Protein Design by Optimization of a Sequence-Structure Quality Function. - Steven E. Brenner; Alan Berry (ISMB, 1994)

A Specification for Defining and Annotating Regions of Macromolecular Structures. - Steven E. Brenner; Tim J. P. Hubbard (ISMB, 1995)

SCOP: a structural classification of proteins database. - Tim J. P. Hubbard; Alexey G. Murzin; Steven E. Brenner; Cyrus Chothia (Nucleic Acids Res., 1997)

The PRESAGE database for structural genomics. - Steven E. Brenner; Derren Barken; Michael Levitt 001 (Nucleic Acids Res., 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 ASTRAL compendium for protein structure and sequence analysis. - Steven E. Brenner; Patrice Koehl; Michael Levitt 001 (Nucleic Acids Res., 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)

Genome Annotation and Protein Structure. - Steven E. Brenner (CSB, 2002)

ASTRAL compendium enhancements. - John-Marc Chandonia; Nigel S. Walker; Loredana Lo Conte; Patrice Koehl; Michael Levitt 001; 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)

SCOR: a Structural Classification of RNA database. - Peter S. Klosterman; Makio Tamura; Stephen R. Holbrook; Steven E. Brenner (Nucleic Acids Res., 2002)

Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison. - Richard E. Green; Steven E. Brenner (Proc. IEEE, 2002)

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 (ISMB (Supplement of Bioinformatics), 2003)

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)

The ASTRAL Compendium in 2004. - John-Marc Chandonia; Gary Chung Hon; Nigel S. Walker; Loredana Lo Conte; Patrice Koehl; Michael Levitt 001; Steven E. Brenner (Nucleic Acids Res., 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)

An alternative model of amino acid replacement. - Gavin E. Crooks; Steven E. Brenner (Bioinform., 2005)

Pairwise alignment incorporating dipeptide covariation. - Gavin E. Crooks; Richard E. Green; Steven E. Brenner (Bioinform., 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)

PLoS Computational Biology: A New Community Journal. - Philip E. Bourne; Steven E. Brenner; Michael B. Eisen (PLoS Comput. Biol., 2005)

Protein Molecular Function Prediction by Bayesian Phylogenomics. - Barbara E. Engelhardt; Michael I. Jordan; Kathryn E. Muratore; Steven E. Brenner (PLoS Comput. Biol., 2005)

A graphical model for predicting protein molecular function. - Barbara E. Engelhardt; Michael I. Jordan; Steven E. Brenner (ICML, 2006)

ANDY: a general, fault-tolerant tool for database searching on computer clusters. - Andrew Smith; John-Marc Chandonia; Steven E. Brenner (Bioinform., 2006)

MeRNA: a database of metal ion binding sites in RNA structures. - Liliana R. Stefan; Rui Zhang 017; Aaron G. Levitan; Donna K. Hendrix; Steven E. Brenner; Stephen R. Holbrook (Nucleic Acids Res., 2006)

Developing Computational Biology. - Philip E. Bourne; Steven E. Brenner (PLoS Comput. Biol., 2007)

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)

Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization. - Benjamin J. Blencowe; Steven E. Brenner; Timothy R. Hughes; Quaid Morris (Pacific Symposium on Biocomputing, 2009)

Alignment-free local structural search by writhe decomposition. - Degui Zhi; Maxim Shatsky; Steven E. Brenner (Bioinform., 2010)

The Future of Genome-Based Medicine. - Quaid Morris; Steven E. Brenner; Jennifer Listgarten; Oliver Stegle (Pacific Symposium on Biocomputing, 2013)

Session introduction. - Oliver Stegle; Steven E. Brenner; Quaid Morris; Jennifer Listgarten (Pacific Symposium on Biocomputing, 2013)

Session introduction. - Jennifer Listgarten; Oliver Stegle; Quaid Morris; Steven E. Brenner; Leopold Parts (Pacific Symposium on Biocomputing, 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)

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; et al. (Nat., 2014)

Session introduction. - Joel T. Dudley; Jennifer Listgarten; Oliver Stegle; Steven E. Brenner; Leopold Parts (Pacific Symposium on Biocomputing, 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)

Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation. - Philip E. Bourne; Steven E. Brenner; Michael B. Eisen (PLoS Comput. Biol., 2015)

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 (PSB, 2016)

Session Introduction. - Drena Dobbs; Steven E. Brenner; Vasant G. Honavar; Robert L. Jernigan; Alain Laederach; Quaid Morris (PSB, 2016)

Session Introduction. - Alexander A. Morgan; Sean D. Mooney; Bruce J. Aronow; Steven E. Brenner (PSB, 2016)

Session Introduction. - Alexander A. Morgan; Dana C. Crawford; Joshua C. Denny; Sean D. Mooney; Bruce J. Aronow; Steven E. Brenner (PSB, 2017)

Session Introduction. - Dana C. Crawford; Alexander A. Morgan; Joshua C. Denny; Bruce J. Aronow; Steven E. Brenner (PSB, 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. - Steven E. Brenner; Martha L. Bulyk; Dana C. Crawford; Jill P. Mesirov; Alexander A. Morgan; Predrag Radivojac (PSB, 2019)

Session Introduction. - Gamze Gürsoy; Arif Ozgun Harmanci; Haixu Tang; Erman Ayday; Steven E. Brenner (PSB, 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. - Steven E. Brenner; Martha L. Bulyk; Dana C. Crawford; Alexander A. Morgan; Predrag Radivojac; Nicholas P. Tatonetti (PSB, 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 (PSB, 2020)

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 (PSB, 2021)

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)