Managing Director, Bioinformatics
M_Biochem-Central Admin
An extensive two-decade career blending computational and biological realms in genomics under the overarching theme of ’big data.'
Publications
clonevdjseq: A workflow and bioinformatics management system for sequencing, archiving, and analysis of VDJ sequences from clonal libraries.
BMC bioinformatics
High-volume hybridoma sequencing on the NeuroMabSeq platform enables efficient generation of recombinant monoclonal antibodies and scFvs for neuroscience research.
Scientific reports
NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research.
bioRxiv : the preprint server for biology
Human soft tissue sarcomas harbor an intratumoral viral microbiome which is linked with natural killer cell infiltrate and prognosis.
Journal for immunotherapy of cancer
Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries.
Global health action
Biofilms preserve the transmissibility of a multi-drug resistance plasmid.
NPJ biofilms and microbiomes
A two-stage digestion of whole murine knee joints for single-cell RNA sequencing.
Osteoarthritis and cartilage open
Comparative Transcriptional Analyses in the Nucleus Accumbens Identifies RGS2 as a Key Mediator of Depression-Related Behavior.
Biological psychiatry
Effects of pairing on color change and central gene expression in lined seahorses.
Genes, brain, and behavior
Sex disparate gut microbiome and metabolome perturbations precede disease progression in a mouse model of Rett syndrome.
Communications biology
Dual transcriptomic analysis reveals metabolic changes associated with differential persistence of human pathogenic bacteria in leaves of Arabidopsis and lettuce.
G3 (Bethesda, Md.)
Establishment of quantitative RNAi-based forward genetics in Entamoeba histolytica and identification of genes required for growth.
PLoS pathogens
Protective heterologous T cell immunity in COVID-19 induced by the trivalent MMR and Tdap vaccine antigens.
Med (New York, N.Y.)
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias).
Systematic biology
Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis.
Blood cancer discovery
Wilson Disease: Intersecting DNA Methylation and Histone Acetylation Regulation of Gene Expression in a Mouse Model of Hepatic Copper Accumulation.
Cellular and molecular gastroenterology and hepatology
The auxin-producing Bacillus thuringiensis RZ2MS9 promotes the growth and modifies the root architecture of tomato (Solanum lycopersicum cv. Micro-Tom).
Archives of microbiology
Protective heterologous T cell immunity in COVID-19 induced by MMR and Tdap vaccine antigens.
bioRxiv : the preprint server for biology
Disruption of global hypothalamic microRNA (miR) profiles and associated behavioral changes in California mice (Peromyscus californicus) developmentally exposed to endocrine disrupting chemicals.
Hormones and behavior
Chromatin accessibility in canine stromal cells and its implications for canine somatic cell reprogramming.
Stem cells translational medicine
Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent.
Frontiers in genetics
Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmon (Oncorhynchus tshawytscha).
Conservation physiology
MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques (Macaca mulatta).
Comparative medicine
Complete Genome Sequence of Bacillus sp. Strain RZ2MS9, a Multitrait Plant Growth Promoter.
Microbiology resource announcements
Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities.
Journal of biomolecular techniques : JBT
Proximal femoral head transcriptome reveals novel candidate genes related to epiphysiolysis in broiler chickens.
BMC genomics
Additional Evidence for DDB2 T338M as a Genetic Risk Factor for Ocular Squamous Cell Carcinoma in Horses.
International journal of genomics
Transcriptome Analysis of Salmonella Heidelberg after Exposure to Cetylpyridinium Chloride, Acidified Calcium Hypochlorite, and Peroxyacetic Acid.
Journal of food protection
Fatherhood alters gene expression within the MPOA.
Environmental epigenetics
Obesity treatment by epigallocatechin-3-gallate-regulated bile acid signaling and its enriched Akkermansia muciniphila.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology
High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-Producing Escherichia coli O177:H- (fliCH25) Isolates Harboring Virulent stx2 and Multiple Plasmids.
Genome announcements
Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women.
The Journal of nutrition
Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis.
Molecular ecology resources
Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).
Journal of biomolecular techniques : JBT
Erratum to: Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus.
Journal of molecular evolution
Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus.
Journal of molecular evolution
Full Mitochondrial Genome Sequence of the Sugar Beet Wireworm Limonius californicus (Coleoptera: Elateridae), a Common Agricultural Pest.
Genome announcements
Mitochondrial Genome Sequence of the Galápagos Endemic Land Snail Naesiotus nux.
Genome announcements
Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance.
Molecular biology and evolution
The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards.
Molecular ecology
Fecal Microbial Community Structure Is Stable over Time and Related to Variation in Macronutrient and Micronutrient Intakes in Lactating Women.
The Journal of nutrition
Draft Genome Sequence of Pseudomonas sp. nov. H2.
Genome announcements
Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp.
Pathogens and disease
Elevated dairy fat intake in lactating women alters milk lipid and fatty acids without detectible changes in expression of genes related to lipid uptake or synthesis.
Nutrition research (New York, N.Y.)
Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures.
Bioresource technology
Influence of organic loading rate and solid retention time on polyhydroxybutyrate production from hybrid poplar hydrolysates using mixed microbial cultures.
Bioresource technology
Draft Genome Sequence of Pseudomonas moraviensis R28-S.
Genome announcements
Microbiota of the seminal fluid from healthy and infertile men.
Fertility and sterility
SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching.
Journal of data mining in genomics & proteomics
Sex-specific transcriptional responses of the zebrafish (Danio rerio) brain selenoproteome to acute sodium selenite supplementation.
Physiological genomics
A forward genetic screen reveals that calcium-dependent protein kinase 3 regulates egress in Toxoplasma.
PLoS pathogens
Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers.
Reproductive toxicology (Elmsford, N.Y.)
An improved algorithm for the detection of genomic variation using short oligonucleotide expression microarrays.
Molecular ecology resources
Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio).
BMC genomics
mcaGUI: microbial community analysis R-Graphical User Interface (GUI).
Bioinformatics (Oxford, England)
Only skin deep: shared genetic response to the deadly chytrid fungus in susceptible frog species.
Molecular ecology
Global analysis of phase variation in Myxococcus xanthus.
Molecular microbiology
OTUbase: an R infrastructure package for operational taxonomic unit data.
Bioinformatics (Oxford, England)
Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome.
PloS one
GSEA-SNP identifies genes associated with Johne's disease in cattle.
Mammalian genome : official journal of the International Mammalian Genome Society
Alterations in the developing testis transcriptome following embryonic vinclozolin exposure.
Reproductive toxicology (Elmsford, N.Y.)
Meta-analysis of transcripts associated with race-specific resistance to stripe rust in wheat demonstrates common induction of blue copper-binding protein, heat-stress transcription factor, pathogen-induced WIR1A protein, and ent-kaurene synthase transcri
Functional & integrative genomics
Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array.
BMC genomics
Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio).
Physiological genomics
Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat-Puccinia striiformis f. sp. tritici interaction.
Molecular plant pathology
Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio).
Comparative biochemistry and physiology. Part D, Genomics & proteomics