Steven E. Brenner

According to our database, Steven E. Brenner authored at least 49 papers between 1994 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning.

John-Marc Chandonia, Lindsey Guan, Shiangyi Lin, Changhua Yu, Naomi K. Fox, Steven E. Brenner

Nucleic Acids Res., 2022

2021

Computational Challenges and Artificial Intelligence in Precision Medicine.

Olga Afanasiev, Joanne Berghout, Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jonathan H. Chen, Roxana Daneshjou, Lukasz Kidzinski

Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021

2020

Navigating Ethical Quandaries with the Privacy Dilemma of Biomedical Datasets.

Gamze Gürsoy, Megan Doerr, John Wilbanks, Jennifer K. Wagner, Haixu Tang, Steven E. Brenner

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

Session Introduction.

Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2019

SCOPe: classification of large macromolecular structures in the structural classification of proteins - extended database.

John-Marc Chandonia, Naomi K. Fox, Steven E. Brenner

Nucleic Acids Res., 2019

Session Introduction.

Gamze Gürsoy, Arif Ozgun Harmanci, Haixu Tang, Erman Ayday, Steven E. Brenner

Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

Session introduction.

Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac

Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

2018

Putting benchmarks in their rightful place: The heart of computational biology.

Bjoern Peters, Steven E. Brenner, Edwin Wang, Donna K. Slonim, Maricel G. Kann

PLoS Comput. Biol., 2018

Session Introduction.

Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

2017

Session Introduction.

Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

2016

Session Introduction.

Alexander A. Morgan, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Session Introduction.

Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

Use of Genome Data in Newborns as a Starting Point for Life-Long Precision Medicine.

Steven E. Brenner, Stephen Kingsmore, Sean D. Mooney, Robert Nussbaum, Jennifer Puck

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015

Ten Years of <i>PLoS^‡ Computational Biology: </i> A Decade of Appreciation and Innovation.

Philip E. Bourne, Steven E. Brenner, Michael B. Eisen

PLoS Comput. Biol., 2015

SIFTER search: a web server for accurate phylogeny-based protein function prediction.

Sayed M. Sahraeian, Kevin R. Luo, Steven E. Brenner

Nucleic Acids Res., 2015

Session introduction.

Joel T. Dudley, Jennifer Listgarten, Oliver Stegle, Steven E. Brenner, Leopold Parts

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2014

Comparative analysis of regulatory information and circuits across distant species Open.

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

Nat., 2014

SCOPe: Structural Classification of Proteins - extended, integrating SCOP and ASTRAL data and classification of new structures.

Naomi K. Fox, Steven E. Brenner, John-Marc Chandonia

Nucleic Acids Res., 2014

Session introduction.

Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts

Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

2013

Session introduction.

Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

The Future of Genome-Based Medicine.

Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

2010

Alignment-free local structural search by writhe decomposition.

Degui Zhi, Maxim Shatsky, Steven E. Brenner

Bioinform., 2010

2009

Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization.

Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008

Data growth and its impact on the SCOP database: new developments.

Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin

Nucleic Acids Res., 2008

2007

Developing Computational Biology.

Philip E. Bourne, Steven E. Brenner

PLoS Comput. Biol., 2007

2006

MeRNA: a database of metal ion binding sites in RNA structures.

Liliana R. Stefan, Rui Zhang, Aaron G. Levitan, Donna K. Hendrix, Steven E. Brenner, Stephen R. Holbrook

Nucleic Acids Res., 2006

ANDY: a general, fault-tolerant tool for database searching on computer clusters.

Andrew Smith, John-Marc Chandonia, Steven E. Brenner

Bioinform., 2006

A graphical model for predicting protein molecular function.

Barbara E. Engelhardt, Michael I. Jordan, Steven E. Brenner

Proceedings of the Machine Learning, 2006

2005

Protein Molecular Function Prediction by Bayesian Phylogenomics.

Barbara E. Engelhardt, Michael I. Jordan, Kathryn E. Muratore, Steven E. Brenner

PLoS Comput. Biol., 2005

<i>PLoS Computational Biology: </i> A New Community Journal.

Philip E. Bourne, Steven E. Brenner, Michael B. Eisen

PLoS Comput. Biol., 2005

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap.

Gavin A. Price, Gavin E. Crooks, Richard E. Green, Steven E. Brenner

Bioinform., 2005

Pairwise alignment incorporating dipeptide covariation.

Gavin E. Crooks, Richard E. Green, Steven E. Brenner

Bioinform., 2005

An alternative model of amino acid replacement.

Gavin E. Crooks, Steven E. Brenner

Bioinform., 2005

2004

SCOR: Structural Classification of RNA, version 2.0.

Makio Tamura, Donna K. Hendrix, Peter S. Klosterman, Nancy R. B. Schimmelman, Steven E. Brenner, Stephen R. Holbrook

Nucleic Acids Res., 2004

The ASTRAL Compendium in 2004.

John-Marc Chandonia, Gary Chung Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner

Nucleic Acids Res., 2004

SCOP database in 2004: refinements integrate structure and sequence family data.

Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin

Nucleic Acids Res., 2004

2003

Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes.

Richard E. Green, Benjamin P. Lewis, R. Tyler Hillman, Marco Blanchette, Liana F. Lareau, Aaron T. Garnett, Donald C. Rio, Steven E. Brenner

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002

Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison.

Richard E. Green, Steven E. Brenner

Proc. IEEE, 2002

SCOR: a Structural Classification of RNA database.

Peter S. Klosterman, Makio Tamura, Stephen R. Holbrook, Steven E. Brenner

Nucleic Acids Res., 2002

SCOP database in 2002: refinements accommodate structural genomics.

Loredana Lo Conte, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin

Nucleic Acids Res., 2002

ASTRAL compendium enhancements.

John-Marc Chandonia, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner

Nucleic Acids Res., 2002

Genome Annotation and Protein Structure.

Steven E. Brenner

Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002

2000

SCOP: a Structural Classification of Proteins database.

Loredana Lo Conte, Bart Ailey, Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia

Nucleic Acids Res., 2000

The ASTRAL compendium for protein structure and sequence analysis.

Steven E. Brenner, Patrice Koehl, Michael Levitt

Nucleic Acids Res., 2000

1999

SCOP: a Structural Classification of Proteins database.

Tim J. P. Hubbard, Bart Ailey, Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia

Nucleic Acids Res., 1999

The PRESAGE database for structural genomics.

Steven E. Brenner, Derren Barken, Michael Levitt

Nucleic Acids Res., 1999

1997

SCOP: a structural classification of proteins database.

Tim J. P. Hubbard, Alexey G. Murzin, Steven E. Brenner, Cyrus Chothia

Nucleic Acids Res., 1997

1995

A Specification for Defining and Annotating Regions of Macromolecular Structures.

Steven E. Brenner, Tim J. P. Hubbard

Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

1994

Protein Design by Optimization of a Sequence-Structure Quality Function.

Steven E. Brenner, Alan Berry

Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994