Literature DB >> 25748911

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Alyssa C Frazee1, Geo Pertea2, Andrew E Jaffe3, Ben Langmead4, Steven L Salzberg5, Jeffrey T Leek1.   

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Year:  2015        PMID: 25748911      PMCID: PMC4792117          DOI: 10.1038/nbt.3172

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


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  31 in total

1.  Matrix eQTL: ultra fast eQTL analysis via large matrix operations.

Authors:  Andrey A Shabalin
Journal:  Bioinformatics       Date:  2012-04-06       Impact factor: 6.937

2.  Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.

Authors:  Peter A C 't Hoen; Marc R Friedländer; Jonas Almlöf; Michael Sammeth; Irina Pulyakhina; Seyed Yahya Anvar; Jeroen F J Laros; Henk P J Buermans; Olof Karlberg; Mathias Brännvall; Johan T den Dunnen; Gert-Jan B van Ommen; Ivo G Gut; Roderic Guigó; Xavier Estivill; Ann-Christine Syvänen; Emmanouil T Dermitzakis; Tuuli Lappalainen
Journal:  Nat Biotechnol       Date:  2013-09-15       Impact factor: 54.908

3.  EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.

Authors:  Ning Leng; John A Dawson; James A Thomson; Victor Ruotti; Anna I Rissman; Bart M G Smits; Jill D Haag; Michael N Gould; Ron M Stewart; Christina Kendziorski
Journal:  Bioinformatics       Date:  2013-02-21       Impact factor: 6.937

4.  Differential analysis of gene regulation at transcript resolution with RNA-seq.

Authors:  Cole Trapnell; David G Hendrickson; Martin Sauvageau; Loyal Goff; John L Rinn; Lior Pachter
Journal:  Nat Biotechnol       Date:  2012-12-09       Impact factor: 54.908

5.  Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.

Authors:  Liying Yan; Mingyu Yang; Hongshan Guo; Lu Yang; Jun Wu; Rong Li; Ping Liu; Ying Lian; Xiaoying Zheng; Jie Yan; Jin Huang; Ming Li; Xinglong Wu; Lu Wen; Kaiqin Lao; Ruiqiang Li; Jie Qiao; Fuchou Tang
Journal:  Nat Struct Mol Biol       Date:  2013-08-11       Impact factor: 15.369

6.  Global epigenomic reconfiguration during mammalian brain development.

Authors:  Ryan Lister; Eran A Mukamel; Joseph R Nery; Mark Urich; Clare A Puddifoot; Nicholas D Johnson; Jacinta Lucero; Yun Huang; Andrew J Dwork; Matthew D Schultz; Miao Yu; Julian Tonti-Filippini; Holger Heyn; Shijun Hu; Joseph C Wu; Anjana Rao; Manel Esteller; Chuan He; Fatemeh G Haghighi; Terrence J Sejnowski; M Margarita Behrens; Joseph R Ecker
Journal:  Science       Date:  2013-07-04       Impact factor: 47.728

7.  Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome.

Authors:  Robert S Young; Ana C Marques; Charlotte Tibbit; Wilfried Haerty; Andrew R Bassett; Ji-Long Liu; Chris P Ponting
Journal:  Genome Biol Evol       Date:  2012-03-08       Impact factor: 3.416

8.  Differential abundance analysis for microbial marker-gene surveys.

Authors:  Joseph N Paulson; O Colin Stine; Héctor Corrada Bravo; Mihai Pop
Journal:  Nat Methods       Date:  2013-09-29       Impact factor: 28.547

9.  A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers.

Authors:  Sang Cheol Kim; Yeonjoo Jung; Jinah Park; Sooyoung Cho; Chaehwa Seo; Jaesang Kim; Pora Kim; Jehwan Park; Jihae Seo; Jiwoong Kim; Seongjin Park; Insu Jang; Namshin Kim; Jin Ok Yang; Byungwook Lee; Kyoohyoung Rho; Yeonhwa Jung; Juhee Keum; Jinseon Lee; Jungho Han; Sangeun Kang; Sujin Bae; So-Jung Choi; Sujin Kim; Jong-Eun Lee; Wankyu Kim; Jhingook Kim; Sanghyuk Lee
Journal:  PLoS One       Date:  2013-02-06       Impact factor: 3.240

10.  Transcriptome and genome sequencing uncovers functional variation in humans.

Authors:  Tuuli Lappalainen; Michael Sammeth; Marc R Friedländer; Peter A C 't Hoen; Jean Monlong; Manuel A Rivas; Mar Gonzàlez-Porta; Natalja Kurbatova; Thasso Griebel; Pedro G Ferreira; Matthias Barann; Thomas Wieland; Liliana Greger; Maarten van Iterson; Jonas Almlöf; Paolo Ribeca; Irina Pulyakhina; Daniela Esser; Thomas Giger; Andrew Tikhonov; Marc Sultan; Gabrielle Bertier; Daniel G MacArthur; Monkol Lek; Esther Lizano; Henk P J Buermans; Ismael Padioleau; Thomas Schwarzmayr; Olof Karlberg; Halit Ongen; Helena Kilpinen; Sergi Beltran; Marta Gut; Katja Kahlem; Vyacheslav Amstislavskiy; Oliver Stegle; Matti Pirinen; Stephen B Montgomery; Peter Donnelly; Mark I McCarthy; Paul Flicek; Tim M Strom; Hans Lehrach; Stefan Schreiber; Ralf Sudbrak; Angel Carracedo; Stylianos E Antonarakis; Robert Häsler; Ann-Christine Syvänen; Gert-Jan van Ommen; Alvis Brazma; Thomas Meitinger; Philip Rosenstiel; Roderic Guigó; Ivo G Gut; Xavier Estivill; Emmanouil T Dermitzakis
Journal:  Nature       Date:  2013-09-15       Impact factor: 49.962

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  236 in total

1.  Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum.

Authors:  Xi Sun; Hongxiang Zheng; Jinlu Li; Luning Liu; Xiansheng Zhang; Na Sui
Journal:  Front Bioeng Biotechnol       Date:  2020-04-15

2.  Paneth Cell Multipotency Induced by Notch Activation following Injury.

Authors:  Shiyan Yu; Kevin Tong; Yanlin Zhao; Iyshwarya Balasubramanian; George S Yap; Ronaldo P Ferraris; Edward M Bonder; Michael P Verzi; Nan Gao
Journal:  Cell Stem Cell       Date:  2018-06-07       Impact factor: 24.633

3.  Polyester: simulating RNA-seq datasets with differential transcript expression.

Authors:  Alyssa C Frazee; Andrew E Jaffe; Ben Langmead; Jeffrey T Leek
Journal:  Bioinformatics       Date:  2015-04-28       Impact factor: 6.937

Review 4.  Cancer transcriptome profiling at the juncture of clinical translation.

Authors:  Marcin Cieślik; Arul M Chinnaiyan
Journal:  Nat Rev Genet       Date:  2017-12-27       Impact factor: 53.242

5.  Expression profiling of snoRNAs in normal hematopoiesis and AML.

Authors:  Wayne A Warner; David H Spencer; Maria Trissal; Brian S White; Nichole Helton; Timothy J Ley; Daniel C Link
Journal:  Blood Adv       Date:  2018-01-23

6.  Modes of genetic adaptations underlying functional innovations in the rumen.

Authors:  Xiangyu Pan; Yudong Cai; Zongjun Li; Xianqing Chen; Rasmus Heller; Nini Wang; Yu Wang; Chen Zhao; Yong Wang; Han Xu; Songhai Li; Ming Li; Cunyuan Li; Shengwei Hu; Hui Li; Kun Wang; Lei Chen; Bin Wei; Zhuqing Zheng; Weiwei Fu; Yue Yang; Tingting Zhang; Zhuoting Hou; Yueyang Yan; Xiaoyang Lv; Wei Sun; Xinyu Li; Shisheng Huang; Lixiang Liu; Shengyong Mao; Wenqing Liu; Jinlian Hua; Zhipeng Li; Guojie Zhang; Yulin Chen; Xihong Wang; Qiang Qiu; Brian P Dalrymple; Wen Wang; Yu Jiang
Journal:  Sci China Life Sci       Date:  2020-11-05       Impact factor: 6.038

7.  Silencing long non-coding RNA NEAT1 enhances the suppression of cell growth, invasion, and apoptosis of bladder cancer cells under cisplatin chemotherapy.

Authors:  Wenchao Zhao; Wenqi Li; Xin Jin; Tianli Niu; Yuanfei Cao; Peng Zhou; Minghua Zheng
Journal:  Int J Clin Exp Pathol       Date:  2019-02-01

8.  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

9.  Alcohol Activates Scabrous-Notch to Influence Associated Memories.

Authors:  Emily Petruccelli; Michael Feyder; Nicolas Ledru; Yanabah Jaques; Edward Anderson; Karla R Kaun
Journal:  Neuron       Date:  2018-10-25       Impact factor: 17.173

10.  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Authors:  Mihaela Pertea; Daehwan Kim; Geo M Pertea; Jeffrey T Leek; Steven L Salzberg
Journal:  Nat Protoc       Date:  2016-08-11       Impact factor: 13.491

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