Research articles and articles on the graphical presentation of research data

Points of View

A series of articles dealing with the fundamental aspects of data presentation published by Nature Methods.

Plotting symbol. Choose distinct symbols that overlap without ambiguity and communicate relationships in data. Krzywinski M, Wong B. Nat Methods. 10: 451 (2013).

Visualizing biological data. Data visualization is increasingly important, but it requires clear objectives and improved implementation. Wong B. Nat Methods. 9: 1131 (2012).

Pencil and paper. A unique set of tools facilitate thinking and hypothesis generation. Wong B, Kjærgaard RS. Nat Methods. 9: 1037 (2012).

Power of the plane. Two-dimensional visualizations of multivariate data are most effective when combined. Gehlenborg M, Wong B. Nat Methods. 9: 935 (2012).

Into the third dimension. Three-dimensional visualizations are effective for spatial data but rarely for other data types. Gehlenborg N, Wong B. Nat Methods. 9: 851 (2012).

Mapping quantitative data to color. Data structure informs choice of color maps. Gehlenborg N, Wong B. Nat Methods. 9: 769 (2012).

Representing genomic structural variation. Techniques for displaying relations between distant genomic positions. Nielsen C, Wong B. Nat Methods. 9: 631 (2012).

Representing genomic structural variation. Techniques for displaying relations between distant genomic positions. Nielsen C, Wong B. Nat Methods. 9: 631 (2012).

Managing deep data in genome browsers. Techniques are at hand for taming the ever-growing number of data tracks. Nielsen C, Wong B. Nat Methods. 9: 521 (2012).

Representing the genome. The choice of visual representation of the linear genome is guided by the question being asked. Nielsen C, Wong B. Nat Methods. 9: 423 (2012).

Integrating data. Different analytical tasks require different visual representations. Gehlenborg N, Wong B. Nat Methods. 9: 315 (2012).

Heat maps. Heat maps are useful for visualizing multivariate data but must be applied properly. Gehlenborg N, Wong B. Nat Methods. 9: 213 (2012).

Networks. We describe graphing techniques to support exploration of networks. Gehlenborg N, Wong B. Nat Methods. 9: 115 (2012).

Data exploration. Enhancement of pattern discovery through graphical representation of data. Shoresh N, Wong B. Nat Methods. 9: 5 (2012).

The design process. Use good design to balance self-expression with the need to satisfy an audience in a logical manner. Wong B. Nat Methods. 8: 987 (2011).

Salience to relevance. Ensure that viewers notice the right content by making relevant information most noticeable. Wong B. Nat Methods. 8: 889 (2011).

Layout. Proper layout reveals the hierarchical relationship of informational elements. Wong B. Nat Methods. 8: 783 (2011).

Arrows. Use well-proportioned arrows sparingly and consistently as a guide through complex information. Wong B. Nat Methods. 8: 701 (2011).

Simplify to clarify. Simplify your presentation to improve clarity. Wong B. Nat Methods. 8: 611 (2011).

Avoiding color. Choose colors appropriately to avoid bias and unwanted artifacts in visuals. Wong B. Nat Methods. 8: 525 (2011).

Color blindness. Make your graphics accessible to those with color vision deficiencies. Wong B. Nat Methods. 8: 441 (2011).

The overview figure. An economic overview figure to convey general concepts helps readers understand a research study. Wong B. Nat Methods. 8: 441 (2011).

Typography. Choose typefaces, sizes and spacing to clarify the structure and meaning of the text. Wong B. Nat Methods. 8: 277 (2011).

Points of review (Part 2). Examples of figure redesigns. Wong B. Nat Methods. 8: 189 (2011).

Points of review (part 1). Examples of figure redesigns. Wong B. Nat Methods. 8: 101 (2011).

Negative space. Whitespace is a powerful way of improving visual appeal and emphasizing content. Wong B. Nat Methods. 8: 1 (2011).

Gestalt principles (part 2). Exploit perceptual phenomena to meaningfully arrange elements on the page. Wong B. Nat Methods. 7: 941 (2010).

Gestalt principles (part 1). Exploit perceptual phenomena to meaningfully arrange elements on the page. Wong B. Nat Methods. 7: 863 (2010).

Salience. Use salience to differentiate graphical symbols and speed up figure reading. Wong B. Nat Methods. 7: 773 (2010).

Design of data figures. Improve figure decoding by using strong visual cues to encode data. Wong B. Nat Methods. 7: 665 (2010).

Color Coding. Choose colors appropriately to avoid bias and unwanted artifacts in visuals. Wong B. Nat Methods. 7: 573 (2010).

Research articles

Genetic and transcriptional evolution alters cancer cell line drug response. Uri Ben-David, Benjamin Siranosian, Gavin Ha, Helen Tang, Yaara Oren, Kunihiko Hinohara, Craig A. Strathdee, Joshua Dempster, Nicholas J. Lyons, Robert Burns, Anwesha Nag, Guillaume Kugener, Beth Cimini, Peter Tsvetkov, Yosef E. Maruvka, Ryan O’Rourke, Anthony Garrity, Andrew A. Tubelli, Pratiti Bandopadhayay, Aviad Tsherniak, Francisca Vazquez, Bang Wong, Chet Birger, Mahmoud Ghandi, Aaron R. Thorner, Joshua A. Bittker, Matthew Meyerson, Gad Getz, Rameen Beroukhim & Todd R. Golub. Nature 560, 325–330 (2018)

GeNets: a unified web platform for network-based genomic analyses. Taibo Li, April Kim, Joseph Rosenbluh, Heiko Horn, Liraz Greenfeld, David An, Andrew Zimmer, Arthur Liberzon, Jon Bistline, Ted Natoli, Yang Li, Aviad Tsherniak, Rajiv Narayan, Aravind Subramanian, Ted Liefeld, Bang Wong, Dawn Thompson, Sarah Calvo, Steve Carr, Jesse Boehm, Jake Jaffe, Jill Mesirov, Nir Hacohen, Aviv Regev & Kasper Lage. Nature Methods 15, 543–546 (2018)

 A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Aravind Subramanian, Rajiv Narayan, Steven M. Corsello, David D. Peck, Ted E. Natoli, Xiaodong Lu, Joshua Gould, John F. Davis, Andrew A. Tubelli, Jacob K. Asiedu, David L. Lahr, Jodi E. Hirschman, Zihan Liu, Melanie Donahue, Bina Julian, Mariya Khan, David Wadden, Ian C. Smith, Daniel Lam, Arthur Liberzon, Courtney Toder, Mukta Bagul, Marek Orzechowski, Oana M. Enache, Federica Piccioni, Sarah A. Johnson, Nicholas J. Lyons, Alice H. Berger,  Alykhan F. Shamji, Angela N. Brooks, Anita Vrcic, Corey Flynn, Jacqueline Rosains, David Y. Takeda, Roger Hu, Desiree Davison, Justin Lamb, Kristin Ardlie, Larson Hogstrom, Peyton Greenside, Nathanael S. Gray, Paul A. Clemons, Serena Silver, Xiaoyun Wu, Wen-Ning Zhao, Willis Read-Button, Xiaohua Wu, Stephen J. Haggarty, Lucienne V. Ronco , Jesse S. Boehm, Stuart L. Schreiber, John G. Doench, Joshua A. Bittker, David E. Root, Bang Wong, Todd R. Golub. Cell 171, 1437-1452  (2017)

The Drug Repurposing Hub: a next-generation drug library and information resource. Corsello SM, Bittker JA, Liu Z, Gould J, McCarren P, Hirschman JE, Johnston SE, Vrcic A, Wong B, Khan M, Asiedu J, Narayan R, Mader CC, Subramanian A, Golub TR. Nat Med. 7:405-408 (2017)

High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines. Yu C, Mannan AM, Yvone GM, Wong B, Garraway LA, Shamji AF, Palmer MA, Foley MA, Winckler W, Schreiber SL, Kung AL, Golub TR  Nat. Biotechnology 34, 419–423 (2016)

Quantitative visualization of alternative exon expression from RNA-seq data. Katz, Y., Wang, E.T., Silterra, J., Schwartz, S., Wong, B., Thorvaldsdóttir, H., Robinson, J.T., Mesirov, J.P., Airoldi, E.M. and Burge, C.B. Bioinformatics 31: 2400-2402 (2015)

Genetic modifiers of EGFR dependence in non-small cell lung cancer. Sharifnia T, Rusu V, Piccioni F, Bagul M, Imielinski M, Cherniack AD,  Pedamallu CS, Wong B, Wilson FH, Garraway LA, Altshuler D, Golub TR, Root DE, Subramanian A, Meyerson M. PNAS 111 (52), 18661–18666 (2014)

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta J, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GS, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Nat Biotechnology 32, 479–484 (2014)

Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B, Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JA Jr, Whitesell L, Lindquist S. Science 341, 6143 (2013)

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals. 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 BE, Nusbaum C, Hacohen N, Regev A, Amit I. Mol Cell 47: 810-822 (2012)

Leveraging electronic health records to support chronic disease management: the need for temporal data views. Samal, Lipika; Wright, Adam; Wong, Bang T.; Linder, Jeffrey A.; Bates, David W. Informatics in Primary Care. 19 (2): 65-74 (2011).

Cleavage by granzyme B is strongly predictive of autoantigen status: implications for initiation of autoimmunity. Casciola-Rosen L, Andrade F, Ulanet D, Wong B, Rosen. A. J. Exp. Med. 190:815-826 (1999).

Serial changes in surfactant-associated proteins in lung and serum before and after onset of ARDS. Greene KE, Wright JR, Steinberg KP, Ruzinski JT, Caldwell E, Wong B, Hull W, Whitsett JA, Akino T, Kuroki Y, Nagae H, Hudson LD, Martin TR. Am. J. Respir. Crit. Care Med. 160(6):1843-1850 (1999).

Molecular expression of the alpha-chemokine rabbit GRO in Escherichia coli and characterization of its production by lung cells in vitro and in vivo. Johnson MC, Kajikawa O, Goodman RB, Wong VA, Mongovin SM, Wong B, Fox-Dewhurst R, Martin TR. J. Biol. Chem. 271(18):10853-10858 (1996).

Reviews

Looks matter (Book review). Kjærgaard, RS, Wong B. Cell 149: 1420-1421 (2012).

Visual Representation of Scientific Information (Published presentation). Wong, B. Sci. Signal., 4: pt1 (2011). Slideshow.

More on color blindness (Correspondence). Wong, B. Nat Methods. 8: 891 (2011).

Visualization biological data: now and in the Future. 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. Nat. Methods, 7(3s), S2-S4 (2010).

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