Items where Subject is "transcriptomes"

Paper

Anaparthy, N., Ho, Y. J., Martelotto, L., Hammell, M., Hicks, J. (January 2019) Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harb Perspect Med, 9 (10). ISSN 2157-1422

BRAIN Initiative Cell Census Network (BICCN) (October 2021) A multimodal cell census and atlas of the mammalian primary motor cortex. Nature, 598 (7879). pp. 86-102. ISSN 0028-0836

Bakken, Trygve E, Jorstad, Nikolas L, Hu, Qiwen, Lake, Blue B, Tian, Wei, Kalmbach, Brian E, Crow, Megan, Hodge, Rebecca D, Krienen, Fenna M, Sorensen, Staci A, Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian D, Aldridge, Andrew I, Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa G, Crichton, Kirsten, Daigle, Tanya L, Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas T, Herb, Brian R, Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang Eric, Liu, Christine S, Liu, Hanqing, Lucero, Jacinta D, Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy A, Moussa, Marmar, Nery, Joseph R, Nicovich, Philip R, Niu, Sheng-Yong, Orvis, Joshua, Osteen, Julia K, Owen, Scott, Palmer, Carter R, Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora M, Rimorin, Christine, Rivkin, Angeline, Romanow, William J, Sedeño-Cortés, Adriana E, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna Marie, Zhang, Renee, Ament, Seth A, Behrens, M Margarita, Bravo, Hector Corrada, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick R, Höllt, Thomas, Horwitz, Gregory D, Keene, C Dirk, Kharchenko, Peter V, Ko, Andrew L, Lelieveldt, Boudewijn P, Luo, Chongyuan, Mukamel, Eran A, Pinto-Duarte, António, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard H, Smith, Kimberly, Spain, William J, White, Owen R, Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan Z, McCarroll, Steven A, Ting, Jonathan T, Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph R, Linnarsson, Sten, Lein, Ed S (October 2021) Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature, 598 (7879). pp. 111-119. ISSN 0028-0836

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

Bergmann, J. H., Li, J., Eckersley-Maslin, M. A., Rigo, F., Freier, S. M., Spector, D. L. (September 2015) Regulation of the ESC transcriptome by nuclear long non-coding RNAs. Genome Res, 25 (9). pp. 1336-1346. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Breschi, A., Davis, C., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Munoz, M., Garrido, D., Reverter, F., Gingeras, T. R., Guigo, R. (March 2018) The molecular basis of the cellular taxonomy of the human body. Human Genomics, 12 (Supple). Meeting Abstract A107. ISSN 1473-9542

Breschi, A., Gingeras, T. R., Guigo, R. (July 2017) Comparative transcriptomics in human and mouse. Nat Rev Genet, 18 (7). pp. 425-440. ISSN 1471-0056

Brown, J. B., Boley, N., Eisman, R., May, G. E., Stoiber, M. H., Duff, M. O., Booth, B. W., Wen, J., Park, S., Suzuki, A. M., Wan, K. H., Yu, C., Zhang, D., Carlson, J. W., Cherbas, L., Eads, B. D., Miller, D., Mockaitis, K., Roberts, J., Davis, C. A., Frise, E., Hammonds, A. S., Olson, S., Shenker, S., Sturgill, D., Samsonova, A. A., Weiszmann, R., Robinson, G., Hernandez, J., Andrews, J., Bickel, P. J., Carninci, P., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Lai, E. C., Oliver, B., Perrimon, N., Graveley, B. R., Celniker, S. E. (March 2014) Diversity and dynamics of the Drosophila transcriptome. Nature, 512 (7515). pp. 393-399. ISSN 0028-0836

Caiado, F., Maia-Silva, D., Jardim, C., Schmolka, N., Carvalho, T., Reforco, C., Faria, R., Kolundzija, B., Simoes, A. E., Baubec, T., Vakoc, C. R., da Silva, M. G., Manz, M. G., Schumacher, T. N., Norell, H., Silva-Santos, B. (November 2019) Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection. Nat Commun, 10 (1). p. 4986. ISSN 2041-1723

Carter, Jason A, Strömich, Léonie, Peacey, Matthew, Chapin, Sarah R, Velten, Lars, Steinmetz, Lars M, Brors, Benedikt, Pinto, Sheena, Meyer, Hannah V (August 2022) Transcriptomic diversity in human medullary thymic epithelial cells. Nature Communications, 13 (1). p. 4296. ISSN 2041-1723

Castel, S. E., Cervera, A., Mohammadi, P., Aguet, F., Reverter, F., Wolman, A., Guigo, R., Iossifov, I., Vasileva, A., Lappalainen, T. (August 2018) Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat Genet, 50 (9). pp. 1327-1334. ISSN 1061-4036

Chandran, D., Scanlon, M. J., Ohtsu, K., Timmermans, M. C., Schnable, P. S., Wildermuth, M. C. (October 2015) Laser Microdissection-Mediated Isolation and In Vitro Transcriptional Amplification of Plant RNA. Curr Protoc Mol Biol, 112. 25A 3.1-25A 3.23. ISSN 1934-3647 (Electronic)1934-3647 (Linking)

Chatterjee, Deeptiman, Costa, Caique Almeida Machado, Wang, Xian-Feng, Jevitt, Allison, Huang, Yi-Chun, Deng, Wu-Min (November 2022) Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model. eLife, 11. e80956. ISSN 2050-084X

Chen, Xiaoyin, Fischer, Stephan, Zhang, Aixin, Gillis, Jesse, Zador, Anthony (2022) Modular cell type organization of cortical areas revealed by in situ sequencing. bioRxiv. (Submitted)

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

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

Czech, Benjamin, Preall, Jonathan B, McGinn, Jon, Hannon, Gregory J (2013) A Transcriptome-wide RNAi Screen in the Drosophila Ovary Reveals Factors of the Germline piRNA Pathway. Molecular Cell, 50 (5). pp. 749-761. ISSN 1097-2765

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

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., Kraus, W. L. (April 2013) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell, 50 (2). pp. 212-22. ISSN 1097-2765

Deck, Courtney A., McKay, Sheldon J., Fiedler, Tristan J., LeMoine, Christophe M. R., Kajimura, Makiko, Nawata, C. Michele, Wood, Chris M., Walsh, Patrick J. (October 2013) Transcriptome responses in the rectal gland of fed and fasted spiny dogfish shark (Squalus acanthias) determined by suppression subtractive hybridization. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. ISSN 1744-117X

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

Dobin, Alexander, Gingeras, Thomas (November 2013) Comment on TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions by Kim et al. BioRxiv. (Unpublished)

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

Dreyer, Stephan B, Upstill-Goddard, Rosie, Paulus-Hock, Viola, Paris, Clara, Lampraki, Eirini-Maria, Dray, Eloise, Serrels, Bryan, Caligiuri, Giuseppina, Rebus, Selma, Plenker, Dennis, Galluzzo, Zachary, Brunton, Holly, Cunningham, Richard, Tesson, Mathias, Nourse, Craig, Bailey, Ulla-Maja, Jones, Marc, Moran-Jones, Kim, Wright, Derek W, Duthie, Fraser, Oien, Karin, Evers, Lisa, McKay, Colin J, McGregor, Grant A, Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephan, Dziubinski, Michele L, Candido, Juliana, Balkwill, Frances, Barry, Simon T, Grützmann, Robert, Rahib, Lola, Glasgow Precision Oncology Laboratory,, Australian Pancreatic Cancer Genome Initiative, Johns, Amber, Pajic, Marina, Froeling, Fieke EM, Beer, Phillip, Musgrove, Elizabeth A, Petersen, Gloria M, Ashworth, Alan, Frame, Margaret C, Crawford, Howard C, Simeone, Diane M, Lord, Chris, Mukhopadhyay, Debabrata, Pilarsky, Christian, Tuveson, David A, Cooke, Susanna L, Jamieson, Nigel B, Morton, Jennifer P, Sansom, Owen J, Bailey, Peter J, Biankin, Andrew V, Chang, David K (January 2021) Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer. Gastroenterology, 160 (1). 362-377.e13. ISSN 0016-5085

Dubois, M., Claeys, H., den Broeck, L. V., Inze, D. (February 2017) Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought. Plant Cell Environ, 40 (2). pp. 180-189. ISSN 1365-3040 (Electronic)0140-7791 (Linking)

Fang, Han, Huang, Yi-Fei, Radhakrishnan, Aditya, Siepel, Adam, Lyon, Gholson J., Schatz, Michael C. (February 2018) Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Systems, 6 (2). pp. 180-191. ISSN 2405-4712

Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G. J., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., Dumais, E., Gingeras, T. R. (February 2009) Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature, 457 (7232). pp. 1028-1032. ISSN 0028-0836

Fischer, Stephan, Crow, Megan, Harris, Benjamin D, Gillis, Jesse (July 2021) Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. Nature Protocols. ISSN 1754-2189

Fiskus, Warren, Mill, Christopher P, Nabet, Behnam, Perera, Dimuthu, Birdwell, Christine, Manshouri, Taghi, Lara, Bernardo, Kadia, Tapan M, DiNardo, Courtney, Takahashi, Koichi, Daver, Naval, Bose, Prithviraj, Masarova, Lucia, Pemmaraju, Naveen, Kornblau, Steven, Borthakur, Gautam, Montalban-Bravo, Guillermo, Manero, Guillermo Garcia, Sharma, Sunil, Stubbs, Matthew, Su, Xiaoping, Green, Michael R, Coarfa, Cristian, Verstovsek, Srdan, Khoury, Joseph D, Vakoc, Christopher R, Bhalla, Kapil N (May 2021) Superior efficacy of co-targeting GFI1/KDM1A and BRD4 against AML and post-MPN secondary AML cells. Blood Cancer Journal, 11 (5). p. 98. ISSN 2044-5385

Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., Huang, L., Hetzer, M. W., Navlakha, S. (December 2018) Predicting age from the transcriptome of human dermal fibroblasts. Genome Biol, 19 (1). p. 221. ISSN 1474-7596 (Public Dataset)

Gearty, Sofia V, Dündar, Friederike, Zumbo, Paul, Espinosa-Carrasco, Gabriel, Shakiba, Mojdeh, Sanchez-Rivera, Francisco J, Socci, Nicholas D, Trivedi, Prerak, Lowe, Scott W, Lauer, Peter, Mohibullah, Neeman, Viale, Agnes, DiLorenzo, Teresa P, Betel, Doron, Schietinger, Andrea (November 2021) An autoimmune stem-like CD8 T cell population drives type 1 diabetes. Nature. ISSN 0028-0836

Gerstein, M. B., Rozowsky, J., Yan, K. K., Wang, D., Cheng, C., Brown, J. B., Davis, C. A., Hillier, L., Sisu, C., Li, J. J., Pei, B., Harmanci, A. O., Duff, M. O., Djebali, S., Alexander, R. P., Alver, B. H., Auerbach, R., Bell, K., Bickel, P. J., Boeck, M. E., Boley, N. P., Booth, B. W., Cherbas, L., Cherbas, P., Di, C., Dobin, A., Drenkow, J., Ewing, B., Fang, G., Fastuca, M., Feingold, E. A., Frankish, A., Gao, G., Good, P. J., Guigo, R., Hammonds, A., Harrow, J., Hoskins, R. A., Howald, C., Hu, L., Huang, H., Hubbard, T. J., Huynh, C., Jha, S., Kasper, D., Kato, M., Kaufman, T. C., Kitchen, R. R., Ladewig, E., Lagarde, J., Lai, E., Leng, J., Lu, Z., MacCoss, M., May, G., McWhirter, R., Merrihew, G., Miller, D. M., Mortazavi, A., Murad, R., Oliver, B., Olson, S., Park, P. J., Pazin, M. J., Perrimon, N., Pervouchine, D., Reinke, V., Reymond, A., Robinson, G., Samsonova, A., Saunders, G. I., Schlesinger, F., Sethi, A., Slack, F. J., Spencer, W. C., Stoiber, M. H., Strasbourger, P., Tanzer, A., Thompson, O. A., Wan, K. H., Wang, G., Wang, H., Watkins, K. L., Wen, J., Wen, K., Xue, C., Yang, L., Yip, K., Zaleski, C., Zhang, Y., Zheng, H., Brenner, S. E., Graveley, B. R., Celniker, S. E., Gingeras, T. R., Waterston, R. (August 2014) Comparative analysis of the transcriptome across distant species. Nature, 512 (7515). pp. 445-8. ISSN 0028-0836

Gingeras, T. R. (February 2012) Patience is a virtue. Nature, 482 (7385). pp. 310-311. ISSN 0028-0836

Gingeras, T. R. (April 2009) Missing lincs in the transcriptome. Nature Biotechnology, 27 (4). pp. 346-347. ISSN 1087-0156

Graveley, B. R., Brooks, A. N., Carlson, J., Duff, M. O., Landolin, J. M., Yang, L., Artieri, C. G., van Baren, M. J., Boley, N., Booth, B. W., Brown, J. B., Cherbas, L., Davis, C. A., Dobin, A., Li, R. H., Lin, W., Malone, J. H., Mattiuzzo, N. R., Miller, D., Sturgill, D., Tuch, B. B., Zaleski, C., Zhang, D. Y., Blanchette, M., Dudoit, S., Eads, B., Green, R. E., Hammonds, A., Jiang, L. C., Kapranov, P., Langton, L., Perrimon, N., Sandler, J. E., Wan, K. H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P. J., Brenner, S. E., Brent, M. R., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Oliver, B., Celniker, S. E. (March 2011) The developmental transcriptome of Drosophila melanogaster. Nature, 471 (7339). pp. 473-479. ISSN 0028-0836

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

Gunner, G., Cheadle, L., Johnson, K. M., Ayata, P., Badimon, A., Mondo, E., Nagy, M. A., Liu, L., Bemiller, S. M., Kim, K. W., Lira, S. A., Lamb, B. T., Tapper, A. R., Ransohoff, R. M., Greenberg, M. E., Schaefer, A., Schafer, D. P. (July 2019) Sensory lesioning induces microglial synapse elimination via ADAM10 and fractalkine signaling. Nat Neurosci, 22 (7). pp. 1075-1088. ISSN 1097-6256 (Print)1097-6256

Haas, Brian J, Dobin, Alexander, Ghandi, Mahmoud, Van Arsdale, Anne, Tickle, Timothy, Robinson, James T, Gillani, Riaz, Kasif, Simon, Regev, Aviv (May 2023) Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. Cell Reports: Methods, 3 (5). p. 100467. ISSN 2667-2375

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

Holt, C., Campbell, M., Keays, D. A., Edelman, N., Kapusta, A., Maclary, E., Domyan, E. T., Suh, A., Warren, W. C., Yandell, M., Gilbert, M. T. P., Shapiro, M. D. (May 2018) Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia). G3-Genes Genomes Genetics, 8 (5). pp. 1391-1398. ISSN 2160-1836

Horvath, D. P., Patel, S., Doǧramaci, M., Chao, W. S., Anderson, J. V., Foley, M. E., Scheffler, B., Lazo, G., Dorn, K., Yan, C., Childers, A., Schatz, M., Marcus, S. (May 2018) Gene Space and Transcriptome Assemblies of Leafy Spurge (Euphorbia esula) Identify Promoter Sequences, Repetitive Elements, High-Quality Markers, and a Full-Length Chloroplast Genome. Weed Science, 66 (3). pp. 355-367. ISSN 00431745 (ISSN)

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

Huang, Z. J., Paul, A. (June 2019) The diversity of GABAergic neurons and neural communication elements. Nat Rev Neurosci, 29 (9). pp. 563-572. ISSN 1471-003x

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

Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, Dawe, R Kelly (August 2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373 (6555). pp. 655-662. ISSN 0036-8075

Jiang, H., Zhang, J., Han, Z., Yang, J., Ge, C., Wu, Q. (March 2017) Revealing new insights into different phosphorus-starving responses between two maize (Zea mays) inbred lines by transcriptomic and proteomic studies. Scientific Reports, 7. p. 44294. ISSN 20452322

Jiang, L. C., Schlesinger, F. J., Davis, C. A., Zhang, Y., Li, R. H., Salit, M., Gingeras, T. R., Oliver, B. (September 2011) Synthetic spike-in standards for RNA-seq experiments. Genome Research, 21 (9). pp. 1543-1551. ISSN 1088-9051 (Public Dataset)

Jiao, Y. N., Leebens-Mack, J., Ayyampalayam, S., Bowers, J. E., McKain, M. R., McNeal, J., Rolf, M., Ruzicka, D. R., Wafula, E., Wickett, N. J., Wu, X. L., Zhang, Y., Wang, J., Zhang, Y. T., Carpenter, E. J., Deyholos, M. K., Kutchan, T. M., Chanderbali, A. S., Soltis, P. S., Stevenson, D. W., McCombie, R., Pires, J. C., Wong, G. K. S., Soltis, D. E., dePamphilis, C. W. (January 2012) A genome triplication associated with early diversification of the core eudicots. Genome Biology, 13 (1). R3. ISSN 1474-7596

Jorstad, Nikolas L, Close, Jennie, Johansen, Nelson, Yanny, Anna Marie, Barkan, Eliza R, Travaglini, Kyle J, Bertagnolli, Darren, Campos, Jazmin, Casper, Tamara, Crichton, Kirsten, Dee, Nick, Ding, Song-Lin, Gelfand, Emily, Goldy, Jeff, Hirschstein, Daniel, Kiick, Katelyn, Kroll, Matthew, Kunst, Michael, Lathia, Kanan, Long, Brian, Martin, Naomi, McMillen, Delissa, Pham, Trangthanh, Rimorin, Christine, Ruiz, Augustin, Shapovalova, Nadiya, Shehata, Soraya, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Callaway, Edward M, Hof, Patrick R, Keene, C Dirk, Levi, Boaz P, Linnarsson, Sten, Mitra, Partha P, Smith, Kimberly, Hodge, Rebecca D, Bakken, Trygve E, Lein, Ed S (October 2023) Transcriptomic cytoarchitecture reveals principles of human neocortex organization. Science, 382 (6667). eadf6812. ISSN 0036-8075

Jorstad, Nikolas L, Song, Janet HT, Exposito-Alonso, David, Suresh, Hamsini, Castro-Pacheco, Nathan, Krienen, Fenna M, Yanny, Anna Marie, Close, Jennie, Gelfand, Emily, Long, Brian, Seeman, Stephanie C, Travaglini, Kyle J, Basu, Soumyadeep, Beaudin, Marc, Bertagnolli, Darren, Crow, Megan, Ding, Song-Lin, Eggermont, Jeroen, Glandon, Alexandra, Goldy, Jeff, Kiick, Katelyn, Kroes, Thomas, McMillen, Delissa, Pham, Trangthanh, Rimorin, Christine, Siletti, Kimberly, Somasundaram, Saroja, Tieu, Michael, Torkelson, Amy, Feng, Guoping, Hopkins, William D, Höllt, Thomas, Keene, C Dirk, Linnarsson, Sten, McCarroll, Steven A, Lelieveldt, Boudewijn P, Sherwood, Chet C, Smith, Kimberly, Walsh, Christopher A, Dobin, Alexander, Gillis, Jesse, Lein, Ed S, Hodge, Rebecca D, Bakken, Trygve E (October 2023) Comparative transcriptomics reveals human-specific cortical features. Science, 382 (6667). eade9516. ISSN 0036-8075

Kalish, B. T., Cheadle, L., Hrvatin, S., Nagy, M. A., Rivera, S., Crow, M., Gillis, J., Kirchner, R., Greenberg, M. E. (January 2018) Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement. Proc Natl Acad Sci U S A, 115 (5). E1051-E1060. ISSN 0027-8424

Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., Gingeras, T. R. (2004) Novel RNAs identified from a in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research, 14 (3). pp. 331-342. ISSN 10889051 (ISSN) (Public Dataset)

Kapranov, P., Cawley, S., Bekiranov, S., Ng, H. H., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Narayanan, B., Helt, G., Struhl, K., Gingeras, T. R. (November 2003) Hidden complexities of the human genome revealed by unbiased mapping of transcriptome. American Journal of Human Genetics, 73 (5). p. 419. ISSN 0002-9297

Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermüller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H., Gingeras, T. R. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316 (5830). pp. 1484-1488. ISSN 00368075 (ISSN)

Kim, Y. C., Wu, Q., Chen, J., Xuan, Z., Jung, Y.-C., Zhang, M. Q., Rowley, J. D., Wang, S. M. (May 2009) The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A, 106 (20). pp. 8278-8283.

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Conference or Workshop Item

Caligiuri, Giuseppina, Thalappillil, Jennifer, Hinds, Juliene, Courtois, Elise T, Flynn, William F, Robson, Paul, Dobin, Alexander, Park, Youngkyu, Tuveson, David A (2022) Spatial transcriptomics reveals heterogeneity and pathway dependencies of cancer associated fibroblasts in pancreatic ductal adenocarcinoma. In: Annual Meeting of the American-Association-for-Cancer-Research (AACR), APR 08-13, 2022, New Orleans, LA.

Church, G., Flicek, P., Ribbs, R., Mardis, E. (September 2010) PERSONAL GENOMES. In: 2010 meeting on PERSONAL GENOMES, September 10–September 12, 2010.

Muzumdar, Sukalp, Ballouz, Sara, Lam, Fung, Degrange, Maureen, Kreuzburg, Samantha, Chong, Hey, Zerbe, Christa, Jongco, Artemio, Gillis, Jesse (2022) A granular view of X-linked chronic granulomatous disease exploiting single-cell transcriptomics. In: Immunology Meeting, MAY 06-10, 2022, Portland, OR.

Nattestad, Maria, Ng, Karen, Goodwin, Sara, Baslan, Timour, Sedlazeck, Fritz, Gurtowski, James, Hutton, Elizabeth, Sundaravadanam, Yogi, Garvin, Tyler, Alford, Marley, Tseng, Elizabeth, Rescheneder, Philipp, Chin, Jason, Beck, Timothy, Kramer, Melissa, McPherson, John, Hicks, James, Schatz, Michael C, McCombie, William R (2016) Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research, 2016 Apr 16-20, New Orleans, LA.

Regan, C., Hao, Y., Preall, J. (July 2019) Stromal cell plasticity and immune surveillance revealed by single-cell transcriptomics. In: AACR Annual Meeting 2019.

Thesis

Harris, Benjamin D (October 2021) Atlas level scRNAseq analysis reveals the functional landscape of cell types. PhD thesis, Cold Spring Harbor Laboratory.

Lu, Shaina (September 2021) The replicability of spatially-resolved transcriptomics for modern neuroscience. 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.

Wunderlich, Cole (September 2023) Quantifying Transposable Element Expression in Single-Cell RNA Sequencing Data. PhD thesis, Cold Spring Harbor Laboratory.