The University of Chicago Header Logo

Search Result Details

Back to Search Results
This page shows the details of why an item matched the keywords from your search.
Search Results
Stephens, Matthew
One or more keywords matched the following properties of Stephens, Matthew
PropertyValue
full name Matthew Stephens
label Stephens, Matthew
last name Stephens
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 TypeName
Concept Alleles
Concept Amino Acid Sequence
Concept Computer Simulation
Concept Base Sequence
Concept Asia, Southeastern
Concept Drug Synergism
Concept Genes
Concept Genes, Bacterial
Concept Genes, Lethal
Concept Genes, Recessive
Concept Oncogenes
Concept Factor Analysis, Statistical
Concept Molecular Sequence Data
Concept Repetitive Sequences, Nucleic Acid
Concept Selection, Genetic
Concept Sex Characteristics
Concept Stress, Physiological
Concept Species Specificity
Concept Regulatory Sequences, Nucleic Acid
Concept RNA Splicing
Concept Social Problems
Concept Sensitivity and Specificity
Concept Software
Concept Genome
Concept United States
Concept RNA Splice Sites
Concept Transcription Initiation Site
Concept Sequence Alignment
Concept Case-Control Studies
Concept Alternative Splicing
Concept Sequence Analysis, DNA
Concept Protein Structure, Tertiary
Concept Genes, Reporter
Concept Consensus Sequence
Concept Sequence Deletion
Concept Sample Size
Concept Genome, Plant
Concept Simvastatin
Concept Sepsis
Concept Genetic Association Studies
Concept Genetic Pleiotropy
Concept Single-Cell Analysis
Concept Biodiversity
Concept Amino Acid Substitution
Concept Oligonucleotide Array Sequence Analysis
Concept High-Throughput Nucleotide Sequencing
Concept Sex Factors
Concept Models, Statistical
Concept Sterol Regulatory Element Binding Proteins
Concept Open Reading Frames
Concept Genome, Human
Concept Gene Silencing
Concept Endangered Species
Concept Transcriptome
Concept Genome-Wide Association Study
Concept Molecular Sequence Annotation
Concept Induced Pluripotent Stem Cells
Concept Data Interpretation, Statistical
Concept India
Concept Organ Specificity
Concept Signal Transduction
Concept Statistical Distributions
Concept Genes, Neurofibromatosis 1
Concept Conserved Sequence
Concept Sequence Analysis, RNA
Concept Polymorphism, Single Nucleotide
Concept RNA Stability
Concept Quantitative Trait Loci
Concept Genetic Loci
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 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 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 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 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 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 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 BAYESIAN LARGE-SCALE MULTIPLE REGRESSION WITH SUMMARY STATISTICS FROM GENOME-WIDE ASSOCIATION STUDIES.
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 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 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 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 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 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 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 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.
Academic Article Organism-Wide Analysis of Sepsis Reveals Mechanisms of Systemic Inflammation.
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 GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.
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 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 Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions.
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 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.
Academic Article Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca.
Search Criteria
  • India
  • s
  • biodiversity