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Sheridan, M. A., Yunusov, D., Balaraman, V., Alexenko, A. P., Yabe, S., Verjovski-Almeida, S., Schust, D. J., Franz, A. W., Sadovsky, Y., Ezashi, T., Roberts, R. M. (2017) Vulnerability of primitive human placental trophoblast to Zika virus. Proc Natl Acad Sci U S A, 114 (9). E1587-e1596. ISSN 0027-8424

Teng, M., Love, M. I., Davis, C. A., Djebali, S., Dobin, A., Graveley, B. R., Li, S., Mason, C. E., Olson, S., Pervouchine, D., Sloan, C. A., Wei, X., Zhan, L., Irizarry, R. A. (2016) A benchmark for RNA-seq quantification pipelines. Genome Biol, 17 (1). p. 74. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Dobin, A., Gingeras, T. R. (2016) Optimizing RNA-Seq Mapping with STAR. Methods Mol Biol, 1415. pp. 245-262. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

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)

Chakrabortty, S. K., Prakash, A., Nechooshtan, G., Hearn, S., Gingeras, T. R. (2015) Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. RNA, 21 (11). pp. 1966-1979. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Dobin, A., Gingeras, T. R. (2015) Mapping RNA-seq Reads with STAR. Curr Protoc Bioinformatics, 51. 11.14.1-11.14.19. ISSN 1934-340X (Electronic)1934-3396 (Linking)

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. (2015) Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun, 6. p. 5903. ISSN 2041-1723

Lin, S., Lin, Y., Nery, J. R., Urich, M. A., Breschi, A., Davis, C. A., Dobin, A., Zaleski, C., Beer, M. A., Chapman, W. C., Gingeras, T. R., Ecker, J. R., Snyder, M. P. (2014) Comparison of the transcriptional landscapes between human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America, 111 (48). pp. 17224-17229. ISSN 0027-8424

Cheng, Y., Ma, Z., Kim, B. H., Wu, W., Cayting, P., Boyle, A. P., Sundaram, V., Xing, X., Dogan, N., Li, J., Euskirchen, G., Lin, S., Lin, Y., Visel, A., Kawli, T., Yang, X., Patacsil, D., Keller, C. A., Giardine, B., Kundaje, A., Wang, T., Pennacchio, L. A., Weng, Z., Hardison, R. C., Snyder, M. P., Consortium, Mouse ENCODE (2014) Principles of regulatory information conservation between mouse and human. Nature, 515 (7527). pp. 371-5. ISSN 0028-0836

Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., Shen, Y., Pervouchine, D. D., Djebali, S., Thurman, R. E., Kaul, R., Rynes, E., Kirilusha, A., Marinov, G. K., Williams, B. A., Trout, D., Amrhein, H., Fisher-Aylor, K., Antoshechkin, I., DeSalvo, G., See, L. H., Fastuca, M., Drenkow, J., Zaleski, C., Dobin, A., Prieto, P., Lagarde, J., Bussotti, G., Tanzer, A., Denas, O., Li, K., Bender, M. A., Zhang, M., Byron, R., Groudine, M. T., McCleary, D., Pham, L., Ye, Z., Kuan, S., Edsall, L., Wu, Y. C., Rasmussen, M. D., Bansal, M. S., Kellis, M., Keller, C. A., Morrissey, C. S., Mishra, T., Jain, D., Dogan, N., Harris, R. S., Cayting, P., Kawli, T., Boyle, A. P., Euskirchen, G., Kundaje, A., Lin, S., Lin, Y., Jansen, C., Malladi, V. S., Cline, M. S., Erickson, D. T., Kirkup, V. M., Learned, K., Sloan, C. A., Rosenbloom, K. R., Lacerda de Sousa, B., Beal, K., Pignatelli, M., Flicek, P., Lian, J., Kahveci, T., Lee, D., Kent, W. J., Ramalho Santos, M., Herrero, J., Notredame, C., Johnson, A., Vong, S., Lee, K., Bates, D., Neri, F., Diegel, M., Canfield, T., Sabo, P. J., Wilken, M. S., Reh, T. A., Giste, E., Shafer, A., Kutyavin, T., Haugen, E., Dunn, D., Reynolds, A. P., Neph, S., Humbert, R., Hansen, R. S., De Bruijn, M. (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515 (7527). pp. 355-64. 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. (2014) Comparative analysis of the transcriptome across distant species. Nature, 512 (7515). pp. 445-8. ISSN 0028-0836

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., Dunham, I., Elnitski, L. L., Farnham, P. J., Feingold, E. A., Gerstein, M., Giddings, M. C., Gilbert, D. M., Gingeras, T. R., Green, E. D., Guigo, R., Hubbard, T., Kent, J., Lieb, J. D., Myers, R. M., Pazin, M. J., Ren, B., Stamatoyannopoulos, J., Weng, Z., White, K. P., Hardison, R. C. (2014) Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America, 111 (33). E3366-E3366. ISSN 10916490 (ISSN)

Bassett, A. R., Akhtar, A., Barlow, D. P., Bird, A. P., Brockdorff, N., Duboule, D., Ephrussi, A., Ferguson-Smith, A. C., Gingeras, T. R., Haerty, W., Higgs, D. R., Miska, E. A., Ponting, C. P. (2014) Considerations when investigating IncRNA function in vivo. Elife, 3. ISSN 2050-084X

Fagegaltier, D., Konig, A., Gordon, A., Lai, E. C., Gingeras, T. R., Hannon, G. J., Shcherbata, H. R. (2014) A Genome-Wide Survey of Sexually Dimorphic Expression of Drosophila miRNAs Identifies the Steroid Hormone-Induced miRNA let-7 as a Regulator of Sexual Identity. Genetics, 198 (2). pp. 647-668. ISSN 0016-6731

Abdelhamid, R. F., Plessy, C., Yamauchi, Y., Taoka, M., de Hoon, M., Gingeras, T. R., Isobe, T., Carninci, P. (2014) Multiplicity of 5' Cap Structures Present on Short RNAs. PLoS One, 9 (7). e102895. ISSN 1932-6203

Weissmueller, S., Manchado, E., Saborowski, M., Morris, J. P. th, Wagenblast, E., Davis, C. A., Moon, S. H., Pfister, N. T., Tschaharganeh, D. F., Kitzing, T., Aust, D., Markert, E. K., Wu, J., Grimmond, S. M., Pilarsky, C., Prives, C., Biankin, A. V., Lowe, S. W. (2014) Mutant p53 Drives Pancreatic Cancer Metastasis through Cell-Autonomous PDGF Receptor beta Signaling. Cell, 157 (2). pp. 382-94. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Morikawa, H., Ohkura, N., Vandenbon, A., Itoh, M., Nagao-Sato, S., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A. R., Standley, D. M., Date, H., Sakaguchi, S., FANTOM Consortium, (2014) Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America, 111 (14). pp. 5289-94. ISSN 0027-8424

Gingeras, T. R. (2014) Conservation and novel functions of non-coding RNAs. Prion, 8 (Supple). pp. 8-9. ISSN 1933-68961933-690X

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., Dunham, I., Elnitski, L. L., Farnham, P. J., Feingold, E. A., Gerstein, M., Giddings, M. C., Gilbert, D. M., Gingeras, T. R., Green, E. D., Guigo, R., Hubbard, T., Kent, J., Lieb, J. D., Myers, R. M., Pazin, M. J., Ren, B., Stamatoyannopoulos, J. A., Weng, Z. P., White, K. P., Hardison, R. C. (2014) Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America, 111 (17). pp. 6131-6138. ISSN 0027-8424

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O., Jorgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Muller, F., Forrest, A. R., Carninci, P., Rehli, M., Sandelin, A., FANTOM Consortium, (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507 (7493). pp. 455-61. ISSN 0028-0836

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. (2014) A promoter-level mammalian expression atlas. Nature, 507 (7493). pp. 462-470. ISSN 14764687

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. (2014) Diversity and dynamics of the Drosophila transcriptome. Nature, 512 (7515). pp. 393-399. ISSN 0028-0836

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

Engström, P. G., Steijger, T., Sipos, B., Grant, G. R., Kahles, A., Rätsch, G., Goldman, N., Hubbard, T. J., Harrow, J., Guigó, R., Bertone, P., Alioto, T., Behr, J., Bohnert, R., Campagna, D., Davis, C. A., Dobin, A., Gingeras, T. R., Jean, G., Kosarev, P., Li, S., Liu, J., Mason, C. E., Molodtsov, V., Ning, Z., Ponstingl, H., Prins, J. F., Ribeca, P., Seledtsov, I., Solovyev, V., Valle, G., Vitulo, N., Wang, K., Wu, T. D., Zeller, G. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods, 10 (12). pp. 1185-1191. ISSN 15487091 (ISSN)

Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S. E., Behr, J., Bertone, P., Bohnert, R., Bucher, P., Cloonan, N., Derrien, T., Djebali, S., Du, J., Dudoit, S., Gerstein, M., Gingeras, T. R., Gonzalez, D., Grimmond, S. M., Guigó, R., Habegger, L., Harrow, J., Hubbard, T. J., Iseli, C., Jean, G., Kahles, A., Lagarde, J., Leng, J., Lefebvre, G., Lewis, S., Mortazavi, A., Niermann, P., Rätsch, G., Reymond, A., Ribeca, P., Richard, H., Rougemont, J., Rozowsky, J., Sammeth, M., Sboner, A., Schulz, M. H., Searle, S. M. J., Solorzano, N. D., Solovyev, V., Stanke, M., Stevenson, B. J., Stockinger, H., Valsesia, A., Weese, D., White, S., Wold, B. J., Wu, J., Wu, T. D., Zeller, G., Zerbino, D., Zhang, M. Q. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184. ISSN 15487091 (ISSN)

Schlesinger, F., Smith, A. D., Gingeras, T. R., Hannon, G. J., Hodges, E. (2013) De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements. Genome Research, 23 (10). pp. 1601-1614. ISSN 10889051 (ISSN)

Plummer, P. N., Freeman, R., Taft, R. J., Vider, J., Sax, M., Umer, B. A., Gao, D. C., Johns, C., Mattick, J. S., Wilto, S. D., Ferro, V., McMillan, N. A. J., Swarbrick, A., Mittal, V., Mellick, A. S. (2013) MicroRNAs Regulate Tumor Angiogenesis Modulated by Endothelial Progenitor Cells. Cancer Research, 73 (1). pp. 341-352. ISSN 0008-5472

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T. R. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29 (1). pp. 15-21. ISSN 1367-4803

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)

Livyatan, I., Harikumar, A., Nissim-Rafinia, M., Duttagupta, R., Gingeras, T. R., Meshorer, E. (2013) Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation. Nucleic Acids Research, 41 (12). pp. 6300-6315. ISSN 03051048 (ISSN)

Batut, P., Gingeras, T. R. (2013) RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs. Current Protocols in Molecular Biology (SUPPL). Unit25B. ISSN 19343639 (ISSN)

Cheng, C., Alexander, R., Min, R. Q., Leng, J., Yip, K. Y., Rozowsky, J., Yan, K. K., Dong, X. J., Djebali, S., Ruan, Y. J., Davis, C. A., Carninci, P., Lassman, T., Gingeras, T. R., Guigo, R., Birney, E., Weng, Z. P., Snyder, M., Gerstein, M. (2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research, 22 (9). pp. 1658-1667. ISSN 1088-9051

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F., Alioto, T., Antoshechkin, I., Baer, M. T., Bar, N. S., Batut, P., Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. J., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L. H., Shahab, A., Skancke, J., Suzuki, A. M., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S. E., Hannon, G., Giddings, M. C., Ruan, Y., Wold, B., Carninci, P., Guig, R., Gingeras, T. R. (2012) Landscape of transcription in human cells. Nature, 489 (7414). pp. 101-108. ISSN 0028-0836

Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., Sanyal, A., Shoresh, N., Simon, J. M., Song, L., Trinklein, N. D., Altshuler, R. C., Birney, E., Brown, J. B., Cheng, C., Djebali, S., Dong, X. J., Ernst, J., Furey, T. S., Gerstein, M., Giardine, B., Greven, M., Hardison, R. C., Harris, R. S., Herrero, J., Hoffman, M. M., Iyer, S., Kellis, M., Kheradpour, P., Lassmann, T., Li, Q. H., Lin, X., Marinov, G. K., Merkel, A., Mortazavi, A., Parker, S. C. J., Reddy, T. E., Rozowsky, J., Schlesinger, F., Thurman, R. E., Wang, J., Ward, L. D., Whitfield, T. W., Wilder, S. P., Wu, W., Xi, H. L. S., Yip, K. Y., Zhuang, J. L., Bernstein, B. E., Green, E. D., Gunter, C., Snyder, M., Pazin, M. J., Lowdon, R. F., Dillon, L. A. L., Adams, L. B., Kelly, C. J., Zhang, J., Wexler, J. R., Good, P. J., Feingold, E. A., Crawford, G. E., Dekker, J., Elnitski, L., Farnham, P. J., Giddings, M. C., Gingeras, T. R., Guigo, R., Hubbard, T. J., Kent, W. J., Lieb, J. D., Margulies, E. H., Myers, R. M., Stamatoyannopoulos, J. A., Tenenbaum, S. A., Weng, Z. P., White, K. P., Wold, B., Yu, Y., Wrobel, J., Risk, B. A., Gunawardena, H. P., Kuiper, H. C., Maier, C. W., Xie, L., Chen, X., Mikkelsen, T. S., Gillespie, S. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836

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. (2012) Modeling gene expression using chromatin features in various cellular contexts. Genome Biology, 13 (9).

Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T. R., Guigo, R. (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs. Genome Research, 22 (9). pp. 1616-1625. ISSN 1088-9051

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. (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

Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., Canfield, T., Giste, E., Johnson, A., Zhang, M., Balasundaram, G., Byron, R., Roach, V., Sabo, P. J., Sandstrom, R., Stehling, A. S., Thurman, R. E., Weissman, S. M., Cayting, P., Hariharan, M., Lian, J., Cheng, Y., Landt, S. G., Ma, Z., Wold, B. J., Dekker, J., Crawford, G. E., Keller, C. A., Wu, W., Morrissey, C., Kumar, S. A., Mishra, T., Jain, D., Byrska-Bishop, M., Blankenberg, D., Lajoiel, B. R., Jain, G., Sanyal, A., Chen, K. B., Denas, O., Taylor, J., Blobel, G. A., Weiss, M. J., Pimkin, M., Deng, W., Marinov, G. K., Williams, B. A., Fisher-Aylor, K. I., Desalvo, G., Kiralusha, A., Trout, D., Amrhein, H., Mortazavi, A., Edsall, L., McCleary, D., Kuan, S., Shen, Y., Yue, F., Ye, Z., Davis, C. A., Zaleski, C., Jha, S., Xue, C., Dobin, A., Lin, W., Fastuca, M., Wang, H., Guigo, R., Djebali, S., Lagarde, J., Ryba, T., Sasaki, T., Malladi, V. S., Cline, M. S., Kirkup, V. M., Learned, K., Rosenbloom, K. R., Kent, W. J., Feingold, E. A., Good, P. J., Pazin, M., Lowdon, R. F., Adams, L. B. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology, 13 (8).

Lasa, I., Toledo-Arana, A., Gingeras, T. R. (2012) An effort to make sense of antisense transcription in bacteria. RNA Biology, 9 (8). pp. 1039-1044. ISSN 1547-6286

Ramaswami, G., Lin, W., Piskol, R., Tan, M. H., Davis, C., Li, J. B. (2012) Accurate identification of human Alu and non-Alu RNA editing sites. Nature Methods, 9 (6). 579-+. ISSN 1548-7091

Lin, W., Piskol, R., Tan, M. H., Li, J. B. (2012) Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science, 335 (6074). 1302; author reply 1302. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Kowalczyk, M. S., Higgs, D. R., Gingeras, T. R. (2012) Molecular biology: RNA discrimination. Nature, 482 (7385). pp. 310-1. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

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

Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J. M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R. R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J., Tress, M. L., Gelpí, J. L., Orozco, M., Valencia, A., van Berkum, N. L., Lajoie, B. R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S. E., Guigó, R., Gingeras, T. R. (2012) Evidence for transcript networks composed of chimeric RNA's in human cells. PLoS ONE, 7 (1). ISSN 19326203 (ISSN)

Li, G., Ruan, X. A., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P. C., Poh, H. M., Goh, Y., Lim, J., Zhang, J., Sim, H. S., Peh, S. Q., Mulawadi, F. H., Ong, C. T., Orlov, Y. L., Hong, S., Zhang, Z., Landt, S. G., Raha, D., Euskirchen, G., Wei, C-L., Ge, W., Wang, H., Davis, C. A., Fisher-Aylor, K. I., Mortazavi, A., Gerstein, M., Gingeras, T. R., Wold, B., Sun, Yi, Fullwood, M. J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., Ruan, Y. (2012) Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell, 148 (1–2). pp. 84-98. ISSN 0092-8674

Lasa, I., Toledo-Arana, A., Dobin, A., Villanueva, M., de los Mozos, I. R., Vergara-Irigaray, M., Segura, V., Fagegaltier, D., Penades, J. R., Valle, J., Solano, C., Gingeras, T. R. (2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 20172-20177. ISSN 0027-8424

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

Clark, M. B., Amaral, P. P., Schlesinger, F. J., Dinger, M. E., Taft, R. J., Rinn, J. L., Ponting, C. P., Stadler, P. F., Morris, K. V., Morillon, A., Rozowsky, J. S., Gerstein, M. B., Wahlestedt, C., Hayashizaki, Y., Carninci, P., Gingeras, T. R., Mattick, J. S. (2011) The reality of pervasive transcription. Plos Biology, 9 (7). ISSN 15449173

Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X. L., Wang, L., Issner, R., Coyne, M. J., Durham, T., Ku, M. C., Truong, T., Ward, L. D., Altshuler, R. C., Lin, M. F., Kellis, M., Davis, C. A., Kapranov, P., Dobin, A., Zaleski, C., Schlesinger, F., Batut, P., Chakrabortty, S., Jha, S., Lin, W., Drenkow, J., Wang, H. E., Bell, K. G., Gao, H., Bell, I., Dumais, E., Dumais, J., Antonarakis, S. E., Ucla, C., Borel, C., Guigo, R., Djebali, S., Lagarde, J., Kingswood, C., Ribeca, P., Sammeth, M., Alioto, T., Merkel, A., Tilgner, H., Carninci, P., Hayashizaki, Y., Lassmann, T., Takahashi, H., Abdelhamid, R. F., Hannon, G., Fejes-Toth, K., Preall, J., Gordon, A., Sotirova, V., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Ruan, Y. J., Ruan, X. A., Shahab, A., Poh, W. T., Wei, C. L., Furey, T. S., Boyle, A. P., Sheffield, N. C., Song, L. Y., Shibata, Y., Vales, T., Winter, D., Zhang, Z. C., London, D., Wang, T. Y., Keefe, D., Iyer, V. R., Lee, B. K., McDaniell, R. M., Liu, Z., Battenhouse, A., Bhinge, A. A., Lieb, J. D., Grasfeder, L. L., Showers, K. A., Giresi, P. G., Kim, S. K. C., Shestak, C., Pauli, F., Reddy, T. E., Gertz, J. (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). Plos Biology, 9 (4). ISSN 1544-9173

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. (2011) The developmental transcriptome of Drosophila melanogaster. Nature, 471 (7339). pp. 473-479. ISSN 0028-0836

Deng, X., Hiatt, J. B., Nguyen, D. K., Ercan, S., Sturgill, D., Hillier, L. W., Schlesinger, F., Davis, C. A., Reinke, V. J., Gingeras, T. R., Shendure, J., Waterston, R. H., Oliver, B., Lieb, J. D., Disteche, C. M. (2011) Balance of the x restored: evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nature Genetics, 43 (12). pp. 1179-85. ISSN 10614036 (ISSN)

Lu, Y., Xue, C. (2011) The power of the purse and budgetary accountability: Experiences from subnational governments in china. Public Administration and Development, 31 (5). pp. 351-362. ISSN 02712075 (ISSN)

Cherbas, L., Willingham, A., Zhang, D., Yang, L., Zou, Y., Eads, B. D., Carlson, J. W., Landolin, J. M., Kapranov, P., Dumais, J., Samsonova, A., Choi, J. H., Roberts, J., Davis, C. A., Tang, H., Van Baren, M. J., Ghosh, S., Dobin, A., Bell, K. G., Lin, W., Langton, L., Duff, M. O., Tenney, A. E., Zaleski, C., Brent, M. R., Hoskins, R. A., Kaufman, T. C., Andrews, J., Graveley, B. R., Perrimon, N., Celniker, S. E., Gingeras, T. R., Cherbas, P. (2011) The transcriptional diversity of 25 Drosophila cell lines. Genome Research, 21 (2). pp. 301-314. ISSN 10889051 (ISSN)

Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L. J., Lin, M. F., Washietl, S., Arshinoff, B. I., Ay, F., Meyer, P. E., Robine, N., Washington, N. L., Di Stefano, L., Berezikov, E., Brown, C. D., Candeias, R., Carlson, J. W., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, M. Y., Will, S., Alekseyenko, A. A., Artieri, C., Booth, B. W., Brooks, A. N., Dai, Q., Davis, C. A., Duff, M. O., Feng, X., Gorchakov, A. A., Gu, T. T., Henikoff, J. G., Kapranov, P., Li, R. H., MacAlpine, H. K., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Powell, S. K., Riddle, N. C., Sakai, A., Samsonova, A., Sandler, J. E., Schwartz, Y. B., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, K. H., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowdon, R., Ahmad, K., Andrews, J., Berger, B., Brenner, S. E., Brent, M. R., Cherbas, L., Elgin, S. C. R., Gingeras, T. R., Grossman, R., Hoskins, R. A., Kaufman, T. C., Kent, W., Kuroda, M. I., Orr-Weaver, T., Perrimon, N., Pirrotta, V., Posakony, J. W., Ren, B., Russell, S., Cherbas, P., Graveley, B. R., Lewis, S., Micklem, G., Oliver, B., Park, P. J., Celniker, S. E., Henikoff, S., Karpen, G. H., Lai, E. C., MacAlpine, D. M., Stein, L. D., White, K. P., Kellis, M. (2010) Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science, 330 (6012). pp. 1787-1797. ISSN 0036-8075

Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, Md, Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D., Hornig, N., Orlando, V., Bell, I., Gao, H., Dumais, J., Kapranov, P., Wang, H., Davis, C. A., Gingeras, T. R., Kawai, J., Daub, C. O., Hayashizaki, Y., Gustincich, S., Carninci, P. (2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods, 7 (7). pp. 528-34. ISSN 15487091 (ISSN)

Amid, C., Frankish, A., Aken, B., Ezkurdia, I., Kokocinsk, F., Gilbert, J., White, S., Carninci, P., Gingeras, T. R., Guigo, R., Searle, S., Tress, M. L., Harrow, J., Hubbard, T. (2010) From identification to validation to gene count. Genome Biology, 11 (Suppl ). ISSN 1474-760X

Yang, A., Zhu, Z., Kettenbach, A., Kapranov, P., McKeon, F., Gingeras, T. R., Struhl, K. (2010) Genome-wide mapping indicates that p73 and p63 Co-occupy target sites and have similar DNA-binding profiles in vivo. PLoS ONE, 5 (7). ISSN 19326203 (ISSN)

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology, 10 (9). R101. ISSN 1474-7596

Gingeras, T. R. (2009) Implications of chimaeric non-co-linear transcripts. Nature, 461 (7261). pp. 206-11. ISSN 1476-4687 (Electronic)

Makrythanasis, P., Kapranov, P., Bartoloni, L., Reymond, A., Deutsch, S., Guigo, R., Denoeud, F., Drenkow, J., Rossier, C., Ariani, F., Capra, V., Excoffier, L., Renieri, A., Gingeras, T. R., Antonarakis, S. E. (2009) Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Human Mutation, 30 (9). E866-79. ISSN 1059-7794

Celniker, S. E., Dillon, L. A., Gerstein, M. B., Gunsalus, K. C., Henikoff, S., Karpen, G. H., Kellis, M., Lai, E. C., Lieb, J. D., MacAlpine, D. M., Micklem, G., Piano, F., Snyder, M., Stein, L. D., White, K. P., Waterston, R. H. (2009) Unlocking the secrets of the genome. Nature, 459 (7249). pp. 927-30. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

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

Zhang, X., Lian, Z., Padden, C., Gerstein, M. B., Rozowsky, J., Snyder, M., Gingeras, T. R., Kapranov, P., Weissman, S. M., Newburger, P. E. (2009) A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood, 113 (11). pp. 2526-34. ISSN 1528-0020 (Electronic)

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. (2009) Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature, 457 (7232). pp. 1028-1032. ISSN 0028-0836

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology, 10 (9). R101. ISSN 1465-6906

Rada-Iglesias, A., Ameur, A., Kapranov, P., Enroth, S., Komorowski, J., Gingeras, T. R., Wadelius, C. (2008) Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Research, 18 (3). pp. 380-92. ISSN 10889051 (ISSN)

Djebali, S., Kapranov, P., Foissac, S., Lagarde, J., Reymond, A., Ucla, C., Wyss, C., Drenkow, J., Dumais, E., Murray, R. R., Lin, C., Szeto, D., Denoeud, F., Calvo, M., Frankish, A., Harrow, J., Makrythanasis, P., Vidal, M., Salehi-Ashtiani, K., Antonarakis, S. E., Gingeras, T. R., Guigo, R. (2008) Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nature Methods, 5 (7). pp. 629-35. ISSN 15487091 (ISSN)

Efroni, S., Duttagupta, R., Cheng, J., Dehghani, H., Hoeppner, D. J., Dash, C., Bazett-Jones, D. P., Le Grice, S., McKay, R. D. G., Buetow, K. H., Gingeras, T. R., Misteli, T., Meshorer, E. (2008) Global Transcription in Pluripotent Embryonic Stem Cells. Cell Stem Cell, 2 (5). pp. 437-447. ISSN 19345909 (ISSN)

Gingeras, T. R. (2008) Mapping the strand-specific transcriptome of fission yeast. Nature Genetics, 40 (8). pp. 935-936. ISSN 1061-4036

Jones, P. A., Archer, T. K., Baylin, S. B., Beck, S., Berger, S., Bernstein, B. E., Carpten, J. D., Clark, S. J., Costello, J. F., Doerge, R. W., Esteller, M., Feinberg, A. P., Gingeras, T. R., Greally, J. M., Henikoff, S., Herman, J. G., Jackson-Grusby, L., Jenuwein, T., Jirtle, R. L., Kim, Y. J., Laird, P. W., Lim, B., Martienssen, R., Polyak, K., Stunnenberg, H., Tlsty, T. D., Tycko, B., Ushijima, T., Zhu, J., Pirrotta, V., Allis, C. D., Elgin, S. C., Rine, J., Wu, C. (2008) Moving AHEAD with an international human epigenome project. Nature, 454 (7205). pp. 711-715. ISSN 00280836 (ISSN)

Johnson, D. S., Li, W., Gordon, D. B., Bhattacharjee, A., Curry, B., Ghosh, J., Brizuela, L., Carroll, J. S., Brown, M., Flicek, P., Koch, C. M., Dunham, I., Bieda, M., Xu, X., Farnham, P. J., Kapranov, P., Nix, D. A., Gingeras, T. R., Zhang, X., Holster, H., Jiang, N., Green, R. D., Song, J. S., McCuine, S. A., Anton, E., Nguyen, L., Trinklein, N. D., Ye, Z., Ching, K., Hawkins, D., Ren, B., Scacheri, P. C., Rozowsky, J., Karpikov, A., Euskirchen, G., Weissman, S., Gerstein, M., Snyder, M., Yang, A., Moqtaderi, Z., Hirsch, H., Shulha, H. P., Fu, Y., Weng, Z., Struhl, K., Myers, R. M., Lieb, J. D., Liu, X. S. (2008) Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research, 18 (3). pp. 393-403. ISSN 10889051 (ISSN)

Li, X. Y., MacArthur, S., Bourgon, R., Nix, D., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Luengo Hendriks, C. L., Hou, C. C., Ogawa, N., Inwood, W., Sementchenko, V., Beaton, A., Weiszmann, R., Celniker, S. E., Knowles, D. W., Gingeras, T. R., Speed, T. P., Eisen, M. B., Biggin, M. D. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biology, 6 (2). 0365-0388. ISSN 1544-9173

Rada-Iglesias, A., Ameur, A., Kapranov, P., Enroth, S., Komorowski, J., Gingeras, T. R., Wadelius, C. (2007) Genome-wide gene regulatory networks for USF1 and USF2 in liver cells - implications for familial combined hyperlipidemia. European Journal of Clinical Investigation, 37. p. 76. ISSN 0014-2972

Sasaki, D., Kondo, S., Maeda, N., Gingeras, T. R., Hasegawa, Y., Hayashizaki, Y. (2007) Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: Causes of signal variation and false positive signals. Genomics, 89 (4). pp. 541-551. ISSN 08887543 (ISSN)

Rozowsky, J. S., Newburger, D., Sayward, F., Wu, J., Jordan, G., Korbel, J. O., Nagalakshmi, U., Yang, J., Zheng, D., Guigó, R., Gingeras, T. R., Weissman, S., Miller, P., Snyder, M., Gerstein, M. B. (2007) The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci. Genome Research, 17 (6). pp. 732-745. ISSN 10889051 (ISSN)

Ghosh, S., Hirsch, H. A., Sekinger, E. A., Kapranov, P., Struhl, K., Gingeras, T. R. (2007) Differential analysis for high density tiling microarray data. BMC Bioinformatics, 8. ISSN 14712105 (ISSN)

Kapranov, P., Willingham, A. T., Gingeras, T. R. (2007) Genome-wide transcription and the implications for genomic organization. Nature Reviews Genetics, 8 (6). pp. 413-423. ISSN 14710056 (ISSN)

Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P., Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C. J., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sunyaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Shahab, A., Flamm, C., Fried, C., Hackermüller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Siepel, A. C. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146). pp. 799-816. ISSN 00280836 (ISSN)

Gingeras, T. R. (2007) Origin of phenotypes: Genes and transcripts. Genome Research, 17 (6). pp. 682-690. ISSN 10889051 (ISSN)

Denoeud, F., Kapranov, P., Ucla, C., Frankish, A., Castelo, R., Drenkow, J., Lagarde, J., Alioto, T., Manzano, C., Chrast, J., Dike, S., Wyss, C., Henrichsen, C. N., Holroyd, N., Dickson, M. C., Taylor, R., Hance, Z., Foissac, S., Myers, R. M., Rogers, J., Hubbard, T., Harrow, J., Guigó, R., Gingeras, T. R., Antonarakis, S. E., Reymond, A. (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research, 17 (6). pp. 746-759. ISSN 10889051 (ISSN)

Zheng, D., Frankish, A., Baertsch, R., Kapranov, P., Reymond, A., Siew, W. C., Lu, Y., Denoeud, F., Antonarakis, S. E., Snyder, M., Ruan, Y., Wei, C. L., Gingeras, T. R., Guigó, R., Harrow, J., Gerstein, M. B. (2007) Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution. Genome Research, 17 (6). pp. 839-851. ISSN 10889051 (ISSN)

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)

Washietl, S., Pedersen, J. S., Korbel, J. O., Stocsits, C., Gruber, A. R., Hackermüller, J., Hertel, J., Lindemeyer, M., Reiche, K., Tanzer, A., Ucla, C., Wyss, C., Antonarakis, S. E., Denoeud, F., Lagarde, J., Drenkow, J., Kapranov, P., Gingeras, T. R., Guigó, R., Snyder, M., Gerstein, M. B., Reymond, A., Hofacker, I. L., Stadler, P. F. (2007) Structured RNAs in the ENCODE selected regions of the human genome. Genome Research, 17 (6). pp. 852-864. ISSN 10889051 (ISSN)

Carroll, J. S., Meyer, C. A., Song, J., Li, W., Geistlinger, T. R., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G. F., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, E. A., Silver, P. A., Gingeras, T. R., Liu, X. S., Brown, M. (2006) Genome-wide analysis of estrogen receptor binding sites. Nature Genetics, 38 (11). pp. 1289-1297. ISSN 1061-4036

Ghosh, S., Hirsch, H. A., Sekinger, E., Struhl, K., Gingeras, T. R. (2006) Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. BMC Bioinformatics, 7. ISSN 1471-2105

Manak, J. R., Dike, S., Sementchenko, V., Kapranov, P., Biemar, F., Long, J., Cheng, J., Bell, I., Ghosh, S., Piccolboni, A., Gingeras, T. R. (2006) Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nature Genetics, 38 (10). pp. 1151-1158. ISSN 10614036 (ISSN)

Liu, W., Putnam, A. L., Xu-yu, Z., Szot, G. L., Lee, M. R., Zhu, S., Gottlieb, P. A., Kapranov, P., Gingeras, T. R., De St. Groth, B. F., Clayberger, C., Soper, D. M., Ziegler, S. F., Bluestone, J. A. (2006) CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. Journal of Experimental Medicine, 203 (7). pp. 1701-1711. ISSN 00221007 (ISSN)

Guigó, R., Flicek, P., Abril, J. F., Reymond, A., Lagarde, J., Denoeud, F., Antonarakis, S., Ashburner, M., Bajic, V. B., Birney, E., Castelo, R., Eyras, E., Ucla, C., Gingeras, T. R., Harrow, J., Hubbard, T., Lewis, S. E., Reese, M. G. (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology, 7 Supp. S2.1-31. ISSN 14656914 (ISSN)

Zhang, M., Drenkow, J., Lankford, C. S. R., Frucht, D. M., Rabin, R. L., Gingeras, T. R., Venkateshan, C., Schwartzkopff, F., Clouse, K. A., Dayton, A. I. (2006) HIV regulation of the IL-7R: A viral mechanism for enhancing HIV-1 replication in human macrophages in vitro. Journal of Leukocyte Biology, 79 (6). pp. 1328-1338. ISSN 07415400 (ISSN)

Schumacher, A., Kapranov, P., Kaminsky, Z., Flanagan, J., Assadzadeh, A., Yau, P., Virtanen, C., Winegarden, N., Cheng, J., Gingeras, T., Petronis, A. (2006) Microarray-based DNA methylation profiling: Technology and applications. Nucleic Acids Research, 34 (2). pp. 528-542. ISSN 03051048 (ISSN)

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)

Yang, A., Zhu, Z., Kapranov, P., McKeon, F., Church, G. M., Gingeras, T. R., Struhl, K. (2006) Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Molecular Cell, 24 (4). pp. 593-602. ISSN 10972765 (ISSN)

Willingham, A. T., Gingeras, T. R. (2006) TUF Love for "Junk" DNA. Cell, 125 (7). pp. 1215-1220. ISSN 00928674 (ISSN)

Willingham, A. T., Dike, S., Cheng, J., Manak, J. R., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Duttagupta, R., Ganesh, M., Ghosh, S., Helt, G., Nix, D., Piccolboni, A., Sementchenko, V., Tammana, H., Kapranov, P., Gingeras, T. R. (2006) Transcriptional landscape of the human and fly genomes: Nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 101-110. ISSN 00917451 (ISSN)

Gingeras, T. R. (2006) The multitasking genome. Nature Genetics, 38 (6). pp. 608-609. ISSN 10614036 (ISSN)

Kapranov, P., Drenkow, J., Cheng, J., Long, J., Helt, G., Dike, S., Gingeras, T. R. (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Research, 15 (7). pp. 987-997. ISSN 10889051 (ISSN)

Gingeras, T. R., Higuchi, R., Kricka, L. J., Lo, Y. M. D., Wittwer, C. T. (2005) Fifty years of molecular (DNA/RNA) diagnostics. Clinical Chemistry, 51 (3). pp. 661-671. ISSN 00099147 (ISSN)

Bernstein, Bradley E., Kamal, Michael, Lindblad-Toh, Kerstin, Bekiranov, Stefan, Bailey, Dione K., Huebert, Dana J., McMahon, Scott, Karlsson, Elinor K., Kulbokas Iii, Edward J., Gingeras, Thomas R., Schreiber, Stuart L., Lander, Eric S. (2005) Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse. Cell, 120 (2). pp. 169-181. ISSN 0092-8674

Jeon, Y., Bekiranov, S., Karnani, N., Kapranov, P., Ghosh, S., MacAlpine, D., Lee, C., Deog, S. H., Gingeras, T. R., Dutta, A. (2005) Temporal profile of replication of human chromosomes. Proceedings of the National Academy of Sciences of the United States of America, 102 (18). pp. 6419-6424. ISSN 00278424 (ISSN)

Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., Sementchenko, V., Piccolboni, A., Bekiranov, S., Bailey, D. K., Ganesh, M., Ghosh, S., Bell, I., Gerhard, D. S., Gingeras, T. R. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308 (5725). pp. 1149-1154. ISSN 00368075 (ISSN)

Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P. T., Kruger, A. F., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S. (2005) The transcriptional landscape of the mammalian genome. Science, 309 (5740). pp. 1559-1563. ISSN 10959203 (ISSN)

Lian, Z., Lian, J., Urban, A. E., Colangelo, C., Kluger, Y., Zhang, X. Q., Konpe, D., Snyder, M., Newburger, P., Gingeras, T. R., Weissman, S. S. (2004) Global analysis of gene networks involved in hematopoiesis. Blood, 104 (11). 137B-137B. ISSN 0006-4971

ENCODE Project Consortium, (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-40. ISSN 0036-8075

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)

Gingeras, T. R. (2004) RNA reference materials for gene expression studies. Difficult first steps. Clinical Chemistry, 50 (8). pp. 1289-1290. ISSN 00099147 (ISSN)

Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., Wheeler, R., Wong, B., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Helt, G., Struhl, K., Gingeras, T. R. (2004) Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs. Cell, 116 (4). pp. 499-509. ISSN 0092-8674

Kampa, D., Kapranov, P., Cawley, S., Bekiranov, S., Ng, H. H., Sekinger, E. A., 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. (2003) Global mapping of functionally-important and regulatory regions on human chromosomes 21 and 22 reveal novel regulatory networks in the human genome. American Journal of Human Genetics, 73 (5). p. 185. ISSN 0002-9297

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. (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., Sementchenko, V. I., Gingeras, T. R. (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

Shi, S., Nathan, C., Schnappinger, D., Drenkow, J., Fuortes, M., Block, E., Ding, A., Gingeras, T. R., Schoolnik, G., Akira, S., Takeda, K., Ehrt, S. (2003) MyD88 primes macrophages for full-scale activation by interferon-γ yet mediates few responses to Mycobacterium tuberculosis. Journal of Experimental Medicine, 198 (7). pp. 987-997. ISSN 00221007 (ISSN)

Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P. A., Gingeras, T. R. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296 (5569). pp. 916-919. ISSN 00368075 (ISSN)

Dalma-Weiszhausz, D. D., Chicurel, M. E., Gingeras, T. R. (2002) Microarrays and genetic epidemiology: A multipurpose tool for a multifaceted field. Genetic Epidemiology, 23 (1). pp. 4-20. ISSN 07410395 (ISSN)

Dong, S. L., Wang, E., Hsie, L., Cao, Y. X., Chen, X. G., Gingeras, T. R. (2001) Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Research, 11 (8). pp. 1418-1424. ISSN 1088-9051

Kato-Maeda, M., Rhee, J. T., Gingeras, T. R., Salamon, H., Drenkow, J., Smittipat, N., Small, P. M. (2001) Comparing genomes within the species Mycobacterium tuberculosis. Genome Research, 11 (4). pp. 547-554. ISSN 10889051 (ISSN)

Rosenow, C., Saxena, R. M., Durst, M., Gingeras, T. R. (2001) Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches. Nucleic Acids Research, 29 (22). ISSN 13624962 (ISSN)

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)

Corbeil, J., Sheeter, D., Genini, D., Rought, S., Leoni, L., Du, P., Ferguson, M., Masys, D. R., Welsh, J. B., Fink, J. L., Sasik, R., Huang, D., Drenkow, J., Richman, D. D., Gingeras, T. R. (2001) Temporal gene regulation during HIV-1 infection of human CD4+ T cells. Genome Research, 11 (7). pp. 1198-1204. ISSN 10889051 (ISSN)

Belcher, C. E., Drenkow, J., Kehoe, B., Gingeras, T. R., McNamara, N., Lemjabbar, H., Basbaum, C., Relman, D. A. (2000) The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proceedings of the National Academy of Sciences of the United States of America, 97 (25). pp. 13847-13852. ISSN 0027-8424

Hacker, C., Thomas, D., Doshi, J., Kimberly, R. P., Gingeras, T. R., Patil, N. (2000) Single nucleotide polymorphism discovery in candidate genes for rheumatoid arthritis. American Journal of Human Genetics, 67 (4). p. 335. ISSN 0002-9297

Gingeras, T. R., Rosenow, C. (2000) Studying microbial genomes with high-density oligonucleotide arrays. ASM News, 66 (8). pp. 463-469. ISSN 0044-7897

Gingeras, T. R. (2000) Using high-density oligonucleotide arrays in hypothesis- and discovery-driven studies of selected host-pathogen interactions. Faseb Journal, 14 (8). A1584-A1584. ISSN 0892-6638

Belcher, C., Drenkow, J., Gingeras, T. R., McNamara, N., Basbaum, C., Relman, D. (2000) A role for mucin in Bordetella pertussis pathogenesis is revealed in the transcriptional profile of infected human bronchial epithelial cells. Pediatric Research, 47 (4). 257A-257A. ISSN 0031-3998

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)

Salamon, H., Kato-Maeda, M., Small, P. M., Drenkow, J., Gingeras, T. R. (2000) Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data. Genome Research, 10 (12). pp. 2044-2054. ISSN 10889051 (ISSN)

Kuritzkes, D. R., Shugarts, D., Bakhtiari, M., Poticha, D., Johnson, J., Rubin, M., Gingeras, T. R., Kennedy, M., Eron, J. J. (2000) Emergence of dual resistance to zidovudine and lamivudine in HIV-1- infected patients treated with zidovudine plus lamivudine as initial therapy. Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology, 23 (1). pp. 26-34. ISSN 10779450 (ISSN)

Lindblad-Toh, K., Winchester, E., Daly, M. J., Wang, D. G., Hirschhorn, J. N., Laviolette, J. P., Ardlie, K., Reich, D. E., Robinson, E., Sklar, P., Shah, N., Thomas, D., Fan, J. B., Gingeras, T. R., Warrington, J., Patil, N., Hudson, T. J., Lander, E. S. (2000) Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nature Genetics, 24 (4). pp. 381-386. ISSN 10614036 (ISSN)

Paxton, W. A., Kang, S., Liu, R., Landau, N. R., Gingeras, T. R., Wu, L., Mackay, C. R., Koup, R. A. (1999) HIV-1 infectability of CD4+ lymphocytes with relation to β-chemokines and the CCR5 coreceptor. Immunology Letters, 66 (1-3). pp. 71-75. ISSN 01652478 (ISSN)

Lipshutz, R. J., Fodor, S. P. A., Gingeras, T. R., Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nature Genetics, 21 (1 SUPP). pp. 20-24. ISSN 10614036 (ISSN)

Troesch, A., Nguyen, H., Miyada, C. G., Desvarenne, S., Gingeras, T. R., Kaplan, P. M., Cros, P., Mabilat, C. (1999) Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. Journal of Clinical Microbiology, 37 (1). pp. 49-55. ISSN 00951137 (ISSN)

Zhu, H., Cong, J. P., Mamtora, G., Gingeras, T. R., Shenk, T. (1998) Cellular gene expression altered by human cytomegalovirus: Global monitoring with oligonucleotide arrays. Proceedings of the National Academy of Sciences of the United States of America, 95 (24). pp. 14470-14475. ISSN 00278424 (ISSN)

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)

Gingeras, T. R., Ghandour, G., Wang, E., Berno, A., Small, P. M., Drobniewski, F., Alland, D., Desmond, E., Holodniy, M., Drenkow, J. (1998) Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Research, 8 (5). pp. 435-448. ISSN 10889051 (ISSN)

Zhu, H., Cong, J. P., Mamtora, G., Gingeras, T. R., Shenk, T. (1998) Use of differential display and dna array technology to assess the effect of human cytomegalovirus infection on signal transduction pathways. Faseb Journal, 12 (8). ISSN 08926638 (ISSN)

Winters, M. A., Shafer, R. W., Jellinger, R. A., Mamtora, G., Gingeras, T. R., Merigan, T. C. (1997) Human immunodeficiency virus type 1 reverse transcriptase genotype and drug susceptibility changes in infected individuals receiving dideoxyinosine monotherapy for 1 to 2 years. Antimicrobial Agents and Chemotherapy, 41 (4). pp. 757-762. ISSN 0066-4804

Kozal, M. J., Shah, N., Shen, N., Yang, R., Fucini, R., Merigan, T. C., Richman, D. D., Morris, D., Hubbell, E., Chee, M., Gingeras, T. R. (1996) Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nature Medicine, 2 (7). pp. 753-759. ISSN 10788956 (ISSN)

Decker, D. J., Linton, P. J., Zaharevitz, S., Biery, M., Gingeras, T. R., Klinman, N. R. (1995) Defining subsets of naive and memory B cells based on the ability of their progeny to somatically mutate in vitro. Immunity, 2 (2). pp. 195-203. ISSN 10747613 (ISSN)

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

Fahy, E., Biery, M., Goulden, M., Ghosh, S. S., Gingeras, T. R. (1994) Issues of variability, carryover contamination, and detection in 3SR-based assays. PCR Methods and Applications, 3 (5). S83-S94. ISSN 10549803 (ISSN)

Stillman, C. A., Linton, P. J., Koutz, P. J., Decker, D. J., Klinman, N. R., Gingeras, T. R. (1994) Specific immunoglobulin cDNA clones produced from hybridoma cell lines and murine spleen fragment cultures by 3SR amplification. PCR Methods and Applications, 3 (6). pp. 320-331. ISSN 10549803 (ISSN)

Gingeras, T. R., Ghosh, S., Blumeyer, K., Eis, P., Millar, D. (1993) A Spectrofluorometric Method for Measurement of Restriction Endonuclease activity based on Fluorescence Polarization. Journal of Cellular Biochemistry, 17C (Suppl). p. 173. ISSN 0730-2312

Decker, D. J., Linton, P. J., Gingeras, T. R., Klinman, N. R. (1993) In vitro analysis of somatically mutated B-cells. Journal of Cellular Biochemistry, 53 (S17B). p. 170. ISSN 0730-2312

Gingeras, T. R. (1993) Novel amplification targets for 3SR. Clinical Chemistry, 39 (4). pp. 726-727. ISSN 00099147 (ISSN)

Richman, D. D., Guatelli, J. C., Grimes, J., Tsiatis, A., Gingeras, T. R. (1991) Detection of mutations associated with zidovudine resistance in human immunodeficiency virus by use of the polymerase chain reaction. Journal of Infectious Diseases, 164 (6). pp. 1075-1081. ISSN 00221899 (ISSN)

Fahy, E., Kwoh, D. Y., Gingeras, T. R. (1991) Self-sustained sequence replication (3SR): An isothermal transcription-based amplification system alternative to PCR. Genome Research, 1 (1). pp. 25-33. ISSN 10889051 (ISSN)

Gingeras, T. R., Prodanovich, P., Latimer, T., Guatelli, J. C., Richman, D. D., Barringer, K. J. (1991) Use of self-sustained sequence replication amplification reaction to analyze and detect mutations in zidovudine-resistant human immunodeficiency virus. Journal of Infectious Diseases, 164 (6). pp. 1066-1074. ISSN 00221899 (ISSN)

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)

Ghosh, S. S., Obermiller, P. S., Kwoh, T. J., Gingeras, T. R. (1990) Analysis of substrate specificity of the PaeR7 endonuclease: Effect of base methylation on the kinetics of cleavage. Nucleic Acids Research, 18 (17). pp. 5063-5068. ISSN 03051048 (ISSN)

Barringer, K. J., Orgel, L., Wahl, G., Gingeras, T. R. (1990) Blunt-end and single-strand ligations by Escherichia coli ligase: influence on an in vitro amplication scheme. Gene, 89 (1). pp. 117-122. ISSN 0378-1119

Davis, G. R., Blumeyer, K., DiMichele, L. J., Whitfield, K. M., Chappelle, H., Riggs, N., Ghosh, S. S., Kao, P. M., Fahy, E., Kwoh, D. Y., Guatelli, J. C., Spector, S. A., Richman, D. D., Gingeras, T. R. (1990) Detection of human immunodeficiency virus type 1 in AIDS patients using amplification-mediated hybridization analyses: Reproducibility and quantitative limitations. Journal of Infectious Diseases, 162 (1). pp. 13-20. ISSN 00221899 (ISSN)

Guatelli, J. C., Whitfield, K. M., Kwoh, D. Y., Barringer, K. J., Richman, D. D., Gingeras, T. R. (1990) Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proceedings of the National Academy of Sciences of the United States of America, 87 (5). pp. 1874-1878. ISSN 00278424 (ISSN)

Gingeras, T. R., Richman, D. D., Kwoh, D. Y., Guatelli, J. C. (1990) Methodologies for in vitro nucleic acid amplification and their applications. Veterinary Microbiology, 24 (3-4). pp. 235-251. ISSN 03781135 (ISSN)

Gingeras, T. R., Whitfield, K. M., Kwoh, D. Y. (1990) Unique features of the self-sustained sequence replication (3SR) reaction in the in vitro amplification of nucleic acids. Annales de Biologie Clinique, 48 (7). pp. 498-501. ISSN 00033898 (ISSN)

Guatelli, J. C., Gingeras, T. R., Richman, D. D. (1989) Nucleic acid amplification in vitro: Detection of sequences with low copy numbers and application to diagnosis of human immunodeficiency virus type 1 infection. Clinical Microbiology Reviews, 2 (2). pp. 217-226. ISSN 08938512 (ISSN)

Kwoh, D. Y., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichelle, L. J., Gingeras, T. R. (1989) Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proceedings of the National Academy of Sciences of the United States of America, 86 (4). pp. 1173-1177. ISSN 00278424 (ISSN)

Kwoh, T. J., Obermiller, P. S., McCue, A. W., Kwoh, D. Y., Sullivan, S. A., Gingeras, T. R. (1988) Introduction and expression of the bacterial PaeR7 restriction endonuclease gene in mouse cells containing the PaeR7 methylase. Nucleic Acids Research, 16 (24). pp. 11489-11506. ISSN 03051048 (ISSN)

Ghosh, S. S., Gingeras, T. R., Davis, G. R., Musso, G. F., Kwoh, D. Y., Kao, P. M. (1987) Covalent attachment of nucleic acids to solid supports - chemistries of coupling and hybridization characteristics. Abstracts of Papers of the American Chemical Society, 194. 68-MBTD. ISSN 0065-7727

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)

Gingeras, T. R., Kwoh, D. Y., Davis, G. R. (1987) Hybridization properties of immobilized nucleic acids. Nucleic Acids Research, 15 (13). pp. 5373-5390. ISSN 03051048 (ISSN)

Kwoh, T. J., Kwoh, D. Y., McCue, A. W., Davis, G. R., Patrick, D., Gingeras, T. R. (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)

Ellis, S. B., Brust, P. F., Koutz, P. J., Waters, A. F., Harpold, M. M., Gingeras, T. R. (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)

Theriault, G., Roy, P. H., Howard, K. A., Benner, J. S., Brooks, J. E., Waters, A. F., Gingeras, T. R. (1985) Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products. Nucleic Acids Research, 13 (23). pp. 8441-8461. ISSN 03051048 (ISSN)

Gingeras, T. R., Brooks, J. E. (1983) Cloned restriction/modification system from Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 80 (2). pp. 402-406. ISSN 00278424 (ISSN)

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

Brooks, J. E., Blumenthal, R. M., Gingeras, T. R. (1983) The isolation and characterization of the Esherichia Coli DNA adenine methylase (dam) gene. Nucleic Acids Research, 11 (3). pp. 837-851. ISSN 03051048 (ISSN)

Roberts, R. J., Sciaky, D., Gelinas, R. E., Jiang, B. D., Yen, C. E., Kelly, M. M., Bullock, P. A., Parsons, B. L., Oneill, K. E., Gingeras, T. R. (1982) Information-Content of the Adenovirus-2 Genome. Cold Spring Harbor Symposia on Quantitative Biology, 47. pp. 1025-1037. ISSN 0091-7451

Gingeras, T. R., Sciaky, D., Gelinas, R. E., Bing-Dong, J., Yen, C. E., Kelly, M. M., Bullock, P. A., Parsons, B. L., O'Neill, K., Roberts, R. J. (1982) Nucleotide sequences from the adenovirus-2 genome. Journal of Biological Chemistry, 257 (22). pp. 13475-13491. ISSN 00219258 (ISSN)

Fitzgerlad, G. F., Daly, C., Brown, L. R., Gingeras, T. R. (1982) ScrFi: A new sequence-specific endonuclease from Streptococcus cremoris. Nucleic Acids Research, 10 (24). pp. 8171-8179. ISSN 03051048 (ISSN)

Gingeras, T. R., Rice, P., Roberts, R. J. (1982) A semi-automated method for the reading of nucleic acid sequencing gels. Nucleic Acids Research, 10 (1). pp. 103-114. ISSN 03051048 (ISSN)

Gingeras, T. R., Greenough, L., Schildkraut, I., Roberts, R. J. (1981) Two new restriction endonucleases from Proteus vulgaris. Nucleic Acids Research, 9 (18). pp. 4525-4536. ISSN 03051048 (ISSN)

Gingeras, T. R. (1980) Restriction endonucleases and their recognition sequences. Biochemical Society Transactions, 8 (3). pp. 397-398. ISSN 03005127 (ISSN)

Gingeras, T. R., Roberts, R. J. (1980) Steps toward computer analysis of nucleotide sequences. Science, 209 (4463). pp. 1322-1328. ISSN 00368075 (ISSN)

Gingeras, T. R., Milazzo, J. P., Sciaky, D., Roberts, R. J. (1979) Computer programs for the assembly of DNA sequences. Nucleic Acids Research, 7 (2). pp. 529-45. ISSN 0305-1048 (Print)0305-1048

Zain, S., Gingeras, T. R., Bullock, P., Wong, G., Gelinas, R. E. (1979) Determination and analysis of adenovirus-2 DNA sequences which may include signals for late messenger RNA processing. Journal of Molecular Biology, 135 (2). pp. 413-433. ISSN 00222836 (ISSN)

Gingeras, T. R., Milazzo, J. P., Roberts, R. J. (1978) A computer assisted method for the determination of restriction enzyme recognition sites. Nucleic Acids Research, 5 (11). pp. 4105-4128. ISSN 03051048 (ISSN)

Gingeras, T. R., Myers, P. A., Olson, J. A., Hanberg, F. A., Roberts, R. J. (1978) A new specific endonuclease present in Xanthomonas holcicola, Xanthomonas papavericola and Brevibacterium luteum. Journal of Molecular Biology, 118 (1). pp. 113-122. ISSN 0022-2836

Gelti Douka, H., Gingeras, T. R., Kambysellis, M. P. (1974) Yolk proteins in Drosophila: identification and site of synthesis. Journal of Experimental Zoology, 187 (1). pp. 167-172. ISSN 0022104X (ISSN)

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.

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

Book Section

Mack, D. H., Tom, E. Y., Mahadev, M., Dong, H., Mittmann, M., Dee, S., Levine, A. J., Gingeras, T. R., Lockhart, D. L. (1998) Deciphering Molecular Circuitry using high-density DNA arrays. In: The Biology of Tumors. Springer, New York, pp. 85-108. ISBN 9780306459320

Fahy, E., Barringer, K. J., Kwoh, D. Y., Prodanovich, P., Gingeras, T. R. (1996) The self-sustained sequence replication (3SR) reaction and its application to the detection of mutations associated with Zidovudine resistance in HIV-1. In: PCR Protocols and Applications: Laboratory Manual. Academic Press, New York. ISBN 9780080886718

Ghosh, S. S., Fahy, E., Gingeras, T. R. (1995) 13 - The Self-Sustained Sequence Replication Reaction and Its Application in Clinical Diagnostics and Molecular Biology. In: Molecular Methods for Virus Detection. Academic Press, San Diego, pp. 287-314. ISBN 978-0-12-748920-9

Gingeras, T. R., Biery, M., Goulden, M., Ghosh, S. S., Fahy, E. (1995) Optimization and Characterization of 3SR-based Assays. In: PCR primer: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 653-666. ISBN 9780879694487

Ghosh, S. S., Fahy, E., Gingeras, T. R. (1995) The self-sustained sequence replication (3SR) reaction: Its practice and applications. In: Molecular Methods for Virus Detection. Academic Press, San Diego, pp. 287-313. ISBN 9780080536897

Gingeras, T. R., Koutz, P. J., Linton, P. J., Decker, D. J., Klinman, N. R., Stillman, C. A. (1994) Production of antibodies of monoclonal specificity without the use of hybridoma cell lines. In: Methods in DNA amplification. Plenum Press, New York. ISBN 9780306449086

Gingeras, T. R. (1991) Restriction-modification systems. Genetic sentries and useful systems in the study of molecular genetics. In: Modern Microbial Genetics. Wiley-Liss, New York, pp. 301-322. ISBN 9780471568452

Kwoh, D. Y., Kwoh, T. J., Gingeras, T. R. (1991) Transcription-based amplification system. In: Methods in Gene Technology. Jai Press, London, pp. 285-299. ISBN 9781559382632

Gingeras, T. R., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichele, L. J., Kwoh, D. Y. (1990) Transcription-based amplification system and the detection of its RNA products by the bead-based sandwich hybridization system. In: PCR Protocols and Applications: Laboratory Manual. Academic Press, New York, pp. 245-252.

Kwoh, D. Y., Gingeras, T. R. (1988) The use of transcription-based amplification systems in the diagnosis of HIV-1 infections. In: Applied virology research. Springer. ISBN 9780306446689

Roberts, R. J., Akusjarvi, G., Alestrom, P., Gelinas, R. E., Gingeras, T., Sciaky, D., Pettersson, U. (1986) A consensus sequence for the adenovirus-2 genome. In: Adenovirus DNA: The Viral Genome and Its Expression. Springer, pp. 1-51. ISBN 9780898387582

Gingeras, T. R. (1984) Organizational expression of a type II restriction-modified system from Pseudomonas aeruginosa. In: Metabolism and Enzymology of Nucleic Acids. Slovak Academy of Sciences, pp. 267-276.

Gingeras, T. R. (1983) Computers and DNA sequences: A natural combination. In: Statistical analysis of DNA sequence data. M. Dekker, New York, pp. 15-44. ISBN 9780824770327

Gingeras, T. R. (1982) The isolation and characterization of the E. coli dam methylase gene. In: Metabolism and Enzymology of Nucleic Acids. Slovak Academy of Sciences, pp. 320-340.

Gingeras, T. R., Roberts, R. J. (1981) Computer assisted methods for nucleic acid sequencing. In: Genetic Engineering: Principles and Methods. Plenum Press, pp. 319-338. ISBN 9780306439193

Gingeras, T. R. (1980) Restriction endonucleases and their role in genomic analysis. In: Gene structure and expression. Ohio State University Biosciences Colloquia. Ohio State University Press, pp. 3-20.

Conference or Workshop Item

Gingeras, T. R. (2012) Important lessons from a complex genome. In: 22nd IUBMB & 37th FEBS Congress, Sept 4th-9th 2012, Seville, Spain.

Thesis

Batut, Philippe (2014) Promoter Evolution in Drosophila: Non-Coding Transcription & Transposon-Driven Innovation. PhD thesis, Cold Spring Harbor Laboratory.

Patent

Thomas Gingeras (1999) Mycobacterial rpoB sequences. United States Patent 7108968. .

Thomas Gingeras (1991) Prenatal sex determination of bovine cells using male-specific oligonucleotides. United States Patent 5055393. .

This list was generated on Wed Mar 29 15:01:35 2017 EDT.
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