Antonis Rokas

Affiliations

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA. xingxingshen@zju.edu.cn antonis.rokas@vanderbilt.edu.

Publications (90)

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota.

Science advances

Avec: Xing-Xing Shen , Jacob L Steenwyk , Abigail L LaBella , Dana A Opulente , Xiaofan Zhou , Jacek Kominek , Yuanning Li , Marizeth Groenewald , Chris T Hittinger , Antonis Rokas

Developing a theoretical evolutionary framework to solve the mystery of parturition initiation.

eLife

Avec: Antonis Rokas , Sam Mesiano , Ortal Tamam , Abigail LaBella , Ge Zhang , Louis Muglia

Transcriptomic, Protein-DNA Interaction, and Metabolomic Studies of VosA, VelB, and WetA in Aspergillus nidulans Asexual Spores.

mBio

Avec: Ming-Yueh Wu , Matthew E Mead , Mi-Kyung Lee , George F Neuhaus , Donovon A Adpressa , Julia I Martien , Ye-Eun Son , Heungyun Moon , Daniel Amador-Noguez , Kap-Hoon Han , Antonis Rokas , Sandra Loesgen , Jae-Hyuk Yu , Hee-Soo Park

An investigation of irreproducibility in maximum likelihood phylogenetic inference.

Nature communications

Avec: Xing-Xing Shen , Yuanning Li , Chris Todd Hittinger , Xue-Xin Chen , Antonis Rokas

Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues.

G3 (Bethesda, Md.)

Avec: Jiyun M Moon , John A Capra , Patrick Abbot , Antonis Rokas

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

BMC research notes

Avec: Jacob L Steenwyk , Antonis Rokas

Unearthing fungal chemodiversity and prospects for drug discovery.

Current opinion in microbiology

Avec: Claudio Greco , Nancy P Keller , Antonis Rokas

Biosynthetic gene clusters and the evolution of fungal chemodiversity.

Natural product reports

Avec: Antonis Rokas , Matthew E Mead , Jacob L Steenwyk , Huzefa A Raja , Nicholas H Oberlies

Into the wild: new yeast genomes from natural environments and new tools for their analysis.

FEMS yeast research

Avec: D Libkind , D Peris , F A Cubillos , J L Steenwyk , D A Opulente , Q K Langdon , A Rokas , C T Hittinger

Pathogenic Allodiploid Hybrids of Aspergillus Fungi.

Current biology : CB

Avec: Jacob L Steenwyk , Abigail L Lind , Laure N A Ries , Thaila F Dos Reis , Lilian P Silva , Fausto Almeida , Rafael W Bastos , Thais Fernanda de Campos Fraga da Silva , Vania L D Bonato , André Moreira Pessoni , Fernando Rodrigues , Huzefa A Raja , Sonja L Knowles , Nicholas H Oberlies , Katrien Lagrou , Gustavo H Goldman , Antonis Rokas

Wheldone: Characterization of a Unique Scaffold from the Coculture of

Organic letters

Avec: Sonja L Knowles , Huzefa A Raja , Israa H Isawi , Laura Flores-Bocanegra , Patricia H Reggio , Cedric J Pearce , Joanna E Burdette , Antonis Rokas , Nicholas H Oberlies

Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways.

Microbiology spectrum

Avec: Min Jin Kwon , Charlotte Steiniger , Timothy C Cairns , Jennifer H Wisecaver , Abigail L Lind , Carsten Pohl , Carmen Regner , Antonis Rokas , Vera Meyer

Microbiome-associated human genetic variants impact phenome-wide disease risk.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Robert H George Markowitz , Abigail Leavitt LaBella , Mingjian Shi , Antonis Rokas , John A Capra , Jane F Ferguson , Jonathan D Mosley , Seth R Bordenstein

The influence of the number of tree searches on maximum likelihood inference in phylogenomics.

Systematic biology

Avec: Chao Liu , Xiaofan Zhou , Yuanning Li , Chris Todd Hittinger , Ronghui Pan , Jinyan Huang , Xue-Xin Chen , Antonis Rokas , Yun Chen , Xing-Xing Shen

Genomic and Phenotypic Trait Variation of the Opportunistic Human Pathogen Aspergillus flavus and Its Close Relatives.

Microbiology spectrum

Avec: E Anne Hatmaker , Manuel Rangel-Grimaldo , Huzefa A Raja , Hadi Pourhadi , Sonja L Knowles , Kevin Fuller , Emily M Adams , Jorge D Lightfoot , Rafael W Bastos , Gustavo H Goldman , Nicholas H Oberlies , Antonis Rokas

Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen.

bioRxiv : the preprint server for biology

Avec: Jacob L Steenwyk , Sonja Knowles , Rafael W Bastos , Charu Balamurugan , David Rinker , Matthew E Mead , Christopher D Roberts , Huzefa A Raja , Yuanning Li , Ana Cristina Colabardini , Patrícia Alves de Castro , Thaila Fernanda Dos Reis , David Canóvas , Rafael Luperini Sanchez , Katrien Lagrou , Egídio Torrado , Fernando Rodrigues , Nicholas H Oberlies , Xiaofan Zhou , Gustavo H Goldman , Antonis Rokas

The evolution of gestation length in eutherian mammals.

bioRxiv : the preprint server for biology

Avec: Thodoris Danis , Antonis Rokas

Strain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence.

bioRxiv : the preprint server for biology

Avec: David C Rinker , Thomas J C Sauters , Karin Steffen , Adiyantara Gumilang , Huzefa A Raja , Manuel Rangel-Grimaldo , Camila Figueiredo Pinzan , Patrícia Alves de Castro , Thaila Fernanda Dos Reis , Endrews Delbaje , Jos Houbraken , Gustavo H Goldman , Nicholas H Oberlies , Antonis Rokas

Strain heterogeneity in a non-pathogenic Aspergillus fungus highlights factors associated with virulence.

Communications biology

Convergent reductive evolution in bee-associated lactic acid bacteria.

Applied and environmental microbiology

Avec: Ana Pontes , Marie-Claire Harrison , Antonis Rokas , Carla Gonçalves

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

Genome biology and evolution

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

Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata.

Molecular plant pathology

Avec: Mingshuang Wang , Huilan Fu , Xing-Xing Shen , Ruoxin Ruan , Antonis Rokas , Hongye Li

The Aspergillus fumigatus Mismatch Repair

mSphere

Avec: Thaila Fernanda Dos Reis , Lilian Pereira Silva , Patrícia Alves de Castro , Rafaela Andrade do Carmo , Marjorie Mendes Marini , José Franco da Silveira , Beatriz Henriques Ferreira , Fernando Rodrigues , Abigail Lee Lind , Antonis Rokas , Gustavo H Goldman

Eukaryotic Acquisition of a Bacterial Operon.

Cell

Avec: Jacek Kominek , Drew T Doering , Dana A Opulente , Xing-Xing Shen , Xiaofan Zhou , Jeremy DeVirgilio , Amanda B Hulfachor , Marizeth Groenewald , Mcsean A Mcgee , Steven D Karlen , Cletus P Kurtzman , Antonis Rokas , Chris Todd Hittinger

The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins.

Genome biology and evolution

Avec: Zackery A Ely , Jiyun M Moon , Gregory R Sliwoski , Amandeep K Sangha , Xing-Xing Shen , Abigail L Labella , Jens Meiler , John A Capra , Antonis Rokas

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

Bioinformatics (Oxford, England)

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

The evolution of the GALactose utilization pathway in budding yeasts.

Trends in genetics : TIG

Avec: Marie-Claire Harrison , Abigail L LaBella , Chris Todd Hittinger , Antonis Rokas

Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus.

Microbiology spectrum

Avec: Jacob L Steenwyk , Matthew E Mead , Patrícia Alves de Castro , Clara Valero , André Damasio , Renato A C Dos Santos , Abigail L Labella , Yuanning Li , Sonja L Knowles , Huzefa A Raja , Nicholas H Oberlies , Xiaofan Zhou , Oliver A Cornely , Frieder Fuchs , Philipp Koehler , Gustavo H Goldman , Antonis Rokas

Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases.

mBio

Avec: Noah P Bradley , Katherine L Wahl , Jacob L Steenwyk , Antonis Rokas , Brandt F Eichman

Evolution of the human pathogenic lifestyle in fungi.

Nature microbiology

Avec: Antonis Rokas

Saccharomycotina yeasts defy longstanding macroecological patterns.

bioRxiv : the preprint server for biology

Avec: Kyle T David , Marie-Claire Harrison , Dana A Opulente , Abigail L LaBella , John F Wolters , Xiaofan Zhou , Xing-Xing Shen , Marizeth Groenewald , Matt Pennell , Chris Todd Hittinger , Antonis Rokas

Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum.

Current biology : CB

Avec: Yuanning Li , Hongyue Liu , Jacob L Steenwyk , Abigail L LaBella , Marie-Claire Harrison , Marizeth Groenewald , Xiaofan Zhou , Xing-Xing Shen , Tao Zhao , Chris Todd Hittinger , Antonis Rokas

The dawn of relaxed phylogenetics.

PLoS biology

Avec: Jacob L Steenwyk , Antonis Rokas

Incongruence in the phylogenomics era.

Nature reviews. Genetics

Avec: Jacob L Steenwyk , Yuanning Li , Xiaofan Zhou , Xing-Xing Shen , Antonis Rokas

Extensive intragenomic variation in the internal transcribed spacer region of fungi.

iScience

Avec: Michael J Bradshaw , M Catherine Aime , Antonis Rokas , Autumn Maust , Swarnalatha Moparthi , Keila Jellings , Alexander M Pane , Dylan Hendricks , Binod Pandey , Yuanning Li , Donald H Pfister

Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes.

Nature aging

Avec: Mei Tao , Jiani Chen , Chunlai Cui , Yandong Xu , Jingxiu Xu , Zheyi Shi , Jiaqi Yun , Junwei Zhang , Guo-Zheng Ou , Chao Liu , Yun Chen , Zeng-Rong Zhu , Ronghui Pan , Suhong Xu , Xue-Xin Chen , Antonis Rokas , Yang Zhao , Sibao Wang , Jianhua Huang , Xing-Xing Shen

A genome-informed higher rank classification of the biotechnologically important fungal subphylum

Studies in mycology

Avec: M Groenewald , C T Hittinger , K Bensch , D A Opulente , X-X Shen , Y Li , C Liu , A L LaBella , X Zhou , S Limtong , S Jindamorakot , P Gonçalves , V Robert , K H Wolfe , C A Rosa , T Boekhout , N Čadež , G Éter , J P Sampaio , M-A Lachance , A M Yurkov , H-M Daniel , M Takashima , K Boundy-Mills , D Libkind , K Aoki , T Sugita , A Rokas

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

G3 (Bethesda, Md.)

Avec: Alec Brown , Jacob L Steenwyk , Antonis Rokas

Machine learning enables identification of an alternative yeast galactose utilization pathway.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Marie-Claire Harrison , Emily J Ubbelohde , Abigail L LaBella , Dana A Opulente , John F Wolters , Xiaofan Zhou , Xing-Xing Shen , Marizeth Groenewald , Chris Todd Hittinger , Antonis Rokas

Aspergillus fumigatus conidial surface-associated proteome reveals factors for fungal evasion and host immunity modulation.

Nature microbiology

Avec: Camila Figueiredo Pinzan , Clara Valero , Patrícia Alves de Castro , Jefferson Luiz da Silva , Kayleigh Earle , Hong Liu , Maria Augusta Crivelente Horta , Olaf Kniemeyer , Thomas Krüger , Annica Pschibul , Derya Nur Cömert , Thorsten Heinekamp , Axel A Brakhage , Jacob L Steenwyk , Matthew E Mead , Nico Hermsdorf , Scott G Filler , Nathalia Gonsales da Rosa-Garzon , Endrews Delbaje , Michael J Bromley , Hamilton Cabral , Camila Diehl , Claudia B Angeli , Giuseppe Palmisano , Ashraf S Ibrahim , David C Rinker , Thomas J C Sauters , Karin Steffen , Adiyantara Gumilang , Antonis Rokas , Sara Gago , Thaila F Dos Reis , Gustavo H Goldman

Evolutionary origin and population diversity of a cryptic hybrid pathogen.

Nature communications

Avec: Jacob L Steenwyk , Sonja Knowles , Rafael W Bastos , Charu Balamurugan , David Rinker , Matthew E Mead , Christopher D Roberts , Huzefa A Raja , Yuanning Li , Ana Cristina Colabardini , Patrícia Alves de Castro , Thaila Fernanda Dos Reis , Adiyantara Gumilang , María Almagro-Molto , Alexandre Alanio , Dea Garcia-Hermoso , Endrews Delbaje , Laís Pontes , Camila Figueiredo Pinzan , Angélica Zaninelli Schreiber , David Canóvas , Rafael Sanchez Luperini , Katrien Lagrou , Egídio Torrado , Fernando Rodrigues , Nicholas H Oberlies , Xiaofan Zhou , Gustavo H Goldman , Antonis Rokas

Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence.

Systematic biology

Avec: Xiaofan Zhou , Sarah Lutteropp , Lucas Czech , Alexandros Stamatakis , Moritz Von Looz , Antonis Rokas

Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation.

BioEssays : news and reviews in molecular, cellular and developmental biology

Avec: Jiyun M Moon , John A Capra , Patrick Abbot , Antonis Rokas

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss.

Genetics

Avec: Max A B Haase , Jacek Kominek , Dana A Opulente , Xing-Xing Shen , Abigail L LaBella , Xiaofan Zhou , Jeremy DeVirgilio , Amanda Beth Hulfachor , Cletus P Kurtzman , Antonis Rokas , Chris Todd Hittinger

Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin.

Genetics

Avec: Ana Cristina Colabardini , Fang Wang , Zhiqiang Dong , Lakhansing Pardeshi , Marina Campos Rocha , Jonas Henrique Costa , Thaila Fernanda Dos Reis , Alec Brown , Qais Z Jaber , Micha Fridman , Taicia Fill , Antonis Rokas , Iran Malavazi , Koon Ho Wong , Gustavo Henrique Goldman

ggpubfigs: Colorblind-Friendly Color Palettes and ggplot2 Graphic System Extensions for Publication-Quality Scientific Figures.

Microbiology resource announcements

Avec: Jacob L Steenwyk , Antonis Rokas

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

PLoS biology

Avec: Abigail Leavitt LaBella , Dana A Opulente , Jacob L Steenwyk , Chris Todd Hittinger , Antonis Rokas

Aspergillus fumigatus G-Protein Coupled Receptors GprM and GprJ Are Important for the Regulation of the Cell Wall Integrity Pathway, Secondary Metabolite Production, and Virulence.

mBio

Avec: Aílton Pereira da Costa Filho , Guilherme Thomaz Pereira Brancini , Patrícia Alves de Castro , Clara Valero , Jaire Alves Ferreira Filho , Lilian Pereira Silva , Marina Campos Rocha , Iran Malavazi , João Guilherme de Moraes Pontes , Taícia Fill , Roberto Nascimento Silva , Fausto Almeida , Jacob L Steenwyk , Antonis Rokas , Thaila F Dos Reis , Laure N A Ries , Gustavo H Goldman

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

Genome biology and evolution

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

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

PLoS biology

Avec: Jacob L Steenwyk , Dayna C Goltz , Thomas J Buida , Yuanning Li , Xing-Xing Shen , Antonis Rokas

Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus.

mBio

Avec: Maria Augusta C Horta , Jacob L Steenwyk , Matthew E Mead , Luciano H Braz Dos Santos , Shu Zhao , John G Gibbons , Marina Marcet-Houben , Toni Gabaldón , Antonis Rokas , Gustavo H Goldman

HGT is widespread in insects and contributes to male courtship in lepidopterans.

Cell

Avec: Yang Li , Zhiguo Liu , Chao Liu , Zheyi Shi , Lan Pang , Chuzhen Chen , Yun Chen , Ronghui Pan , Wenwu Zhou , Xue-Xin Chen , Antonis Rokas , Jianhua Huang , Xing-Xing Shen

Aspergillus fumigatus FhdA Transcription Factor Is Important for Mitochondrial Activity and Codon Usage Regulation during the Caspofungin Paradoxical Effect.

Antimicrobial agents and chemotherapy

Avec: Ana Cristina Colabardini , Norman Van Rhijn , Abigail L LaBella , Clara Valero , Lauren Dineen , Antonis Rokas , Gustavo H Goldman

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

G3 (Bethesda, Md.)

Avec: Miya Hugaboom , Elizabeth Anne Hatmaker , Abigail L LaBella , Antonis Rokas

Genomic and ecological factors shaping specialism and generalism across an entire subphylum.

bioRxiv : the preprint server for biology

Avec: Dana A Opulente , Abigail Leavitt LaBella , Marie-Claire Harrison , John F Wolters , Chao Liu , Yonglin Li , Jacek Kominek , Jacob L Steenwyk , Hayley R Stoneman , Jenna VanDenAvond , Caroline R Miller , Quinn K Langdon , Margarida Silva , Carla Gonçalves , Emily J Ubbelohde , Yuanning Li , Kelly V Buh , Martin Jarzyna , Max A B Haase , Carlos A Rosa , Neža Čadež , Diego Libkind , Jeremy H DeVirgilio , Amanda Beth Hulfachor , Cletus P Kurtzman , José Paulo Sampaio , Paula Gonçalves , Xiaofan Zhou , Xing-Xing Shen , Marizeth Groenewald , Antonis Rokas , Chris Todd Hittinger

Draft genomes of

Microbiology resource announcements

Avec: E Anne Hatmaker , Jonathan E Schmitz , Antonis Rokas

Mitochondrial Genome Diversity across the Subphylum Saccharomycotina.

bioRxiv : the preprint server for biology

Avec: John F Wolters , Abigail L LaBella , Dana A Opulente , Antonis Rokas , Chris Todd Hittinger

Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning.

Microbiology spectrum

Avec: Olivia Riedling , Allison S Walker , Antonis Rokas

The cell morphological diversity of Saccharomycotina yeasts.

FEMS yeast research

Avec: Christina M Chavez , Marizeth Groenewald , Amanda B Hulfachor , Gideon Kpurubu , Rene Huerta , Chris Todd Hittinger , Antonis Rokas

Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes.

Fungal genetics and biology : FG & B

Avec: Ruby Ye , Megan Biango-Daniels , Jacob L Steenwyk , Antonis Rokas , Nicolas Louw , Robert Nardella , Benjamin E Wolfe

Diverse signatures of convergent evolution in cacti-associated yeasts.

bioRxiv : the preprint server for biology

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

GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions.

Bioinformatics (Oxford, England)

Avec: Abin Abraham , Abigail L Labella , Mary Lauren Benton , Antonis Rokas , John A Capra

Genetic effects on the timing of parturition and links to fetal birth weight.

Nature genetics

Avec: Pol Solé-Navais , Christopher Flatley , Valgerdur Steinthorsdottir , Marc Vaudel , Julius Juodakis , Jing Chen , Triin Laisk , Abigail L LaBella , David Westergaard , Jonas Bacelis , Ben Brumpton , Line Skotte , Maria C Borges , Øyvind Helgeland , Anubha Mahajan , Matthias Wielscher , Frederick Lin , Catherine Briggs , Carol A Wang , Gunn-Helen Moen , Robin N Beaumont , Jonathan P Bradfield , Abin Abraham , Gudmar Thorleifsson , Maiken E Gabrielsen , Sisse R Ostrowski , Dominika Modzelewska , Ellen A Nohr , Elina Hypponen , Amit Srivastava , Octavious Talbot , Catherine Allard , Scott M Williams , Ramkumar Menon , Beverley M Shields , Gardar Sveinbjornsson , Huan Xu , Mads Melbye , William Lowe , Luigi Bouchard , Emily Oken , Ole B Pedersen , Daniel F Gudbjartsson , Christian Erikstrup , Erik Sørensen , Auteur inconnu , Auteur inconnu , Auteur inconnu , Rolv T Lie , Kari Teramo , Mikko Hallman , Thorhildur Juliusdottir , Hakon Hakonarson , Henrik Ullum , Andrew T Hattersley , Line Sletner , Mario Merialdi , Sheryl L Rifas-Shiman , Thora Steingrimsdottir , Denise Scholtens , Christine Power , Jane West , Mette Nyegaard , John A Capra , Anne H Skogholt , Per Magnus , Ole A Andreassen , Unnur Thorsteinsdottir , Struan F A Grant , Elisabeth Qvigstad , Craig E Pennell , Marie-France Hivert , Geoffrey M Hayes , Marjo-Riitta Jarvelin , Mark I McCarthy , Deborah A Lawlor , Henriette S Nielsen , Reedik Mägi , Antonis Rokas , Kristian Hveem , Kari Stefansson , Bjarke Feenstra , Pål Njolstad , Louis J Muglia , Rachel M Freathy , Stefan Johansson , Ge Zhang , Bo Jacobsson

Saccharomycotina yeasts defy long-standing macroecological patterns.

Proceedings of the National Academy of Sciences of the United States of America

Phylogenomics reveals extensive misidentification of fungal strains from the genus

Microbiology spectrum

Avec: Jacob L Steenwyk , Charu Balamurugan , Huzefa A Raja , Carla Gonçalves , Ningxiao Li , Frank Martin , Judith Berman , Nicholas H Oberlies , John G Gibbons , Gustavo H Goldman , David M Geiser , Jos Houbraken , David S Hibbett , Antonis Rokas

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.

Science (New York, N.Y.)

Avec: Dana A Opulente , Abigail Leavitt LaBella , Marie-Claire Harrison , John F Wolters , Chao Liu , Yonglin Li , Jacek Kominek , Jacob L Steenwyk , Hayley R Stoneman , Jenna VanDenAvond , Caroline R Miller , Quinn K Langdon , Margarida Silva , Carla Gonçalves , Emily J Ubbelohde , Yuanning Li , Kelly V Buh , Martin Jarzyna , Max A B Haase , Carlos A Rosa , Neža ČCadež , Diego Libkind , Jeremy H DeVirgilio , Amanda Beth Hulfachor , Cletus P Kurtzman , José Paulo Sampaio , Paula Gonçalves , Xiaofan Zhou , Xing-Xing Shen , Marizeth Groenewald , Antonis Rokas , Chris Todd Hittinger

Genomic factors shaping codon usage across the Saccharomycotina subphylum.

G3 (Bethesda, Md.)

Avec: Bryan Zavala , Lauren Dineen , Kaitlin J Fisher , Dana A Opulente , Marie-Claire Harrison , John F Wolters , Xing-Xing Shen , Xiaofan Zhou , Marizeth Groenewald , Chris Todd Hittinger , Antonis Rokas , Abigail Leavitt LaBella

Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework.

Yeast (Chichester, England)

Avec: Marie-Claire Harrison , Dana A Opulente , John F Wolters , Xing-Xing Shen , Xiaofan Zhou , Marizeth Groenewald , Chris Todd Hittinger , Antonis Rokas , Abigail Leavitt LaBella

Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci.

Nature communications

Avec: Abigail L LaBella , Abin Abraham , Yakov Pichkar , Sarah L Fong , Ge Zhang , Louis J Muglia , Patrick Abbot , Antonis Rokas , John A Capra

Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens

Frontiers in genetics

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

Toward a Fully Resolved Fungal Tree of Life.

Annual review of microbiology

Avec: Timothy Y James , Jason E Stajich , Chris Todd Hittinger , Antonis Rokas

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

PLoS biology

Avec: Jacob L Steenwyk , Dana A Opulente , Jacek Kominek , Xing-Xing Shen , Xiaofan Zhou , Abigail L Labella , Noah P Bradley , Brandt F Eichman , Neža Čadež , Diego Libkind , Jeremy DeVirgilio , Amanda Beth Hulfachor , Cletus P Kurtzman , Chris Todd Hittinger , Antonis Rokas

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

PLoS genetics

Avec: Abigail L LaBella , Dana A Opulente , Jacob L Steenwyk , Chris Todd Hittinger , Antonis Rokas

Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication.

Evolution, medicine, and public health

Avec: Samuel P Smith , Julie B Phillips , Maddison L Johnson , Patrick Abbot , John A Capra , Antonis Rokas

Rapid Phenotypic and Metabolomic Domestication of Wild

mBio

Avec: Ina Bodinaku , Jason Shaffer , Allison B Connors , Jacob L Steenwyk , Megan N Biango-Daniels , Erik K Kastman , Antonis Rokas , Albert Robbat , Benjamin E Wolfe

Nutritional Heterogeneity Among

Frontiers in microbiology

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

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

Systematic biology

Avec: Xing-Xing Shen , Jacob L Steenwyk , Antonis Rokas

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

Genetics

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

A genome-scale phylogeny of the kingdom Fungi.

Current biology : CB

Avec: Yuanning Li , Jacob L Steenwyk , Ying Chang , Yan Wang , Timothy Y James , Jason E Stajich , Joseph W Spatafora , Marizeth Groenewald , Casey W Dunn , Chris Todd Hittinger , Xing-Xing Shen , Antonis Rokas

Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of

bioRxiv : the preprint server for biology

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

PLoS genetics

Avec: Abigail L LaBella , Dana A Opulente , Jacob L Steenwyk , Chris Todd Hittinger , Antonis Rokas

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships.

PLoS biology

Avec: Alexander K Tice , David Žihala , Tomáš Pánek , Robert E Jones , Eric D Salomaki , Serafim Nenarokov , Fabien Burki , Marek Eliáš , Laura Eme , Andrew J Roger , Antonis Rokas , Xing-Xing Shen , Jürgen F H Strassert , Martin Kolísko , Matthew W Brown

Aspergillus fumigatus Acetate Utilization Impacts Virulence Traits and Pathogenicity.

mBio

Avec: Laure Nicolas Annick Ries , Patricia Alves de Castro , Lilian Pereira Silva , Clara Valero , Thaila Fernanda Dos Reis , Raquel Saborano , Iola F Duarte , Gabriela Felix Persinoti , Jacob L Steenwyk , Antonis Rokas , Fausto Almeida , Jonas Henrique Costa , Taicia Fill , Sarah Sze Wah Wong , Vishukumar Aimanianda , Fernando José Santos Rodrigues , Relber A Gonçales , Cláudio Duarte-Oliveira , Agostinho Carvalho , Gustavo H Goldman

An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function.

Science advances

Avec: Jacob L Steenwyk , Megan A Phillips , Feng Yang , Swapneeta S Date , Todd R Graham , Judith Berman , Chris Todd Hittinger , Antonis Rokas

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

Genetics

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

Mosaic patterns of selection in genomic regions associated with diverse human traits.

PLoS genetics

Avec: Abin Abraham , Abigail L LaBella , John A Capra , Antonis Rokas

Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth.

BMC medicine

Avec: Abin Abraham , Brian Le , Idit Kosti , Peter Straub , Digna R Velez-Edwards , Lea K Davis , J M Newton , Louis J Muglia , Antonis Rokas , Cosmin A Bejan , Marina Sirota , John A Capra

How has horizontal gene transfer shaped the evolution of insect genomes?

Environmental microbiology

Avec: Chao Liu , Yang Li , Yun Chen , Xue-Xin Chen , Jianhua Huang , Antonis Rokas , Xing-Xing Shen

COVID-19-Associated Pulmonary Aspergillosis Isolates Are Genomically Diverse but Similar to Each Other in Their Responses to Infection-Relevant Stresses.

Microbiology spectrum

Avec: Matthew E Mead , Patrícia Alves de Castro , Jacob L Steenwyk , Jean-Pierre Gangneux , Martin Hoenigl , Juergen Prattes , Riina Rautemaa-Richardson , Hélène Guegan , Caroline B Moore , Cornelia Lass-Flörl , Florian Reizine , Clara Valero , Norman Van Rhijn , Michael J Bromley , Antonis Rokas , Gustavo H Goldman , Sara Gago , Auteur inconnu

Mitochondrial genome diversity across the subphylum Saccharomycotina.

Frontiers in microbiology

Avec: John F Wolters , Abigail L LaBella , Dana A Opulente , Antonis Rokas , Chris Todd Hittinger

Réseau de co-auteurs

Jacob L Steenwyk 40 collaborations

Xing-Xing Shen 28 collaborations

Chris Todd Hittinger 24 collaborations

Xiaofan Zhou 20 collaborations

Gustavo H Goldman 19 collaborations

Abigail L LaBella 18 collaborations

Dana A Opulente 17 collaborations

Yuanning Li 16 collaborations

Marizeth Groenewald 13 collaborations

Matthew E Mead 13 collaborations

Huzefa A Raja 11 collaborations

Nicholas H Oberlies 11 collaborations

Patrícia Alves de Castro 11 collaborations

Marie-Claire Harrison 11 collaborations

John A Capra 10 collaborations

John F Wolters 10 collaborations

Thaila Fernanda Dos Reis 7 collaborations

Clara Valero 7 collaborations

Jacek Kominek 6 collaborations

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Chao Liu 6 collaborations

Carla Gonçalves 6 collaborations

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Sonja L Knowles 5 collaborations

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Abin Abraham 5 collaborations

Patrick Abbot 4 collaborations

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None None 4 collaborations

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Lilian P Silva 3 collaborations

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