A5066110547- Animal Virus Infections Studies
- SARS-CoV-2 and COVID-19 Research
- Genomics and Phylogenetic Studies
- Viral gastroenteritis research and epidemiology
- Virus-based gene therapy research
- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- Microbial infections and disease research
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Antimicrobial Resistance in Staphylococcus
- Physiological and biochemical adaptations
- Computational Drug Discovery Methods
- Heat shock proteins research
- Bacterial Identification and Susceptibility Testing
- Fish Ecology and Management Studies
- Genetics, Aging, and Longevity in Model Organisms
- Viral Infections and Vectors
- Genetic diversity and population structure
- Machine Learning in Bioinformatics
- Bacteriophages and microbial interactions
- vaccines and immunoinformatics approaches
- Zoonotic diseases and public health
- Vector-borne infectious diseases
- CRISPR and Genetic Engineering
New York State College of Veterinary Medicine
2025
Cornell University
2024-2025
Temple University
2021-2024
Abstract Inference and interpretation of evolutionary processes, in particular the types targets natural selection affecting coding sequences, are critically influenced by assumptions built into statistical models tests. If certain aspects substitution process (even when they not direct interest) presumed absent or modeled with too crude a simplification, estimates key model parameters can become biased, often systematically, lead to poor performance. Previous work established that failing...
ABSTRACT Equine Erythroparvovirus 1 is a parvovirus that was identified in the blood of four horses United States. Here, we report one genome from horse New York State. This may represent new species within genus .
Recombination contributes to the genetic diversity found in coronaviruses and is known be a prominent mechanism whereby they evolve. It apparent, both from controlled experiments genome sequences sampled nature, that patterns of recombination are non-random this likely attributable combination sequence features favour occurrence break points at specific genomic sites, selection disfavouring survival recombinants within which favourable intra-genome interactions have been disrupted. Here we...
Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity historical demographic comparisons other shark species. The exhibited low variation, 8.7% 2.77 Gbp in runs homozygosity (ROH) > 1 Mbp 74.4% ROH >100 kbp. 4.98 had considerably...
A canine coronavirus (CCoV) has now been reported from two independent human samples Malaysia (respiratory, collected in 2017–2018; CCoV-HuPn-2018) and Haiti (urine, 2017); these viruses were nearly genetically identical. In an effort to identify any novel adaptations associated with this apparent shift tropism we carried out detailed evolutionary analyses of the spike gene virus context related Alphacoronavirus 1 species. The 0-domain retains homology CCoV2b (enteric infections)...
Abstract Feline coronaviruses (FCoVs) commonly cause mild enteric infections in felines worldwide (termed feline coronavirus [FECV]), with around 12 per cent developing into deadly infectious peritonitis (FIP; virus [FIPV]). Genomic differences between FECV and FIPV have been reported, yet the putative genotypic basis of highly pathogenic phenotype remains unclear. Here, we used state-of-the-art molecular evolutionary genetic statistical techniques to identify compare natural selection...
Using a phylogenetic framework to characterize natural selection, we investigate the hypothesis that zoonotic viruses require adaptation prior zoonosis sustain human-to-human transmission. Examining emergence of Ebola virus, Marburg influenza A SARS-CoV, and SARS-CoV-2, find no evidence change in intensity selection immediately host switch, compared with typical within reservoir hosts. We conclude extensive pre-zoonotic is not necessary for transmission viruses. In contrast, reemergence H1N1...
ABSTRACT Background Fever of unknown origin (FUO) without a respiratory component is frequent clinical presentation in horses. Multiple pathogens, both tick‐borne and enteric, can be involved as etiologic agents. An additional potential mechanism intestinal barrier dysfunction. Objectives This case–control study aimed to detect associate microbial taxa blood with disease state. Study Design Areas known for high prevalence diseases humans were chosen survey horses FUO, which was defined fever...
ABSTRACT Staphylococcus pseudintermedius is a common representative of the normal skin microbiota dogs and cats but also causative agent variety infections. Although primarily canine/feline bacterium, recent studies suggest an expanded host range including humans. This paper details population genomic analyses largest yet assembled sequenced collection S. isolates from across USA Canada assesses these within larger global genetic context. We then employ pan-genome-wide association study...
An important unmet need revealed by the COVID-19 pandemic is near-real-time identification of potentially fitness-altering mutations within rapidly growing SARS-CoV-2 lineages. Although powerful molecular sequence analysis methods are available to detect and characterize patterns natural selection modestly sized gene-sequence datasets, computational complexity these their sensitivity sequencing errors render them effectively inapplicable in large-scale genomic surveillance contexts....
Small heat shock proteins (sHSPs) emerged early in evolution and occur all domains of life nearly species, including humans. Mutations four sHSPs (HspB1, HspB3, HspB5, HspB8) are associated with neuromuscular disorders. The aim this study is to investigate the evolutionary forces shaping these during vertebrate evolution. We performed comparative analyses on a set orthologous sHSP sequences, based ratio non-synonymous: synonymous substitution rates for each codon. found that had been...
Feline Coronaviruses (FCoVs) commonly cause mild enteric infections in felines worldwide (termed Enteric Coronavirus [FECV]), with around 12% developing into deadly Infectious Peritonitis (FIP; Virus [FIPV]). Genomic differences between FECV and FIPV have been reported, yet the putative genotypic basis of highly pathogenic phenotype remains unclear. Here, we used state-of-the-art molecular evolutionary genetic statistical techniques to identify compare natural selection pressure sequences,...
Abstract Inference and interpretation of evolutionary processes, in particular the types targets natural selection affecting coding sequences, are critically influenced by assumptions built into statistical models tests. If certain aspects substitution process (even when they not direct interest) presumed absent or modeled with too crude a simplification, estimates key model parameters can become biased, often systematically, lead to poor performance. Previous work established that failing...
An important component of efforts to manage the ongoing COVID19 pandemic is R apid A ssessment how natural selection contributes emergence and proliferation potentially dangerous S ARS-CoV-2 lineages CL ades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based analyses rapidly growing clade-focused genome surveillance datasets, such as those produced following initial detection variants. From datasets automatically generates down-sampled codon alignments individual...
Abstract Recombination contributes to the genetic diversity found in coronaviruses and is known be a prominent mechanism whereby they evolve. It apparent, both from controlled experiments genome sequences sampled nature, that patterns of recombination are non-random this likely attributable combination sequence features favour occurrence breakpoints at specific genomic sites, selection disfavouring survival recombinants within which favourable intra-genome interactions have been disrupted....
Abstract Background Protein–protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present publicly available, automated pipeline to predict genome-wide protein–protein produce high-quality multimeric structural models. Results Application of our method the Human Yeast genomes yield interaction networks similar quality common experimental...
Infections caused by antimicrobial-resistant
ABSTRACT There are several examples of coronaviruses in the Betacoronavirus subgenus Embecovirus that have jumped from an animal to human host. Studying how evolutionary factors shape non-human hosts may provide insight into coronavirus host-switching potential. Equids, such as horses and donkeys, susceptible equine (ECoVs). With increased testing prevalence, ECoV genome sequences become available for molecular analyses, especially those United States America (USA). To date, no analyses been...
ABSTRACT A recent study reported the occurrence of Canine Coronavirus (CCoV) in nasopharyngeal swabs from a small number patients hospitalized with pneumonia during 2017-18 period Sarawak, Malaysia. Because genome sequence for one these isolates is available, we conducted comparative evolutionary analyses spike gene this strain (CCoV-HuPn-2018), other available Alphacoronavirus 1 sequences. The most N-terminus subdomain (0-domain) CCoV-HuPn-2018 protein has similarity to Transmissible...
Abstract Small heat shock proteins (sHSPs) emerged early in evolution and occur all domains of life nearly species, including humans. Mutations four sHSPs (HspB1, HspB3, HspB5, HspB8) are associated with neuromuscular disorders. The aim this study is to investigate the evolutionary forces shaping these during vertebrate evolution. We performed comparative analyses on a set orthologous sHSP sequences, based ratio non-synonymous: synonymous substitution rates for each codon. found that had...
Abstract Protein-protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present publicly available, automated pipeline to predict genome-wide protein-protein produce high-quality multimeric structural models. Application of our method the Human Yeast genomes yield interaction networks similar quality common experimental methods. We...