Scholars@Duke
Andrew Scott Allen

Andrew Scott Allen

Professor of Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Integrative Genomics
asallen@duke.edu
Duke Box 103854, Durham, NC 27710
3 Genome Ct, 1245 MSRB III, Durham, NC 27705

Scholarly Works - Journal articles

Modeling gene regulatory perturbations via deep learning from high-throughput reporter assays.

Journal article bioRxiv · March 31, 2026 Assessing likely variant effects on phenotypes is of critical importance in diagnostic settings, and while much progress has been made in interpreting genic mutations based on our understanding of coding sequence, noncoding variants can be much more challe ... Full text Link to item Cite

Cell modeling and rescue of a novel noncoding genetic cause of glycogen storage disease IX.

Journal article Genet Med Open · 2026 PURPOSE: Delayed diagnosis of Mendelian disease prevents early therapeutic intervention that could improve symptoms and prognosis. One major contributing challenge is functional interpretation of noncoding variants that alter splicing. Here, we aimed to be ... Full text Link to item Cite

Bayesian estimation of allele-specific expression in the presence of phasing uncertainty.

Journal article Bioinformatics · June 2, 2025 MOTIVATION: Allele-specific expression (ASE) analyses aim to detect imbalanced expression of maternal versus paternal copies of an autosomal gene. Such allelic imbalance can result from a variety of cis-acting causes, including disruptive mutations within ... Full text Link to item Cite

Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER.

Journal article Cell Genom · February 12, 2025 Single-cell RNA sequencing CRISPR (perturb-seq) screens enable high-throughput investigation of the genome, allowing for characterization of thousands of genomic perturbations on gene expression. Ambient gRNAs, which are contaminating gRNAs, are a major so ... Full text Link to item Cite

Promoter Deletion Leading to Allele Specific Expression in a Genetically Unsolved Case of Primary Ciliary Dyskinesia.

Journal article Am J Med Genet A · February 2025 Variation in the non-coding genome represents an understudied mechanism of disease and it remains challenging to predict if single nucleotide variants, small insertions and deletions, or structural variants in non-coding genomic regions will be detrimental ... Full text Link to item Cite

Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER.

Journal article bioRxiv · September 4, 2024 Recent technological developments in single-cell RNA-seq CRISPR screens enable high-throughput investigation of the genome. Through transduction of a gRNA library to a cell population followed by transcriptomic profiling by scRNA-seq, it is possible to cha ... Full text Link to item Cite

Deciphering the impact of genomic variation on function.

Journal article Nature · September 2024 Our genomes influence nearly every aspect of human biology-from molecular and cellular functions to phenotypes in health and disease. Studying the differences in DNA sequence between individuals (genomic variation) could reveal previously unknown mechanism ... Full text Open Access Link to item Cite

Bayesian Estimation of Allele-Specific Expression in the Presence of Phasing Uncertainty.

Journal article bioRxiv · August 13, 2024 MOTIVATION: Allele-specific expression (ASE) analyses aim to detect imbalanced expression of maternal versus paternal copies of an autosomal gene. Such allelic imbalance can result from a variety of cis-acting causes, including disruptive mutations within ... Full text Link to item Cite

Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome.

Journal article BMC Genomics · March 12, 2024 BACKGROUND: There are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen ... Full text Link to item Cite

The role of copy number variants in the genetic architecture of common familial epilepsies.

Journal article Epilepsia · March 2024 OBJECTIVE: Copy number variants (CNVs) contribute to genetic risk and genetic etiology of both rare and common epilepsies. Whereas many studies have explored the role of CNVs in sporadic or severe cases, fewer have been done in familial generalized and foc ... Full text Link to item Cite

DYNATE: Localizing rare-variant association regions via multiple testing embedded in an aggregation tree.

Journal article Genet Epidemiol · February 2024 Rare-variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggr ... Full text Link to item Cite

Ultra-rare genetic variation in relapsing polychondritis: a whole-exome sequencing study.

Journal article Ann Rheum Dis · January 11, 2024 OBJECTIVE: Relapsing polychondritis (RP) is a systemic inflammatory disease of unknown aetiology. The objective of this study was to examine the contribution of rare genetic variations to RP. METHODS: We performed a case-control exome-wide rare variant ass ... Full text Link to item Cite

Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens.

Journal article Nat Genet · December 2023 Clinical response to adoptive T cell therapies is associated with the transcriptional and epigenetic state of the cell product. Thus, discovery of regulators of T cell gene networks and their corresponding phenotypes has potential to improve T cell therapi ... Full text Link to item Cite

Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations.

Journal article Nat Commun · November 2, 2023 Cerebral Cavernous Malformations (CCMs) are vascular malformations of the central nervous system which can lead to moderate to severe neurological phenotypes in patients. A majority of CCM lesions are driven by a cancer-like three-hit mutational mechanism, ... Full text Link to item Cite

Prevalence and significance of clonal hematopoiesis of indeterminate potential in lung transplant recipients.

Journal article BMC Pulm Med · October 30, 2023 BACKGROUND: Clonal hematopoiesis of indeterminate potential (CHIP), the age-related acquisition of somatic mutations that leads to an expanded blood cell clone, has been associated with development of a pro-inflammatory state. An enhanced or dysregulated i ... Full text Link to item Cite

Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals.

Journal article Nat Commun · July 20, 2023 Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure disorders share genetic risk factors, we pooled CNV data from 10,590 individuals with seizure disorders, 16 ... Full text Link to item Cite

Analysing an allelic series of rare missense variants of CACNA1I in a Swedish schizophrenia cohort.

Journal article Brain · June 3, 2022 CACNA1I is implicated in the susceptibility to schizophrenia by large-scale genetic association studies of single nucleotide polymorphisms. However, the channelopathy of CACNA1I in schizophrenia is unknown. CACNA1I encodes CaV3.3, a neuronal voltage-gated ... Full text Link to item Cite

Ancestry adjustment improves genome-wide estimates of regional intolerance.

Journal article Genetics · May 31, 2022 Genomic regions subject to purifying selection are more likely to carry disease-causing mutations than regions not under selection. Cross species conservation is often used to identify such regions but with limited resolution to detect selection on short e ... Full text Link to item Cite

Novel Fluorescence-Based High-Throughput FLIPR Assay Utilizing Membrane-Tethered Genetic Calcium Sensors to Identify T-Type Calcium Channel Modulators.

Journal article ACS Pharmacol Transl Sci · March 11, 2022 T-type voltage-gated Ca2+ channels have been implicated in many human disorders, and there has been increasing interest in developing highly selective and potent T-type Ca2+ channel modulators for potential clinical use. However, the unique biophysical pro ... Full text Link to item Cite

Association of ultra-rare coding variants with genetic generalized epilepsy: A case-control whole exome sequencing study.

Journal article Epilepsia · March 2022 OBJECTIVE: We aimed to identify genes associated with genetic generalized epilepsy (GGE) by combining large cohorts enriched with individuals with a positive family history. Secondarily, we set out to compare the association of genes independently with fam ... Full text Link to item Cite

Focused goodness of fit tests for gene set analyses.

Journal article Brief Bioinform · January 17, 2022 Gene set-based signal detection analyses are used to detect an association between a trait and a set of genes by accumulating signals across the genes in the gene set. Since signal detection is concerned with identifying whether any of the genes in the gen ... Full text Link to item Cite

A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors.

Journal article Bioinformatics · December 22, 2021 MOTIVATION: Conservation is broadly used to identify biologically important (epi)genomic regions. In the case of tumor growth, preferential conservation of DNA methylation can be used to identify areas of particular functional importance to the tumor. Howe ... Full text Link to item Cite

Targeted long-read sequencing identifies missing disease-causing variation.

Journal article Am J Hum Genet · August 5, 2021 Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate stru ... Full text Link to item Cite

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism.

Journal article Hum Genomics · July 13, 2021 BACKGROUND: Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observa ... Full text Link to item Cite

Sub-genic intolerance, ClinVar, and the epilepsies: A whole-exome sequencing study of 29,165 individuals.

Journal article Am J Hum Genet · June 3, 2021 Both mild and severe epilepsies are influenced by variants in the same genes, yet an explanation for the resulting phenotypic variation is unknown. As part of the ongoing Epi25 Collaboration, we performed a whole-exome sequencing analysis of 13,487 epileps ... Full text Link to item Cite

Correcting signal biases and detecting regulatory elements in STARR-seq data.

Journal article Genome Res · May 2021 High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure regulatory element activity across the entire human genome at once. The resulting data, however, present substantial ... Full text Link to item Cite

Diverse genetic causes of polymicrogyria with epilepsy.

Journal article Epilepsia · April 2021 OBJECTIVE: We sought to identify novel genes and to establish the contribution of known genes in a large cohort of patients with nonsyndromic sporadic polymicrogyria and epilepsy. METHODS: We enrolled participants with polymicrogyria and their parents thro ... Full text Link to item Cite

Neurogranin, Encoded by the Schizophrenia Risk Gene NRGN, Bidirectionally Modulates Synaptic Plasticity via Calmodulin-Dependent Regulation of the Neuronal Phosphoproteome.

Journal article Biol Psychiatry · February 1, 2021 BACKGROUND: Neurogranin (Ng), encoded by the schizophrenia risk gene NRGN, is a calmodulin-binding protein enriched in the postsynaptic compartments, and its expression is reduced in the postmortem brains of patients with schizophrenia. Experience-dependen ... Full text Link to item Cite

Casual Genetic Variants in Stillbirth

Journal article Obstetrical and Gynecological Survey · February 1, 2021 Full text Cite

Secondary analysis of case-control association studies: Insights on weighting-based inference motivate a new specification test.

Journal article Stat Med · September 30, 2020 Case-control sampling is frequently used in genetic association studies to examine the relationship between disease and genetic exposures. Such designs usually collect extensive information on phenotypes beyond the primary disease, whose associations with ... Full text Link to item Cite

Causal Genetic Variants in Stillbirth.

Journal article N Engl J Med · September 17, 2020 BACKGROUND: In the majority of cases, the cause of stillbirth remains unknown despite detailed clinical and laboratory evaluation. Approximately 10 to 20% of stillbirths are attributed to chromosomal abnormalities. However, the causal nature of single-nucl ... Full text Link to item Cite

Incorporating external information to improve sparse signal detection in rare-variant gene-set-based analyses.

Journal article Genet Epidemiol · June 2020 Featured Publication Gene-set analyses are used to assess whether there is any evidence of association with disease among a set of biologically related genes. Such an analysis typically treats all genes within the sets similarly, even though there is substantial, external, inf ... Full text Link to item Cite

Arfgef1 haploinsufficiency in mice alters neuronal endosome composition and decreases membrane surface postsynaptic GABAA receptors.

Journal article Neurobiol Dis · February 2020 Featured Publication ARFGEF1 encodes a guanine exchange factor involved in intracellular vesicle trafficking, and is a candidate gene for childhood genetic epilepsies. To model ARFGEF1 haploinsufficiency observed in a recent Lennox Gastaut Syndrome patient, we studied a frames ... Full text Link to item Cite

Bayesian estimation of genetic regulatory effects in high-throughput reporter assays.

Journal article Bioinformatics · January 15, 2020 Featured Publication MOTIVATION: High-throughput reporter assays dramatically improve our ability to assign function to noncoding genetic variants, by measuring allelic effects on gene expression in the controlled setting of a reporter gene. Unlike genetic association tests, s ... Full text Link to item Cite

Rare-variant collapsing analyses for complex traits: guidelines and applications.

Journal article Nat Rev Genet · December 2019 Featured Publication The first phase of genome-wide association studies (GWAS) assessed the role of common variation in human disease. Advances optimizing and economizing high-throughput sequencing have enabled a second phase of association studies that assess the contribution ... Full text Link to item Cite

Quantitative analysis of phenotypic elements augments traditional electroclinical classification of common familial epilepsies.

Journal article Epilepsia · November 2019 Featured Publication OBJECTIVE: Classification of epilepsy into types and subtypes is important for both clinical care and research into underlying disease mechanisms. A quantitative, data-driven approach may augment traditional electroclinical classification and shed new ligh ... Full text Link to item Cite

Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach.

Journal article Genome Biol Evol · October 1, 2019 Featured Publication Changes in transcriptional regulation are thought to be a major contributor to the evolution of phenotypic traits, but the contribution of changes in chromatin accessibility to the evolution of gene expression remains almost entirely unknown. To address th ... Full text Link to item Cite

Exome-Based Rare-Variant Analyses in CKD.

Journal article J Am Soc Nephrol · June 2019 Featured Publication BACKGROUND: Studies have identified many common genetic associations that influence renal function and all-cause CKD, but these explain only a small fraction of variance in these traits. The contribution of rare variants has not been systematically examine ... Full text Link to item Cite

Efficient estimation of grouped survival models.

Journal article BMC Bioinformatics · May 28, 2019 Featured Publication BACKGROUND: Time- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For example, drug-induced toxicities a ... Full text Link to item Cite

A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS.

Journal article Genome Res · May 2019 Large-scale sequencing efforts in amyotrophic lateral sclerosis (ALS) have implicated novel genes using gene-based collapsing methods. However, pathogenic mutations may be concentrated in specific genic regions. To address this, we developed two collapsing ... Full text Link to item Cite

Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons.

Journal article FASEB J · April 2019 Overexpression of mouse neurogenin ( Neurog) 2 alone or in combination with mouse Neurog2/1 in human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) can rapidly produce high-yield excitatory neurons. Here, we report a detaile ... Full text Link to item Cite

Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance.

Journal article Am J Hum Genet · February 7, 2019 Featured Publication Different parts of a gene can be of differential importance to development and health. This regional heterogeneity is also apparent in the distribution of disease-associated mutations, which often cluster in particular regions of disease-associated genes. ... Full text Link to item Cite

Genome-wide association study (GWAS) of human host factors influencing viral severity of herpes simplex virus type 2 (HSV-2).

Journal article Genes Immun · February 2019 Featured Publication Herpes simplex virus type 2 (HSV-2) is an incurable viral infection with severity ranging from asymptomatic to frequent recurrences. The viral shedding rate has been shown as a reproducible HSV-2 severity end point that correlates with lesion rates. We use ... Full text Link to item Cite

Family-based association tests for rare variants with censored traits.

Journal article PLoS One · 2019 Featured Publication We propose a set of family-based burden and kernel tests for censored traits (FamBAC and FamKAC). Here, censored traits refer to time-to-event outcomes, for instance, age-at-onset of a disease. To model censored traits in family-based designs, we used the ... Full text Link to item Cite

Arfgef1 haploinsufficiency in mice alters neuronal endosome composition and decreases membrane surface postsynaptic GABA A receptors

Journal article · 2019 ARFGEF1 encodes a guanine exchange factor involved in intracellular vesicle trafficking, and is a candidate gene for childhood genetic epilepsies. To model ARFGEF1 haploinsufficiency observed in a recent Lennox Gastaut Syndrome patient, we studied a frame ... Full text Cite

Human genome-wide measurement of drug-responsive regulatory activity.

Journal article Nat Commun · December 21, 2018 Featured Publication Environmental stimuli commonly act via changes in gene regulation. Human-genome-scale assays to measure such responses are indirect or require knowledge of the transcription factors (TFs) involved. Here, we present the use of human genome-wide high-through ... Full text Link to item Cite

Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration.

Journal article EMBO J · December 3, 2018 Featured Publication A set of glutamylases and deglutamylases controls levels of tubulin polyglutamylation, a prominent post-translational modification of neuronal microtubules. Defective tubulin polyglutamylation was first linked to neurodegeneration in the Purkinje cell dege ... Full text Link to item Cite

bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.

Journal article Bioinformatics · October 15, 2018 Featured Publication SUMMARY: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings am ... Full text Link to item Cite

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.

Journal article PLoS Comput Biol · October 2018 Featured Publication Here we present an open-source R package 'meaRtools' that provides a platform for analyzing neuronal networks recorded on Microelectrode Arrays (MEAs). Cultured neuronal networks monitored with MEAs are now being widely used to characterize in vitro models ... Full text Link to item Cite

Somatic SLC35A2 variants in the brain are associated with intractable neocortical epilepsy.

Journal article Ann Neurol · June 2018 Featured Publication OBJECTIVE: Somatic variants are a recognized cause of epilepsy-associated focal malformations of cortical development (MCD). We hypothesized that somatic variants may underlie a wider range of focal epilepsy, including nonlesional focal epilepsy (NLFE). Th ... Full text Link to item Cite

De novo and inherited private variants in MAP1B in periventricular nodular heterotopia.

Journal article PLoS Genet · May 2018 Featured Publication Periventricular nodular heterotopia (PVNH) is a malformation of cortical development commonly associated with epilepsy. We exome sequenced 202 individuals with sporadic PVNH to identify novel genetic risk loci. We first performed a trio-based analysis and ... Full text Link to item Cite

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.

Journal article Neuron · March 21, 2018 Featured Publication To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 ... Full text Link to item Cite

Genetic Polymorphisms of CFH and ARMS2 Do Not Predict Response to Antioxidants and Zinc in Patients with Age-Related Macular Degeneration: Independent Statistical Evaluations of Data from the Age-Related Eye Disease Study.

Journal article Ophthalmology · March 2018 Featured Publication PURPOSE: Considerable controversy has erupted in recent years regarding whether genotyping should be part of standard care for patients with age-related macular degeneration (AMD) who are being considered for treatment with antioxidants and zinc. We aimed ... Full text Link to item Cite

De novo variants in the alternative exon 5 of SCN8A cause epileptic encephalopathy.

Journal article Genet Med · February 2018 Featured Publication PurposeAs part of the Epilepsy Genetics Initiative, we re-evaluated clinically generated exome sequence data from 54 epilepsy patients and their unaffected parents to identify molecular diagnoses not provided in the initial diagnostic interpretation.Method ... Full text Link to item Cite

Facilitating the Calculation of the Efficient Score Using Symbolic Computing.

Journal article Am Stat · 2018 Featured Publication The score statistic continues to be a fundamental tool for statistical inference. In the analysis of data from high-throughput genomic assays, inference on the basis of the score usually enjoys greater stability, considerably higher computational efficienc ... Full text Link to item Cite

A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations.

Journal article PLoS Genet · November 2017 Featured Publication Trio exome sequencing has been successful in identifying genes with de novo mutations (DNMs) causing epileptic encephalopathy (EE) and other neurodevelopmental disorders. Here, we evaluate how well a case-control collapsing analysis recovers genes causing ... Full text Link to item Cite

Mapping eQTL by leveraging multiple tissues and DNA methylation.

Journal article BMC Bioinformatics · October 18, 2017 Featured Publication BACKGROUND: DNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variation and gene expression, and this rel ... Full text Link to item Cite

Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly.

Journal article Cold Spring Harb Mol Case Stud · September 2017 Featured Publication Hemimegalencephaly (HME) is a heterogeneous cortical malformation characterized by enlargement of one cerebral hemisphere. Somatic variants in mammalian target of rapamycin (mTOR) regulatory genes have been implicated in some HME cases; however, ∼70% have ... Full text Open Access Link to item Cite

Phenotypic analysis of 303 multiplex families with common epilepsies.

Journal article Brain · August 1, 2017 Featured Publication Gene identification in epilepsy has mainly been limited to large families segregating genes of major effect and de novo mutations in epileptic encephalopathies. Many families that present with common non-acquired focal epilepsies and genetic generalized ep ... Full text Link to item Cite

An Exome Sequencing Study to Assess the Role of Rare Genetic Variation in Pulmonary Fibrosis.

Journal article Am J Respir Crit Care Med · July 1, 2017 Featured Publication RATIONALE: Idiopathic pulmonary fibrosis (IPF) is an increasingly recognized, often fatal lung disease of unknown etiology. OBJECTIVES: The aim of this study was to use whole-exome sequencing to improve understanding of the genetic architecture of pulmonar ... Full text Link to item Cite

Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data.

Journal article Eur J Hum Genet · June 2017 Featured Publication The classic epileptic encephalopathies, including infantile spasms (IS) and Lennox-Gastaut syndrome (LGS), are severe seizure disorders that usually arise sporadically. De novo variants in genes mainly encoding ion channel and synaptic proteins have been f ... Full text Link to item Cite

Transversions have larger regulatory effects than transitions.

Journal article BMC Genomics · May 19, 2017 Featured Publication BACKGROUND: Transversions (Tv's) are more likely to alter the amino acid sequence of proteins than transitions (Ts's), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the two different types of mutations h ... Full text Link to item Cite

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.

Journal article Bioinformatics · May 15, 2017 Featured Publication MOTIVATION: The accurate interpretation of genetic variants is critical for characterizing genotype-phenotype associations. Because the effects of genetic variants can depend strongly on their local genomic context, accurate genome annotations are essentia ... Full text Link to item Cite

Evaluating genetic susceptibility to Staphylococcus aureus bacteremia in African Americans using admixture mapping.

Journal article Genes Immun · March 2017 Featured Publication The incidence of Staphylococcus aureus bacteremia (SAB) is significantly higher in African American (AA) than in European-descended populations. We used admixture mapping (AM) to test the hypothesis that genomic variations with different frequencies in Eur ... Full text Link to item Cite

Leveraging population information in family-based rare variant association analyses of quantitative traits.

Journal article Genet Epidemiol · February 2017 Featured Publication Confounding due to population substructure is always a concern in genetic association studies. Although methods have been proposed to adjust for population stratification in the context of common variation, it is unclear how well these approaches will work ... Full text Link to item Cite

Ultra-rare genetic variation in common epilepsies: a case-control sequencing study.

Journal article Lancet Neurol · February 2017 Featured Publication BACKGROUND: Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilep ... Full text Link to item Cite

Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.

Journal article PLoS One · 2017 Featured Publication There is broad agreement that genetic mutations occurring outside of the protein-coding regions play a key role in human disease. Despite this consensus, we are not yet capable of discerning which portions of non-coding sequence are important in the contex ... Full text Link to item Cite

Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy.

Journal article Am J Hum Genet · August 4, 2016 Featured Publication Hypothalamic hamartoma (HH) with gelastic epilepsy is a well-recognized drug-resistant epilepsy syndrome of early life.(1) Surgical resection allows limited access to the small deep-seated lesions that cause the disease. Here, we report the results of a se ... Full text Link to item Cite

De Novo Mutations in SLC1A2 and CACNA1A Are Important Causes of Epileptic Encephalopathies.

Journal article Am J Hum Genet · August 4, 2016 Featured Publication Epileptic encephalopathies (EEs) are the most clinically important group of severe early-onset epilepsies. Next-generation sequencing has highlighted the crucial contribution of de novo mutations to the genetic architecture of EEs as well as to their under ... Full text Link to item Cite

Exploiting expression patterns across multiple tissues to map expression quantitative trait loci.

Journal article BMC Bioinformatics · June 24, 2016 Featured Publication BACKGROUND: In order to better understand complex diseases, it is important to understand how genetic variation in the regulatory regions affects gene expression. Genetic variants found in these regulatory regions have been shown to activate transcription ... Full text Link to item Cite

Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls.

Journal article PLoS Genet · May 2016 Featured Publication Next-generation sequencing of DNA provides an unprecedented opportunity to discover rare genetic variants associated with complex diseases and traits. However, the common practice of first calling underlying genotypes and then treating the called values as ... Full text Link to item Cite

Polymorphisms in HLA Class II Genes Are Associated With Susceptibility to Staphylococcus aureus Infection in a White Population.

Journal article J Infect Dis · March 1, 2016 Featured Publication BACKGROUND: Staphylococcus aureus can cause life-threatening infections. Human susceptibility to S. aureus infection may be influenced by host genetic variation. METHODS: A genome-wide association study (GWAS) in a large health plan-based cohort included b ... Full text Link to item Cite

The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes.

Journal article Genome Biol · January 18, 2016 Featured Publication Ranking human genes based on their tolerance to functional genetic variation can greatly facilitate patient genome interpretation. It is well established, however, that different parts of proteins can have different functions, suggesting that it will ultim ... Full text Link to item Cite

The RBMX gene as a candidate for the Shashi X-linked intellectual disability syndrome.

Journal article Clin Genet · October 2015 Featured Publication A novel X-linked intellectual disability (XLID) syndrome with moderate intellectual disability and distinguishing craniofacial dysmorphisms had been previously mapped to the Xq26-q27 interval. On whole exome sequencing in the large family originally report ... Full text Link to item Cite

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity.

Journal article PLoS Genet · September 2015 Featured Publication Noncoding sequence contains pathogenic mutations. Yet, compared with mutations in protein-coding sequence, pathogenic regulatory mutations are notoriously difficult to recognize. Most fundamentally, we are not yet adept at recognizing the sequence stretche ... Full text Link to item Cite

Incorporating Functional Information in Tests of Excess De Novo Mutational Load.

Journal article Am J Hum Genet · August 6, 2015 Featured Publication A number of recent studies have investigated the role of de novo mutations in various neurodevelopmental and neuropsychiatric disorders. These studies attempt to implicate causal genes by looking for an excess load of de novo mutations within those genes. ... Full text Link to item Cite

The genetics of neuropsychiatric diseases: looking in and beyond the exome.

Journal article Annu Rev Neurosci · July 8, 2015 Featured Publication Next-generation sequencing, which allows genome-wide detection of rare and de novo mutations, is transforming neuropsychiatric disease genetics through identifying on an unprecedented scale genes and protein-coding mutations that confer risk. Although unde ... Full text Link to item Cite

Testing for risk and protective trends in genetic analyses of HIV acquisition.

Journal article Biostatistics · April 2015 Featured Publication Host genetics studies of HIV-1 acquisition are critically important for the identification of new targets for drug and vaccine development. Analyses of such studies typically focus on pairwise comparisons of three different groups: HIV-1 positive individua ... Full text Link to item Cite

Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways.

Journal article Science · March 27, 2015 Featured Publication Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease with no effective treatment. We report the results of a moderate-scale sequencing study aimed at increasing the number of genes known to contribute to predisposition for ALS. We perf ... Full text Link to item Cite

Testing the effect of rare compound-heterozygous and recessive mutations in case--parent sequencing studies.

Journal article Genet Epidemiol · March 2015 Featured Publication Compound heterozygous mutations are mutations that occur on different copies of genes and may completely "knock-out" gene function. Compound heterozygous mutations have been implicated in a large number of diseases, but there are few statistical methods fo ... Full text Link to item Cite

De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies.

Journal article Am J Hum Genet · October 2, 2014 Featured Publication Emerging evidence indicates that epileptic encephalopathies are genetically highly heterogeneous, underscoring the need for large cohorts of well-characterized individuals to further define the genetic landscape. Through a collaboration between two consort ... Full text Link to item Cite

An evaluation of copy number variation detection tools from whole-exome sequencing data.

Journal article Hum Mutat · July 2014 Featured Publication Copy number variation (CNV) has been found to play an important role in human disease. Next-generation sequencing technology, including whole-genome sequencing (WGS) and whole-exome sequencing (WES), has become a primary strategy for studying the genetic b ... Full text Link to item Cite

A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting.

Journal article BMC Infect Dis · February 13, 2014 BACKGROUND: Humans vary in their susceptibility to acquiring Staphylococcus aureus infection, and research suggests that there is a genetic basis for this variability. Several recent genome-wide association studies (GWAS) have identified variants that may ... Full text Open Access Link to item Cite

Robust regression analysis of copy number variation data based on a univariate score.

Journal article PLoS One · 2014 Featured Publication MOTIVATION: The discovery that copy number variants (CNVs) are widespread in the human genome has motivated development of numerous algorithms that attempt to detect CNVs from intensity data. However, all approaches are plagued by high false discovery rate ... Full text Link to item Cite

De novo mutations in epileptic encephalopathies.

Journal article Nature · September 12, 2013 Featured Publication Epileptic encephalopathies are a devastating group of severe childhood epilepsy disorders for which the cause is often unknown. Here we report a screen for de novo mutations in patients with two classical epileptic encephalopathies: infantile spasms (n = 1 ... Full text Link to item Cite

Sequencing studies in human genetics: design and interpretation.

Journal article Nat Rev Genet · July 2013 Featured Publication Next-generation sequencing is becoming the primary discovery tool in human genetics. There have been many clear successes in identifying genes that are responsible for Mendelian diseases, and sequencing approaches are now poised to identify the mutations t ... Full text Link to item Cite

A longitudinal examination of the psychoeducational, neurocognitive, and psychiatric functioning in children with 22q11.2 deletion syndrome.

Journal article Res Dev Disabil · May 2013 Featured Publication The present study sought to examine the longitudinal psychoeducational, neurocognitive, and psychiatric outcomes of children and adolescents with chromosome 22q11.2 deletion syndrome (22q11DS), a population with a high incidence of major psychiatric illnes ... Full text Link to item Cite

Leveraging prior information to detect causal variants via multi-variant regression.

Journal article PLoS Comput Biol · 2013 Featured Publication Although many methods are available to test sequence variants for association with complex diseases and traits, methods that specifically seek to identify causal variants are less developed. Here we develop and evaluate a Bayesian hierarchical regression m ... Full text Link to item Cite

Genic intolerance to functional variation and the interpretation of personal genomes.

Journal article PLoS Genet · 2013 Featured Publication A central challenge in interpreting personal genomes is determining which mutations most likely influence disease. Although progress has been made in scoring the functional impact of individual mutations, the characteristics of the genes in which those mut ... Full text Link to item Cite

Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus.

Journal article G3 (Bethesda) · June 2012 Featured Publication Exposure to Staphylococcus aureus has a variety of outcomes, from asymptomatic colonization to fatal infection. Strong evidence suggests that host genetics play an important role in susceptibility, but the specific host genetic factors involved are not kno ... Full text Open Access Link to item Cite

Stratification-score matching improves correction for confounding by population stratification in case-control association studies.

Journal article Genet Epidemiol · April 2012 Featured Publication Proper control of confounding due to population stratification is crucial for valid analysis of case-control association studies. Fine matching of cases and controls based on genetic ancestry is an increasingly popular strategy to correct for such confound ... Full text Link to item Cite

A weighted accumulation test for associating rare genetic variation with quantitative phenotypes.

Journal article BMC Proc · November 29, 2011 Featured Publication Currently there is a great deal of interest in developing methods for testing the role that rare variation plays in disease development. Here we propose a weighted association test that accumulates genetic variation across a signaling pathway. We evaluate ... Full text Link to item Cite

SVA: software for annotating and visualizing sequenced human genomes.

Journal article Bioinformatics · July 15, 2011 Featured Publication SUMMARY: Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. ... Full text Link to item Cite

Control for confounding in case-control studies using the stratification score, a retrospective balancing score.

Journal article Am J Epidemiol · April 1, 2011 Featured Publication The stratification score for a case-control study is the probability of disease modeled as a function of potential confounders. The authors show that the stratification score is a retrospective balancing score and thus plays a similar role in case-control ... Full text Link to item Cite

Aging-related atherosclerosis is exacerbated by arterial expression of tumor necrosis factor receptor-1: evidence from mouse models and human association studies.

Journal article Hum Mol Genet · July 15, 2010 Featured Publication Aging is believed to be among the most important contributors to atherosclerosis, through mechanisms that remain largely obscure. Serum levels of tumor necrosis factor (TNF) rise with aging and have been correlated with the incidence of myocardial infarcti ... Full text Open Access Link to item Cite

Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB.

Journal article Int J Neuropsychopharmacol · July 2010 Featured Publication In a previous study we showed that genetic variation in HTR2A, which encodes the serotonin 2A receptor, influenced outcome of citalopram treatment in patients with major depressive disorder. Since chronic administration of citalopram, which selectively and ... Full text Link to item Cite

SNPs in CAST are associated with Parkinson disease: a confirmation study.

Journal article Am J Med Genet B Neuropsychiatr Genet · June 5, 2010 Featured Publication Using data from the National Institutes of Neurological disease and Stroke's (NINDS) study of Parkinson disease (PD), we recently reported that single nucleotide polymorphisms (SNPs) in a region containing the Calpastatin (CAST) gene were associated with P ... Full text Link to item Cite

Testing gene-treatment interactions in pharmacogenetic studies.

Journal article J Biopharm Stat · March 2010 Featured Publication Drug-related side effects are one of the leading causes of death and illness in the developed world. Finding genes that modify drug response has the potential to significantly improve drug delivery, by identifying both individuals that can benefit from the ... Full text Link to item Cite

Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB.

Journal article The international journal of neuropsychopharmacology / official scientific journal of the Collegium Internationale Neuropsychopharmacologicum (CINP) · January 2010 Featured Publication In a previous study we showed that genetic variation in HTR2A, which encodes the serotonin 2A receptor, influenced outcome of citalopram treatment in patients with major depressive disorder. Since chronic administration of citalopram, which selectively and ... Cite

Fast and robust association tests for untyped SNPs in case-control studies.

Journal article Hum Hered · 2010 Featured Publication Genome-wide association studies (GWASs) aim to genotype enough single nucleotide polymorphisms (SNPs) to effectively capture common genetic variants across the genome. Even though the number of SNPs genotyped in such studies can exceed a million, there is ... Full text Link to item Cite

Genome-wide association analysis of rheumatoid arthritis data via haplotype sharing.

Journal article BMC Proc · December 15, 2009 Featured Publication We present computationally simple association tests based on haplotype sharing that can be easily applied to genome-wide association studies, while allowing use of fast (but not likelihood-based) haplotyping algorithms, and properly accounting for the unce ... Full text Link to item Cite

Effect of population stratification on the identification of significant single-nucleotide polymorphisms in genome-wide association studies.

Journal article BMC Proc · December 15, 2009 Featured Publication The North American Rheumatoid Arthritis Consortium case-control study collected case participants across the United States and control participants from New York. More than 500,000 single-nucleotide polymorphisms (SNPs) were genotyped in the sample of 2000 ... Full text Link to item Cite

A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease.

Journal article Genet Epidemiol · December 2009 Featured Publication The large number of markers considered in a genome-wide association study (GWAS) has resulted in a simplification of analyses conducted. Most studies are analyzed one marker at a time using simple tests like the trend test. Methods that account for the spe ... Full text Link to item Cite

Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients.

Journal article Pharmacogenet Genomics · September 2009 Featured Publication OBJECTIVES: Suicidal ideation is an uncommon but worrisome symptom than can emerge during antidepressant treatment. We have described earlier the association between treatment-emergent suicidal ideation (TESI) and markers in genes encoding glutamate recept ... Full text Link to item Cite

A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity.

Journal article Ann Hum Genet · September 2009 Featured Publication Association methods based on haplotype similarity (HS) can overcome power and stability issues encountered in standard haplotype analyses. Current HS methods can be generally classified into evolutionary and two-sample approaches. We propose a new regressi ... Full text Link to item Cite

Invited keynote talk: Haplotype sharing for genome-wide case-control association studies

Journal article Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · August 27, 2008 The computational demands imposed by the large number of markers considered in a genome-wide association study (GWAS) have resulted in an extreme simplification in the types of analyses conducted. While sophisticated methodology may be used to adjust for m ... Full text Cite

Determinants of exhaled nitric oxide levels in healthy, nonsmoking African American adults.

Journal article J Allergy Clin Immunol · February 2008 Featured Publication BACKGROUND: Asthma is a significant cause of morbidity and mortality for African Americans. Fraction of exhaled nitric oxide (FeNO) levels are increased in patients with asthma, and airway levels of nitric oxide metabolites regulate airway inflammation and ... Full text Link to item Cite

Robust estimation and testing of haplotype effects in case-control studies.

Journal article Genet Epidemiol · January 2008 Featured Publication Haplotype-based analyses are thought to play a major role in the study of common complex diseases. This has led to the development of a variety of statistical methods for detecting disease-haplotype associations from case-control study data. However, haplo ... Full text Link to item Cite

Response to Lee et al.

Journal article American Journal of Human Genetics · 2008 Featured Publication Full text Cite

A simple and improved correction for population stratification in case-control studies.

Journal article Am J Hum Genet · May 2007 Featured Publication Population stratification remains an important issue in case-control studies of disease-marker association, even within populations considered to be genetically homogeneous. Campbell et al. (Nature Genetics 2005;37:868-872) illustrated this by showing that ... Full text Link to item Cite

Inference on haplotype/disease association using parent-affected-child data: the projection conditional on parental haplotypes method.

Journal article Genet Epidemiol · April 2007 Featured Publication We develop a method that allows inference on parameters in log-linear models of the relative risk of disease given an individual's haplotypes, that can be used to analyze case-parent trio data. Our methods are robust to population stratification and can al ... Full text Link to item Cite

Simple methods for assessing haplotype-environment interactions in case-only and case-control studies.

Journal article Genet Epidemiol · January 2007 Featured Publication For investigating haplotype-environment interactions in case-control studies, one can implement statistical methods based either on a retrospective likelihood (modeling the probability of haplotype and environment conditional on disease status) or a prospe ... Full text Link to item Cite

Statistical models for haplotype sharing in case-parent trio data.

Journal article Hum Hered · 2007 Featured Publication BACKGROUND: Haplotype sharing statistics have been introduced in an ad-hoc way, often relying heavily on permutation testing. As a result, applying these approaches to whole genome association studies or to evaluate their properties in extensive simulation ... Full text Link to item Cite

Summary of contributions to GAW15 Group 13: candidate gene association studies.

Journal article Genet Epidemiol · 2007 Featured Publication Here we summarize the contributions to Group 13 of the Genetic Analysis Workshop 15 held in St. Pete Beach, Florida, on November 12-14, 2006. The focus of this group was to identify candidate genes associated with rheumatoid arthritis or surrogate outcomes ... Full text Link to item Cite

Association mapping via a class of haplotype-sharing statistics.

Journal article BMC Proc · 2007 Featured Publication We present a class of haplotype-sharing statistics useful for association mapping in case-parent trio data. The framework presented allows derivation of novel tests as well as new simplified variance estimators for previously proposed tests. We give an ove ... Full text Link to item Cite

Inference for case-control studies when exposure status is both informatively missing and misclassified.

Journal article Stat Med · December 15, 2006 Featured Publication In case-control studies, it is common for a categorical exposure variable to be misclassified. It is also common for exposure status to be informatively missing for some individuals, in that the probability of missingness may be related to exposure. Proced ... Full text Link to item Cite

Genetic association tests based on ranks (GATOR) for quantitative traits with and without censoring.

Journal article Genet Epidemiol · April 2006 Featured Publication Linkage disequilibrium mapping of quantitative traits is a powerful method for dissecting the genetic etiology of complex phenotypes. Quantitative traits, however, often exhibit characteristics that make their use problematic. For example, the distribution ... Full text Link to item Cite

Journal of the American Statistical Association: Comment

Journal article Journal of the American Statistical Association · March 1, 2006 Full text Cite

Comment

Journal article Journal of the American Statistical Association · March 1, 2006 Full text Cite

Robust testing of haplotype/disease association.

Journal article BMC Genet · December 30, 2005 Featured Publication Haplotypes, the combination of closely linked alleles that fall on the same chromosome, show great promise for studying the genetic components of complex diseases. However, when only multilocus genotype data are available, statistical approaches need to be ... Full text Link to item Cite

Application of a rank-based genetic association test to age-at-onset data from the Collaborative Study on the Genetics of Alcoholism study.

Journal article BMC Genet · December 30, 2005 Featured Publication Association studies of quantitative traits have often relied on methods in which a normal distribution of the trait is assumed. However, quantitative phenotypes from complex human diseases are often censored, highly skewed, or contaminated with outlying va ... Full text Open Access Link to item Cite

Physician-diagnosed depression as a correlate of hospitalizations in patients receiving long-term hemodialysis.

Journal article Am J Kidney Dis · October 2005 Featured Publication BACKGROUND: Hospital admissions consume a large proportion of costs for the end-stage renal disease (ESRD) program in the United States. We investigated whether a physician diagnosis of depression increases the risk for hospitalization or death in patients ... Full text Link to item Cite

Locally-efficient robust estimation of haplotype-disease association in family-based studies

Journal article Biometrika · September 1, 2005 Modelling human genetic variation is critical to understanding the genetic basis of complex disease. The Human Genome Project has discovered millions of binary DNA sequence variants, called single nucleotide polymorphisms, and millions more may exist. As c ... Full text Cite

Genetic association studies in cardiology.

Journal article Am Heart J · June 2005 Featured Publication The last decade has witnessed the emergence of the genetic association study into the mainstream clinical literature. Technological advances and the Human Genome Project have resulted in widespread interest in exploring these new variables in clinical dise ... Full text Link to item Cite

Long-term survival estimates for imatinib versus interferon-alpha plus low-dose cytarabine for patients with newly diagnosed chronic-phase chronic myeloid leukemia.

Journal article Cancer · December 1, 2004 Featured Publication BACKGROUND: The authors estimated survival among patients with chronic myeloid leukemia for a cost-effectiveness analysis of imatinib versus interferon-alpha plus low-dose cytarabine (IFN+LDAC). METHODS: Two-year survival and cytogenetic response were dete ... Full text Link to item Cite

Adjusting for covariates on a slippery slope: linkage analysis of change over time.

Journal article BMC Genet · December 31, 2003 BACKGROUND: We analyzed the Genetic Analysis Workshop 13 (GAW13) simulated data to contrast and compare different methods for the genetic linkage analysis of hypertension and change in blood pressure over time. We also examined methods for incorporating co ... Full text Link to item Cite

Bootstrap calibration of TRANSMIT for informative missingness of parental genotype data.

Journal article BMC Genet · December 31, 2003 Featured Publication Informative missingness of parental genotype data occurs when the genotype of a parent influences the probability of the parent's genotype data being observed. Informative missingness can occur in a number of plausible ways and can affect both the validity ... Full text Link to item Cite

Changes in CD4+ T-cell differentiation phenotype during structured treatment interruption in patients with chronic HIV-1 infection.

Journal article J Acquir Immune Defic Syndr · December 15, 2003 Markers of maturation and activation were measured on peripheral CD4+ T cells in chronically HIV-1-infected patients in a randomized, controlled pilot study of structured treatment interruption (STI). Eight subjects underwent 2 cycles of 1 month off and 1 ... Full text Link to item Cite

Characteristics of treated hypertension in incident hemodialysis and peritoneal dialysis patients.

Journal article Am J Kidney Dis · December 2003 Featured Publication BACKGROUND: The treatment of hypertension in dialysis patients is prevalent and poorly characterized. beta-Blockers and calcium channel blockers (CCBs) have been associated with reduced all-cause and cardiovascular mortality. This study describes the treat ... Full text Link to item Cite

Reduction of myocardial ischemic injury following coronary intervention (the MC-1 to Eliminate Necrosis and Damage trial).

Journal article Am J Cardiol · September 15, 2003 Myocardial ischemic injury complicating acute myocardial infarction (AMI) and coronary revascularization procedures remains an unresolved clinical dilemma. In preclinical studies, treatment with pyridoxal-5'-phosphate monohydrate (MC-1), a vitamin B6 metab ... Full text Link to item Cite

Power calculations for large multi-arm placebo-controlled studies of dichotomous outcomes.

Journal article Stat Med · June 30, 2003 Featured Publication Several statistical methods can be used to test for differences in placebo-controlled dichotomous multi-arm studies. These tests include linear and quadratic trends, Dunnett's test, Hochberg's test, and the overall chi-square test. We computed the power of ... Full text Link to item Cite

Informative missingness in genetic association studies: case-parent designs.

Journal article Am J Hum Genet · March 2003 Featured Publication We consider the effect of informative missingness on association tests that use parental genotypes as controls and that allow for missing parental data. Parental data can be informatively missing when the probability of a parent being available for study i ... Full text Link to item Cite

Missing data in the 2 x 2 table: patterns and likelihood-based analysis for cross-sectional studies with supplemental sampling.

Journal article Stat Med · February 28, 2003 Featured Publication Standard measures of crude association in the context of a cross-sectional study are the risk difference, relative risk and odds ratio as derived from a 2x 2 table. Most such studies are subject to missing data on disease, exposure, or both, introducing bi ... Full text Link to item Cite

Joint models for toxicology studies with dose-dependent number of implantations.

Journal article Risk Anal · December 2002 Featured Publication Many chemicals interfere with the natural reproductive processes in mammals. The chemicals may prevent the fertilization of an egg or keep a zygote from implanting in the uterine wall. For this reason, toxicology studies with pre-implantation exposure ofte ... Full text Link to item Cite

Estimating crude or common odds ratios in case-control studies with informatively missing exposure data.

Journal article Am J Epidemiol · February 1, 2002 Featured Publication In case-control studies, the crude odds ratio derived from a 2 x 2 table and the common odds ratio adjusted for stratification variables are staple measures of exposure-disease association. While missing exposure data are encountered in the majority of suc ... Full text Link to item Cite

Involving the male partner for interpreting the basal body temperature graph.

Journal article Obstet Gynecol · July 2001 Featured Publication OBJECTIVE: To determine if the male cohabiting partner of a woman may serve as a control for exogenous influences on basal body temperature (BBT). METHODS: Twelve couples from the Atlanta area were enrolled for a total of 41 couple-cycles. Couples recorded ... Full text Link to item Cite

Alcohol consumption is negatively associated with the prevalence of coronary heart disease in the New Mexico Elder Health Survey.

Journal article J Am Geriatr Soc · April 1999 Featured Publication OBJECTIVE: To compare the prevalence of coronary heart disease (CHD) and the effects of various risk factors, including alcohol consumption, on prevalence rates in a randomly selected sample of older Hispanic and non-Hispanic white (NHW) men and women. DES ... Full text Link to item Cite

Prevalences of type 2 diabetes, the insulin resistance syndrome, and coronary heart disease in an elderly, biethnic population.

Journal article Diabetes Care · June 1998 Featured Publication OBJECTIVE: To compare the prevalences of type 2 diabetes, the various cardiovascular risk factors encompassing the insulin resistance syndrome (IRS), and coronary heart disease (CHD) in elderly Hispanics compared with non-Hispanic whites. RESEARCH DESIGN A ... Full text Link to item Cite

Outcome of recruitment and report on participation rate in the New Mexico Elder Health Survey.

Journal article Ethn Dis · 1998 Featured Publication The purpose of this paper is to report on the outcome of recruitment and participation rate in the New Mexico Elder Health Survey. This survey is the first community based epidemiological survey to examine health and health related issues of elderly (65 ye ... Link to item Cite