Computational and Evolutionary Systems Biology
Scholarship Keywords
evolutionary theory, population genetics, bioinformatics, data science, systems biology, modeling & simulation, evolutionary biology, computational biology
Interim Council Member
Working Groups
Manager:
Affiliation,
Infrastructure
Member:
Communications,
Finance
Works
- scribl: A system for the semantic capture of relationships in biological literature Zenodo 2025 DOI (software)
- PyPop: Python for Population Genomics Zenodo 2025 DOI (software)
- scribl: A system for the semantic capture of relationships in biological literature Journal of Open Source Software 2024 URL DOI (journal-article)
- PyPop: a mature open-source software pipeline for population genomics Frontiers in Immunology 2024 URL DOI (journal-article)
- PyPop: A mature open-source software pipeline for population genomics Zenodo 2024 DOI (preprint)
- Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise Nature Communications 2019 URL DOI (journal-article)
- Python for the life sciences: A gentle introduction to python for life scientists Python for the Life Sciences: A Gentle Introduction to Python for Life Scientists 2019 URL DOI (book)
- Ribosome profiling of genetically diverse Saccharomyces cerevisiae strains harboring the [PSI+] prion 2019 URL DOI (data-set)
- A new paradigm for the scientific enterprise: nurturing the ecosystem F1000Research 2018 URL DOI (journal-article)
- Inhibiting mitochondrial phosphate transport as an unexploited antifungal strategy Nature Chemical Biology 2018 URL DOI (journal-article)
- How do we build a human-centered open science? The Winnower 2016 URL DOI (working-paper)
- A Fungal-Selective Cytochrome bc
1 Inhibitor Impairs Virulence and Prevents the Evolution of Drug Resistance Cell Chemical Biology 2016 URL DOI (journal-article) - Luminidependens (LD) is an Arabidopsis protein with prion behavior Proceedings of the National Academy of Sciences of the United States of America 2016 URL DOI (journal-article)
- COSMOS: cloud enabled NGS analysis OpenAlex 2015 DOI (other)
- Scalable and cost-effective NGS genotyping in the cloud BMC Medical Genomics 2015 URL DOI (journal-article)
- Science and technology consortia in U.S. biomedical research: A paradigm shift in response to unsustainable academic growth BioEssays 2015 URL DOI (journal-article)
- COSMOS: Python library for massively parallel workflows Bioinformatics 2014 URL DOI (journal-article)
- An evolutionarily conserved prion-like element converts wild fungi from metabolic specialists to generalists Cell 2014 URL DOI (journal-article)
- Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformation of metabolism Cell 2014 URL DOI (journal-article)
- Erratum: Inhibiting GPI anchor biosynthesis in fungi stresses the endoplasmic reticulum and enhances immunogenicity (ACS Chemical Biology (2012) 7 (1520-1528) DOI: 10.1021/cb300235m) ACS Chemical Biology 2014 URL DOI (journal-article)
- Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit Bmc Genomics 2014 URL DOI (journal-article)
- PLAAC: A web and command-line application to identify proteins with prion-like amino acid composition Bioinformatics 2014 URL DOI (journal-article)
- Fitness Trade-offs Restrict the Evolution of Resistance to Amphotericin B Plos Biology 2013 URL DOI (journal-article)
- Fresh Insights from RNA-Seq Analysis into Black Widow Spider Venom Composition and Evolution Integrative and Comparative Biology 2013 URL (journal-article)
- Heritable remodeling of yeast multicellularity by an environmentally responsive prion Cell 2013 URL DOI (journal-article)
- Yeast Reveal a "Druggable" Rsp5/Nedd4 Network that Ameliorates α-Synuclein Toxicity in Neurons. 2013 URL DOI (journal-article)
- Inhibiting GPI anchor biosynthesis in fungi stresses the endoplasmic reticulum and enhances immunogenicity ACS Chemical Biology 2012 URL DOI (journal-article)
- Prions are a common mechanism for phenotypic inheritance in wild yeasts Nature 2012 URL DOI (journal-article)
- A community standard for immunogenomic data reporting and analysis: proposal for a STrengthening the REporting of Immunogenomic Studies statement. 2011 URL DOI (journal-article)
- A hierarchical analysis of selection at the HLA-DPB1 locus reveals the action of balancing selection operating on DP serological categories Tissue Antigens 2010 URL (journal-article)
- The spontaneous appearance rate of the yeast prion [PSI+] and its implications for the evolution of the evolvability properties of the [PSI+] system Genetics 2010 URL DOI (journal-article)
- Toward a community standard for immunogenetics data reporting and analysis Tissue Antigens 2010 URL (journal-article)
- HLA-A, -B, -C, and-DRB1 allele and haplotype frequencies distinguish Eastern European Americans from the general European American population Tissue Antigens 2009 URL DOI (journal-article)
- IDAWG - THE IMMUNOGENOMIC DATA-ANALYSIS WORKING GROUP. Human Immunology 2009 URL DOI (journal-article)
- The evolution of reversible switches in the presence of irreversible mimics Evolution 2009 URL DOI (journal-article)
- Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies Human Immunology 2008 URL DOI (journal-article)
- GLOBAL PATTERNS OF POLYMORPHISM AND SELECTION AT THE CLASSICAL HLA LOCI: A META-ANALYSIS OF 497 POPULATION STUDIES Human Immunology 2008 URL DOI (journal-article)
- Selection at the amino acid level for HLA class I and class II loci Tissue Antigens 2008 URL (journal-article)
- 14th International HLA and Immunogenetics Workshop: Report of progress in methodology, data collection, and analyses Tissue Antigens 2007 URL DOI (journal-article)
- HLA Haplotypes in Singapore: A Study of Mothers and Their Cord Blood Units Human Immunology 2007 URL DOI (journal-article)
- HLA-A, -B, -C, -DRB1 allele and haplotype frequencies in an African American population Tissue Antigens 2007 URL DOI (journal-article)
- PyPop update - A software pipeline for large-scale multilocus population genomics Tissue Antigens 2007 URL DOI (journal-article)
- Population genetic analyses of the 13th IHW anthropology data Human Immunology 2005 DOI (journal-article)
- Signatures of demographic history and natural selection in the human MHC - a comparative study Tissue Antigens 2005 URL (journal-article)
- Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci Tissue Antigens 2004 URL DOI (journal-article)
- High resolution HLA-DRB1 identification of a caucasian population Human Immunology 2004 URL DOI (journal-article)
- PyPop: a software framework for population genomics: analyzing large-scale multi-locus genotype data. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003 URL (journal-article)
- Therapeutic engineering: Models of individual variability in drug systems Computers and Their Applications 2001 URL (journal-article)