Research

Publications

• conference proceeding

  • A glycan shield on chimpanzee CD4 protects against infection by primate lentiviruses (HIV/SIV). Journal of Medical Primatology. 222-223.2020
  • Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 487-498.2019

• journal article

  • Regulation of human interferon signaling by transposon exonization. Cell.2024
  • Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses.2024
  • Macrophages derived from human induced pluripotent stem cells (iPSCs) serve as a high-fidelity cellular model for investigating HIV-1, dengue, and influenza viruses. Journal of Virology.2024
  • Structurally divergent and recurrently mutated regions of primate genomes. Cell.2024
  • Human mRNA in saliva can correctly identify individuals harboring acute infection. mBio.2023
  • Quantification of virus-infected cells using RNA FISH-Flow. STAR Protocols.2023
  • How avian influenza viruses spill over to mammals. eLife.2023
  • Identifying animal viruses in humans. Science. 982-983.2023
  • High rates of observed face mask use at Colorado universities align with students' opinions about masking and support the safety and viability of in-person higher education during the COVID-19 pandemic. BMC Public Health.2023
  • RNase L activation in the cytoplasm induces aberrant processing of mRNAs in the nucleus. PLoS Pathogens.2022
  • Primate hemorrhagic fever-causing arteriviruses are poised for spillover to humans. Cell. 3980-+.2022
  • Monkeypox emergency: Urgent questions and perspectives. Cell. 3279-3281.2022
  • Human ACE2 Polymorphisms from Different Human Populations Modulate SARS-CoV-2 Infection. Viruses.2022
  • Estimating the effect of non-pharmaceutical interventions on US SARS-CoV-2 infections in the first year of the pandemic. Royal Society Open Science.2022
  • Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities (vol 118, e2104547118, 2021). Proceedings of the National Academy of Sciences of USA.2022
  • Nuku, a family of primate retrocopies derived fromKU70. G3: Genes, Genomes, Genetics.2021
  • RNase L limits host and viral protein synthesis via inhibition of mRNA export. Science Advances.2021
  • Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities. Proceedings of the National Academy of Sciences of USA.2021
  • Positive natural selection in primate genes of the type I interferon response. BMC Ecology.2021
  • Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. eLife.2021
  • Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities.2021
  • Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers.2021
  • Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 487-498.2020
  • dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA. Viruses.2019
  • TRIM5αRestricts Flavivirus Replication by Targeting the Viral Protease for Proteasomal Degradation. Cell Reports. 3269-+.2019
  • A glycan shield on chimpanzee CD4 protects against infection by primate lentiviruses (HIV/SIV). Proceedings of the National Academy of Sciences of USA. 11460-11469.2019
  • A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species. Proceedings of the National Academy of Sciences of USA. 11351-11360.2019
  • Selective use of primate CD4 receptors by HIV-1. PLoS Biology.2019
  • How host genetics dictates successful viral zoonosis. PLoS Biology.2019
  • Species-Specific Deamidation of cGAS by Herpes Simplex Virus UL37 Protein Facilitates Viral Replication. Cell Host and Microbe. 234-+.2018
  • Control of yeast retrotransposons mediated through nucleoporin evolution. PLoS Genetics.2018
  • Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir. eLife.2018
  • Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes. PLoS Pathogens.2018
  • Owl monkey CCR5 reveals synergism between CD4 and CCR5 in HIV-1 entry. Virology. 180-186.2017
  • Nuclear TRIM25 Specifically Targets Influenza Virus Ribonucleoproteins to Block the Onset of RNA Chain Elongation. Cell Host and Microbe. 627-+.2017
  • Modulation of LINE-1 Retrotransposition by a Human SAMHD1 Polymorphism.. Virology Reports. 53-60.2016
  • Non-human Primate Schlafen11 Inhibits Production of Both Host and Viral Proteins. PLoS Pathogens.2016
  • XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts. PLoS Pathogens.2016
  • An Intrinsically Disordered Region of the DNA Repair Protein Nbs1 Is a Species-Specific Barrier to Herpes Simplex Virus 1 in Primates. Cell Host and Microbe. 178-188.2016
  • ADAPTIVE EVOLUTION At the mercy of viruses. eLife.2016
  • A putative SUMO interacting motif in the B30.2/SPRY domain of rhesus macaque TRIM5 alpha important for NF-kappa B/AP-1 signaling and HIV-1 restriction. Heliyon.2016
  • Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. eLife.2015
  • Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast. PLoS Genetics.2015
  • Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses. Journal of Virology. 11643-11653.2015
  • Identification of Owl Monkey CD4 Receptors Broadly Compatible with Early-Stage HIV-1 Isolates. Journal of Virology. 8611-8622.2015
  • The Effect of Species Representation on the Detection of Positive Selection in Primate Gene Data Sets. Molecular Biology and Evolution. 1091-1096.2015
  • Rapid evolution ofBRCA1 andBRCA2 in humans and other primates. BMC Evolutionary Biology.2014
  • Effects of human SAMHD1 polymorphisms on HIV-1 susceptibility. Virology. 34-44.2014
  • Widespread Sequence Variations in VAMP1 across Vertebrates Suggest a Potential Selective Pressure from Botulinum Neurotoxins. PLoS Pathogens.2014
  • Reply to Schmitt et al.: Data-filtering schemes for avoiding double-counting in circle sequencing. Proceedings of the National Academy of Sciences of USA. E1561-E1561.2014
  • Positive selection of primate genes that promote HIV-1 replication. Virology. 291-298.2014
  • Analyzing machupo virus-receptor binding by molecular dynamics simulations. PeerJ.2014
  • High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proceedings of the National Academy of Sciences of USA. 19872-19877.2013
  • Recent host-shifts in ranaviruses: signatures of positive selection in the viral genome. Journal of General Virology. 2082-2093.2013
  • D316 is critical for the enzymatic activity and HIV-1 restriction potential of human and rhesus APOBEC3B. Virology. 31-39.2013
  • Dual Host-Virus Arms Races Shape an Essential Housekeeping Protein. PLoS Biology.2013
  • Generation of an HIV Resistant T-cell Line by Targeted "Stacking" of Restriction Factors. Molecular Therapy. 786-795.2013
  • An Evolutionary Screen Highlights Canonical and Noncanonical Candidate Antiviral Genes within the PrimateTRIM Gene Family. Genome Biology and Evolution. 2141-2154.2013
  • A cross-species view on viruses. Current Opinion in Virology. 561-568.2012
  • Evidence for ACE2-Utilizing Coronaviruses (CoVs) Related to Severe Acute Respiratory Syndrome CoV in Bats. Journal of Virology. 6350-6353.2012
  • Evolutionary Reconstructions of the Transferrin Receptor of Caniforms Supports Canine Parvovirus Being a Re-emerged and Not a Novel Pathogen in Dogs. PLoS Pathogens.2012
  • HIV-1 Capsid-Targeting Domain of Cleavage and Polyadenylation Specificity Factor 6. Journal of Virology. 3851-3860.2012
  • Species-Specific Features of DARC, the Primate Receptor for Plasmodium vivax and Plasmodium knowlesi. Molecular Biology and Evolution. 445-449.2012
  • Identification of a Genomic Reservoir for NewTRIM Genes in Primate Genomes. PLoS Genetics.2011
  • Two-stepping through time: mammals and viruses. Trends in Microbiology. 286-294.2011
  • Ancient and Recent Adaptive Evolution of Primate Non-Homologous End Joining Genes. PLoS Genetics.2010
  • An expanded clade of rodentTrim5 genes. Virology. 473-483.2009
  • Molecular evolution of the antiretroviralTRIM5 gene. Immunogenetics. 163-176.2009
  • Discordant evolution of the adjacent antiretroviral genesTRIM22 andTRIM5 in mammals. PLoS Pathogens. 1918-1929.2007
  • Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis. Proceedings of the National Academy of Sciences of USA. 17614-17619.2006
  • High-frequency persistence of an impaired allele of the retroviral defense geneTRIM5α in humans. Current Biology. 95-100.2006
  • High-frequency persistence of an impaired allele of the retroviral defense gene TRIM5alpha in humans.. Current Biology. 95-100.2006
  • Positive selection of primateTRIM5α identifies a critical species-specific retroviral restriction domain. Proceedings of the National Academy of Sciences of USA. 2832-2837.2005
  • Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biology. 1278-1285.2004
  • Mcm10 and Cdc45 cooperate in origin activation inSaccharomyces cerevisiae. Journal of Molecular Biology. 195-202.2004
  • Mcm10 and Cdc45 Cooperate in Origin Activation in Saccharomyces cerevisiae. Journal of Molecular Biology. 195-202.2004
  • The hexameric eukaryotic MCM helicase: Building symmetry from nonidentical parts. Journal of Biological Chemistry. 34833-34836.2000
  • Mcm10 and the MCM2-7 complex interact to initiate DNA synthesis and to release replication factors from origins. Genes and Development. 913-926.2000
  • 2ND OPINIONS. The Veterinary Record. 56-56.1986
  • FACILITATION OF INDIVIDUAL FORELIMB MOTOR UNITS BY SINGLE INTRACORTICAL MICROSTIMULI IN BEHAVING MONKEYS. The Journal of Physiology. P19-P20.1983
  • DR OR MR. The Veterinary Record. 22-22.1978

Teaching

• BCHM 6901 - Research in Biochemistry
  Primary Instructor - Fall 2022 / Spring 2023
  May be repeated up to 15 total credit hours.
• MCDB 3160 - Infectious Disease
  Primary Instructor - Fall 2018 / Fall 2019 / Fall 2021 / Fall 2022 / Fall 2023
  Illustrate how cutting edge tools in genomics can be used to study, monitor and cure disease caused by new and re-emerging human pathogens such as SARS/MERS, Ebola virus, Neisseria meningitides, influenza virus and malaria parasites. Technologies covered will include genome sequencing, annotation, transcriptomics, phylogenetics and genotyping of microbial populations. An integrated approach to this topic will be presented, with these concepts threaded throughout: natural history and evolution of pathogens, molecular biology, immunology, epidemiology, public health and clinical diagnosis. There may be some overlap with material covered in MCDB 1030 and MCDB 4750.
• MCDB 5201 - Graduate Lab in Molecular Evolution
  Primary Instructor - Fall 2018
  Ever wonder what functional clues might reside in the DNA sequence of your favorite gene? In this course, graduate students will learn the fundamentals of phylogenetics with an emphasis on evolutionary models that infer selective pressures in protein-coding DNA sequences (genes). During the course, students will be working on their favorite gene and using it as a case study for applying all of the concepts that we will cover. By the end of the course they will have generated a publication-quality summary figure, along with appropriate supplemental figures, of the selective pressures shaping their favorite gene. Additionally, they will learn how to design and execute an experimental approach based off of findings from the evolutionary analysis.
• MCDB 6000 - Introduction to Laboratory Methods
  Primary Instructor - Spring 2019 / Spring 2020 / Fall 2020 / Spring 2021 / Fall 2021 / Spring 2022 / Spring 2023 / Spring 2024 / Fall 2024
  Introduces methodology and techniques used in biological research. Designed as a tutorial between a few students and one faculty member. Students are expected to read original research papers, discuss findings, and to plan and execute experiments in selected areas. May be repeated up to 15 total credit hours.

Background

• Ph.D.,Cornell University2003
• B.S.,University of Kansas1996

• NIH Director’s Pioneer Award (DP1),conferred byNational Institutes of Health,2022
• NIH Director’s Pioneer Award (DP1),conferred byNational Institutes of Health,2018
• Avant-Garde Award for HIV/AIDS Research,conferred byNational Institute on Drug Abuse,2018
• Richard M. Elliott Memorial Award in Virology,conferred byMRC-University of Glasgow Centre for Virus Research,2018
• Investigators in Pathogenesis of Infectious Diseases,conferred byBurroughs Wellcome Fund,2013
• Kavli Frontiers of Science Fellow,conferred byNational Academy of Sciences,2011
• Presidential Early Career Awards for Scientists and Engineers,conferred byPresident of the United States of America,2010
• Sloan Research Fellowship-Molecular Biology,conferred byAlfred P. Sloan Foundation,2009

Other Profiles

• http://orcid.org/0000-0002-6965-1085

• https://scholar.google.com/citations?user=XY7DNtgAAAAJ&hl=en&oi=ao