Matthew Stephens

发表

msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots

Garrett Hellenthal, Matthew Stephens, M. Stephens, 2007, Bioinform..

High Pressure Testing Of Composite Solid Rocket Propellant Mixtures: Burner Facility Characterization

Matthew Stephens, Rodolphe Carro, Jason Arvanetes, 2005 .

A likelihood-based scoring method for peptide identification using mass spectrometry

Qunhua Li, Matthew Stephens, Jimmy K. Eng, 2012, 1301.2467.

Variational Inference of Population Structure in Large SNP Datasets

Matthew Stephens, Anil Raj, Jonathan K. Pritchard, 2013, bioRxiv.

Alignment and testing of critical interface fixtures for the James Webb Space Telescope

Adam Sutton, Matthew Stephens, James Parker, 2017, Optical Engineering + Applications.

A Fast Algorithm for Maximum Likelihood Estimation of Mixture Proportions Using Sequential Quadratic Programming

Mihai Anitescu, Matthew Stephens, Peter Carbonetto, 2018, Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.

False discovery rates: a new deal

Matthew Stephens, M. Stephens, 2016, bioRxiv.

BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS.

Matthew Stephens, Xiaoquan Wen, M. Stephens, 2011, The annals of applied statistics.

USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA.

Matthew Stephens, Xiaoquan Wen, M. Stephens, 2010, The annals of applied statistics.

A comparison of bayesian methods for haplotype reconstruction from population genotype data.

Peter Donnelly, Matthew Stephens, P. Donnelly, 2003, American journal of human genetics.

UNIFYING AND GENERALIZING METHODS FOR REMOVING UNWANTED VARIATION BASED ON NEGATIVE CONTROLS.

David Gerard, Matthew Stephens, M. Stephens, 2017, Statistica Sinica.

Efficient Algorithms for Multivariate Linear Mixed Models in Genome-wide Association Studies

Xiang Zhou, Matthew Stephens, M. Stephens, 2013, Nature Methods.

A simple new approach to variable selection in regression, with application to genetic fine-mapping

Matthew Stephens, Peter Carbonetto, Gao T. Wang, 2018, bioRxiv.

Superfamilies of Evolved and Designed Networks

Peter Donnelly, Matthew Stephens, Jonathan K. Pritchard, 2004 .

Detailed modeling of positive selection improves detection of cancer driver genes

Matthew Stephens, Yuwen Liu, Chuan He, 2019, Nature Communications.

A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.

Paul Scheet, Matthew Stephens, M. Stephens, 2006, American journal of human genetics.

Virtual Testing Applied to Door Latch Performance Evaluation

Matthew Stephens, John Hutchinson, Keith Friedman, 2016 .

Bayesian large-scale multiple regression with summary statistics from genome-wide association studies

Xiang Zhu, Matthew Stephens, M. Stephens, 2016, bioRxiv.

Flexible signal denoising via flexible empirical Bayes shrinkage

Matthew Stephens, Peter Carbonetto, Zhengrong Xing, 2016 .

Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation.

David Gerard, Matthew Stephens, M. Stephens, 2017, Biostatistics.

A new sequence logo plot to highlight enrichment and depletion

Matthew Stephens, Kushal K. Dey, Dongyue Xie, 2017, BMC Bioinformatics.

Visualizing the structure of RNA-seq expression data using grade of membership models

Matthew Stephens, Kushal K Dey, Chiaowen Joyce Hsiao, 2016, bioRxiv.

CorShrink: Empirical Bayes shrinkage estimation of correlations, with applications

Matthew Stephens, Kushal K Dey, 2018 .

Variance Adaptive Shrinkage (vash): Flexible Empirical Bayes estimation of variances

Matthew Stephens, Mengyin Lu, M. Stephens, 2016, bioRxiv.

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

Xiang Zhou, Matthew Stephens, Peter Carbonetto, 2012, PLoS genetics.

ebnm: An R Package for Solving the Empirical Bayes Normal Means Problem

Matthew Stephens, Jason Willwerscheid, M. Stephens, 2021 .

Multi-scale Poisson process approaches for differential expression analysis of high-throughput sequencing data

Matthew Stephens, Ester Pantaleo, Francesca Luca, 2021, 2106.13634.

Non-negative matrix factorization algorithms greatly improve topic model fits pdf

Matthew Stephens, Zihao Wang, Peter Carbonetto, 2021, ArXiv.

Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes

Matthew Stephens, M. Stephens, Xiang Zhu, 2018, Nature Communications.

Next generation analytic tools for large scale genetic epidemiology studies of complex diseases

Kathryn Roeder, Peter Kraft, Matthew Stephens, 2012, Genetic epidemiology.

Evidence for substantial fine-scale variation in recombination rates across the human genome

Dana C Crawford, Matthew Stephens, Deborah A Nickerson, 2004, Nature Genetics.

Ancestral Inference in Population Genetics Models with Selection (with Discussion)

Peter Donnelly, Matthew Stephens, P. Donnelly, 2003 .

Reply to Zhang et al.

Peter Donnelly, Matthew Stephens, Nicholas J. Smith, 2001 .

Assigning African elephant DNA to geographic region of origin: applications to the ivory trade.

Matthew Stephens, M. Stephens, E. Ostrander, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Automating resequencing-based detection of insertion-deletion polymorphisms

Matthew Stephens, Deborah A Nickerson, D. Nickerson, 2006, Nature Genetics.

Genome-Wide Association of Lipid-Lowering Response to Statins in Combined Study Populations

Paul T. Williams, Russell A. Wilke, Matthew Stephens, 2010, PloS one.

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding

Matthew Stephens, Jonathan K. Pritchard, Yoav Gilad, 2015, PloS one.

Epigenetic Modifications are Associated with Inter-species Gene Expression Variation in Primates

Emily R. Davenport, Matthew Stephens, Jonathan K. Pritchard, 2014 .

WAVELET-BASED GENETIC ASSOCIATION ANALYSIS OF FUNCTIONAL PHENOTYPES ARISING FROM HIGH-THROUGHPUT SEQUENCING ASSAYS.

Matthew Stephens, Heejung Shim, M. Stephens, 2013, The annals of applied statistics.

Smoothing via Adaptive Shrinkage (smash): denoising Poisson and heteroskedastic Gaussian signals

Matthew Stephens, Zhengrong Xing, M. Stephens, 2016 .

Visualizing spatial population structure with estimated effective migration surfaces

Matthew Stephens, John Novembre, Desislava Petkova, 2014, Nature Genetics.

The genetic architecture of gene expression levels in wild baboons

Matthew Stephens, Jenny Tung, Yoav Gilad, 2014, bioRxiv.

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Mary Goldman, Brian Craft, Jingchun Zhu, 2016, Nature Communications.

Linkage Disequilibrium-Based Quality Control for Large-Scale Genetic Studies

Paul Scheet, Matthew Stephens, 2008, PLoS genetics.

Fast and Accurate Estimation of the Population-Scaled Mutation Rate, θ, From Microsatellite Genotype Data

Matthew Stephens, Arindam RoyChoudhury, M. Stephens, 2007, Genetics.

Epigenetic modifications are associated with inter-species gene expression variation in primates

Xiang Zhou, Emily R. Davenport, Matthew Stephens, 2014, bioRxiv.

False Discovery Rates: A New Deal

Matthew Stephens, 2016 .

Dealing with multimodal posteriors and non-identifiabilit y in mixture models

Matthew Stephens, 1999 .

Comparative RNA sequencing reveals substantial genetic variation in endangered primates.

Páll Melsted, Matthew Stephens, Joseph K. Pickrell, 2012, Genome research.

Dissecting the regulatory architecture of gene expression QTLs

Matthew Stephens, Jean-Baptiste Veyrieras, Jacob F. Degner, 2012, Genome Biology.

Estimating Time to the Common Ancestor for a Beneficial Allele

Matthew Stephens, John Novembre, Graham Coop, 2016, bioRxiv.

STATISTICAL INFERENCE OF TRANSMISSION FIDELITY OF DNA METHYLATION PATTERNS OVER SOMATIC CELL DIVISIONS IN MAMMALS.

Matthew Stephens, Audrey Qiuyan Fu, Charles D. Laird, 2010 .

A large-scale genome-wide enrichment analysis identifies new trait-associated genes, pathways and tissues across 31 human phenotypes*

Matthew Stephens, M. Stephens, X Zhu, 2017, bioRxiv.

Genotyping Polyploids from Messy Sequencing Data

Matthew Stephens, L. F. V. Ferrão, David Gerard, 2018, Genetics.

Automating sequence-based detection and genotyping of SNPs from diploid samples

Paul Scheet, Matthew Stephens, Deborah A Nickerson, 2006, Nature Genetics.

Variation in Human Recombination Rates and Its Genetic Determinants

Yongtao Guan, Matthew Stephens, Molly Przeworski, 2011, PloS one.

Insights into recombination from population genetic variation.

Matthew Stephens, M. Stephens, G. Hellenthal, 2006, Current opinion in genetics & development.

Combating the Illegal Trade in African Elephant Ivory with DNA Forensics

Matthew Stephens, M. Stephens, S. Wasser, 2008, Conservation biology : the journal of the Society for Conservation Biology.

STATISTICAL INFERENCE OF TRANSMISSION FIDELITY OF DNA METHYLATION PATTERNS OVER SOMATIC CELL DIVISIONS IN MAMMALS.

Matthew Stephens, Audrey Qiuyan Fu, M. Stephens, 2010, The annals of applied statistics.

Genetic Analyses Support the Contribution of mRNA N6-methyladenosine (m6A) Modification to Human Disease Heritability

Matthew Stephens, Chuan He, Xin He, 2020, Nature Genetics.

Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases

Andrew B. Nobel, Fred A. Wright, Ivan Rusyn, 2015, Scientific Reports.

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels

Matthew Stephens, Joseph K. Pickrell, Jonathan K. Pritchard, 2012, PLoS genetics.

Interactions between Glucocorticoid Treatment and Cis-Regulatory Polymorphisms Contribute to Cellular Response Phenotypes

Matthew Stephens, Xiaoquan Wen, Francesca Luca, 2011, PLoS genetics.

Practical Issues in Imputation-Based Association Mapping

Yongtao Guan, Matthew Stephens, M. Stephens, 2008, PLoS genetics.

A simple model-based approach to inferring and visualizing cancer mutation signatures

Satoru Miyano, Yuichi Shiraishi, Matthew Stephens, 2015 .

Absence of the TAP2 Human Recombination Hotspot in Chimpanzees

Matthew Stephens, Molly Przeworski, Yoav Gilad, 2004, PLoS biology.

Discovery and characterization of variance QTLs in human induced pluripotent stem cells

Matthew Stephens, John D Blischak, Yoav Gilad, 2019, PLoS genetics.

Empirical Bayes estimation of normal means, accounting for uncertainty in estimated standard errors

Matthew Stephens, Mengyin Lu, M. Stephens, 2019, 1901.10679.

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

John D. Blischak, Matthew Stephens, Yoav Gilad, 2019, bioRxiv.

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

Matthew Stephens, Jonathan K. Pritchard, Yoav Gilad, 2015 .