Literature DB >> 25166867

Guided visual exploration of genomic stratifications in cancer.

Marc Streit1, Alexander Lex2, Samuel Gratzl1, Christian Partl3, Dieter Schmalstieg3, Hanspeter Pfister2, Peter J Park4, Nils Gehlenborg4,5.   

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Year:  2014        PMID： 25166867      PMCID： PMC4196637          DOI： 10.1038/nmeth.3088

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


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  6 in total

1.  StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization.

Authors:  A Lex; M Streit; H-J Schulz; C Partl; D Schmalstieg; P J Park; N Gehlenborg
Journal:  Comput Graph Forum       Date:  2012-06-25       Impact factor: 2.078

2.  Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.

Authors:  Roel G W Verhaak; Katherine A Hoadley; Elizabeth Purdom; Victoria Wang; Yuan Qi; Matthew D Wilkerson; C Ryan Miller; Li Ding; Todd Golub; Jill P Mesirov; Gabriele Alexe; Michael Lawrence; Michael O'Kelly; Pablo Tamayo; Barbara A Weir; Stacey Gabriel; Wendy Winckler; Supriya Gupta; Lakshmi Jakkula; Heidi S Feiler; J Graeme Hodgson; C David James; Jann N Sarkaria; Cameron Brennan; Ari Kahn; Paul T Spellman; Richard K Wilson; Terence P Speed; Joe W Gray; Matthew Meyerson; Gad Getz; Charles M Perou; D Neil Hayes
Journal:  Cancer Cell       Date:  2010-01-19       Impact factor: 31.743

3.  LineUp: visual analysis of multi-attribute rankings.

Authors:  Samuel Gratzl; Alexander Lex; Nils Gehlenborg; Hanspeter Pfister; Marc Streit
Journal:  IEEE Trans Vis Comput Graph       Date:  2013-12       Impact factor: 4.579

4.  Comprehensive molecular characterization of clear cell renal cell carcinoma.

Authors: 
Journal:  Nature       Date:  2013-06-23       Impact factor: 49.962

Review 5.  Visualizing multidimensional cancer genomics data.

Authors:  Michael P Schroeder; Abel Gonzalez-Perez; Nuria Lopez-Bigas
Journal:  Genome Med       Date:  2013-01-31       Impact factor: 11.117

6.  Network-based stratification of tumor mutations.

Authors:  Matan Hofree; John P Shen; Hannah Carter; Andrew Gross; Trey Ideker
Journal:  Nat Methods       Date:  2013-09-15       Impact factor: 28.547
  6 in total
  10 in total

1.  Intertumoral Heterogeneity within Medulloblastoma Subgroups.

Authors:  Florence M G Cavalli; Marc Remke; Ladislav Rampasek; John Peacock; David J H Shih; Betty Luu; Livia Garzia; Jonathon Torchia; Carolina Nor; A Sorana Morrissy; Sameer Agnihotri; Yuan Yao Thompson; Claudia M Kuzan-Fischer; Hamza Farooq; Keren Isaev; Craig Daniels; Byung-Kyu Cho; Seung-Ki Kim; Kyu-Chang Wang; Ji Yeoun Lee; Wieslawa A Grajkowska; Marta Perek-Polnik; Alexandre Vasiljevic; Cecile Faure-Conter; Anne Jouvet; Caterina Giannini; Amulya A Nageswara Rao; Kay Ka Wai Li; Ho-Keung Ng; Charles G Eberhart; Ian F Pollack; Ronald L Hamilton; G Yancey Gillespie; James M Olson; Sarah Leary; William A Weiss; Boleslaw Lach; Lola B Chambless; Reid C Thompson; Michael K Cooper; Rajeev Vibhakar; Peter Hauser; Marie-Lise C van Veelen; Johan M Kros; Pim J French; Young Shin Ra; Toshihiro Kumabe; Enrique López-Aguilar; Karel Zitterbart; Jaroslav Sterba; Gaetano Finocchiaro; Maura Massimino; Erwin G Van Meir; Satoru Osuka; Tomoko Shofuda; Almos Klekner; Massimo Zollo; Jeffrey R Leonard; Joshua B Rubin; Nada Jabado; Steffen Albrecht; Jaume Mora; Timothy E Van Meter; Shin Jung; Andrew S Moore; Andrew R Hallahan; Jennifer A Chan; Daniela P C Tirapelli; Carlos G Carlotti; Maryam Fouladi; José Pimentel; Claudia C Faria; Ali G Saad; Luca Massimi; Linda M Liau; Helen Wheeler; Hideo Nakamura; Samer K Elbabaa; Mario Perezpeña-Diazconti; Fernando Chico Ponce de León; Shenandoah Robinson; Michal Zapotocky; Alvaro Lassaletta; Annie Huang; Cynthia E Hawkins; Uri Tabori; Eric Bouffet; Ute Bartels; Peter B Dirks; James T Rutka; Gary D Bader; Jüri Reimand; Anna Goldenberg; Vijay Ramaswamy; Michael D Taylor
Journal:  Cancer Cell       Date:  2017-06-12       Impact factor: 31.743

2.  Integrated genomic characterization of papillary thyroid carcinoma.

Authors: 
Journal:  Cell       Date:  2014-10-23       Impact factor: 41.582

3.  From Visual Exploration to Storytelling and Back Again.

Authors:  S Gratzl; A Lex; N Gehlenborg; N Cosgrove; M Streit
Journal:  Comput Graph Forum       Date:  2016-07-04       Impact factor: 2.078

4.  NSD1- and NSD2-damaging mutations define a subset of laryngeal tumors with favorable prognosis.

Authors:  Suraj Peri; Evgeny Izumchenko; Adrian D Schubert; Michael J Slifker; Karen Ruth; Ilya G Serebriiskii; Theresa Guo; Barbara A Burtness; Ranee Mehra; Eric A Ross; David Sidransky; Erica A Golemis
Journal:  Nat Commun       Date:  2017-11-24       Impact factor: 14.919

5.  Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.

Authors:  Marc Streit; Samuel Gratzl; Holger Stitz; Andreas Wernitznig; Thomas Zichner; Christian Haslinger
Journal:  Bioinformatics       Date:  2019-09-01       Impact factor: 6.937

6.  Vials: Visualizing Alternative Splicing of Genes.

Authors:  Hendrik Strobelt; Bilal Alsallakh; Joseph Botros; Brant Peterson; Mark Borowsky; Hanspeter Pfister; Alexander Lex
Journal:  IEEE Trans Vis Comput Graph       Date:  2016-01       Impact factor: 4.579

7.  OncoThreads: visualization of large-scale longitudinal cancer molecular data.

Authors:  Theresa A Harbig; Sabrina Nusrat; Tali Mazor; Qianwen Wang; Alexander Thomson; Hans Bitter; Ethan Cerami; Nils Gehlenborg
Journal:  Bioinformatics       Date:  2021-07-12       Impact factor: 6.937

8.  The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations.

Authors:  HoJoon Lee; Jennifer Palm; Susan M Grimes; Hanlee P Ji
Journal:  Genome Med       Date:  2015-10-27       Impact factor: 11.117

9.  Interactive visual exploration and refinement of cluster assignments.

Authors:  Michael Kern; Alexander Lex; Nils Gehlenborg; Chris R Johnson
Journal:  BMC Bioinformatics       Date:  2017-09-12       Impact factor: 3.169

10.  Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance.

Authors:  Melanie Maria Obermeier; Wisnu Adi Wicaksono; Julian Taffner; Alessandro Bergna; Anja Poehlein; Tomislav Cernava; Stefanie Lindstaedt; Mario Lovric; Christina Andrea Müller Bogotá; Gabriele Berg
Journal:  ISME J       Date:  2020-11-11       Impact factor: 10.302
  10 in total

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