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Steven E. Brenner
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- affiliation: University of California Berkeley, USA
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Journal Articles
- 2022
- [j29]John-Marc Chandonia
, Lindsey Guan
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. Nucleic Acids Res. 50(D1): 553-559 (2022) - 2019
- [j28]John-Marc Chandonia
SCOPe: classification of large macromolecular structures in the structural classification of proteins - extended database. Nucleic Acids Res. 47(Database-Issue): D475-D481 (2019) - 2018
- [j27]Bjoern Peters, Steven E. Brenner, Edwin Wang, Donna K. Slonim
Putting benchmarks in their rightful place: The heart of computational biology. PLoS Comput. Biol. 14(11) (2018) - 2015
- [j26]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): W141-W147 (2015) - [j25]Philip E. Bourne, Steven E. Brenner, Michael B. Eisen
Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation. PLoS Comput. Biol. 11(6) (2015) - 2014
- [j24]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): 304-309 (2014) - [j23]Alan P. Boyle
Comparative analysis of regulatory information and circuits across distant species Open. Nat. 512(7515): 453-456 (2014) - 2010
- [j22]Degui Zhi, Maxim Shatsky, Steven E. Brenner:
Alignment-free local structural search by writhe decomposition. Bioinform. 26(9): 1176-1184 (2010) - 2008
- [j21]Antonina Andreeva
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36(Database-Issue): 419-425 (2008) - 2007
- [j20]Philip E. Bourne, Steven E. Brenner:
Developing Computational Biology. PLoS Comput. Biol. 3(9) (2007) - 2006
- [j19]Andrew Smith, John-Marc Chandonia
ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinform. 22(5): 618-620 (2006) - [j18]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): 131-134 (2006) - 2005
- [j17]Gavin E. Crooks, Steven E. Brenner:
An alternative model of amino acid replacement. Bioinform. 21(7): 975-980 (2005) - [j16]Gavin E. Crooks, Richard E. Green
Pairwise alignment incorporating dipeptide covariation. Bioinform. 21(19): 3704-3710 (2005) - [j15]Gavin A. Price, Gavin E. Crooks, Richard E. Green
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinform. 21(20): 3824-3831 (2005) - [j14]Philip E. Bourne, Steven E. Brenner, Michael B. Eisen
PLoS Computational Biology: A New Community Journal. PLoS Comput. Biol. 1(1) (2005) - [j13]Barbara E. Engelhardt
Protein Molecular Function Prediction by Bayesian Phylogenomics. PLoS Comput. Biol. 1(5) (2005) - 2004
- [j12]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): 182-184 (2004) - [j11]John-Marc Chandonia
The ASTRAL Compendium in 2004. Nucleic Acids Res. 32(Database-Issue): 189-192 (2004) - [j10]Antonina Andreeva
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32(Database-Issue): 226-229 (2004) - 2002
- [j9]John-Marc Chandonia
ASTRAL compendium enhancements. Nucleic Acids Res. 30(1): 260-263 (2002) - [j8]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): 264-267 (2002) - [j7]Peter S. Klosterman, Makio Tamura, Stephen R. Holbrook, Steven E. Brenner:
SCOR: a Structural Classification of RNA database. Nucleic Acids Res. 30(1): 392-394 (2002) - [j6]Richard E. Green
Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison. Proc. IEEE 90(12): 1834-1847 (2002) - 2000
- [j5]Steven E. Brenner, Patrice Koehl
The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res. 28(1): 254-256 (2000) - [j4]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): 257-259 (2000) - 1999
- [j3]Steven E. Brenner, Derren Barken, Michael Levitt:
The PRESAGE database for structural genomics. Nucleic Acids Res. 27(1): 251-253 (1999) - [j2]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): 254-256 (1999) - 1997
- [j1]Tim J. P. Hubbard, Alexey G. Murzin, Steven E. Brenner, Cyrus Chothia:
SCOP: a structural classification of proteins database. Nucleic Acids Res. 25(1): 236-239 (1997)
Conference and Workshop Papers
- 2021
- [c21]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 - 2020
- [c20]Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti:
Session Introduction. PSB 2020: 547-550 - [c19]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: 736-738 - 2019
- [c18]Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac:
Session introduction. PSB 2019: 220-223 - [c17]Gamze Gürsoy, Arif Ozgun Harmanci, Haixu Tang, Erman Ayday, Steven E. Brenner:
Session Introduction. PSB 2019: 386-390 - 2018
- [c16]Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. PSB 2018: 389-399 - 2017
- [c15]Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. PSB 2017: 348-355 - 2016
- [c14]Alexander A. Morgan, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner:
Session Introduction. PSB 2016: 243-248 - [c13]Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris:
Session Introduction. PSB 2016: 429-432 - [c12]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: 568-575 - 2015
- [c11]Joel T. Dudley, Jennifer Listgarten, Oliver Stegle, Steven E. Brenner, Leopold Parts:
Session introduction. Pacific Symposium on Biocomputing 2015: 342-346 - 2014
- [c10]Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts:
Session introduction. Pacific Symposium on Biocomputing 2014: 247-249 - 2013
- [c9]Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten:
Session introduction. Pacific Symposium on Biocomputing 2013: 171-174 - [c8]Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle:
The Future of Genome-Based Medicine. Pacific Symposium on Biocomputing 2013: 456-458 - 2009
- [c7]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: 545-548 - 2007
- [c6]Degui Zhi, Maxim Shatsky, Steven E. Brenner:
Alignment-Free Local Structural Search by Writhe Decomposition. WABI 2007: 194-195 - 2006
- [c5]Barbara E. Engelhardt, Michael I. Jordan
A graphical model for predicting protein molecular function. ICML 2006: 297-304 - 2003
- [c4]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: 118-121 - 2002
- [c3]Steven E. Brenner:
Genome Annotation and Protein Structure. CSB 2002: 4 - 1995
- [c2]Steven E. Brenner, Tim J. P. Hubbard:
A Specification for Defining and Annotating Regions of Macromolecular Structures. ISMB 1995: 66-74 - 1994
- [c1]Steven E. Brenner, Alan Berry:
Protein Design by Optimization of a Sequence-Structure Quality Function. ISMB 1994: 44-52
Coauthor Index
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