Models, Genetic

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  Subject Areas on Research

  • (Session Introduction) Joint Learning from Multiple Types of Genomic Data 
  • . Loss of sexual recombination and segregation is associated with increased diversification in evening primroses. 
  • 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. 
  • A Modified Integrated Genetic Model for Risk Prediction in Younger Patients with Acute Myeloid Leukemia. 
  • A bayesian analysis strategy for cross-study translation of gene expression biomarkers. 
  • A biometric latent curve analysis of memory decline in older men of the NAS-NRC twin registry. 
  • A bivariate frailty model with a cure fraction for modeling familial correlations in diseases. 
  • A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila. 
  • A case-only approach for assessing gene by sex interaction in human longevity. 
  • A change in the structure of Vbeta chromatin associated with TCR beta allelic exclusion. 
  • A cline in seed dormancy helps conserve the environment experienced during reproduction across the range of Arabidopsis thaliana. 
  • A comparative study of asymmetric migration events across a marine biogeographic boundary. 
  • A comparison of major histocompatibility complex SNPs in Han Chinese residing in Taiwan and Caucasians. 
  • A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region. 
  • A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information. 
  • A framework phylogeny of the American oak clade based on sequenced RAD data. 
  • A functional analysis of the spacer of V(D)J recombination signal sequences. 
  • A functional genomics predictive network model identifies regulators of inflammatory bowel disease. 
  • A gene expression signature of confinement in peripheral blood of red wolves (Canis rufus). 
  • A genetic algorithm for variable selection in logistic regression analysis of radiotherapy treatment outcomes. 
  • A genetic risk score based on direct associations with coronary heart disease improves coronary heart disease risk prediction in the Atherosclerosis Risk in Communities (ARIC), but not in the Rotterdam and Framingham Offspring, Studies. 
  • A genetic stochastic process model for genome-wide joint analysis of biomarker dynamics and disease susceptibility with longitudinal data. 
  • A genome-wide search for linkage to asthma phenotypes in the genetics of asthma international network families: evidence for a major susceptibility locus on chromosome 2p. 
  • A genomewide scan for early-onset coronary artery disease in 438 families: the GENECARD Study. 
  • A genomic regulatory network for development. 
  • A genomic screen of autism: evidence for a multilocus etiology. 
  • A genomic strategy to elucidate modules of oncogenic pathway signaling networks. 
  • A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. 
  • A human model for multigenic inheritance: phenotypic expression in Hirschsprung disease requires both the RET gene and a new 9q31 locus. 
  • A hybrid bayesian approach for genome-wide association studies on related individuals. 
  • A hybrid framework for genome wide epistasis discovery. 
  • A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan. 
  • A latent model for prioritization of SNPs for functional studies. 
  • A logistic regression model for measuring gene-longevity associations. 
  • A long-range flexible billboard model of gene activation. 
  • A mechanistic study of evolvability using the mitogen-activated protein kinase cascade. 
  • A meta-analysis of MTHFR C677T and A1298C polymorphisms and risk of acute lymphoblastic leukemia in children. 
  • A model for RAS mutation patterns in cancers: finding the sweet spot. 
  • A model for alignment of Env V1 and V2 hypervariable domains from human and simian immunodeficiency viruses. 
  • A molecular basis for inositol polyphosphate synthesis in Drosophila melanogaster. 
  • A mosaic analysis system with Cre or Tomato expression in the mouse. 
  • A multi-locus molecular phylogeny of the Lepidoziaceae: laying the foundations for a stable classification. 
  • A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. 
  • A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. 
  • A multistate model for the genetic analysis of the ageing process. 
  • A mutation in a mitochondrial transmembrane protein is responsible for the pleiotropic hematological and skeletal phenotype of flexed-tail (f/f) mice. 
  • A network-heuristic approach to improve the impact of genomic data on drug discovery. 
  • A non-canonical RNA degradation pathway suppresses RNAi-dependent epimutations in the human fungal pathogen Mucor circinelloides. 
  • A pathway-based classification of human breast cancer. 
  • A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. 
  • A predictive model for transcriptional control of physiology in a free living cell. 
  • A probabilistic learning approach to whole-genome operon prediction. 
  • A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. 
  • A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity. 
  • A reversible color polyphenism in American peppered moth (Biston betularia cognataria) caterpillars. 
  • A second-generation genomic screen for multiple sclerosis. 
  • A semiparametric model for vQTL mapping. 
  • A simple and improved correction for population stratification in case-control studies. 
  • A simple formula useful for positional cloning. 
  • A simple genetic incompatibility causes hybrid male sterility in mimulus. 
  • A sparse transmission disequilibrium test for haplotypes based on Bradley-Terry graphs. 
  • A statistical framework for cross-tissue transcriptome-wide association analysis. 
  • A stochastic evolutionary model for protein structure alignment and phylogeny. 
  • A study in scarlet: MC1R as the main predictor of red hair and exemplar of the flip-flop effect. 
  • A study of the repetitive structure and distribution of short motifs in human genomic sequences. 
  • A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. 
  • A test of the chromosomal rearrangement model of speciation in Drosophila pseudoobscura. 
  • A three-generation approach in biodemography is based on the developmental profiles and the epigenetics of female gametes. 
  • A truncated isoform of c-Mpl with an essential C-terminal peptide targets the full-length receptor for degradation. 
  • A user's guide to the encyclopedia of DNA elements (ENCODE). 
  • A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma. 
  • A whole blood gene expression-based signature for smoking status. 
  • A whole more than the sum of its synthetic parts. 
  • A zebrafish model for the Shwachman-Diamond syndrome (SDS). 
  • Abnormal osmotic regulation in trpv4-/- mice. 
  • Accounting for linkage in family-based tests of association with missing parental genotypes. 
  • Activated cAMP-response element-binding protein regulates neuronal expression of presenilin-1. 
  • Adaptive evolution drives the diversification of zinc-finger binding domains. 
  • Adaptive evolution: evaluating empirical support for theoretical predictions. 
  • Adeno-associated virus-mediated antiangiogenic gene therapy with thrombospondin-1 type 1 repeats and endostatin. 
  • Adenovirus inhibition of cellular protein synthesis involves inactivation of cap-binding protein. 
  • Adenylyl cyclase-associated protein Aca1 regulates virulence and differentiation of Cryptococcus neoformans via the cyclic AMP-protein kinase A cascade. 
  • Advances to Bayesian network inference for generating causal networks from observational biological data. 
  • African-American heredity prostate cancer study: a model for genetic research. 
  • Age at onset in two common neurodegenerative diseases is genetically controlled. 
  • Age-of-onset heterogeneity in Huntington disease families. 
  • Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent. 
  • Allelic loss at the tuberous sclerosis 2 locus in spontaneous tumors in the Eker rat. 
  • Alternative translation of osteopontin generates intracellular and secreted isoforms that mediate distinct biological activities in dendritic cells. 
  • Amplification of cDNA ends based on template-switching effect and step-out PCR. 
  • An "almost exhaustive" search-based sequential permutation method for detecting epistasis in disease association studies. 
  • An analysis paradigm for investigating multi-locus effects in complex disease: examination of three GABA receptor subunit genes on 15q11-q13 as risk factors for autistic disorder. 
  • An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference. 
  • An exploration of genetic association tests for disease risk and age at onset. 
  • An imprinted PEG1/MEST antisense expressed predominantly in human testis and in mature spermatozoa. 
  • An improved genetic algorithm for designing optimal temporal patterns of neural stimulation. 
  • An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer. 
  • Analyses on mutation patterns, detection of population bottlenecks, and suggestion of deleterious-compensatory evolution among members of the genus Potyvirus. 
  • Analysis of muscle creatine kinase regulatory elements in recombinant adenoviral vectors. 
  • Anastral spindle assembly: a mathematical model. 
  • Ancestral population genomics: the coalescent hidden Markov model approach. 
  • Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates. 
  • Ancient single origin for Malagasy primates. 
  • Antitermination by bacteriophage lambda Q protein. 
  • Application of Bayesian inference using Gibbs sampling to item-response theory modeling of multi-symptom genetic data. 
  • Application of a rank-based genetic association test to age-at-onset data from the Collaborative Study on the Genetics of Alcoholism study. 
  • Approximating selective sweeps. 
  • Arabidopsis iba response5 suppressors separate responses to various hormones. 
  • Assessing genetic association with human survival at multi-allelic loci. 
  • Assessment of LD matrix measures for the analysis of biological pathway association. 
  • Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers. 
  • Association of LEP G2548A and LEPR Q223R polymorphisms with cancer susceptibility: evidence from a meta-analysis. 
  • Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans. 
  • Association test for X-linked QTL in family-based designs. 
  • Associations, populations, and the truth: recommendations for genetic association studies in Arthritis & Rheumatism. 
  • Assortative mating for antisocial behavior: developmental and methodological implications. 
  • Autonomous Boolean modelling of developmental gene regulatory networks. 
  • Autosomal admixture levels are informative about sex bias in admixed populations. 
  • Bacteriophage T4 helicase loader protein gp59 functions as gatekeeper in origin-dependent replication in vivo. 
  • BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. 
  • Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. 
  • Bayesian analysis of mutational spectra. 
  • Bayesian and maximum likelihood estimation of genetic maps. 
  • Bayesian estimation of genomic distance. 
  • Between-site differences in the scale of dispersal and gene flow in red oak. 
  • Beyond 2/3 and 1/3: The Complex Signatures of Sex-Biased Admixture on the X Chromosome. 
  • Beyond Arabidopsis. Translational biology meets evolutionary developmental biology. 
  • Bidirectional excision in methyl-directed mismatch repair. 
  • Bimodal quantitative relationships between histone modifications for X-linked and autosomal loci. 
  • Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. 
  • Biological and/or genetic factors in alcoholism. 
  • Biological clocks and the coordination theory of RNA operons and regulons. 
  • Both heptad repeats of human respiratory syncytial virus fusion protein are potent inhibitors of viral fusion. 
  • Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program. 
  • CFTR haplotype analysis reveals genetic heterogeneity in the etiology of congenital bilateral aplasia of the vas deferens. 
  • Caenorhabditis elegans DNA mismatch repair gene msh-2 is required for microsatellite stability and maintenance of genome integrity. 
  • Calcineurin is required for virulence of Cryptococcus neoformans. 
  • Calcium Channel Mutations in Cardiac Arrhythmia Syndromes. 
  • Callipyge mutation affects gene expression in cis: a potential role for chromatin structure. 
  • Cardiac rupture after myocardial infarction: new insights from murine models. 
  • Cardiovascular genomics: estimating the total number of genes expressed in the human cardiovascular system. 
  • Catabolism of branched-chain amino acids in heart failure: insights from genetic models. 
  • Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors. 
  • Cell cycle dependence of group VIA calcium-independent phospholipase A2 activity. 
  • Centromere identity in Drosophila is not determined in vivo by replication timing. 
  • Chromatin and DNA replication. 
  • Chromosome aberrations resulting from double-strand DNA breaks at a naturally occurring yeast fragile site composed of inverted ty elements are independent of Mre11p and Sae2p. 
  • Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair. 
  • Chronic mild stress-induced anhedonia: greater effect in a genetic rat model of depression. 
  • Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. 
  • Clinical application of exome sequencing in undiagnosed genetic conditions. 
  • Co-occurrence of ADHD and low IQ has genetic origins. 
  • Coevolution of self-fertilization and inbreeding depression. I. Mutation-selection balance at one and two loci. 
  • Coevolution of self-fertilization and inbreeding depression. II. Symmetric overdominance in viability. 
  • Coevolution of the major histocompatibility complex and the t-complex in the mouse. I. Generation and maintenance of high complementarity associations. 
  • Coevolution of the major histocompatibility complex and the t-complex in the mouse. II. Modification of response to sharing of histocompatibility antigens. 
  • Combined genotype and haplotype tests for region-based association studies. 
  • Combining location and expression data for principled discovery of genetic regulatory network models. 
  • Comparative genomics as a tool for gene discovery. 
  • Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. 
  • Comparative tests of evolutionary trade-offs in a palinurid lobster acoustic system. 
  • Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene Loci and calibration points, with application to a radiation of cute-looking mouse lemur species. 
  • Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow. 
  • Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors. 
  • Complete genomic screen for disease susceptibility loci in nuclear families. 
  • Complete genomic screen in late-onset familial Alzheimer disease. Evidence for a new locus on chromosome 12. 
  • Complete genomic screen in late-onset familial Alzheimer's disease. 
  • Complex gene-gene interactions in multiple sclerosis: a multifactorial approach reveals associations with inflammatory genes. 
  • Complex genetic interactions in a quantitative trait locus. 
  • Complexity reduction in context-dependent DNA substitution models. 
  • Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. 
  • Computational and experimental analyses reveal previously undetected coding exons of the KRIT1 (CCM1) gene. 
  • Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. 
  • Conflicting processes in the evolution of body size and development time. 
  • Connecting recombination, nucleotide diversity and species divergence in Drosophila. 
  • Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. 
  • Contrasts between adaptive coding and noncoding changes during human evolution. 
  • Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. 
  • Contribution of chromosomal polymorphisms to the G-matrix of Mimulus guttatus. 
  • Control elements within the PWS/AS imprinting box and their function in the imprinting process. 
  • Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes. 
  • Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. 
  • Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution 
  • Coupled mutagenesis screens and genetic mapping in zebrafish. 
  • Crossover interference on nucleolus organizing region-bearing chromosomes in Arabidopsis. 
  • Cryptococcus neoformans mitochondrial superoxide dismutase: an essential link between antioxidant function and high-temperature growth. 
  • Crystal structure of the transcription activator BmrR bound to DNA and a drug. 
  • Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes. 
  • Cyclin D1 G870A polymorphism and breast cancer risk: a meta-analysis comprising 9,911 cases and 11,171 controls. 
  • Cyclin D1 inhibits peroxisome proliferator-activated receptor gamma-mediated adipogenesis through histone deacetylase recruitment. 
  • DNA CpG methylation inhibits binding of NF-kappa B proteins to the HIV-1 long terminal repeat cognate DNA motifs. 
  • DNA polymerase zeta introduces multiple mutations when bypassing spontaneous DNA damage in Saccharomyces cerevisiae. 
  • DNA replication. 
  • DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. 
  • Dating the emergence of pandemic influenza viruses. 
  • Decreased physical function and increased pain sensitivity in mice deficient for type IX collagen. 
  • Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification. 
  • Deep-coverage whole genome sequences and blood lipids among 16,324 individuals. 
  • Defending information-free genocentrism. 
  • Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (genus Oplurus). 
  • Deleterious mutations and genetic variation for flower size in Mimulus guttatus. 
  • Density dependence and population differentiation of genetic architecture in Impatiens capensis in natural environments. 
  • Design, expression, and immunogenicity of a soluble HIV trimeric envelope fragment adopting a prefusion gp41 configuration. 
  • Destabilization of yeast micro- and minisatellite DNA sequences by mutations affecting a nuclease involved in Okazaki fragment processing (rad27) and DNA polymerase delta (pol3-t). 
  • Detection and localization of a single binary trait locus in experimental populations. 
  • Determining centromere identity: cyclical stories and forking paths. 
  • Differences in (G+C) content between species: a commentary on Forsdyke's "chromosomal viewpoint" of speciation. 
  • Different models, different trees: the geographic origin of PTLV-I. 
  • Differential display RT-PCR for identifying novel gene expression in the lung. 
  • Differential expression analysis for RNAseq using Poisson mixed models. 
  • Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis. 
  • Dinucleotide repeats in the Drosophila and human genomes have complex, length-dependent mutation processes. 
  • Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B. 
  • Discordant on/off switching of gene expression in myocytes during cardiac hypertrophy in vivo. 
  • Disruption of lysosome function promotes tumor growth and metastasis in Drosophila. 
  • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. 
  • Distinct stress responses of two functional laccases in Cryptococcus neoformans are revealed in the absence of the thiol-specific antioxidant Tsa1. 
  • Distribution and abundance of microsatellites in the yeast genome can Be explained by a balance between slippage events and point mutations. 
  • Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. 
  • Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. 
  • Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. 
  • Diversity in the weapons of sexual selection: horn evolution in the beetle genus Onthophagus (Coleoptera: Scarabaeidae). 
  • Do asexual polyploid lineages lead short evolutionary lives? A case study from the fern genus Astrolepis 
  • Do-it-yourself RNAi made easy? 
  • Does evolutionary theory need a rethink? 
  • Double-strand break repair in tandem repeats during bacteriophage T4 infection. 
  • Double-strand breaks associated with repetitive DNA can reshape the genome. 
  • Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. 
  • Drosophila as a model for the identification of genes causing adult human heart disease. 
  • Drosophila follicle cell amplicons as models for metazoan DNA replication: a cyclinE mutant exhibits increased replication fork elongation. 
  • Drosophila spastin regulates synaptic microtubule networks and is required for normal motor function. 
  • Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. 
  • Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models. 
  • Ectomycorrhizal fungal community in a tropical forest dominated by the Neotropical Dipterocarp, Pakaraimea dipterocarpaceae 
  • Editorial: studying hormonal regulation by microarrays: distinguishing the trees from the forest. 
  • Effect of mutagen-induced cell lethality on the dose response of germline mutations. 
  • Effects of covariates: a summary of Group 5 contributions. 
  • Effects of inversions on within- and between-species recombination and divergence. 
  • Efficient estimation of grouped survival models. 
  • Embryonic lethal abnormal visual RNA-binding proteins involved in growth, differentiation, and posttranscriptional gene expression. 
  • Endonucleolytic function of MutLalpha in human mismatch repair. 
  • Energy-efficient waveform shapes for neural stimulation revealed with a genetic algorithm. 
  • Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. 
  • Epistasis and balanced polymorphism influencing complex trait variation. 
  • Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. 
  • Escape from adaptive conflict after duplication in an anthocyanin pathway gene. 
  • Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. 
  • Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. 
  • Estimating FST and kinship for arbitrary population structures. 
  • Estimating genomic coexpression networks using first-order conditional independence. 
  • Estimating haplotype relative risks on human survival in population-based association studies. 
  • Estimation of the transition/transversion rate bias and species sampling. 
  • Eukaryotic mRNPs may represent posttranscriptional operons. 
  • Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach. 
  • Evaluating genetic association among ovarian, breast, and endometrial cancer: evidence for a breast/ovarian cancer relationship. 
  • Evaluating haplotype effects in case-control studies via penalized-likelihood approaches: prospective or retrospective analysis? 
  • Evaluation of genotype-specific survival using joint analysis of genetic and non-genetic subsamples of longitudinal data. 
  • Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in Drosophila pseudoobscura and D. persimilis. 
  • Evidence for Dobzhansky-Muller incompatibilites contributing to the sterility of hybrids between Mimulus guttatus and M. nasutus. 
  • Evolution of a polyphenism by genetic accommodation. 
  • Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana 
  • Evolution of leaf form in marsileaceous ferns: evidence for heterochrony 
  • Evolution of resistance and progression to disease during clonal expansion of cancer. 
  • Evolutionary design on a budget: robustness and optimality of bacteriophage T7. 
  • Evolutionary dynamics of self-incompatibility alleles in Brassica. 
  • Evolutionary dynamics of tumor progression with random fitness values. 
  • Evolutionary genetics of plant adaptation. 
  • Evolutionary rate variation in anthocyanin pathway genes. 
  • Evolving sensitivity. 
  • Exact moment calculations for genetic models with migration, mutation, and drift. 
  • Exon 10b of the NF1 gene represents a mutational hotspot and harbors a recurrent missense mutation Y489C associated with aberrant splicing. 
  • Expansion of adult beta-cell mass in response to increased metabolic demand is dependent on HNF-4alpha. 
  • Experimental determination of rates of concerted evolution. 
  • Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. 
  • Explicit equilibrium modeling of transcription-factor binding and gene regulation. 
  • Exploration of a hypothesized independent association of a common 9p21.3 gene variant and ischemic stroke in patients with and without angiographic coronary artery disease. 
  • Extrapolating weak selection in evolutionary games. 
  • Extreme selective sweeps independently targeted the X chromosomes of the great apes. 
  • Facial pain with localized and widespread manifestations: separate pathways of vulnerability. 
  • Failure of the ILD to determine data combinability for slow loris phylogeny. 
  • Familial antiphospholipid antibody syndrome: criteria for disease and evidence for autosomal dominant inheritance. 
  • Family-based association tests for rare variants with censored traits. 
  • Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence. 
  • Flanking nuclear matrix attachment regions synergize with the T cell receptor delta enhancer to promote V(D)J recombination. 
  • Flying at the head of the pack: Wnt biology in Drosophila. 
  • From genotype to phenotype: systems biology meets natural variation. 
  • From the Cover: mitotic gene conversion events induced in G1-synchronized yeast cells by gamma rays are similar to spontaneous conversion events. 
  • Functional assessment of variants in the TSC1 and TSC2 genes identified in individuals with Tuberous Sclerosis Complex. 
  • Functional conservation of human Spastin in a Drosophila model of autosomal dominant-hereditary spastic paraplegia. 
  • Functional evolution of an anthocyanin pathway enzyme during a flower color transition. 
  • Functional polymorphisms of matrix metalloproteinase-9 are associated with risk of occurrence and metastasis of lung cancer. 
  • G-protein-coupled receptor (GPCR) kinase phosphorylation and beta-arrestin recruitment regulate the constitutive signaling activity of the human cytomegalovirus US28 GPCR. 
  • Gene conversion and crossing over along the 405-kb left arm of Saccharomyces cerevisiae chromosome VII. 
  • Gene expression phenotypic models that predict the activity of oncogenic pathways. 
  • Gene flow between Drosophila pseudoobscura and D. persimilis. 
  • Gene flow biases population genetic inference of recombination rate. 
  • Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). 
  • Gene transfer and expression in rat cardiac transplants. 
  • Gene-gene interaction between FGF20 and MAOB in Parkinson disease. 
  • Gene-trait similarity regression for multimarker-based association analysis. 
  • Genealogical histories in structured populations. 
  • Genealogy-dependent variation in viability among self-incompatibility genotypes. 
  • Generation of recombinant adeno-associated virus vectors by a complete adenovirus-mediated approach. 
  • Genes, demography, and life span: the contribution of demographic data in genetic studies on aging and longevity. 
  • Genetic Consequences of Biologically Altered Environments. 
  • Genetic Data from Nearly 63,000 Women of European Descent Predicts DNA Methylation Biomarkers and Epithelial Ovarian Cancer Risk. 
  • Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci. 
  • Genetic analysis of durations: correlated frailty model applied to survival of Danish twins. 
  • Genetic ancestry-smoking interactions and lung function in African Americans: a cohort study. 
  • Genetic animal models of depression and ethanol preference provide support for cholinergic and serotonergic involvement in depression and alcoholism. 
  • Genetic architecture of gene expression traits across diverse populations. 
  • Genetic assimilation and accommodation: Models and mechanisms. 
  • Genetic association models are robust to common population kinship estimation biases. 
  • Genetic association tests based on ranks (GATOR) for quantitative traits with and without censoring. 
  • Genetic editing of colonic organoids provides a molecularly distinct and orthotopic preclinical model of serrated carcinogenesis. 
  • Genetic effects in the leukotriene biosynthesis pathway and association with atherosclerosis. 
  • Genetic evidence reveals temporal change in hybridization patterns in a wild baboon population. 
  • Genetic factors in susceptibility to death: a comparative analysis of bivariate survival models. 
  • Genetic interactions of TGA transcription factors in the regulation of pathogenesis-related genes and disease resistance in Arabidopsis. 
  • Genetic investigation of quantitative traits related to autism: use of multivariate polygenic models with ascertainment adjustment. 
  • Genetic linkage studies in Alzheimer's disease families. 
  • Genetic loci for retinal arteriolar microcirculation. 
  • Genetic model for longitudinal studies of aging, health, and longevity and its potential application to incomplete data. 
  • Genetic models of human vascular disease. 
  • Genetic models reveal origin, persistence and non-redundant functions of IL-17-producing γδ T cells. 
  • Genetic nature of individual frailty: comparison of two approaches. 
  • Genetic network identification using convex programming. 
  • Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling. 
  • Genetic organization, length conservation, and evolution of RNA polymerase II carboxyl-terminal domain. 
  • Genetic polymorphisms and the risk of stroke after cardiac surgery. 
  • Genetic profiling to predict recurrence of early cervical cancer. 
  • Genetic selection for enhanced serine metabolism in cancer development. 
  • Genetic signatures of exceptional longevity in humans. 
  • Genetic simulation tools for post-genome wide association studies of complex diseases. 
  • Genetic variability in beta-defensins is not associated with susceptibility to Staphylococcus aureus bacteremia. 
  • Genetic variants in miR-196a2 and miR-499 are associated with susceptibility to esophageal squamous cell carcinoma in Chinese Han population. 
  • Genetic variations in the mTOR gene contribute toward gastric adenocarcinoma susceptibility in an Eastern Chinese population. 
  • Genetics of gene expression responses to temperature stress in a sea urchin gene network. 
  • Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. 
  • Genome-wide linkage screen in familial Parkinson disease identifies loci on chromosomes 3 and 18. 
  • Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins. 
  • Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. 
  • Genomewide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus). 
  • Genomic approaches for understanding the genetics of complex disease. 
  • Genomic organization, expression, and localization of murine Ran-binding protein 2 (RanBP2) gene. 
  • Genomics and genetics of human and primate y chromosomes. 
  • Genotype-based association test for general pedigrees: the genotype-PDT. 
  • Geographic selection in the small heat shock gene complex differentiating populations of Drosophila pseudoobscura. 
  • Geographical variation in postzygotic isolation and its genetic basis within and between two Mimulus species. 
  • Germline mutations in glial cell line-derived neurotrophic factor (GDNF) and RET in a Hirschsprung disease patient. 
  • Glutathione-S-transferase gene polymorphisms (GSTM1, GSTT1, GSTP1) and idiopathic male infertility: novel perspectives versus facts. 
  • Growth arrest and DNA damage-inducible protein GADD34 assembles a novel signaling complex containing protein phosphatase 1 and inhibitor 1. 
  • HDL-cholesterol levels and risk of age-related macular degeneration: a multiethnic genetic study using Mendelian randomization. 
  • HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC. 
  • Half of the variation in susceptibility to mortality is genetic: findings from Swedish twin survival data. 
  • Haplotype associations with quantitative traits in the presence of complex multilocus and heterogeneous effects. 
  • Heritability of death from coronary heart disease: a 36-year follow-up of 20 966 Swedish twins. 
  • Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. 
  • High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. 
  • Historical effects on beta diversity and community assembly in Amazonian trees. 
  • History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). 
  • Homeostasis and dynamic stability of the phenotype link robustness and plasticity. 
  • Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia. 
  • How Darwinian reductionism refutes genetic determinism. 
  • How accurately can we control the FDR in analyzing microarray data? 
  • How heritable is individual susceptibility to death? The results of an analysis of survival data on Danish, Swedish and Finnish twins. 
  • How long can humans live? Lower bound for biological limit of human longevity calculated from Danish twin data using correlated frailty model. 
  • How the effects of aging and stresses of life are integrated in mortality rates: insights for genetic studies of human health and longevity. 
  • Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species. 
  • Human genetic admixture. 
  • Human promoters are intrinsically directional. 
  • Human retroviral gag- and gag-pol-like proteins interact with the transforming growth factor-beta receptor activin receptor-like kinase 1. 
  • Human strand-specific mismatch repair occurs by a bidirectional mechanism similar to that of the bacterial reaction. 
  • Hybridization can facilitate species invasions, even without enhancing local adaptation. 
  • Hypothesis-independent pathway analysis implicates GABA and acetyl-CoA metabolism in primary open-angle glaucoma and normal-pressure glaucoma. 
  • Identification and utilization of arbitrary correlations in models of recombination signal sequences. 
  • Identification of a novel trimeric autotransporter adhesin in the cryptic genospecies of Haemophilus. 
  • Identification of quantitative trait loci and a candidate locus for freezing tolerance in controlled and outdoor environments in the overwintering crucifer Boechera stricta. 
  • Identification of significant association and gene-gene interaction of GABA receptor subunit genes in autism. 
  • Identification of susceptibility loci contributing to a complex disease using conventional segregation, linkage, and association methods. 
  • Identification of the mating-type (MAT) locus that controls sexual reproduction of Blastomyces dermatitidis. 
  • Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii. 
  • Identification of virulence mutants of the fungal pathogen Cryptococcus neoformans using signature-tagged mutagenesis. 
  • Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays. 
  • Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral. 
  • IgA and IgG antineutrophil cytoplasmic antibody engagement of Fc receptor genetic variants influences granulomatosis with polyangiitis. 
  • Impact of measurement error on testing genetic association with quantitative traits. 
  • Importance sampling for the infinite sites model. 
  • Imprinting evolution and the price of silence. 
  • Imprinting of PEG3, the human homologue of a mouse gene involved in nurturing behavior. 
  • Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance. 
  • Inbreeding depression in non-human primates: a historical review of methods used and empirical data. 
  • Incongruence between genetic and morphological diversity in Microcebus griseorufus of Beza Mahafaly. 
  • Incorporating Functional Information in Tests of Excess De Novo Mutational Load. 
  • Incorporating epigenetic mechanisms to advance fetal programming theories. 
  • Increased efficiency of case-control association analysis by using allele-sharing and covariate information. 
  • Increased vascular smooth muscle contractility in TRPC6-/- mice. 
  • Individual variation in inbreeding depression: the roles of inbreeding history and mutation. 
  • Inductive determination of allele frequency spectrum probabilities in structured populations. 
  • Inference on haplotype/disease association using parent-affected-child data: the projection conditional on parental haplotypes method. 
  • Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. 
  • Influence of network topology and data collection on network inference. 
  • Influence of serotonin transporter promoter region polymorphisms on hippocampal volumes in late-life depression. 
  • InfoEvolve: moving from data to knowledge using information theory and genetic algorithms. 
  • Informative missingness in genetic association studies: case-parent designs. 
  • Informative priors based on transcription factor structural class improve de novo motif discovery. 
  • Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data. 
  • Instability of a plasmid-borne inverted repeat in Saccharomyces cerevisiae. 
  • Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes. 
  • Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. 
  • Integrating statistical genetic and geospatial methods brings new power to phylogeography. 
  • Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. 
  • Integration of plasmids into the bacteriophage T4 genome. 
  • Interactions of TLC1 (which encodes the RNA subunit of telomerase), TEL1, and MEC1 in regulating telomere length in the yeast Saccharomyces cerevisiae. 
  • Interpretation of simultaneous linkage and family-based association tests in genome screens. 
  • Interpreting analyses of continuous covariates in affected sibling pair linkage studies. 
  • Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis. 
  • Interval mapping of viability loci causing heterosis in Arabidopsis. 
  • Intrachromosomal gene conversion and the maintenance of sequence homogeneity among repeated genes. 
  • Intrachromosomal triplication of 2q11.2-q21 in a severely malformed infant: case report and review of triplications and their possible mechanism. 
  • Intragenic duplication and divergence in the spectrin superfamily of proteins. 
  • Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association. 
  • Intratumor heterogeneity in evolutionary models of tumor progression. 
  • Inverted DNA repeats channel repair of distant double-strand breaks into chromatid fusions and chromosomal rearrangements. 
  • Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT). 
  • Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction. 
  • Investigation of Notch3 as a candidate gene for bipolar disorder using brain hyperintensities as an endophenotype. 
  • Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. 
  • Is epigenetic inheritance a counterexample to the central dogma? 
  • Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. 
  • Large recurrent microdeletions associated with schizophrenia. 
  • Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair. 
  • Lattice animal model of chromosome organization 
  • Leveraging population information in family-based rare variant association analyses of quantitative traits. 
  • Life after the screen: making sense of many P-values. 
  • Life history in a model system: opening the black box with Arabidopsis thaliana. 
  • Likelihoods from summary statistics: recent divergence between species. 
  • Limited family structure and breast cancer risk. 
  • Linearity Versus nonlinearity of offspring-parent regression: an experimental study of Drosophila melanogaster. 
  • Linkage analysis with gene-environment interaction: model illustration and performance of ordered subset analysis. 
  • Linkage disequilibrium and haplotype tagging polymorphisms in the Tau H1 haplotype. 
  • Linkage of familial Wilms' tumor predisposition to chromosome 19 and a two-locus model for the etiology of familial tumors. 
  • Linkage of genes for laminin B1 and B2 subunits on chromosome 1 in mouse. 
  • Local frequency dependence and global coexistence. 
  • Localization of a cryptic binding site for tenascin on fibronectin. 
  • Localizing multiple X chromosome-linked retinitis pigmentosa loci using multilocus homogeneity tests. 
  • Long poly(A) tracts in the human genome are associated with the Alu family of repeated elements. 
  • Long-distance dispersal and genetic structure of natural populations: an assessment of the inverse isolation hypothesis in peat mosses. 
  • Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae. 
  • Lotka's game in predator-prey theory: linking populations to individuals. 
  • Markov Chain Monte Carlo approaches to analysis of genetic and environmental components of human developmental change and G x E interaction. 
  • Mathematical modeling: epidemiology meets systems biology. 
  • Mating-type-specific and nonspecific PAK kinases play shared and divergent roles in Cryptococcus neoformans. 
  • Maximal stimulation of meiotic recombination by a yeast transcription factor requires the transcription activation domain and a DNA-binding domain. 
  • Maximum-likelihood estimation of rates of recombination within mating-type regions. 
  • Mcl-1 promotes survival of thymocytes by inhibition of Bak in a pathway separate from Bcl-2. 
  • Mdm2 regulates p53 mRNA translation through inhibitory interactions with ribosomal protein L26. 
  • Measurements of excision repair tracts formed during meiotic recombination in Saccharomyces cerevisiae. 
  • Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. 
  • Measuring the genetic influence in modulating the human life span: gene-environment interaction and the sex-specific genetic effect. 
  • Mechanism of insulin gene regulation by the pancreatic transcription factor Pdx-1: application of pre-mRNA analysis and chromatin immunoprecipitation to assess formation of functional transcriptional complexes. 
  • Mechanisms of DNA-mismatch correction. 
  • Meiotic chromosome distribution in Drosophila oocytes: roles of two kinesin-related proteins. 
  • Meiotic mutants that cause a polar decrease in recombination on the X chromosome in Caenorhabditis elegans. 
  • Meiotic recombination hot spots and cold spots. 
  • Meiotic recombination involving heterozygous large insertions in Saccharomyces cerevisiae: formation and repair of large, unpaired DNA loops. 
  • Meiotic sister chromatid recombination. 
  • Metaphors and the role of genes in development. 
  • Metazoan operons accelerate recovery from growth-arrested states. 
  • Methods for interaction analyses using family-based case-control data: conditional logistic regression versus generalized estimating equations. 
  • Methods for large-scale single mediator hypothesis testing: Possible choices and comparisons. 
  • Methylation of TFPI-2 gene is not the sole cause of its silencing. 
  • MicroRNAs preferentially target the genes with high transcriptional regulation complexity. 
  • Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. 
  • Microsatellite mutation models: insights from a comparison of humans and chimpanzees. 
  • Model selection in binary trait locus mapping. 
  • Modeling RAS phenotype in colorectal cancer uncovers novel molecular traits of RAS dependency and improves prediction of response to targeted agents in patients. 
  • Modeling biological systems using Dynetica--a simulator of dynamic networks. 
  • Modeling the Ames test. 
  • Modeling the effects of biologically incorporated radionuclides and chronic low-dose ionizing radiation exposure on both cancer and chronic non-cancer diseases. 
  • Molecular Clocks without Rocks: New Solutions for Old Problems. 
  • Molecular evolution of X-linked accessory gland proteins in Drosophila pseudoobscura. 
  • Molecular evolution of a Drosophila homolog of human BRCA2. 
  • Molecular insights into the phylogeny and subgeneric classification of Frullania Raddi (Frullaniaceae, Porellales). 
  • Molecular phylogeny of the Entomophthoromycota: 
  • Molecular structures of crossover and noncrossover intermediates during gap repair in yeast: implications for recombination. 
  • Morning glory as a powerful model in ecological genomics: tracing adaptation through both natural and artificial selection. 
  • Morphological and genomic characterization of Filobasidiella depauperata: a homothallic sibling species of the pathogenic cryptococcus species complex. 
  • Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. 
  • Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes. 
  • Multiethnic genome-wide association study of cerebral white matter hyperintensities on MRI. 
  • Multiethnic polygenic risk scores improve risk prediction in diverse populations. 
  • Multifactorial/threshold models and their application to cleft lip and cleft palate. 
  • Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana. 
  • Multilocus test for introgression between the cactophilic species Drosophila mojavensis and Drosophila arizonae. 
  • Multiple colonisations of the western Indian Ocean by Pteropus fruit bats (Megachiroptera: Pteropodidae): the furthest islands were colonised first. 
  • Multiple origins of high reciprocal symbiotic specificity at an intercontinental spatial scale among gelatinous lichens (Collemataceae, Lecanoromycetes). 
  • Multiple, conserved cryptic recombination signals in VH gene segments: detection of cleavage products only in pro B cells. 
  • Multistage designs in the genomic era: providing balance in complex disease studies. 
  • Mutation detection with MutH, MutL, and MutS mismatch repair proteins. 
  • Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. 
  • Mutational origin of new mating type specificities in flowering plants. 
  • Myocyte-enriched calcineurin-interacting protein, MCIP1, inhibits cardiac hypertrophy in vivo. 
  • NOS2A, TLR4, and IFNGR1 interactions influence pulmonary tuberculosis susceptibility in African-Americans. 
  • Natural and orthogonal model for estimating gene-gene interactions applied to cutaneous melanoma. 
  • Natural selection of memory-one strategies for the iterated prisoner's dilemma. 
  • Natural selection on a leaf-shape polymorphism in the ivyleaf morning glory (Ipomoea hederacea). 
  • Neurofibromatosis Type 1 and tumorigenesis: molecular mechanisms and therapeutic implications. 
  • Neuronal activity-regulated gene transcription in synapse development and cognitive function. 
  • New tools for studying integration and modularity. 
  • Newborn, carrier, and early childhood screening recommendations for fragile X. 
  • Nicotine abstinence genotyping: assessing the impact on smoking cessation clinical trials. 
  • Nitrosation and oxidation in the regulation of gene expression. 
  • Non-additive and epistatic effects of HLA polymorphisms contributing to risk of adult glioma. 
  • Noncoding transcription controls downstream promoters to regulate T-cell receptor alpha recombination. 
  • Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. 
  • Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria). 
  • Nonlinear developmental processes as sources of dominance. 
  • North American origin and recent European establishments of the amphi-Atlantic peat moss Sphagnum angermanicum. 
  • Nucleo-cytoplasmic interactions that control nuclear envelope breakdown and entry into mitosis in the sea urchin zygote. 
  • Nucleosome Turnover Regulates Histone Methylation Patterns over the Genome. 
  • Nucleotide bias of DCL and AGO in plant anti-virus gene silencing. 
  • Oct4 RNA interference induces trophectoderm differentiation in mouse embryonic stem cells. 
  • On the evolution of genetic incompatibility systems. III. Introduction of weak gametophytic self-incompatibility under partial inbreeding. 
  • On the evolution of genetic incompatibility systems. V. Origin of sporophytic self-incompatibility in response to overdominance in viability. 
  • On the evolution of genetic incompatibility systems. VI. A three-locus modifier model for the origin of gametophytic self-incompatibility. 
  • On the origin of self-incompatibility haplotypes: transition through self-compatible intermediates. 
  • Optimal sequence selection in proteins of known structure by simulated evolution. 
  • Orai proteins interact with TRPC channels and confer responsiveness to store depletion. 
  • Ordered subset analysis for case-control studies. 
  • Ordered subset analysis in genetic linkage mapping of complex traits. 
  • Ordered-subset analysis (OSA) for family-based association mapping of complex traits. 
  • Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics. 
  • Overexpression of bone morphogenetic protein 10 in myocardium disrupts cardiac postnatal hypertrophic growth. 
  • Overlapping specificities of base excision repair, nucleotide excision repair, recombination, and translesion synthesis pathways for DNA base damage in Saccharomyces cerevisiae. 
  • PI3K/Akt and apoptosis: size matters. 
  • PINA is essential for growth and positively influences NIMA function in Aspergillus nidulans. 
  • PRM1 and KAR5 function in cell-cell fusion and karyogamy to drive distinct bisexual and unisexual cycles in the Cryptococcus pathogenic species complex. 
  • Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. 
  • Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method. 
  • Palindromic sequences in heteroduplex DNA inhibit mismatch repair in yeast. 
  • Partial correction of endogenous DeltaF508 CFTR in human cystic fibrosis airway epithelia by spliceosome-mediated RNA trans-splicing. 
  • Pathway-Structured Predictive Model for Cancer Survival Prediction: A Two-Stage Approach. 
  • Pathway-based identification of SNPs predictive of survival. 
  • Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. 
  • Patterns of chromosomal alterations in breast ductal carcinoma in situ. 
  • Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling? 
  • Persistence and reversal of plasmid-mediated antibiotic resistance. 
  • Perspectives on Unidirectional versus Divergent Transcription. 
  • Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. 
  • Phenotypic homogeneity provides increased support for linkage on chromosome 2 in autistic disorder. 
  • PhyloOncology: Understanding cancer through phylogenetic analysis. 
  • Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA. 
  • Phylogenetic analysis of vertebrate lactate dehydrogenase (LDH) multigene families. 
  • Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta). 
  • Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. 
  • Phylogeographic structure and cryptic speciation in the trans-Antarctic moss Pyrrhobryum mnioides. 
  • Phylogeography's past, present, and future: 10 years after Avise, 2000. 
  • Physical and cDNA mapping in the DBH region of human chromosome 9q34. 
  • Pleiotropic effects of an allele producing white flowers in Ipomoea purpurea. 
  • Polychaetoid is required to restrict segregation of sensory organ precursors from proneural clusters in Drosophila. 
  • Polygenic model of DNA repair genetic polymorphisms in human breast cancer risk. 
  • Polymorphisms and haplotypes of the NBS1 gene are associated with risk of sporadic breast cancer in non-Hispanic white women  
  • Polymorphisms of LIG4 and XRCC4 involved in the NHEJ pathway interact to modify risk of glioma. 
  • Polymorphisms of vitamin D receptor gene protect against the risk of head and neck cancer. 
  • Population dynamics of a meiotic/mitotic expansion model for the fragile X syndrome. 
  • Population genetic inference using a fixed number of segregating sites: a reassessment. 
  • Population genetics, pleiotropy, and the preferential fixation of mutations during adaptive evolution. 
  • Population history in Arabidopsis halleri using multilocus analysis. 
  • Population outbreaks in a discrete world. 
  • Population-genomic inference of the strength and timing of selection against gene flow. 
  • Positional cloning uncovers mutations in PLCE1 responsible for a nephrotic syndrome variant that may be reversible. 
  • Positive patches and negative noodles: linking RNA processing to transcription? 
  • Positive selection on MMP3 regulation has shaped heart disease risk. 
  • Positive selection on a human-specific transcription factor binding site regulating IL4 expression. 
  • Post hoc Analysis for Detecting Individual Rare Variant Risk Associations Using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies. 
  • Potentially functional genetic variants in PLIN2, SULT2A1 and UGT1A9 genes of the ketone pathway and survival of nonsmall cell lung cancer. 
  • Potentially functional variants in the core nucleotide excision repair genes predict survival in Japanese gastric cancer patients. 
  • Power and sample size calculations for SNP association studies with censored time-to-event outcomes. 
  • Precisely modeling zero-inflated count phenotype for rare variants. 
  • Predicted group II intron lineages E and F comprise catalytically active ribozymes. 
  • Predicting the response to simultaneous selection: genetic architecture and physiological constraints. 
  • Prediction of a time-to-event trait using genome wide SNP data. 
  • Preface to the special issue: ecological and evolutionary genomics of populations in nature. 
  • Preserved heart function and maintained response to cardiac stresses in a genetic model of cardiomyocyte-targeted deficiency of cyclooxygenase-2. 
  • Prevalence of transcription promoters within archaeal operons and coding sequences. 
  • Primary immunodeficiency mutation databases. 
  • Principal components of heritability from neurocognitive domains differ between families with schizophrenia and control subjects. 
  • Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models. 
  • Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. 
  • Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae). 
  • Promoter logic. 
  • Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution 
  • Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling. 
  • Protein prediction for trait mapping in diverse populations. 
  • Puzzling role of genetic risk factors in human longevity: "risk alleles" as pro-longevity variants. 
  • Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. 
  • Quantitative modeling of transcription factor binding specificities using DNA shape. 
  • Quantitative models of hybrid dysgenesis: rapid evolution under transposition, extrachromosomal inheritance, and fertility selection. 
  • RB regulates transcription of the p21/WAF1/CIP1 gene. 
  • RNA regulons: coordination of post-transcriptional events. 
  • RNA-DNA hybrid formation at a bacteriophage T4 replication origin. 
  • Rank order metrics for quantifying the association of sequence features with gene regulation. 
  • Rapamycin antifungal action is mediated via conserved complexes with FKBP12 and TOR kinase homologs in Cryptococcus neoformans. 
  • Rapid evolution of social learning. 
  • Rebellious teens? Genetic and environmental influences on the social attitudes of adolescents. 
  • Recent divergence, intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi-Atlantic peatmoss populations. 
  • Receptor-specific ubiquitination of beta-arrestin directs assembly and targeting of seven-transmembrane receptor signalosomes. 
  • Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae. 
  • Recombination-dependent DNA replication stimulated by double-strand breaks in bacteriophage T4. 
  • Reconstructing the temporal ordering of biological samples using microarray data. 
  • Reduced dermatopontin expression is a molecular link between uterine leiomyomas and keloids. 
  • Reducing environmental bias when measuring natural selection. 
  • Regional management units for marine turtles: a novel framework for prioritizing conservation and research across multiple scales. 
  • Regulation of V(D)J recombination: a dominant role for promoter positioning in gene segment accessibility. 
  • Regulation of chromatin accessibility for V(D)J recombination. 
  • Relaxed constraint and evolutionary rate variation between basic helix-loop-helix floral anthocyanin regulators in Ipomoea. 
  • Relaxed natural selection alone does not permit transposable element expansion within 4,000 generations in Escherichia coli. 
  • Reliability of transcriptional cycles and the yeast cell-cycle oscillator. 
  • Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection. 
  • Replication of TCF4 through association and linkage studies in late-onset Fuchs endothelial corneal dystrophy. 
  • Replication studies in longevity: puzzling findings in Danish centenarians at the 3'APOB-VNTR locus. 
  • Review. The strength and genetic basis of reproductive isolating barriers in flowering plants. 
  • Ribonucleotides in DNA: hidden in plain sight. 
  • Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement. 
  • Ring chromosomes and rDNA magnification in Drosophila. 
  • Robust analysis of secondary phenotypes in case-control genetic association studies. 
  • Robust estimation and testing of haplotype effects in case-control studies. 
  • Role for topoisomerase 1 in transcription-associated mutagenesis in yeast. 
  • Roles of RAD6 epistasis group members in spontaneous polzeta-dependent translesion synthesis in Saccharomyces cerevisiae. 
  • SNP selection in genome-wide association studies via penalized support vector machine with MAX test. 
  • SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease. 
  • SNPselector: a web tool for selecting SNPs for genetic association studies. 
  • STIM1 signalling controls store-operated calcium entry required for development and contractile function in skeletal muscle. 
  • Sample size for FDR-control in microarray data analysis. 
  • Scaling in ordered and critical random boolean networks. 
  • Score-based adjustment for confounding by population stratification in genetic association studies. 
  • Segregation and linkage analysis of alpha-N-acetyl-D-glucosaminidase (NAG) levels in a black family. 
  • Segregation at three loci explains familial and population risk in Hirschsprung disease. 
  • Semiparametric tests for identifying differentially methylated loci with case-control designs using Illumina arrays. 
  • SeqSIMLA2: simulating correlated quantitative traits accounting for shared environmental effects in user-specified pedigree structure. 
  • Sequence divergence impedes crossover more than noncrossover events during mitotic gap repair in yeast. 
  • Sequence signatures of a recent chromosomal rearrangement in Drosophila mojavensis. 
  • Sequencing studies in human genetics: design and interpretation. 
  • Sequential synthesis of small capped RNA transcripts in vitro by vesicular stomatitis virus. 
  • Serotonin transporter gene moderates the development of emotional problems among children following bullying victimization. 
  • Sex-specific gene and pathway modeling of inherited glioma risk. 
  • Sex-specific incompatibility generates locus-specific rates of introgression between species. 
  • Sib-pair linkage analysis in late onset Alzheimer's disease. 
  • Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective. 
  • Simple methods for assessing haplotype-environment interactions in case-only and case-control studies. 
  • Simultaneous consideration of multiple candidate protein biomarkers for long-term risk for cardiovascular events. 
  • Single nucleus multi-omics regulatory landscape of the murine pituitary. 
  • Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa. 
  • Small eye (Sey): a mouse model for the genetic analysis of craniofacial abnormalities. 
  • Somatic deletion of the neurofibromatosis type 1 gene in a neurofibrosarcoma supports a tumour suppressor gene hypothesis. 
  • Spatial Measures of Genetic Heterogeneity During Carcinogenesis. 
  • Spatial Moran models, II: cancer initiation in spatially structured tissue. 
  • Spatial models for hybrid zones. 
  • Speciation by reinforcement: a model derived from studies of Drosophila. 
  • Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs. 
  • Sporadic, Global Linkage Disequilibrium Between Unlinked Segregating Sites. 
  • Stage- and ribosome-specific alterations in nascent chain-Sec61p interactions accompany translocation across the ER membrane. 
  • Statistical analysis of antigen receptor spectratype data. 
  • Statistical analysis of genetic interactions in Tn-Seq data. 
  • Statistical analysis of skin tumor data from Tg.AC mouse bioassays. 
  • Statistical methods for studying modularity: a reply to Mitteroecker and Bookstein. 
  • Statistical models for haplotype sharing in case-parent trio data. 
  • Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum. 
  • Stochastic segment models of eukaryotic promoter regions. 
  • Strand-specific mismatch repair in mammalian cells. 
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. 
  • Strategy for investigating interactions between measured genes and measured environments. 
  • Stratification-score matching improves correction for confounding by population stratification in case-control association studies. 
  • Strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS): explanation and elaboration. 
  • Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration. 
  • Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration. 
  • Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. 
  • Strong founder effect in Drosophila pseudoobscura colonizing New Zealand from North America. 
  • Strong genetic effects on cross-situational antisocial behaviour among 5-year-old children according to mothers, teachers, examiner-observers, and twins' self-reports. 
  • Strong reinforcing selection in a Texas wildflower. 
  • Strong selection genome-wide enhances fitness tradeoffs across environments and episodes of selection 
  • Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. 
  • Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex. 
  • Subfunctionalization: How often does it occur? How long does it take? 
  • Superimmunity: characterization of a new gene in the immunity region of P1. 
  • Survival Outcomes in Cancer Patients Predicted by a Partial EMT Gene Expression Scoring Metric. 
  • Systems approaches to identifying gene regulatory networks in plants. 
  • Tagging ribozyme reaction sites to follow trans-splicing in mammalian cells. 
  • Tcra gene recombination is supported by a Tcra enhancer- and CTCF-dependent chromatin hub. 
  • Tcrd Rearrangement Redirects a Processive Tcra Recombination Program to Expand the Tcra Repertoire. 
  • Testing for contributions of mitochondrial DNA mutations to complex diseases. 
  • Testing the effect of rare compound-heterozygous and recessive mutations in case--parent sequencing studies. 
  • The APL test: extension to general nuclear families and haplotypes and examination of its robustness. 
  • The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth. 
  • The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. 
  • The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing 
  • The cyclophilin-like domain of Ran-binding protein-2 modulates selectively the activity of the ubiquitin-proteasome system and protein biogenesis. 
  • The effect of oxidative metabolism on spontaneous Pol zeta-dependent translesion synthesis in Saccharomyces cerevisiae. 
  • The effective rate of influenza reassortment is limited during human infection. 
  • The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support. 
  • The evolution of a complex eucaryotic gene. 
  • The evolution of homing endonuclease genes and group I introns in nuclear rDNA. 
  • The evolutionary dynamics of alpha-satellite. 
  • The evolutionary dynamics of self-incompatibility systems. 
  • The evolutionary history of ferns inferred from 25 low‐copy nuclear genes 
  • The founding of Mauritian endemic coffee trees by a synchronous long-distance dispersal event. 
  • The g-value paradox. 
  • The generation of ordered sets of cosmid DNA clones from human chromosome region 11p. 
  • The genetic architecture of selection at the human dopamine receptor D4 (DRD4) gene locus. 
  • The genetic basis of developmental abnormalities in interpopulation hybrids of the moss Ceratodon purpureus. 
  • The genetic component of discrete disability traits: an analysis using liability models with age-dependent thresholds. 
  • The genetics of speciation by reinforcement. 
  • The genetics of the J wave patterns. 
  • The genome empowerment scale: An assessment of parental empowerment in families with undiagnosed disease. 
  • The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. 
  • The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing. 
  • The heritability of breast cancer: a Bayesian correlated frailty model applied to Swedish twins data. 
  • The heritability of human longevity: a population-based study of 2872 Danish twin pairs born 1870-1900. 
  • The impact of disregarding family structure on genome-wide association analysis of complex diseases in cohorts with simple pedigrees. 
  • The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. 
  • The molecular basis of quantitative genetic variation in central and secondary metabolism in Arabidopsis. 
  • The more you test, the more you find: The smallest P-values become increasingly enriched with real findings as more tests are conducted. 
  • The nature of robustness in development. 
  • The neutral theory and natural selection in the HLA region. 
  • The origins of defective interfering particles of the negative-strand RNA viruses. 
  • The p47 GTPases Igtp and Irgb10 map to the Chlamydia trachomatis susceptibility locus Ctrq-3 and mediate cellular resistance in mice. 
  • The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks. 
  • The putative glucose 6-phosphate translocase gene is mutated in essentially all cases of glycogen storage disease type I non-a. 
  • The relationship between retinal arteriolar and venular calibers is genetically mediated, and each is associated with risk of cardiovascular disease. 
  • The retinitis pigmentosa GTPase regulator (RPGR) interacts with novel transport-like proteins in the outer segments of rod photoreceptors. 
  • The robustness of the transcriptional response to alterations in morphogenetic gradients. 
  • The roles of positive and negative selection in the molecular evolution of insect endosymbionts. 
  • The statistics of bulk segregant analysis using next generation sequencing. 
  • The telomere hypothesis of cellular aging. 
  • The tight linkage between DNA replication and double-strand break repair in bacteriophage T4. 
  • The tor pathway regulates gene expression by linking nutrient sensing to histone acetylation. 
  • The utrophin A 5'-untranslated region confers internal ribosome entry site-mediated translational control during regeneration of skeletal muscle fibers. 
  • The voltage-dependent anion channel (VDAC) binds tissue-type plasminogen activator and promotes activation of plasminogen on the cell surface. 
  • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. 
  • Theoretical and practical advances in genome halving. 
  • Theories of kin and group selection: a population genetics perspective. 
  • Tissue-specific expression and regulation of the alternatively-spliced forms of lysyl hydroxylase 2 (LH2) in human kidney cells and skin fibroblasts. 
  • Topoisomerase I is essential in Cryptococcus neoformans: role In pathobiology and as an antifungal target. 
  • Toward an animal model for antisocial behavior: parallels between mice and humans. 
  • Towards a genetic theory for the evolution of the sex ratio. III. Parental and sibling control of brood investment ratio under partial sib-mating. 
  • Trait-to-gene: a computational method for predicting the function of uncharacterized genes. 
  • Transcriptional network of multiple capsule and melanin genes governed by the Cryptococcus neoformans cyclic AMP cascade. 
  • Transcriptome analysis of mouse stem cells and early embryos. 
  • Transcriptome profiling of genes involved in neural tube closure during human embryonic development using long serial analysis of gene expression (long-SAGE). 
  • Truncating BRCA1 mutations are uncommon in a cohort of hereditary prostate cancer families with evidence of linkage to 17q markers. 
  • Two cyclophilin A homologs with shared and distinct functions important for growth and virulence of Cryptococcus neoformans. 
  • Two types of recombination hotspots in bacteriophage T4: one requires DNA damage and a replication origin and the other does not. 
  • Two-locus genome-wide linkage scan for prostate cancer susceptibility genes with an interaction effect. 
  • Type 2 diabetes: evidence for linkage on chromosome 20 in 716 Finnish affected sib pairs. 
  • Type I glycogen storage diseases: disorders of the glucose-6-phosphatase complex. 
  • Understanding of basic mechanisms of beta-cell function and survival: prelude to new diabetes therapies. 
  • Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. 
  • Using comparative genomic data to test for fast-X evolution. 
  • Using extremal events to characterize noisy time series. 
  • Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. 
  • Validation of a genomic classifier for prediction of metastasis and prostate cancer-specific mortality in African-American men following radical prostatectomy in an equal access healthcare setting. 
  • Variants in PPP3R1 and MAPT are associated with more rapid functional decline in Alzheimer's disease: the Cache County Dementia Progression Study. 
  • Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): phylogenetic implications. 
  • Variations of focal regions versus numbers and positions of sources in two-dimensional media. 
  • Vertebrate sex determination: evolutionary plasticity of a fundamental switch. 
  • WRN helicase is a synthetic lethal target in microsatellite unstable cancers. 
  • Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution. 
  • Whole genomewide linkage screen for neural tube defects reveals regions of interest on chromosomes 7 and 10. 
  • Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae). 
  • X-LRT: a likelihood approach to estimate genetic risks and test association with X-linked markers using a case-parents design. 
  • X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription. 
  • Yeast base excision repair: interconnections and networks. 
  • alpha AD alpha hybrids of Cryptococcus neoformans: evidence of same-sex mating in nature and hybrid fitness. 
  • c-IAP1 is cleaved by caspases to produce a proapoptotic C-terminal fragment. 
  • dUTP incorporation into genomic DNA is linked to transcription in yeast. 
  • gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels. 
• 

  Keywords of People

  • Bejsovec, Amy, Associate Professor of Biology, Biology
  • Berchuck, Andrew, James M. Ingram Distinguished Professor of Gynecologic Oncology, Obstetrics and Gynecology, Gynecologic Oncology
  • Ciofani, Maria, Associate Professor of Integrative Immunobiology, Cell Biology
  • Erickson, Harold Paul, James B. Duke Distinguished Professor Emeritus, Cell Biology
  • Ferrari, Guido, Professor in Surgery, Molecular Genetics and Microbiology
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Hogan, Brigid L. M., Research Professor of Cell Biology, Cell Biology
  • Krangel, Michael S., George Barth Geller Distinguished Professor of Immunology, Integrative Immunobiology
  • Liu, Yutao, Adjunct Assistant Professor in the Department of Medicine, Medicine, Medical Genetics
  • Noor, Mohamed A. F., Professor of Biology, Duke University
  • Shinohara, Mari L., Professor of Integrative Immunobiology, Cell Biology
  • Velkey, John Matthew, Assistant Professor of the Practice of Medical Education in the Department of Cell Biology, Cell Biology
  • Wray, Gregory Allan, Professor of Biology, Evolutionary Anthropology
  • Yoder, Anne Daphne, Braxton Craven Distinguished Professor of Evolutionary Biology, Duke Science & Society