The COMBREX Project: Design, Methodology, and Initial Results
- Brian P. Anton
- Yi-Chien Chang
- Peter Brown
- Han-Pil Choi
- Lina L. Faller
- Jyotsna Guleria
- Zhenjun Hu
- Niels Klitgord
- Varun Mazumdar
- Mark McGettrick
- Lais Osmani
- Revonda Pokrzywa
- John Rachlin
- Rajeswari Swaminathan
- Caitlin Monahan
- Krista Rochussen
- Kevin Tao
- Ashok S. Bhagwat
- Steven E. Brenner
- Linda Columbus
- Alexey Fomenkov
- Giovanni Gadda
- Richard D. Morgan
- Andrei L. Osterman
- Dmitry A. Rodionov
- Irina A. Rodionova
- Kenneth E. Rudd
- Dieter Söll
- James Spain
- Shuang-yong Xu
- Alex Bateman
- Robert M. Blumenthal
- J. Martin Bollinger
- Iddo Friedberg
- Michael Y. Galperin
- Julien Gobeill
- Daniel Haft
- John Hunt
- Peter Karp
- William Klimke
- Carsten Krebs
- Maria J. Martin
- Jeffrey H. Miller
- Claire O'Donovan
- Bernhard Palsson
- Patrick Ruch
- Aaron Setterdahl
- Granger Sutton
- John Tate
- Alexander Yakunin
- Dmitri Tchigvintsev
- Germán Plata
- Jie Hu
- Russ Greiner, Dept of Computing Science; PI of AICML
- David Horn
- Kimmen Sjölander
- Steven L. Salzberg
- Dennis Vitkup
- Stanley Letovsky
- Daniel Segrè
- Charles DeLisi
- Richard J. Roberts
- Martin Steffen
- Simon Kasif
COMBREX (COMputational BRidges to EXperiments, http://combrex.bu.edu) is an NIH-funded enterprise that has brought computational and experimental biologists together, with the goal of greatly improving our overall understanding of microbial protein function [1],[2]. Since its inception, it has made significant progress toward the following goals: identifying the minority of proteins that have already been experimentally characterized, serving as a public repository of novel protein function predictions made by diverse methods, producing a clear chain of evidence from experiment to prediction, identifying (âÃÂÃÂrecommendingâÃÂÃÂ) those functional predictions whose verification will contribute most to our overall understanding of protein function, and actually funding the experiments to test function. The recommendation system is a proof of concept based on active learning principles and includes, for a given protein, criteria including phylogenetic distribution of its protein family, biological and clinical phenotypes associated with it, the availability of protein structure data, and its sequence distance from experimentally determined proteins or from the other proteins in its family.
Citation
B. Anton, Y. Chang, P. Brown, H. Choi, L. Faller, J. Guleria, Z. Hu, N. Klitgord, V. Mazumdar, M. McGettrick, L. Osmani, R. Pokrzywa, J. Rachlin, R. Swaminathan, C. Monahan, K. Rochussen, K. Tao, A. Bhagwat, S. Brenner, L. Columbus, A. Fomenkov, G. Gadda, R. Morgan, A. Osterman, D. Rodionov, I. Rodionova, K. Rudd, D. Söll, J. Spain, S. Xu, A. Bateman, R. Blumenthal, J. Bollinger, I. Friedberg, M. Galperin, J. Gobeill, D. Haft, J. Hunt, P. Karp, W. Klimke, C. Krebs, M. Martin, J. Miller, C. O'Donovan, B. Palsson, P. Ruch, A. Setterdahl, G. Sutton, J. Tate, A. Yakunin, D. Tchigvintsev, G. Plata, J. Hu, R. Greiner, D. Horn, K. Sjölander, S. Salzberg, D. Vitkup, S. Letovsky, D. Segrè, C. DeLisi, R. Roberts, M. Steffen, S. Kasif. "The COMBREX Project: Design, Methodology, and Initial Results". PLOS Biology, 11(8), pp e1001638, August 2013.Keywords: | bioinformatics, machine learning, COMBREX |
Category: | In Journal |
Web Links: | DOI |
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BibTeX
@article{Anton+al:PlosBiology13, author = {Brian P. Anton and Yi-Chien Chang and Peter Brown and Han-Pil Choi and Lina L. Faller and Jyotsna Guleria and Zhenjun Hu and Niels Klitgord and Varun Mazumdar and Mark McGettrick and Lais Osmani and Revonda Pokrzywa and John Rachlin and Rajeswari Swaminathan and Caitlin Monahan and Krista Rochussen and Kevin Tao and Ashok S. Bhagwat and Steven E. Brenner and Linda Columbus and Alexey Fomenkov and Giovanni Gadda and Richard D. Morgan and Andrei L. Osterman and Dmitry A. Rodionov and Irina A. Rodionova and Kenneth E. Rudd and Dieter Söll and James Spain and Shuang-yong Xu and Alex Bateman and Robert M. Blumenthal and J. Martin Bollinger and Iddo Friedberg and Michael Y. Galperin and Julien Gobeill and Daniel Haft and John Hunt and Peter Karp and William Klimke and Carsten Krebs and Maria J. Martin and Jeffrey H. Miller and Claire O'Donovan and Bernhard Palsson and Patrick Ruch and Aaron Setterdahl and Granger Sutton and John Tate and Alexander Yakunin and Dmitri Tchigvintsev and Germán Plata and Jie Hu and Russ Greiner and David Horn and Kimmen Sjölander and Steven L. Salzberg and Dennis Vitkup and Stanley Letovsky and Daniel Segrè and Charles DeLisi and Richard J. Roberts and Martin Steffen and Simon Kasif}, title = {The COMBREX Project: Design, Methodology, and Initial Results}, Volume = "11", Number = "8", Pages = { e1001638}, journal = {PLOS Biology}, year = 2013, }Last Updated: February 10, 2020
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