Computational Biology Concept

subject area of

• A Catalog of Reference Genomes from the Human Microbiome  Journal Articles
• A Comprehensive Expression Analysis of the Arabidopsis Proline-rich Extensin-like Receptor Kinase Gene Family using Bioinformatic and Experimental Approaches  Journal Articles
• A Computational Model of the Functional Role of the Ventral-Striatal D2 Receptor in the Expression of Previously Acquired Behaviors  Journal Articles
• A FLEXIBLE NONPARAMETRIC APPROACH TO FIND CANDIDATE GENES ASSOCIATED WITH DISEASE IN MICROARRAY EXPERIMENTS  Journal Articles
• A Human Protein Interaction Network Shows Conservation of Aging Processes between Human and Invertebrate Species  Journal Articles
• A New Family of Giardial Cysteine-Rich Non-VSP Protein Genes and a Novel Cyst Protein  Journal Articles
• A Novel Non-canonical Forkhead-associated (FHA) Domain-binding Interface Mediates the Interaction between Rad53 and Dbf4 Proteins  Journal Articles
• A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis  Journal Articles
• A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring  Journal Articles
• A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history  Journal Articles
• A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia  Journal Articles
• A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach  Journal Articles
• Adaptive modelling of gene regulatory network using Bayesian information criterion‐guided sparse regression approach  Journal Articles
• Amplification of MUC1 in prostate cancer metastasis and CRPC development  Journal Articles
• An atypical proprotein convertase in Giardia lamblia differentiation  Journal Articles
• Analysis of Transcriptome Differences between Resistant and Susceptible Strains of the Citrus Red Mite Panonychus citri (Acari: Tetranychidae)  Journal Articles
• Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array  Journal Articles
• AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods  Journal Articles
• Antimicrobial resistance surveillance in the genomic age  Journal Articles
• Application of metabolomics to the study of irritable bowel syndrome  Journal Articles
• Association of common variants in the human eyes shut ortholog (EYS) with statin‐induced myopathy: Evidence for additional functions of EYS  Journal Articles
• Automated Identification of Depsipeptide Natural Products by an Informatic Search Algorithm  Journal Articles
• BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species  Journal Articles
• Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.  Journal Articles
• Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins  Journal Articles
• Bioinformatics of antimicrobial resistance in the age of molecular epidemiology  Journal Articles
• Biomedical Signal and Image Processing for Clinical Decision Support Systems 2014  Journal Articles
• CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database  Journal Articles
• Characterizing Transcriptional Networks in Male Rainbow Darter (Etheostoma caeruleum) that Regulate Testis Development over a Complete Reproductive Cycle  Journal Articles
• Chemical and biosynthetic evolution of the antimycin-type depsipeptides  Journal Articles
• Chlamydia pneumoniae CopD Translocator Protein Plays a Critical Role in Type III Secretion (T3S) and Infection  Journal Articles
• Clinical Outcome Prediction in Aneurysmal Subarachnoid Hemorrhage Using Bayesian Neural Networks with Fuzzy Logic Inferences  Journal Articles
• Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin  Journal Articles
• Comments on “Evolutionary dynamics of RNA-like replicator systems”  Journal Articles
• Community-wide hackathons to identify central themes in single-cell multi-omics  Journal Articles
• Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems  Journal Articles
• Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs  Journal Articles
• Computational cognitive neuroscience  Journal Articles
• Critical assessment of automated flow cytometry data analysis techniques  Journal Articles
• Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity.  Journal Articles
• Cross‐species discovery of syncretic drug combinations that potentiate the antifungal fluconazole  Journal Articles
• DELPHI: accurate deep ensemble model for protein interaction sites prediction  Journal Articles
• DNA and the revolutions of molecular evolution, computational biology, and bioinformatics  Journal Articles
• Deciphering epitope specificities within polyserum using affinity selection of random peptides and a novel algorithm based on pattern recognition theory  Journal Articles
• Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery  Journal Articles
• Directionality in the evolution of influenza A haemagglutinin  Journal Articles
• Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella  Journal Articles
• Discovery of novel bacterial toxins by genomics and computational biology  Journal Articles
• Do common in silico tools predict the clinical consequences of amino‐acid substitutions in the CFTR gene?  Journal Articles
• Editorial  Journal Articles
• Effects of contact structure on the transient evolution of HIV virulence  Journal Articles
• Estimating Blood Flow in Skeletal Muscle Arteriolar Trees Reconstructed from In Vivo Data  Conferences
• Estimating blood flow in skeletal muscle arteriolar trees reconstructed from in vivo data using the Fry approach  Journal Articles
• Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss  Journal Articles
• Evaluation of the Disease Liability of CFTR Variants  Journal Articles
• Experimental Screening of Dihydrofolate Reductase Yields a “Test Set” of 50,000 Small Molecules for a Computational Data-Mining and Docking Competition  Journal Articles
• Exploration of Nonribosomal Peptide Families with an Automated Informatic Search Algorithm  Journal Articles
• Extracting Haplotypes from Diploid Organisms  Journal Articles
• Fast computation of neighbor seeds  Journal Articles
• Fast estimation of time-varying infectious disease transmission rates  Journal Articles
• Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial  Journal Articles
• Flexibility of “Polyunsaturated Fatty Acid Chains” and Peptide Backbones:  A Comparative ab Initio Study  Journal Articles
• Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences  Journal Articles
• Gene-centric Meta-analysis in 87,736 Individuals of European Ancestry Identifies Multiple Blood-Pressure-Related Loci  Journal Articles
• Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads  Journal Articles
• Genetic variants of MARCO are associated with susceptibility to pulmonary tuberculosis in a Gambian population  Journal Articles
• Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family  Journal Articles
• Genome-Wide Association Studies—Data Generation, Storage, Interpretation, and Bioinformatics  Journal Articles
• Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining  Journal Articles
• Genotypic and Phenotypic Analyses of Two “Isogenic” Strains of the Human Fungal Pathogen Cryptococcus neoformans var. neoformans  Journal Articles
• Hepatic gene expression profiling in zebrafish (Danio rerio) exposed to the fungicide chlorothalonil  Journal Articles
• Heterologous expression-facilitated natural products’ discovery in actinomycetes  Journal Articles
• Heterotachy and long-branch attraction in phylogenetics  Journal Articles
• Holotestoid: A computational model for testing hypotheses about echinoid skeleton form and growth  Journal Articles
• How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish  Journal Articles
• Human Chromosome 7: DNA Sequence and Biology  Journal Articles
• Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry  Journal Articles
• Identification of CD8+ T Cell Epitopes in the West Nile Virus Polyprotein by Reverse-Immunology Using NetCTL  Journal Articles
• Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum.  Journal Articles
• Identification, Structure, and Function of a Novel Type VI Secretion Peptidoglycan Glycoside Hydrolase Effector-Immunity Pair  Journal Articles
• Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance  Journal Articles
• Improved Compressed Sensing-Based Algorithm for Sparse-View CT Image Reconstruction  Journal Articles
• Imputation of missing genotypes: an empirical evaluation of IMPUTE  Journal Articles
• In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences.  Journal Articles
• Integrated gene and species phylogenies from unaligned whole genome protein sequences  Journal Articles
• Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models  Journal Articles
• Interpreting Metabolomic Profiles using Unbiased Pathway Models  Journal Articles
• Introducing the GEV Activation Function for Highly Unbalanced Data to Develop COVID-19 Diagnostic Models  Journal Articles
• Iron and citrate export by a major facilitator superfamily pump regulates metabolism and stress resistance inSalmonellaTyphimurium  Journal Articles
• Key Developments in Endocrine Disrupter Research and Human Health  Journal Articles
• Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration  Journal Articles
• Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an ¹⁸O-Labeled “Universal” Reference Sample  Journal Articles
• Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function  Journal Articles
• Low‐depth sequencing for copy number abnormalities in multiple myeloma supersedes fluorescent in situ hybridization in scope and resolution  Journal Articles
• MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons  Journal Articles
• Mapping of Steroids Binding to 17β-Hydroxysteroid Dehydrogenase Type 1 Using Monte Carlo Energy Minimization Reveals Alternative Binding Modes  Journal Articles
• Metabolic and co-expression network-based analyses associated with nitrate response in rice  Journal Articles
• Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA  Journal Articles
• Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells  Journal Articles
• MiR-204 down-regulation elicited perturbation of a gene target signature common to human cholangiocarcinoma and gastric cancer  Journal Articles
• MicroRNAs 146a/b-5 and 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes  Journal Articles
• Minimum Information about a Biosynthetic Gene cluster  Journal Articles
• Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities  Journal Articles
• Modular Evolution and the Origins of Symmetry: Reconstruction of a Three-Fold Symmetric Globular Protein  Journal Articles
• Molecular and phylogenetic approaches for assessing sources of Cryptosporidium contamination in water  Journal Articles
• Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila  Journal Articles
• Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades  Journal Articles
• Molecular signatures for the phylum Synergistetes and some of its subclades  Journal Articles
• Monte Carlo-energy minimization of correolide in the Kv1.3 channel: possible role of potassium ion in ligand-receptor interactions.  Journal Articles
• Mountain Pine Beetles Colonizing Historical and Naïve Host Trees Are Associated with a Bacterial Community Highly Enriched in Genes Contributing to Terpene Metabolism  Journal Articles
• Mouse Models of Lung Fibrosis  Journal Articles
• Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes  Journal Articles
• Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins  Journal Articles
• Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes  Journal Articles
• Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition  Journal Articles
• Novel approaches to discovery of antibacterial agents  Journal Articles
• Novel function discovery through sequence and structural data mining  Journal Articles
• ORFcor: Identifying and Accommodating ORF Prediction Inconsistencies for Phylogenetic Analysis  Journal Articles
• Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of Pseudomonas aeruginosa  Journal Articles
• On selection in finite populations  Journal Articles
• PITHIA: Protein Interaction Site Prediction Using Multiple Sequence Alignments and Attention  Journal Articles
• PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction.  Journal Articles
• PROGRAM DESCRIPTION  Journal Articles
• Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters  Journal Articles
• Pathbase: a database of mutant mouse pathology  Journal Articles
• Pathbase: a new reference resource and database for laboratory mouse pathology  Journal Articles
• Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C  Journal Articles
• Phenomics: expanding the role of clinical evaluation in genomic studies.  Journal Articles
• Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures  Journal Articles
• Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae  Journal Articles
• Plant DNA sequences from feces: potential means for assessing diets of wild primates  Journal Articles
• Pollux: platform independent error correction of single and mixed genomes  Journal Articles
• Population Genetics Without Intraspecific Data  Journal Articles
• Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population  Journal Articles
• Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos  Journal Articles
• Predicting Protein Interaction Sites Using PITHIA  Journal Articles
• Predicting Protein–Protein Interactions Using SPRINT  Journal Articles
• Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment  Journal Articles
• Prediction of plant lncRNA by ensemble machine learning classifiers  Journal Articles
• Preface to the special issue on computational cognitive neuroscience  Journal Articles
• Preface to the special issue: Computational cognitive neuroscience  Journal Articles
• Prevalence Estimates of Polycystic Kidney and Liver Disease by Population Sequencing  Journal Articles
• Processing of Serum Proteins Underlies the Mass Spectral Fingerprinting of Myocardial Infarction  Journal Articles
• Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas  Journal Articles
• Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties  Journal Articles
• Recommendations From the International Stroke Genetics Consortium, Part 2  Journal Articles
• Regulation of a Novel Gene Cluster Involved in Secondary Metabolite Production in Streptomyces coelicolor  Journal Articles
• Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson's disease.  Journal Articles
• Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells  Journal Articles
• SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria  Journal Articles
• Scoring alignments by embedding vector similarity  Journal Articles
• Searching for Substitution Rate Heterogeneity  Journal Articles
• Secretome proteins as candidate biomarkers for aggressive thyroid carcinomas  Journal Articles
• Sensitivity of the dynamics of the general Rosenzweig–MacArthur model to the mathematical form of the functional response: a bifurcation theory approach  Journal Articles
• Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray  Journal Articles
• Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans  Journal Articles
• Simple sequence in brain and nervous system specific proteins  Journal Articles
• SpEED: fast computation of sensitive spaced seeds  Journal Articles
• Stem cell gene expression programs influence clinical outcome in human leukemia  Journal Articles
• Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data  Journal Articles
• Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d  Journal Articles
• Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements  Journal Articles
• Systems-Level Chemical Biology to Accelerate Antibiotic Drug Discovery  Journal Articles
• Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease  Journal Articles
• The Composite Genome of the Legume Symbiont Sinorhizobium meliloti  Journal Articles
• The Comprehensive Antibiotic Resistance Database  Journal Articles
• The LASSO and Sparse Least Squares Regression Methods for SNP Selection in Predicting Quantitative Traits  Journal Articles
• The Transcription Factor Encyclopedia  Journal Articles
• The effect of sampling from subdivided populations on species identification with DNA barcodes using a Bayesian statistical approach  Journal Articles
• The impact of cigarette smoke exposure, COPD, or asthma status on ABC transporter gene expression in human airway epithelial cells  Journal Articles
• The origin of life is a spatially localized stochastic transition  Journal Articles
• Unified approach to optimal estimation of mean and standard deviation from sample summaries  Journal Articles
• Update of the spectrum of GJB2 mutations in 107 patients with nonsyndromic hearing loss in the Fujian population of China.  Journal Articles
• Use of Buffy Coat miRNA Profiling for Breast Cancer Prediction in Healthy Women  Journal Articles
• Use of an Interactive Tool to Assess Patients' Willingness-to-Pay  Journal Articles
• Virtual Histology of Cortical Thickness and Shared Neurobiology in 6 Psychiatric Disorders  Journal Articles
• mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics  Journal Articles
• “From Protein Toxins to Applied Toxicological Testing” virtual workshop identifies the need for a bioinformatic framework to assess novel food protein safety  Conferences