Literature DB >> 25203036

The devil in the details of RNA-seq.

Anton Kratz1, Piero Carninci1.   

Abstract

Year:  2014        PMID: 25203036     DOI: 10.1038/nbt.3015

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


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  5 in total

Review 1.  Microarray technology: beyond transcript profiling and genotype analysis.

Authors:  Jörg D Hoheisel
Journal:  Nat Rev Genet       Date:  2006-03       Impact factor: 53.242

Review 2.  Reuse of public genome-wide gene expression data.

Authors:  Johan Rung; Alvis Brazma
Journal:  Nat Rev Genet       Date:  2012-12-27       Impact factor: 53.242

3.  The regulated retrotransposon transcriptome of mammalian cells.

Authors:  Geoffrey J Faulkner; Yasumasa Kimura; Carsten O Daub; Shivangi Wani; Charles Plessy; Katharine M Irvine; Kate Schroder; Nicole Cloonan; Anita L Steptoe; Timo Lassmann; Kazunori Waki; Nadine Hornig; Takahiro Arakawa; Hazuki Takahashi; Jun Kawai; Alistair R R Forrest; Harukazu Suzuki; Yoshihide Hayashizaki; David A Hume; Valerio Orlando; Sean M Grimmond; Piero Carninci
Journal:  Nat Genet       Date:  2009-04-19       Impact factor: 38.330

4.  A promoter-level mammalian expression atlas.

Authors:  Alistair R R Forrest; Hideya Kawaji; Michael Rehli; J Kenneth Baillie; Michiel J L de Hoon; Vanja Haberle; Timo Lassmann; Ivan V Kulakovskiy; Marina Lizio; Masayoshi Itoh; Robin Andersson; Christopher J Mungall; Terrence F Meehan; Sebastian Schmeier; Nicolas Bertin; Mette Jørgensen; Emmanuel Dimont; Erik Arner; Christian Schmidl; Ulf Schaefer; Yulia A Medvedeva; Charles Plessy; Morana Vitezic; Jessica Severin; Colin A Semple; Yuri Ishizu; Robert S Young; Margherita Francescatto; Intikhab Alam; Davide Albanese; Gabriel M Altschuler; Takahiro Arakawa; John A C Archer; Peter Arner; Magda Babina; Sarah Rennie; Piotr J Balwierz; Anthony G Beckhouse; Swati Pradhan-Bhatt; Judith A Blake; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; A Maxwell Burroughs; Andrea Califano; Carlo V Cannistraci; Daniel Carbajo; Yun Chen; Marco Chierici; Yari Ciani; Hans C Clevers; Emiliano Dalla; Carrie A Davis; Michael Detmar; Alexander D Diehl; Taeko Dohi; Finn Drabløs; Albert S B Edge; Matthias Edinger; Karl Ekwall; Mitsuhiro Endoh; Hideki Enomoto; Michela Fagiolini; Lynsey Fairbairn; Hai Fang; Mary C Farach-Carson; Geoffrey J Faulkner; Alexander V Favorov; Malcolm E Fisher; Martin C Frith; Rie Fujita; Shiro Fukuda; Cesare Furlanello; Masaaki Furino; Jun-ichi Furusawa; Teunis B Geijtenbeek; Andrew P Gibson; Thomas Gingeras; Daniel Goldowitz; Julian Gough; Sven Guhl; Reto Guler; Stefano Gustincich; Thomas J Ha; Masahide Hamaguchi; Mitsuko Hara; Matthias Harbers; Jayson Harshbarger; Akira Hasegawa; Yuki Hasegawa; Takehiro Hashimoto; Meenhard Herlyn; Kelly J Hitchens; Shannan J Ho Sui; Oliver M Hofmann; Ilka Hoof; Furni Hori; Lukasz Huminiecki; Kei Iida; Tomokatsu Ikawa; Boris R Jankovic; Hui Jia; Anagha Joshi; Giuseppe Jurman; Bogumil Kaczkowski; Chieko Kai; Kaoru Kaida; Ai Kaiho; Kazuhiro Kajiyama; Mutsumi Kanamori-Katayama; Artem S Kasianov; Takeya Kasukawa; Shintaro Katayama; Sachi Kato; Shuji Kawaguchi; Hiroshi Kawamoto; Yuki I Kawamura; Tsugumi Kawashima; Judith S Kempfle; Tony J Kenna; Juha Kere; Levon M Khachigian; Toshio Kitamura; S Peter Klinken; Alan J Knox; Miki Kojima; Soichi Kojima; Naoto Kondo; Haruhiko Koseki; Shigeo Koyasu; Sarah Krampitz; Atsutaka Kubosaki; Andrew T Kwon; Jeroen F J Laros; Weonju Lee; Andreas Lennartsson; Kang Li; Berit Lilje; Leonard Lipovich; Alan Mackay-Sim; Ri-ichiroh Manabe; Jessica C Mar; Benoit Marchand; Anthony Mathelier; Niklas Mejhert; Alison Meynert; Yosuke Mizuno; David A de Lima Morais; Hiromasa Morikawa; Mitsuru Morimoto; Kazuyo Moro; Efthymios Motakis; Hozumi Motohashi; Christine L Mummery; Mitsuyoshi Murata; Sayaka Nagao-Sato; Yutaka Nakachi; Fumio Nakahara; Toshiyuki Nakamura; Yukio Nakamura; Kenichi Nakazato; Erik van Nimwegen; Noriko Ninomiya; Hiromi Nishiyori; Shohei Noma; Shohei Noma; Tadasuke Noazaki; Soichi Ogishima; Naganari Ohkura; Hiroko Ohimiya; Hiroshi Ohno; Mitsuhiro Ohshima; Mariko Okada-Hatakeyama; Yasushi Okazaki; Valerio Orlando; Dmitry A Ovchinnikov; Arnab Pain; Robert Passier; Margaret Patrikakis; Helena Persson; Silvano Piazza; James G D Prendergast; Owen J L Rackham; Jordan A Ramilowski; Mamoon Rashid; Timothy Ravasi; Patrizia Rizzu; Marco Roncador; Sugata Roy; Morten B Rye; Eri Saijyo; Antti Sajantila; Akiko Saka; Shimon Sakaguchi; Mizuho Sakai; Hiroki Sato; Suzana Savvi; Alka Saxena; Claudio Schneider; Erik A Schultes; Gundula G Schulze-Tanzil; Anita Schwegmann; Thierry Sengstag; Guojun Sheng; Hisashi Shimoji; Yishai Shimoni; Jay W Shin; Christophe Simon; Daisuke Sugiyama; Takaai Sugiyama; Masanori Suzuki; Naoko Suzuki; Rolf K Swoboda; Peter A C 't Hoen; Michihira Tagami; Naoko Takahashi; Jun Takai; Hiroshi Tanaka; Hideki Tatsukawa; Zuotian Tatum; Mark Thompson; Hiroo Toyodo; Tetsuro Toyoda; Elvind Valen; Marc van de Wetering; Linda M van den Berg; Roberto Verado; Dipti Vijayan; Ilya E Vorontsov; Wyeth W Wasserman; Shoko Watanabe; Christine A Wells; Louise N Winteringham; Ernst Wolvetang; Emily J Wood; Yoko Yamaguchi; Masayuki Yamamoto; Misako Yoneda; Yohei Yonekura; Shigehiro Yoshida; Susan E Zabierowski; Peter G Zhang; Xiaobei Zhao; Silvia Zucchelli; Kim M Summers; Harukazu Suzuki; Carsten O Daub; Jun Kawai; Peter Heutink; Winston Hide; Tom C Freeman; Boris Lenhard; Vladimir B Bajic; Martin S Taylor; Vsevolod J Makeev; Albin Sandelin; David A Hume; Piero Carninci; Yoshihide Hayashizaki
Journal:  Nature       Date:  2014-03-27       Impact factor: 49.962

5.  An integrated encyclopedia of DNA elements in the human genome.

Authors: 
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

  5 in total
  16 in total

1.  Discovering New Biology through Sequencing of RNA.

Authors:  Andreas P M Weber
Journal:  Plant Physiol       Date:  2015-09-09       Impact factor: 8.340

2.  Maximizing the Utility of Archival Formalin-Fixed Paraffin-Embedded Blocks for Nucleic Acid Analysis.

Authors:  Sarah R Greytak; Kelly B Engel; Helen M Moore
Journal:  Biopreserv Biobank       Date:  2018-07-13       Impact factor: 2.300

Review 3.  Immune cell profiling to guide therapeutic decisions in rheumatic diseases.

Authors:  Joerg Ermann; Deepak A Rao; Nikola C Teslovich; Michael B Brenner; Soumya Raychaudhuri
Journal:  Nat Rev Rheumatol       Date:  2015-06-02       Impact factor: 20.543

4.  Statistical Methods in Integrative Genomics.

Authors:  Sylvia Richardson; George C Tseng; Wei Sun
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5.  PennDiff: detecting differential alternative splicing and transcription by RNA sequencing.

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6.  Gene expression in retinal ischemic post-conditioning.

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7.  Cross Platform Standardisation of an Experimental Pipeline for Use in the Identification of Dysregulated Human Circulating MiRNAs.

Authors:  Helena Kelly; Tim Downing; Nina L Tuite; Terry J Smith; Michael J Kerin; Róisín M Dwyer; Eoin Clancy; Thomas Barry; Kate Reddington
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8.  RNAseq Analyses Identify Tumor Necrosis Factor-Mediated Inflammation as a Major Abnormality in ALS Spinal Cord.

Authors:  David G Brohawn; Laura C O'Brien; James P Bennett
Journal:  PLoS One       Date:  2016-08-03       Impact factor: 3.240

9.  Getting the most out of RNA-seq data analysis.

Authors:  Tsung Fei Khang; Ching Yee Lau
Journal:  PeerJ       Date:  2015-10-29       Impact factor: 2.984

10.  Limits of Peripheral Blood Mononuclear Cells for Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis.

Authors:  Laiping Wong; Kaiyu Jiang; Yanmin Chen; Teresa Hennon; Lucy Holmes; Carol A Wallace; James N Jarvis
Journal:  Sci Rep       Date:  2016-07-07       Impact factor: 4.379

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