Literature DB >> 20458303

Advancing RNA-Seq analysis.

Brian J Haas, Michael C Zody.   

Abstract

Mesh:

Year:  2010        PMID: 20458303     DOI: 10.1038/nbt0510-421

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


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  15 in total

1.  Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.

Authors:  Moran Yassour; Tommy Kaplan; Hunter B Fraser; Joshua Z Levin; Jenna Pfiffner; Xian Adiconis; Gary Schroth; Shujun Luo; Irina Khrebtukova; Andreas Gnirke; Chad Nusbaum; Dawn-Anne Thompson; Nir Friedman; Aviv Regev
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-10       Impact factor: 11.205

2.  The transcriptional landscape of the yeast genome defined by RNA sequencing.

Authors:  Ugrappa Nagalakshmi; Zhong Wang; Karl Waern; Chong Shou; Debasish Raha; Mark Gerstein; Michael Snyder
Journal:  Science       Date:  2008-05-01       Impact factor: 47.728

3.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

4.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.

Authors:  Mitchell Guttman; Ido Amit; Manuel Garber; Courtney French; Michael F Lin; David Feldser; Maite Huarte; Or Zuk; Bryce W Carey; John P Cassady; Moran N Cabili; Rudolf Jaenisch; Tarjei S Mikkelsen; Tyler Jacks; Nir Hacohen; Bradley E Bernstein; Manolis Kellis; Aviv Regev; John L Rinn; Eric S Lander
Journal:  Nature       Date:  2009-02-01       Impact factor: 49.962

Review 5.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

6.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

7.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Authors:  Cole Trapnell; Brian A Williams; Geo Pertea; Ali Mortazavi; Gordon Kwan; Marijke J van Baren; Steven L Salzberg; Barbara J Wold; Lior Pachter
Journal:  Nat Biotechnol       Date:  2010-05-02       Impact factor: 54.908

8.  Annotating genomes with massive-scale RNA sequencing.

Authors:  France Denoeud; Jean-Marc Aury; Corinne Da Silva; Benjamin Noel; Odile Rogier; Massimo Delledonne; Michele Morgante; Giorgio Valle; Patrick Wincker; Claude Scarpelli; Olivier Jaillon; François Artiguenave
Journal:  Genome Biol       Date:  2008-12-16       Impact factor: 13.583

9.  TopHat: discovering splice junctions with RNA-Seq.

Authors:  Cole Trapnell; Lior Pachter; Steven L Salzberg
Journal:  Bioinformatics       Date:  2009-03-16       Impact factor: 6.937

10.  Full-length messenger RNA sequences greatly improve genome annotation.

Authors:  Brian J Haas; Natalia Volfovsky; Christopher D Town; Maxim Troukhan; Nickolai Alexandrov; Kenneth A Feldmann; Richard B Flavell; Owen White; Steven L Salzberg
Journal:  Genome Biol       Date:  2002-05-30       Impact factor: 13.583

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  77 in total

1.  IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly.

Authors:  Wei Li; Jianxing Feng; Tao Jiang
Journal:  J Comput Biol       Date:  2011-09-27       Impact factor: 1.479

2.  CEDER: accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq.

Authors:  Lin Wan; Fengzhu Sun
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2012 Sep-Oct       Impact factor: 3.710

3.  Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.

Authors:  Sheng Li; Scott W Tighe; Charles M Nicolet; Deborah Grove; Shawn Levy; William Farmerie; Agnes Viale; Chris Wright; Peter A Schweitzer; Yuan Gao; Dewey Kim; Joe Boland; Belynda Hicks; Ryan Kim; Sagar Chhangawala; Nadereh Jafari; Nalini Raghavachari; Jorge Gandara; Natàlia Garcia-Reyero; Cynthia Hendrickson; David Roberson; Jeffrey Rosenfeld; Todd Smith; Jason G Underwood; May Wang; Paul Zumbo; Don A Baldwin; George S Grills; Christopher E Mason
Journal:  Nat Biotechnol       Date:  2014-08-24       Impact factor: 54.908

4.  RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis.

Authors:  Zhihui Xia; Huimin Xu; Jinling Zhai; Dejun Li; Hongli Luo; Chaozu He; Xi Huang
Journal:  Plant Mol Biol       Date:  2011-08-03       Impact factor: 4.076

5.  RNA-Seq unleashed.

Authors:  Matthew K Iyer; Arul M Chinnaiyan
Journal:  Nat Biotechnol       Date:  2011-07-11       Impact factor: 54.908

Review 6.  Next-generation transcriptome assembly.

Authors:  Jeffrey A Martin; Zhong Wang
Journal:  Nat Rev Genet       Date:  2011-09-07       Impact factor: 53.242

7.  RNA-seq methods for identifying differentially expressed gene in human pancreatic islet cells treated with pro-inflammatory cytokines.

Authors:  Bo Li; Chang Long Bi; Ning Lang; Yu Ze Li; Chao Xu; Ying Qi Zhang; Ai Xia Zhai; Zhi Feng Cheng
Journal:  Mol Biol Rep       Date:  2014-03-12       Impact factor: 2.316

8.  Approaches to Fungal Genome Annotation.

Authors:  Brian J Haas; Qiandong Zeng; Matthew D Pearson; Christina A Cuomo; Jennifer R Wortman
Journal:  Mycology       Date:  2011-10-03

Review 9.  Quantitative analysis of 5HT(2C) receptor RNA editing patterns in psychiatric disorders.

Authors:  Richard T O'Neil; Ronald B Emeson
Journal:  Neurobiol Dis       Date:  2011-09-03       Impact factor: 5.996

10.  Solexa sequencing based transcriptome analysis of Helicoverpa armigera larvae.

Authors:  Jigang Li; Xiumin Li; Yongli Chen; Zhongxiang Yang; Sandui Guo
Journal:  Mol Biol Rep       Date:  2012-10-12       Impact factor: 2.316

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