subject area of

• A Java API for working with PubChem datasets  Academic Article
• A bacterial metapopulation adapts locally to phage predation despite global dispersal  Academic Article
• A bioinformatic assay for pluripotency in human cells  Academic Article
• A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana  Academic Article
• A comparison of match-only algorithms for the analysis of plasmodium falciparum oligonucleotide arrays  Academic Article
• A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes  Academic Article
• A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses  Academic Article
• A computational approach to correct arginine-to-proline conversion in quantitative proteomics  Academic Article
• A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data  Academic Article
• A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells  Academic Article
• A covering method for detecting genetic associations between rare variants and common phenotypes  Academic Article
• A gene wiki for community annotation of gene function  Academic Article
• A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue  Academic Article
• A new member of the 4-methylideneimidazole-5-one-containing aminomutase family from the enediyne kedarcidin biosynthetic pathway  Academic Article
• A new perspective on V3 phenotype prediction  Academic Article
• A note on generalized genome scan meta-analysis statistics  Academic Article
• A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9  Academic Article
• A novel method for finding tRNA genes  Academic Article
• A phosphopantetheinylating polyketide synthase producing a linear polyene to initiate enediyne antitumor antibiotic biosynthesis  Academic Article
• A population response analysis approach to assign class II HLA-epitope restrictions  Academic Article
• A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites  Academic Article
• A quantitative protein interaction network for the ErbB receptors using protein microarrays  Academic Article
• A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in setaria  Academic Article
• Active site binding modes of curcumin in HIV-1 protease and integrase  Academic Article
• Agonist antibody that induces human malignant cells to kill one another  Academic Article
• An application and empirical comparison of statistical analysis methods for associating rare variants to a complex phenotype  Academic Article
• An archaeal antioxidant: Characterization of a dps-like protein from sulfolobus solfataricus  Academic Article
• An ensemble method for gene discovery based on DNA microarray data  Academic Article
• An in vivo screen to identify candidate neurogenic genes in the developing Xenopus visual system  Academic Article
• An online resource for GPCR structure determination and analysis  Academic Article
• Analysis of large-scale sequencing of small RNAs  Academic Article
• Analysis of microtubule dynamic instability using a plus-end growth marker  Academic Article
• Analysis of stop-gain and frameshift variants in human innate immunity genes  Academic Article
• Analyzing molecular interactions  Academic Article
• Applications of beta-mixture models in bioinformatics  Academic Article
• Applying genomics to organ transplantation medicine in both discovery and validation of biomarkers  Academic Article
• Arrayed protein library technology for therapeutic biologic discovery  Academic Article
• Assigning function to yeast proteins by integration of technologies  Academic Article
• AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context  Academic Article
• AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading  Academic Article
• Automatic annotation of matrix-assisted laser desorption/ionization n-glycan spectra  Academic Article
• Autonomous metabolomics for rapid metabolite identification in global profiling  Academic Article
• Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics  Academic Article
• Biobanking: an important resource for precision medicine in glioblastoma  Academic Article
• Biochemistry. Integrative structural biology  Academic Article
• Biodiversity and biogeography of phages in modern stromatolites and thrombolites  Academic Article
• Biogps: An extensible and customizable portal for querying and organizing gene annotation resources  Academic Article
• Bioinformatic analysis of circadian gene oscillation in mouse aorta  Academic Article
• Bioinformatic identification of genes suppressing genome instability  Academic Article
• Bioinformatics and HIV latency  Academic Article
• Bioinformatics: the next frontier of metabolomics  Academic Article
• Biosynthesis of the enediyne antitumor antibiotic c-1027 involves a new branching point in chorismate metabolism  Academic Article
• Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement  Academic Article
• C-S bond cleavage by a polyketide synthase domain  Academic Article
• CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma  Academic Article
• CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses  Academic Article
• Can the false-discovery rate be misleading?  Academic Article
• Cancer proteomics by quantitative shotgun proteomics  Academic Article
• Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers  Academic Article
• Characterization of sporulation histidine kinases of bacillus anthracis  Academic Article
• Coarse grain lipid-protein molecular interactions and diffusion with MsbA flippase  Academic Article
• Coevolution and subsite decomposition for the design of resistance-evading HIV-1 protease inhibitors  Academic Article
• Collecting and organizing systematic sets of protein data  Academic Article
• Combining h/d exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase  Academic Article
• Combining metabolite-based pharmacophores with Bayesian machine learning models for mycobacterium tuberculosis drug discovery  Academic Article
• Composition and structure of the 80S ribosome from the green alga Chlamydomonas reinhardtii: 80S ribosomes are conserved in plants and animals  Academic Article
• Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold  Academic Article
• Computational coevolution of antiviral drug resistance  Academic Article
• Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells  Academic Article
• Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy  Academic Article
• Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic hiv vaccine epitope  Academic Article
• Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5  Academic Article
• Computational design of proteins targeting the conserved stem region of influenza hemagglutinin  Academic Article
• Computational design of self-assembling register-specific collagen heterotrimers  Academic Article
• Computational fragment-based binding site identification by ligand competitive saturation  Academic Article
• Computational functional group mapping for drug discovery  Academic Article
• Computational reconstruction of multidomain proteins using atomic force microscopy data  Academic Article
• Computational tools for epitope vaccine design and evaluation  Academic Article
• Crowdsourcing for bioinformatics  Academic Article
• Crowdsourcing in biomedicine: challenges and opportunities  Academic Article
• Crystal and solution structures of a prokaryotic m16b peptidase: An open and shut case  Academic Article
• Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 Å resolution  Academic Article
• Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme  Academic Article
• Current advances in molecular, biochemical, and computational modeling analysis of microalgal triacylglycerol biosynthesis  Academic Article
• DNA binding-dependent glucocorticoid receptor activity promotes adipogenesis via Kruppel-like factor 15 gene expression  Academic Article
• DNA-based photonic logic gates: AND, NAND, and INHIBIT  Academic Article
• Deep mutational scanning: assessing protein function on a massive scale  Academic Article
• Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease  Academic Article
• Defining the rna internal loops preferred by benzimidazole derivatives via 2D combinatorial screening and computational analysis  Academic Article
• Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase: comparisons with methane monooxygenase  Academic Article
• Detecting individual sites subject to episodic diversifying selection  Academic Article
• Differential gene expression in lps/ifn gamma activated microglia and macrophages: In vitro versus in vivo  Academic Article
• Digital orthodoxy of human data collection  Academic Article
• Discovering disease-associated enzymes by proteome reactivity profiling  Academic Article
• Discovery and functional characterization of a neomorphic PTEN mutation  Academic Article
• Discovery of acetylcholinesterase peripheral anionic site ligands through computational refinement of a directed library  Academic Article
• Discovery of highly potent, selective, and brain-penetrable leucine-rich repeat kinase 2 (LRRK2) small molecule inhibitors  Academic Article
• Discovery of novel drugs for promising targets  Academic Article
• Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms  Academic Article
• Dizeez: an online game for human gene-disease annotation  Academic Article
• Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation  Academic Article
• Dose-response in a high density three-dimensional liver device with real-time bioenergetic and metabolic flux quantification  Academic Article
• Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface  Academic Article
• Dynamics in cryo em reconstructions visualized with maximum-likelihood derived variance maps  Academic Article
• Early emergence of negative regulation of the tyrosine kinase Src by the C-terminal Src kinase  Academic Article
• Ecto-Fc MS identifies ligand-receptor interactions through extracellular domain Fc fusion protein baits and shotgun proteomic analysis  Academic Article
• Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet  Academic Article
• Electrostatic aspects of protein-protein interactions  Academic Article
• Enabling drug discovery project decisions with integrated computational chemistry and informatics  Academic Article
• Engineered DNA sequence syntax inspector  Academic Article
• Enhancing the selectivity of kinase inhibitors in oncology: a chemical biology perspective  Academic Article
• Enrich: software for analysis of protein function by enrichment and depletion of variants  Academic Article
• Enrichment of regulatory signals in conserved non-coding genomic sequence  Academic Article
• Envelope: Interactive software for modeling and fitting complex isotope distributions  Academic Article
• Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation  Academic Article
• Eugene: a domain specific language for specifying and constraining synthetic biological parts, devices, and systems  Academic Article
• Evidence-based annotation of the malaria parasite's genome using comparative expression profiling  Academic Article
• Evolution of the TIR, tolls and TLRs: functional inferences from computational biology  Academic Article
• Evolutionary analysis of HIV-1 protease inhibitors: methods for design of inhibitors that evade resistance  Academic Article
• Expanding the proteome: Disordered and alternatively folded proteins  Academic Article
• Extent of protein-protein interactions and quasi-equivalence in viral capsids  Academic Article
• Factor Xa active site substrate specificity with substrate phage display and computational molecular modeling  Academic Article
• Fast, cheap and out of control: a zero curation model for ontology development  Academic Article
• FoldEco: A model for proteostasis in E. coli  Academic Article
• FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A  Academic Article
• Function and dynamics of macromolecular complexes explored by integrative structural and computational biology  Academic Article
• Functional metagenomic profiling of nine biomes  Academic Article
• GeneDig: a web application for accessing genomic and bioinformatics knowledge  Academic Article
• Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes  Academic Article
• Genomic studies of transcription factor-DNA interactions  Academic Article
• Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?  Academic Article
• Glioma-propagating cells as an in vitro screening platform: PLK1 as a case study  Academic Article
• Glycomics: An integrated systems approach to structure-function relationships of glycans  Academic Article
• GuavaH: a compendium of host genomic data in HIV biology and disease  Academic Article
• Ha novel approach to investigate tissue-specific trinucleotide repeat instability  Academic Article
• Hi-Fi transmission of periodic signals amid cell-to-cell variability  Academic Article
• Hierarchical and multi-resolution representation of protein flexibility  Academic Article
• Hierarchical and programmable one-pot synthesis of oligosaccharides  Academic Article
• High confidence fission yeast SUMO conjugates identified by tandem denaturing affinity purification  Academic Article
• High-throughput assays for promiscuous inhibitors  Academic Article
• Hotspot-centric de novo design of protein binders  Academic Article
• Human germline antibody gene segments encode polyspecific antibodies  Academic Article
• IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform  Academic Article
• IHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website  Academic Article
• Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements  Academic Article
• Identification of an HIV-1 clade A envelope that exhibits broad antigenicity and neutralization sensitivity and elicits antibodies targeting three distinct epitopes  Academic Article
• Identification of direct residue contacts in protein-protein interaction by message passing  Academic Article
• Identification of rare cancer driver mutations by network reconstruction  Academic Article
• Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay  Academic Article
• Identification of the thiazolyl peptide GE37468 gene cluster from Streptomyces ATCC 55365 and heterologous expression in Streptomyces lividans  Academic Article
• Improving the TFold test for differential shotgun proteomics  Academic Article
• In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen  Academic Article
• In silico discovery of transcription regulatory elements in plasmodium falciparum  Academic Article
• In silico qtl mapping of basal liver iron levels in inbred mouse strains  Academic Article
• Increased hydrophobicity at the n terminus/membrane interface impairs gating of the severe combined immunodeficiency-related orai1 mutant  Academic Article
• Informatics and multiplexing of intact protein identification in bacteria and the archaea  Academic Article
• Informatics enhanced SNP microarray analysis of 30 miscarriage samples compared to routine cytogenetics  Academic Article
• Informatics-based, highly accurate, noninvasive prenatal paternity testing  Academic Article
• Integrated computational and experimental analysis of the neuroendocrine transcriptome in genetic hypertension identifies novel control points for the cardiometabolic syndrome  Academic Article
• Integrating computation and visualization for biomolecular analysis: an example using Python and AVS  Academic Article
• Interaction fidelity in two-component signaling  Academic Article
• Interdependency of brassinosteroid and auxin signaling in Arabidopsis  Academic Article
• Interoperability with Moby 1.0: it's better than sharing your toothbrush  Academic Article
• Ionomics and the study of the plant ionome  Academic Article
• Kinomics-structural biology and chemogenomics of kinase inhibitors and targets  Academic Article
• Large-scale integration of human genetic and physical maps  Academic Article
• Leveraging two-way prob-level block design for identifying differential gene expression with high-density oligonucleotide arrays  Academic Article
• Local quality assessment in homology models using statistical potentials and support vector machines  Academic Article
• Low-molecular-weight protein tyrosine phosphatases of bacillus subtilis  Academic Article
• Machine learning models and pathway genome data base for trypanosoma cruzi drug discovery  Academic Article
• Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion  Academic Article
• Meta- and orthogonal integration of influenza "OMICs'' data defines a role for UBR4 in virus budding  Academic Article
• Meta-analysis of untargeted metabolomic data from multiple profiling experiments  Academic Article
• Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression  Academic Article
• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals  Academic Article
• Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity  Academic Article
• MicroRNA regulation of molecular networks mapped by global microRNA, mRNA, and protein expression in activated T lymphocytes  Academic Article
• Microtask crowdsourcing for disease mention annotation in PubMed abstracts  Academic Article
• Minimum information about a biosynthetic gene cluster  Academic Article
• Mining the Giardia genome and proteome for conserved and unique basal body proteins  Academic Article
• Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains  Academic Article
• Mobile elements create structural variation: Analysis of a complete human genome  Academic Article
• Model of the alpha L beta 2 integrin I-domain/ICAM-1 DI interface suggests that subtle changes in loop orientation determine ligand specificity  Academic Article
• Multiscale coarse-graining of the protein energy landscape  Academic Article
• Networks link antigenic and receptor-binding sites of influenza hemagglutinin: Mechanistic insight into fitter strain propagation  Academic Article
• Nmr structure determination of the conserved hypothetical protein tm1816 from thermotoga maritima  Academic Article
• Non-invasive prenatal detection of trisomy 13 using a single nucleotide polymorphism- and informatics-based approach  Academic Article
• OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing  Academic Article
• Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing  Academic Article
• Orphan receptor GPR158 is an allosteric modulator of RGS7 catalytic activity with an essential role in dictating its expression and localization in the brain  Academic Article
• Outcome of the first wwPDB Hybrid/Integrative Methods Task Force Workshop  Academic Article
• PDZ domain binding selectivity is optimized across the mouse proteome  Academic Article
• PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data  Academic Article
• Parallel identification of new genes in Saccharomyces cerevisiae  Academic Article
• Perspective on computational and structural aspects of kinase discovery from IPK2014  Academic Article
• Phase-locked signals elucidate circuit architecture of an oscillatory pathway  Academic Article
• Platensimycin and platencin biosynthesis in Streptomyces platensis, showcasing discovery and characterization of novel bacterial diterpene synthases  Academic Article
• Predicting PDZ domain-peptide interactions from primary sequences  Academic Article
• Predicting structurally conserved contacts for homologous proteins using sequence conservation filters  Academic Article
• Proliferating cell nuclear antigen loaded onto double-stranded DNA: Dynamics, minor groove interactions and functional implications  Academic Article
• Protein analysis by shotgun/bottom-up proteomics  Academic Article
• Protein identification using 2D-LC-MS/MS  Academic Article
• Protein interaction mapping for target validation: The need for an integrated combinatory process involving complementary approaches  Academic Article
• Protein-protein docking with F(2)Dock 2.0 and GB-rerank  Academic Article
• Proteomic analysis of tumor necrosis factor-alpha (TNF-α)-induced L6 myotube secretome reveals novel TNF-α-dependent myokines in diabetic skeletal muscle  Academic Article
• Proteomics by mass spectrometry: approaches, advances, and applications  Academic Article
• Pseudopodium-enriched atypical kinase 1 regulates the cytoskeleton and cancer progession  Academic Article
• Purdue ionomics information management system. An integrated functional genomics platform  Academic Article
• Putting proteins in context  Academic Article
• Quantitative analysis of brain nuclear phosphoproteins identifies developmentally regulated phosphorylation events  Academic Article
• Quantitative analysis of human pluripotency and neural specification by in-depth (phospho) proteomic profiling  Academic Article
• RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis  Academic Article
• Recognition templates for predicting adenylate-binding sites in proteins  Academic Article
• Regulatory networks define phenotypic classes of human stem cell lines  Academic Article
• Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery  Academic Article
• Rhesus macaque B-cell responses to an HIV-1 trimer vaccine revealed by unbiased longitudinal repertoire analysis  Academic Article
• Rigid body refinement of protein complexes with long-range distance restraints from pulsed dipolar ESR  Academic Article
• Rosetta predictions in casp5: Successes, failures, and prospects for complete automation  Academic Article
• Rosettaremodel: A generalized framework for flexible backbone protein design  Academic Article
• SG-ADVISER CNV: copy-number variant annotation and interpretation  Academic Article
• Scripps Genome ADVISER: annotation and distributed variant interpretation SERver  Academic Article
• Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations  Academic Article
• Semen-specific genetic characteristics of human immunodeficiency virus type 1 env  Academic Article
• Sequence and structure signatures of cancer mutation hotspots in protein kinases  Academic Article
• Sequence interpretation. Functional annotation of mouse genome sequences  Academic Article
• Shape complementarity of protein-protein complexes at multiple resolutions  Academic Article
• Signaling between chloroplasts and the nucleus: can a systems biology approach bring clarity to a complex and highly regulated pathway?  Academic Article
• Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics  Academic Article
• Software tools for macromolecular microscopy  Academic Article
• Solution structures of the putative anti-σ-factor antagonist TM1442 from Thermotoga maritima in the free and phosphorylated states  Academic Article
• Solution x-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on pcna  Academic Article
• Statistical coupling analysis-guided library design for the discovery of mutant luciferases  Academic Article
• Structural analysis of mammalian cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene: insight into partial enzymatic activity  Academic Article
• Structural biology: form and function instructions  Academic Article
• Structural disorder in expanding the functionome of aminoacyl-tRNA synthetases  Academic Article
• Structure and regulatory mechanism of Aquifex aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation  Academic Article
• Structure of concatenated HAMP domains provides a mechanism for signal transduction  Academic Article
• Structures of virus and virus-like particles  Academic Article
• Symptom-driven idiopathic disease gene identification  Academic Article
• Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast  Academic Article
• Synergy of NMR, computation, and x-ray crystallography for structural biology  Academic Article
• TagDock: an efficient rigid body docking algorithm for oligomeric protein complex model construction and experiment planning  Academic Article
• Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain loci  Academic Article
• The 2.5 Å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation  Academic Article
• The Chlamydomonas genome reveals the evolution of key animal and plant functions  Academic Article
• The Geropathology Research Network: An interdisciplinary approach for integrating pathology into research on aging  Academic Article
• The Life Sciences Semantic Web is full of creeps!  Academic Article
• The NS5A protein of hepatitis C virus is a zinc metalloprotein  Academic Article
• The challenge of protein structure determination - lessons from structural genomics  Academic Article
• The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins  Academic Article
• The crystal structure of avian cd1 reveals a smaller, more primordial antigen-binding pocket compared to mammalian cd1  Academic Article
• The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins  Academic Article
• The fragile breakage versus random breakage models of chromosome evolution  Academic Article
• The gene wiki: Community intelligence applied to human gene annotation  Academic Article
• The implicitome: a resource for rationalizing gene-disease associations  Academic Article
• The mammalian Doublesex homolog DMRT6 coordinates the transition between mitotic and meiotic developmental programs during spermatogenesis  Academic Article
• The origin of enantioselectivity in aldolase antibodies: crystal structure, site-directed mutagenesis, and computational analysis  Academic Article
• The origins of asymmetry in the folding transition states of protein L and protein G  Academic Article
• The predicted binding site and dynamics of peptide inhibitors to the Methuselah GPCR from Drosophila melanogaster  Academic Article
• The proteome of mouse brain microvessel membranes and basal lamina  Academic Article
• The sequence of the human genome  Academic Article
• The third acgg-db meeting report: Towards an international collaborative infrastructure for glycobioinformatics  Academic Article
• The transcription factor encyclopedia  Academic Article
• The wisdom of the commons: Ensemble tree classifiers for prostate cancer prognosis  Academic Article
• Therapeutic targeting of casein kinase 1δ in breast cancer  Academic Article
• Three-dimensional structural view of the central metabolic network of Thermotoga maritima  Academic Article
• Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network  Academic Article
• Total synthesis and biological investigation of (-)-promysalin  Academic Article
• Towards precise classification of cancers based on robust gene functional expression profiles  Academic Article
• Transcriptional profiling identifies the signaling axes of IGF and transforming growth factor-β as involved in the pathogenesis of osteosarcoma  Academic Article
• Unifying model for molecular determinants of the preselection Vβ repertoire  Academic Article
• Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse  Academic Article
• Using AutoDock for ligand-receptor docking  Academic Article
• Variant interpretation: functional assays to the rescue  Academic Article
• Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes  Academic Article
• Windex: A toolset for indexing helices  Academic Article
• XCMS2: Processing tandem mass spectrometry data for metabolite identification and structural characterization  Academic Article
• YADA: a tool for taking the most out of high-resolution spectra  Academic Article
• ZiF-Predict: a web tool for predicting DNA-binding specificity in C2H2 zinc finger proteins  Academic Article
• Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB  Academic Article
• cellPACK: a virtual mesoscope to model and visualize structural systems biology  Academic Article
• ePMV embeds molecular modeling into professional animation software environments  Academic Article
• plusTipTracker: Quantitative image analysis software for the measurement of microtubule dynamics  Academic Article
• uPy: a ubiquitous CG Python API with biological-modeling applications  Academic Article