Bioinformatics

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  Subject Areas on Research

  • - : Exploring the outer limits of bacterial pseudogenes 
  • A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data. 
  • A Forecasting Model of Disease Prevalence Based on the McKendrick-von Foerster Equation. 
  • A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal. 
  • A Resource of Mapped Human Bacterial Artificial Chromosome Clones 
  • A Standard MIGS/MIMS Compliant XML Schema: Toward the Development of the Genomic Contextual Data Markup Language (GCDML) 
  • A behavioral summary for completely random nets 
  • A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. 
  • A compact CMOS biochip immunosensor towards the detection of a single bacteria. 
  • A comparative analysis of the information content in long and short SAGE libraries. 
  • A comparison of methods for RNA extraction from lymphocytes for RT-PCR. 
  • A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes. 
  • A critical analysis of computational protein design with sparse residue interaction graphs. 
  • A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. 
  • A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans. 
  • A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs. 
  • A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation. 
  • A kinetic model for the intramolecular distribution of 15N in uric acid in patients with primary gout fed 15N-glycine 
  • A mathematical model of glutathione metabolism. 
  • A methodology for tracking solute distribution in a mathematical model of the kidney 
  • A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. 
  • A novel cross-disciplinary multi-institute approach to translational cancer research: Lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC) 
  • A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme. 
  • A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status. 
  • A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data. 
  • A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. 
  • A preliminary gene map for the Van der Woude syndrome critical region derived from 900 kb of genomic sequence at 1q32-q41. 
  • A protocol for imaging alternative splicing regulation in vivo using fluorescence reporters in transgenic mice. 
  • A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data. 
  • A second locus for hereditary hemorrhagic telangiectasia maps to chromosome 12. 
  • A semiclassical theory for nerve excitation by a low intensity electromagnetic field 
  • A semiclassical theory for nerve excitation by a low intensity electromagnetic field. 
  • A stele-enriched gene regulatory network in the Arabidopsis root. 
  • A study of the repetitive structure and distribution of short motifs in human genomic sequences. 
  • A synthetic Escherichia coli predator-prey ecosystem. 
  • A transcription factor affinity-based code for mammalian transcription initiation. 
  • A xanthine oxidase/colloidal gold enzyme electrode for amperometric biosensor applications 
  • Abrupt population changes along smooth environmental gradients 
  • Advances to Bayesian network inference for generating causal networks from observational biological data. 
  • Advantages of mRNA amplification for microarray analysis. 
  • Age trends in the prevalence of cervical squamous intraepithelial lesions among HIV-positive women in Cameroon: a cross-sectional study. 
  • Alginate encapsulation is a highly reproducible method for tumor cell implantation in dorsal skinfold chambers. 
  • Algorithm for backrub motions in protein design. 
  • All-Atom Contacts: A New Approach to Structure Validation 
  • Alternative ion channel splicing in mesial temporal lobe epilepsy and Alzheimer's disease. 
  • An RNA tertiary switch by modifying how helices are tethered. 
  • An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes. 
  • An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. 
  • An assay for human chorionic gonadotrophin using the capillary fill immunosensor. 
  • An asymptotic solution for traveling waves of a nonlinear-diffusion Fisher's equation 
  • An effective algorithm of motif finding problem. 
  • An efficient parallel algorithm for accelerating computational protein design. 
  • An encyclopedia of mouse DNA elements (Mouse ENCODE). 
  • An improved ontological representation of dendritic cells as a paradigm for all cell types. 
  • An individualized predictor of health and disease using paired reference and target samples. 
  • An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer. 
  • An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. 
  • An ionically based mapping model with memory for cardiac restitution. 
  • An optimization algorithm for a distributed-loop model of an avian urine concentrating mechanism. 
  • Analysis of biological macromolecules and particles by field-flow fractionation. 
  • Analysis of the mouse transcriptome for genes involved in the function of the nervous system. 
  • Angiogenesis: an adaptive dynamic biological patterning problem. 
  • Annotating the human genome with Disease Ontology. 
  • Application of a miniature biochip using the molecular beacon probe in breast cancer gene BRCA1 detection. 
  • Applications of a rat multiple tissue gene expression data set. 
  • Assembly and characterization of heterochromatin and euchromatin on human artificial chromosomes. 
  • Assessment of protein dynamics and DNA repair following generation of DNA double-strand breaks at defined genomic sites. 
  • Automatic annotation of spatial expression patterns via sparse Bayesian factor models. 
  • Avianbase: a community resource for bird genomics. 
  • BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. 
  • BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies. 
  • BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. 
  • Bacterial artificial chromosome cloning and mapping of a 630-kb human extrachromosomal structure. 
  • Bacterial infection remodels the DNA methylation landscape of human dendritic cells. 
  • Bacterial temporal dynamics enable optimal design of antibiotic treatment. 
  • Balancing selection and trans-specific polymorphisms. 
  • BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. 
  • Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. 
  • Bayesian consensus clustering. 
  • Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies. 
  • Bayesian joint analysis of heterogeneous genomics data. 
  • Bayesian network-response regression. 
  • Bayesian segmentation of protein secondary structure. 
  • Beyond a 'skeleton': Understanding cellular functions of the cytoskeleton 
  • Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. 
  • Bifurcation study of blood flow control in the kidney. 
  • Biological control with nonlocal interactions 
  • Biological pathway selection through Bayesian integrative modeling 
  • Biotinylated tags for recovery and characterization of ribonucleoprotein complexes. 
  • Boolean Analysis of Histocompatibility Data and Genetic Mapping 
  • Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer. 
  • CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions. 
  • CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. 
  • Callipyge mutation affects gene expression in cis: a potential role for chromatin structure. 
  • Cancer characterization and feature set extraction by discriminative margin clustering. 
  • Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers. 
  • Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. 
  • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. 
  • Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. 
  • Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. 
  • Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. 
  • Checkpoints couple transcription network oscillator dynamics to cell-cycle progression 
  • Checkpoints couple transcription network oscillator dynamics to cell-cycle progression. 
  • Chemical carcinogenesis and toxicity models: matching complexity to objectives. 
  • Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes 
  • Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. 
  • Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila. 
  • Cloud-based solution to identify statistically significant MS peaks differentiating sample categories. 
  • Clustering gene expression time series data using an infinite Gaussian process mixture model. 
  • Colonoscopy-based colorectal cancer modeling in mice with CRISPR–Cas9 genome editing and organoid transplantation 
  • Community assembly and food web stability 
  • Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen 
  • Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. 
  • Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. 
  • Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. 
  • Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. 
  • Comparative genomics reveals molecular features unique to the songbird lineage. 
  • Comparative genomics search for losses of long-established genes on the human lineage. 
  • Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. 
  • Comparing reference-based RNA-Seq mapping methods for non-human primate data. 
  • Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. 
  • Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling. 
  • Complexity reduction in context-dependent DNA substitution models. 
  • Composition and organization of active centromere sequences in complex genomes. 
  • Computational and experimental identification of novel human imprinted genes. 
  • Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity. 
  • Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5. 
  • Computational inference of neural information flow networks. 
  • Computing van der Waals energies in the context of the rotamer approximation. 
  • Conduction of feedback-mediated signal in a computational model of coupled nephrons. 
  • Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom. 
  • Constructal law: Pleasure, golden ratio, animal locomotion and the design of pedestrian evacuation. Comment on "The emergence of design in pedestrian dynamics: Locomotion, self-organization, walking paths and the constructal law" by A. Miguel 
  • Constructal law: pleasure, golden ratio, animal locomotion and the design of pedestrian evacuation: comment on "The emergence of design in pedestrian dynamics: locomotion, self-organization, walking paths and the constructal law" by A. Miguel. 
  • Control and modulation of fluid flow in the rat kidney. 
  • Cooperation between Polycomb and androgen receptor during oncogenic transformation 
  • Coordinated posttranscriptional mRNA population dynamics during T-cell activation. 
  • Coping with Viral Diversity in HIV Vaccine Design: A Response to Nickle et al. 
  • Coping with viral diversity in HIV vaccine design: a response to Nickle et al. 
  • Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. 
  • Correction to: Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling 
  • Correction: Bang-Bang Control of Feeding: Role of Hypothalamic and Satiety Signals 
  • Coupling spatial segregation with synthetic circuits to control bacterial survival. 
  • Crystal structure of YbaK protein fromHaemophilus influenzae (HI1434) at 1.8 ? resolution: Functional implications 
  • Crystal structure of Yeco fromHaemophilus influenzae (HI0319) reveals a methyltransferase fold and a boundS-adenosylhomocysteine 
  • Crystallization of a fragment of human fibronectin: introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine. 
  • Crystallization of the purine salvage enzyme adenine phosphoribosyltransferase. 
  • Culture and the Constructal-Law evolution of the human and machine species. Comment on "An evolutionary framework for cultural change: Selectionism versus communal exchange" by L. Gabora 
  • Culture and the Constructal-Law evolution of the human and machine species: comment on "An evolutionary framework for cultural change: selectionism versus communal exchange" by L. Gabora. 
  • Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. 
  • DADOS-Prospective: an open source application for Web-based prospective data collection. 
  • DIG--a system for gene annotation and functional discovery. 
  • DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. 
  • Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility. 
  • Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. 
  • Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans. 
  • Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations. 
  • Dependence of paracentric inversion rate on tract length. 
  • Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. 
  • Design and implementation of high-throughput RNAi screens in cultured Drosophila cells. 
  • Design in nature, thermodynamics, and the constructal law: comment on "Life, hierarchy, and the thermodynamic machinery of planet Earth" by A. Kleidon. 
  • Detecting differential copy number variation between groups of samples. 
  • Developing a synthetic psychosocial stress measure and harmonizing CVD-risk data: a way forward to GxE meta- and mega-analyses. 
  • Development of human protein reference database as an initial platform for approaching systems biology in humans. 
  • Developmental control of gene copy number by repression of replication initiation and fork progression. 
  • Developmental control of the DNA replication and transcription programs. 
  • Different methods of sample preparation influence sensitivity of Mycobacterium tuberculosis and Borrelia burgdorferi PCR. 
  • Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. 
  • Digital atlasing and standardization in the mouse brain. 
  • Digital image analysis for rapid quantification of total RNA and cDNA for SMART-PCR. 
  • Dissecting the regulatory architecture of gene expression QTLs. 
  • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. 
  • Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy. 
  • Distinguishing direct versus indirect transcription factor-DNA interactions. 
  • Domain prediction with probabilistic directional context. 
  • Drivers of Inter-individual Variation in Dengue Viral Load Dynamics. 
  • Drug detoxification dynamics explain the postantibiotic effect. 
  • Dynamic DNA methylation across diverse human cell lines and tissues. 
  • Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. 
  • Editorial Foreword 
  • Effect of dimensionality on Lotka-Volterra predator-prey dynamics: Individual based simulation results 
  • Effect of pegloticase on renal function in patients with chronic kidney disease: a post hoc subgroup analysis of 2 randomized, placebo-controlled, phase 3 clinical trials. 
  • Effect of tubular inhomogeneities on feedback-mediated dynamics of a model of a thick ascending limb. 
  • Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin. 
  • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. 
  • Efficiency, selectivity, and robustness of nucleocytoplasmic transport. 
  • Enabling functional genomics with genome engineering. 
  • Encoding of naturalistic stimuli by local field potential spectra in networks of excitatory and inhibitory neurons. 
  • Energy driven cascade recognition for selective detection of nucleic acids with high discrimination factor at room temperature. 
  • Enhancement of transport selectivity through nano-channels by non-specific competition. 
  • Epigenetic assimilation in the aging human brain. 
  • Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer. 
  • Errata: BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies (Genome Research (2015) 25 (155-166)) 
  • Erratum 
  • Erratum 
  • Erratum to: Host lifestyle affects human microbiota on daily timescales. 
  • Erratum: A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat (Genome Research (1999) 9, (AP1-AP8)) 
  • Erratum: Applications of a rat multiple tissue gene expression data set (Genome Research (2004) vol. 14 (742-749)) 
  • Erratum: Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets (Genome Research (2012) 22 (386-397)) 
  • Erratum: RIP-Chip: The isolation and identification of mRNAs, microRNAS and protein components of ribonucleoprotein complexes from cell extracts (Nature Protocols (2006) vol. 1 (302-307) 10.1038/nprot.2006.47) 
  • Establishing reporting standards for metabolomic and metabonomic studies: a call for participation. 
  • Estimating genomic coexpression networks using first-order conditional independence. 
  • Estimating the Probability of Polyreactive Antibodies 4E10 and 2F5 Disabling a gp41 Trimer after T Cell-HIV Adhesion 
  • Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping 
  • Evaluating cell-surface expression and measuring activation of mammalian odorant receptors in heterologous cells. 
  • Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping. 
  • Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1. 
  • Existence and uniqueness of solutions to a mathematical model of the urine concentrating mechanism 
  • Expanding the diversity of DNA base modifications with N⁶-methyldeoxyadenosine. 
  • Explant culture of adult zebrafish hearts for epicardial regeneration studies. 
  • Explicit equilibrium modeling of transcription-factor binding and gene regulation. 
  • Expressed sequence tag analysis in Cycas, the most primitive living seed plant. 
  • Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster. 
  • Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images 
  • Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. 
  • Extrapolating weak selection in evolutionary games. 
  • Extrema-weighted feature extraction for functional data. 
  • F-Seq: a feature density estimator for high-throughput sequence tags. 
  • Fabrication of an autoclavable one-way valve for venting fermentation gases. 
  • Familial and sporadic idiopathic pulmonary fibrosis: making the diagnosis from peripheral blood. 
  • Fast gap-free enumeration of conformations and sequences for protein design. 
  • Feedback-mediated dynamics in a model of a compliant thick ascending limb. 
  • Field-induced forces at dielectric interfaces as a possible mechanism of RF hearing effects. 
  • Finite element modelling of pulsatile blood flow in idealized model of human aortic arch: study of hypotension and hypertension. 
  • Fluorescence in situ hybridization method for measuring transfection efficiency. 
  • Focal delivery of neurotrophins into the central nervous system using fluorescent latex microspheres. 
  • From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. 
  • From spiking neuron models to linear-nonlinear models. 
  • Functional genomics of membrane transporters in human populations 
  • GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. 
  • Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation 
  • Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. 
  • Gene selection using iterative feature elimination random forests for survival outcomes. 
  • Generation and customization of biosynthetic excitable tissues for electrophysiological studies and cell-based therapies. 
  • Generation of orthotopic and heterotopic human pancreatic cancer xenografts in immunodeficient mice. 
  • Genetic engineering of a single-chain antibody fragment for surface immobilization in an optical biosensor. 
  • Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology. 
  • Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies. 
  • Genome accessibility is widely preserved and locally modulated during mitosis. 
  • Genome annotation assessment in Drosophila melanogaster. 
  • Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. 
  • Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors. 
  • Genome-scale phylogenetic function annotation of large and diverse protein families 
  • Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. 
  • Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). 
  • Genome-wide prediction of imprinted murine genes. 
  • Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. 
  • Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. 
  • Genomic approaches for understanding the genetics of complex disease. 
  • Genomic characterization of large heterochromatic gaps in the human genome assembly. 
  • Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. 
  • Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. 
  • Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles. 
  • Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. 
  • Group Theoretical and Combinatorial Analysis of Histocompatibility and Switching Algebra 
  • HPV clearance and the neglected role of stochasticity. 
  • Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. 
  • Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. 
  • Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies. 
  • High heritability of metabolomic profiles in families burdened with premature cardiovascular disease. 
  • High prevalence of hypertension and cardiovascular disease risk factors among medical students at Makerere University College of Health Sciences, Kampala, Uganda 
  • High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer. 
  • High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. 
  • High-resolution mapping of open chromatin in the rice genome. 
  • High-throughput genotyping with single nucleotide polymorphisms. 
  • High-throughput inference of protein-protein interfaces from unassigned NMR data. 
  • High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. 
  • Highly active zinc-finger nucleases by extended modular assembly. 
  • Host lifestyle affects human microbiota on daily timescales. 
  • Human and mouse alpha-synuclein genes: comparative genomic sequence analysis and identification of a novel gene regulatory element. 
  • Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants. 
  • Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing. 
  • IDENTIFYING PATTERNS OF DNA FOR TUMOR DIAGNOSIS USING CAPILLARY ELECTROPHORESIS-AMPLIFIED FRAGMENT LENGTH POLYMORPHISM (CE-AFLP) SCREENING 
  • IN SILICO PHENOTYPIC SCREENING METHOD OF MUTANTS BASED ON STATISTICAL MODELING OF GENETICALLY MIXED SAMPLES 
  • Identification and isolation of differentially expressed genes from very small tissue samples. 
  • Identification and utilization of arbitrary correlations in models of recombination signal sequences. 
  • Identification of co-regulated transcripts affecting male body size in Drosophila. 
  • Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. 
  • Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals. 
  • Identifying candidate causal variants responsible for altered activity of the ABCB1 multidrug resistance gene. 
  • Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins. 
  • Importance sampling for the infinite sites model. 
  • Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. 
  • Improved energy bound accuracy enhances the efficiency of continuous protein design. 
  • Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. 
  • In silico evolution of functional modules in biochemical networks 
  • In vivo optical molecular imaging and analysis in mice using dorsal window chamber models applied to hypoxia, vasculature and fluorescent reporters. 
  • In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors. 
  • Infectious pathogen detection arrays: viral detection in cell lines and postmortem brain tissue. 
  • Instrumenting the health care enterprise for discovery research in the genomic era 
  • Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. 
  • Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. 
  • Integrating statistical pair potentials into protein complex prediction. 
  • Integrative Pathway Analysis Using Graph-Based Learning with Applications to TCGA Colon and Ovarian Data. 
  • Integrative pathway analysis using Graph-Based learning with applications to TCGA colon and ovarian data 
  • Interpolated markov chains for eukaryotic promoter recognition. 
  • Joint eQTL assessment of whole blood and dura mater tissue from individuals with Chiari type I malformation. 
  • K r /K c but not d N /d S correlates positively with body mass in birds, raising implications for inferring lineage-specific selection 
  • Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage 
  • LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. 
  • Laser capture microdissection in 2-D co-culture models as a tool to study tumor-stroma interactions. 
  • Leveraging prior information to detect causal variants via multi-variant regression. 
  • Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling. 
  • Linear Latent Structure Analysis and Modelling of Multiple Categorical Variables 
  • Localization of the C-terminus of rat glutathione S-transferase A1-1: crystal structure of mutants W21F and W21F/F220Y. 
  • Localized delivery of DNA to the cells by viral collagen-loaded silica colloidal crystals. 
  • MAGI: a Node. js web service for fast MicroRNA-Seq Analysis in a GPU Infrastructure 
  • MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. 
  • Magnetic separation to concentrate the estrogen receptor from adipose tissue for western analysis. 
  • Managing Multi-center Flow Cytometry Data for Immune Monitoring. 
  • Mapping nucleosome positions using DNase-seq. 
  • Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. 
  • Mathematical model insights into arsenic detoxification 
  • Mathematical model insights into arsenic detoxification. 
  • Mathematical modeling of renal hemodynamics in physiology and pathophysiology. 
  • Mathematical modeling of the effects of glutathione on arsenic methylation. 
  • Maximization of signal derived from cDNA microarrays. 
  • Medical cost trajectories and onsets of cancer and noncancer diseases in US elderly population. 
  • Meeting Report: The Fifth Genomic Standards Consortium (GSC) Workshop 
  • Memory capacity of networks with stochastic binary synapses. 
  • Mesoscopic hydrogel molding to control the 3D geometry of bioartificial muscle tissues. 
  • Metabolic pattern formation in the tumor microenvironment. 
  • Metabolic rewiring drives resistance to targeted cancer therapy. 
  • Methods for generating and colonizing gnotobiotic zebrafish. 
  • Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers 
  • Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group. 
  • Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study. 
  • Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data. 
  • Modeling Glucose Metabolism in the Kidney. 
  • Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies. 
  • Modeling endocrine control of the pituitary-ovarian axis: androgenic influence and chaotic dynamics. 
  • Modeling glucose metabolism and lactate production in the kidney. 
  • Modifier genetics in neuropsychiatric disease: challenges and opportunities 
  • Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. 
  • Molprobity's ultimate rotamer-library distributions for model validation. 
  • Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitrite. 
  • Multistable dynamics mediated by tubuloglomerular feedback in a model of coupled nephrons. 
  • Myocardial infarction and intramyocardial injection models in swine. 
  • NMR structural inference of symmetric homo-oligomers. 
  • Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair. 
  • Network-based SNP meta-analysis identifies joint and disjoint genetic features across common human diseases. 
  • Neuron's eye view: Inferring features of complex stimuli from neural responses. 
  • Neuroprosthetic Decoder Training as Imitation Learning. 
  • Next generation distributed computing for cancer research. 
  • Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications. 
  • Noise reduction by diffusional dissipation in a minimal quorum sensing motif. 
  • Novel computational methods for increasing PCR primer design effectiveness in directed sequencing 
  • Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation. 
  • Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans. 
  • On the maternal transmission of immunity: A ‘molecular attention’ hypothesis 
  • OntologyWidget - a reusable, embeddable widget for easily locating ontology terms. 
  • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. 
  • Optical aberrations and objective choice in multicolor confocal microscopy. 
  • Optical immunosensing systems--meeting the market needs. 
  • Optimized regimen for expression of heat-inducible Cre in mice. 
  • Optogenetic manipulation of neural circuits and behavior in Drosophila larvae. 
  • Ordinary Differential Equation Models for Adoptive Immunotherapy. 
  • Origin of bistability underlying mammalian cell cycle entry. 
  • Osteoprotegerin in bone metastases: mathematical solution to the puzzle. 
  • Overcoming Barriers in the Implementation of Personalized Medicine into Clinical Practice 
  • PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. 
  • Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression. 
  • Parametric modeling of cellular state transitions as measured with flow cytometry. 
  • Parametric modeling of cellular state transitions as measured with flow cytometry. 
  • Pathway analysis using random forests classification and regression. 
  • Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species 
  • Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. 
  • Performance of in-line microfluidic mixers in laminar flow for high-throughput flow cytometry. 
  • Phase-independent rhythmic analysis of genome-wide expression patterns. 
  • Phenotypic signatures arising from unbalanced bacterial growth. 
  • Phylogenetic footprint analysis of IGF2 in extant mammals. 
  • Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. 
  • Phylogeographic ancestral inference using the coalescent model on haplotype trees. 
  • Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. 
  • Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. 
  • Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans. 
  • Post-translational regulation enables robust p53 regulation. 
  • Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome. 
  • Predicting gene structure changes resulting from genetic variants via exon definition features. 
  • Preparation of N-succinimidyl 3-[*I]iodobenzoate: an agent for the indirect radioiodination of proteins. 
  • Prevalence and correlates of proteinuria in Kampala, Uganda: a cross-sectional pilot study. 
  • Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. 
  • Principles of microRNA regulation of a human cellular signaling network. 
  • Principles that govern competition or co-existence in Rho-GTPase driven polarization. 
  • Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum. 
  • Probabilistic fluorescence-based synapse detection. 
  • Processing Oscillatory Signals by Incoherent Feedforward Loops. 
  • Propagation of Fluctuations in Biochemical Systems, I: Linear SSC Networks 
  • Propagation of fluctuations in biochemical systems, I: linear SSC networks. 
  • Propagation of fluctuations in biochemical systems, II: nonlinear chains 
  • Protein design using continuous rotamers. 
  • Protein loop closure using orientational restraints from NMR data. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Pulling the genome in opposite directions to dissect gene networks 
  • Pyruvate aldolases in chiral carbon-carbon bond formation. 
  • Quantifying the effects of elastic collisions and non-covalent binding on glutamate receptor trafficking in the post-synaptic density 
  • Quantum mechanics simulation of protein dynamics on long timescale. 
  • RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. 
  • RNA-Seq optimization with eQTL gold standards. 
  • RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. 
  • RS-SNP: a random-set method for genome-wide association studies. 
  • Race and sex differences in small-molecule metabolites and metabolic hormones in overweight and obese adults. 
  • Random forests for genetic association studies. 
  • Rank order metrics for quantifying the association of sequence features with gene regulation. 
  • Rapid 16S ribosomal DNA sequencing from a single colony without DNA extraction or purification. 
  • Rapid purification of microtubule motor domain proteins expressed in bacteria. 
  • Reconstructing the temporal ordering of biological samples using microarray data. 
  • Reconstruction of cell population dynamics using CFSE. 
  • Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. 
  • Reducing mass degeneracy in SAR by MS by stable isotopic labeling. 
  • Regression analysis of multiple protein structures. 
  • Reliability of transcriptional cycles and the yeast cell-cycle oscillator 
  • Removable cranial windows for long-term imaging in awake mice. 
  • Rescue of targeted regions of mammalian chromosomes by in vivo recombination in yeast. 
  • Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio) by transcriptome profiling. 
  • Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. 
  • Risk of dislocation using large- vs. small-diameter femoral heads in total hip arthroplasty 
  • SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. 
  • SNPselector: a web tool for selecting SNPs for genetic association studies. 
  • SNiPA: an interactive, genetic variant-centered annotation browser. 
  • SPR biosensors: simultaneously removing thermal and bulk-composition effects1This paper was presented at the Fifth World Congress on Biosensors, Berlin, Germany, 3–5 June 1998.1 
  • STDP in a bistable synapse model based on CaMKII and associated signaling pathways. 
  • SVA: software for annotating and visualizing sequenced human genomes. 
  • Sample size for FDR-control in microarray data analysis. 
  • Search for organising principles: understanding in systems biology. 
  • Security Assessment of Cyberphysical Digital Microfluidic Biochips. 
  • Segregation and mixing in degenerate diffusion in population dynamics 
  • Self monitoring of blood glucose - a survey of diabetes UK members with type 2 diabetes who use SMBG 
  • Sensitive DNA detection and SNP discrimination using ultrabright SERS nanorattles and magnetic beads for malaria diagnostics. 
  • Sensitivity enhancement of optical immunosensors by the use of a surface plasmon resonance fluoroimmunoassay. 
  • Sequence specificity incompletely defines the genome-wide occupancy of Myc. 
  • Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. 
  • Sequential gene profiling of basal cell carcinomas treated with imiquimod in a placebo-controlled study defines the requirements for tissue rejection. 
  • Serial dilution curve: a new method for analysis of reverse phase protein array data. 
  • Sex differences in hepatic one-carbon metabolism. 
  • Signal duration and the time scale dependence of signal integration in biochemical pathways. 
  • SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements. 
  • Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. 
  • Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes. 
  • SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization. 
  • Spatial Measures of Genetic Heterogeneity During Carcinogenesis. 
  • Spatial preferences of microRNA targets in 3' untranslated regions. 
  • Stability selection for regression-based models of transcription factor-DNA binding specificity. 
  • Stability, instability in delay equations modeling human respiration. 
  • Stable oscillations in single species growth models with hereditary effects 
  • Stakeholder Perspectives on Public Health Genomics Applications for Sickle Cell Disease: A Methodology for a Human Heredity and Health in Africa (H3Africa) Qualitative Research Study 
  • State dependence of stimulus-induced variability tuning in macaque MT. 
  • Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. 
  • Statistical analysis of RNA backbone. 
  • Statistical analysis of antigen receptor spectratype data. 
  • Statistical estimation of statistical mechanical models: helix-coil theory and peptide helicity prediction. 
  • Stochastic model for analysis of longitudinal data on aging and mortality. 
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. 
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. 
  • Stratified pathway analysis to identify gene sets associated with oral contraceptive use and breast cancer. 
  • Structural analysis, identification, and design of calcium-binding sites in proteins. 
  • Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin. 
  • Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing. 
  • Structure validation by Calpha geometry: phi,psi and Cbeta deviation. 
  • Supporting the SBML layout extension 
  • Synchronization in stress p53 network. 
  • Synchronous luminescence: a new detection technique for multiple fluorescent probes used for DNA sequencing. 
  • Systematic assessment of imputation performance using the 1000 Genomes reference panels. 
  • Systematic solution to homo-oligomeric structures determined by NMR. 
  • T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. 
  • THE EFFECT OF THE ORGANISMS' BODY SIZE AND ENERGY RESERVES IN MODELS FOR POPULATION DYNAMICS 
  • Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). 
  • Target domain definition and classification in CASP8. 
  • Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network. 
  • Taste and pheromone perception in mammals and flies. 
  • Temporal control of self-organized pattern formation without morphogen gradients in bacteria. 
  • Ten Simple Rules for Effective Statistical Practice. 
  • The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes. 
  • The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. 
  • The Bioinformatics Open Source Conference (BOSC) 2013. 
  • The Bioperl toolkit: Perl modules for the life sciences. 
  • The E6-Ap ubiquitin-protein ligase (UBE3A) gene is localized within a narrowed Angelman syndrome critical region. 
  • The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. 
  • The PLOS Computational Biology Software Section. 
  • The STEDMAN project: biophysical, biochemical and metabolic effects of a behavioral weight loss intervention during weight loss, maintenance, and regain. 
  • The biochemistry of acetaminophen hepatotoxicity and rescue: a mathematical model. 
  • The cis-Pro touch-turn: a rare motif preferred at functional sites. 
  • The constructal law and the evolution of design in nature. 
  • The constructal law makes biology and economics be like physics 
  • The constructal unification of biological and geophysical design. 
  • The continuum of causality in human genetic disorders. 
  • The cyclophilins. 
  • The distribution of variation in regulatory gene segments, as present in MHC class II promoters. 
  • The effect of polar lipids on tear film dynamics. 
  • The effects of health histories on stochastic process models of aging and mortality. 
  • The elements of stem cell self-renewal: a genetic perspective. 
  • The evolutionary dynamics of alpha-satellite. 
  • The human olfactory transcriptome. 
  • The influence of a consumer-wearable activity tracker on sedentary time and prolonged sedentary bouts: secondary analysis of a randomized controlled trial. 
  • The inoculum effect and band-pass bacterial response to periodic antibiotic treatment. 
  • The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. 
  • The penultimate rotamer library. 
  • The role of local backrub motions in evolved and designed mutations. 
  • The statistics of bulk segregant analysis using next generation sequencing. 
  • The surface of beta-sheet proteins contains amphiphilic regions which may provide clues about protein folding. 
  • The transport of organelles in axons 
  • The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms. 
  • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. 
  • Transfer Function Analysis of Dynamic Blood Flow Control in the Rat Kidney. 
  • Translational Bioinformatics: Past, Present, and Future. 
  • Tubular fluid flow and distal NaCl delivery mediated by tubuloglomerular feedback in the rat kidney 
  • Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation. 
  • Unsupervised Bayesian linear unmixing of gene expression microarrays. 
  • Using context to improve protein domain identification. 
  • Virtual Patients and Sensitivity Analysis of the Guyton Model of Blood Pressure Regulation: Towards Individualized Models of Whole-Body Physiology 
  • WGAViewer: software for genomic annotation of whole genome association studies. 
  • WebGLORE: a web service for Grid LOgistic REgression. 
  • Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. 
  • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. 
  • Whole-genome reconstruction and mutational signatures in gastric cancer. 
  • ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. 
  • bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens. 
  • cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. 
  • comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. 
  • lambda RNA internal standards quantify sensitivity and amplification efficiency of mammalian gene expression profiling. 
  • lumi: a pipeline for processing Illumina microarray. 
  • meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays. 
  • nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. 
  • permGPU: Using graphics processing units in RNA microarray association studies. 
  • rqt: an R package for gene-level meta-analysis. 
  • stpm: an R package for stochastic process model. 
  • λRNA internal standards quantify sensitivity and amplification efficiency of mammalian gene expression profiling 
• 

  Keywords of People

  • Arnold, Matthias, Adjunct Assistant Professor in the Department of Psychiatry and Behavioral Sciences, Psychiatry & Behavioral Sciences, Behavioral Medicine
  • Coronado Sroka, Eduardo, Student, Statistical Science
  • Hong, Julian, House Staff, Radiation Oncology
  • Kibbe, Warren Alden, Professor - Track V in Biostatistics and Bioinformatics, Biostatistics & Bioinformatics
  • Tchapyjnikov, Dmitry, Assistant Professor - Track IV of Pediatrics, Pediatrics, Neurology
  • Tenenbaum, Jessica Dale, Assistant Professor - Track V of Biostatistics & Bioinformatics, Duke Science & Society
  • Wu, Qingrong, Professor of Radiation Oncology, Radiation Oncology
  • Yin, Fang-Fang, Professor in Radiation Oncology, Radiation Oncology