E., Tanyi, J. L., Li, C., Yuan, C. X., Zhang, D., Yuan, H., Hua, K., Lu, Y., Katsaros, D., Huang, Q., Montone, K., Fan, Y., Coukos, G., Boyd, J., Sood, A. K., Rebbeck, T., Mills, G. B., Dang, C. V., Zhang, L. (2015) Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. Cancer Cell, 28 (4). pp. 529-540. ISSN 1535-6108

Yang, F., Bui, H. T., Pautler, M., Llaca, V., Johnston, R., Lee, B. H., Kolbe, A., Sakai, H., Jackson, D. (January 2015) A Maize Glutaredoxin Gene, Abphyl2, Regulates Shoot Meristem Size and Phyllotaxy. Plant Cell, 27 (1). pp. 121-131. ISSN 1040-4651

Yang, Yang, Paul, Anirban, Bach, Thao Nguyen, Huang, Z Josh, Zhang, Michael Q (July 2021) Single-cell alternative polyadenylation analysis delineates GABAergic neuron types. BMC Biology, 19 (1). p. 144. ISSN 1741-7007

Yao, Zizhen, Liu, Hanqing, Xie, Fangming, Fischer, Stephan, Adkins, Ricky S, Aldridge, Andrew I, Ament, Seth A, Bartlett, Anna, Behrens, M Margarita, Van den Berge, Koen, Bertagnolli, Darren, de Bézieux, Hector Roux, Biancalani, Tommaso, Booeshaghi, A Sina, Bravo, Héctor Corrada, Casper, Tamara, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Crichton, Kirsten, Crow, Megan, Dee, Nick, Dougherty, Elizabeth L, Doyle, Wayne I, Dudoit, Sandrine, Fang, Rongxin, Felix, Victor, Fong, Olivia, Giglio, Michelle, Goldy, Jeff, Hawrylycz, Mike, Herb, Brian R, Hertzano, Ronna, Hou, Xiaomeng, Hu, Qiwen, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, Li, Yang Eric, Lucero, Jacinta D, Luo, Chongyuan, Mahurkar, Anup, McMillen, Delissa, Nadaf, Naeem M, Nery, Joseph R, Nguyen, Thuc Nghi, Niu, Sheng-Yong, Ntranos, Vasilis, Orvis, Joshua, Osteen, Julia K, Pham, Thanh, Pinto-Duarte, Antonio, Poirion, Olivier, Preissl, Sebastian, Purdom, Elizabeth, Rimorin, Christine, Risso, Davide, Rivkin, Angeline C, Smith, Kimberly, Street, Kelly, Sulc, Josef, Svensson, Valentine, Tieu, Michael, Torkelson, Amy, Tung, Herman, Vaishnav, Eeshit Dhaval, Vanderburg, Charles R, van Velthoven, Cindy, Wang, Xinxin, White, Owen R, Huang, Z Josh, Kharchenko, Peter V, Pachter, Lior, Ngai, John, Regev, Aviv, Tasic, Bosiljka, Welch, Joshua D, Gillis, Jesse, Macosko, Evan Z, Ren, Bing, Ecker, Joseph R, Zeng, Hongkui, Mukamel, Eran A (October 2021) A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature, 598 (7879). pp. 103-110. ISSN 0028-0836

Young, D., O'Neill, K., Broek, D., Wigler, M. H. (June 1991) The adenylyl cyclase-encoding gene from Saccharomyces kluyveri. Gene, 102 (1). pp. 129-32. ISSN 0378-1119

Young, D., O'Neill, K., Jessell, T., Wigler, M. H. (July 1988) Characterization of the rat mas oncogene and its high-level expression in the hippocampus and cerebral cortex of rat brain. Proc Natl Acad Sci U S A, 85 (14). pp. 5339-42. ISSN 0027-8424

Young, D., Riggs, M., Field, J., Vojtek, A., Broek, D., Wigler, M. H. (October 1989) The adenylyl cyclase gene from Schizosaccharomyces pombe. Proc Natl Acad Sci U S A, 86 (20). pp. 7989-93. ISSN 0027-8424

Young, D., Waitches, G., Birchmeier, C., Fasano, O., Wigler, M. H. (1986) Isolation and characterization of a new cellular oncogene encoding a protein with multiple potential transmembrane domains. Cell, 45 (5). pp. 711-720.

Yu, M., Lin, G., Arshadi, N., Kalatskaya, I., Xue, B., Haider, S., Nguyen, F., Boutros, P. C., Elson, A., Muthuswamy, L. B., Tonks, N. K., Muthuswamy, S. K. (October 2012) Expression profiling during mammary epithelial cell 3D morphogenesis identifies PTPRO as a novel regulator of morphogenesis and ErbB2 mediated transformation. Mol Cell Biol, 32 (19). pp. 3913-3924. ISSN 1098-5549 (Electronic)0270-7306 (Linking)

Yu, Duonan, dos Santos, Camila O, Zhao, Guowei, Jiang, Jing, Amigo, Julio D, Khandros, Eugene, Dore, Louis C, Yao, Yu, D'Souza, Janine, Zhang, Zhe, Ghaffari, Saghi, Choi, John, Friend, Sherree, Tong, Wei, Orange, Jordan S, Paw, Barry H, Weiss, Mitchell J (August 2010) miR-451 protects against erythroid oxidant stress by repressing 14-3-3zeta. Genes and Development, 24 (15). pp. 1620-1633. ISSN 0890-9369

Zebell, S. G. (October 2020) Excising the Mystery of Single-Guide RNA Processing. Plant Physiol, 184 (2). pp. 572-573. ISSN 0032-0889 (Print)0032-0889

Zelko, I., Kobayashi, R., Negishi, M. (May 2000) Repression of phenobarbital-responsive enhancer module in the Cyp2b10 gene by estrogen receptor-related receptor ERR. Faseb Journal, 14 (8). A1433-A1433. ISSN 0892-6638

Zeng, P. Y., Vakoc, C. R., Chen, Z. C., Blobel, G. A., Berger, S. L. (2006) In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation. Biotechniques, 41 (6). pp. 694-698. ISSN 07366205 (ISSN)

Zhang, M. Q. (August 1999) Large-scale gene expression data analysis: a new challenge to computational biologists. Genome Research, 9 (8). pp. 681-8. ISSN 1088-9051 (Print)

Zhang, M. Q. (June 1999) Promoter analysis of co-regulated genes in the yeast genome. Computers & Chemistry, 23 (3-4). pp. 233-50. ISSN 0097-8485 (Print)

Zhang, Y., Mei, P. C., Lou, R., Zhang, M. Q., Wu, G. Y., Qiang, B. Q., Zhang, Z. G., Shen, Y. (October 2002) Gene expression profiling in developing human hippocampus. Journal of Neuroscience Research, 70 (2). pp. 200-208. ISSN 0360-4012

Zhang, R, Atwal, GS, Lim, WK (March 2021) Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. Patterns, 2 (3). p. 100211. ISSN 2666-3899

Zhao, Y., Lin, P., Liufu, Z., Yang, H., Lyu, Y., Shen, X., Wu, C. I., Tang, T. (April 2018) Regulation of large number of weak targets - New insights from twin-microRNAs. Genome Biology and Evolution, 10 (5). pp. 1255-1264. ISSN 17596653 (ISSN)

Zhao, R., Nakamura, T., Fu, Y., Lazar, Z., Spector, D. L. (November 2011) Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nature Cell Biology, 13 (11). 1295-1304 . ISSN 1465-7392

Zhong, T., Luke, M. M., Arndt, K. T. (January 1996) Transcriptional regulation of the yeast DnaJ homologue SIS1. Journal of Biological Chemistry , 271 (3). pp. 1349-56. ISSN 0021-9258

Zhong, Y. (1996) Behavior-specific genes? Trends in Genetics, 12 (3). pp. 116-117. ISSN 01689525 (ISSN)

Zhu, X., Lin, C. R., Prefontaine, G. G., Tollkuhn, J., Rosenfeld, M. G. (June 2005) Genetic control of pituitary development and hypopituitarism. Curr Opin Genet Dev, 15 (3). pp. 332-40. ISSN 0959-437X (Print)0959-437X (Linking)

Zhu, Y., Pak, D., Qin, Y., McCormack, S. G., Kim, M. J., Baumgart, J. P., Velamoor, V., Auberson, Y. P., Osten, P., Van Aelst, L., Sheng, M., Zhu, J. J. (2005) Rap2-JNK removes synaptic AMPA receptors during depotentiation. Neuron, 46 (6). pp. 905-916. ISSN 08966273 (ISSN)

Zhu, Chuanmei, Liu, Lei, Crowell, Olivia, Zhao, Hui, Brutnell, Thomas P, Jackson, David, Kellogg, Elizabeth A (2021) The CLV3 Homolog in Setaria viridis Selectively Controls Inflorescence Meristem Size. Frontiers in Plant Science, 12. p. 636749. ISSN 1664-462X

Zuber, J., Rappaport, A. R., Luo, W., Wang, E., Chen, C., Vaseva, A. V., Shi, J., Weissmueller, S., Fellman, C., Taylor, M. J., Weissenboeck, M., Graeber, T. G., Kogan, S. C., Vakoc, C. R., Lowe, S. W. (August 2011) An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance. Genes & Development, 25 (15). pp. 1628-1640. ISSN 0890-9369

van der Horst, E. H., Degenhardt, Y. Y., Strelow, A., Slavin, A., Chinn, L., Orf, J., Rong, M., Li, S., See, L. H., Nguyen, K. Q., Hoey, T., Wesche, H., Powers, S. (November 2005) Metastatic properties and genomic amplification of the tyrosine kinase gene ACK1. Proceedings of the National Academy of Sciences of the United States of America, 102 (44). pp. 15901-6. ISSN 0027-8424

Book Section

Groover, A., Jackson, David (2002) Live-Cell Imaging of GFP in Plants. In: Arabidopsis: A Lab Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 262-279. ISBN 0-87969-573-0

Hicks, J. B., Strathern, J. N., Klar, A. J. (1982) Cloning by complementation in yeast: the mating type genes. In: Genetic engineering: principles and methods. Plenum Press, New York, pp. 219-248.

Jackson, D. P. (1992) In-situ hybridisation in plants. In: Molecular Plant Pathology: A Practical Approach. Practical Approach Series, 1 (85). Oxford University Press. ISBN 978-0-19-963102-5

Kessler, M., Gunnery, S., Laspia, M. F., Rice, A. P., Mathews, M. B. (1991) The Role of the Tar Region and Tat Protein in Hiv-Directed Gene Expression. In: Genetic structure and regulation of HIV. Harvard Aids Institute Series on Gene Regulation of Human Retroviruses (ED.). Raven Press, New York, pp. 75-96.

McClintock, Barbara (December 1961) Further studies of the suppressor-mutator system of control of gene action in maize. In: Annual Report of the Director of the Department of Genetics Carnegie Institution of Washington Year Book No. 60, 1960-1961. Carnegie Institution of Washington, Washington, D.C., pp. 469-476.

McClintock, Barbara (1968) Genetic systems regulating gene expression during development. In: Developmental Biology. Supplement 1: The 26th symposium of the society for developmental biology. Developmental Biology. Supplement 1: The 26th Symposium of the Society for Developmental Biology (June, 1967), Control Mechanisms in Developmental Processes . Academic Press, New York, pp. 84-112.

McClintock, Barbara (1980) Modified gene expressions induced by transposable elements. In: Mobilization and reassembly of genetic information: Proceedings of the Miami Winter Symposium, January, 1980. Academic Press, New York, pp. 11-19.

McClintock, Barbara (December 1966) Regulation of pattern of gene expression by controlling elements in maize. In: Carnegie Institution of Washington Year Book 65, 1965-1966. Carnegie Institution of Washington, Washington, D.C., pp. 568-578.

McClintock, Barbara (1971) The contribution of one component of a control system to versatility of gene expression. In: Carnegie Institution of Washington Year Book 70, 1970-1971. Carnegie Institution of Washington, Washington, D.C., pp. 5-17.

Spector, D. L. (2007) Nuclear Organization and Gene Expression. In: From DNA to Proteins: The Multiple Levels of Regulation, The Biomedical & Life Sciences Collection. Henry Stewart Talks Ltd, London.

Spector, David L. (1997) Genes and transcripts in the interphase nucleus. In: Nuclear organization, chromatin structure and gene expression. Oxford University Press, Oxford, pp. 169-184. ISBN 0198549237

Taparowsky, E., Suard, Y., Fasano, O., Shimizu, K., Goldfarb, M., Wigler, M. H. (1983) Activation of the Human H-Ras Gene. In: Recombinant DNA applications to human disease. Banbury report, 14 (ED.). Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 123-134. ISBN 0879692146

Wang, Yalin, Dubnau, Josh, Tully, Tim, Zhong, Yi (2007) Chapter 3 - Genetics in learning and memory. In: Neurobiology of Learning and Memory (Second Edition). Academic Press, Burlington, pp. 103-127. ISBN 978-0-12-372540-0

Wigler, M. H., Fasano, O., Taparowsky, E., Powers, S., Kataoka, T., Birnbaum, D., Shimizu, K., Goldfarb, M. (1984) Structure and Activation of Ras Genes. In: Oncogenes and viral genes. Cancer cells, 2 (ED.). Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 419-424. ISBN 0879691697

Wigler, M. H., Powers, S., Kataoka, T., Toda, T., Fasano, O., Matsumoto, K., Uno, I., Ishikawa, T., Broach, J. (1985) Function of Yeast Ras Genes. In: Genetics, cell differentiation, and cancer. Bristol-Myers cancer symposia, 7 (ED.). Academic Press, Orlando, pp. 153-164.

Conference or Workshop Item

Feigman, Mary J, Moss, Matthew A, Chen, Chen, Cyrill, Samantha L, Ciccone, Michael, Trousdell, Marygrace, Yang, Shih Ting, Frey, Wesley D, Wilkinson, John E, dos Santos, Camila O (June 2020) Pregnancy reprograms the epigenome of mammary epithelial cells and blocks the development of premalignant mammary lesions in response to cMYC-overexpression. In: AACR Special Conference on the Evolving Landscape of Cancer Modeling.

Zhu, J., Zhang, M. Q. (January 2000) Cluster, function and promoter: analysis of yeast expression array. In: Pacific Symposium on Biocomputing.

Book

Thor, A., Anderson, P., Raschid, L., Navlakha, S., Saha, B., Khuller, S., Zhang, X. N. (October 2011) Link prediction for annotation graphs using graph summarization. Lecture Notes in Computer Science, 7031 L (Part 1). Springer, pp. 714-729. ISBN 03029743 (ISSN); 9783642250729 (ISBN)

Wang, D., Pan, E., Fang, G., Kumari, S., He, F., Ware, D., Maslov, S., Gerstein, M. (September 2013) Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between arabidopsis and poplar. 2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 . ACM, pp. 689-690. ISBN 9781450324342 (ISBN)

Thesis

Bodnar, M. S. (March 2013) The Dynamics of Pluripotency Genes Upon Differentiation of Mouse Embryonic Stem Cells. PhD thesis, Cold Spring Harbor Laboratory.

Eckersley-Maslin, Melanie A. (January 2014) Characteristics of random monoallelic gene expression during embryonic stem cell differentiation. PhD thesis, Cold Spring Harbor Laboratory.

Finigan, P. (August 2011) The origin of novel phenotypic variation in Arabidopsis allopolyploids. PhD thesis, Cold Spring Harbor Laboratory.

Gutbrod, Michael J. (November 2019) Chromosomal Functions of RNA Interference and Small RNAs in Early Mammalian Development. PhD thesis, Cold Spring Harbor Laboratory.

Muratani, M. (April 2005) Regulation of Gene Expression by the Ubiquitin-Proteasome System. PhD thesis, Cold Spring Harbor Laboratory.

Pautler, Michael (August 2013) Meristem size and determinacy in Maize. PhD thesis, Cold Spring Harbor Laboratory.

Rappaport, A. R. (2011) Dissecting tumor suppressor and tumor maintenance genes in poor prognosis AML. PhD thesis, Cold Spring Harbor Laboratory.

Werner, Jonathan M (December 2023) Transcriptomic approaches for investigating developmental lineage: exploiting the X-chromosome as a marker for lineage specification and quantifying the lineage fidelity of neural organoid systems. PhD thesis, Cold Spring Harbor Laboratory.

Yordanov, Georgi Nenov (July 2019) Myc and Spdef: two transcription factors hijacked by pancreatic cancer. PhD thesis, Cold Spring Harbor.

Video

Gillis, J. (November 2012) Talk from Jessie Gillis at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Hammell, C. M. (November 2012) Talk from Chris Hammell at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Mills, A. A. (November 2011) Talk from Alea Mills at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Spector, D. L. (November 2012) Talk from David Spector at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Vakoc, C. R. (November 2012) Talk from Chris Vakoc at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Dataset

Mistry, M., Gillis, J., Pavlidis, P. (2013) Data and design files for 6 public datasets used in "Genome-wide expression profiling of schizophrenia using a large combined cohort" Mistry, M. and Gillis, J. and Pavlidis, P. (2013) Molecular Psychiatry, 18 (2). pp. 215-225. [Dataset]