Items where Community is "Dobin Lab"

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Paper

Wang, L., Lu, Z., Delabastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Xu, X., Ortiz-Ramirez, C., Marco, C.F., Goodwin, S., Dobin, A., Birnbaum, K. D., Jackson, D. P., Martienssen, R. A., McCombie, W. R., Micklos, D. A., Schatz, M. C., Ware, D. H., Gingeras, T. R. (March 2020) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science, 11 (289). ISSN 1664-462X (Public Dataset)

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

Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., Regev, A. (October 2019) Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol, 20 (1). p. 213. ISSN 1474-7596

Ballouz, S., Dobin, A., Gillis, J. A. (August 2019) Is it time to change the reference genome? Genome Biol, 20 (1). ISSN 1474-7596

Zhang, Q., Chao, T. C., Patil, V. S., Qin, Y., Tiwari, S. K., Chiou, J., Dobin, A., Tsai, C. M., Li, Z., Dang, J., Gupta, S., Urdahl, K., Nizet, V., Gingeras, T. R., Gaulton, K. J., Rana, T. M. (March 2019) The long noncoding RNA ROCKI regulates inflammatory gene expression. Embo j, 38 (8). Article number e100041. ISSN 0261-4189

Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

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

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. (April 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. (April 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)

Dobin, A., Gingeras, T. R. (September 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. (January 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. (November 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 (November 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. (November 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. (August 2014) Comparative analysis of the transcriptome across distant species. Nature, 512 (7515). pp. 445-8. ISSN 0028-0836

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. (December 2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods, 10 (12). pp. 1185-1191. ISSN 15487091 (ISSN)

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T. R. (January 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)

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. (September 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. (September 2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836

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. (August 2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology, 13 (8).

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. (January 2012) Evidence for transcript networks composed of chimeric RNA's in human cells. PLoS ONE, 7 (1). ISSN 19326203 (ISSN)

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. (December 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

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. (April 2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). Plos Biology, 9 (4). ISSN 1544-9173 (Public Dataset)

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

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) (Public Dataset)

This list was generated on Tue Aug 11 21:55:15 2020 EDT.
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