List of works by Steven E. Brenner

A continuous fluorescence assay for the characterization of Nudix hydrolases

scientific article published on 07 March 2013

A generalized affine gap model significantly improves protein sequence alignment accuracy

scientific article

A large-scale evaluation of computational protein function prediction

scientific article

A method for the alignment of heterogeneous macromolecules from electron microscopy

scientific article published on 30 December 2008

A novel PRRT2 pathogenic variant in a family with Paroxysmal Kinesigenic Dyskinesia and Benign Familial Infantile Seizures

scientific article

A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70

scientific article

A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III.

scientific article published on 28 July 2016

A quantitative methodology for the de novo design of proteins

scientific article

A rust‐fungus Nudix hydrolase effector decaps <scp>mRNA</scp><i>in vitro</i> and interferes with plant immune pathways

scientific article published in 2023

A tour of structural genomics.

scientific article

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

scientific article published on 5 January 2006

ASTRAL compendium enhancements

scientific article

Alignment-free local structural search by writhe decomposition

scientific article

Aluminum may mediate Alzheimer's disease through liver toxicity, with aberrant hepatic synthesis of ceruloplasmin and ATPase7B, the resultant excess free copper causing brain oxidation, beta-amyloid aggregation and Alzheimer disease

scientific article published on 20 December 2012

Aluminum neurotoxicity is reduced by dantrolene and dimethyl sulfoxide in cultured rat hippocampal neurons

scientific article

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

scientific article

An alternative model of amino acid replacement

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An unappreciated role for RNA surveillance

scientific article published in 2004

Antioxidants and risk of Alzheimer disease.

scientific article

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

scientific article published on 03 September 2019

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

scientific article published on 17 August 2019

Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge

scientific article published on 03 July 2019

Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016

scientific article published on 01 September 2019

Association of gut microbiota with post-operative clinical course in Crohn's disease

scientific article

Automated multi-model reconstruction from single-particle electron microscopy data

scientific article

Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs

scientific article

BLAST, Blitz, BLOCKS and BEAUTY: sequence comparison on the net.

scientific article

Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported

scientific journal article

Be prepared for the big genome leak

scientific article

Biases in Illumina transcriptome sequencing caused by random hexamer priming

scientific article

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

scientific article published on 03 September 2019

Classification of multi-helical DNA-binding domains and application to predict the DBD structures of sigma factor, LysR, OmpR/PhoB, CENP-B, Rapl, and Xy1S/Ada/AraC.

scientific article

Clomiphene citrate induced ovulation and intrauterine insemination: effect of timing of human chorionic gonadotropin injection in relation to the spontaneous LH surge on pregnancy rates

scientific article

Combined immunodeficiency due to MALT1 mutations, treated by hematopoietic cell transplantation

scientific article

Common sense for our genomes

scientific article published in October 2007

Comparative analysis of regulatory information and circuits across distant species

scientific article

Comparative analysis of the transcriptome across distant species

scientific article

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

scientific article

Conservation of an RNA regulatory map between Drosophila and mammals

scientific article

Currently used medicines for Alzheimer's disease are not very effective.

scientific article published in December 2007

DNA recognition code of transcription factors

scientific article

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

scientific article (publication date: 2008)

Developing computational biology

scientific article published on September 2007

Distribution of protein folds in the three superkingdoms of life.

scientific article

Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge

scientific article published on 12 July 2019

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans

scientific article (publication date: 7 January 2003)

Expectations from structural genomics

scientific article

Gene duplications in H. influenzae.

scientific article published in November 1995

Genome-scale phylogenetic function annotation of large and diverse protein families

scientific article

Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members

scientific article published on February 2009

Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs.

scientific article published in June 2004

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila

scientific article

Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila

scientific article

High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris

scientific article

Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans

scientific article

Identification of functional elements and regulatory circuits by Drosophila modENCODE

scientific article (publication date: 24 December 2010)

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

scientific article published in January 2005

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

scientific article published on 23 May 2017

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

scientific article

Measurements of protein sequence-structure correlations.

scientific article

Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily

scientific article published on 17 June 2013

Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors

scientific article published on 15 October 2015

Multisystem Anomalies in Severe Combined Immunodeficiency with Mutant BCL11B

scientific journal article

Natural cycle cryo-thaw transfer may improve pregnancy outcome

scientific article

Newborn Sequencing in Genomic Medicine and Public Health

scientific article

Newborn screening for SCID identifies patients with ataxia telangiectasia

scientific article

Nijmegen breakage syndrome detected by newborn screening for T cell receptor excision circles (TRECs)

scientific article

Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society

scientific article published on 14 February 2017

Optimal and fast rotational alignment of volumes with missing data in Fourier space

scientific article

Outcome of a workshop on applications of protein models in biomedical research

scientific article (publication date: 13 February 2009)

PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS THERAPY.

scientific article published on January 2014

PLoS Computational Biology: a new community journal

scientific article

PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY.

scientific article

Pairwise alignment incorporating dipeptide covariation.

scientific article

Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society

scientific article published on 21 January 2016

Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5

scientific article published on 17 August 2019

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.

scientific article

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.

scientific article published in January 2015

Phylogenetic molecular function annotation

scientific article published on January 2009

Planning the human variome project: the Spain report.

scientific article published in April 2009

Population statistics of protein structures: lessons from structural classifications

scientific article published on June 1997

Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization.

scientific article published in January 2009

Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

scientific article published on 24 June 2019

Protein molecular function prediction by Bayesian phylogenomics

scientific article

Protein secondary structure: entropy, correlations and prediction

scientific article

Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions

scientific journal article

RNA structural motifs: building blocks of a modular biomolecule

scientific article published on August 2005

Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

scientific article

Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible

scientific article

Reports from CAGI: The Critical Assessment of Genome Interpretation.

scientific article published in September 2017

Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation

scientific article published on 26 August 2019

SCOP database in 2002: refinements accommodate structural genomics

scientific article

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

scientific article (publication date: 2004)

SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data

scientific article

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database

scientific article published on 30 November 2016

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

scientific article

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

scientific article published on 01 January 2022

SCOR: Structural Classification of RNA, version 2.0.

scientific article

SCOR: a Structural Classification of RNA database

scientific article

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

scientific article published on 15 May 2015

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

scientific article

Severe hypertriglyceridemia and pancreatitis following hormone replacement prior to cryothaw transfer

scientific article

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap

scientific article

Structural genomics and structural biology: compare and contrast

scientific article

Structural genomics of minimal organisms and protein fold space

scientific article published in January 2005

Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes

scientific article

Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family

scientific article

Sulfotransferases and sulfatases in mycobacteria

scientific article

Survey of large protein complexes in D. vulgaris reveals great structural diversity

scholarly article

Target selection and deselection at the Berkeley Structural Genomics Center

scientific article published in February 2006

Target selection for structural genomics

scientific article

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

scientific article published on 24 June 2015

The ASTRAL Compendium in 2004

scientific article

The Bioperl toolkit: Perl modules for the life sciences

scientific article

The COMBREX project: design, methodology, and initial results

scientific article

The PRESAGE database for structural genomics

scientific article published on January 1999

The RNA Ontology Consortium: an open invitation to the RNA community

scientific article published on 16 February 2006

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

scientific article published in March 2007

The coupling of alternative splicing and nonsense-mediated mRNA decay.

scientific article published on January 2007

The developmental transcriptome of Drosophila melanogaster

scientific article (publication date: 24 March 2011)

The evolution of function within the Nudix homology clan

scientific article

The evolving roles of alternative splicing

scientific article published on June 2004

The future of genome-based medicine.

scientific article published in January 2013

The impact of structural genomics: expectations and outcomes

scientific article

The role of exome sequencing in newborn screening for inborn errors of metabolism

scientific article published on 10 August 2020

The value of protein structure classification information-Surveying the scientific literature.

scientific article

Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns

scientific article

USE OF GENOME DATA IN NEWBORNS AS A STARTING POINT FOR LIFE-LONG PRECISION MEDICINE.

scientific article

Understanding protein structure: using scop for fold interpretation

scientific article

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

scientific article published on 14 March 2007

VIPdb, a genetic Variant Impact Predictor Database

scientific article published on 17 August 2019

WebLogo: A Sequence Logo Generator

scientific article (publication date: June 2004)

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

scientific article

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