selected scholarly activity
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conferences
- “From Protein Toxins to Applied Toxicological Testing” virtual workshop identifies the need for a bioinformatic framework to assess novel food protein safety. Regulatory Toxicology and Pharmacology. 105146-105146. 2022
- CHARACTERIZATION OF THE PROTOSPACER TARGETS OF Clostridium botulinum CRISPR-CAS SPACER ARRAYS. Toxicon. S74-S75. 2021
- Effects of Marijuana Smoke Exposure and LABA/GCS Intervention on the Transcriptome and Pro-Inflammatory Cytokine Production of Airway Epithelial Cells In Vitro. American Journal of Respiratory and Critical Care Medicine. 2019
- ATP Binding Cassette (ABC) Transporter Expression in Human Airway Epithelial Cells: A Meta-Analysis of Gene Expression from Bronchial Brushings. American Journal of Respiratory and Critical Care Medicine. 2018
- Estrogen Receptor Beta Is a Novel Target in Acute Myeloid Leukemia. Blood. 1395-1395. 2015
- Discrimination of Insoluble-Carbohydrate Binding Proteins and Their Binding Sites Using a 3D Motif Detection Method. Proceedings. IEEE International Conference on Bioinformatics and Biomedicine. 207-213. 2008
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journal articles
- COVID‐19 severity gradient differentially dysregulates clinically relevant drug processing genes in nasopharyngeal swab samples. British Journal of Clinical Pharmacology. 90:2137-2158. 2024
- AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods. Briefings in Bioinformatics. 25:bbae229. 2024
- Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples. ISME Communications. 4:ycae024. 2024
- Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells. Methods in molecular biology (Clifton, N.J.). 2813:79-94. 2024
- Cannabis smoke suppresses antiviral immune responses to influenza A in mice. ERJ Open Research. 9:00219-2023. 2023
- Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus). iScience. 26:108319-108319. 2023
- Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenzae isolates associated with paediatric otitis media and upper respiratory infection. BMC Infectious Diseases. 23:596. 2023
- Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains. Nature Communications. 14:5475. 2023
- Phylogenomic Analysis of 155 Helminth Species Reveals Widespread Absence of Oxygen Metabolic Capacity. Genome Biology and Evolution. 15:evad135. 2023
- A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information. Genome Biology and Evolution. 15:evad129. 2023
- Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome. Viruses. 15:1116-1116. 2023
- Comparative analysis of adenylate isopentenyl transferase genes in plant growth-promoting bacteria and plant pathogenic bacteria. Vaccine Reports. 9:e13955-e13955. 2023
- Identification and characterization of a novel peptide from rainbow trout (Oncorhynchus mykiss) with antimicrobial activity against Streptococcus iniae. Developmental and Comparative Immunology. 137:104518-104518. 2022
- Identification of TFPI as a receptor reveals recombination-driven receptor switching in Clostridioides difficile toxin B variants. Nature Communications. 13:6786. 2022
- Glutamine Metabolism Mediates Sensitivity to Respiratory Complex II Inhibition in Acute Myeloid Leukemia. Molecular Cancer Research. 20:1659-1673. 2022
- Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways. iScience. 25:104614-104614. 2022
- Structures of distant diphtheria toxin homologs reveal functional determinants of an evolutionarily conserved toxin scaffold. Communications Biology. 5:375. 2022
- Potentiation of long-acting β2-agonist and glucocorticoid responses in human airway epithelial cells by modulation of intracellular cAMP. Respiratory Research. 22:266. 2021
- PathFams: statistical detection of pathogen-associated protein domains. BMC Genomics. 22:663. 2021
- Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways 2021
- Metabolic flexibility determines human NK cell functional fate in the tumor microenvironment. Cell Metabolism. 33:1205-1220.e5. 2021
- Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. iScience. 24:102477-102477. 2021
- PhyloCorrelate: inferring bacterial gene–gene functional associations through large-scale phylogenetic profiling. Bioinformatics. 37:17-22. 2021
- Unraveling the Zoonotic Origin and Transmission of SARS-CoV-2. Trends in Ecology and Evolution. 36:180-184. 2021
- AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology. GigaScience. 10:giab006. 2021
- Development and validation of an open-source, disposable, 3D-printed in vitro environmental exposure system for Transwell culture inserts. ERJ Open Research. 7:00705-2020. 2021
- Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster. Frontiers in Microbiology. 12:787726. 2021
- Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLoS Pathogens. 16:e1009181-e1009181. 2020
- Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus. Journal of General Virology. 101:1251-1260. 2020
- Slr4, a newly identified S‐layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Molecular Microbiology. 114:979-990. 2020
- Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis. Scientific Reports. 10:19052. 2020
- Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status. ERJ Open Research. 6:00128-2020. 2020
- Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue. European Respiratory Journal. 56:2001123-2001123. 2020
- Phylogenomics of 8,839Clostridioides difficilegenomes reveals recombination-driven evolution and diversification of toxin A and B 2020
- High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. The ISME Journal. 14:1857-1872. 2020
- Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens. mSystems. 5:e00145-e00120. 2020
- Genome Sequence of the Fish Brain Bacterium Clostridium tarantellae. Microbiology Resource Announcements. 9:e01575-e01519. 2020
- An assessment of genome annotation coverage across the bacterial tree of life. Microbial Genomics. 6. 2020
- The C. difficile toxin B membrane translocation machinery is an evolutionarily conserved protein delivery apparatus. Nature Communications. 11:432. 2020
- A study of nitric oxide dynamics in a growing biofilm using a density dependent reaction-diffusion model. Journal of Theoretical Biology. 485:110053-110053. 2020
- ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells. Frontiers in Cellular and Infection Microbiology. 10:487. 2020
- Effect of long-acting β-agonists/glucocorticoids on human airway epithelial cell cytokine, transcriptomic and oxidative stress responses to cannabis smoke. ERJ Open Research. 6:00265-2019. 2020
- High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress. Frontiers in Physiology. 11:588313. 2020
- Metagenomic and chemical characterization of soil cobalamin production. The ISME Journal. 14:53-66. 2020
- Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties. Bioinformatics. 35:5063-5065. 2019
- Transcriptomic and barrier responses of human airway epithelial cells exposed to cannabis smoke. Physiological Reports. 7:e14249. 2019
- Exploring the Evolution of Virulence Factors through Bioinformatic Data Mining. mSystems. 4:e00162-e00119. 2019
- AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Research (NAR). 47:4442-4448. 2019
- Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins. Scientific Reports. 9:1634. 2019
- The impact of cigarette smoke exposure, COPD, or asthma status on ABC transporter gene expression in human airway epithelial cells. Scientific Reports. 9:153. 2019
- A comparative analysis of cannabis and tobacco smoke exposure on human airway epithelial cell gene expression, immune phenotype, and response to formoterol and budesonide treatment 2019
- Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database : the journal of biological databases and curation. 2019:baz085. 2019
- Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses. Microbiome. 6:1. 2018
- Metagenomic Sequencing of Wastewater from a South African Research Farm. Microbiology Resource Announcements. 7:e01323-e01318. 2018
- Identification of a diphtheria toxin‐like gene family beyond the Corynebacterium genus. FEBS Letters. 592:2693-2705. 2018
- Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil. Microbiology Resource Announcements. 6:e00632-e00618. 2018
- Discovery of novel bacterial toxins by genomics and computational biology. Toxicon. 147:2-12. 2018
- Genomic insights into the evolution and ecology of botulinum neurotoxins. FEMS Immunology and Medical Microbiology. 76. 2018
- Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium. Cell Host and Microbe. 23:169-176.e6. 2018
- Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing height. eLife. 6:e29329. 2017
- Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution. Scientific Reports. 7:16843. 2017
- Newly identified relatives of botulinum neurotoxins shed light on their molecular evolution 2017
- Estrogen Receptor β Is a Novel Target in Acute Myeloid Leukemia. Molecular Cancer Therapeutics. 16:2618-2626. 2017
- Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti. mSystems. 2:e00035-e00017. 2017
- Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella. Nature Communications. 8:521. 2017
- The Skin Microbiome of Cohabiting Couples. mSystems. 2:e00043-e00017. 2017
- Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk. Nature Genetics. 49:1202-1210. 2017
- Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function. Bioinformatics. 33:1338-1345. 2017
- Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity. Environmental Microbiology. 19:1189-1208. 2017
- Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences. PLoS ONE. 12:e0172545-e0172545. 2017
- Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems. Microbial Genomics. 2:e000080. 2016
- Novel function discovery through sequence and structural data mining. Current Opinion in Structural Biology. 38:53-61. 2016
- MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. Journal of Biology. 13:92. 2015
- mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens. Bioinformatics. 31:590-592. 2015
- Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production. The ISME Journal. 9:461-471. 2015
- Botulinum neurotoxin homologs in non‐Clostridium species. FEBS Letters. 589:342-348. 2015
- Remote homology and the functions of metagenomic dark matter. Frontiers in Genetics. 6:234. 2015
- Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Philosophical Transactions of the Royal Society of London. Biological Sciences. 368:20130029-20130029. 2013
- Prediction of molecular mimicry candidates in human pathogenic bacteria. Virulence. 4:453-466. 2013
- Horizontal Gene Transfer Contributed to the Evolution of Extracellular Surface Structures: The Freshwater Polyp Hydra Is Covered by a Complex Fibrous Cuticle Containing Glycosaminoglycans and Proteins of the PPOD and SWT (Sweet Tooth) Families. PLoS ONE. 7:e52278-e52278. 2012
- Modular Evolution and the Origins of Symmetry: Reconstruction of a Three-Fold Symmetric Globular Protein. Folding and Design. 20:161-171. 2012
- Nuclear Targeting of Methyl-Recycling Enzymes in Arabidopsis thaliana Is Mediated by Specific Protein Interactions. Molecular Plant. 5:231-248. 2012
- Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. BMC Molecular and Cell Biology. 10:23. 2010
- Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster. BMC Ecology and Evolution. 8:316. 2008
- Assessing the evolution of gene expression using microarray data. Evolutionary Bioinformatics. 2008:139-152. 2008
- Assessing the Evolution of Gene Expression Using Microarray Data. Evolutionary Bioinformatics. 4:EBO.S628-EBO.S628. 2008
- Functional Divergence in the Arabidopsis -1,3-Glucanase Gene Family Inferred by Phylogenetic Reconstruction of Expression States. Molecular Biology and Evolution (MBE). 24:1045-1055. 2007
- Cold-Active Winter Rye Glucanases with Ice-Binding Capacity. Plant Physiology. 141:1459-1472. 2006
- Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions. Nature Biotechnology. 24:852-855. 2006
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preprints
- Nasopharyngeal metatranscriptomics reveals host-pathogen signatures of pediatric sinusitis 2024
- Identification of a botulinum neurotoxin-like gene cluster inBacillus toyonensis 2023
- Identification of divergent botulinum neurotoxin homologs in Paeniclostridium ghonii 2022
- AncientClostridiumDNA and variants of tetanus neurotoxins associated with human archaeological remains 2022