Antonis Rokas (A Rokas)

Loop profile Ciência ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 117

Top Venues

mBio

bioRxiv : the preprint server for biology

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

PLoS biology

Vanderbilt University

University of Edinburgh (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Vanderbilt University

United States

Professor :: Department of Biological Sciences

Education History

University of Edinburgh

United Kingdom

PHD :: Institute of Cell, Animal and Population Biology

Publications

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 van Rhijn, Michael J Bromley, Antonis Rokas, Gustavo Henrique Goldman, Sara Gago, null null
COVID-19-Associated Pulmonary Aspergillosis Isolates Are Genomically Diverse but Similar to Each Other in Their Responses to Infection-Relevant Stresses. Microbiology spectrum (2023)
Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, Brian Looney, Zachary Konkel, Jason C Slot, Yuichi Sakamoto, Jacob L Steenwyk, Antonis Rokas, Juan Carro, Susana Camarero, Patricia Ferreira, Gonzalo Molpeceres, Francisco Javier Ruiz-Dueñas, Ana Serrano, Bernard Henrissat, Elodie Drula, Karen W Hughes, Juan L Mata, Noemia Kazue Ishikawa, Ruby Vargas-Isla, Shuji Ushijima, Chris A Smith, John Donoghue, Steven Ahrendt, William Andreopoulos, Guifen He, Kurt M LaButti, Anna Lipzen, Vivian Ng, Robert Riley, Laura Sandor, Kerrie Barry, Angel T Martínez, Yang Xiao, John G Gibbons, Kazuhisa Terashima, Igor V Grigoriev, David S Hibbett
A global phylogenomic analysis of the shiitake genus Lentinula . Proceedings of the National Academy of Sciences of the United States of America 120 (10) (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, Brian Looney, Zachary Konkel, Jason C Slot, Yuichi Sakamoto, Jacob L Steenwyk, Antonis Rokas, Juan Carro, Susana Camarero, Patricia Ferreira, Gonzalo Molpeceres, Francisco Javier Ruiz-Dueñas, Ana Serrano, Bernard Henrissat, Elodie Drula, Karen W Hughes, Juan L Mata, Noemia Kazue Ishikawa, Ruby Vargas-Isla, Shuji Ushijima, Chris A Smith, John Donoghue, Steven Ahrendt, William Andreopoulos, Guifen He, Kurt M LaButti, Anna Lipzen, Vivian Ng, Robert Riley, Laura Sandor, Kerrie Barry, Angel T Martínez, Yang Xiao, John G Gibbons, Kazuhisa Terashima, Igor V Grigoriev, David S Hibbett
A global phylogenomic analysis of the shiitake genus Lentinula . Proceedings of the National Academy of Sciences of the United States of America 120 (10) (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
E Anne Hatmaker, Jonathan E Schmitz, Antonis Rokas
Draft genomes of Aspergillus nomiae and Aspergillus tamarii isolates from human eye infections. Microbiology resource announcements (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Jacob L Steenwyk, Yuanning Li, Xiao-Fan Zhou, Xing-Xing Shen, Antonis Rokas
Incongruence in the phylogenomics era. Nature reviews. Genetics (2023)
Pol Sole Navais, Christopher Flatley, Valgerdur Steinthorsdottir, Marc Vaudel, Julius Juodakis, Jing Chen, Triin Laisk, Abigail Leavitt LaBella, David Westergaard, Jonas Bacelis, Ben Michael Brumpton, Line Skotte, Maria C Borges, Øyvind Helgeland, Anubha Mahajan, Matthias Wielscher, Frederick T J Lin, Catherine Briggs, Carol A Wang, Gunn-Helen Moen, Robin N Beaumont, Jonathan P Bradfield, Abin Abraham, Gudmar Thorleifsson, Maiken E Gabrielsen, Sisse Rye Ostrowski, Dominika Modzelewska, Ellen A Nohr, Elina Hyppӧnen, Amit Srivastava, Octavious Talbot, Catherine Allard, Scott M Williams, Ramkumar Menon, Beverley M Shields, Gardar Sveinbjornsson, Huan Xu, Mads Melbye, William L Lowe, Luigi Bouchard, Emily Oken, Ole Birger Vesterager Pedersen, Daníel F Guðbjartsson, Christian Erikstrup, Erik Sørensen, null null, null null, null null, 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 M Scholtens, Christine Power, Jane West, Mette Nygaard, John A Capra, Anne Heidi Skogholt, Per Magnus, Ole Andreas Andreassen, Unnur Thorsteinsdottir, Struan F A Grant, Elisabeth Qvigstad, Craig E Pennell, Marie-France Hivert, M Geoffrey Hayes, Marjo-Riitta Jarvelin, Mark I McCarthy, Deborah A Lawlor, Henriette Svarre Nielsen, Reedik Mägi, Antonis Rokas, Kristian Hveem, Kári Stefánsson, Bjarke Feenstra, Pal Rasmus Njolstad, Louis J Muglia, Rachel M Freathy, Stefan E Johansson, Ge Zhang, Bo Jacobsson
Author Correction: Genetic effects on the timing of parturition and links to fetal birth weight. Nature genetics (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Katrina Ngo, Tristen H Gittens, David I Gonzalez, E Anne Hatmaker, Simcha Plotkin, Mason Engle, Geofrey A Friedman, Melissa Goldin, Remington E Hoerr, Brandt F Eichman, Antonis Rokas, Mary Lauren Benton, Katherine L Friedman
A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae . bioRxiv : the preprint server for biology (2023)
Jacob L Steenwyk, Antonis Rokas
The dawn of relaxed phylogenetics. PLoS biology 21 (1) (2023)
Pol Sole Navais, Christopher Flatley, Valgerdur Steinthorsdottir, Marc Vaudel, Julius Juodakis, Jing Chen, Triin Laisk, Abigail Leavitt LaBella, David Westergaard, Jonas Bacelis, Ben Michael Brumpton, Line Skotte, Maria C Borges, Øyvind Helgeland, Anubha Mahajan, Matthias Wielscher, Frederick T J Lin, Catherine Briggs, Carol A Wang, Gunn-Helen Moen, Robin N Beaumont, Jonathan P Bradfield, Abin Abraham, Gudmar Thorleifsson, Maiken E Gabrielsen, Sisse Rye Ostrowski, Dominika Modzelewska, Ellen A Nohr, Elina Hyppӧnen, Amit Srivastava, Octavious Talbot, Catherine Allard, Scott M Williams, Ramkumar Menon, Beverley M Shields, Gardar Sveinbjornsson, Huan Xu, Mads Melbye, William L Lowe, Luigi Bouchard, Emily Oken, Ole Birger Vesterager Pedersen, Daníel F Guðbjartsson, Christian Erikstrup, Erik Sørensen, null null, null null, null null, 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 M Scholtens, Christine Power, Jane West, Mette Nygaard, John A Capra, Anne Heidi Skogholt, Per Magnus, Ole Andreas Andreassen, Unnur Thorsteinsdottir, Struan F A Grant, Elisabeth Qvigstad, Craig E Pennell, Marie-France Hivert, M Geoffrey Hayes, Marjo-Riitta Jarvelin, Mark I McCarthy, Deborah A Lawlor, Henriette Svarre Nielsen, Reedik Mägi, Antonis Rokas, Kristian Hveem, Kári Stefánsson, Bjarke Feenstra, Pal Rasmus Njolstad, Louis J Muglia, Rachel M Freathy, Stefan E Johansson, Ge Zhang, Bo Jacobsson
Genetic effects on the timing of parturition and links to fetal birth weight. Nature genetics (2023)
Katrina Ngo, Tristen H Gittens, David I Gonzalez, E Anne Hatmaker, Simcha Plotkin, Mason Engle, Geofrey A Friedman, Melissa Goldin, Remington E Hoerr, Brandt F Eichman, Antonis Rokas, Mary Lauren Benton, Katherine L Friedman
A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae . bioRxiv : the preprint server for biology (2023)
Clara Valero, Camila Figueiredo Pinzan, Patrícia Alves de Castro, Norman van Rhijn, Kayleigh Earle, Hong Liu, Maria Augusta Crivelente Horta, Olaf Kniemeyer, Thomas Krüger, Annica Pschibul, Derya Nur Coemert, Thorsten Heinekamp, Axel A Brakhage, Jacob L Steenwyk, Matthew E Mead, Antonis Rokas, Scott G Filler, Nathalia Gonsales da Rosa-Garzon, Hamilton Cabral, Endrews Deljabe, Michael J Bromley, Claudia B Angeli, Giuseppe Palmisano, Ashraf S Ibrahim, Sara Gago, Thaila F Dos Reis, Gustavo Henrique Goldman
A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis. bioRxiv : the preprint server for biology (2023)
Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, Brian Looney, Zachary Konkel, Jason C Slot, Yuichi Sakamoto, Jacob L Steenwyk, Antonis Rokas, Juan Carro, Susana Camarero, Patricia Ferreira, Gonzalo Molpeceres, Francisco Javier Ruiz-Dueñas, Ana Serrano, Bernard Henrissat, Elodie Drula, Karen W Hughes, Juan L Mata, Noemia Kazue Ishikawa, Ruby Vargas-Isla, Shuji Ushijima, Chris A Smith, John Donoghue, Steven Ahrendt, William Andreopoulos, Guifen He, Kurt M LaButti, Anna Lipzen, Vivian Ng, Robert Riley, Laura Sandor, Kerrie Barry, Angel T Martínez, Yang Xiao, John G Gibbons, Kazuhisa Terashima, Igor V Grigoriev, David S Hibbett
A global phylogenomic analysis of the shiitake genus Lentinula . Proceedings of the National Academy of Sciences of the United States of America 120 (10) (2023)
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, Xiao-Fan Zhou, Gustavo H Goldman, Antonis Rokas
Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen. bioRxiv : the preprint server for biology (2023)
Jacob L Steenwyk, Antonis Rokas
The dawn of relaxed phylogenetics. PLoS biology 21 (1) (2023)
Thodoris Danis, Antonis Rokas
The evolution of gestation length in eutherian mammals. bioRxiv : the preprint server for biology (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, Brian Looney, Zachary Konkel, Jason C Slot, Yuichi Sakamoto, Jacob L Steenwyk, Antonis Rokas, Juan Carro, Susana Camarero, Patricia Ferreira, Gonzalo Molpeceres, Francisco Javier Ruiz-Dueñas, Ana Serrano, Bernard Henrissat, Elodie Drula, Karen W Hughes, Juan L Mata, Noemia Kazue Ishikawa, Ruby Vargas-Isla, Shuji Ushijima, Chris A Smith, John Donoghue, Steven Ahrendt, William Andreopoulos, Guifen He, Kurt M LaButti, Anna Lipzen, Vivian Ng, Robert Riley, Laura Sandor, Kerrie Barry, Angel T Martínez, Yang Xiao, John G Gibbons, Kazuhisa Terashima, Igor V Grigoriev, David S Hibbett
A global phylogenomic analysis of the shiitake genus Lentinula . Proceedings of the National Academy of Sciences of the United States of America 120 (10) (2023)
Gustavo Henrique Goldman, Clara Valero, Camila Pinzan, Patrícia de Castro, Norman van van Rhijn, Kayleigh Earle, Hong Liu, Maria Augusta Horta, Olaf Kniemeyer, Thomas Krueger, Annica Pschibul, Derya Coemert, Thorsten Heinekamp, Axel A Brakhage, Jacob Steenwyk, Matthew Mead, Antonis Rokas, Scott Filler, Nathalia da Rosa-Garzon, Endrews Delbaje, Michael J Bromley, Claudia B Angeli, Giuseppe Palmisano, Ashraf S Ibrahim, Sara Gago, Thaila Does Reis
A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis. Research square (2023)
Carla Gonçalves, Marie-Claire Harrison, Jacob L Steenwyk, Dana A Opulente, Abigail Leavitt LaBella, John F Wolters, Xiao-Fan Zhou, Xing-Xing Shen, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas
Diverse signatures of convergent evolution in cacti-associated yeasts. bioRxiv : the preprint server for biology (2023)
Charu Balamurugan, Jacob L Steenwyk, Gustavo Henrique Goldman, Antonis Rokas
The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. bioRxiv : the preprint server for biology (2023)
Rishitha L Nalabothu, Kaitlin J Fisher, Abigail Leavitt LaBella, Taylor A Meyer, Dana A Opulente, John F Wolters, Antonis Rokas, Chris Todd Hittinger
Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts. Molecular biology and evolution (2023)
Olivia Riedling, Allison S Walker, Antonis Rokas
Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning. bioRxiv : the preprint server for biology (2023)
Jacob L Steenwyk, Antonis Rokas
The dawn of relaxed phylogenetics. PLoS biology 21 (1) (2023)
Charu Balamurugan, Jacob L Steenwyk, Gustavo Henrique Goldman, Antonis Rokas
The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. bioRxiv : the preprint server for biology (2023)
Kyle T David, Marie-Claire Harrison, Dana A Opulente, Abigail Leavitt LaBella, John F Wolters, Xiao-Fan Zhou, Xing-Xing Shen, Marizeth Groenewald, Matthew W Pennell, Chris Todd Hittinger, Antonis Rokas
Saccharomycotina yeasts defy longstanding macroecological patterns. bioRxiv : the preprint server for biology (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Yuanning Li, Xing-Xing Shen, Benjamin Evans, Casey W Dunn, Antonis Rokas
Rooting the Animal Tree of Life. Molecular biology and evolution 38 (10) (2022)
Alec Brown, Matthew E Mead, Jacob L Steenwyk, Gustavo Henrique Goldman, Antonis Rokas
Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. Frontiers in fungal biology 3 (2022)
Matthew E Mead, Jacob L Steenwyk, Lilian P Silva, Patrícia A de Castro, Nauman Saeed, Falk Hillmann, Gustavo Henrique Goldman, Antonis Rokas
An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi. Genetics 218 (2) (2022)
Megan A Phillips, Jacob L Steenwyk, Xing-Xing Shen, Antonis Rokas
Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum. Genome biology and evolution 13 (10) (2022)
Noah P Bradley, Katherine L Wahl, Jacob L Steenwyk, Antonis Rokas, Brandt F Eichman
Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases. mBio 13 (2) (2022)
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 Henrique Goldman, Nicholas H Oberliels, Antonis Rokas
Genomic and Phenotypic Trait Variation of the Opportunistic Human Pathogen Aspergillus flavus and Its Close Relatives. Microbiology spectrum (2022)
Jacob L Steenwyk, Thomas J Buida, Carla Gonçalves, Dayna C Goltz, Grace Morales, Matthew E Mead, Abigail Leavitt LaBella, Christina M Chavez, Jonathan E Schmitz, Maria Hadjifrangiskou, Yuanning Li, Antonis Rokas
BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Genetics 221 (3) (2022)
Robert H George Markowitz, Abigail Leavitt LaBella, Mingjian Shi, Antonis Rokas, John A Capra, Jane F Ferguson, Jonathan D Mosley, Seth R Bordenstein
Microbiome-associated human genetic variants impact phenome-wide disease risk. Proceedings of the National Academy of Sciences of the United States of America 119 (26) (2022)
Jacob L Steenwyk, Megan A Phillips, Feng Yang, Swapneeta S Date, Todd R Graham, Judith Berman, Chris Todd Hittinger, Antonis Rokas
An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. Science advances 8 (18) (2022)
Alec Brown, Matthew E Mead, Jacob L Steenwyk, Gustavo Henrique Goldman, Antonis Rokas
Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. Frontiers in fungal biology 3 (2022)
Maria Augusta Crivelente 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 Henrique Goldman
Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus. mBio 13 (4) (2022)
Alec Brown, Matthew E Mead, Jacob L Steenwyk, Gustavo Henrique Goldman, Antonis Rokas
Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. Frontiers in fungal biology 3 (2022)
Jacob L Steenwyk, Dayna C Goltz, Thomas J Buida, Yuanning Li, Xing-Xing Shen, Antonis Rokas
OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. PLoS biology 20 (10) (2022)
Miya Hugaboom, E Anne Hatmaker, Abigail Leavitt LaBella, Antonis Rokas
Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi. G3 (Bethesda, Md.) (2022)
E Anne Hatmaker, Delaney L Miller, Irene L G Newton, Antonis Rokas
Draft Genome Sequence of an Aspergillus Strain Isolated from a Honey Bee Pupa. Microbiology resource announcements 11 (11) (2022)
Abin Abraham, Abigail Leavitt LaBella, John A Capra, Antonis Rokas
Mosaic patterns of selection in genomic regions associated with diverse human traits. PLoS genetics 18 (11) (2022)
Antonis Rokas
Evolution of the human pathogenic lifestyle in fungi. Nature microbiology 7 (5) (2022)
Alec Brown, Matthew E Mead, Jacob L Steenwyk, Gustavo Henrique Goldman, Antonis Rokas
Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. Frontiers in fungal biology 3 (2022)
Ana Cristina Colabardini, Norman van van Rhijn, Abigail L LaBella, Clara Valero, Lauren Dineen, Antonis Rokas, Gustavo Henrique Goldman
Aspergillus fumigatus FhdA Transcription Factor Is Important for Mitochondrial Activity and Codon Usage Regulation during the Caspofungin Paradoxical Effect. Antimicrobial agents and chemotherapy 66 (9) (2022)
Abigail Leavitt LaBella, Dana A Opulente, Jacob L Steenwyk, Chris Todd Hittinger, Antonis Rokas
Signatures of optimal codon usage in metabolic genes inform budding yeast ecology. PLoS biology 19 (4) (2021)
Mary Lauren Benton, Abin Abraham, Abigail Leavitt LaBella, Patrick Abbot, Antonis Rokas, Anthony Capra
The influence of evolutionary history on human health and disease. Nature reviews. Genetics 22 (5) (2021)
Jacob L Steenwyk, Antonis Rokas
orthofisher: a broadly applicable tool for automated gene identification and retrieval. G3 (Bethesda, Md.) 11 (9) (2021)
Min Jin Kwon, Charlotte Steiniger, Timothy C Cairns, Jennifer H Wisecaver, Abigail L Lind, Carsten Freidank-Pohl, Carmen Regner, Antonis Rokas, Vera Meyer
Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways. Microbiology spectrum 9 (2) (2021)
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 Henrique Goldman, Antonis Rokas
Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus. Microbiology spectrum 9 (1) (2021)
Jacob L Steenwyk, Antonis Rokas
ggpubfigs: Colorblind-Friendly Color Palettes and ggplot2 Graphic System Extensions for Publication-Quality Scientific Figures. Microbiology resource announcements 10 (44) (2021)
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
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS biology 19 (8) (2021)
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
Transcriptomic, Protein-DNA Interaction, and Metabolomic Studies of VosA, VelB, and WetA in Aspergillus nidulans Asexual Spores. mBio 12 (1) (2021)
Xing-Xing Shen, Yuanning Li, Chris Todd Hittinger, Xue-Xin Chen, Antonis Rokas
An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nature communications 11 (1) (2020)
Antonis Rokas, Sam Mesiano, Ortal Tamam, Abigail Leavitt LaBella, Ge Zhang, Louis J Muglia
Developing a theoretical evolutionary framework to solve the mystery of parturition initiation. eLife 9 (2020)
Abigail Leavitt LaBella, Abin Abraham, Yakov Pichkar, Sarah L Fong, Ge Zhang, Louis J Muglia, Patrick Abbot, Antonis Rokas, Anthony Capra
Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nature communications 11 (1) (2020)
E Anne Hatmaker, Xiaofan Zhou, Matthew E Mead, Heungyun Moon, Jae-Hyuk Yu, Antonis Rokas
Revised Transcriptome-Based Gene Annotation for Aspergillus flavus Strain NRRL 3357. Microbiology resource announcements 9 (49) (2020)
Julie C Dunning Hotopp, David A Baltrus, Vincent M Bruno, John J Dennehy, Steven R Gill, Julia A Maresca, Jelle Matthijnssens, Irene L G Newton, Catherine Putonti, David A Rasko, Antonis Rokas, Simon Roux, Jason E Stajich, Kenneth M Stedman, Frank J Stewart, J Cameron Thrash
Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements. Microbiology resource announcements 9 (36) (2020)
Yuanning Li, Kyle T David, Xing-Xing Shen, Jacob L Steenwyk, Kenneth M Halanych, Antonis Rokas
Feature frequency profile-based phylogenies are inaccurate. Proceedings of the National Academy of Sciences of the United States of America 117 (50) (2020)
Milton T Drott, R W Bastos, Antonis Rokas, L N A Ries, T Gabaldón, Gustavo Henrique Goldman, Nancy P Keller, C Greco
Diversity of Secondary Metabolism in Aspergillus nidulans Clinical Isolates. mSphere 5 (2) (2020)
Jacob L Steenwyk, Matthew E Mead, Sonja L Knowles, Huzefa A Raja, Christopher D Roberts, Oliver Bader, Jos Houbraken, Gustavo Henrique Goldman, Nicholas H Oberliels, Antonis Rokas
Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species. Genetics 216 (2) (2020)
Xing-Xing Shen, Jacob L Steenwyk, Abigail Leavitt LaBella, Dana A Opulente, Xiaofan Zhou, Jacek Kominek, Yuanning Li, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas
Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Science advances 6 (45) (2020)
Antonis Rokas, Matthew E Mead, Jacob L Steenwyk, Nicholas H Oberliels, Gustavo Henrique Goldman
Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity. PLoS pathogens 16 (2) (2020)
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 Oberliels
Wheldone: Characterization of a Unique Scaffold from the Coculture of Aspergillus fischeri and Xylaria flabelliformis. Organic letters 22 (5) (2020)
Rafael Wesley Bastos, Clara Valero, Lilian Pereira Silva, Taylor Schoen, Milton T Drott, Verônica Brauer, Rafael Silva-Rocha, Abigail Lind, Jacob L Steenwyk, Antonis Rokas, Fernando Rodrigues, Agustin Resendiz-Sharpe, Katrien Lagrou, Marina Marcet-Houben, Toni Gabaldón, Erin McDonnell, Ian Reid, Adrian Tsang, Berl R Oakley, Flávio Vieira Loures, Fausto Almeida, Anna Huttenlocher, Nancy P Keller, Laure Nicolas Annick Ries, Gustavo Henrique Goldman
Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans. mSphere 5 (2) (2020)
Renato Augusto Corrêa Dos Santos, Olga Rivero-Menendez, Jacob L Steenwyk, Matthew E Mead, Gustavo Henrique Goldman, Ana Alastruey-Izquierdo, Antonis Rokas
Draft Genome Sequences of Four Aspergillus Section Fumigati Clinical Strains. Microbiology resource announcements 9 (40) (2020)
Sonja L Knowles, Matthew E Mead, Lilian Pereira Silva, Huzefa A Raja, Jacob L Steenwyk, Gustavo Henrique Goldman, Nicholas H Oberliels, Antonis Rokas
Gliotoxin, a Known Virulence Factor in the Major Human Pathogen Aspergillus fumigatus, Is Also Biosynthesized by Its Nonpathogenic Relative Aspergillus fischeri. mBio 11 (1) (2020)
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 Henrique Goldman
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 11 (5) (2020)
Laure N A Ries, Lakhansing Pardeshi, Zhiqiang Dong, Kaeling Tan, Jacob L Steenwyk, Ana Cristina Colabardini, Jaire A Ferreira Filho, Patricia A de Castro, Lilian Pereira Silva, Nycolas W Preite, Fausto Almeida, Leandro Jose de Assis, Renato A C Dos Santos, Paul Bowyer, Michael J Bromley, Rebecca A Owens, Sean Doyle, Marilene Demasi, Diego C R Hernández, Luis Eduardo Soares Netto, Monica T Pupo, Antonis Rokas, Flavio V Loures, Koon Ho Wong, Gustavo Henrique Goldman
The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence. PLoS pathogens 16 (7) (2020)
Jacob L Steenwyk, Thomas J Buida, Yuanning Li, Xing-Xing Shen, Antonis Rokas
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. PLoS biology 18 (12) (2020)
Samuel P Smith, Julie B Phillips, Maddison L Johnson, Patrick Abbot, John A Capra, Antonis Rokas
Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication. Evolution, medicine, and public health 2019 (1) (2019)
Jiyun M Moon, John A Capra, Patrick Abbot, 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 41 (9) (2019)
Abigail Leavitt LaBella, Dana A Opulente, Jacob L Steenwyk, Chris Todd Hittinger, Antonis Rokas
Variation and selection on codon usage bias across an entire subphylum. PLoS genetics 15 (7) (2019)
Yuyu Wang, Xiao-Fan Zhou, Liming Wang, Xingyue Liu, Ding Yang, Antonis Rokas
Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. International journal of molecular sciences 20 (5) (2019)
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 Henrique Goldman
The Aspergillus fumigatus Mismatch Repair MSH2 Homolog Is Important for Virulence and Azole Resistance. mSphere 4 (4) (2019)
Matthew E Mead, Huzefa A Raja, Jacob L Steenwyk, Sonja L Knowles, Nicholas H Oberliels, Antonis Rokas
Draft Genome Sequence of the Griseofulvin-Producing Fungus Xylaria flabelliformis Strain G536. Microbiology resource announcements 8 (38) (2019)
David A Baltrus, Christina A Cuomo, John J Dennehy, Julie C Dunning Hotopp, Julia A Maresca, Irene L G Newton, David A Rasko, Antonis Rokas, Simon Roux, Jason E Stajich
Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity. Microbiology resource announcements 8 (36) (2019)
Antonis Rokas, Jennifer H Wisecaver, Abigail L Lind
The birth, evolution and death of metabolic gene clusters in fungi. Nature reviews. Microbiology 16 (12) (2019)
Ina Bodinaku, Jason Shaffer, Allison B Connors, Jacob L Steenwyk, Megan N Biango-Daniels, Erik K Kastman, Antonis Rokas, Albert Robbat, Benjamin E Wolfe
Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese. mBio 10 (5) (2019)
Jiyun M Moon, John A Capra, Patrick Abbot, Antonis Rokas
Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. G3 (Bethesda, Md.) 9 (8) (2019)
Jacob L Steenwyk, Xing-Xing Shen, Abigail L Lind, Gustavo Henrique Goldman, Antonis Rokas
A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium. mBio 10 (4) (2019)
Sonja L Knowles, Ngoc Vu, Daniel A Todd, Huzefa A Raja, Antonis Rokas, Qibin Zhang, Nicholas H Oberliels
Orthogonal Method for Double-Bond Placement via Ozone-Induced Dissociation Mass Spectrometry (OzID-MS). Journal of natural products 82 (12) (2019)
Jacob L Steenwyk, Dana A Opulente, Jacek Kominek, Xing-Xing Shen, Xiao-Fan Zhou, Abigail Leavitt LaBella, Noah P Bradley, Brandt F Eichman, Neža Čadež, Diego Libkind, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P Kurtzman, Chris Todd Hittinger, Antonis Rokas
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS biology 17 (5) (2019)
Jacob L Steenwyk, Antonis Rokas
Treehouse: a user-friendly application to obtain subtrees from large phylogenies. BMC research notes 12 (1) (2019)
Matthew E Mead, Sonja L Knowles, Huzefa A Raja, Sarah R Beattie, Caitlin H Kowalski, Jacob L Steenwyk, Lilian P Silva, Jessica Chiaratto, Laure N A Ries, Gustavo Henrique Goldman, Robert A Cramer, Nicholas H Oberlies, Antonis Rokas
Characterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus fischeri, a Close Relative of the Major Human Fungal Pathogen Aspergillus fumigatus. mSphere 4 (1) (2019)
Ella Shtifman Segal, Vladimir Gritsenko, Anton Levitan, Bhawna Yadav, Naama Dror, Jacob L Steenwyk, Yael Silberberg, Kevin Mielich, Antonis Rokas, Neil A R Gow, Reinhard Kunze, Roded Sharan, Judith Berman
Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans. mBio 9 (5) (2018)
Jiyun M Moon, David M Aronoff, John A Capra, Patrick Abbot, Antonis Rokas
Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology. G3 (Bethesda, Md.) 8 (4) (2018)
Katherine Young Bezold Lamm, Maddison L Johnson, Julie Baker Phillips, Michael B Muntifering, Jeanne M James, Helen N Jones, Raymond W Redline, Antonis Rokas, Louis J Muglia
Inverted formin 2 regulates intracellular trafficking, placentation, and pregnancy outcome. eLife 7 (2018)
Fang Yun Lim, Tae Hyung Won, Nicholas Raffa, Joshua A Baccile, Jen Wisecaver, Antonis Rokas, Frank C Schroeder, Nancy P Keller
Fungal Isocyanide Synthases and Xanthocillin Biosynthesis in Aspergillus fumigatus. mBio 9 (3) (2018)
Ming-Yueh Wu, Matthew E Mead, Mi-Kyung Lee, Erin M Ostrem Loss, Sun-Chang Kim, Antonis Rokas, Jae-Hyuk Yu
Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi. mBio 9 (4) (2018)
Tadeusz Krassowski, Aisling Y Coughlan, Xing-Xing Shen, Xiaofan Zhou, Jacek Kominek, Dana A Opulente, Robert Riley, Igor V Grigoriev, Nikunj Maheshwari, Denis C Shields, Cletus P Kurtzman, Chris Todd Hittinger, Antonis Rokas, Kenneth H Wolfe
Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature communications 9 (1) (2018)
David J Krause, Jacek Kominek, Dana A Opulente, Xing-Xing Shen, Xiaofan Zhou, Quinn K Langdon, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P Kurtzman, Antonis Rokas, Chris Todd Hittinger
Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proceedings of the National Academy of Sciences of the United States of America 115 (43) (2018)
Johanna M Huusko, Minna K Karjalainen, Britney E Graham, Ge Zhang, Emily G Farrow, Neil A Miller, Bo Jacobsson, Haley R Eidem, Jeffrey C Murray, Bruce Bedell, Patrick J Breheny, Noah W Brown, Frans L Bødker, Nadia K Litterman, Pan-Pan Jiang, Laura Russell, David A Hinds, Youna Hu, null null, Antonis Rokas, Kari Teramo, Kaare Christensen, Scott M Williams, Mika Rämet, Stephen F Kingsmore, Kelli K Ryckman, Mikko Hallman, Louis J Muglia
Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth. PLoS genetics 14 (7) (2018)
Haley R Eidem, Jacob L Steenwyk, Jennifer H Wisecaver, John A Capra, Patrick Abbot, Antonis Rokas
integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth. BMC medical genomics 11 (1) (2018)
Aaron L Fidler, Sergei P Boudko, Antonis Rokas, Billy G Hudson
The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution. Journal of cell science 131 (7) (2018)

Antonis Rokas.css-eqlu8i{font-size:small;padding-left:4px;} (A Rokas)

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Antonis Rokas (A Rokas)