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Data Visualization Initiative

The Data Visualization Initiative at the Broad Institute consists of a community of people dedicated to exploring and finding visualization solutions to complex data. We collaborate with researchers in the Broad community to apply graphical techniques to communicate research findings and to explore data as the scientific story is unfolding.

We are committed to sharing our solutions through publications, hands-on workshops, and professional conferences.

 

Select Projects

  • VIZBI. An international initiative aimed at raising the global standard of bioinformatics software. Central to this effort is a conference series supported by the Broad Institute, EMBL-Heidelberg Germany, EMBO and the NIH (5R13LM010987-05). For more information about VIZBI and to view past conference talks and poster presentations, visit www.vizbi.org
  • The ‘Points of View’ articles published by Nature Methods. The series of 40+ articles deals with the fundamental aspects of visual presentation applicable to anyone who works with the visual representation of data. Everything from choice of colors, fonts, graph type and design to overall layout can influence data interpretation. The articles are intended to help researchers display data clearly with minimal bias. Please find a complete list of articles below.
  • Vis Skunkworks at Broad. Established with a grant from SPARC this program brings together expertise in design, computational biology, and interactive-software development to rapidly develop visualization concepts from back-of-the-napkin ideas to working prototypes. A hallmark of the project are “mini-sabbaticals” where members of the Broad community come to the skunkworks to explore their own ideas, seek advice or contribute to current visualization projects.
  • The CMap CLUE Apps. An ecosystem of computational and visualization tools being developed to explore the Connectivity Map and related data.
  • CURSOR. Best characterized as a “peak explorer” this web-based software enables researchers to quickly locate regions of the genome where the data suggest something interesting is happening.
  • GENETS. A web platform for the analysis and visualization of biological pathways.

 

Team

Bang Wong, Creative Director
Noam Shoresh, Sr Group Leader, Epigenomics
Mariya Khan, Visual Designer, Connectivity Map
Liraz Greenfeld, Software Engineer, KDUX

 

Alumni

Miriah Meyer, Assistant Professor, School of Computing, University of Utah
Janet Iwasa, Research Assistant Professor, Biochemistry, University of Utah
Peter Torpey, Media Experience Artist, The nth Art
Daniel Kohn, Artist, Kohnworkshop
Ryo Sakai, Visualization researcher

 

Publications

Visualization

  1. Katz Y Wang E Silterra J Schwartz S Wong B Thorvaldsdóttir H Robinson J Mesirov J Airoldi E Burge C, Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics (Oxford, England). 2015 vol: 31 (14) pp: 2400-2.
  2. Meyer M Wong B Styczynski M Munzner T Pfister H. Pathline : A Tool For Comparative Functional Genomics. Eurographics/ IEEE-VGTC Symposium on Visualization. 2010 vol: 29 (3)

Points of View articles

  1. Krzywinski, M. & Wong, B. Plotting symbol. Nat Methods. 10: 451 (2013)
  2. Wong, B. Visualizing biological data. Nat Methods. 9: 1131 (2012)
  3. Wong, B. & Kjærgaard, RS. Pencil and paper. Nat Methods. 9: 1037 (2012)
  4. Gehlenborg, N & Wong, B. Power of the plane. Nat Methods. 9: 935 (2012)
  5. Gehlenborg, N & Wong, B. Into the third dimension. Nat Methods. 9: 851 (2012)
  6. Gehlenborg, N & Wong, B. Mapping quantitative data to color. Nat Methods. 9: 769 (2012)
  7. Nielsen, C. & Wong, B. Representing genomic structural variation. Nat Methods. 9: 631 (2012)
  8. Nielsen, C & Wong, B. Managing deep data in genome browsers. Nat Methods. 9: 521 (2012)
  9. Nielsen, C & Wong, B. Representing the genome. Nat Methods. 9: 423 (2012)
  10. Gehlenborg, N & Wong, B. Integrating data. Nat Methods. 9: 315 (2012)
  11. Gehlenborg, N & Wong, B. Heat maps. Nat Methods. 9: 213 (2012)
  12. Gehlenborg, N & Wong, B. Networks. Nat Methods. 9: 115 (2012)
  13. Shoresh, N & Wong, B. Data exploration. Nat Methods. 9: 5 (2012)
  14. Wong, B. Visual Representation of Scientific Information. Sci. Signaling 4: 1 (2011).
  15. Wong, B. The design process. Nat Methods. 8: 987 (2011)
  16. Wong, B. Correspondence: More on color blindness. Nat Methods. 8: 891 (2011)
  17. Wong, B. Salience to relevance. Nat Methods. 8: 889 (2011)
  18. Wong, B. Layout. Nat Methods. 8: 783 (2011)
  19. Wong, B. Arrows. Nat Methods. 8: 701 (2011)
  20. Wong, B. Simplify to clarify. Nat Methods. 8: 611 (2011)
  21. Wong, B. Avoiding color. Nat Methods. 8: 525 (2011)
  22. Wong, B. Color blindness. Nat Methods. 8: 441 (2011)
  23. Wong, B. The overview figure. Nat Methods. 8: 441 (2011)
  24. Wong, B. Typography. Nat Methods. 8: 277 (2011)
  25. Wong, B. Points of review (part 2). Nat Methods. 8: 189 (2011)
  26. Wong, B. Points of review (part 1). Nat Methods. 8: 101 (2011)
  27. Wong, B. Negative space. Nat Methods. 8: 1 (2011)
  28. Wong, B. Gestalt principles (part 2). Nat Methods. 7: 941 (2010)
  29. Wong, B. Gestalt principles (part 1). Nat Methods. 7: 863 (2010)
  30. Wong, B. Salience. Nat Methods. 7: 773 (2010)
  31. Wong, B. Design of data figures. Nat Methods. 7: 665 (2010)
  32. Wong, B. Color Coding. Nat Methods. 7: 573 (2010)

Research articles

  1. Yu C Mannan A Yvone G Ross K Zhang Y Marton M Taylor B Crenshaw A Gould J Tamayo P Weir B Tsherniak A Wong B Garraway L Shamji A Palmer M Foley M Winckler W Schreiber S Kung A Golub T. High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines. Nature biotechnology 2016 vol: 34 (4) pp: 419-23
  2. Sharifnia T Rusu V Piccioni F Bagul M Imielinski M Cherniack A Pedamallu C Wong B Wilson F Garraway L Altshuler D Golub T Root D Subramanian A Meyerson M. Genetic modifiers of EGFR dependence in non-small cell lung cancer. PNAS: 111 (52) pp: 18661-6 (2014)
  3. Lohr J Adalsteinsson V Cibulskis K Choudhury A Rosenberg M Cruz-Gordillo P Francis J Zhang C Shalek A Satija R Trombetta J Lu D Tallapragada N Tahirova N Kim S Blumenstiel B Sougnez C Lowe A Wong B Auclair D Van Allen E Nakabayashi M Lis R Lee G Li T Chabot M Ly A Taplin M Clancy T Loda M Regev A Meyerson M Hahn W Kantoff P Golub T Getz G Boehm J Love J. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nature biotechnology 2014 vol: 32 (5) pp: 479-84
  4. Sandro Santagata, Marc L. Mendillo, Yun-chi Tang, Aravind Subramanian, Casey C. Perley, Stephane P. Roche, Bang Wong, Rajiv Narayan, Hyoungtae Kwon, Martina Koeva, Angelika Amon, Todd R. Golub, John A. Porco Jr., Luke Whitesell, Susan Lindquist. Tight Coordination of Protein Translation and HSF1 Activation Supports the Anabolic Malignant State. Science 341, 6143 (2013).
  5. Garber M Yosef N Goren A Raychowdhury R Thielke A Guttman M Robinson J Minie B Chevrier N Itzhaki Z Blecher-Gonen R Bornstein C Amann-Zalcenstein D Weiner A Friedrich D Meldrim J Ram O Cheng C Gnirke A Fisher S Friedman N Wong B Bernstein B Nusbaum C Hacohen N Regev A Amit I. A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals. Molecular Cell 2012 vol: 47 (5) pp: 810-822

Reviews

  1. Looks matter (Book review). Kjærgaard, RS, Wong B. Cell 149: 1420-1421 (2012)
  2. O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Hériché JK, Nielsen CB, North C, Olson AJ, Procter JB, Shattuck DW, Walter T, Wong B. Visualizing biological data-now and in the future. Nat Methods. 7: S2-4 (2010).