JS
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