Steven E. Brenner

49 papers A* 1A 2C 1Misc 15Journal 28Unranked 2
YearRankTypeTitle / Venue / Authors
2022 J jnl
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning.
Nucleic Acids Res.
John-Marc Chandonia, Lindsey Guan, Shiangyi Lin, Changhua Yu, Naomi K. Fox, Steven E. Brenner
2021 Misc conf
Computational Challenges and Artificial Intelligence in Precision Medicine.
PSB
Olga Afanasiev, Joanne Berghout, Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jonathan H. Chen, Roxana Daneshjou, Lukasz Kidzinski
2020 Misc conf
Navigating Ethical Quandaries with the Privacy Dilemma of Biomedical Datasets.
PSB
Gamze Gürsoy, Megan Doerr, John Wilbanks, Jennifer K. Wagner, Haixu Tang, Steven E. Brenner
2020 Misc conf
Session Introduction.
PSB
Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti
2019 J jnl
SCOPe: classification of large macromolecular structures in the structural classification of proteins - extended database.
Nucleic Acids Res.
John-Marc Chandonia, Naomi K. Fox, Steven E. Brenner
2019 Misc conf
Session Introduction.
PSB
Gamze Gürsoy, Arif Ozgun Harmanci, Haixu Tang, Erman Ayday, Steven E. Brenner
2019 Misc conf
Session introduction.
PSB
Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac
2018 J jnl
Putting benchmarks in their rightful place: The heart of computational biology.
PLoS Comput. Biol.
Bjoern Peters, Steven E. Brenner, Edwin Wang, Donna K. Slonim, Maricel G. Kann
2018 Misc conf
Session Introduction.
PSB
Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner
2017 Misc conf
Session Introduction.
PSB
Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner
2016 Misc conf
Session Introduction.
PSB
Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
2016 Misc conf
Session Introduction.
PSB
Alexander A. Morgan, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner
2016 Misc conf
Use of Genome Data in Newborns as a Starting Point for Life-Long Precision Medicine.
PSB
Steven E. Brenner, Stephen Kingsmore, Sean D. Mooney, Robert Nussbaum, Jennifer Puck
2015 J jnl
SIFTER search: a web server for accurate phylogeny-based protein function prediction.
Nucleic Acids Res.
Sayed M. Sahraeian, Kevin R. Luo, Steven E. Brenner
2015 Misc conf
Session introduction.
Pacific Symposium on Biocomputing
Joel T. Dudley, Jennifer Listgarten, Oliver Stegle, Steven E. Brenner, Leopold Parts
2015 J jnl
Ten Years of
PLoS Comput. Biol.
Philip E. Bourne, Steven E. Brenner, Michael B. Eisen
2014 J jnl
Comparative analysis of regulatory information and circuits across distant species Open.
Nat.
Alan P. Boyle, Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W. Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel S. Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, Michael Snyder
2014 J jnl
SCOPe: Structural Classification of Proteins - extended, integrating SCOP and ASTRAL data and classification of new structures.
Nucleic Acids Res.
Naomi K. Fox, Steven E. Brenner, John-Marc Chandonia
2014 Misc conf
Session introduction.
Pacific Symposium on Biocomputing
Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts
2013 Misc conf
Session introduction.
Pacific Symposium on Biocomputing
Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten
2013 Misc conf
The Future of Genome-Based Medicine.
Pacific Symposium on Biocomputing
Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle
2010 J jnl
Alignment-free local structural search by writhe decomposition.
Bioinform.
Degui Zhi, Maxim Shatsky, Steven E. Brenner
2009 Misc conf
Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization.
Pacific Symposium on Biocomputing
Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris
2008 J jnl
Data growth and its impact on the SCOP database: new developments.
Nucleic Acids Res.
Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin
2007 C conf
Alignment-Free Local Structural Search by Writhe Decomposition.
WABI
Degui Zhi, Maxim Shatsky, Steven E. Brenner
2007 J jnl
Developing Computational Biology.
PLoS Comput. Biol.
Philip E. Bourne, Steven E. Brenner
2006 A* conf
A graphical model for predicting protein molecular function.
ICML
Barbara E. Engelhardt, Michael I. Jordan, Steven E. Brenner
2006 J jnl
ANDY: a general, fault-tolerant tool for database searching on computer clusters.
Bioinform.
Andrew Smith, John-Marc Chandonia, Steven E. Brenner
2006 J jnl
MeRNA: a database of metal ion binding sites in RNA structures.
Nucleic Acids Res.
Liliana R. Stefan, Rui Zhang, Aaron G. Levitan, Donna K. Hendrix, Steven E. Brenner, Stephen R. Holbrook
2005 J jnl
An alternative model of amino acid replacement.
Bioinform.
Gavin E. Crooks, Steven E. Brenner
2005 J jnl
Pairwise alignment incorporating dipeptide covariation.
Bioinform.
Gavin E. Crooks, Richard E. Green, Steven E. Brenner
2005 J jnl
Protein Molecular Function Prediction by Bayesian Phylogenomics.
PLoS Comput. Biol.
Barbara E. Engelhardt, Michael I. Jordan, Kathryn E. Muratore, Steven E. Brenner
2005 J jnl
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap.
Bioinform.
Gavin A. Price, Gavin E. Crooks, Richard E. Green, Steven E. Brenner
2004 J jnl
SCOP database in 2004: refinements integrate structure and sequence family data.
Nucleic Acids Res.
Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin
2004 J jnl
SCOR: Structural Classification of RNA, version 2.0.
Nucleic Acids Res.
Makio Tamura, Donna K. Hendrix, Peter S. Klosterman, Nancy R. B. Schimmelman, Steven E. Brenner, Stephen R. Holbrook
2004 J jnl
The ASTRAL Compendium in 2004.
Nucleic Acids Res.
John-Marc Chandonia, Gary Chung Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner
2003 — conf
Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes.
ISMB (Supplement of Bioinformatics)
Richard E. Green, Benjamin P. Lewis, R. Tyler Hillman, Marco Blanchette, Liana F. Lareau, Aaron T. Garnett, Donald C. Rio, Steven E. Brenner
2002 J jnl
ASTRAL compendium enhancements.
Nucleic Acids Res.
John-Marc Chandonia, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner
2002 J jnl
Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison.
Proc. IEEE
Richard E. Green, Steven E. Brenner
2002 — conf
Genome Annotation and Protein Structure.
CSB
Steven E. Brenner
2002 J jnl
SCOP database in 2002: refinements accommodate structural genomics.
Nucleic Acids Res.
Loredana Lo Conte, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin
2002 J jnl
SCOR: a Structural Classification of RNA database.
Nucleic Acids Res.
Peter S. Klosterman, Makio Tamura, Stephen R. Holbrook, Steven E. Brenner
2000 J jnl
SCOP: a Structural Classification of Proteins database.
Nucleic Acids Res.
Loredana Lo Conte, Bart Ailey, Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia
2000 J jnl
The ASTRAL compendium for protein structure and sequence analysis.
Nucleic Acids Res.
Steven E. Brenner, Patrice Koehl, Michael Levitt
1999 J jnl
SCOP: a Structural Classification of Proteins database.
Nucleic Acids Res.
Tim J. P. Hubbard, Bart Ailey, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia
1999 J jnl
The PRESAGE database for structural genomics.
Nucleic Acids Res.
Steven E. Brenner, Derren Barken, Michael Levitt
1997 J jnl
SCOP: a structural classification of proteins database.
Nucleic Acids Res.
Tim J. P. Hubbard, Alexey G. Murzin, Steven E. Brenner, Cyrus Chothia
1995 A conf
A Specification for Defining and Annotating Regions of Macromolecular Structures.
ISMB
Steven E. Brenner, Tim J. P. Hubbard
1994 A conf
Protein Design by Optimization of a Sequence-Structure Quality Function.
ISMB
Steven E. Brenner, Alan Berry