ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference von Steenwyk, Jacob L, Buida, 3rd, Thomas J, Li, Yuanning, Shen, Xing-Xing, Rokas, Antonis

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The promise and pitfalls of synteny in phylogenomics von Steenwyk, Jacob L, King, Nicole

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The dawn of relaxed phylogenetics von Steenwyk, Jacob L, Rokas, Antonis

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OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees von Steenwyk, Jacob L, Goltz, Dayna C, Buida, Thomas J, Li, Yuanning, Shen, Xing-Xing, Rokas, Antonis

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Evolutionary Divergence in DNA Damage Responses among Fungi von Steenwyk, Jacob L

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Know the enemy and know yourself: Addressing cryptic fungal pathogens of humans and beyond von Steenwyk, Jacob L, Rokas, Antonis, Goldman, Gustavo H

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Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum von Shen, Xing-Xing, Opulente, Dana A., Kominek, Jacek, Zhou, Xiaofan, Steenwyk, Jacob L., Buh, Kelly V., Haase, Max A.B., Wisecaver, Jennifer H., Wang, Mingshuang, Doering, Drew T., Boudouris, James T., Schneider, Rachel M., Langdon, Quinn K., Ohkuma, Moriya, Endoh, Rikiya, Takashima, Masako, Manabe, Ri-ichiroh, Čadež, Neža, Libkind, Diego, Rosa, Carlos A., DeVirgilio, Jeremy, Hulfachor, Amanda Beth, Groenewald, Marizeth, Kurtzman, Cletus P., Hittinger, Chris Todd, Rokas, Antonis

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Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity von Rokas, Antonis, Mead, Matthew E, Steenwyk, Jacob L, Oberlies, Nicholas H, Goldman, Gustavo H

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Variation and selection on codon usage bias across an entire subphylum von LaBella, Abigail L, Opulente, Dana A, Steenwyk, Jacob L, Hittinger, Chris Todd, Rokas, Antonis

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Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts von Steenwyk, Jacob L, Opulente, Dana A, Kominek, Jacek, Shen, Xing-Xing, Zhou, Xiaofan, Labella, Abigail L, Bradley, Noah P, Eichman, Brandt F, Čadež, Neža, Libkind, Diego, DeVirgilio, Jeremy, Hulfachor, Amanda Beth, Kurtzman, Cletus P, Hittinger, Chris Todd, Rokas, Antonis

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Signatures of optimal codon usage in metabolic genes inform budding yeast ecology von LaBella, Abigail Leavitt, Opulente, Dana A, Steenwyk, Jacob L, Hittinger, Chris Todd, Rokas, Antonis

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Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation von Steenwyk, Jacob L, Rokas, Antonis

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orthofisher: a broadly applicable tool for automated gene identification and retrieval von Steenwyk, Jacob L, Rokas, Antonis

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Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species von Steenwyk, Jacob L, Mead, Matthew E, Knowles, Sonja L, Raja, Huzefa A, Roberts, Christopher D, Bader, Oliver, Houbraken, Jos, Goldman, Gustavo H, Oberlies, Nicholas H, Rokas, Antonis

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Treehouse: a user-friendly application to obtain subtrees from large phylogenies von Steenwyk, Jacob L, Rokas, Antonis

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CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair von O'Meara, Matthew J, Rapala, Jackson R, Nichols, Connie B, Alexandre, A Christina, Billmyre, R Blake, Steenwyk, Jacob L, Alspaugh, J Andrew, O'Meara, Teresa R

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Correction: Variation and selection on codon usage bias across an entire subphylum von LaBella, Abigail L, Opulente, Dana A, Steenwyk, Jacob L, Hittinger, Chris Todd, Rokas, Antonis

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Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota von Shen, Xing-Xing, Steenwyk, Jacob L, LaBella, Abigail L, Opulente, Dana A, Zhou, Xiaofan, Kominek, Jacek, Li, Yuanning, Groenewald, Marizeth, Hittinger, Chris T, Rokas, Antonis

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Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases von Bradley, Noah P, Wahl, Katherine L, Steenwyk, Jacob L, Rokas, Antonis, Eichman, Brandt F

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Regulation of gliotoxin biosynthesis and protection in Aspergillus species von de Castro, Patrícia Alves, Colabardini, Ana Cristina, Moraes, Maísa, Horta, Maria Augusta Crivelente, Knowles, Sonja L, Raja, Huzefa A, Oberlies, Nicholas H, Koyama, Yasuji, Ogawa, Masahiro, Gomi, Katsuya, Steenwyk, Jacob L, Rokas, Antonis, Gonçales, Relber A, Duarte-Oliveira, Cláudio, Carvalho, Agostinho, Ries, Laure N A, Goldman, Gustavo H

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