Literature DB >> 19333237

The UCSC Cancer Genomics Browser.

Jingchun Zhu, J Zachary Sanborn, Stephen Benz, Christopher Szeto, Fan Hsu, Robert M Kuhn, Donna Karolchik, John Archie, Marc E Lenburg, Laura J Esserman, W James Kent, David Haussler, Ting Wang.   

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Year:  2009        PMID： 19333237      PMCID： PMC5027375          DOI： 10.1038/nmeth0409-239

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


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  5 in total

1.  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

2.  Genomic and transcriptional aberrations linked to breast cancer pathophysiologies.

Authors:  Koei Chin; Sandy DeVries; Jane Fridlyand; Paul T Spellman; Ritu Roydasgupta; Wen-Lin Kuo; Anna Lapuk; Richard M Neve; Zuwei Qian; Tom Ryder; Fanqing Chen; Heidi Feiler; Taku Tokuyasu; Chris Kingsley; Shanaz Dairkee; Zhenhang Meng; Karen Chew; Daniel Pinkel; Ajay Jain; Britt Marie Ljung; Laura Esserman; Donna G Albertson; Frederic M Waldman; Joe W Gray
Journal:  Cancer Cell       Date:  2006-12       Impact factor: 31.743

3.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Authors: 
Journal:  Nature       Date:  2008-09-04       Impact factor: 49.962

4.  The UCSC Genome Browser Database: 2008 update.

Authors:  D Karolchik; R M Kuhn; R Baertsch; G P Barber; H Clawson; M Diekhans; B Giardine; R A Harte; A S Hinrichs; F Hsu; K M Kober; W Miller; J S Pedersen; A Pohl; B J Raney; B Rhead; K R Rosenbloom; K E Smith; M Stanke; A Thakkapallayil; H Trumbower; T Wang; A S Zweig; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2007-12-17       Impact factor: 16.971

5.  High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

Authors:  Suet F Chin; Andrew E Teschendorff; John C Marioni; Yanzhong Wang; Nuno L Barbosa-Morais; Natalie P Thorne; Jose L Costa; Sarah E Pinder; Mark A van de Wiel; Andrew R Green; Ian O Ellis; Peggy L Porter; Simon Tavaré; James D Brenton; Bauke Ylstra; Carlos Caldas
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583
  5 in total
  104 in total

1.  LayerCake: a tool for the visual comparison of viral deep sequencing data.

Authors:  Michael Correll; Adam L Bailey; Alper Sarikaya; David H O'Connor; Michael Gleicher
Journal:  Bioinformatics       Date:  2015-07-07       Impact factor: 6.937

2.  JBrowse: a next-generation genome browser.

Authors:  Mitchell E Skinner; Andrew V Uzilov; Lincoln D Stein; Christopher J Mungall; Ian H Holmes
Journal:  Genome Res       Date:  2009-07-01       Impact factor: 9.043

Review 3.  Making sense of cancer genomic data.

Authors:  Lynda Chin; William C Hahn; Gad Getz; Matthew Meyerson
Journal:  Genes Dev       Date:  2011-03-15       Impact factor: 11.361

Review 4.  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

5.  The EMT modulator SNAI1 contributes to AML pathogenesis via its interaction with LSD1.

Authors:  Catherine L Carmichael; Jueqiong Wang; Thao Nguyen; Oluseyi Kolawole; Aissa Benyoucef; Charlotte De Mazière; Anna R Milne; Sona Samuel; Kevin Gillinder; Soroor Hediyeh-Zadeh; Anh N Q Vo; Yizhou Huang; Kathy Knezevic; William R L McInnes; Benjamin J Shields; Helen Mitchell; Matthew E Ritchie; Tim Lammens; Beatrice Lintermans; Pieter Van Vlierberghe; Nicholas C Wong; Katharina Haigh; Julie A I Thoms; Emma Toulmin; David J Curtis; Ethan P Oxley; Ross A Dickins; Dominik Beck; Andrew Perkins; Matthew P McCormack; Melissa J Davis; Geert Berx; Johannes Zuber; John E Pimanda; Benjamin T Kile; Steven Goossens; Jody J Haigh
Journal:  Blood       Date:  2020-08-20       Impact factor: 22.113

Review 6.  Collection, integration and analysis of cancer genomic profiles: from data to insight.

Authors:  Jianjiong Gao; Giovanni Ciriello; Chris Sander; Nikolaus Schultz
Journal:  Curr Opin Genet Dev       Date:  2014-02-27       Impact factor: 5.578

7.  Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society.

Authors:  Rehan Akbani; Karl-Friedrich Becker; Neil Carragher; Ted Goldstein; Leanne de Koning; Ulrike Korf; Lance Liotta; Gordon B Mills; Satoshi S Nishizuka; Michael Pawlak; Emanuel F Petricoin; Harvey B Pollard; Bryan Serrels; Jingchun Zhu
Journal:  Mol Cell Proteomics       Date:  2014-04-28       Impact factor: 5.911

8.  Paracrine WNT5A Signaling Inhibits Expansion of Tumor-Initiating Cells.

Authors:  Nicholas Borcherding; David Kusner; Ryan Kolb; Qing Xie; Wei Li; Fang Yuan; Gabriel Velez; Ryan Askeland; Ronald J Weigel; Weizhou Zhang
Journal:  Cancer Res       Date:  2015-03-13       Impact factor: 12.701

9.  Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.

Authors:  Charles J Vaske; Stephen C Benz; J Zachary Sanborn; Dent Earl; Christopher Szeto; Jingchun Zhu; David Haussler; Joshua M Stuart
Journal:  Bioinformatics       Date:  2010-06-15       Impact factor: 6.937

10.  Disease gene characterization through large-scale co-expression analysis.

Authors:  Allen Day; Jun Dong; Vincent A Funari; Bret Harry; Samuel P Strom; Dan H Cohn; Stanley F Nelson
Journal:  PLoS One       Date:  2009-12-31       Impact factor: 3.240
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