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Literature DB >> 24296473

Genomics: the state of the art in RNA-seq analysis.

Ian Korf¹.

Abstract

Mesh：

Year: 2013 PMID： 24296473 DOI： 10.1038/nmeth.2735

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

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6 in total

1. mGene: accurate SVM-based gene finding with an application to nematode genomes.

Authors: Gabriele Schweikert; Alexander Zien; Georg Zeller; Jonas Behr; Christoph Dieterich; Cheng Soon Ong; Petra Philips; Fabio De Bona; Lisa Hartmann; Anja Bohlen; Nina Krüger; Sören Sonnenburg; Gunnar Rätsch
Journal: Genome Res Date: 2009-06-29 Impact factor: 9.043

2. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Authors: Keith R Bradnam; Joseph N Fass; Anton Alexandrov; Paul Baranay; Michael Bechner; Inanç Birol; Sébastien Boisvert; Jarrod A Chapman; Guillaume Chapuis; Rayan Chikhi; Hamidreza Chitsaz; Wen-Chi Chou; Jacques Corbeil; Cristian Del Fabbro; T Roderick Docking; Richard Durbin; Dent Earl; Scott Emrich; Pavel Fedotov; Nuno A Fonseca; Ganeshkumar Ganapathy; Richard A Gibbs; Sante Gnerre; Elénie Godzaridis; Steve Goldstein; Matthias Haimel; Giles Hall; David Haussler; Joseph B Hiatt; Isaac Y Ho; Jason Howard; Martin Hunt; Shaun D Jackman; David B Jaffe; Erich D Jarvis; Huaiyang Jiang; Sergey Kazakov; Paul J Kersey; Jacob O Kitzman; James R Knight; Sergey Koren; Tak-Wah Lam; Dominique Lavenier; François Laviolette; Yingrui Li; Zhenyu Li; Binghang Liu; Yue Liu; Ruibang Luo; Iain Maccallum; Matthew D Macmanes; Nicolas Maillet; Sergey Melnikov; Delphine Naquin; Zemin Ning; Thomas D Otto; Benedict Paten; Octávio S Paulo; Adam M Phillippy; Francisco Pina-Martins; Michael Place; Dariusz Przybylski; Xiang Qin; Carson Qu; Filipe J Ribeiro; Stephen Richards; Daniel S Rokhsar; J Graham Ruby; Simone Scalabrin; Michael C Schatz; David C Schwartz; Alexey Sergushichev; Ted Sharpe; Timothy I Shaw; Jay Shendure; Yujian Shi; Jared T Simpson; Henry Song; Fedor Tsarev; Francesco Vezzi; Riccardo Vicedomini; Bruno M Vieira; Jun Wang; Kim C Worley; Shuangye Yin; Siu-Ming Yiu; Jianying Yuan; Guojie Zhang; Hao Zhang; Shiguo Zhou; Ian F Korf
Journal: Gigascience Date: 2013-07-22 Impact factor: 6.524

3. Sequence-specific error profile of Illumina sequencers.

Authors: Kensuke Nakamura; Taku Oshima; Takuya Morimoto; Shun Ikeda; Hirofumi Yoshikawa; Yuh Shiwa; Shu Ishikawa; Margaret C Linak; Aki Hirai; Hiroki Takahashi; Md Altaf-Ul-Amin; Naotake Ogasawara; Shigehiko Kanaya
Journal: Nucleic Acids Res Date: 2011-05-16 Impact factor: 16.971

4. AUGUSTUS: ab initio prediction of alternative transcripts.

Authors: Mario Stanke; Oliver Keller; Irfan Gunduz; Alec Hayes; Stephan Waack; Burkhard Morgenstern
Journal: Nucleic Acids Res Date: 2006-07-01 Impact factor: 16.971

5. Systematic evaluation of spliced alignment programs for RNA-seq data.

Authors: Pär G Engström; Tamara Steijger; Botond Sipos; Gregory R Grant; André Kahles; Gunnar Rätsch; Nick Goldman; Tim J Hubbard; Jennifer Harrow; Roderic Guigó; Paul Bertone
Journal: Nat Methods Date: 2013-11-03 Impact factor: 28.547

6. Assessment of transcript reconstruction methods for RNA-seq.

Authors: Josep F Abril; Pär G Engström; Felix Kokocinski; Tamara Steijger; Tim J Hubbard; Roderic Guigó; Jennifer Harrow; Paul Bertone
Journal: Nat Methods Date: 2013-11-03 Impact factor: 28.547

6 in total

9 in total

Review 1. A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases.

Authors: Ahsan Naveed; Sajjad Ur-Rahman; Sabahat Abdullah; Muhammad Ammar Naveed
Journal: Mol Biotechnol Date: 2017-12 Impact factor: 2.695

2. Investigating the Transcriptomic and Expression Presence-Absence Variation Exist in Japanese Eel (Anguilla japonica), a Primitive Teleost.

Authors: Yung-Sen Huang; Chung-Yen Lin; Wen-Chih Cheng
Journal: Mar Biotechnol (NY) Date: 2021-10-29 Impact factor: 3.619

3. Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq.

Authors: Anto P Rajkumar; Per Qvist; Ross Lazarus; Francesco Lescai; Jia Ju; Mette Nyegaard; Ole Mors; Anders D Børglum; Qibin Li; Jane H Christensen
Journal: BMC Genomics Date: 2015-07-25 Impact factor: 3.969

4. Comprehensive analysis of Panax ginseng root transcriptomes.

Authors: Murukarthick Jayakodi; Sang-Choon Lee; Yun Sun Lee; Hyun-Seung Park; Nam-Hoon Kim; Woojong Jang; Hyun Oh Lee; Ho Jun Joh; Tae-Jin Yang
Journal: BMC Plant Biol Date: 2015-06-12 Impact factor: 4.215

Review 5. Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation.

Authors: Andreas Kloetgen; Philipp C Münch; Arndt Borkhardt; Jessica I Hoell; Alice C McHardy
Journal: Brief Funct Genomics Date: 2014-06-20 Impact factor: 4.241