Visualizing biological data—now and in the future

Methods and tools for visualizing biological data have improved considerably over the last decades, but they are still inadequate for some high-throughput data sets. For most users, a key challenge is to benefit from the deluge of data without being overwhelmed by it. This challenge is still largely unfulfilled and will require the development of truly integrated and highly useable tools.

[1]  Mark A. Ragan,et al.  Advanced computing for systems biology , 2006, Briefings Bioinform..

[2]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[3]  Christopher J. Lee,et al.  POAVIZ: A Partial Order Multiple Sequence Alignment Visualizer , 2003, Bioinform..

[4]  Ben Shneiderman,et al.  Designing the User Interface: Strategies for Effective Human-Computer Interaction , 1998 .

[5]  Ivica Letunic,et al.  Visualization of multiple alignments, phylogenies and gene family evolution , 2010, Nature Methods.

[6]  Miguel Ángel García-Ruíz,et al.  An overview of auditory display to assist comprehension of molecular information , 2006, Interact. Comput..

[7]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[8]  Stephan Saalfeld,et al.  CATMAID: collaborative annotation toolkit for massive amounts of image data , 2009, Bioinform..

[9]  David J. Reiss,et al.  The Gaggle: An open-source software system for integrating bioinformatics software and data sources , 2006, BMC Bioinformatics.

[10]  I. Dubchak,et al.  Visualizing genomes: techniques and challenges , 2010, Nature Methods.

[11]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[12]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[13]  Matthew A. Hibbs,et al.  Visualization of omics data for systems biology , 2010, Nature Methods.

[14]  D. Goodsell,et al.  Visualization of macromolecular structures , 2010, Nature Methods.

[15]  Chris North,et al.  An insight-based methodology for evaluating bioinformatics visualizations , 2005, IEEE Transactions on Visualization and Computer Graphics.

[16]  David Haussler,et al.  The UCSC Genome Browser database: update 2010 , 2009, Nucleic Acids Res..

[17]  B. Schneirdeman,et al.  Designing the User Interface: Strategies for Effective Human-Computer Interaction , 1998 .

[18]  Stijn van Dongen,et al.  Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data , 2007, PLoS Comput. Biol..

[19]  Maryann E Martone,et al.  The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. , 2008, Journal of structural biology.

[20]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[21]  Kristin A. Cook,et al.  Illuminating the Path: The Research and Development Agenda for Visual Analytics , 2005 .

[22]  Alexandre Gillet,et al.  Tangible interfaces for structural molecular biology. , 2005, Structure.

[23]  Chris North,et al.  Realizing embodied interaction for visual analytics through large displays , 2007, Comput. Graph..

[24]  Anne E Carpenter,et al.  Visualization of image data from cells to organisms , 2010, Nature Methods.

[25]  Matthew Suderman,et al.  Tools for visually exploring biological networks , 2007, Bioinform..

[26]  Barbara Mirel,et al.  Supporting cognition in systems biology analysis: findings on users' processes and design implications , 2009 .

[27]  Inanç Birol,et al.  ABySS-Explorer: Visualizing Genome Sequence Assemblies , 2009, IEEE Transactions on Visualization and Computer Graphics.

[28]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.