Computational Biology

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  Subject Areas on Research

  • 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. 
  • A Fringe-modified Notch signal affects specification of mesoderm and endoderm in the sea urchin embryo. 
  • A Genome-Wide Association Study Identifies Two Novel Susceptible Regions for Squamous Cell Carcinoma of the Head and Neck. 
  • A Machine-Learning-Based Drug Repurposing Approach Using Baseline Regularization. 
  • A Multidimensional Bioinformatic Platform for the Study of Human Response to Surgery. 
  • A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. 
  • A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks. 
  • A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. 
  • A comparative analysis of the information content in long and short SAGE libraries. 
  • A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits. 
  • A computational analysis of antisense off-targets in prokaryotic organisms. 
  • A computational method to classify variants of uncertain significance using functional assay data with application to BRCA1. 
  • A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays. 
  • A draft genome sequence of the elusive giant squid, Architeuthis dux. 
  • A five-gene hedgehog signature developed as a patient preselection tool for hedgehog inhibitor therapy in medulloblastoma. 
  • A five-gene phylogeny of Pezizomycotina. 
  • A framework for annotating human genome in disease context. 
  • A framework for integrating the songbird brain. 
  • 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 genetic memory initiates the epigenetic loop necessary to preserve centromere position. 
  • A genetic stochastic process model for genome-wide joint analysis of biomarker dynamics and disease susceptibility with longitudinal data. 
  • A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. 
  • A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. 
  • A genomic regulatory network for development. 
  • A glutaminase isoform switch drives therapeutic resistance and disease progression of prostate cancer. 
  • A gradient-directed Monte Carlo approach for protein design. 
  • A hybrid framework for genome wide epistasis discovery. 
  • A leave-one-out cross-validation SAS macro for the identification of markers associated with survival. 
  • A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression. 
  • A mathematical model of the methionine cycle. 
  • A multidisciplinary approach to probing enthalpy-entropy compensation and the interfacial mobility model. 
  • A new method to accurately identify single nucleotide variants using small FFPE breast samples. 
  • A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease. 
  • A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement. 
  • A permutation-based multiple testing method for time-course microarray experiments. 
  • A phylogenetic transform enhances analysis of compositional microbiota data. 
  • A power-law dependence of bacterial invasion on mammalian host receptors. 
  • A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers. 
  • A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. 
  • 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 synthetic biology challenge: making cells compute. 
  • A whole genome approach for discovering the genetic basis of blood group antigens: independent confirmation for P1 and Xg^a . 
  • ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves. 
  • Absence of a simple code: how transcription factors read the genome. 
  • Active learning for computational chemogenomics. 
  • Active-learning strategies in computer-assisted drug discovery. 
  • AglQ is a novel component of the Haloferax volcanii N-glycosylation pathway. 
  • All-atom contacts: a new approach to structure validation. 
  • An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. 
  • An ERCC4 regulatory variant predicts grade-3 or -4 toxicities in patients with advanced non-small cell lung cancer treated by platinum-based therapy. 
  • An active learning approach for rapid characterization of endothelial cells in human tumors. 
  • An age-independent gene signature for monitoring acute rejection in kidney transplantation. 
  • 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 application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. 
  • An approach to modelling in immunology. 
  • An atlas of genetic influences on human blood metabolites. 
  • An embryonic system to assess direct and indirect Wnt transcriptional targets. 
  • An evaluation of copy number variation detection tools from whole-exome sequencing data. 
  • An international bioinformatics infrastructure to underpin the Arabidopsis community. 
  • An overview of genomic data analysis. 
  • Analysis of the Rab GTPase Interactome in Dendritic Cells Reveals Anti-microbial Functions of the Rab32 Complex in Bacterial Containment. 
  • Analytic gain in probabilistic decompression sickness models. 
  • Angiogenesis: an adaptive dynamic biological patterning problem. 
  • Annotating the human genome with Disease Ontology. 
  • Antigen receptor repertoire profiling from RNA-seq data. 
  • Application of combined omics platforms to accelerate biomedical discovery in diabesity. 
  • Application of proteomic marker ensembles to subcellular organelle identification. 
  • Aquatic models, genomics and chemical risk management. 
  • Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. 
  • Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements. 
  • Assessing transcription factor motif drift from noisy decoy sequences. 
  • Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches. 
  • Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis. 
  • Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. 
  • Automated constraint-based nucleotide sequence selection for DNA computation. 
  • Automatic annotation of spatial expression patterns via sparse Bayesian factor models. 
  • 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. 
  • BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. 
  • Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions. 
  • Bayesian network-response regression. 
  • Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data. 
  • Best practices and lessons learned from reuse of 4 patient-derived metabolomics datasets in Alzheimer's disease. 
  • Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. 
  • Bile acid aspiration associated with lung chemical profile linked to other biomarkers of injury after lung transplantation. 
  • BioWarehouse: a bioinformatics database warehouse toolkit. 
  • Biochemistry. Exciting structures. 
  • Bioinformatic challenges in targeted proteomics. 
  • Bioinformatic design of A-kinase anchoring protein-in silico: a potent and selective peptide antagonist of type II protein kinase A anchoring. 
  • Bioinformatics Associated With Conjoined Twin Separation. 
  • Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation. 
  • Biology by design: reduction and synthesis of cellular components and behaviour. 
  • Bone-associated gene evolution and the origin of flight in birds. 
  • Bottom up: a modular view of immunology. 
  • Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding. 
  • Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer. 
  • Building Statistical Models to Analyze Species Distributions 
  • CRISPR-Cas "Non-Target" Sites Inhibit On-Target Cutting Rates. 
  • CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer. 
  • Cancer Data Science and Computational Medicine. 
  • Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research. 
  • Cancer Moonshot Data and Technology Team: Enabling a National Learning Healthcare System for Cancer to Unleash the Power of Data. 
  • Carbonic anhydrase and CO2 sensing during Cryptococcus neoformans growth, differentiation, and virulence. 
  • Causal network inference from gene transcriptional time-series response to glucocorticoids. 
  • Cell-free DNA diagnostics in transplantation utilizing next generation sequencing. 
  • Cell-internalization SELEX: method for identifying cell-internalizing RNA aptamers for delivering siRNAs to target cells. 
  • Centralized biorepositories for genetic and genomic research. 
  • Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types. 
  • Characterization of the Saccharomyces cerevisiae ATP-Interactome using the iTRAQ-SPROX Technique. 
  • Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. 
  • Chemical interrogation of the malaria kinome. 
  • Cheminformatic Analysis of Natural Product Fragments. 
  • Chemotactic movement of a polarity site enables yeast cells to find their mates. 
  • Chromatin signatures of the Drosophila replication program. 
  • Circular RNAs are abundant, conserved, and associated with ALU repeats. 
  • ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis. 
  • Clinically focused exome sequencing identifies an homozygous mutation that confers DOCK8 deficiency. 
  • Clustering gene expression time series data using an infinite Gaussian process mixture model. 
  • Co-regulation of nuclear respiratory factor-1 by NFkappaB and CREB links LPS-induced inflammation to mitochondrial biogenesis. 
  • Coarse and reliable geometric alignment for protein docking. 
  • Collaborating with Undergraduates To Contribute to Biochemistry Community Resources. 
  • Combining MALDI-FTMS and bioinformatics for rapid peptidomic comparisons. 
  • Combining gene expression, demographic and clinical data in modeling disease: a case study of bipolar disorder and schizophrenia. 
  • Comparative Loss-of-Function Screens Reveal ABCE1 as an Essential Cellular Host Factor for Efficient Translation of Paramyxoviridae and Pneumoviridae. 
  • Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing. 
  • Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. 
  • Comparative genomics as a tool for gene discovery. 
  • Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. 
  • Comparative proteomic characterization of articular cartilage tissue from normal donors and patients with osteoarthritis. 
  • Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. 
  • Completeness of HIV-1 Envelope Glycan Shield at Transmission Determines Neutralization Breadth. 
  • Comprehensive Characterization of Cancer Driver Genes and Mutations. 
  • Comprehensive genomic profiling of pancreatic acinar cell carcinomas identifies recurrent RAF fusions and frequent inactivation of DNA repair genes. 
  • Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. 
  • Computation in neural systems. Editorial. 
  • Computation of mutual information from Hidden Markov Models. 
  • Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. 
  • Computational Analysis of Targeting SARS-CoV-2, Viral Entry Proteins ACE2 and TMPRSS2, and Interferon Genes by Host MicroRNAs. 
  • Computational Methods for RNA Structure Validation and Improvement. 
  • Computational analysis of antibody dynamics identifies recent HIV-1 infection. 
  • Computational analysis of core promoters in the Drosophila genome. 
  • Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors. 
  • Computational and experimental identification of novel human imprinted genes. 
  • Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. 
  • Computational design of a biologically active enzyme. 
  • Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5. 
  • Computational immunology--from bench to virtual reality. 
  • Computational modelling and analysis of the molecular network regulating sporulation initiation in Bacillus subtilis. 
  • Computational prediction of efficient splice sites for trans-splicing ribozymes. 
  • Computational protein engineering. 
  • Computational tools for understanding sequence variability in recombination signals. 
  • Computing van der Waals energies in the context of the rotamer approximation. 
  • Contrasts between adaptive coding and noncoding changes during human evolution. 
  • Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. 
  • Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. 
  • Critical assessment of automated flow cytometry data analysis techniques. 
  • Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. 
  • Cross-study projections of genomic biomarkers: an evaluation in cancer genomics. 
  • Cryptic phosphorylation in nucleoside natural product biosynthesis. 
  • Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow. 
  • DNA methylation alterations in response to pesticide exposure in vitro. 
  • Decision tree classification of proteins identified by mass spectrometry of blood serum samples from people with and without lung cancer. 
  • Design and Analysis of Large-Scale Biological Rhythm Studies: A Comparison of Algorithms for Detecting Periodic Signals in Biological Data 
  • Detecting and characterizing circular RNAs. 
  • Detection of viruses via statistical gene expression analysis. 
  • Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors. 
  • Development of a quantitative morphological assessment of toxicant-treated zebrafish larvae using brightfield imaging and high-content analysis. 
  • Development of human protein reference database as an initial platform for approaching systems biology in humans. 
  • Differential display of hepatic mRNA from killifish (Fundulus heteroclitus) inhabiting a Superfund estuary. 
  • Differential regulation of genes by retrotransposons in rice promoters. 
  • Differentially Expressed miRNAs in Hepatocellular Carcinoma Target Genes in the Genetic Information Processing and Metabolism Pathways. 
  • Digital atlasing and standardization in the mouse brain. 
  • Discovering sequences with potential regulatory characteristics. 
  • Discovering the landscape of protein modifications. 
  • Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. 
  • Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs. 
  • Domain prediction with probabilistic directional context. 
  • Domain-oriented edge-based alignment of protein interaction networks. 
  • Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma. 
  • Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. 
  • Dysregulation of DGCR6 and DGCR6L: psychopathological outcomes in chromosome 22q11.2 deletion syndrome. 
  • Dysregulation of fatty acid synthesis and glycolysis in non-Hodgkin lymphoma. 
  • Effects of premature termination codon polymorphisms in the Drosophila pseudoobscura subclade. 
  • Effects of virtual environment platforms on emotional responses. 
  • Electrotaxis of Glioblastoma and Medulloblastoma Spheroidal Aggregates. 
  • Enhanced protein fold recognition through a novel data integration approach. 
  • Enhancement of transport selectivity through nano-channels by non-specific competition. 
  • EuroPhenome: a repository for high-throughput mouse phenotyping data. 
  • Evaluation of EEG features in decoding individual finger movements from one hand. 
  • Evidence of a genetic link between endometriosis and ovarian cancer. 
  • Evidence-ranked motif identification. 
  • Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. 
  • Exosome markers associated with immune activation and oxidative stress in HIV patients on antiretroviral therapy. 
  • Expanding studies of chromosome structure and function in the era of T2T genomics. 
  • Experimental design of time series data for learning from dynamic Bayesian networks. 
  • Exploring motif composition of eukaryotic promoter regions. 
  • Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. 
  • Extrapolating weak selection in evolutionary games. 
  • Extrema-weighted feature extraction for functional data. 
  • Extreme selective sweeps independently targeted the X chromosomes of the great apes. 
  • False positives in multiplex PCR-based next-generation sequencing have unique signatures. 
  • Fast molecular shape matching using contact maps. 
  • Fibroblast growth factor-2 (FGF2) and syndecan-1 (SDC1) are potential biomarkers for putative circulating CD15+/CD30+ cells in poor outcome Hodgkin lymphoma patients. 
  • Finding diagnostic biomarkers in proteomic spectra. 
  • Finding our way through phenotypes. 
  • Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing. 
  • FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows. 
  • FlyRNAi: the Drosophila RNAi screening center database. 
  • Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. 
  • From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. 
  • Functional analysis of novel SNPs and mutations in human and mouse genomes. 
  • Functional variants in DCAF4 associated with lung cancer risk in European populations. 
  • Fungal community analysis by large-scale sequencing of environmental samples. 
  • Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination. 
  • Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues". 
  • GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. 
  • Gene Expression Profiling of Cutaneous Injured and Non-Injured Nociceptors in SNI Animal Model of Neuropathic Pain. 
  • Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen. 
  • Gene prediction and verification in a compact genome with numerous small introns. 
  • Generating mammalian sirtuin tools for protein-interaction analysis. 
  • Genetic and bioinformatic analyses of the expression and function of PI3K regulatory subunit PIK3R3 in an Asian patient gastric cancer library. 
  • Genetic and structural analyses of affinity maturation in the humoral response to HIV-1. 
  • Genetic composition of the Bacillus subtilis SOS system. 
  • Genetic modifiers of the severity of sickle cell anemia identified through a genome-wide association study. 
  • Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies. 
  • Genetic variants in fanconi anemia pathway genes BRCA2 and FANCA predict melanoma survival. 
  • Genetic variation in the prostaglandin E2 pathway is associated with primary graft dysfunction. 
  • Genetics. Enhancing gene regulation. 
  • Genome accessibility is widely preserved and locally modulated during mitosis. 
  • Genome annotation assessment in Drosophila melanogaster. 
  • Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity. 
  • Genome technologies and personalized dental medicine. 
  • Genome-wide Analysis Identifies Novel Loci Associated with Ovarian Cancer Outcomes: Findings from the Ovarian Cancer Association Consortium. 
  • Genome-wide analysis of miRNA signature in the APPswe/PS1ΔE9 mouse model of alzheimer's disease. 
  • Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. 
  • Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. 
  • Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. 
  • Genome-wide quantification of the effects of DNA methylation on human gene regulation. 
  • Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. 
  • Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study. 
  • Global search for chromosomal abnormalities in infiltrating ductal carcinoma of the breast using array-comparative genomic hybridization. 
  • Gradient lasso for Cox proportional hazards model. 
  • Guidelines for Genome-Scale Analysis of Biological Rhythms. 
  • Halogen Substitution Influences Ketamine Metabolism by Cytochrome P450 2B6: In Vitro and Computational Approaches. 
  • Heterogeneity of tumor-induced gene expression changes in the human metabolic network. 
  • 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-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability. 
  • Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). 
  • Hybrid error correction and de novo assembly of single-molecule sequencing reads. 
  • Identification and analysis of eukaryotic promoters: recent computational approaches. 
  • Identification and utilization of arbitrary correlations in models of recombination signal sequences. 
  • Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data. 
  • Identification of Long Noncoding RNAs Associated to Human Disease Susceptibility. 
  • Identification of amygdala-expressed genes associated with autism spectrum disorder. 
  • Identification of an HIV-1 clade A envelope that exhibits broad antigenicity and neutralization sensitivity and elicits antibodies targeting three distinct epitopes. 
  • Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models. 
  • Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. 
  • Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. 
  • Identification of functional elements and regulatory circuits by Drosophila modENCODE. 
  • Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus. 
  • Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. 
  • Identification of new genetic variants of HLA-DQB1 associated with human longevity and lipid homeostasis-a cross-sectional study in a Chinese population. 
  • Identification of the sex genes in an early diverged fungus. 
  • Identification of variants in CNGA3 as cause for achromatopsia by exome sequencing of a single patient. 
  • Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. 
  • Identifying novel transcriptional components controlling energy metabolism. 
  • Immune Tolerance-Adjusted Personalized Immunogenicity Prediction for Pompe Disease. 
  • Immune control of tuberculosis by IFN-gamma-inducible LRG-47. 
  • Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology. 
  • Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method. 
  • Improving the modeling of disease data from the government surveillance system: a case study on malaria in the Brazilian Amazon. 
  • Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models. 
  • Increased expression of programmed death ligand 1 (PD-L1) in human pituitary tumors. 
  • Individual-scale variation, species-scale differences: inference needed to understand diversity. 
  • Influence of network topology and data collection on network inference. 
  • InfoEvolve: moving from data to knowledge using information theory and genetic algorithms. 
  • Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline. 
  • Insights from molecular signature of in vivo cardiac c-Kit(+) cells following cardiac injury and β-catenin inhibition. 
  • Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer. 
  • Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. 
  • Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. 
  • Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. 
  • Integrative computational immunogenomic profiling of cortisol-secreting adrenocortical carcinoma. 
  • Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. 
  • Intragenic modifiers of hereditary spastic paraplegia due to spastin gene mutations. 
  • Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. 
  • Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. - Accepted at pacific symposium on biocomputing, 2016 
  • Iso-risk air no decompression limits after scoring marginal decompression sickness cases as non-events. 
  • Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data. 
  • Joint effect of multiple common SNPs predicts melanoma susceptibility. 
  • Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. 
  • KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. 
  • Kernel canonical correlation analysis for assessing gene-gene interactions and application to ovarian cancer. 
  • Know Me! Unraveling the Riddle of Calcific Aortic Valve Disease by Bioinformatics. 
  • Label propagation defines signaling networks associated with recurrently mutated cancer genes. 
  • Laminin alpha 2 enables glioblastoma stem cell growth. 
  • Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. 
  • Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers. 
  • Latent goal models for dynamic strategic interaction. 
  • Learning protein-DNA interaction landscapes by integrating experimental data through computational models. 
  • Linking big: the continuing promise of evolutionary synthesis. 
  • Lipidomics reveals a remarkable diversity of lipids in human plasma. 
  • Local encoding of computationally designed enzyme activity. 
  • Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. 
  • Longitudinal multi-omics of host-microbe dynamics in prediabetes. 
  • Making sense of microarrays. 
  • Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. 
  • Mapping nucleosome positions using DNase-seq. 
  • Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. 
  • Mathematical methods for diffusion MRI processing. 
  • Mathematical modeling of the Phoenix Rising pathway. 
  • Measuring similarity between dynamic ensembles of biomolecules. 
  • Meeting report: high-throughput technologies for in vivo imaging agents. 
  • Memory capacity of networks with stochastic binary synapses. 
  • Metabolomic analysis of insulin resistance across different mouse strains and diets. 
  • Metabolomic profiling reveals mitochondrial-derived lipid biomarkers that drive obesity-associated inflammation. 
  • Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results. 
  • Metallomics: Emerging Investigators 2019. 
  • Methodologies for Following EMT In Vivo at Single Cell Resolution. 
  • Micro flow bio-molecular computation. 
  • Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study. 
  • Minimal PAM specificity of a highly similar SpCas9 ortholog. 
  • Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). 
  • Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. 
  • Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies. 
  • Modeling false positive error making patterns in radiology trainees for improved mammography education. 
  • Modeling flow cytometry data for cancer vaccine immune monitoring. 
  • Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. 
  • Modulation of network excitability by persistent activity: how working memory affects the response to incoming stimuli. 
  • Module-based association analysis for omics data with network structure. 
  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. 
  • Molecular evolution of the junctophilin gene family. 
  • Multi-omics integration in biomedical research - A metabolomics-centric review. 
  • Multi-trait genome-wide association study identifies new loci associated with optic disc parameters. 
  • Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes. 
  • Multifactorial determinants of protein expression in prokaryotic open reading frames. 
  • Multiple chronic pain states are associated with a common amino acid-changing allele in KCNS1. 
  • Mutational analysis of the tyrosine phosphatome in colorectal cancers. 
  • Mutational profile and prognostic significance of TP53 in diffuse large B-cell lymphoma patients treated with R-CHOP: report from an International DLBCL Rituximab-CHOP Consortium Program Study. 
  • Mutations within the mepA operator affect binding of the MepR regulatory protein and its induction by MepA substrates in Staphylococcus aureus. 
  • Mutual information in random Boolean models of regulatory networks. 
  • NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. 
  • NEIBank: genomics and bioinformatics resources for vision research. 
  • National Cancer Institute Prostate Cancer Genetics Workshop. 
  • National Heart, Lung, And Blood Institute Clinical Proteomics Working Group report. 
  • Natural positive selection and north-south genetic diversity in East Asia. 
  • NeXML: rich, extensible, and verifiable representation of comparative data and metadata. 
  • Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans. 
  • Neuron's eye view: Inferring features of complex stimuli from neural responses. 
  • Neuroprosthetic decoder training as imitation learning 
  • New fossils of the oldest North American euprimate Teilhardina brandti (Omomyidae) from the paleocene-eocene thermal maximum. 
  • New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. 
  • New techniques for DNA sequence classification. 
  • New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics. 
  • Next-generation computational genetic analysis: multiple complement alleles control survival after Candida albicans infection. 
  • Next‐generation polyploid phylogenetics: Rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing 
  • Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. 
  • Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping. 
  • Nucleotide excision repair as a marker for susceptibility to tobacco-related cancers: a review of molecular epidemiological studies. 
  • OPEN DATA FOR DISCOVERY SCIENCE. 
  • OligoCalc: an online oligonucleotide properties calculator. 
  • Open source tools and toolkits for bioinformatics: significance, and where are we? 
  • Optimized mixed Markov models for motif identification. 
  • Osteoprotegerin in bone metastases: mathematical solution to the puzzle. 
  • PGC-1α, a potential therapeutic target for early intervention in Parkinson's disease. 
  • Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. 
  • Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies. 
  • Pathway analysis using random forests classification and regression. 
  • Pathway analysis using random forests with bivariate node-split for survival outcomes. 
  • Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. 
  • Pedigree generation for analysis of genetic linkage and association. 
  • Pedigree selection and information content. 
  • Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. 
  • Peritoneal and subperitoneal stroma may facilitate regional spread of ovarian cancer. 
  • Personal Omics for Precision Health 
  • Personal genomes in progress: from the human genome project to the personal genome project. 
  • Phenex: ontological annotation of phenotypic diversity. 
  • PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases. 
  • Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. 
  • Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure. 
  • Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. 
  • Potential for expanded power in linkage studies using the ALLEGRO and MERLIN software programs. 
  • Practical approach to determine sample size for building logistic prediction models using high-throughput data. 
  • Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China. 
  • PrimerZ: streamlined primer design for promoters, exons and human SNPs. 
  • Principles of microRNA regulation of a human cellular signaling network. 
  • Principles that govern competition or co-existence in Rho-GTPase driven polarization. 
  • Probabilistic fluorescence-based synapse detection. 
  • Probabilistic pharmacokinetic models of decompression sickness in humans: Part 2, coupled perfusion-diffusion models. 
  • Processing Oscillatory Signals by Incoherent Feedforward Loops. 
  • Programmable mutually exclusive alternative splicing for generating RNA and protein diversity. 
  • Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution 
  • Properties of overlapping genes are conserved across microbial genomes. 
  • Protein Serine/Threonine Phosphatases: Keys to Unlocking Regulators and Substrates. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite. 
  • Proteomic Profiling of Human Hepatic Stellate Cell Line LX2 Responses to Irradiation and TGF-β1. 
  • Proteomic analysis of urinary extracellular vesicles reveal biomarkers for neurologic disease. 
  • Putative biomarkers for predicting tumor sample purity based on gene expression data. 
  • QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. 
  • Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response. 
  • Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane. 
  • Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step. 
  • Quantitative modeling of transcription factor binding specificities using DNA shape. 
  • Quorum-sensing regulation of a copper toxicity system in Pseudomonas aeruginosa. 
  • RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). 
  • RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. 
  • Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex. 
  • Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. 
  • RasGRP1 is a potential biomarker to stratify anti-EGFR therapy response in colorectal cancer. 
  • Recessive mutations in the α3 (VI) collagen gene COL6A3 cause early-onset isolated dystonia. 
  • Recommendations from the international stroke genetics consortium, part 2: biological sample collection and storage. 
  • Reconstructing spatiotemporal gene expression data from partial observations. 
  • Recovering ensembles of chromatin conformations from contact probabilities. 
  • Regulators of G-Protein signaling RGS10 and RGS17 regulate chemoresistance in ovarian cancer cells. 
  • Reliability of transcriptional cycles and the yeast cell-cycle oscillator. 
  • Reliable genotypic tropism tests for the major HIV-1 subtypes. 
  • Report on the Fifth International Workshop on Chromosome 9 held at Eynsham, Oxfordshire, UK, September 4-6, 1996. 
  • Residue-level prediction of HIV-1 antibody epitopes based on neutralization of diverse viral strains. 
  • Response nonlinearities in networks of spiking neurons. 
  • Response of human thalamic neurons to high-frequency stimulation. 
  • Retinitis pigmentosa associated with rhodopsin mutations: Correlation between phenotypic variability and molecular effects. 
  • Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. 
  • Revolution and renaissance. 
  • RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. 
  • Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model. 
  • Secrets of the perioptome: new tools for a new concept. 
  • Shrinkage estimation for robust and efficient screening of single-SNP association from case-control genome-wide association studies. 
  • Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. 
  • Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo. 
  • Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. 
  • SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization. 
  • Spatial preferences of microRNA targets in 3' untranslated regions. 
  • Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate. 
  • Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. 
  • Statistical challenges in preprocessing in microarray experiments in cancer. 
  • Statistical considerations for analysis of microarray experiments. 
  • Statistical methods for assessment of added usefulness of new biomarkers. 
  • Strong impact of natural-selection-free heterogeneity in genetics of age-related phenotypes. 
  • Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes. 
  • Structure-based high-throughput epitope analysis of hexon proteins in B and C species human adenoviruses (HAdVs). 
  • Subcellular organelle lipidomics in TLR-4-activated macrophages. 
  • Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. 
  • Systems Genetics Approach to Biomarker Discovery: GPNMB and Heart Failure in Mice and Humans. 
  • Systems biology approaches to defining transcription regulatory networks in halophilic archaea. 
  • Systems biology. 
  • Target domain definition and classification in CASP8. 
  • Temporal Patterns in Sheep Fetal Heart Rate Variability Correlate to Systemic Cytokine Inflammatory Response: A Methodological Exploration of Monitoring Potential Using Complex Signals Bioinformatics. 
  • Ten Simple Rules for Effective Statistical Practice. 
  • The 2015 Bioinformatics Open Source Conference (BOSC 2015). 
  • The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018). 
  • The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. 
  • The Bioinformatics Open Source Conference (BOSC) 2013. 
  • The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. 
  • The Bioperl toolkit: Perl modules for the life sciences. 
  • The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. 
  • The Chlamydia trachomatis Protease CPAF Contains a Cryptic PDZ-Like Domain with Similarity to Human Cell Polarity and Tight Junction PDZ-Containing Proteins. 
  • The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science. 
  • The ENCODE (ENCyclopedia Of DNA Elements) Project. 
  • The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. 
  • The Gene Ontology in 2010: extensions and refinements. 
  • The Genome 10K Project: a way forward. 
  • The LabBase system for data management in large scale biology research laboratories. 
  • The MetJ regulon in gammaproteobacteria determined by comparative genomics methods. 
  • The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency. 
  • The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants. 
  • The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. 
  • The coming age of data-driven medicine: translational bioinformatics' next frontier. 
  • The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. 
  • The genome of the sea urchin Stongylocentrotus purpuratus 
  • The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches. 
  • The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. 
  • The molecular basis of quantitative genetic variation in central and secondary metabolism in Arabidopsis. 
  • The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. 
  • The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. 
  • The persistence potential of transferable plasmids. 
  • The statistics of bulk segregant analysis using next generation sequencing. 
  • The teleost anatomy ontology: anatomical representation for the genomics age. 
  • Thinking outside the gate: single-cell assessments in multiple dimensions. 
  • Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. 
  • Toward computational systems biology. 
  • Towards an integrated ecosystem of R packages for the analysis of population genetic data. 
  • Transcription Factor RUNX1 Regulates Platelet PCTP (Phosphatidylcholine Transfer Protein): Implications for Cardiovascular Events: Differential Effects of RUNX1 Variants. 
  • Transcriptional analyses of adult and pediatric adamantinomatous craniopharyngioma reveals similar expression signatures regarding potential therapeutic targets. 
  • Transcriptome analysis of mouse stem cells and early embryos. 
  • Transcriptomic and Proteomic Analysis of Clear Cell Foci (CCF) in the Human Non-Cirrhotic Liver Identifies Several Differentially Expressed Genes and Proteins with Functions in Cancer Cell Biology and Glycogen Metabolism. 
  • Translating genomic biomarkers into clinically useful diagnostics. 
  • Translational Bioinformatics: Past, Present, and Future. 
  • Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. 
  • Transversions have larger regulatory effects than transitions. 
  • Understanding the Cellular and Molecular Mechanisms of Physical Activity-Induced Health Benefits. 
  • Unique microRNA profile in end-stage heart failure indicates alterations in specific cardiovascular signaling networks. 
  • Use of bioinformatic tools in primer validation. 
  • Using DNA duplex stability information for transcription factor binding site discovery. 
  • Using DNase digestion data to accurately identify transcription factor binding sites. 
  • Using cauliflower to find conserved non-coding regions in Arabidopsis. 
  • Using extremal events to characterize noisy time series. 
  • Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. 
  • Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution. 
  • Vaginal deployment and tenofovir delivery by microbicide gels. 
  • Validation of three-dimensional conduction models using experimental mapping: are we getting closer? 
  • Visual annotation of the gene database. 
  • Visual presentation as a welcome alternative to textual presentation of gene annotation information. 
  • WASABI: an automated sequence processing system for multigene phylogenies. 
  • Waddling and toddling: the biomechanical effects of an immature gait. 
  • What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). 
  • What is mzXML good for? 
  • Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. 
  • Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. 
  • Whole-genome sequencing of bloodstream Staphylococcus aureus isolates does not distinguish bacteraemia from endocarditis. 
  • Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation. 
  • Workshop on cancer biometrics: identifying biomarkers and surrogates of cancer in patients: a meeting held at the Masur Auditorium, National Institutes of Health. 
  • ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. 
  • Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation. 
  • apex: phylogenetics with multiple genes. 
  • dictyBase: a new Dictyostelium discoideum genome database. 
  • hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine. 
  • meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays. 
  • minotaur: A platform for the analysis and visualization of multivariate results from genome scans with R Shiny. 
  • p38 MAPK is essential for secondary axis specification and patterning in sea urchin embryos. 
• 

  Keywords of People

  • Bryan, Jordan, Student, Statistical Science
  • Gounley, John, Affiliate, Biomedical Engineering
  • Grimsrud, Paul, Assistant Professor in Medicine, Medicine, Endocrinology, Metabolism, and Nutrition
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Hogan, Brigid L. M., George Barth Geller Distinguished Professor for Research in Molecular Biology, Cell Biology
  • Ji, Zhicheng, Assistant Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Kelsoe, Garnett H., James B. Duke Distinguished Professor of Immunology, Immunology
  • Li, Yi-Ju, Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Ma, Li, Associate Professor of Statistical Science, Biostatistics & Bioinformatics
  • Magwene, Paul Mitaari, Professor of Biology, Biology
  • McLendon, Roger Edwin, Professor of Pathology, Pathology
  • Ochoa, Alejandro, Assistant Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Pang, Herbert, Adjunct Assistant Professor in the Department of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Pornmongkolsuk, Ratchanon "RP", Student, School of Medicine
  • Randles, Amanda, Alfred Winborne and Victoria Stover Mordecai Assistant Professor of Biomedical Sciences, Thomas Lord Department of Mechanical Engineering and Materials Science
  • Soderling, Scott Haydn, George Barth Geller Distinguished Professor of Molecular Biology, Cell Biology
  • Taylor, Gregory Alan, Professor in Medicine, Immunology
  • Wray, Gregory Allan, Professor of Biology, Evolutionary Anthropology
  • Yan, Hai, Adjunct Professor of Pathology, Pathology