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Subject Areas on Research
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1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function.
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A Fringe-modified Notch signal affects specification of mesoderm and endoderm in the sea urchin embryo.
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A Genome-Wide Association Study Identifies Two Novel Susceptible Regions for Squamous Cell Carcinoma of the Head and Neck.
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A Machine-Learning-Based Drug Repurposing Approach Using Baseline Regularization.
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A Multidimensional Bioinformatic Platform for the Study of Human Response to Surgery.
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A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.
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A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks.
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A case study in the functional consequences of scaling the sizes of realistic cortical models.
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A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.
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A comparative analysis of the information content in long and short SAGE libraries.
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A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits.
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A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome.
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A computational analysis of antisense off-targets in prokaryotic organisms.
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A computational method to classify variants of uncertain significance using functional assay data with application to BRCA1.
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A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays.
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A draft genome sequence of the elusive giant squid, Architeuthis dux.
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A five-gene hedgehog signature developed as a patient preselection tool for hedgehog inhibitor therapy in medulloblastoma.
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A five-gene phylogeny of Pezizomycotina.
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A framework for annotating human genome in disease context.
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A framework for integrating the songbird brain.
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A framework phylogeny of the American oak clade based on sequenced RAD data.
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A functional analysis of the spacer of V(D)J recombination signal sequences.
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A genetic memory initiates the epigenetic loop necessary to preserve centromere position.
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A genetic stochastic process model for genome-wide joint analysis of biomarker dynamics and disease susceptibility with longitudinal data.
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A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function.
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A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function.
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A genomic regulatory network for development.
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A glutaminase isoform switch drives therapeutic resistance and disease progression of prostate cancer.
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A gradient-directed Monte Carlo approach for protein design.
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A hybrid framework for genome wide epistasis discovery.
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A leave-one-out cross-validation SAS macro for the identification of markers associated with survival.
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A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression.
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A mathematical model of the methionine cycle.
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A multidisciplinary approach to probing enthalpy-entropy compensation and the interfacial mobility model.
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A new method to accurately identify single nucleotide variants using small FFPE breast samples.
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A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease.
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A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement.
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A permutation-based multiple testing method for time-course microarray experiments.
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A phylogenetic transform enhances analysis of compositional microbiota data.
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A power-law dependence of bacterial invasion on mammalian host receptors.
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A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers.
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A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.
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A study of the repetitive structure and distribution of short motifs in human genomic sequences.
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A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily.
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A synthetic biology challenge: making cells compute.
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A whole genome approach for discovering the genetic basis of blood group antigens: independent confirmation for P1 and Xga
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ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves.
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Absence of a simple code: how transcription factors read the genome.
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Active learning for computational chemogenomics.
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Active-learning strategies in computer-assisted drug discovery.
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AglQ is a novel component of the Haloferax volcanii N-glycosylation pathway.
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All-atom contacts: a new approach to structure validation.
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An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease.
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An ERCC4 regulatory variant predicts grade-3 or -4 toxicities in patients with advanced non-small cell lung cancer treated by platinum-based therapy.
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An active learning approach for rapid characterization of endothelial cells in human tumors.
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An age-independent gene signature for monitoring acute rejection in kidney transplantation.
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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.
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An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings.
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An approach to modelling in immunology.
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An atlas of genetic influences on human blood metabolites.
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An embryonic system to assess direct and indirect Wnt transcriptional targets.
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An evaluation of copy number variation detection tools from whole-exome sequencing data.
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An international bioinformatics infrastructure to underpin the Arabidopsis community.
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An overview of genomic data analysis.
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Analysis of the Rab GTPase Interactome in Dendritic Cells Reveals Anti-microbial Functions of the Rab32 Complex in Bacterial Containment.
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Analytic gain in probabilistic decompression sickness models.
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Angiogenesis: an adaptive dynamic biological patterning problem.
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Annotating the human genome with Disease Ontology.
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Antigen receptor repertoire profiling from RNA-seq data.
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Application of combined omics platforms to accelerate biomedical discovery in diabesity.
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Application of proteomic marker ensembles to subcellular organelle identification.
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Aquatic models, genomics and chemical risk management.
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Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences.
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Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements.
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Assessing transcription factor motif drift from noisy decoy sequences.
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Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.
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Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis.
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Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.
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Automated constraint-based nucleotide sequence selection for DNA computation.
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Automatic annotation of spatial expression patterns via sparse Bayesian factor models.
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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.
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BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells.
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Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions.
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Bayesian network-response regression.
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Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data.
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Best practices and lessons learned from reuse of 4 patient-derived metabolomics datasets in Alzheimer's disease.
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Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.
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Bile acid aspiration associated with lung chemical profile linked to other biomarkers of injury after lung transplantation.
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BioWarehouse: a bioinformatics database warehouse toolkit.
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Biochemistry. Exciting structures.
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Bioinformatic challenges in targeted proteomics.
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Bioinformatic design of A-kinase anchoring protein-in silico: a potent and selective peptide antagonist of type II protein kinase A anchoring.
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Bioinformatic jujutsu to defeat an endometrial transcriptomic foe.
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Bioinformatics Associated With Conjoined Twin Separation.
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Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation.
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Biology by design: reduction and synthesis of cellular components and behaviour.
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Bone-associated gene evolution and the origin of flight in birds.
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Bottom up: a modular view of immunology.
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Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding.
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Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer.
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Building Statistical Models to Analyze Species Distributions
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CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer.
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Cancer Data Science and Computational Medicine.
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Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research.
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Cancer Moonshot Data and Technology Team: Enabling a National Learning Healthcare System for Cancer to Unleash the Power of Data.
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Carbonic anhydrase and CO2 sensing during Cryptococcus neoformans growth, differentiation, and virulence.
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Causal network inference from gene transcriptional time-series response to glucocorticoids.
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Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers.
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Cell-free DNA diagnostics in transplantation utilizing next generation sequencing.
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Cell-internalization SELEX: method for identifying cell-internalizing RNA aptamers for delivering siRNAs to target cells.
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Centralized biorepositories for genetic and genomic research.
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Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types.
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Characterization of the Saccharomyces cerevisiae ATP-Interactome using the iTRAQ-SPROX Technique.
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Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor.
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Chemical interrogation of the malaria kinome.
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Cheminformatic Analysis of Natural Product Fragments.
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Chemotactic movement of a polarity site enables yeast cells to find their mates.
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Chromatin signatures of the Drosophila replication program.
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Circular RNAs are abundant, conserved, and associated with ALU repeats.
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ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis.
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Clinically focused exome sequencing identifies an homozygous mutation that confers DOCK8 deficiency.
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Clustering gene expression time series data using an infinite Gaussian process mixture model.
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Co-regulation of nuclear respiratory factor-1 by NFkappaB and CREB links LPS-induced inflammation to mitochondrial biogenesis.
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Coarse and reliable geometric alignment for protein docking.
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Collaborating with Undergraduates To Contribute to Biochemistry Community Resources.
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Combining MALDI-FTMS and bioinformatics for rapid peptidomic comparisons.
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Combining gene expression, demographic and clinical data in modeling disease: a case study of bipolar disorder and schizophrenia.
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Comparative Loss-of-Function Screens Reveal ABCE1 as an Essential Cellular Host Factor for Efficient Translation of Paramyxoviridae and Pneumoviridae.
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Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing.
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Comparative genomic analysis of fungal genomes reveals intron-rich ancestors.
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Comparative genomics as a tool for gene discovery.
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Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.
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Comparative proteomic characterization of articular cartilage tissue from normal donors and patients with osteoarthritis.
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Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.
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Completeness of HIV-1 Envelope Glycan Shield at Transmission Determines Neutralization Breadth.
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Comprehensive Characterization of Cancer Driver Genes and Mutations.
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Comprehensive genomic profiling of pancreatic acinar cell carcinomas identifies recurrent RAF fusions and frequent inactivation of DNA repair genes.
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Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.
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Computation in neural systems. Editorial.
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Computation of mutual information from Hidden Markov Models.
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Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
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Computational Analysis of Targeting SARS-CoV-2, Viral Entry Proteins ACE2 and TMPRSS2, and Interferon Genes by Host MicroRNAs.
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Computational Methods for RNA Structure Validation and Improvement.
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Computational analysis of antibody dynamics identifies recent HIV-1 infection.
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Computational analysis of core promoters in the Drosophila genome.
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Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.
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Computational and experimental identification of novel human imprinted genes.
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Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
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Computational design of a biologically active enzyme.
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Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5.
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Computational immunology--from bench to virtual reality.
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Computational prediction of efficient splice sites for trans-splicing ribozymes.
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Computational protein engineering.
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Computational tools for understanding sequence variability in recombination signals.
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Computing van der Waals energies in the context of the rotamer approximation.
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Contrasts between adaptive coding and noncoding changes during human evolution.
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Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design.
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Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest.
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Critical assessment of automated flow cytometry data analysis techniques.
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Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer.
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Cross-study projections of genomic biomarkers: an evaluation in cancer genomics.
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Cryptic phosphorylation in nucleoside natural product biosynthesis.
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Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.
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DNA methylation alterations in response to pesticide exposure in vitro.
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Decision tree classification of proteins identified by mass spectrometry of blood serum samples from people with and without lung cancer.
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Design and Analysis of Large-Scale Biological Rhythm Studies: A Comparison of Algorithms for Detecting Periodic Signals in Biological Data
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Detecting and characterizing circular RNAs.
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Detection of viruses via statistical gene expression analysis.
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Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors.
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Development of a quantitative morphological assessment of toxicant-treated zebrafish larvae using brightfield imaging and high-content analysis.
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Development of human protein reference database as an initial platform for approaching systems biology in humans.
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Differential display of hepatic mRNA from killifish (Fundulus heteroclitus) inhabiting a Superfund estuary.
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Differential regulation of genes by retrotransposons in rice promoters.
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Differentially Expressed miRNAs in Hepatocellular Carcinoma Target Genes in the Genetic Information Processing and Metabolism Pathways.
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Digital atlasing and standardization in the mouse brain.
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Discovering sequences with potential regulatory characteristics.
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Discovering the landscape of protein modifications.
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Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble.
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Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs.
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Domain prediction with probabilistic directional context.
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Domain-oriented edge-based alignment of protein interaction networks.
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Down-regulation of microRNAs controlling tumourigenic factors in follicular thyroid carcinoma.
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Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.
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Dysregulation of DGCR6 and DGCR6L: psychopathological outcomes in chromosome 22q11.2 deletion syndrome.
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Dysregulation of fatty acid synthesis and glycolysis in non-Hodgkin lymphoma.
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Effects of premature termination codon polymorphisms in the Drosophila pseudoobscura subclade.
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Effects of virtual environment platforms on emotional responses.
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Electrotaxis of Glioblastoma and Medulloblastoma Spheroidal Aggregates.
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Emerging Technologies for Gut Microbiome Research.
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Enhanced protein fold recognition through a novel data integration approach.
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Enhancement of transport selectivity through nano-channels by non-specific competition.
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EuroPhenome: a repository for high-throughput mouse phenotyping data.
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Evaluation of EEG features in decoding individual finger movements from one hand.
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Evidence of a genetic link between endometriosis and ovarian cancer.
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Evidence-ranked motif identification.
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Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.
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Evolutionary dynamics and information hierarchies in biological systems.
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Exosome markers associated with immune activation and oxidative stress in HIV patients on antiretroviral therapy.
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Expanding studies of chromosome structure and function in the era of T2T genomics.
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Experimental design of time series data for learning from dynamic Bayesian networks.
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Exploring motif composition of eukaryotic promoter regions.
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Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases.
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Extrapolating weak selection in evolutionary games.
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Extrema-weighted feature extraction for functional data.
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Extreme selective sweeps independently targeted the X chromosomes of the great apes.
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False positives in multiplex PCR-based next-generation sequencing have unique signatures.
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Fast molecular shape matching using contact maps.
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Fibroblast growth factor-2 (FGF2) and syndecan-1 (SDC1) are potential biomarkers for putative circulating CD15+/CD30+ cells in poor outcome Hodgkin lymphoma patients.
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Finding diagnostic biomarkers in proteomic spectra.
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Finding our way through phenotypes.
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Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing.
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FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows.
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FlyRNAi: the Drosophila RNAi screening center database.
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Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase.
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From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.
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Functional analysis of novel SNPs and mutations in human and mouse genomes.
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Functional variants in DCAF4 associated with lung cancer risk in European populations.
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Fungal community analysis by large-scale sequencing of environmental samples.
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Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination.
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Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues".
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GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis.
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Gene Expression Profiling of Cutaneous Injured and Non-Injured Nociceptors in SNI Animal Model of Neuropathic Pain.
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Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen.
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Gene prediction and verification in a compact genome with numerous small introns.
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Generating mammalian sirtuin tools for protein-interaction analysis.
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Genetic and bioinformatic analyses of the expression and function of PI3K regulatory subunit PIK3R3 in an Asian patient gastric cancer library.
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Genetic and structural analyses of affinity maturation in the humoral response to HIV-1.
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Genetic composition of the Bacillus subtilis SOS system.
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Genetic modifiers of the severity of sickle cell anemia identified through a genome-wide association study.
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Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.
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Genetic variants in fanconi anemia pathway genes BRCA2 and FANCA predict melanoma survival.
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Genetic variation in the prostaglandin E2 pathway is associated with primary graft dysfunction.
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Genetics. Enhancing gene regulation.
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Genome accessibility is widely preserved and locally modulated during mitosis.
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Genome annotation assessment in Drosophila melanogaster.
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Genome technologies and personalized dental medicine.
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Genome-wide Analysis Identifies Novel Loci Associated with Ovarian Cancer Outcomes: Findings from the Ovarian Cancer Association Consortium.
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Genome-wide analysis of miRNA signature in the APPswe/PS1ΔE9 mouse model of alzheimer's disease.
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Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.
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Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
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Genome-wide quantification of the effects of DNA methylation on human gene regulation.
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Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.
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Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study.
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Global search for chromosomal abnormalities in infiltrating ductal carcinoma of the breast using array-comparative genomic hybridization.
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Gradient lasso for Cox proportional hazards model.
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Guidelines for Genome-Scale Analysis of Biological Rhythms.
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Halogen Substitution Influences Ketamine Metabolism by Cytochrome P450 2B6: In Vitro and Computational Approaches.
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Heterogeneity of tumor-induced gene expression changes in the human metabolic network.
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High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer.
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High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability.
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Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).
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Hybrid error correction and de novo assembly of single-molecule sequencing reads.
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Identification and analysis of eukaryotic promoters: recent computational approaches.
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Identification and utilization of arbitrary correlations in models of recombination signal sequences.
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Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data.
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Identification of Brassinosteroid Target Genes by Chromatin Immunoprecipitation Followed by High-Throughput Sequencing (ChIP-seq) and RNA-Sequencing.
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Identification of Long Noncoding RNAs Associated to Human Disease Susceptibility.
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Identification of amygdala-expressed genes associated with autism spectrum disorder.
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Identification of an HIV-1 clade A envelope that exhibits broad antigenicity and neutralization sensitivity and elicits antibodies targeting three distinct epitopes.
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Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models.
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Identification of cell cycle-regulated, putative hyphal genes in Candida albicans.
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Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.
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Identification of functional elements and regulatory circuits by Drosophila modENCODE.
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Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus.
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Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus.
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Identification of new genetic variants of HLA-DQB1 associated with human longevity and lipid homeostasis-a cross-sectional study in a Chinese population.
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Identification of the sex genes in an early diverged fungus.
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Identification of variants in CNGA3 as cause for achromatopsia by exome sequencing of a single patient.
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Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites.
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Identifying novel transcriptional components controlling energy metabolism.
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Immune Tolerance-Adjusted Personalized Immunogenicity Prediction for Pompe Disease.
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Immune control of tuberculosis by IFN-gamma-inducible LRG-47.
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Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology.
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Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method.
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Improving the modeling of disease data from the government surveillance system: a case study on malaria in the Brazilian Amazon.
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Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models.
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Increased expression of programmed death ligand 1 (PD-L1) in human pituitary tumors.
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Individual-scale variation, species-scale differences: inference needed to understand diversity.
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Influence of network topology and data collection on network inference.
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InfoEvolve: moving from data to knowledge using information theory and genetic algorithms.
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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline.
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Insights from molecular signature of in vivo cardiac c-Kit(+) cells following cardiac injury and β-catenin inhibition.
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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.
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Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.
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Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.
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Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets.
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Integrative computational immunogenomic profiling of cortisol-secreting adrenocortical carcinoma.
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Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability.
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Intragenic modifiers of hereditary spastic paraplegia due to spastin gene mutations.
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Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors.
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Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. - Accepted at pacific symposium on biocomputing, 2016
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Iso-risk air no decompression limits after scoring marginal decompression sickness cases as non-events.
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Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data.
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Joint effect of multiple common SNPs predicts melanoma susceptibility.
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Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.
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KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program.
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Kernel canonical correlation analysis for assessing gene-gene interactions and application to ovarian cancer.
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Know Me! Unraveling the Riddle of Calcific Aortic Valve Disease by Bioinformatics.
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Label propagation defines signaling networks associated with recurrently mutated cancer genes.
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Laminin alpha 2 enables glioblastoma stem cell growth.
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Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana.
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Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers.
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Learning protein-DNA interaction landscapes by integrating experimental data through computational models.
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Linking big: the continuing promise of evolutionary synthesis.
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Lipidomics reveals a remarkable diversity of lipids in human plasma.
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Local encoding of computationally designed enzyme activity.
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Logical computation using algorithmic self-assembly of DNA triple-crossover molecules.
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Longitudinal multi-omics of host-microbe dynamics in prediabetes.
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Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment.
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Mapping nucleosome positions using DNase-seq.
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Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.
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Mathematical methods for diffusion MRI processing.
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Mathematical modeling of the Phoenix Rising pathway.
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Measuring similarity between dynamic ensembles of biomolecules.
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Meeting report: high-throughput technologies for in vivo imaging agents.
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Memory capacity of networks with stochastic binary synapses.
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Metabolomic analysis of insulin resistance across different mouse strains and diets.
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Metabolomic profiling reveals mitochondrial-derived lipid biomarkers that drive obesity-associated inflammation.
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Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results.
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Metallomics: Emerging Investigators 2019.
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Methodologies for Following EMT In Vivo at Single Cell Resolution.
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Micro flow bio-molecular computation.
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Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study.
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Minimal PAM specificity of a highly similar SpCas9 ortholog.
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Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).
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Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains.
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Misexpression of ptf1a in cortical pyramidal cells in vivo promotes an inhibitory peptidergic identity.
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Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies.
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Modeling false positive error making patterns in radiology trainees for improved mammography education.
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Modeling flow cytometry data for cancer vaccine immune monitoring.
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Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.
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Modulation of network excitability by persistent activity: how working memory affects the response to incoming stimuli.
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Module-based association analysis for omics data with network structure.
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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
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Molecular evolution of the junctophilin gene family.
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Multi-omics integration in biomedical research - A metabolomics-centric review.
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Multi-trait genome-wide association study identifies new loci associated with optic disc parameters.
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Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.
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Multifactorial determinants of protein expression in prokaryotic open reading frames.
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Multiple chronic pain states are associated with a common amino acid-changing allele in KCNS1.
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Mutational analysis of the tyrosine phosphatome in colorectal cancers.
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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.
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Mutations within the mepA operator affect binding of the MepR regulatory protein and its induction by MepA substrates in Staphylococcus aureus.
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Mutual information in random Boolean models of regulatory networks.
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NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data.
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NEIBank: genomics and bioinformatics resources for vision research.
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National Cancer Institute Prostate Cancer Genetics Workshop.
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National Heart, Lung, And Blood Institute Clinical Proteomics Working Group report.
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Natural positive selection and north-south genetic diversity in East Asia.
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NeXML: rich, extensible, and verifiable representation of comparative data and metadata.
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Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans.
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Neuron's eye view: Inferring features of complex stimuli from neural responses.
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Neuroprosthetic decoder training as imitation learning
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New fossils of the oldest North American euprimate Teilhardina brandti (Omomyidae) from the paleocene-eocene thermal maximum.
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New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.
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New techniques for DNA sequence classification.
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New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics.
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Next-generation computational genetic analysis: multiple complement alleles control survival after Candida albicans infection.
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Next‐generation polyploid phylogenetics: Rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing
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Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.
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Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping.
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Nucleotide excision repair as a marker for susceptibility to tobacco-related cancers: a review of molecular epidemiological studies.
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OPEN DATA FOR DISCOVERY SCIENCE.
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OligoCalc: an online oligonucleotide properties calculator.
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Open source tools and toolkits for bioinformatics: significance, and where are we?
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Optimized mixed Markov models for motif identification.
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Osteoprotegerin in bone metastases: mathematical solution to the puzzle.
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PGC-1α, a potential therapeutic target for early intervention in Parkinson's disease.
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Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas.
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Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies.
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Pathway analysis using random forests classification and regression.
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Pathway analysis using random forests with bivariate node-split for survival outcomes.
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Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification.
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Pedigree generation for analysis of genetic linkage and association.
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Pedigree selection and information content.
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Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
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Peritoneal and subperitoneal stroma may facilitate regional spread of ovarian cancer.
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Personal Omics for Precision Health
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Personal genomes in progress: from the human genome project to the personal genome project.
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Phenex: ontological annotation of phenotypic diversity.
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PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases.
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Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.
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Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.
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Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes.
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Potential for expanded power in linkage studies using the ALLEGRO and MERLIN software programs.
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Practical approach to determine sample size for building logistic prediction models using high-throughput data.
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Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China.
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PrimerZ: streamlined primer design for promoters, exons and human SNPs.
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Principles of microRNA regulation of a human cellular signaling network.
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Principles that govern competition or co-existence in Rho-GTPase driven polarization.
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Probabilistic fluorescence-based synapse detection.
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Probabilistic pharmacokinetic models of decompression sickness in humans: Part 2, coupled perfusion-diffusion models.
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Processing Oscillatory Signals by Incoherent Feedforward Loops.
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Programmable mutually exclusive alternative splicing for generating RNA and protein diversity.
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Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
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Properties of overlapping genes are conserved across microbial genomes.
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Protein Serine/Threonine Phosphatases: Keys to Unlocking Regulators and Substrates.
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Protein-Protein Docking Benchmark 2.0: an update.
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Proteogenomic and metabolomic characterization of human glioblastoma.
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Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite.
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Proteomic Profiling of Human Hepatic Stellate Cell Line LX2 Responses to Irradiation and TGF-β1.
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Proteomic analysis of urinary extracellular vesicles reveal biomarkers for neurologic disease.
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Putative biomarkers for predicting tumor sample purity based on gene expression data.
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QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants.
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Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response.
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Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane.
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Quantitative determinants of aerobic glycolysis identify flux through the enzyme GAPDH as a limiting step.
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Quantitative modeling of transcription factor binding specificities using DNA shape.
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Quorum-sensing regulation of a copper toxicity system in Pseudomonas aeruginosa.
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RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
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RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
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Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex.
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Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection.
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RasGRP1 is a potential biomarker to stratify anti-EGFR therapy response in colorectal cancer.
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Recommendations from the international stroke genetics consortium, part 2: biological sample collection and storage.
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Reconstructing spatiotemporal gene expression data from partial observations.
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Recovering ensembles of chromatin conformations from contact probabilities.
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Regulators of G-Protein signaling RGS10 and RGS17 regulate chemoresistance in ovarian cancer cells.
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Reliability of transcriptional cycles and the yeast cell-cycle oscillator.
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Reliable genotypic tropism tests for the major HIV-1 subtypes.
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Report of the fifth international workshop on human chromosome 1 mapping 1999.
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Report on the Fifth International Workshop on Chromosome 9 held at Eynsham, Oxfordshire, UK, September 4-6, 1996.
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Residue-level prediction of HIV-1 antibody epitopes based on neutralization of diverse viral strains.
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Response nonlinearities in networks of spiking neurons.
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Response of human thalamic neurons to high-frequency stimulation.
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Retinitis pigmentosa associated with rhodopsin mutations: Correlation between phenotypic variability and molecular effects.
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Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA.
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Revolution and renaissance.
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RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data.
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Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model.
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Secrets of the perioptome: new tools for a new concept.
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Session Introduction: Digital health technology data in biocomputing: Research efforts and considerations for expanding access.
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Shrinkage estimation for robust and efficient screening of single-SNP association from case-control genome-wide association studies.
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Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.
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Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo.
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Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis.
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SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization.
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Spatial preferences of microRNA targets in 3' untranslated regions.
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Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate.
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Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.
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Statistical challenges in preprocessing in microarray experiments in cancer.
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Statistical considerations for analysis of microarray experiments.
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Statistical methods for assessment of added usefulness of new biomarkers.
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Strong impact of natural-selection-free heterogeneity in genetics of age-related phenotypes.
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Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes.
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Structure-based high-throughput epitope analysis of hexon proteins in B and C species human adenoviruses (HAdVs).
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Subcellular organelle lipidomics in TLR-4-activated macrophages.
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Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
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Systems Genetics Approach to Biomarker Discovery: GPNMB and Heart Failure in Mice and Humans.
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Systems biology approaches to defining transcription regulatory networks in halophilic archaea.
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Systems biology.
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Target domain definition and classification in CASP8.
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Temporal Patterns in Sheep Fetal Heart Rate Variability Correlate to Systemic Cytokine Inflammatory Response: A Methodological Exploration of Monitoring Potential Using Complex Signals Bioinformatics.
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Ten Simple Rules for Effective Statistical Practice.
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The 2015 Bioinformatics Open Source Conference (BOSC 2015).
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The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018).
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The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome.
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The Bioinformatics Open Source Conference (BOSC) 2013.
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The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.
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The Bioperl toolkit: Perl modules for the life sciences.
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The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community.
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The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.
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The Chlamydia trachomatis Protease CPAF Contains a Cryptic PDZ-Like Domain with Similarity to Human Cell Polarity and Tight Junction PDZ-Containing Proteins.
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The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science.
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The ENCODE (ENCyclopedia Of DNA Elements) Project.
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The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.
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The Gene Ontology in 2010: extensions and refinements.
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The Genome 10K Project: a way forward.
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The LabBase system for data management in large scale biology research laboratories.
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The MetJ regulon in gammaproteobacteria determined by comparative genomics methods.
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The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency.
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The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants.
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The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods.
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The coming age of data-driven medicine: translational bioinformatics' next frontier.
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The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.
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The genome of the sea urchin Stongylocentrotus purpuratus
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The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches.
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The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues.
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The molecular basis of quantitative genetic variation in central and secondary metabolism in Arabidopsis.
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The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.
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The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.
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The persistence potential of transferable plasmids.
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The statistics of bulk segregant analysis using next generation sequencing.
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The teleost anatomy ontology: anatomical representation for the genomics age.
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Thinking outside the gate: single-cell assessments in multiple dimensions.
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Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.
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Toward computational systems biology.
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Towards an integrated ecosystem of R packages for the analysis of population genetic data.
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Transcription Factor RUNX1 Regulates Platelet PCTP (Phosphatidylcholine Transfer Protein): Implications for Cardiovascular Events: Differential Effects of RUNX1 Variants.
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Transcriptional analyses of adult and pediatric adamantinomatous craniopharyngioma reveals similar expression signatures regarding potential therapeutic targets.
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Transcriptome analysis of mouse stem cells and early embryos.
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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.
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Translating genomic biomarkers into clinically useful diagnostics.
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Translational Bioinformatics: Past, Present, and Future.
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Translational bioinformatics in mental health: open access data sources and computational biomarker discovery.
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Transversions have larger regulatory effects than transitions.
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Uncertainty-Gated Stochastic Sequential Model for EHR Mortality Prediction.
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Understanding the Cellular and Molecular Mechanisms of Physical Activity-Induced Health Benefits.
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Unique microRNA profile in end-stage heart failure indicates alterations in specific cardiovascular signaling networks.
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Use of bioinformatic tools in primer validation.
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Use of immuno-LCM to identify the in situ expression profile of cellular constituents of the tumor microenvironment.
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Using DNA duplex stability information for transcription factor binding site discovery.
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Using DNase digestion data to accurately identify transcription factor binding sites.
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Using cauliflower to find conserved non-coding regions in Arabidopsis.
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Using extremal events to characterize noisy time series.
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Using nurses' natural language entries to build a concept-oriented terminology for patients' chief complaints in the emergency department.
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Using secondary structure to identify ribosomal numts: cautionary examples from the human genome.
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Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.
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Vaginal deployment and tenofovir delivery by microbicide gels.
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Validation of three-dimensional conduction models using experimental mapping: are we getting closer?
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Visual annotation of the gene database.
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Visual presentation as a welcome alternative to textual presentation of gene annotation information.
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WASABI: an automated sequence processing system for multigene phylogenies.
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Waddling and toddling: the biomechanical effects of an immature gait.
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What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae).
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What is mzXML good for?
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Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum.
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Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios.
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Whole-genome sequencing of bloodstream Staphylococcus aureus isolates does not distinguish bacteraemia from endocarditis.
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Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation.
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Workshop on cancer biometrics: identifying biomarkers and surrogates of cancer in patients: a meeting held at the Masur Auditorium, National Institutes of Health.
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ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
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Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation.
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apex: phylogenetics with multiple genes.
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dictyBase: a new Dictyostelium discoideum genome database.
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hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine.
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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
-
Bobay, Benjamin,
Research Associate, Senior,
Radiology
-
Bryan, Jordan,
Student,
Statistical Science
-
Gounley, John,
Affiliate,
Biomedical Engineering
-
Grimsrud, Paul,
Assistant Professor in Medicine,
Medicine, Endocrinology, Metabolism, and Nutrition
-
Haase, Steven B.,
Professor of Biology,
Biology
-
Hartemink, Alexander J.,
Professor in the Department of Computer Science,
Biology
-
Hogan, Brigid L. M.,
Research Professor of Cell 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