Jacob Steenwyk

Publications

• OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
• Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans
• Biosynthetic gene clusters, secondary metabolite profiles, and cards of virulence in the closest nonpathogenic relatives of Aspergillus fumigatus
• A portrait of budding yeasts: A symbol of the arts, sciences and a whole greater than the sum of its parts
• An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi
• Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus
• Extensive sequence divergence of non-coding regions between Aspergillus fumigatus, a major fungal pathogen of humans, and its relatives
• Resistance-guided mining of bacterial genotoxins defines a family of DNA glycosylases
• ggpubfigs: Colorblind-Friendly Color Palettes and ggplot2 Graphic System Extensions for Publication-Quality Scientific Figures
• Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits
• ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
• Feature Frequency Profile-based phylogenies are inaccurate
• The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence
• Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese
• Treehouse: a user-friendly application to obtain subtrees from large phylogenies
• Recurrent Loss of abaA, a Master Regulator of Asexual Development in Filamentous Fungi, Correlates with Changes in Genomic and Morphological Traits
• Gliotoxin, a known virulence factor in the major human pathogen Aspergillus fumigatus, is also biosynthesized by the non-pathogenic relative A. fischeri
• Draft Genome Sequences of Four Aspergillus Section Fumigati Clinical Strains
• Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species
• PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data
• Feature frequency profile-based phylogenies are inaccurate
• ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
• Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity
• Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus and Aspergillus fumigatiaffinis
• A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny
• Evolutionary Divergence in DNA Damage Responses among Fungi
• A genome-scale phylogeny of the kingdom Fungi
• Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
• Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus
• Lack of universal mutational biases in a fungal phylum
• Signatures of optimal codon usage predict metabolic ecology in budding yeasts
• BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data
• Aspergillus fumigatus acetate utilisation impacts virulence traits and pathogenicity
• Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus
• Signatures of optimal codon usage in metabolic genes inform budding yeast ecology
• OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
• PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
• Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
• BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data
• orthofisher: a broadly applicable tool for automated gene identification and retrieval
• Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases
• Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum
• An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function
• Biosynthetic gene clusters and the evolution of fungal chemodiversity
• Into the wild: new yeast genomes from natural environments and new tools for their analysis
• Gliotoxin, a Known Virulence Factor in the Major Human Pathogen Aspergillus fumigatus, Is Also Biosynthesized by Its Nonpathogenic Relative Aspergillus fischeri
• Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum
• Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus
• An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function
• Aspergillus fumigatus Acetate Utilization Impacts Virulence Traits and Pathogenicity
• Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest
• Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains
• Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation
• integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
• A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium
• Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
• Characterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus fischeri , a Close Relative of the Major Human Fungal Pathogen Aspergillus fumigatus
• Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
• A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium
• Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation
• Variation and selection on codon usage bias across an entire subphylum
• Draft Genome Sequence of the Griseofulvin-Producing Fungus Xylaria flabelliformis Strain G536
• Nutritional Heterogeneity Among Aspergillus fumigatus Strains Has Consequences for Virulence in a Strain- and Host-Dependent Manner
• Mapping the Fungal Battlefield: Using in situ Chemistry and Deletion Mutants to Monitor Interspecific Chemical Interactions Between Fungi
• Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
• integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
• Latch Verified Bulk-RNA Seq toolkit: a cloud-based suite of workflows for bulk RNA-seq quality control, analysis, and functional enrichment
• Phylogenomics reveals extensive misidentification of fungal strains from the genusAspergillus
• The dawn of relaxed phylogenetics
• A global phylogenomic analysis of the shiitake genus Lentinula
• COVID-19-Associated Pulmonary Aspergillosis Isolates Are Genomically Diverse but Similar to Each Other in Their Responses to Infection-Relevant Stresses
• The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing
• Incongruence in the phylogenomics era
• CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair
• CryptoCEN: A Co-Expression Network forCryptococcus neoformansreveals novel proteins involved in DNA damage repair
• Diverse signatures of convergent evolution in cacti-associated yeasts
• A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences
• Know the enemy and know yourself: Addressing cryptic fungal pathogens of humans and beyond
• OrthoFlow: phylogenomic analysis and diagnostics with one command
• Orthoflow: phylogenomic analysis and diagnostics with one command
• Genome-wide patterns of non-coding sequence variation in the major fungal pathogenAspergillus fumigatus
• Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum
• Natural trait variation across Saccharomycotina species
• Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus
• The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi
• Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
• Genome-wide patterns of non-coding and protein-coding sequence variation in the major fungal pathogen Aspergillus fumigatus
• Genome-wide patterns of noncoding and protein-coding sequence variation in the major fungal pathogen Aspergillus fumigatus
• The promise and pitfalls of synteny in phylogenomics
• The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution
• Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage
• The discovery of a new lifespan-extending gene in insects
• Genomic and phenotypic heterogeneity of clinical isolates of the human pathogensAspergillus fumigatus, Aspergillus lentulusandAspergillus fumigatiaffinis
• Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates ofAspergillus fumigatus
• Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi
• Clonal-aggregative multicellularity entrained by salinity in one of the closest relative of animals
• PhyKIT: A Multitool for Phylogenomics
• RCVT: a novel diagnostic to quantify compositional biases among taxa for phylogenomics
• OrthoHMM: Improved Inference of Ortholog Groups using Hidden Markov Models
• ClipKIT in the Browser: Fast Online Trimming of Multiple Sequence Alignments for Phylogenetics
• From Genes to Genomes: Opportunities and Challenges for Synteny-based Phylogenies
• From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics
• From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics
• RCVT: a diagnostic to quantify compositional biases among taxa for large phylogenomic studies
• ClipKIT in the browser: fast online trimming of multiple sequence alignments for phylogenetics
• The role of metabolism in shaping enzyme structures over 400 million years
• Discovery of additional ancient genome duplications in yeasts
• PAQman: reference-free ensemble evaluation of long-read eukaryotic genome assemblies
• Environmentally regulated clonal-aggregative multicellularity in a choanoflagellate
• Integrative phylogenomics positions sponges at the root of the animal tree
• Stable Hypermutators Revealed by the Genomic Landscape of Genes Involved in Genome Stability Among Yeast Species