P. Stenson

发表

Effect of predicted protein-truncating genetic variants on the human transcriptome

Emily K. Tsang, Jared L. Nedzel, Pedro G. Ferreira, 2015, Science.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Lisa M. D'Souza, Colin N. Dewey, Martin S. Taylor, 2004, Nature.

Analysis of protein-coding genetic variation in 60,706 humans

Andrew J. Hill, Ami Levy Moonshine, J. Danesh, 2015, bioRxiv.

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

Tom R. Gaunt, Hashem A. Shihab, J. Gough, 2012, Human mutation.

The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution

P. Stenson, D. Cooper, M. Mort, 2012, Current protocols in bioinformatics.

The Human Gene Mutation Database: 2008 update

P. Stenson, D. Cooper, M. Mort, 2009, Genome Medicine.

Human Gene Mutation Database (HGMD

P. Stenson, D. Cooper, M. Mort, 2003 .

Human Gene Mutation Database (HGMD®): 2003 update

P. Stenson, D. Cooper, M. Mort, 2003, Human mutation.

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

P. Stenson, D. Cooper, M. Mort, 2017, Human Genetics.

Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes

P. Stenson, D. Cooper, A. Phillips, 2011, Human mutation.

AMELIE 3: Fully Automated Mendelian Patient Reanalysis at Under 1 Alert per Patient per Year

S. Nelson, E. Ashley, M. Wheeler, 2021, medRxiv.

CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency

J. Casanova, P. Stenson, D. Cooper, 2018, Front. Immunol..

AMELIE accelerates Mendelian patient diagnosis directly from the primary literature

Gill Bejerano, Johannes Birgmeier, Peter D. Stenson, 2017, bioRxiv.

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature

M. Diekhans, Alexander J. Ratner, G. Bejerano, 2020, Science Translational Medicine.

AMELIE 2 speeds up Mendelian diagnosis by matching patient phenotype & genotype to primary literature

M. Diekhans, Alexander J. Ratner, G. Bejerano, 2019, bioRxiv.

Elucidating Common Structural Features of Human Pathogenic Variations Using Large‐Scale Atomic‐Resolution Protein Networks

Haiyuan Yu, P. Stenson, D. Cooper, 2014, Human mutation.

Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.

C. Tyler-Smith, Yali Xue, Q. Ayub, 2012, American journal of human genetics.

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

David N. Messina, Ryan D. Hernandez, Jeffery P. Demuth, 2007, Science.

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

P. Stenson, D. Cooper, M. Mort, 2013, Human Genetics.

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

P. Stenson, D. Cooper, M. Mort, 2010, Human mutation.

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

H. Carter, R. Karchin, P. Stenson, 2013, BMC Genomics.

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

Karsten M. Borgwardt, M. Daly, D. MacArthur, 2015, Human mutation.

PIVOTAL: Prioritizing variants of uncertain significance with spatial genomic patterns in the 3D proteome

Haiyuan Yu, P. Stenson, D. Cooper, 2020, bioRxiv.

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

Shayne D. Wierbowski, A. Clark, Haiyuan Yu, 2019, Nature Communications.

The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting

P. Stenson, D. Cooper, M. Mort, 2020, Human Genetics.

Human Gene Mutation Database—A biomedical information and research resource

P. Stenson, D. Cooper, M. Krawczak, 2000, Human mutation.

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST‐Indel)

David L. Masica, R. Karchin, P. Stenson, 2015, Human mutation.

The Human Gene Mutation Database (HGMD) and Its Exploitation in the Study of Mutational Mechanisms

P. Stenson, D. Cooper, N. Chuzhanova, 2005, Current protocols in bioinformatics.

Insights into hominid evolution from the gorilla genome sequence

Albert J. Vilella, Gregory E. Jordan, Petra C. Schwalie, 2012, Nature.

Meiotic recombination favors the spreading of deleterious mutations in human populations

P. Stenson, D. Cooper, L. Duret, 2011, Human mutation.

A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations

Matthew Mort, Peter D. Stenson, Xiaomu Wei, 2014, PLoS genetics.

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

Jian Wang, Tao Wang, Yan Li, 2011, Nature Biotechnology.

The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalised genomics

Matthew Mort, Peter D Stenson, David N Cooper, 2009, Human Genomics.

iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations

Haiyuan Yu, P. Stenson, D. Cooper, 2017, Genome Biology.

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

Jacques Fellay, Peter D. Stenson, David N. Cooper, 2018, Proceedings of the National Academy of Sciences.

Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073

Ken Chen, Joshua M. Korn, Afidalina Tumian, 2010 .

AVADA Improves Automated Genetic Variant Database 2 Construction Directly from Full Text Literature 3

G. Bejerano, P. Stenson, D. Cooper, 2019 .

AVADA Improves Automated Genetic Variant Database

G. Bejerano, P. Stenson, D. Cooper, 2019 .

Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes

J. Casanova, P. Stenson, D. Cooper, 2020, Proceedings of the National Academy of Sciences.

S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing

Gill Bejerano, Joseph M Paggi, Karthik A Jagadeesh, 2019, Nature Genetics.

Human Gene Mutation Database: towards a comprehensive central mutation database

P. Stenson, D. Cooper, M. Mort, 2007, Journal of Medical Genetics.

Identifying novel high-impact rare disease-causing mutations, genes and pathways in exomes of Ashkenazi Jewish inflammatory bowel disease patients

H. Ostrer, M. Daly, J. Rioux, 2020, medRxiv.

Single base‐pair substitutions at the translation initiation sites of human genes as a cause of inherited disease

Matthew Mort, Michael Krawczak, Amke Caliebe, 2011, Human mutation.

Identification of Discriminative Gene-level and Protein-level Features Associated with Gain-of-Function and Loss-of-Function Mutations

P. Stenson, D. Cooper, A. Schlessinger, 2021, bioRxiv.

SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data

J. Casanova, P. Stenson, D. Cooper, 2019, Nucleic acids research.

S-CAP extends clinical-grade pathogenicity prediction to genetic variants that affect RNA splicing

Joseph M. Paggi, G. Bejerano, P. Stenson, 2018, bioRxiv.

Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations.

Larry N. Singh, J. Mullikin, H. Kong, 2015, American journal of human genetics.

Genome-wide prediction of pathogenic gain-and loss-of-function variants from ensemble learning of diverse feature set

P. Stenson, D. Cooper, A. Schlessinger, 2022 .

Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach

B. Peters, R. Drmanac, P. Stenson, 2015, Human Genomics.

Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns

A. Chakravarti, R. Karchin, P. Stenson, 2015, bioRxiv.

Gross rearrangement breakpoint database (GRaBD™)

P. Stenson, D. Cooper, M. Krawczak, 2004, Human mutation.

X-CAP improves pathogenicity prediction of stopgain variants

G. Bejerano, P. Stenson, D. Cooper, 2022, Genome Medicine.

The human gene damage index as a gene-level approach to prioritizing exome variants

Jean-Michel Claverie, Lluis Quintana-Murci, Patrick Nitschke, 2015, Proceedings of the National Academy of Sciences.

Complete ascertainment of intragenic copy number mutations (CNMs) in the CFTR gene and its implications for CNM formation at other autosomal loci

P. Stenson, D. Cooper, N. Chuzhanova, 2010, Human mutation.

Distinct sequence features underlie microdeletions and gross deletions in the human genome

Huiying Zhao, J. Tainer, P. Stenson, 2021, Human mutation.

Changes in primary DNA sequence complexity influence the phenotypic consequences of mutations in human gene regulatory regions

P. Stenson, D. Cooper, M. Krawczak, 2000, Human Genetics.

Using Exome Data to Identify Malignant Hyperthermia

J. Mullikin, P. Stenson, D. Cooper, 2013 .

Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections

Huiying Zhao, J. Tainer, P. Stenson, 2022, Human Genetics.

Using Exome Data to Identify Malignant Hyperthermia Susceptibility Mutations

J. Mullikin, P. Stenson, D. Cooper, 2013, Anesthesiology.

Interpreting Secondary Cardiac Disease Variants in an Exome Cohort

Larry N. Singh, J. Mullikin, P. Stenson, 2013, Circulation. Cardiovascular genetics.

Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set

P. Stenson, D. Cooper, A. Schlessinger, 2022, bioRxiv.

A comprehensive knowledgebase of known and predicted human genetic variants associated with COVID-19 susceptibility and severity

P. Stenson, C. S. Bayrak, Y. Itan, 2022, medRxiv.

Supplement for “X-CAP improves pathogenicity prediction of stopgain substitutions”

G. Bejerano, P. Stenson, D. Cooper, 2022 .

Identifying shared genetic factors underlying epilepsy and congenital heart disease in Europeans

P. Stenson, D. Cooper, C. S. Bayrak, 2022, Human Genetics.

Delineating the Hemostaseome as an aid to individualize the analysis of the hereditary basis of thrombotic and bleeding disorders

P. Stenson, D. Cooper, K. Fechtel, 2011, Human Genetics.

Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions

P. Stenson, D. Cooper, N. Chuzhanova, 2005, Human mutation.

Genome-wide detection of human variants that disrupt intronic branchpoints

J. Casanova, P. Stenson, D. Cooper, 2022, bioRxiv.

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

P. Stenson, D. Cooper, M. Mort, 2017, Human Genetics.

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

Gill Bejerano, Aaron M Wenger, Harendra Guturu, 2016, Nature Genetics.

An integrated map of genetic variation from 1,092 human genomes

Kenny Q. Ye, Mauricio O. Carneiro, Francisco M. De La Vega, 2012, Nature.

Meta‐Analysis of gross insertions causing human genetic disease: Novel mutational mechanisms and the role of replication slippage

Peter D Stenson, David N Cooper, Nadia Chuzhanova, 2005, Human mutation.

mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome

Matthew Mort, Alberto Paccanaro, Haiyuan Yu, 2016, Human mutation.

Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach

Andrew P. Stubbs, B. Peters, R. Drmanac, 2015, Human Genomics.

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures

M. Diekhans, R. Karchin, P. Stenson, 2013, Human Genetics.

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

P. Stenson, D. Cooper, M. Mort, 2013, Human Genetics.

CRAVAT: cancer-related analysis of variants toolkit

Hannah Carter, Mark Diekhans, Peter D. Stenson, 2013, Bioinform..

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures

Mark Diekhans, Peter D. Stenson, Rachel Karchin, 2013, Human Genetics.

Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants.

P. Stenson, D. Cooper, A. Schlessinger, 2021, American journal of human genetics.

Analysis of missense variants in the human genome reveals widespread gene-specific clustering and improves prediction of pathogenicity

P. Stenson, D. Cooper, C. Rivolta, 2022, American journal of human genetics.

Complex gene rearrangements caused by serial replication slippage

P. Stenson, D. Cooper, N. Chuzhanova, 2005, Human mutation.

Compensatory epistasis explored by molecular dynamics simulations

P. Stenson, D. Cooper, L. Azevedo, 2021, Human Genetics.

Databases in human and medical genetics

S. Sherry, D. Maglott, M. Feolo, 2010 .

Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides

Matthew Mort, Peter D Stenson, David N Cooper, 2010, Human Genomics.

Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity

Michael Krawczak, Peter D Stenson, David N Cooper, 2005, Human mutation.

Exome Aggregation Consortium

Adam Kiezun, Sergio Islas-Andrade, Pierre Fontanillas, 2016 .

Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns.

A. Chakravarti, R. Karchin, P. Stenson, 2015, Human molecular genetics.

The mutation significance cutoff: gene-level thresholds for variant predictions

Lluis Quintana-Murci, Lei Shang, Yuval Itan, 2016, Nature Methods.

Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes

Leo Goodstadt, Heming Xing, Peter D Stenson, 2004, Genome Biology.

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

Cheng Wang, Biao Li, Sean D. Mooney, 2014, PLoS Comput. Biol..

Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes

J. Casanova, P. Stenson, D. Cooper, 2019, Proceedings of the National Academy of Sciences.

SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data

Peng Zhang, Yuval Itan, Jean-Laurent Casanova, 2018, bioRxiv.

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties.

Aleksandar Milosavljevic, Peter D Stenson, David N Cooper, 2008, Genome research.

AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature

Gill Bejerano, Johannes Birgmeier, Maximilian Haeussler, 2019, Genetics in Medicine.

The genetic structure of the Turkish population reveals high levels of variation and admixture

J. Casanova, P. Stenson, D. Cooper, 2021, Proceedings of the National Academy of Sciences.

AVADA Enables Automated Genetic Variant Curation Directly from the Full Text Literature

David Neil Cooper, Maximilian Haeussler, Gill Bejerano, 2018, bioRxiv.

HGMD: the human gene mutation database

P. Stenson, D. Cooper, M. Krawczak, 2002 .

A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease

P. Stenson, D. Cooper, C. Férec, 2005, Human Genetics.

Phylogenomic analyses provide insights into primate evolution

T. Marquès-Bonet, K. Farh, Ming Li, 2023, Science.

iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations

Haiyuan Yu, P. Stenson, D. Cooper, 2017, Genome Biology.

AVADA: Towards Automated Pathogenic Variant Evidence Retrieval Directly from the Full Text Literature

G. Bejerano, P. Stenson, D. Cooper, 2019, Genetics in Medicine.

Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients

Judy H. Cho, H. Ostrer, M. Daly, 2023, Nature communications.

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

J. Casanova, J. Fellay, P. Stenson, 2018, Proceedings of the National Academy of Sciences.

The Human Gene Mutation Database: 2008 update

P. Stenson, D. Cooper, M. Mort, 2009, Genome Medicine.

The mutation significance cutoff: gene-level thresholds for variant predictions

P. Stenson, Shen-Ying Zhang, L. Quintana-Murci, 2016, Nature Methods.

The landscape of rare genetic variation associated with inflammatory bowel disease and Parkinson’s disease comorbidity

P. Stenson, Y. Itan, J. Burisch, 2024, Genome medicine.