Literature DB >> 23138293

NGS analyses by visualization with Trackster.

Jeremy Goecks, Nate Coraor, Anton Nekrutenko, James Taylor.   

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Year:  2012        PMID： 23138293      PMCID： PMC3889118          DOI： 10.1038/nbt.2404

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


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  16 in total

1.  Artemis: sequence visualization and annotation.

Authors:  K Rutherford; J Parkhill; J Crook; T Horsnell; P Rice; M A Rajandream; B Barrell
Journal:  Bioinformatics       Date:  2000-10       Impact factor: 6.937

2.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

3.  Savant: genome browser for high-throughput sequencing data.

Authors:  Marc Fiume; Vanessa Williams; Andrew Brook; Michael Brudno
Journal:  Bioinformatics       Date:  2010-06-20       Impact factor: 6.937

Review 4.  Signal integration in the endoplasmic reticulum unfolded protein response.

Authors:  David Ron; Peter Walter
Journal:  Nat Rev Mol Cell Biol       Date:  2007-07       Impact factor: 94.444

Review 5.  Visualizing genomes: techniques and challenges.

Authors:  Cydney B Nielsen; Michael Cantor; Inna Dubchak; David Gordon; Ting Wang
Journal:  Nat Methods       Date:  2010-02-25       Impact factor: 28.547

6.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Authors:  Cole Trapnell; Adam Roberts; Loyal Goff; Geo Pertea; Daehwan Kim; David R Kelley; Harold Pimentel; Steven L Salzberg; John L Rinn; Lior Pachter
Journal:  Nat Protoc       Date:  2012-03-01       Impact factor: 13.491

7.  Mammalian microRNAs predominantly act to decrease target mRNA levels.

Authors:  Huili Guo; Nicholas T Ingolia; Jonathan S Weissman; David P Bartel
Journal:  Nature       Date:  2010-08-12       Impact factor: 49.962

Review 8.  Signalling pathways in the unfolded protein response: development from yeast to mammals.

Authors:  Kazutoshi Mori
Journal:  J Biochem       Date:  2009-10-27       Impact factor: 3.387

9.  Galaxy: a web-based genome analysis tool for experimentalists.

Authors:  Daniel Blankenberg; Gregory Von Kuster; Nathaniel Coraor; Guruprasad Ananda; Ross Lazarus; Mary Mangan; Anton Nekrutenko; James Taylor
Journal:  Curr Protoc Mol Biol       Date:  2010-01

10.  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
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  16 in total

1.  Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations.

Authors:  Vahan Simonyan; Jeremy Goecks; Raja Mazumder
Journal:  PDA J Pharm Sci Technol       Date:  2016-12-14

2.  The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.

Authors:  Thomas A Darde; Olivier Sallou; Emmanuelle Becker; Bertrand Evrard; Cyril Monjeaud; Yvan Le Bras; Bernard Jégou; Olivier Collin; Antoine D Rolland; Frédéric Chalmel
Journal:  Nucleic Acids Res       Date:  2015-04-16       Impact factor: 16.971

3.  Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

Authors:  Peter J A Cock; Björn A Grüning; Konrad Paszkiewicz; Leighton Pritchard
Journal:  PeerJ       Date:  2013-09-17       Impact factor: 2.984

4.  The personal genome browser: visualizing functions of genetic variants.

Authors:  Liran Juan; Mingxiang Teng; Tianyi Zang; Yafeng Hao; Zhenxing Wang; Chengwu Yan; Yongzhuang Liu; Jie Li; Tianjiao Zhang; Yadong Wang
Journal:  Nucleic Acids Res       Date:  2014-05-05       Impact factor: 16.971

5.  FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

Authors:  Malte Mader; Ronald Simon; Stefan Kurtz
Journal:  J Clin Bioinforma       Date:  2014-03-31

6.  Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines.

Authors:  Jeremy Goecks; Bassel F El-Rayes; Shishir K Maithel; H Jean Khoury; James Taylor; Michael R Rossi
Journal:  Cancer Med       Date:  2015-01-04       Impact factor: 4.452

7.  NEUROD2 Regulates Stim1 Expression and Store-Operated Calcium Entry in Cortical Neurons.

Authors:  Gokhan Guner; Gizem Guzelsoy; Fatma Sadife Isleyen; Gulcan Semra Sahin; Cansu Akkaya; Efil Bayam; Eser Ilgin Kotan; Alkan Kabakcioglu; Gulayse Ince-Dunn
Journal:  eNeuro       Date:  2017-03-09

8.  Web-based visual analysis for high-throughput genomics.

Authors:  Jeremy Goecks; Carl Eberhard; Tomithy Too; Anton Nekrutenko; James Taylor
Journal:  BMC Genomics       Date:  2013-06-13       Impact factor: 3.969

Review 9.  Next-generation sequence assembly: four stages of data processing and computational challenges.

Authors:  Sara El-Metwally; Taher Hamza; Magdi Zakaria; Mohamed Helmy
Journal:  PLoS Comput Biol       Date:  2013-12-12       Impact factor: 4.475

10.  RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.

Authors:  Audrey M Michel; James P A Mullan; Vimalkumar Velayudhan; Patrick B F O'Connor; Claire A Donohue; Pavel V Baranov
Journal:  RNA Biol       Date:  2016-01-29       Impact factor: 4.652
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