Academic lineage
Video highlight
Extensive intragenomic variation in the internal transcribed spacer region of fungi
- Michael J Bradshaw, M Catherine Aime, Antonis Rokas, …, Binod Pandey, Yuanning Li, Donald H Pfister
- None, 10.1016/j.isci.2023.107317
Draft genomes of Aspergillus nomiae and Aspergillus tamarii isolates from human eye infections
- E Anne Hatmaker, Jonathan E Schmitz, Antonis Rokas, E Anne Hatmaker, Jonathan E Schmitz, Antonis Rokas
- None, 10.1128/mra.00391-23
Author Correction: Genetic effects on the timing of parturition and links to fetal birth weight
- Christopher Flatley, Valgerdur Steinthorsdottir, Marc Vaudel, …, Stefan Johansson, Ge Zhang, Bo Jacobsson
- Nat Genet, 10.1038/s41588-023-01412-z
Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts
- Rishitha L Nalabothu, Kaitlin J Fisher, Abigail Leavitt LaBella, …, John F Wolters, Antonis Rokas, Chris Todd Hittinger
- Mol Biol Evol, 10.1093/molbev/msad111
A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae
- Katrina Ngo, Tristen H Gittens, David I Gonzalez, …, Antonis Rokas, Mary Lauren Benton, Katherine L Friedman
- None, 10.1101/2023.03.20.533556
Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives
- Alec Brown, Matthew E Mead, Jacob L Steenwyk, …, Jacob L Steenwyk, Gustavo H Goldman, Antonis Rokas
- None, 10.3389/ffunb.2022.802494
A global phylogenomic analysis of the shiitake genus Lentinula
- Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, …, Kazuhisa Terashima, Igor V Grigoriev, David Hibbett
- Proc Natl Acad Sci U S A, 10.1073/pnas.2214076120
The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi
- Charu Balamurugan, Jacob L Steenwyk, Gustavo H Goldman, …, Jacob L Steenwyk, Gustavo H Goldman, Antonis Rokas
- None, 10.1101/2023.01.17.524442
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions
- Abin Abraham, Abigail L LaBella, Mary Lauren Benton, …, Mary Lauren Benton, Antonis Rokas, John A Capra
- Bioinformatics, 10.1093/bioinformatics/btad037
How has horizontal gene transfer shaped the evolution of insect genomes?
- Liu Chao, Yang Li, Yun Chen, …, Jianhua Huang, Antonis Rokas, Xing-Xing Shen
- Environ Microbiol, 10.1111/1462-2920.16311
Mosaic patterns of selection in genomic regions associated with diverse human traits
- Abin Abraham, Abigail L LaBella, John A Capra, …, Abigail L LaBella, John A Capra, Antonis Rokas
- PLoS Genet, 10.1371/journal.pgen.1010494
Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum
- Yuanning Li, Hongyue Liu, Jacob L Steenwyk, …, Tao Zhao, Chris Todd Hittinger, Antonis Rokas
- Curr Biol, 10.1016/j.cub.2022.10.025
Genomic and Phenotypic Trait Variation of the Opportunistic Human Pathogen Aspergillus flavus and Its Close Relatives
- E Anne Hatmaker, Manuel Rangel-Grimaldo, Huzefa A Raja, …, Gustavo H Goldman, Nicholas H Oberlies, Antonis Rokas
- Microbiol Spectr, 10.1128/spectrum.03069-22
Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi
- Miya Hugaboom, E Anne Hatmaker, Abigail L LaBella, …, Elizabeth Anne Hatmaker, Abigail L LaBella, Antonis Rokas
- G3 (Bethesda), 10.1093/g3journal/jkac285
Draft Genome Sequence of an Aspergillus Strain Isolated from a Honey Bee Pupa
- E Anne Hatmaker, Delaney L Miller, Irene Newton, …, Delaney L Miller, Irene Newton, Antonis Rokas
- None, 10.1128/mra.00798-22
Aspergillus fumigatus FhdA Transcription Factor Is Important for Mitochondrial Activity and Codon Usage Regulation during the Caspofungin Paradoxical Effect
- Ana Cristina Colabardini, Norman Van Rhijn, Abigail L LaBella, …, Lauren Dineen, Antonis Rokas, Gustavo H Goldman
- Antimicrob Agents Chemother, 10.1128/aac.00701-22
HGT is widespread in insects and contributes to male courtship in lepidopterans
- Yang Li, Zhiguo Liu, Chao Liu, …, Antonis Rokas, Jianhua Huang, Xing-Xing Shen
- Cell, 10.1016/j.cell.2022.06.014
Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus
- Maria Augusta C Horta, Jacob L Steenwyk, Matthew E Mead, …, Toni Gabaldón, Antonis Rokas, Gustavo H Goldman
- mBio, 10.1128/mbio.01519-22
Microbiome-associated human genetic variants impact phenome-wide disease risk
- Robert H George Markowitz, Abigail Leavitt LaBella, Mingjian Shi, …, Jane F Ferguson, Jonathan D Mosley, Seth R Bordenstein
- Proc Natl Acad Sci U S A, 10.1073/pnas.2200551119
Evolution of the human pathogenic lifestyle in fungi
- Antonis Rokas
- Nat Microbiol, 10.1038/s41564-022-01112-0
An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function
- Jacob L Steenwyk, Megan A Phillips, Feng Yang, …, Judith Berman, Chris Todd Hittinger, Antonis Rokas
- Sci Adv, 10.1126/sciadv.abn0105
Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases
- Noah P Bradley, Katherine L Wahl, Jacob L Steenwyk, Antonis Rokas, Brandt F Eichman
- mBio, 10.1128/mbio.03297-21
Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin
- Ana Cristina Colabardini, Fang Wang, Zhiqiang Dong, …, Iran Malavazi, Koon Ho Wong, Gustavo Henrique Goldman
- Genetics, 10.1093/genetics/iyab183
orthofisher: a broadly applicable tool for automated gene identification and retrieval
- Jacob L Steenwyk, Antonis Rokas
- G3 (Bethesda), 10.1093/g3journal/jkab250
Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus
- Jacob L Steenwyk, Matthew E Mead, Patrícia Alves de Castro, …, Philipp Koehler, Gustavo H Goldman, Antonis Rokas
- Microbiol Spectr, 10.1128/spectrum.00010-21
The influence of evolutionary history on human health and disease
- Mary Lauren Benton, Abin Abraham, Abigail L LaBella, …, Patrick Abbot, Antonis Rokas, John A Capra
- Nat Rev Genet, 10.1038/s41576-020-00305-9
Developing a theoretical evolutionary framework to solve the mystery of parturition initiation
- Antonis Rokas, Sam Mesiano, Ortal Tamam, Abigail LaBella, Ge Zhang, Louis Muglia
- Elife, 10.7554/elife.58343
Revised Transcriptome-Based Gene Annotation for Aspergillus flavus Strain NRRL 3357
- E Anne Hatmaker, Xiaofan Zhou, Matthew E Mead, Heungyun Moon, Jae-Hyuk Yu, Antonis Rokas
- None, 10.1128/mra.01155-20
Draft Genome Sequences of Four Aspergillus Section Fumigati Clinical Strains
- Renato Augusto Corrêa Dos Santos, Olga Rivero-Menendez, Jacob L Steenwyk, …, Gustavo Henrique Goldman, Ana Alastruey-Izquierdo, Antonis Rokas
- None, 10.1128/mra.00856-20
Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species
- Jacob L Steenwyk, Matthew E Mead, Sonja L Knowles, …, Gustavo H Goldman, Nicholas H Oberlies, Antonis Rokas
- Genetics, 10.1534/genetics.120.303549
Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci
- Abigail L LaBella, Abin Abraham, Yakov Pichkar, …, Patrick Abbot, Antonis Rokas, John A Capra
- Nat Commun, 10.1038/s41467-020-17258-6
The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence
- Laure N A Ries, Lakhansing Pardeshi, Zhiqiang Dong, …, Flavio V Loures, Koon H Wong, Gustavo H Goldman
- PLoS Pathog, 10.1371/journal.ppat.1008645
Diversity of Secondary Metabolism in Aspergillus nidulans Clinical Isolates
- M T Drott, R W Bastos, A Rokas, …, G H Goldman, N P Keller, C Greco
- mSphere, 10.1128/msphere.00156-20
Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity
- Antonis Rokas, Matthew E Mead, Jacob L Steenwyk, Nicholas H Oberlies, Gustavo H Goldman
- PLoS Pathog, 10.1371/journal.ppat.1008315
Wheldone: Characterization of a Unique Scaffold from the Coculture of Aspergillus fischeri and Xylaria flabelliformis
- Sonja L Knowles, Huzefa A Raja, Israa H Isawi, …, Joanna E Burdette, Antonis Rokas, Nicholas H Oberlies
- Org Lett, 10.1021/acs.orglett.0c00219
Gliotoxin, a Known Virulence Factor in the Major Human Pathogen Aspergillus fumigatus, Is Also Biosynthesized by Its Nonpathogenic Relative Aspergillus fischeri
- Sonja L Knowles, Matthew E Mead, Lilian Pereira Silva, …, Gustavo H Goldman, Nicholas H Oberlies, Antonis Rokas
- mBio, 10.1128/mbio.03361-19
Into the wild: new yeast genomes from natural environments and new tools for their analysis
- D Libkind, D Peris, F A Cubillos, …, Q K Langdon, A Rokas, C T Hittinger
- FEMS Yeast Res, 10.1093/femsyr/foaa008
Biosynthetic gene clusters and the evolution of fungal chemodiversity
- Antonis Rokas, Matthew E Mead, Jacob L Steenwyk, Huzefa A Raja, Nicholas H Oberlies
- Nat Prod Rep, 10.1039/c9np00045c
Orthogonal Method for Double-Bond Placement via Ozone-Induced Dissociation Mass Spectrometry (OzID-MS)
- Sonja L Knowles, Ngoc Vu, Daniel A Todd, …, Antonis Rokas, Qibin Zhang, Nicholas H Oberlies
- J Nat Prod, 10.1021/acs.jnatprod.9b00787
Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese
- Ina Bodinaku, Jason Shaffer, Allison B Connors, …, Antonis Rokas, Albert Robbat, Benjamin E Wolfe
- mBio, 10.1128/mbio.02445-19
Draft Genome Sequence of the Griseofulvin-Producing Fungus Xylaria flabelliformis Strain G536
- Matthew E Mead, Huzefa A Raja, Jacob L Steenwyk, Sonja L Knowles, Nicholas H Oberlies, Antonis Rokas
- None, 10.1128/mra.00890-19
Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence
- Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz Von Looz, Antonis Rokas
- Syst Biol, 10.1093/sysbio/syz058
Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity
- David A Baltrus, Christina A Cuomo, John J Dennehy, …, Antonis Rokas, Simon Roux, Jason E Stajich
- None, 10.1128/mra.00954-19
Treehouse: a user-friendly application to obtain subtrees from large phylogenies
- Jacob L Steenwyk, Antonis Rokas
- BMC Res Notes, 10.1186/s13104-019-4577-5
Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation
- Jiyun M Moon, John A Capra, Patrick Abbot, Antonis Rokas
- Bioessays, 10.1002/bies.201900072
Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata
- Mingshuang Wang, Huilan Fu, Xing-Xing Shen, Ruoxin Ruan, Antonis Rokas, Hongye Li
- Mol Plant Pathol, 10.1111/mpp.12848