Jacob Steenwyk

Graduate student (Evolutionary biology not elsewhere classified)

Nashville, TN

My research, conducted as part of the Antonis Rokas Lab at Vanderbilt University, aims to utilize various 'omics approaches to understand the evolution and function of fungal genomes. I implement computational tools to conduct analyses of species relationships, sequence evolution, and mutational variation across the fungal tree of life or populations thereof. These analyses can inform the evolution and/or divergence of traits important to our lives such as pathogenicity and bioindustrial traits like fermentative capacity. More generally, I am most interested in how populations and/or species evolve, diverge, and what genomic elements and traits define them.

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