Literature DB >> 21747384

RNA-Seq unleashed.

Matthew K Iyer, Arul M Chinnaiyan.   

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Year:  2011        PMID: 21747384     DOI: 10.1038/nbt.1915

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  10 in total

1.  Advancing RNA-Seq analysis.

Authors:  Brian J Haas; Michael C Zody
Journal:  Nat Biotechnol       Date:  2010-05       Impact factor: 54.908

2.  De novo assembly and analysis of RNA-seq data.

Authors:  Gordon Robertson; Jacqueline Schein; Readman Chiu; Richard Corbett; Matthew Field; Shaun D Jackman; Karen Mungall; Sam Lee; Hisanaga Mark Okada; Jenny Q Qian; Malachi Griffith; Anthony Raymond; Nina Thiessen; Timothee Cezard; Yaron S Butterfield; Richard Newsome; Simon K Chan; Rong She; Richard Varhol; Baljit Kamoh; Anna-Liisa Prabhu; Angela Tam; YongJun Zhao; Richard A Moore; Martin Hirst; Marco A Marra; Steven J M Jones; Pamela A Hoodless; Inanc Birol
Journal:  Nat Methods       Date:  2010-10-10       Impact factor: 28.547

Review 3.  Computational methods for transcriptome annotation and quantification using RNA-seq.

Authors:  Manuel Garber; Manfred G Grabherr; Mitchell Guttman; Cole Trapnell
Journal:  Nat Methods       Date:  2011-05-27       Impact factor: 28.547

4.  Chimeric transcript discovery by paired-end transcriptome sequencing.

Authors:  Christopher A Maher; Nallasivam Palanisamy; John C Brenner; Xuhong Cao; Shanker Kalyana-Sundaram; Shujun Luo; Irina Khrebtukova; Terrence R Barrette; Catherine Grasso; Jindan Yu; Robert J Lonigro; Gary Schroth; Chandan Kumar-Sinha; Arul M Chinnaiyan
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-10       Impact factor: 11.205

5.  Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Authors:  Sushmita Roy; Jason Ernst; Peter V Kharchenko; Pouya Kheradpour; Nicolas Negre; Matthew L Eaton; Jane M Landolin; Christopher A Bristow; Lijia Ma; Michael F Lin; Stefan Washietl; Bradley I Arshinoff; Ferhat Ay; Patrick E Meyer; Nicolas Robine; Nicole L Washington; Luisa Di Stefano; Eugene Berezikov; Christopher D Brown; Rogerio Candeias; Joseph W Carlson; Adrian Carr; Irwin Jungreis; Daniel Marbach; Rachel Sealfon; Michael Y Tolstorukov; Sebastian Will; Artyom A Alekseyenko; Carlo Artieri; Benjamin W Booth; Angela N Brooks; Qi Dai; Carrie A Davis; Michael O Duff; Xin Feng; Andrey A Gorchakov; Tingting Gu; Jorja G Henikoff; Philipp Kapranov; Renhua Li; Heather K MacAlpine; John Malone; Aki Minoda; Jared Nordman; Katsutomo Okamura; Marc Perry; Sara K Powell; Nicole C Riddle; Akiko Sakai; Anastasia Samsonova; Jeremy E Sandler; Yuri B Schwartz; Noa Sher; Rebecca Spokony; David Sturgill; Marijke van Baren; Kenneth H Wan; Li Yang; Charles Yu; Elise Feingold; Peter Good; Mark Guyer; Rebecca Lowdon; Kami Ahmad; Justen Andrews; Bonnie Berger; Steven E Brenner; Michael R Brent; Lucy Cherbas; Sarah C R Elgin; Thomas R Gingeras; Robert Grossman; Roger A Hoskins; Thomas C Kaufman; William Kent; Mitzi I Kuroda; Terry Orr-Weaver; Norbert Perrimon; Vincenzo Pirrotta; James W Posakony; Bing Ren; Steven Russell; Peter Cherbas; Brenton R Graveley; Suzanna Lewis; Gos Micklem; Brian Oliver; Peter J Park; Susan E Celniker; Steven Henikoff; Gary H Karpen; Eric C Lai; David M MacAlpine; Lincoln D Stein; Kevin P White; Manolis Kellis
Journal:  Science       Date:  2010-12-22       Impact factor: 47.728

6.  Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:  Mark B Gerstein; Zhi John Lu; Eric L Van Nostrand; Chao Cheng; Bradley I Arshinoff; Tao Liu; Kevin Y Yip; Rebecca Robilotto; Andreas Rechtsteiner; Kohta Ikegami; Pedro Alves; Aurelien Chateigner; Marc Perry; Mitzi Morris; Raymond K Auerbach; Xin Feng; Jing Leng; Anne Vielle; Wei Niu; Kahn Rhrissorrakrai; Ashish Agarwal; Roger P Alexander; Galt Barber; Cathleen M Brdlik; Jennifer Brennan; Jeremy Jean Brouillet; Adrian Carr; Ming-Sin Cheung; Hiram Clawson; Sergio Contrino; Luke O Dannenberg; Abby F Dernburg; Arshad Desai; Lindsay Dick; Andréa C Dosé; Jiang Du; Thea Egelhofer; Sevinc Ercan; Ghia Euskirchen; Brent Ewing; Elise A Feingold; Reto Gassmann; Peter J Good; Phil Green; Francois Gullier; Michelle Gutwein; Mark S Guyer; Lukas Habegger; Ting Han; Jorja G Henikoff; Stefan R Henz; Angie Hinrichs; Heather Holster; Tony Hyman; A Leo Iniguez; Judith Janette; Morten Jensen; Masaomi Kato; W James Kent; Ellen Kephart; Vishal Khivansara; Ekta Khurana; John K Kim; Paulina Kolasinska-Zwierz; Eric C Lai; Isabel Latorre; Amber Leahey; Suzanna Lewis; Paul Lloyd; Lucas Lochovsky; Rebecca F Lowdon; Yaniv Lubling; Rachel Lyne; Michael MacCoss; Sebastian D Mackowiak; Marco Mangone; Sheldon McKay; Desirea Mecenas; Gennifer Merrihew; David M Miller; Andrew Muroyama; John I Murray; Siew-Loon Ooi; Hoang Pham; Taryn Phippen; Elicia A Preston; Nikolaus Rajewsky; Gunnar Rätsch; Heidi Rosenbaum; Joel Rozowsky; Kim Rutherford; Peter Ruzanov; Mihail Sarov; Rajkumar Sasidharan; Andrea Sboner; Paul Scheid; Eran Segal; Hyunjin Shin; Chong Shou; Frank J Slack; Cindie Slightam; Richard Smith; William C Spencer; E O Stinson; Scott Taing; Teruaki Takasaki; Dionne Vafeados; Ksenia Voronina; Guilin Wang; Nicole L Washington; Christina M Whittle; Beijing Wu; Koon-Kiu Yan; Georg Zeller; Zheng Zha; Mei Zhong; Xingliang Zhou; Julie Ahringer; Susan Strome; Kristin C Gunsalus; Gos Micklem; X Shirley Liu; Valerie Reinke; Stuart K Kim; LaDeana W Hillier; Steven Henikoff; Fabio Piano; Michael Snyder; Lincoln Stein; Jason D Lieb; Robert H Waterston
Journal:  Science       Date:  2010-12-22       Impact factor: 47.728

7.  Understanding mechanisms underlying human gene expression variation with RNA sequencing.

Authors:  Joseph K Pickrell; John C Marioni; Athma A Pai; Jacob F Degner; Barbara E Engelhardt; Everlyne Nkadori; Jean-Baptiste Veyrieras; Matthew Stephens; Yoav Gilad; Jonathan K Pritchard
Journal:  Nature       Date:  2010-03-10       Impact factor: 49.962

8.  Massive genomic rearrangement acquired in a single catastrophic event during cancer development.

Authors:  Philip J Stephens; Chris D Greenman; Beiyuan Fu; Fengtang Yang; Graham R Bignell; Laura J Mudie; Erin D Pleasance; King Wai Lau; David Beare; Lucy A Stebbings; Stuart McLaren; Meng-Lay Lin; David J McBride; Ignacio Varela; Serena Nik-Zainal; Catherine Leroy; Mingming Jia; Andrew Menzies; Adam P Butler; Jon W Teague; Michael A Quail; John Burton; Harold Swerdlow; Nigel P Carter; Laura A Morsberger; Christine Iacobuzio-Donahue; George A Follows; Anthony R Green; Adrienne M Flanagan; Michael R Stratton; P Andrew Futreal; Peter J Campbell
Journal:  Cell       Date:  2011-01-07       Impact factor: 41.582

9.  Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Authors:  Manfred G Grabherr; Brian J Haas; Moran Yassour; Joshua Z Levin; Dawn A Thompson; Ido Amit; Xian Adiconis; Lin Fan; Raktima Raychowdhury; Qiandong Zeng; Zehua Chen; Evan Mauceli; Nir Hacohen; Andreas Gnirke; Nicholas Rhind; Federica di Palma; Bruce W Birren; Chad Nusbaum; Kerstin Lindblad-Toh; Nir Friedman; Aviv Regev
Journal:  Nat Biotechnol       Date:  2011-05-15       Impact factor: 54.908

10.  Alternative isoform regulation in human tissue transcriptomes.

Authors:  Eric T Wang; Rickard Sandberg; Shujun Luo; Irina Khrebtukova; Lu Zhang; Christine Mayr; Stephen F Kingsmore; Gary P Schroth; Christopher B Burge
Journal:  Nature       Date:  2008-11-27       Impact factor: 49.962

  10 in total
  8 in total

1.  De novo assembly and characterization of Muscovy duck liver transcriptome and analysis of differentially regulated genes in response to heat stress.

Authors:  Tao Zeng; Liping Zhang; Jinjun Li; Deqian Wang; Yong Tian; Lizhi Lu
Journal:  Cell Stress Chaperones       Date:  2015-02-09       Impact factor: 3.667

2.  Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.

Authors:  Berat Z Haznedaroglu; Darryl Reeves; Hamid Rismani-Yazdi; Jordan Peccia
Journal:  BMC Bioinformatics       Date:  2012-07-18       Impact factor: 3.169

3.  Evaluating de Bruijn graph assemblers on 454 transcriptomic data.

Authors:  Xianwen Ren; Tao Liu; Jie Dong; Lilian Sun; Jian Yang; Yafang Zhu; Qi Jin
Journal:  PLoS One       Date:  2012-12-07       Impact factor: 3.240

4.  Association between changes in reproductive activity and D-glucose metabolism in the tephritid fruit fly, Bactrocera dorsalis (Hendel).

Authors:  Daifeng Cheng; Langjie Chen; Chunyan Yi; Guangwen Liang; Yijuan Xu
Journal:  Sci Rep       Date:  2014-12-15       Impact factor: 4.379

5.  Si-CSP9 regulates the integument and moulting process of larvae in the red imported fire ant, Solenopsis invicta.

Authors:  Daifeng Cheng; Yongyue Lu; Ling Zeng; Guangwen Liang; Xiaofang He
Journal:  Sci Rep       Date:  2015-03-18       Impact factor: 4.379

6.  Comparative De Novo Transcriptome Analysis of Fertilized Ovules in Xanthoceras sorbifolium Uncovered a Pool of Genes Expressed Specifically or Preferentially in the Selfed Ovule That Are Potentially Involved in Late-Acting Self-Incompatibility.

Authors:  Qingyuan Zhou; Yuanrun Zheng
Journal:  PLoS One       Date:  2015-10-20       Impact factor: 3.240

7.  A transcriptomic analysis of bermudagrass (Cynodon dactylon) provides novel insights into the basis of low temperature tolerance.

Authors:  Liang Chen; Jibiao Fan; Longxing Hu; Zhengrong Hu; Yan Xie; Yingzi Zhang; Yanhong Lou; Eviatar Nevo; Jinmin Fu
Journal:  BMC Plant Biol       Date:  2015-09-11       Impact factor: 4.215

8.  RNA-Seq for gene identification and transcript profiling of three Stevia rebaudiana genotypes.

Authors:  Junwen Chen; Kai Hou; Peng Qin; Hongchang Liu; Bin Yi; Wenting Yang; Wei Wu
Journal:  BMC Genomics       Date:  2014-07-07       Impact factor: 3.969

  8 in total

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