Bioinformatics Concept

subject area of

• A FLEXIBLE NONPARAMETRIC APPROACH TO FIND CANDIDATE GENES ASSOCIATED WITH DISEASE IN MICROARRAY EXPERIMENTS  Journal Articles
• A Multivariate Growth Curve Model for Ranking Genes in Replicated Time Course Microarray Data  Journal Articles
• A Note on Observation Processes in Epidemic Models  Journal Articles
• A Quantitative Approach to Detect and Overcome PCR Inhibition in Ancient DNA Extracts  Journal Articles
• A comparison of self-reported chronic disease, health awareness and behaviours in social housing residents: cross-sectional study of communities in Ontario and Quebec  Journal Articles
• A comprehensive guide to dynamic analysis of microbial gene expression using the 3D-printed PFIbox and a fluorescent reporter library  Journal Articles
• A delay model for persistent viral infections in replicating cells  Journal Articles
• A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code  Journal Articles
• A multivariate Poisson-log normal mixture model for clustering transcriptome sequencing data  Journal Articles
• A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data  Journal Articles
• A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes  Journal Articles
• A novel strain of cynomolgus macaque cytomegalovirus: implications for host-virus co-evolution  Journal Articles
• A parameterized, continuum electrostatic model for predicting protein pK_a values  Journal Articles
• A phased SNP-based classification of sickle cell anemia HBB haplotypes  Journal Articles
• A physiological model for the evaluation of muscular forces in human locomotion: theoretical aspects  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
• A program to identify prognostic and predictive gene signatures  Journal Articles
• A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations  Journal Articles
• A simple and sensitive method for quantifying human genomic DNA in forensic specimen extracts.  Journal Articles
• A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae  Journal Articles
• A universal bacterial sensor created by integrating a light modulating aptamer complex with photoelectrochemical signal readout  Journal Articles
• A well plate–based multiplexed platform for incorporation of organoids into an organ-on-a-chip system with a perfusable vasculature  Journal Articles
• ALeS: adaptive-length spaced-seed design  Journal Articles
• Access to primary care in adults in a provincial correctional facility in Ontario  Journal Articles
• Adaptive modelling of gene regulatory network using Bayesian information criterion‐guided sparse regression approach  Journal Articles
• Adolescent deliveries in urban Cameroon: a retrospective analysis of the prevalence, 6-year trend and adverse outcomes  Journal Articles
• Allelic Expression Imbalance ofTP53Mutated and Polymorphic Alleles in Head and Neck Tumors  Journal Articles
• An Alternative Formulation for a Distributed Delayed Logistic Equation  Journal Articles
• An alternative delayed population growth difference equation model  Journal Articles
• An augmented phase plane approach for discrete planar maps: Introducing next-iterate operators  Journal Articles
• An examination of the thresholds of enrichment: a resource-based growth model  Journal Articles
• Analytic Calculation of Finite-Population Reproductive Numbers for Direct- and Vector-Transmitted Diseases with Homogeneous Mixing  Journal Articles
• Analytic Models for the Patchy Spread of Plant Disease  Journal Articles
• AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods  Journal Articles
• Assessing the Evolution of Gene Expression Using Microarray Data  Journal Articles
• Assessing the evolution of gene expression using microarray data  Journal Articles
• Asymptotic rates of growth of the extinction probability of a mutant gene  Journal Articles
• Asymptotic rates of growth of the extinction probability of a mutant gene  Journal Articles
• Attractivity of coherent manifolds in metapopulation models  Journal Articles
• Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics  Journal Articles
• Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing  Journal Articles
• Author Correction: The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies  Journal Articles
• BISTABILITY AND LONG-TERM CURE IN A WITHIN-HOST MODEL OF HEPATITIS C  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
• BMC Bioinformatics  Journal
• BMC Genomics  Journal
• BMC Research Notes  Journal
• BMC Systems Biology  Journal
• BOND: Basic OligoNucleotide Design  Journal Articles
• BPG: Seamless, automated and interactive visualization of scientific data  Journal Articles
• Backwards bifurcations and catastrophe in simple models of fatal diseases  Journal Articles
• Bacteremia in febrile cancer patients in Uganda  Journal Articles
• Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.  Journal Articles
• BioSystems  Journal
• BioTechniques  Journal
• Bioinformatics  Journal
• Biology Direct  Journal
• Biomedical Signal and Image Processing for Clinical Decision Support Systems  Journal Articles
• Biomedical Signal and Image Processing for Clinical Decision Support Systems 2014  Journal Articles
• Biosensor integrated brain-on-a-chip platforms: Progress and prospects in clinical translation  Journal Articles
• Biosensors and Bioelectronics  Journal
• Book Reviews  Journal Articles
• Book reviews  Journal Articles
• Briefings in Bioinformatics  Journal
• Bulletin of Mathematical Biology  Journal
• CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery  Journal Articles
• Calibration of individual-based models to epidemiological data: A systematic review  Journal Articles
• Calibration of individual-based models to epidemiological data: A systematic review  Journal Articles
• Cancer Informatics  Journal
• ChIP-on-Chip Analysis of In Vivo Mutant p53 Binding To Selected Gene Promoters  Journal Articles
• Chaos and complexity in measles models: A comparative numerical study  Journal Articles
• Circulating Vaccine Derived Polio Viruses and their Impact on Global Polio Eradication  Journal Articles
• Classical and resource-based competition: a unifying graphical approach  Journal Articles
• Clinical Outcome Prediction in Aneurysmal Subarachnoid Hemorrhage Using Bayesian Neural Networks with Fuzzy Logic Inferences  Journal Articles
• Co-operation between Polymerases and Nucleotide Synthetases in the RNA World  Journal Articles
• Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress  Journal Articles
• Combined effect of M/A constituent and grain boundary on the impact toughness of CGHAZ and ICCGHAZ of E550 grade offshore engineering steel  Journal Articles
• Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection  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
• Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution  Journal Articles
• Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria  Journal Articles
• Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness  Journal Articles
• Comparing the performance of linear and nonlinear principal components in the context of high-dimensional genomic data integration  Journal Articles
• Comparison of health state utility estimates from instrument-based and vignette-based methods: a case study in kidney disease  Journal Articles
• Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems  Journal Articles
• Competition in the presence of a virus in an aquatic system: an SIS model in the chemostat  Journal Articles
• Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths  Journal Articles
• Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools  Journal Articles
• Computational and Mathematical Methods in Medicine  Journal
• Computational haemodynamics in stenotic internal jugular veins  Journal Articles
• Computer simulations of Template-Directed RNA Synthesis driven by temperature cycling in diverse sequence mixtures  Journal Articles
• Computing Maximal Covers for Protein Sequences  Journal Articles
• Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis  Journal Articles
• Correcting Illumina data  Journal Articles
• Cover Image, Volume 85, Issue 8  Journal Articles
• Cross-sectional study of the association between skin tags and vascular risk factors in a bariatric clinic-based cohort of Irish adults with morbid obesity  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
• Cultural influences on palliative family caregiving: service recommendations specific to the Vietnamese in Canada  Journal Articles
• DELPHI: accurate deep ensemble model for protein interaction sites prediction  Journal Articles
• DNA methylation changes in cord blood and the developmental origins of health and disease – a systematic review and replication study  Journal Articles
• DNAzymes as key components of biosensing systems for the detection of biological targets  Journal Articles
• Decreased miR-192 expression in peripheral blood of asthmatic individuals undergoing an allergen inhalation challenge  Journal Articles
• Definition of an electrostatic relay switch critical for the cAMP‐dependent activation of protein kinase A as revealed by the D170A mutant of RIα  Journal Articles
• Delineation of key XRCC4/Ligase IV interfaces for targeted disruption of non-homologous end joining DNA repair  Journal Articles
• Delusion or obsession: Clinical dilemma  Journal Articles
• Derivation and Analysis of a Discrete Predator–Prey Model  Journal Articles
• Derivation and dynamics of discrete population models with distributed delay in reproduction.  Journal Articles
• Detecting natural adaptation of the Streptococcus thermophilus CRISPR-Cas systems in research and classroom settings  Journal Articles
• Development of a community health and wellness pilot in a subsidised seniors’ apartment building in Hamilton, Ontario: Community Health Awareness Program delivered by Emergency Medical Services (CHAP-EMS)  Journal Articles
• Diverticular disease of the right colon  Journal Articles
• Does Counting Different Life Stages Impact Estimates for Extinction Probabilities for Tsetse (Glossina spp)?  Journal Articles
• E-MEM: efficient computation of maximal exact matches for very large genomes  Journal Articles
• E2F1 and KIAA0191 expression predicts breast cancer patient survival  Journal Articles
• Economic (gross cost) analysis of systematically implementing a programme of advance care planning in three Irish nursing homes  Journal Articles
• Effect of light on the growth of non-nitrogen-fixing and nitrogen-fixing phytoplankton in an aquatic system  Journal Articles
• Effects of contact structure on the transient evolution of HIV virulence  Journal Articles
• Efficient Algorithms for Counting and Reporting Segregating Sites in Genomic Sequences  Journal Articles
• Electrochemical DNAzyme-based biosensors for disease diagnosis  Journal Articles
• Electrochemical assisted enhanced nanozymatic activity of functionalized borophene for H2O2 and tetracycline detection  Journal Articles
• Enhancing nutritional environments through access to fruit and vegetables in schools and homes among children and youth: a systematic review  Journal Articles
• Entrapment of horseradish peroxidase in sugar-modified silica monoliths: Toward the development of a biocatalytic sensor  Journal Articles
• Erratum to: Access to primary care in adults in a provincial correctional facility in Ontario  Journal Articles
• Erratum: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression (Genome Research (2011) 21, (645-657) DOI: 10.1101/gr.097378.109)  Journal Articles
• Estimating Initial Epidemic Growth Rates  Journal Articles
• Estimating Number of Clusters Based on a General Similarity Matrix with Application to Microarray Data  Journal Articles
• Estimating the muscle forces generated in the human lower extremity when walking: a physiological solution  Journal Articles
• Estimation of duplication history under a stochastic model for tandem repeats  Journal Articles
• Estimation of weighted log partial area under the ROC curve and its application to MicroRNA expression data  Journal Articles
• Eurasip Journal on Bioinformatics and Systems Biology  Journal
• Evaluating in vivo effectiveness of sotrovimab for the treatment of Omicron subvariant BA.2 versus BA.1: a multicentre, retrospective cohort study  Journal Articles
• Evaluating the evidence for macrophage presence in skeletal muscle and its relation to insulin resistance in obese mice and humans: a systematic review protocol  Journal Articles
• Evaluating the test re-test reliability and inter-subject variability of health care provider manual fluid resuscitation performance  Journal Articles
• Evolution and persistence of influenza A and other diseases  Journal Articles
• Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia  Journal Articles
• Evolutionary Bioinformatics  Journal
• Evolutionary Stability of Minimal Mutation Rates in an Evo-epidemiological Model  Journal Articles
• Evolutionary stability in continuous nonlinear public goods games  Journal Articles
• Expectancy-based rhythmic entrainment as continuous Bayesian inference  Journal Articles
• Exploitative competition in a chemostat for two complementary, and possibly inhibitory, resources  Journal Articles
• Exploitative competition in the chemostat for two perfectly substitutable resources  Journal Articles
• Exploratory analysis of multiple sequence alignments using phylogenies  Journal Articles
• Fast chromosome karyotyping by auction algorithm  Journal Articles
• Fast chromosome karyotyping by auction algorithm  Journal Articles
• Fast computation of neighbor seeds  Journal Articles
• Fast estimation of time-varying infectious disease transmission rates  Journal Articles
• Femtosecond laser nanostructuring for femtosensitive DNA detection  Journal Articles
• Filtering Genes for Cluster and Network Analysis  Journal Articles
• Finite mixtures of matrix variate Poisson-log normal distributions for three-way count data  Journal Articles
• Fitting Epidemic Models to Data: A Tutorial in Memory of Fred Brauer  Journal Articles
• FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures  Journal Articles
• Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network  Journal Articles
• Gene expression profiling in the Cynomolgus macaque Macaca fascicularis shows variation within the normal birth range  Journal Articles
• Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation  Journal Articles
• Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression  Journal Articles
• Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression  Journal Articles
• Generality of the Final Size Formula for an Epidemic of a Newly Invading Infectious Disease  Journal Articles
• Genome Biology  Journal
• Genome Research  Journal
• Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A  Journal Articles
• Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes  Journal Articles
• Genome-wide evidence for selection acting on single amino acid repeats  Journal Articles
• Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses  Journal Articles
• Germline contamination and leakage in whole genome somatic single nucleotide variant detection.  Journal Articles
• Global analysis of a model of plasmid-bearing, plasmid-free competition in a chemostat  Journal Articles
• Global analysis of competition for perfectly substitutable resources with linear response  Journal Articles
• Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis  Journal Articles
• Global dynamics of a chemostat competition model with distributed delay  Journal Articles
• Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933  Journal Articles
• Growth on two limiting essential resources in a self-cycling fermentor  Journal Articles
• Guaranteed parameter estimation of non-linear dynamic systems using high-order bounding techniques with domain and CPU-time reduction strategies  Journal Articles
• HISEA: HIerarchical SEed Aligner for PacBio data  Journal Articles
• HiTEC: accurate error correction in high-throughput sequencing data  Journal Articles
• High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)  Journal Articles
• High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination  Journal Articles
• High-throughput full-length single-cell RNA-seq automation  Journal Articles
• How acceptable is it for HIV positive African, Caribbean and Black women to provide breast milk/fluid samples for research purposes?  Journal Articles
• IEEE/ACM Transactions on Computational Biology and Bioinformatics  Journal
• IET Systems Biology  Journal
• IMA Journal of Mathematical Control and Information  Journal
• INCREASED YIELD OF SMALL DNA FRAGMENTS PURIFIED BY SILICA BINDING  Journal Articles
• Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish  Journal Articles
• Identification and functional analyses of sex determination genes in the sexually dimorphic stag beetle Cyclommatus metallifer  Journal Articles
• Identification of Conflicting Selective Effects on Highly Expressed Genes  Journal Articles
• Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role  Journal Articles
• Improved Compressed Sensing-Based Algorithm for Sparse-View CT Image Reconstruction  Journal Articles
• Improving GRN re‐construction by mining hidden regulatory signals  Journal Articles
• In Vivo Cloning Strategy for Rhizobium Plasmids  Journal Articles
• In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences.  Journal Articles
• Incidental findings in CT imaging of coronary artery bypass grafts: results from a Canadian multicenter prospective cohort  Journal Articles
• Increased Efficiency of Genetic Profiling Through Quantity and Quality Assessment of Fluorescently Labeled Oligonucleotide Primers  Journal Articles
• Induction of immune response in chickens primed in ovo with an inactivated H9N2 avian influenza virus vaccine  Journal Articles
• Inferring sequence regions under functional divergence in duplicate genes  Journal Articles
• Information obtained in cladistic analysis  Journal Articles
• Insight into the evolutionary and domesticated history of the most widely cultivated mushroom Agaricus bisporus via mitogenome sequences of 361 global strains  Journal Articles
• Integrated gene and species phylogenies from unaligned whole genome protein sequences  Journal Articles
• Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome  Journal Articles
• Integration of transcriptional inputs at promoters of the arabinose catabolic pathway  Journal Articles
• Integrative Analysis of Gene Expression Data Including an Assessment of Pathway Enrichment for Predicting Prostate Cancer  Journal Articles
• Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models  Journal Articles
• Interactions Between the Immune System and Cancer: A Brief Review of Non-spatial Mathematical Models  Journal Articles
• Interactions between bacterial surface and nanoparticles govern the performance of “chemical nose” biosensors  Journal Articles
• International Journal of Bioinformatics Research and Applications  Journal
• Interpreting Metabolomic Profiles using Unbiased Pathway Models  Journal Articles
• Joint Classification and Pairing of Human Chromosomes  Journal Articles
• Journal of Bioinformatics and Computational Biology  Journal
• Journal of Biological Systems  Journal
• Journal of Computational Biology  Journal
• Journal of Mathematical Biology  Journal
• Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration  Journal Articles
• LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data  Journal Articles
• LASER: Large genome ASsembly EvaluatoR  Journal Articles
• Label-free detection of nucleic acid and protein microarrays by scanning Kelvin nanoprobe  Journal Articles
• Leveling up evidence syntheses: filling conceptual gaps of the role of midwifery in health systems through a network analysis  Journal Articles
• Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function  Journal Articles
• Live-Cell Nucleocytoplasmic Protein Shuttle Assay Utilizing Laser Confocal Microscopy and FRAP  Journal Articles
• Lone workers attitudes towards their health: views of Ontario truck drivers and their managers  Journal Articles
• MAUI (MBI Analysis User Interface)—An image processing pipeline for Multiplexed Mass Based Imaging  Journal Articles
• MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks  Journal Articles
• Mate Choice and the Origin of Menopause  Journal Articles
• Mathematical Biosciences  Journal
• Mathematical Biosciences and Engineering  Journal
• Mathematical Medicine and Biology  Journal
• Mathematical models of microbial growth and competition in the chemostat regulated by cell-bound extracellular enzymes  Journal Articles
• McMaster Optimal Aging Portal: an evidence-based database for geriatrics-focused health professionals  Journal Articles
• Measurement Properties of Simple Biomechanical Measures of Walking Effort  Journal Articles
• Medical characteristics of the oldest old: retrospective chart review of patients aged 85+ in an academic primary care centre  Journal Articles
• Mental and psychosocial health among youth after their first psychiatric hospitalization: a feasibility study  Journal Articles
• Metabolic and co-expression network-based analyses associated with nitrate response in rice  Journal Articles
• Microfabrication of AngioChip, a biodegradable polymer scaffold with microfluidic vasculature  Journal Articles
• Misclassification of child body mass index from cut-points defined by rounded percentiles instead of Z-scores  Journal Articles
• Model-based clustering of microarray expression data via latent Gaussian mixture models  Journal Articles
• Modeling enculturated bias in entrainment to rhythmic patterns  Journal Articles
• Modeling the Interplay Between Seasonal Flu Outcomes and Individual Vaccination Decisions  Journal Articles
• Modelling in vivo action potential propagation along a giant axon  Journal Articles
• Molecular Systems Biology  Journal
• Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales)  Journal Articles
• Monte Carlo-minimized energy profile of estradiol in the ligand-binding tunnel of 17?-hydroxysteroid dehydrogenase: Atomic mechanisms of steroid recognition  Journal Articles
• Multi-Stability and Multi-Instability Phenomena in a Mathematical Model of Tumor-Immune-Virus Interactions  Journal Articles
• Multicopy gene family evolution on primate Y chromosomes  Journal Articles
• Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment  Journal Articles
• Multimodality cardiac imaging of a ventricular septal rupture post myocardial infarction: a case report  Journal Articles
• Multiple Transmission Pathways and Disease Dynamics in a Waterborne Pathogen Model  Journal Articles
• Multiple spaced seeds for homology search  Journal Articles
• Multiple testing in orthopedic literature: a common problem?  Journal Articles
• Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins  Journal Articles
• Nature Protocols  Journal
• Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition  Journal Articles
• Nitrogen limitation and high density responses in rice suggest a role for ethylene under high density stress  Journal Articles
• Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens  Journal Articles
• Norovirus infections in preterm infants: wide variety of clinical courses  Journal Articles
• Novel subtractive transcription-based amplification of mRNA (STAR) method and its application in search of rare and differentially expressed genes in AD brains  Journal Articles
• OMICS A Journal of Integrative Biology  Journal
• Omics Underpins Novel Clues on VDR Chemoprevention Target in Breast Cancer  Journal Articles
• On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A  Journal Articles
• On inferring evolutionary stability in finite populations using infinite population models  Journal Articles
• On selection in finite populations  Journal Articles
• On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A  Journal Articles
• On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network  Journal Articles
• Opening communication channels with people living with HIV using mobile phone text messaging: insights from the CAMPS trial  Journal Articles
• Origin and evolution of gene families in Bacteria and Archaea  Journal Articles
• PLoS Computational Biology  Journal
• Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters  Journal Articles
• PathFams: statistical detection of pathogen-associated protein domains  Journal Articles
• PedSplit: pedigree management for stratified analysis  Journal Articles
• PhyloCorrelate: inferring bacterial gene–gene functional associations through large-scale phylogenetic profiling  Journal Articles
• Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures  Journal Articles
• Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation  Journal Articles
• Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis  Journal Articles
• Physics of Life Reviews  Journal
• Pollux: platform independent error correction of single and mixed genomes  Journal Articles
• Population growth and competition models with decay and competition consistent delay  Journal Articles
• Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern  Journal Articles
• Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos  Journal Articles
• Predator-mediated competition in the chemostat  Journal Articles
• Predator-prey systems with group defence: The paradox of enrichment revisited  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
• Production and use of antigen tetramers to study antigen-specific B cells  Journal Articles
• Programming gene expression with combinatorial promoters  Journal Articles
• Prospective evaluation of direct approach with a tablet device as a strategy to enhance survey study participant response rate  Journal Articles
• Proteins: Structure, Function and Bioinformatics  Journal
• Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties  Journal Articles
• P�lya-like urns and the Ewens' sampling formula  Journal Articles
• Quantification of protein surfaces, volumes and atom–atom contacts using a constrained Voronoi procedure  Journal Articles
• Quantitative PCR as a Predictor of Aligned Ancient DNA Read Counts Following Targeted Enrichment  Journal Articles
• RACER: Rapid and accurate correction of errors in reads  Journal Articles
• RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions  Journal Articles
• Rapid isolation of DNA from fossil and museum specimens suitable for PCR.  Journal Articles
• Rapid screening of microsatellite markers for polymorphisms using SYBR ^® Green I and a DNA sequencer  Journal Articles
• Relaxation oscillations of a piecewise-smooth slow-fast Bazykin's model with Holling type Ⅰ functional response.  Journal Articles
• Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing  Journal Articles
• Response to Brinkmann et al. “Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States”  Journal Articles
• Rich dynamics of a three-tiered anaerobic food-web in a chemostat with multiple substrate inflow  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
• Rosiglitazone: can meta-analysis accurately estimate excess cardiovascular risk given the available data? Re-analysis of randomized trials using various methodologic approaches  Journal Articles
• Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells  Journal Articles
• SAGE2: parallel human genome assembly  Journal Articles
• SAGE: String-overlap Assembly of GEnomes  Journal Articles
• SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria  Journal Articles
• SHRiMP2: Sensitive yet Practical Short Read Mapping  Journal Articles
• SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome  Journal Articles
• Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA  Journal Articles
• Scoring alignments by embedding vector similarity  Journal Articles
• Seeds for effective oligonucleotide design  Journal Articles
• Sensitivity enhancement of SPR assay of progesterone based on mixed self-assembled monolayers using nanogold particles  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
• Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes  Journal Articles
• Seq-InSite: sequence supersedes structure for protein interaction site prediction  Journal Articles
• Signature proteins that are distinctive of alpha proteobacteria  Journal Articles
• Simple sequences are rare in the Protein Data Bank  Journal Articles
• Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality  Journal Articles
• SpEED: fast computation of sensitive spaced seeds  Journal Articles
• Sparse Canonical Correlation Analysis with Application to Genomic Data Integration  Journal Articles
• Statistical Applications in Genetics and Molecular Biology  Journal
• Statistical models and computational algorithms for discovering relationships in microbiome data  Journal Articles
• Structural Organization of the WD repeat protein-encoding gene HIRA in the DiGeorge syndrome critical region of human chromosome 22.  Journal Articles
• Successful invasion of a food web in a chemostat  Journal Articles
• Surgical versus medical management of patients with acute ischemic mitral regurgitation: a systematic review  Journal Articles
• Surveying the Repair of Ancient DNA from Bones Via High-Throughput Sequencing  Journal Articles
• Susceptibility to chronic pain following nerve injury is genetically affected by CACNG2  Journal Articles
• Systematic narrative review of decision frameworks to select the appropriate modelling approaches for health economic evaluations  Journal Articles
• Systems Level Modeling of the Cell Cycle Using Budding Yeast  Journal Articles
• Systems level modeling of the cell cycle using budding yeast.  Journal Articles
• Testing and Isolation Efficacy: Insights from a Simple Epidemic Model  Journal Articles
• Testing genotypes-phenotype relationships using permutation tests on association rules  Journal Articles
• Tests for differential gene expression using weights in oligonucleotide microarray experiments  Journal Articles
• The Impact of the Allee Effect in Dispersal and Patch-Occupancy Age on the Dynamics of Metapopulations  Journal Articles
• The LASSO and Sparse Least Squares Regression Methods for SNP Selection in Predicting Quantitative Traits  Journal Articles
• The Team to Address Bariatric Care in Canadian Children (Team ABC3): Team Grant Research Proposal  Journal Articles
• The Transcription Factor Encyclopedia  Journal Articles
• The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data  Journal Articles
• The accumulation of mutations in asexual populations and the structure of genealogical trees in the presence of selection  Journal Articles
• The advantages and disadvantages of horizontal gene transfer and the emergence of the first species  Journal Articles
• The association between caregiver well-being and care provided to persons with Alzheimer’s disease and related disorders  Journal Articles
• The dilution effect and the importance of selecting the right internal control genes for RT-qPCR: a paradigmatic approach in fetal sheep  Journal Articles
• The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans.  Journal Articles
• The effect of maternity waiting homes on perinatal mortality is inconclusive: a critical appraisal of existing evidence from Sub-Saharan Africa  Journal Articles
• The effects of disease dispersal and host clustering on the epidemic threshold in plants  Journal Articles
• The effects of population heterogeneity on disease invasion  Journal Articles
• The emotional origins of music  Journal Articles
• The fate of laterally transferred genes: Life in the fast lane to adaptation or death  Journal Articles
• The identification of functional motifs in temporal gene expression analysis  Journal Articles
• The identification of functional motifs in temporal gene expression analysis.  Journal Articles
• The importance of accurately modelling human interactions  Journal Articles
• The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies  Journal Articles
• The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z  Journal Articles
• The odds of duplicate gene persistence after polyploidization  Journal Articles
• The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex  Journal Articles
• The origin of life is a spatially localized stochastic transition  Journal Articles
• The origin recognition complex protein family  Journal Articles
• The origins and genomic diversity of American Civil War Era smallpox vaccine strains  Journal Articles
• The sampling theory of neutral alleles and an urn model in population genetics  Journal Articles
• The spirit of D'Arcy Thompson dwells in empirical morphospace  Journal Articles
• The survival probability of a mutant in a multidimensional population  Journal Articles
• The survival probability of a mutant in a multidimensional population  Journal Articles
• The use of incentives in vulnerable populations for a telephone survey: a randomized controlled trial  Journal Articles
• Towards information processing from nonlinear physical chemistry: A synthetic electrochemical cognitive system  Journal Articles
• Transient oscillations induced by delayed growth response in the chemostat  Journal Articles
• Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny  Journal Articles
• Two-way learning with one-way supervision for gene expression data  Journal Articles
• Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast  Journal Articles
• Uncovering rate variation of lateral gene transfer during bacterial genome evolution  Journal Articles
• Uncovering rate variation of lateral gene transfer during bacterial genome evolution  Journal Articles
• Understanding apparently non-exponential outbreaks Comment on “Mathematical models to characterize early epidemic growth: A review” by Gerardo Chowell et al.  Journal Articles
• Unsupervised statistical clustering of environmental shotgun sequences  Journal Articles
• Using the ratio of means as the effect size measure in combining results of microarray experiments  Journal Articles
• Valection: design optimization for validation and verification studies.  Journal Articles
• Validating a self-report measure of HIV viral suppression: an analysis of linked questionnaire and clinical data from the Canadian HIV Women’s Sexual and Reproductive Health Cohort Study  Journal Articles
• Validation of parent-reported physical activity and sedentary time by accelerometry in young children  Journal Articles
• Validity of tools used for surveying physicians about their interactions with pharmaceutical company: a systematic review  Journal Articles
• Visual detection method for identifying recombinant bacterial colonies.  Journal Articles
• Vitamin D supplementation in children with asthma: a systematic review and meta-analysis  Journal Articles
• Yeast Recombinase FLP Functions Effectively in Human Cells for Construction of Adenovirus Vectors  Journal Articles
• markophylo: Markov chain analysis on phylogenetic trees  Journal Articles
• mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics  Journal Articles
• mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens  Journal Articles
• “Chemical nose” for the visual identification of emerging ocular pathogens using gold nanostars  Journal Articles
• “Colony Sequencing”: Direct Sequencing of Plasmid DNA from Bacterial Colonies  Journal Articles