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445 results

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Page 1
Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Gerstein MB, et al. Among authors: auerbach r. Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424. Nature. 2014. PMID: 25164755 Free PMC article.
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. Lu ZJ, et al. Among authors: auerbach r. Genome Res. 2011 Feb;21(2):276-85. doi: 10.1101/gr.110189.110. Epub 2010 Dec 22. Genome Res. 2011. PMID: 21177971 Free PMC article.
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. Rozowsky J, et al. Among authors: auerbach rk. Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4. Nat Biotechnol. 2009. PMID: 19122651 Free PMC article.
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washing… See abstract for full author list ➔ Gerstein MB, et al. Among authors: auerbach rk. Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Science. 2010. PMID: 21177976 Free PMC article.
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.
Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M. Zhong M, et al. Among authors: auerbach r. PLoS Genet. 2010 Feb 19;6(2):e1000848. doi: 10.1371/journal.pgen.1000848. PLoS Genet. 2010. PMID: 20174564 Free PMC article.
Mapping accessible chromatin regions using Sono-Seq.
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M. Auerbach RK, et al. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31. doi: 10.1073/pnas.0905443106. Epub 2009 Aug 18. Proc Natl Acad Sci U S A. 2009. PMID: 19706456 Free PMC article.
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.
Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M. Lefrançois P, et al. BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37. BMC Genomics. 2009. PMID: 19159457 Free PMC article.
The real cost of sequencing: higher than you think!
Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. Sboner A, et al. Genome Biol. 2011 Aug 25;12(8):125. doi: 10.1186/gb-2011-12-8-125. Genome Biol. 2011. PMID: 21867570 Free PMC article.
445 results