Works matching AU Steenwyk, Jacob L

Results: 37

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage.

Published in:

Molecular Systems Biology, 2025, v. 21, n. 8, p. 1066, doi. 10.1038/s44320-025-00118-0

By:

Feng, Bo;
Li, Yonglin;
Xu, Biyang;
Liu, Hongyue;
Steenwyk, Jacob L;
David, Kyle T;
Tian, Xiaolin;
Gonçalves, Carla;
Opulente, Dana A;
LaBella, Abigail L;
Harrison, Marie-Claire;
Wolters, John F;
Shao, Shengyuan;
Chen, Zhaohao;
Fisher, Kaitlin J;
Groenewald, Marizeth;
Hittinger, Chris Todd;
Shen, Xing-Xing;
Li, Shengying;
Rokas, Antonis

Publication type:

Article

Signatures of optimal codon usage in metabolic genes inform budding yeast ecology.

Published in:

PLoS Biology, 2021, v. 19, n. 4, p. 1, doi. 10.1371/journal.pbio.3001185

By:

LaBella, Abigail Leavitt;
Opulente, Dana A.;
Steenwyk, Jacob L.;
Hittinger, Chris Todd;
Rokas, Antonis

Publication type:

Article

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference.

Published in:

PLoS Biology, 2020, v. 18, n. 12, p. 1, doi. 10.1371/journal.pbio.3001007

By:

Steenwyk, Jacob L.;
Buida III, Thomas J.;
Li, Yuanning;
Shen, Xing-Xing;
Rokas, Antonis

Publication type:

Article

PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2325, doi. 10.1093/bioinformatics/btab096

By:

Steenwyk, Jacob L;
Buida, Thomas J;
Labella, Abigail L;
Li, Yuanning;
Shen, Xing-Xing;
Rokas, Antonis

Publication type:

Article

Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens Aspergillus fumigatus , Aspergillus lentulus , and Aspergillus fumigatiaffinis.

Published in:

Frontiers in Genetics, 2020, v. 11, p. 1, doi. 10.3389/fgene.2020.00459

By:

dos Santos, Renato A. C.;
Steenwyk, Jacob L.;
Rivero-Menendez, Olga;
Mead, Matthew E.;
Silva, Lilian P.;
Bastos, Rafael W.;
Alastruey-Izquierdo, Ana;
Goldman, Gustavo H.;
Rokas, Antonis

Publication type:

Article

Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum.

Published in:

Genome Biology & Evolution, 2021, v. 13, n. 10, p. 1, doi. 10.1093/gbe/evab219

By:

Phillips, Megan A;
Steenwyk, Jacob L;
Shen, Xing-Xing;
Rokas, Antonis

Publication type:

Article

Recurrent Loss of abaA, a Master Regulator of Asexual Development in Filamentous Fungi, Correlates with Changes in Genomic and Morphological Traits.

Published in:

Genome Biology & Evolution, 2020, v. 12, n. 7, p. 1119, doi. 10.1093/gbe/evaa107

By:

Mead, Matthew E;
Borowsky, Alexander T;
Joehnk, Bastian;
Steenwyk, Jacob L;
Shen, Xing-Xing;
Sil, Anita;
Rokas, Antonis

Publication type:

Article

integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth.

Published in:

BMC Medical Genomics, 2018, v. 11, n. 1, p. N.PAG, doi. 10.1186/s12920-018-0426-y

By:

Eidem, Haley R.;
Steenwyk, Jacob L.;
Wisecaver, Jennifer H.;
Capra, John A.;
Abbot, Patrick;
Rokas, Antonis

Publication type:

Article

Know the enemy and know yourself: Addressing cryptic fungal pathogens of humans and beyond.

Published in:

PLoS Pathogens, 2023, v. 19, n. 10, p. 1, doi. 10.1371/journal.ppat.1011704

By:

Steenwyk, Jacob L.;
Rokas, Antonis;
Goldman, Gustavo H.

Publication type:

Article

Regulation of gliotoxin biosynthesis and protection in Aspergillus species.

Published in:

PLoS Genetics, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pgen.1009965

By:

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.

Publication type:

Article

Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts.

Published in:

PLoS Biology, 2019, v. 17, n. 5, p. 1, doi. 10.1371/journal.pbio.3000255

By:

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

Publication type:

Article

Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity.

Published in:

PLoS Pathogens, 2020, v. 16, n. 2, p. 1, doi. 10.1371/journal.ppat.1008315

By:

Rokas, Antonis;
Mead, Matthew E.;
Steenwyk, Jacob L.;
Oberlies, Nicholas H.;
Goldman, Gustavo H.

Publication type:

Article

Variation and selection on codon usage bias across an entire subphylum.

Published in:

PLoS Genetics, 2019, v. 15, n. 7, p. 1, doi. 10.1371/journal.pgen.1008304

By:

Labella, Abigail L.;
Opulente, Dana A.;
Steenwyk, Jacob L.;
Hittinger, Chris Todd;
Rokas, Antonis

Publication type:

Article

Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation.

Published in:

Frontiers in Microbiology, 2018, p. 1, doi. 10.3389/fmicb.2018.00288

By:

Steenwyk, Jacob L.;
Rokas, Antonis

Publication type:

Article

ClipKIT in the browser: fast online trimming of multiple sequence alignments for phylogenetics Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. W1, p. W169, doi. 10.1093/nar/gkaf325

By:

Steenwyk, Jacob L;
Loucks, Jeffrey T;
Buida, Thomas J

Publication type:

Article

Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-3044-0

By:

Steenwyk, Jacob L.;
Soghigian, John S.;
Perfect, John R.;
Gibbons, John G.

Publication type:

Article

The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence.

Published in:

PLoS Pathogens, 2020, v. 16, n. 7, p. 1, doi. 10.1371/journal.ppat.1008645

By:

Ries, Laure N. A.;
Pardeshi, Lakhansing;
Dong, Zhiqiang;
Tan, Kaeling;
Steenwyk, Jacob L.;
Colabardini, Ana Cristina;
Ferreira Filho, Jaire A.;
de Castro, Patricia A.;
Silva, Lilian P.;
Preite, Nycolas W.;
Almeida, Fausto;
de Assis, Leandro J.;
dos Santos, Renato A. C.;
Bowyer, Paul;
Bromley, Michael;
Owens, Rebecca A.;
Doyle, Sean;
Demasi, Marilene;
Hernández, Diego C. R.;
Netto, Luís Eduardo S.

Publication type:

Article

PhyKIT: A Multitool for Phylogenomics.

Published in:

Current Protocols, 2024, v. 4, n. 11, p. 1, doi. 10.1002/cpz1.70016

By:

Steenwyk, Jacob L.;
Martínez‐Redondo, Gemma I.;
Buida, Thomas J.;
Gluck‐Thaler, Emile;
Shen, Xing‐Xing;
Gabaldón, Toni;
Rokas, Antonis;
Fernández, Rosa

Publication type:

Article

Nutritional Heterogeneity Among Aspergillus fumigatus Strains Has Consequences for Virulence in a Strain- and Host-Dependent Manner.

Published in:

Frontiers in Microbiology, 2019, p. N.PAG, doi. 10.3389/fmicb.2019.00854

By:

Ries, Laure Nicolas Annick;
Steenwyk, Jacob L.;
de Castro, Patrícia Alves;
de Lima, Pollyne Borborema Almeida;
Almeida, Fausto;
de Assis, Leandro José;
Manfiolli, Adriana Oliveira;
Takahashi-Nakaguchi, Azusa;
Kusuya, Yoko;
Hagiwara, Daisuke;
Takahashi, Hiroki;
Wang, Xi;
Obar, Joshua J.;
Rokas, Antonis;
Goldman, Gustavo H.

Publication type:

Article

Mapping the Fungal Battlefield: Using in situ Chemistry and Deletion Mutants to Monitor Interspecific Chemical Interactions Between Fungi.

Published in:

Frontiers in Microbiology, 2019, p. N.PAG, doi. 10.3389/fmicb.2019.00285

By:

Knowles, Sonja L.;
Raja, Huzefa A.;
Wright, Allison J.;
Lee, Ann Marie L.;
Caesar, Lindsay K.;
Cech, Nadja B.;
Mead, Matthew E.;
Steenwyk, Jacob L.;
Ries, Laure N. A.;
Goldman, Gustavo H.;
Rokas, Antonis;
Oberlies, Nicholas H.

Publication type:

Article

CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair.

Published in:

PLoS Genetics, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pgen.1011158

By:

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.

Publication type:

Article

Diverse signatures of convergent evolution in cactus-associated yeasts.

Published in:

PLoS Biology, 2024, v. 22, n. 9, p. 1, doi. 10.1371/journal.pbio.3002832

By:

Gonçalves, Carla;
Harrison, Marie-Claire;
Steenwyk, Jacob L.;
Opulente, Dana A.;
LaBella, Abigail L.;
Wolters, John F.;
Zhou, Xiaofan;
Shen, Xing-Xing;
Groenewald, Marizeth;
Hittinger, Chris Todd;
Rokas, Antonis

Publication type:

Article

A taxon-rich and genome-scale phylogeny of Opisthokonta.

Published in:

PLoS Biology, 2024, v. 22, n. 9, p. 1, doi. 10.1371/journal.pbio.3002794

By:

Liu, Hongyue;
Steenwyk, Jacob L.;
Zhou, Xiaofan;
Schultz, Darrin T.;
Kocot, Kevin M.;
Shen, Xing-Xing;
Rokas, Antonis;
Li, Yuanning

Publication type:

Article

The promise and pitfalls of synteny in phylogenomics.

Published in:

PLoS Biology, 2024, v. 22, n. 5, p. 1, doi. 10.1371/journal.pbio.3002632

By:

Steenwyk, Jacob L.;
King, Nicole

Publication type:

Article

Genome-wide patterns of noncoding and protein-coding sequence variation in the major fungal pathogen Aspergillus fumigatus.

Published in:

G3: Genes | Genomes | Genetics, 2024, v. 14, n. 7, p. 1, doi. 10.1093/g3journal/jkae091

By:

Brown, Alec;
Steenwyk, Jacob L;
Rokas, Antonis

Publication type:

Article

The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi.

Published in:

G3: Genes | Genomes | Genetics, 2024, v. 14, n. 5, p. 1, doi. 10.1093/g3journal/jkae063

By:

Balamurugan, Charu;
Steenwyk, Jacob L;
Goldman, Gustavo H;
Rokas, Antonis

Publication type:

Article

Cover Image: A portrait of budding yeasts: A symbol of the arts, sciences and a whole greater than the sum of its parts.

Published in:

Yeast, 2021, v. 38, n. 1, p. i, doi. 10.1002/yea.3551

By:

Steenwyk, Jacob L.

Publication type:

Article

A portrait of budding yeasts: A symbol of the arts, sciences and a whole greater than the sum of its parts.

Published in:

Yeast, 2021, v. 38, n. 1, p. 54, doi. 10.1002/yea.3518

By:

Steenwyk, Jacob L.

Publication type:

Article

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum.

Published in:

Genetics, 2024, v. 226, n. 3, p. 1, doi. 10.1093/genetics/iyae008

By:

Haase, Max A B;
Steenwyk, Jacob L;
Boeke, Jef D

Publication type:

Article

BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data.

Published in:

Genetics, 2022, v. 221, n. 3, p. 1, doi. 10.1093/genetics/iyac079

By:

Steenwyk, Jacob L.;
Buida III, Thomas J.;
Gonçalves, Carla;
Goltz, Dayna C.;
Morales, Grace;
Mead, Matthew E.;
LaBella, Abigail L.;
Chavez, Christina M.;
Schmitz, Jonathan E.;
Hadjifrangiskou, Maria;
Yuanning Li;
Rokas, Antonis

Publication type:

Article

An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi.

Published in:

Genetics, 2021, v. 218, n. 2, p. 1, doi. 10.1093/genetics/iyab066

By:

Mead, Matthew E.;
Steenwyk, Jacob L.;
Silva, Lilian P.;
de Castro, Patrícia A.;
Saeed, Nauman;
Hillmann, Falk;
Goldman, Gustavo H.;
Rokas, Antonis

Publication type:

Article

Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species.

Published in:

Genetics, 2020, v. 216, n. 2, p. 481, doi. 10.1534/genetics.120.303549

By:

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

Publication type:

Article

Treehouse: a user-friendly application to obtain subtrees from large phylogenies.

Published in:

BMC Research Notes, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13104-019-4577-5

By:

Steenwyk, Jacob L.;
Rokas, Antonis

Publication type:

Article

The dawn of relaxed phylogenetics.

Published in:

PLoS Biology, 2023, v. 21, n. 1, p. 1, doi. 10.1371/journal.pbio.3001998

By:

Steenwyk, Jacob L.;
Rokas, Antonis

Publication type:

Article

OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.

Published in:

PLoS Biology, 2022, v. 20, n. 10, p. 1, doi. 10.1371/journal.pbio.3001827

By:

Steenwyk, Jacob L.;
Goltz, Dayna C.;
Buida III, Thomas J.;
Li, Yuanning;
Shen, Xing-Xing;
Rokas, Antonis

Publication type:

Article

Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data.

Published in:

Systematic Biology, 2021, v. 70, n. 5, p. 997, doi. 10.1093/sysbio/syab011

By:

Shen, Xing-Xing;
Steenwyk, Jacob L;
Rokas, Antonis

Publication type:

Article

Correction: Variation and selection on codon usage bias across an entire subphylum.

Published in:

2021

By:

LaBella, Abigail L.;
Opulente, Dana A.;
Steenwyk, Jacob L.;
Hittinger, Chris Todd;
Rokas, Antonis

Publication type:

Correction Notice