Steven E. Brenner

发表

SCOP: a Structural Classification of Proteins database

Tim J. P. Hubbard, Bart Ailey, Steven E. Brenner, 1999, Nucleic Acids Res..

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

Steven E. Brenner, Sayed M. Sahraeian, Kevin R. Luo, 2015, Nucleic Acids Res..

Steven E. Brenner, 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

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

Steven E. Brenner, Richard E. Green, Benjamin P. Lewis, 2003, ISMB.

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

Steven E. Brenner, Naomi Fox, John-Marc Chandonia, 2018, Nucleic Acids Res..

SCOP: a Structural Classification of Proteins database

Tim J. P. Hubbard, Bart Ailey, Steven E. Brenner, 2000, Nucleic Acids Res..

The value of protein structure classification information—Surveying the scientific literature

Steven E. Brenner, Naomi K. Fox, John‐Marc Chandonia, 2015, Proteins.

An alternative model of amino acid replacement

Steven E. Brenner, Gavin E. Crooks, G. Crooks, 2004, Bioinform..

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

Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, 2007, Nucleic Acids Res..

Software Discovery Index Workshop Report

Daniel S. Katz, Phil Bourne, Ian Fore, 2015 .

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

Andrew Smith, Steven E. Brenner, John-Marc Chandonia, 2006, Bioinform..

SCOP: a structural classification of proteins database

Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, 1998, Nucleic Acids Res..

Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework

Steven E. Brenner, Xi Luo, Lea M. Starita, 2019, Genome Medicine.

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

Steven E. Brenner, Quaid Morris, Timothy R. Hughes, 2008, Pacific Symposium on Biocomputing.

Alignment-Free Local Structural Search by Writhe Decomposition

Steven E. Brenner, Degui Zhi, Maxim Shatsky, 2007, WABI.

Pairwise alignment incorporating dipeptide covariation

Steven E. Brenner, Richard E. Green, Gavin E. Crooks, 2005, Bioinform..

Proceedings Of The Third International Conference On Intelligent Systems For Molecular Biology

Steven E. Brenner, Tim Hubbard, T. Hubbard, 1995 .

Developing Computational Biology

Philip E. Bourne, Steven E. Brenner, 2007, PLoS Comput. Biol..

WebLogo: A sequence logo generator - eScholarship

Steven E. Brenner, Gary C. Hon, John-Marc Chandonia, 2004 .

Faculty Opinions recommendation of Secondary structure switching in Cro protein evolution.

Steven E. Brenner, 2004 .

SCOR: Structural Classification of RNA, version 2.0

Steven E. Brenner, Stephen R. Holbrook, Peter S. Klosterman, 2004, Nucleic Acids Res..

Session introduction

Leopold Parts, Oliver Stegle, Steven E. Brenner, 2003, Pacific Symposium on Biocomputing.

Running head: ANDY: database searching on computer clusters

Steven E. Brenner, Andrew P. Smith, John-Marc Chandonia, 2006 .

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

Steven E. Brenner, Naomi Fox, John-Marc Chandonia, 2013, Nucleic Acids Res..

The PRESAGE database for structural genomics

Steven E. Brenner, Michael Levitt, Derren Barken, 1999, Nucleic Acids Res..

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

Rui Zhang, Steven E. Brenner, Stephen R. Holbrook, 2005, Nucleic Acids Res..

Opportunities and Challenges for Interpreting Rare Variation in Clinically Important Genes

Steven E. Brenner, Gregory McInnes, Russ B. Altman, 2020 .

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap

Steven E. Brenner, Richard E. Green, Gavin E. Crooks, 2005, Bioinform..

Protein Design by Optimization of a Sequence-Structure Quality Function

Steven E. Brenner, Alan Berry, S. Brenner, 1994, ISMB.

SCOR: a Structural Classification of RNA database

Steven E. Brenner, Stephen R. Holbrook, Peter S. Klosterman, 2002, Nucleic Acids Res..

Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison

Steven E. Brenner, Richard E. Green, S. Brenner, 2002, Proc. IEEE.

Comparative analysis of regulatory information and circuits across distant species

Peter J. Bickel, Mark Gerstein, Philip Cayting, 2014, Nature.

StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants

Steven E. Brenner, Zhiqiang Hu, Andrew G. Sharo, 2020, bioRxiv.

Methods and algorithms for the design of proteins

Steven E. Brenner, Alan Berry, S. Brenner, 1994 .

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

Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, 2004, Nucleic Acids Res..

Perturbation robustness analyses reveal important parameters in variant interpretation pipelines

Pui-Yan Kwok, Steven E. Brenner, Rajgopal Srinivasan, 2020, bioRxiv.

PLoS Computational Biology: A New Community Journal

Philip E. Bourne, Michael B. Eisen, Steven E. Brenner, 2005, PLoS Comput. Biol..

Introduction to Cgi/Perl: Getting Started With Web Scripts

Steven E. Brenner, Edwin Aoki, 1995 .

Alignment-free local structural search by writhe decomposition

Steven E. Brenner, Degui Zhi, Maxim Shatsky, 2007, WABI.

Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation

Philip E. Bourne, Michael B. Eisen, Steven E. Brenner, 2015, PLoS Comput. Biol..

The ASTRAL compendium for protein structure and sequence analysis

Patrice Koehl, Steven E. Brenner, Michael Levitt, 2000, Nucleic Acids Res..

The Future of Genome-Based Medicine

Oliver Stegle, Steven E. Brenner, Jennifer Listgarten, 2012, Pacific Symposium on Biocomputing.

Protein Molecular Function Prediction by Bayesian Phylogenomics

Michael I. Jordan, Steven E. Brenner, Barbara E. Engelhardt, 2005, PLoS Comput. Biol..

Regulatory RNA: Session Introduction

Vasant Honavar, Robert L. Jernigan, Drena Dobbs, 2016 .

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

ASTRAL compendium enhancements

Patrice Koehl, Steven E. Brenner, Michael Levitt, 2002, Nucleic Acids Res..

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

Edwin Wang, Steven E. Brenner, Maricel G. Kann, 2018, PLoS Comput. Biol..

The ASTRAL Compendium in 2004

Patrice Koehl, Steven E. Brenner, Michael Levitt, 2003, Nucleic Acids Res..

A Specification for Defining and Annotating Regions of Macromolecular Structures

Tim J. P. Hubbard, Steven E. Brenner, 1995, ISMB.

Computational Challenges and Artificial Intelligence in Precision Medicine

Dana C. Crawford, Steven E. Brenner, Joanne Berghout, 2020, PSB.

A graphical model for predicting protein molecular function

Michael I. Jordan, Steven E. Brenner, Barbara E. Engelhardt, 2006, ICML '06.

Sequences and topology: a decade of genomes Editorial overview

Anna Tramontano, Steven E. Brenner, 2005 .

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

Sean D. Mooney, Steven E. Brenner, Stephen Kingsmore, 2016, PSB.

The DOE Systems Biology Knowledgebase (KBase)

Fangfang Xia, Rick Stevens, Mark Gerstein, 2016, bioRxiv.

SCOP database in 2002: refinements accommodate structural genomics

Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, 2002, Nucleic Acids Res..

Meta-Align: A Novel HMM-based Algorithm for Pairwise Alignment of Error-Prone Sequencing Reads

Steven E. Brenner, Degui Zhi, Kentaro Tomii, 2020 .

An SF1 affinity model to identify branch point sequences in human introns

Steven E. Brenner, Marco Blanchette, Donald C. Rio, 2010, Nucleic acids research.

Structural Genomics of Minimal Organisms and Protein Fold Space

Paul D. Adams, Steven E. Brenner, Stephen R. Holbrook, 2005, Journal of Structural and Functional Genomics.

Practical database searching

Steven E. Brenner, 1998 .

SCOP database in 2002

Steven E. Brenner, Alexey G. Murzin, Cyrus Chothia, 2002 .

Be prepared for the big genome leak

Steven E. Brenner, 2013, Nature.

Comparative Analysis of the Transcriptome across Distant Species

Peter J. Bickel, Raymond K. Auerbach, Peter J. Park, 2014, Nature.

Common sense for our genomes

Steven E. Brenner, 2007, Nature.

A novel PRRT2 pathogenic variant in a family with paroxysmal kinesigenic dyskinesia and benign familial infantile seizures

Su Guo, Steven E. Brenner, Igor B. Zhulin, 2018, Cold Spring Harbor molecular case studies.

The Developmental Transcriptome of Drosophila melanogaster

Peter J. Bickel, Li Yang, Thomas R. Gingeras, 2010, Nature.

Target selection for structural genomics

Steven E. Brenner, S. Brenner, 2000, Nature Structural Biology.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

Computational Structural Genomics of a Complete Minimal Organism

Steven E. Brenner, John-Marc Chandonia, David E. Konerding, 2002 .