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Stephens, Matthew

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

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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.

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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.

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

Item Type	Name
Concept	Amidinotransferases
Concept	Agriculture
Concept	Americas
Concept	Adenosine
Concept	Africa, Western
Concept	Adolescent
Concept	Birds
Concept	Africa
Concept	Aged
Concept	Amino Acids
Concept	Algorithms
Concept	Alleles
Concept	Amino Acid Sequence
Concept	Adult
Concept	Antineoplastic Agents
Concept	Asia
Concept	Cell Line, Transformed
Concept	Animals
Concept	Hypoxia
Concept	Carcinoma
Concept	Commerce
Concept	Computer Simulation
Concept	Arthritis, Rheumatoid
Concept	Asthma
Concept	Anti-Inflammatory Agents
Concept	B-Lymphocytes
Concept	Base Sequence
Concept	Bayes Theorem
Concept	DNA Damage
Concept	Pan troglodytes
Concept	China
Concept	Calibration
Concept	Asia, Southeastern
Concept	Bacterial Proteins
Concept	Blastocyst
Concept	Biometry
Concept	Brain
Concept	Child
Concept	Cells
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	Cholesterol
Concept	Diabetes Mellitus, Type 1
Concept	Diabetes Mellitus, Type 2
Concept	Homozygote
Concept	Crime
Concept	Disease
Concept	DNA Transposable Elements
Concept	DNA-Binding Proteins
Concept	DNA, Mitochondrial
Concept	Dexamethasone
Concept	Drug Synergism
Concept	Elephants
Concept	Indians, North American
Concept	Interleukin-2
Concept	Emigration and Immigration
Concept	Crohn Disease
Concept	Diploidy
Concept	Drosophila
Concept	DNA Mutational Analysis
Concept	Dentin
Concept	Europe
Concept	Gene Frequency
Concept	Glucocorticoids
Concept	Chromosomes, Human, Pair 17
Concept	Chromosomes, Human, Pair 19
Concept	Exons
Concept	Dextroamphetamine
Concept	DNA
Concept	Double-Blind Method
Concept	Drosophila melanogaster
Concept	Introns
Concept	Environment
Concept	Methyltransferases
Concept	Gene Expression Regulation
Concept	Genetic Techniques
Concept	Gene Conversion
Concept	Genes
Concept	Genes, Bacterial
Concept	Genes, Lethal
Concept	Genetics, Behavioral
Concept	False Positive Reactions
Concept	Terminology as Topic
Concept	Genes, Recessive
Concept	Genetic Complementation Test
Concept	DNA (Cytosine-5-)-Methyltransferases
Concept	Oncogenes
Concept	Geography
Concept	Heptanoic Acids
Concept	Factor Analysis, Statistical
Concept	Image Interpretation, Computer-Assisted
Concept	Inflammation
Concept	Italy
Concept	Genetics, Medical
Concept	Genetics, Population
Concept	Language
Concept	Leukocytes, Mononuclear
Concept	Lipoproteins, LDL
Concept	Mathematical Computing
Concept	Models, Molecular
Concept	Lipids
Concept	Macaca mulatta
Concept	Muscular Diseases
Concept	Myocardial Infarction
Concept	Models, Genetic
Concept	Models, Theoretical
Concept	Noise
Concept	Polyploidy
Concept	Markov Chains
Concept	Molecular Sequence Data
Concept	Monte Carlo Method
Concept	Middle Aged
Concept	Recombination, Genetic
Concept	Repetitive Sequences, Nucleic Acid
Concept	Molecular Biology
Concept	Mutation
Concept	Nigeria
Concept	Lipopolysaccharides
Concept	Liver
Concept	Selection, Genetic
Concept	Pedigree
Concept	Pattern Recognition, Automated
Concept	Sex Characteristics
Concept	Polynesia
Concept	Stress, Physiological
Concept	Polymorphism, Genetic
Concept	Oxygen
Concept	Parent-Child Relations
Concept	Female
Concept	Probability
Concept	Pregnanolone
Concept	Primates
Concept	Protein Binding
Concept	Genetic Markers
Concept	Hybridization, Genetic
Concept	Transcription Factors
Concept	Regression Analysis
Concept	Haplotypes
Concept	Risk Factors
Concept	Quality Control
Concept	Y Chromosome
Concept	Interferon-gamma
Concept	Species Specificity
Concept	Regulatory Sequences, Nucleic Acid
Concept	Ribosomes
Concept	RNA Splicing
Concept	Cadherins
Concept	Interleukin-6
Concept	Social Problems
Concept	RNA
Concept	Sensitivity and Specificity
Concept	Histones
Concept	Humans
Concept	Cluster Analysis
Concept	Linear Models
Concept	Transcription, Genetic
Concept	Protein Biosynthesis
Concept	Software
Concept	Transients and Migrants
Concept	Interferon Type I
Concept	Genome
Concept	Uganda
Concept	United States
Concept	Tumor Necrosis Factor-alpha
Concept	Terminator Regions, Genetic
Concept	Genetic Variation
Concept	Male
Concept	Multifactorial Inheritance
Concept	RNA Splice Sites
Concept	NF-kappa B
Concept	Transcription Initiation Site
Concept	Principal Component Analysis
Concept	DNA Modification Methylases
Concept	Likelihood Functions
Concept	Artifacts
Concept	NAD(P)H Dehydrogenase (Quinone)
Concept	Causality
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	Genes, Reporter
Concept	National Institutes of Health (U.S.)
Concept	Consensus Sequence
Concept	Helicobacter Infections
Concept	Immediate-Early Proteins
Concept	Sequence Deletion
Concept	Gene Expression Regulation, Developmental
Concept	DNA, Complementary
Concept	Sample Size
Concept	Evolution, Molecular
Concept	Genome, Plant
Concept	Hepatocyte Nuclear Factor 1-alpha
Concept	Simvastatin
Concept	Sepsis
Concept	Fragile X Mental Retardation Protein
Concept	Edar Receptor
Concept	Genetic Association Studies
Concept	Genetic Pleiotropy
Concept	Single-Cell Analysis
Concept	Gene-Environment Interaction
Concept	Ipomoea batatas
Concept	Population Groups
Concept	Biodiversity
Concept	Mitogen-Activated Protein Kinase 14
Concept	Amino Acid Substitution
Concept	Response Elements
Concept	DNA Footprinting
Concept	Internet
Concept	Oligonucleotide Array Sequence Analysis
Concept	Hydroxymethylglutaryl-CoA Reductase Inhibitors
Concept	Databases, Genetic
Concept	Myocytes, Cardiac
Concept	Gene Expression Profiling
Concept	Information Dissemination
Concept	Placebos
Concept	Population Density
Concept	Population Dynamics
Concept	Promoter Regions, Genetic
Concept	Mice
Concept	Gene Flow
Concept	Receptors, Glucocorticoid
Concept	Pyrroles
Concept	Research Design
Concept	RNA, Messenger
Concept	Coffea
Concept	Data Mining
Concept	High-Throughput Nucleotide Sequencing
Concept	Genotyping Techniques
Concept	Tropical Climate
Concept	Sex Factors
Concept	Temperature
Concept	Models, Statistical
Concept	Sterol Regulatory Element Binding Proteins
Concept	Multivariate Analysis
Concept	Open Reading Frames
Concept	Helicobacter pylori
Concept	Reproducibility of Results
Concept	Linkage Disequilibrium
Concept	Genome, Human
Concept	Odds Ratio
Concept	ATP-Binding Cassette Transporters
Concept	Arabidopsis
Concept	DNA Methylation
Concept	Molecular Epidemiology
Concept	Antiporters
Concept	Gene Silencing
Concept	Gene Knockdown Techniques
Concept	Animal Migration
Concept	Genetic Heterogeneity
Concept	Microsatellite Repeats
Concept	Endangered Species
Concept	Workflow
Concept	Transcriptome
Concept	Genome-Wide Association Study
Concept	Mendelian Randomization Analysis
Concept	Molecular Sequence Annotation
Concept	Mutation Rate
Concept	Cell Line, Tumor
Concept	Lipid Metabolism
Concept	Proto-Oncogene Proteins c-fyn
Concept	Toll-Like Receptors
Concept	Induced Pluripotent Stem Cells
Concept	Epigenomics
Concept	Automation
Concept	Cell Line
Concept	Cells, Cultured
Concept	Central African Republic
Concept	Chromatin
Concept	Chromosomes
Concept	Cytosine
Concept	Data Interpretation, Statistical
Concept	Deoxyribonuclease I
Concept	Genetic Testing
Concept	Genotype
Concept	Heterozygote
Concept	Immunity, Innate
Concept	India
Concept	Kinetics
Concept	Genetic Linkage
Concept	Lymphocytes
Concept	Models, Biological
Concept	Monocytes
Concept	Neoplasms
Concept	Organ Specificity
Concept	Papio
Concept	Phenotype
Concept	Phylogeny
Concept	Population
Concept	Democratic Republic of the Congo
Concept	Signal Transduction
Concept	Transcriptional Activation
Concept	Statistical Distributions
Concept	Cytokines
Concept	Genes, Neurofibromatosis 1
Concept	Pravastatin
Concept	Conserved Sequence
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	MicroRNAs
Concept	Quantitative Trait Loci
Concept	Genetic Drift
Concept	Chromosomes, Human, X
Concept	Epigenesis, Genetic
Concept	Genetic Loci
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	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	The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.
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	Response to Cavalli-Sforza interview [Human Biology 82(3):245-266 (June 2010)].
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	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	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	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	fastSTRUCTURE: variational inference of population structure in large SNP data sets.
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	Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
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	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	USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA.
Academic Article	False discovery rates: a new deal.
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	Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation.
Academic Article	Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.
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	A new sequence logo plot to highlight enrichment and depletion.
Academic Article	Estimating recent migration and population-size surfaces.
Academic Article	Discovery and characterization of variance QTLs in human induced pluripotent stem cells.
Academic Article	Regional influences on community structure across the tropical-temperate divide.
Academic Article	Detailed modeling of positive selection improves detection of cancer driver genes.
Academic Article	Bayesian multivariate reanalysis of large genetic studies identifies many new associations.
Academic Article	Creating and sharing reproducible research code the workflowr way.
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	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	Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace's Line.
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	DNA, Ancient
Concept	DNA (Cytosine-5-)-Methyltransferase 1
Concept	RNA, Long Noncoding
Concept	Animal Distribution
Concept	Carcinogenesis
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	GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.
Academic Article	A simple new approach to variable selection in regression, with application to genetic fine mapping.
Academic Article	Discussion of "Confidence Intervals for Nonparametric Empirical Bayes Analysis".
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	UNIFYING AND GENERALIZING METHODS FOR REMOVING UNWANTED VARIATION BASED ON NEGATIVE CONTROLS.
Academic Article	Flexible Signal Denoising via Flexible Empirical Bayes Shrinkage.
Academic Article	Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits.
Academic Article	Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca.

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