Steven E. Brenner

Publication Activity (10 Years)

Years Active: 1994-2022
Publications (10 Years): 13

Top Topics

Computational Challenges

Starting Points

Protein Function Prediction

Top Venues

Pacific Symposium on Biocomputing

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

John-Marc Chandonia, Lindsey Guan, Shiangyi Lin, Changhua Yu, Naomi K. Fox, Steven E. Brenner
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. Nucleic Acids Res. 50 (D1) (2022)
Olga Afanasiev, Joanne Berghout, Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jonathan H. Chen, Roxana Daneshjou, Lukasz Kidzinski
Computational Challenges and Artificial Intelligence in Precision Medicine. PSB (2021)
Gamze Gürsoy, Megan Doerr, John Wilbanks, Jennifer K. Wagner, Haixu Tang, Steven E. Brenner
Navigating Ethical Quandaries with the Privacy Dilemma of Biomedical Datasets. PSB (2020)
Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti
Session Introduction. PSB (2020)
Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac
Session introduction. PSB (2019)
John-Marc Chandonia, Naomi K. Fox, Steven E. Brenner
SCOPe: classification of large macromolecular structures in the structural classification of proteins - extended database. Nucleic Acids Res. 47 (Database-Issue) (2019)
Gamze Gürsoy, Arif O. Harmanci, Haixu Tang, Erman Ayday, Steven E. Brenner
Session Introduction. PSB (2019)
Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner
Session Introduction. PSB (2018)
Bjoern Peters, Steven E. Brenner, Edwin Wang, Donna K. Slonim, Maricel G. Kann
Putting benchmarks in their rightful place: The heart of computational biology. PLoS Comput. Biol. 14 (11) (2018)
Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner
Session Introduction. PSB (2017)
Alexander A. Morgan, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner
Session Introduction. PSB (2016)
Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
Session Introduction. PSB (2016)
Steven E. Brenner, Stephen Kingsmore, Sean D. Mooney, Robert Nussbaum, Jennifer Puck
Use of Genome Data in Newborns as a Starting Point for Life-Long Precision Medicine. PSB (2016)
Philip E. Bourne, Steven E. Brenner, Michael B. Eisen
A Decade of Appreciation and Innovation. PLoS Comput. Biol. 11 (6) (2015)
Joel T. Dudley, Jennifer Listgarten, Oliver Stegle, Steven E. Brenner, Leopold Parts
Session introduction. Pacific Symposium on Biocomputing (2015)
Sayed M. Sahraeian, Kevin R. Luo, Steven E. Brenner
SIFTER search: a web server for accurate phylogeny-based protein function prediction. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts
Session introduction. Pacific Symposium on Biocomputing (2014)
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
Comparative analysis of regulatory information and circuits across distant species Open. Nat. 512 (7515) (2014)
Naomi K. Fox, Steven E. Brenner, John-Marc Chandonia
SCOPe: Structural Classification of Proteins - extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 42 (Database-Issue) (2014)
Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten
Session introduction. Pacific Symposium on Biocomputing (2013)
Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle
The Future of Genome-Based Medicine. Pacific Symposium on Biocomputing (2013)
Degui Zhi, Maxim Shatsky, Steven E. Brenner
Alignment-free local structural search by writhe decomposition. Bioinform. 26 (9) (2010)
Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris
Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization. Pacific Symposium on Biocomputing (2009)
Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36 (Database-Issue) (2008)
Philip E. Bourne, Steven E. Brenner
Developing Computational Biology. PLoS Comput. Biol. 3 (9) (2007)
Degui Zhi, Maxim Shatsky, Steven E. Brenner
Alignment-Free Local Structural Search by Writhe Decomposition. WABI (2007)
Liliana R. Stefan, Rui Zhang, Aaron G. Levitan, Donna K. Hendrix, Steven E. Brenner, Stephen R. Holbrook
MeRNA: a database of metal ion binding sites in RNA structures. Nucleic Acids Res. 34 (Database-Issue) (2006)
Andrew Smith, John-Marc Chandonia, Steven E. Brenner
ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinform. 22 (5) (2006)
Barbara E. Engelhardt, Michael I. Jordan, Steven E. Brenner
A graphical model for predicting protein molecular function. ICML (2006)
Philip E. Bourne, Steven E. Brenner, Michael B. Eisen
A New Community Journal. PLoS Comput. Biol. 1 (1) (2005)
Barbara E. Engelhardt, Michael I. Jordan, Kathryn E. Muratore, Steven E. Brenner
Protein Molecular Function Prediction by Bayesian Phylogenomics. PLoS Comput. Biol. 1 (5) (2005)
Gavin E. Crooks, Richard E. Green, Steven E. Brenner
Pairwise alignment incorporating dipeptide covariation. Bioinform. 21 (19) (2005)
Gavin A. Price, Gavin E. Crooks, Richard E. Green, Steven E. Brenner
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinform. 21 (20) (2005)
Gavin E. Crooks, Steven E. Brenner
An alternative model of amino acid replacement. Bioinform. 21 (7) (2005)
Makio Tamura, Donna K. Hendrix, Peter S. Klosterman, Nancy R. B. Schimmelman, Steven E. Brenner, Stephen R. Holbrook
SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res. 32 (Database-Issue) (2004)
Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32 (Database-Issue) (2004)
John-Marc Chandonia, Gary Chung Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner
The ASTRAL Compendium in 2004. Nucleic Acids Res. 32 (Database-Issue) (2004)
Richard E. Green, Benjamin P. Lewis, R. Tyler Hillman, Marco Blanchette, Liana F. Lareau, Aaron T. Garnett, Donald C. Rio, Steven E. Brenner
Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. ISMB (Supplement of Bioinformatics) (2003)
Loredana Lo Conte, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res. 30 (1) (2002)
Steven E. Brenner
Genome Annotation and Protein Structure. CSB (2002)
John-Marc Chandonia, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner
ASTRAL compendium enhancements. Nucleic Acids Res. 30 (1) (2002)
Peter S. Klosterman, Makio Tamura, Stephen R. Holbrook, Steven E. Brenner
SCOR: a Structural Classification of RNA database. Nucleic Acids Res. 30 (1) (2002)
Richard E. Green, Steven E. Brenner
Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison. Proc. IEEE 90 (12) (2002)
Loredana Lo Conte, Bart Ailey, Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia
SCOP: a Structural Classification of Proteins database. Nucleic Acids Res. 28 (1) (2000)
Steven E. Brenner, Patrice Koehl, Michael Levitt
The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res. 28 (1) (2000)
Tim J. P. Hubbard, Bart Ailey, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia
SCOP: a Structural Classification of Proteins database. Nucleic Acids Res. 27 (1) (1999)
Steven E. Brenner, Derren Barken, Michael Levitt
The PRESAGE database for structural genomics. Nucleic Acids Res. 27 (1) (1999)
Tim J. P. Hubbard, Alexey G. Murzin, Steven E. Brenner, Cyrus Chothia
SCOP: a structural classification of proteins database. Nucleic Acids Res. 25 (1) (1997)
Steven E. Brenner, Tim J. P. Hubbard
A Specification for Defining and Annotating Regions of Macromolecular Structures. ISMB (1995)
Steven E. Brenner, Alan Berry
Protein Design by Optimization of a Sequence-Structure Quality Function. ISMB (1994)