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Stephens, Matthew

One or more keywords matched the following properties of Stephens, Matthew

Property	Value
overview	My lab works on a wide variety of problems at the interface of Statistics and Genetics. We often tackle problems where novel statistical methods are required, or can learn something new compared with existing approaches. Thus, much of our research involves developing new statistical methodology, many of which have a non-trivial computational component. People in my lab tend to come from a quantitative background (e.g., Statistics, Computer Science), with varying levels of formal or informal Biology training.
preferred title	Professor

Property

Value

overview

My lab works on a wide variety of problems at the interface of Statistics and Genetics. We often tackle problems where novel statistical methods are required, or can learn something new compared with existing approaches. Thus, much of our research involves developing new statistical methodology, many of which have a non-trivial computational component. People in my lab tend to come from a quantitative background (e.g., Statistics, Computer Science), with varying levels of formal or informal Biology training.

preferred title

Professor

One or more keywords matched the following items that are connected to Stephens, Matthew

Item Type	Name
Concept	Hypoxia
Concept	Pan troglodytes
Concept	Bacterial Proteins
Concept	Biometry
Concept	Biological Evolution
Concept	Fertility
Concept	Coenzyme A
Concept	Cell Cycle
Concept	Chromosome Mapping
Concept	Chromosomes, Human, Pair 7
Concept	C-Reactive Protein
Concept	Conservation of Natural Resources
Concept	Crossing Over, Genetic
Concept	Homozygote
Concept	Crime
Concept	DNA-Binding Proteins
Concept	Drug Synergism
Concept	Diploidy
Concept	DNA Mutational Analysis
Concept	Glucocorticoids
Concept	Chromosomes, Human, Pair 17
Concept	Chromosomes, Human, Pair 19
Concept	Double-Blind Method
Concept	Environment
Concept	Gene Expression Regulation
Concept	Genetic Techniques
Concept	Gene Conversion
Concept	Genetics, Behavioral
Concept	False Positive Reactions
Concept	Genes, Recessive
Concept	Genetic Complementation Test
Concept	Geography
Concept	Heptanoic Acids
Concept	Image Interpretation, Computer-Assisted
Concept	Genetics, Medical
Concept	Genetics, Population
Concept	Models, Theoretical
Concept	Noise
Concept	Polyploidy
Concept	Recombination, Genetic
Concept	Molecular Biology
Concept	Mutation
Concept	Selection, Genetic
Concept	Pedigree
Concept	Pattern Recognition, Automated
Concept	Sex Characteristics
Concept	Polynesia
Concept	Stress, Physiological
Concept	Polymorphism, Genetic
Concept	Parent-Child Relations
Concept	Female
Concept	Probability
Concept	Pregnanolone
Concept	Primates
Concept	Protein Binding
Concept	Genetic Markers
Concept	Hybridization, Genetic
Concept	Haplotypes
Concept	Species Specificity
Concept	RNA Splicing
Concept	Social Problems
Concept	Histones
Concept	Humans
Concept	Transcription, Genetic
Concept	Protein Biosynthesis
Concept	Genetic Variation
Concept	Male
Concept	Multifactorial Inheritance
Concept	NF-kappa B
Concept	Principal Component Analysis
Concept	Artifacts
Concept	NAD(P)H Dehydrogenase (Quinone)
Concept	Poisson Distribution
Concept	Gene Expression
Concept	Sequence Alignment
Concept	Case-Control Studies
Concept	Human Genome Project
Concept	RNA Interference
Concept	Alternative Splicing
Concept	Sequence Analysis, DNA
Concept	Protein Structure, Tertiary
Concept	National Institutes of Health (U.S.)
Concept	Helicobacter Infections
Concept	Immediate-Early Proteins
Concept	Gene Expression Regulation, Developmental
Concept	Evolution, Molecular
Concept	Genome, Plant
Concept	Hepatocyte Nuclear Factor 1-alpha
Concept	Fragile X Mental Retardation Protein
Concept	Genetic Association Studies
Concept	Genetic Pleiotropy
Concept	Single-Cell Analysis
Concept	Gene-Environment Interaction
Concept	Population Groups
Concept	Mitogen-Activated Protein Kinase 14
Concept	Amino Acid Substitution
Concept	DNA Footprinting
Concept	Oligonucleotide Array Sequence Analysis
Concept	Hydroxymethylglutaryl-CoA Reductase Inhibitors
Concept	Gene Expression Profiling
Concept	Placebos
Concept	Population Density
Concept	Population Dynamics
Concept	Promoter Regions, Genetic
Concept	Gene Flow
Concept	Pyrroles
Concept	Research Design
Concept	High-Throughput Nucleotide Sequencing
Concept	Genotyping Techniques
Concept	Tropical Climate
Concept	Sterol Regulatory Element Binding Proteins
Concept	Helicobacter pylori
Concept	Genome, Human
Concept	DNA Methylation
Concept	Molecular Epidemiology
Concept	Gene Silencing
Concept	Gene Knockdown Techniques
Concept	Genetic Heterogeneity
Concept	Genome-Wide Association Study
Concept	Mendelian Randomization Analysis
Concept	Molecular Sequence Annotation
Concept	Lipid Metabolism
Concept	Proto-Oncogene Proteins c-fyn
Concept	Induced Pluripotent Stem Cells
Concept	Epigenomics
Concept	Chromatin
Concept	Genetic Testing
Concept	Genotype
Concept	Heterozygote
Concept	Immunity, Innate
Concept	Genetic Linkage
Concept	Organ Specificity
Concept	Papio
Concept	Phenotype
Concept	Phylogeny
Concept	Population
Concept	Signal Transduction
Concept	Transcriptional Activation
Concept	Pravastatin
Concept	Sequence Analysis, RNA
Concept	Computational Biology
Concept	Quantitative Trait, Heritable
Concept	Genetic Predisposition to Disease
Concept	Polymorphism, Single Nucleotide
Concept	RNA Stability
Concept	Genomics
Concept	Genetic Drift
Concept	Chromosomes, Human, X
Concept	Epigenesis, Genetic
Concept	HapMap Project
Academic Article	Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.
Academic Article	Traces of human migrations in Helicobacter pylori populations.
Academic Article	The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium.
Academic Article	Genome-wide detection and characterization of positive selection in human populations.
Academic Article	Practical issues in imputation-based association mapping.
Academic Article	RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
Academic Article	Genome-wide association of lipid-lowering response to statins in combined study populations.
Academic Article	Sex-specific and lineage-specific alternative splicing in primates.
Academic Article	Understanding mechanisms underlying human gene expression variation with RNA sequencing.
Academic Article	Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
Academic Article	Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes.
Academic Article	Genome-wide efficient mixed-model analysis for association studies.
Academic Article	Fast and accurate genotype imputation in genome-wide association studies through pre-phasing.
Academic Article	Dissecting the regulatory architecture of gene expression QTLs.
Academic Article	Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein.
Academic Article	The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.
Academic Article	Inferring weak population structure with the assistance of sample group information.
Academic Article	Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
Academic Article	Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation.
Academic Article	Next generation analytic tools for large scale genetic epidemiology studies of complex diseases.
Academic Article	A second generation human haplotype map of over 3.1 million SNPs.
Academic Article	Functional comparison of innate immune signaling pathways in primates.
Academic Article	Variation in human recombination rates and its genetic determinants.
Academic Article	Comparative RNA sequencing reveals substantial genetic variation in endangered primates.
Academic Article	DNase?I sensitivity QTLs are a major determinant of human expression variation.
Academic Article	Absence of the TAP2 human recombination hotspot in chimpanzees.
Academic Article	High-resolution mapping of expression-QTLs yields insight into human gene regulation.
Academic Article	Interpreting principal component analyses of spatial population genetic variation.
Academic Article	Genes mirror geography within Europe.
Academic Article	Genetic, functional and molecular features of glucocorticoid receptor binding.
Academic Article	Response to Cavalli-Sforza interview [Human Biology 82(3):245-266 (June 2010)].
Academic Article	Polygenic modeling with bayesian sparse linear mixed models.
Academic Article	A statistical framework for joint eQTL analysis in multiple tissues.
Academic Article	Automating resequencing-based detection of insertion-deletion polymorphisms.
Academic Article	Mangravite et al. reply.
Academic Article	Insights into recombination from population genetic variation.
Academic Article	Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis.
Academic Article	Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion.
Academic Article	Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.
Academic Article	msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots.
Academic Article	Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data.
Academic Article	Probabilistic segmentation and intensity estimation for microarray images.
Academic Article	Epigenetic modifications are associated with inter-species gene expression variation in primates.
Academic Article	A unified framework for association analysis with multiple related phenotypes.
Academic Article	Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban.
Academic Article	Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns.
Academic Article	An estimate of the average number of recessive lethal mutations carried by humans.
Academic Article	A statin-dependent QTL for GATM expression is associated with statin-induced myopathy.
Academic Article	Imputation-based analysis of association studies: candidate regions and quantitative traits.
Academic Article	The genetic architecture of gene expression levels in wild baboons.
Academic Article	Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease.
Academic Article	A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians.
Academic Article	Bayesian statistical methods for genetic association studies.
Academic Article	fastSTRUCTURE: variational inference of population structure in large SNP data sets.
Academic Article	A comparison of phasing algorithms for trios and unrelated individuals.
Academic Article	A comparison of bayesian methods for haplotype reconstruction from population genotype data.
Academic Article	Automating sequence-based detection and genotyping of SNPs from diploid samples.
Academic Article	A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.
Academic Article	Linkage disequilibrium-based quality control for large-scale genetic studies.
Academic Article	Differential gene induction by type I and type II interferons and their combination.
Academic Article	Evidence for substantial fine-scale variation in recombination rates across the human genome.
Academic Article	Efficient multivariate linear mixed model algorithms for genome-wide association studies.
Academic Article	Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
Academic Article	msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.
Academic Article	A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures.
Academic Article	Visualizing spatial population structure with estimated effective migration surfaces.
Academic Article	Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.
Academic Article	New evidence for hybrid zones of forest and savanna elephants in Central and West Africa.
Academic Article	Assigning African elephant DNA to geographic region of origin: applications to the ivory trade.
Academic Article	STATISTICAL INFERENCE OF TRANSMISSION FIDELITY OF DNA METHYLATION PATTERNS OVER SOMATIC CELL DIVISIONS IN MAMMALS.
Academic Article	BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS.
Academic Article	USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA.
Academic Article	Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances.
Academic Article	Inference of population structure using multilocus genotype data: dominant markers and null alleles.
Academic Article	Promoter shape varies across populations and affects promoter evolution and expression noise.
Academic Article	Visualizing the structure of RNA-seq expression data using grade of membership models.
Academic Article	Correction: Visualizing the structure of RNA-seq expression data using grade of membership models.
Academic Article	Estimating Time to the Common Ancestor for a Beneficial Allele.
Academic Article	WAVELET-BASED GENETIC ASSOCIATION ANALYSIS OF FUNCTIONAL PHENOTYPES ARISING FROM HIGH-THROUGHPUT SEQUENCING ASSAYS.
Academic Article	Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes.
Academic Article	Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.
Academic Article	Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions.
Academic Article	Inference and visualization of DNA damage patterns using a grade of membership model.
Academic Article	Genotyping Polyploids from Messy Sequencing Data.
Academic Article	Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models.
Academic Article	A new sequence logo plot to highlight enrichment and depletion.
Academic Article	Estimating recent migration and population-size surfaces.
Academic Article	Correction: A Unified Framework for Association Analysis with Multiple Related Phenotypes.
Academic Article	Discovery and characterization of variance QTLs in human induced pluripotent stem cells.
Academic Article	Detailed modeling of positive selection improves detection of cancer driver genes.
Academic Article	Evanescent field response to immunoassay layer thickness on planar waveguides.
Academic Article	Bayesian multivariate reanalysis of large genetic studies identifies many new associations.
Academic Article	Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis.
Academic Article	Publisher Correction: Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics.
Academic Article	Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics.
Academic Article	Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability.
Academic Article	Cell type-specific genetic regulation of gene expression across human tissues.
Academic Article	The impact of sex on gene expression across human tissues.
Academic Article	Exploiting the GTEx resources to decipher the mechanisms at GWAS loci.
Academic Article	Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes.
Academic Article	A Fast Algorithm for Maximum Likelihood Estimation of Mixture Proportions Using Sequential Quadratic Programming.
Academic Article	Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis.
Academic Article	Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region.
Academic Article	Fine-mapping from summary data with the "Sum of Single Effects" model.
Concept	Plant Breeding
Concept	Grassland
Concept	Forests
Grant	Multipoint and significance methods for genome-wide association studies
Grant	Statistical analysis of gene expression quantitative trait loci (eQTL)
Grant	Genome analysis: statistical methods and applications
Academic Article	The Bayesian lens and Bayesian blinkers.
Academic Article	A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes.
Academic Article	DISSECTING TUMOR TRANSCRIPTIONAL HETEROGENEITY FROM SINGLE-CELL RNA-SEQ DATA BY GENERALIZED BINARY COVARIANCE DECOMPOSITION.
Academic Article	GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.
Academic Article	A pairwise cytokine code explains the organism-wide response to sepsis.
Academic Article	Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits.

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Dehydrogenase
Quinone