Literature DB >> 28398307

Reproducible RNA-seq analysis using recount2.

Leonardo Collado-Torres1,2,3, Abhinav Nellore4,5,6, Kai Kammers1,2,7, Shannon E Ellis1,2, Margaret A Taub1,2, Kasper D Hansen1,2,8, Andrew E Jaffe1,2,3,9, Ben Langmead1,2,10, Jeffrey T Leek1,2.   

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Year:  2017        PMID: 28398307      PMCID: PMC6742427          DOI: 10.1038/nbt.3838

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


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  35 in total

1.  Toil enables reproducible, open source, big biomedical data analyses.

Authors:  John Vivian; Arjun Arkal Rao; Frank Austin Nothaft; Christopher Ketchum; Joel Armstrong; Adam Novak; Jacob Pfeil; Jake Narkizian; Alden D Deran; Audrey Musselman-Brown; Hannes Schmidt; Peter Amstutz; Brian Craft; Mary Goldman; Kate Rosenbloom; Melissa Cline; Brian O'Connor; Megan Hanna; Chet Birger; W James Kent; David A Patterson; Anthony D Joseph; Jingchun Zhu; Sasha Zaranek; Gad Getz; David Haussler; Benedict Paten
Journal:  Nat Biotechnol       Date:  2017-04-11       Impact factor: 54.908

2.  Flexible expressed region analysis for RNA-seq with derfinder.

Authors:  Leonardo Collado-Torres; Abhinav Nellore; Alyssa C Frazee; Christopher Wilks; Michael I Love; Ben Langmead; Rafael A Irizarry; Jeffrey T Leek; Andrew E Jaffe
Journal:  Nucleic Acids Res       Date:  2016-09-29       Impact factor: 16.971

3.  Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

Authors:  Yael Haberman; Timothy L Tickle; Phillip J Dexheimer; Mi-Ok Kim; Dora Tang; Rebekah Karns; Robert N Baldassano; Joshua D Noe; Joel Rosh; James Markowitz; Melvin B Heyman; Anne M Griffiths; Wallace V Crandall; David R Mack; Susan S Baker; Curtis Huttenhower; David J Keljo; Jeffrey S Hyams; Subra Kugathasan; Thomas D Walters; Bruce Aronow; Ramnik J Xavier; Dirk Gevers; Lee A Denson
Journal:  J Clin Invest       Date:  2014-07-08       Impact factor: 14.808

4.  Human genomics. The human transcriptome across tissues and individuals.

Authors:  Marta Melé; Pedro G Ferreira; Ferran Reverter; David S DeLuca; Jean Monlong; Michael Sammeth; Taylor R Young; Jakob M Goldmann; Dmitri D Pervouchine; Timothy J Sullivan; Rory Johnson; Ayellet V Segrè; Sarah Djebali; Anastasia Niarchou; Fred A Wright; Tuuli Lappalainen; Miquel Calvo; Gad Getz; Emmanouil T Dermitzakis; Kristin G Ardlie; Roderic Guigó
Journal:  Science       Date:  2015-05-08       Impact factor: 47.728

5.  Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Authors:  Robert Petryszak; Maria Keays; Y Amy Tang; Nuno A Fonseca; Elisabet Barrera; Tony Burdett; Anja Füllgrabe; Alfonso Muñoz-Pomer Fuentes; Simon Jupp; Satu Koskinen; Oliver Mannion; Laura Huerta; Karine Megy; Catherine Snow; Eleanor Williams; Mitra Barzine; Emma Hastings; Hendrik Weisser; James Wright; Pankaj Jaiswal; Wolfgang Huber; Jyoti Choudhary; Helen E Parkinson; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2015-10-19       Impact factor: 16.971

6.  Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Authors:  Abhinav Nellore; Andrew E Jaffe; Jean-Philippe Fortin; José Alquicira-Hernández; Leonardo Collado-Torres; Siruo Wang; Robert A Phillips; Nishika Karbhari; Kasper D Hansen; Ben Langmead; Jeffrey T Leek
Journal:  Genome Biol       Date:  2016-12-30       Impact factor: 13.583

7.  Rail-RNA: scalable analysis of RNA-seq splicing and coverage.

Authors:  Abhinav Nellore; Leonardo Collado-Torres; Andrew E Jaffe; José Alquicira-Hernández; Christopher Wilks; Jacob Pritt; James Morton; Jeffrey T Leek; Ben Langmead
Journal:  Bioinformatics       Date:  2017-12-15       Impact factor: 6.937

8.  Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome.

Authors:  Cornelis A Albers; Dirk S Paul; Harald Schulze; Kathleen Freson; Jonathan C Stephens; Peter A Smethurst; Jennifer D Jolley; Ana Cvejic; Myrto Kostadima; Paul Bertone; Martijn H Breuning; Najet Debili; Panos Deloukas; Rémi Favier; Janine Fiedler; Catherine M Hobbs; Ni Huang; Matthew E Hurles; Graham Kiddle; Ingrid Krapels; Paquita Nurden; Claudia A L Ruivenkamp; Jennifer G Sambrook; Kenneth Smith; Derek L Stemple; Gabriele Strauss; Chantal Thys; Chris van Geet; Ruth Newbury-Ecob; Willem H Ouwehand; Cedric Ghevaert
Journal:  Nat Genet       Date:  2012-02-26       Impact factor: 38.330

9.  Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors.

Authors:  Gerald Goh; Ute I Scholl; James M Healy; Murim Choi; Manju L Prasad; Carol Nelson-Williams; John W Kunstman; John W Kuntsman; Reju Korah; Anna-Carinna Suttorp; Dimo Dietrich; Matthias Haase; Holger S Willenberg; Peter Stålberg; Per Hellman; Göran Akerström; Peyman Björklund; Tobias Carling; Richard P Lifton
Journal:  Nat Genet       Date:  2014-04-20       Impact factor: 38.330

10.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Authors:  Daehwan Kim; Geo Pertea; Cole Trapnell; Harold Pimentel; Ryan Kelley; Steven L Salzberg
Journal:  Genome Biol       Date:  2013-04-25       Impact factor: 13.583

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  133 in total

1.  MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease.

Authors:  Jaclyn N Taroni; Peter C Grayson; Qiwen Hu; Sean Eddy; Matthias Kretzler; Peter A Merkel; Casey S Greene
Journal:  Cell Syst       Date:  2019-05-22       Impact factor: 10.304

2.  Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders.

Authors:  David Zhang; Sebastian Guelfi; Sonia Garcia-Ruiz; Beatrice Costa; Regina H Reynolds; Karishma D'Sa; Wenfei Liu; Thomas Courtin; Amy Peterson; Andrew E Jaffe; John Hardy; Juan A Botía; Leonardo Collado-Torres; Mina Ryten
Journal:  Sci Adv       Date:  2020-06-10       Impact factor: 14.136

3.  Identification and characterization of an alternative cancer-derived PD-L1 splice variant.

Authors:  Nadia B Hassounah; Venkat S Malladi; Yi Huang; Samuel S Freeman; Ellen M Beauchamp; Shohei Koyama; Nicholas Souders; Sunil Martin; Glenn Dranoff; Kwok-Kin Wong; Chandra S Pedamallu; Peter S Hammerman; Esra A Akbay
Journal:  Cancer Immunol Immunother       Date:  2018-12-18       Impact factor: 6.968

4.  Improving the value of public RNA-seq expression data by phenotype prediction.

Authors:  Shannon E Ellis; Leonardo Collado-Torres; Andrew Jaffe; Jeffrey T Leek
Journal:  Nucleic Acids Res       Date:  2018-05-18       Impact factor: 16.971

5.  Detecting hidden batch factors through data-adaptive adjustment for biological effects.

Authors:  Haidong Yi; Ayush T Raman; Han Zhang; Genevera I Allen; Zhandong Liu
Journal:  Bioinformatics       Date:  2018-04-01       Impact factor: 6.937

6.  SliceIt: A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome.

Authors:  Sasank Vemuri; Rajneesh Srivastava; Quoseena Mir; Seyedsasan Hashemikhabir; X Charlie Dong; Sarath Chandra Janga
Journal:  Methods       Date:  2019-09-05       Impact factor: 3.608

7.  Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

Authors:  Vinay Swamy; David McGaughey
Journal:  Invest Ophthalmol Vis Sci       Date:  2019-07-01       Impact factor: 4.799

8.  Interpretation of an individual functional genomics experiment guided by massive public data.

Authors:  Young-Suk Lee; Aaron K Wong; Alicja Tadych; Boris M Hartmann; Christopher Y Park; Veronica A DeJesus; Irene Ramos; Elena Zaslavsky; Stuart C Sealfon; Olga G Troyanskaya
Journal:  Nat Methods       Date:  2018-11-26       Impact factor: 28.547

9.  Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.

Authors:  Michael I Love; Charlotte Soneson; Rob Patro
Journal:  F1000Res       Date:  2018-06-27

Review 10.  Cloud computing for genomic data analysis and collaboration.

Authors:  Ben Langmead; Abhinav Nellore
Journal:  Nat Rev Genet       Date:  2018-01-30       Impact factor: 53.242

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