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A Catalog of Reference Genomes from the Human Microbiome Academic Article
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A Comprehensive Expression Analysis of the Arabidopsis Proline-rich Extensin-like Receptor Kinase Gene Family using Bioinformatic and Experimental Approaches Academic Article
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A Computational Model of the Functional Role of the Ventral-Striatal D2 Receptor in the Expression of Previously Acquired Behaviors Academic Article
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A FLEXIBLE NONPARAMETRIC APPROACH TO FIND CANDIDATE GENES ASSOCIATED WITH DISEASE IN MICROARRAY EXPERIMENTS Academic Article
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A Human Protein Interaction Network Shows Conservation of Aging Processes between Human and Invertebrate Species Academic Article
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A New Family of Giardial Cysteine-Rich Non-VSP Protein Genes and a Novel Cyst Protein Academic Article
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A Novel Non-canonical Forkhead-associated (FHA) Domain-binding Interface Mediates the Interaction between Rad53 and Dbf4 Proteins Academic Article
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A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis Academic Article
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A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring Academic Article
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A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history Academic Article
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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 Academic Article
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A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach Academic Article
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Adaptive modelling of gene regulatory network using Bayesian information criterion‐guided sparse regression approach Academic Article
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Amplification of MUC1 in prostate cancer metastasis and CRPC development Academic Article
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An atypical proprotein convertase in Giardia lamblia differentiation Academic Article
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Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array Academic Article
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Antimicrobial resistance surveillance in the genomic age Academic Article
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Application of metabolomics to the study of irritable bowel syndrome Academic Article
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Association of common variants in the human eyes shut ortholog (EYS) with statin-induced myopathy: Evidence for additional functions of EYS Academic Article
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Automated Identification of Depsipeptide Natural Products by an Informatic Search Algorithm Academic Article
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BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species Academic Article
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Bioinformatic analyses identifies novel protein-coding pharmacogenomic markers associated with paclitaxel sensitivity in NCI60 cancer cell lines Academic Article
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Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins Academic Article
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Bioinformatics of antimicrobial resistance in the age of molecular epidemiology Academic Article
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Biomedical Signal and Image Processing for Clinical Decision Support Systems 2014 Academic Article
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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database Academic Article
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Characterizing Transcriptional Networks in Male Rainbow Darter (Etheostoma caeruleum) that Regulate Testis Development over a Complete Reproductive Cycle Academic Article
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Chemical and biosynthetic evolution of the antimycin-type depsipeptides Academic Article
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Chlamydia pneumoniae CopD Translocator Protein Plays a Critical Role in Type III Secretion (T3S) and Infection Academic Article
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Classifying post-traumatic stress disorder using the magnetoencephalographic connectome and machine learning Academic Article
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Clinical Outcome Prediction in Aneurysmal Subarachnoid Hemorrhage Using Bayesian Neural Networks with Fuzzy Logic Inferences Academic Article
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Comments on “Evolutionary dynamics of RNA-like replicator systems” Academic Article
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Community-wide hackathons to identify central themes in single-cell multi-omics Academic Article
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Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs Academic Article
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Computational cognitive neuroscience Academic Article
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Critical assessment of automated flow cytometry data analysis techniques Academic Article
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Cross‐species discovery of syncretic drug combinations that potentiate the antifungal fluconazole Academic Article
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DELPHI: accurate deep ensemble model for protein interaction sites prediction Academic Article
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DNA and the revolutions of molecular evolution, computational biology, and bioinformatics Academic Article
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DataSHIELD: taking the analysis to the data, not the data to the analysis Academic Article
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Deciphering epitope specificities within polyserum using affinity selection of random peptides and a novel algorithm based on pattern recognition theory Academic Article
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Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery Academic Article
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Directionality in the evolution of influenza A haemagglutinin Academic Article
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Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella Academic Article
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Discovery of novel bacterial toxins by genomics and computational biology Academic Article
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Do commonin silicotools predict the clinical consequences of amino-acid substitutions in the CFTR gene? Academic Article
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Editorial Academic Article
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Effects of contact structure on the transient evolution of HIV virulence Academic Article
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Estimating Blood Flow in Skeletal Muscle Arteriolar Trees Reconstructed from In Vivo Data Conference Paper
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Estimating blood flow in skeletal muscle arteriolar trees reconstructed from in vivo data using the Fry approach Academic Article
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Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss Academic Article
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Evaluation of the Disease Liability of CFTR Variants Academic Article
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Experimental Screening of Dihydrofolate Reductase Yields a “Test Set” of 50,000 Small Molecules for a Computational Data-Mining and Docking Competition Academic Article
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Exploration of Nonribosomal Peptide Families with an Automated Informatic Search Algorithm Academic Article
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Extracting Haplotypes from Diploid Organisms Academic Article
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Fast computation of neighbor seeds Academic Article
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Fast estimation of time-varying infectious disease transmission rates Academic Article
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Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial Academic Article
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Flexibility of “Polyunsaturated Fatty Acid Chains” and Peptide Backbones: A Comparative ab Initio Study Academic Article
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Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences Academic Article
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Gene-centric Meta-analysis in 87,736 Individuals of European Ancestry Identifies Multiple Blood-Pressure-Related Loci Academic Article
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Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads Academic Article
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Genetic variants of MARCO are associated with susceptibility to pulmonary tuberculosis in a Gambian population Academic Article
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Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family Academic Article
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Genome-Wide Association Studies—Data Generation, Storage, Interpretation, and Bioinformatics Academic Article
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Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining Academic Article
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Genotypic and Phenotypic Analyses of Two “Isogenic” Strains of the Human Fungal Pathogen Cryptococcus neoformans var. neoformans Academic Article
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Hepatic gene expression profiling in zebrafish (Danio rerio) exposed to the fungicide chlorothalonil Academic Article
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Heterologous expression-facilitated natural products’ discovery in actinomycetes Academic Article
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Heterotachy and long-branch attraction in phylogenetics Academic Article
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Holotestoid: A computational model for testing hypotheses about echinoid skeleton form and growth Academic Article
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How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish Academic Article
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Human Chromosome 7: DNA Sequence and Biology Academic Article
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Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry Academic Article
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Identification of CD8+ T Cell Epitopes in the West Nile Virus Polyprotein by Reverse-Immunology Using NetCTL Academic Article
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Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum. Academic Article
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Identification, Structure, and Function of a Novel Type VI Secretion Peptidoglycan Glycoside Hydrolase Effector-Immunity Pair Academic Article
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Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance Academic Article
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Imputation of missing genotypes: an empirical evaluation of IMPUTE Academic Article
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In Vitro Screening for Drug Repositioning Academic Article
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Integrated gene and species phylogenies from unaligned whole
genome protein sequences Academic Article
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Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models Academic Article
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Interpreting Metabolomic Profiles using Unbiased Pathway Models Academic Article
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Introducing the GEV Activation Function for Highly Unbalanced Data to Develop COVID-19 Diagnostic Models Academic Article
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Iron and citrate export by a major facilitator superfamily pump regulates metabolism and stress resistance in
Salmonella
Typhimurium Academic Article
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Key Developments in Endocrine Disrupter Research and Human Health Academic Article
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Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration Academic Article
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Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an 18O-Labeled “Universal” Reference Sample Academic Article
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Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function Academic Article
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Low‐depth sequencing for copy number abnormalities in multiple myeloma supersedes fluorescent in situ hybridization in scope and resolution Academic Article
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MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons Academic Article
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Mapping of Steroids Binding to 17β-Hydroxysteroid Dehydrogenase Type 1 Using Monte Carlo Energy Minimization Reveals Alternative Binding Modes Academic Article
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Metabolic and co-expression network-based analyses associated with nitrate response in rice Academic Article
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Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA Academic Article
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MiR-204 down-regulation elicited perturbation of a gene target signature common to human cholangiocarcinoma and gastric cancer Academic Article
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MicroRNAs 146a/b-5 and 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes Academic Article
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Minimum Information about a Biosynthetic Gene cluster Academic Article
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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 Academic Article
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Modular Evolution and the Origins of Symmetry: Reconstruction of a Three-Fold Symmetric Globular Protein Academic Article
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Molecular and phylogenetic approaches for assessing sources of Cryptosporidium contamination in water Academic Article
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Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila Academic Article
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Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades Academic Article
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Molecular signatures for the phylum Synergistetes and some of its subclades Academic Article
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Monte Carlo-energy minimization of correolide in the Kv1.3 channel: possible role of potassium ion in ligand-receptor interactions. Academic Article
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Mouse Models of Lung Fibrosis Academic Article
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Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes Academic Article
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Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins Academic Article
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Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes Academic Article
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Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition Academic Article
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Novel approaches to discovery of antibacterial agents Academic Article
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Novel function discovery through sequence and structural data mining Academic Article
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Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of
Pseudomonas aeruginosa Academic Article
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On selection in finite populations Academic Article
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PITHIA: Protein Interaction Site Prediction Using Multiple Sequence Alignments and Attention Academic Article
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PROGRAM DESCRIPTION Academic Article
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Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters Academic Article
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Pathbase: a database of mutant mouse pathology Academic Article
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Pathbase: a new reference resource and database for laboratory mouse pathology Academic Article
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Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C Academic Article
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Phenomics: expanding the role of clinical evaluation in genomic studies. Academic Article
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Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures Academic Article
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Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae Academic Article
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Plant DNA sequences from feces: potential means for assessing diets of wild primates Academic Article
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Pollux: platform independent error correction of single and mixed genomes Academic Article
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Population Genetics Without Intraspecific Data Academic Article
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Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population Academic Article
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Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos Academic Article
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Predicting Protein Interaction Sites Using PITHIA Academic Article
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Predicting Protein–Protein Interactions Using SPRINT Academic Article
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Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment Academic Article
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Prediction of plant lncRNA by ensemble machine learning classifiers Academic Article
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Preface to the special issue on computational cognitive neuroscience Academic Article
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Preface to the special issue: Computational cognitive neuroscience Academic Article
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Prevalence Estimates of Polycystic Kidney and Liver Disease by Population Sequencing Academic Article
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Processing of Serum Proteins Underlies the Mass Spectral Fingerprinting of Myocardial Infarction Academic Article
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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 Academic Article
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Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties Academic Article
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Recommendations From the International Stroke Genetics Consortium, Part 2 Academic Article
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Regulation of a Novel Gene Cluster Involved in Secondary Metabolite Production in
Streptomyces coelicolor Academic Article
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Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells Academic Article
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Searching for Substitution Rate Heterogeneity Academic Article
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Secretome proteins as candidate biomarkers for aggressive thyroid carcinomas Academic Article
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Sensitivity of the dynamics of the general Rosenzweig–MacArthur model to the mathematical form of the functional response: a bifurcation theory approach Academic Article
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Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray Academic Article
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Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans Academic Article
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Simple sequence in brain and nervous system specific proteins Academic Article
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SpEED: fast computation of sensitive spaced seeds Academic Article
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Stem cell gene expression programs influence clinical outcome in human leukemia Academic Article
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Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data Academic Article
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Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d Academic Article
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Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements Academic Article
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Systems-Level Chemical Biology to Accelerate Antibiotic Drug Discovery Academic Article
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease Academic Article
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The Composite Genome of the Legume Symbiont
Sinorhizobium meliloti Academic Article
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The Comprehensive Antibiotic Resistance Database Academic Article
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The LASSO and Sparse Least Squares Regression Methods for SNP Selection in Predicting Quantitative Traits Academic Article
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The Transcription Factor Encyclopedia Academic Article
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The effect of sampling from subdivided populations on species identification with DNA barcodes using a Bayesian statistical approach Academic Article
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The impact of cigarette smoke exposure, COPD, or asthma status on ABC transporter gene expression in human airway epithelial cells Academic Article
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The origin of life is a spatially localized stochastic transition Academic Article
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Unified approach to optimal estimation of mean and standard deviation from sample summaries Academic Article
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Use of Buffy Coat miRNA Profiling for Breast Cancer Prediction in Healthy Women Academic Article
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Use of an Interactive Tool to Assess Patients' Willingness-to-Pay Academic Article
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“From Protein Toxins to Applied Toxicological Testing” virtual workshop identifies the need for a bioinformatic framework to assess novel food protein safety Conference Paper