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Literature DB >> 20195254

Visualizing biological data-now and in the future.

Seán I O'Donoghue¹, Anne-Claude Gavin, Nils Gehlenborg, David S Goodsell, Jean-Karim Hériché, Cydney B Nielsen, Chris North, Arthur J Olson, James B Procter, David W Shattuck, Thomas Walter, Bang Wong.

Abstract

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.

Mesh：

Year: 2010 PMID： 20195254 DOI： 10.1038/nmeth.f.301

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

22 in total

1. Announcing the worldwide Protein Data Bank.

Authors: Helen Berman; Kim Henrick; Haruki Nakamura
Journal: Nat Struct Biol Date: 2003-12

2. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors: Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal: Genome Res Date: 2003-11 Impact factor: 9.043

3. Tangible interfaces for structural molecular biology.

Authors: Alexandre Gillet; Michel Sanner; Daniel Stoffler; Arthur Olson
Journal: Structure Date: 2005-03 Impact factor: 5.006

4. An insight-based methodology for evaluating bioinformatics visualizations.

Authors: Purvi Saraiya; Chris North; Karen Duca
Journal: IEEE Trans Vis Comput Graph Date: 2005 Jul-Aug Impact factor: 4.579

Review 5. Advanced computing for systems biology.

Authors: Kevin Burrage; Lindsay Hood; Mark A Ragan
Journal: Brief Bioinform Date: 2006-09-25 Impact factor: 11.622

Review 6. Tools for visually exploring biological networks.

Authors: Matthew Suderman; Michael Hallett
Journal: Bioinformatics Date: 2007-08-25 Impact factor: 6.937

Review 7. 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

Review 8. Visualization of omics data for systems biology.

Authors: Nils Gehlenborg; Seán I O'Donoghue; Nitin S Baliga; Alexander Goesmann; Matthew A Hibbs; Hiroaki Kitano; Oliver Kohlbacher; Heiko Neuweger; Reinhard Schneider; Dan Tenenbaum; Anne-Claude Gavin
Journal: Nat Methods Date: 2010-03 Impact factor: 28.547

9. Jalview Version 2--a multiple sequence alignment editor and analysis workbench.

Authors: Andrew M Waterhouse; James B Procter; David M A Martin; Michèle Clamp; Geoffrey J Barton
Journal: Bioinformatics Date: 2009-01-16 Impact factor: 6.937

10. The UCSC Genome Browser database: update 2010.

Authors: Brooke Rhead; Donna Karolchik; Robert M Kuhn; Angie S Hinrichs; Ann S Zweig; Pauline A Fujita; Mark Diekhans; Kayla E Smith; Kate R Rosenbloom; Brian J Raney; Andy Pohl; Michael Pheasant; Laurence R Meyer; Katrina Learned; Fan Hsu; Jennifer Hillman-Jackson; Rachel A Harte; Belinda Giardine; Timothy R Dreszer; Hiram Clawson; Galt P Barber; David Haussler; W James Kent
Journal: Nucleic Acids Res Date: 2009-11-11 Impact factor: 16.971

47 in total

Visualizing biological data-now and in the future.

1. Announcing the worldwide Protein Data Bank.

2. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

3. Tangible interfaces for structural molecular biology.

4. An insight-based methodology for evaluating bioinformatics visualizations.

Review 5. Advanced computing for systems biology.

Review 6. Tools for visually exploring biological networks.

Review 7. Visualizing genomes: techniques and challenges.

Review 8. Visualization of omics data for systems biology.

9. Jalview Version 2--a multiple sequence alignment editor and analysis workbench.

10. The UCSC Genome Browser database: update 2010.

1. BioImageXD: an open, general-purpose and high-throughput image-processing platform.

2. NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data.

Review 3. A guide to the visual analysis and communication of biomolecular structural data.

Review 4. Functional adaptations of the transcriptome to mastitis-causing pathogens: the mammary gland and beyond.

5. Biomedical Visual Computing: Case Studies and Challenges.

6. Proteomic and biochemical methods to study the cytoskeletome.

7. Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models.

8. Visual analysis of geocoded twin data puts nature and nurture on the map.

9. Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants.

10. A novel application of motion analysis for detecting stress responses in embryos at different stages of development.