Antonis Rokas

Also affiliated with Evolutionary Genomics (United States), Vanderbilt Health

Biochemistry, Genetics and Molecular BiologyAgricultural and Biological SciencesMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 2%percentile

4.2Author DataRank

Indexed papers

10in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 10 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Microbiology Spectrum(2024)10.1128/spectrum.03980-23

Top 25%

0.799DataRank

Top 25%35 citations

Charu Balamurugan, Huzefa A. Raja, Carla Gonçalves, N. Li, Frank N. Martin +9 more

Papers

Driven by 117 papers — median percentile 47. Top paper: “ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference”.

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

PLoS Biology(2020)10.1371/journal.pbio.3001007

N/A

4.6DataRank · unranked

765 citations

Thomas J. Buida, Yuanning Li, Xing‐Xing Shen, Antonis Rokas, Jacob L. Steenwyk

Rooting the Animal Tree of Life

Molecular Biology and Evolution(2021)10.1093/molbev/msab170

N/A

3.9DataRank · unranked

160 citations

Xing‐Xing Shen, Benjamin Evans, Casey W. Dunn, Antonis Rokas, Yuanning Li

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

Studies in Mycology(2023)10.3114/sim.2023.105.01

N/A

1.6DataRank · unranked

120 citations

Chris Todd Hittinger, Konstanze Bensch, Dana A. Opulente, Xing‐Xing Shen, Yàn Li +23 more

Diversity of Secondary Metabolism in Aspergillus nidulans Clinical Isolates

mSphere(2020)10.1128/msphere.00156-20

N/A

1.4DataRank · unranked

63 citations

Rafael Wesley Bastos, Antonis Rokas, Laure Nicolas Annick Ries, Toni Gabaldón, Gustavo H. Goldman +3 more

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

PLoS Biology(2022)10.1371/journal.pbio.3001827

N/A

1.1DataRank · unranked

36 citations

Dayna Goltz, Thomas J. Buida, Yuanning Li, Xing‐Xing Shen, Antonis Rokas +1 more

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Microbiology Spectrum(2024)10.1128/spectrum.03980-23

Top 25%

0.799DataRank

Top 25%35 citations

Charu Balamurugan, Huzefa A. Raja, Carla Gonçalves, N. Li, Frank N. Martin +9 more

orthofisher: a broadly applicable tool for automated gene identification and retrieval

G3 Genes Genomes Genetics(2021)10.1093/g3journal/jkab250

N/A

0.717DataRank · unranked

52 citations

Antonis Rokas, Jacob L. Steenwyk

A global phylogenomic analysis of the shiitake genus Lentinula

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2214076120

Top 28%

0.704DataRank

Top 28%27 citations

Byoungnam Min, Miguel A. Naranjo-Ortíz, Brian P. Looney, Zachary Konkel, Jason C. Slot +34 more

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

G3 Genes Genomes Genetics(2022)10.1093/g3journal/jkac285

N/A

0.701DataRank · unranked

19 citations

E. Anne Hatmaker, Abigail L. LaBella, Antonis Rokas, Miya B. Hugaboom

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.19.545611

Top 30%

0.672DataRank

Top 30%25 citations

Abigail L. LaBella, Marie‐Claire Harrison, John F. Wolters, Chao Liu, Yonglin Li +27 more

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

Nature Communications(2020)10.1038/s41467-020-17258-6

N/A

0.500DataRank · unranked

16 citations

Abin Abraham, Yakov Pichkar, Sarah Fong, Ge Zhang, Louis J. Muglia +4 more

Mitochondrial genome diversity across the subphylum Saccharomycotina

Frontiers in Microbiology(2023)10.3389/fmicb.2023.1268944

N/A

0.495DataRank · unranked

15 citations

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

Diverse signatures of convergent evolution in cactus-associated yeasts

PLoS Biology(2024)10.1371/journal.pbio.3002832

Top 42%

0.446DataRank

Top 42%15 citations

Marie‐Claire Harrison, Jacob L. Steenwyk, Dana A. Opulente, Abigail L. LaBella, John F. Wolters +6 more

Evolutionary origin and population diversity of a cryptic hybrid pathogen

Nature Communications(2024)10.1038/s41467-024-52639-1

N/A

0.353DataRank · unranked

8 citations

S E Knowles, Rafael Wesley Bastos, Charu Balamurugan, David C. Rinker, Matthew E. Mead +24 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.09.451830

Top 51%

0.342DataRank

Top 51%4 citations

Megan Phillips, Feng Yang, Swapneeta S. Date, Todd R. Graham, Judith Berman +3 more

Genomic factors shaping codon usage across the Saccharomycotina subphylum

G3 Genes Genomes Genetics(2024)10.1093/g3journal/jkae207

N/A

0.322DataRank · unranked

6 citations

Lauren Dineen, Kaitlin J. Fisher, Dana A. Opulente, Marie‐Claire Harrison, John F. Wolters +7 more

Draft Genome Sequences of Four Aspergillus Section Fumigati Clinical Strains

Microbiology Resource Announcements(2020)10.1128/mra.00856-20

Top 56%

0.294DataRank

Top 56%5 citations

Olga Rivero-Menéndez, Jacob L. Steenwyk, Matthew E. Mead, Gustavo H. Goldman, Ana Alastruey‐Izquierdo +2 more

Machine learning illuminates how diet influences the evolution of yeast galactose metabolism

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.20.549758

Top 58%

0.273DataRank

Top 58%5 citations

Emily J. Ubbelohde, Abigail L. LaBella, Dana A. Opulente, John F. Wolters, Xiaofan Zhou +5 more

Diverse signatures of convergent evolution in cacti-associated yeasts

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.14.557833

Top 58%

0.269DataRank

Top 58%5 citations

Marie‐Claire Harrison, Jacob L. Steenwyk, Dana A. Opulente, Abigail L. LaBella, John F. Wolters +6 more

Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research

Scientific Data(2018)10.1038/s41597-018-0004-3

Top 59%

0.261DataRank

Top 59%2 citations

Cristel G. Thomas, Rebecca Liu, Maya Zuhl, Payal Banerjee, Ronald J. Wong +25 more

Tracing the Origin and Evolution of the Fungal Mycophenolic Acid Biosynthesis Pathway

Genome Biology and Evolution(2025)10.1093/gbe/evaf039

N/A

0.208DataRank · unranked

3 citations

Hajar Yaakoub, Arnaud Lanoue, Antoine Géry, Virginie Séguin, Florent Magot +13 more

Draft genomes of Aspergillus nomiae and Aspergillus tamarii isolates from human eye infections

Microbiology Resource Announcements(2023)10.1128/mra.00391-23

Top 70%

0.165DataRank

Top 70%2 citations

Jonathan E. Schmitz, Antonis Rokas, E. Anne Hatmaker

Gestation length both shapes and is shaped by other life history traits in terrestrial eutherian mammals

Evolution Letters(2025)10.1093/evlett/qraf028

N/A

0.104DataRank · unranked

1 citations

Dana Lin, Daniel S. Caetano, Gregory F. Funston, Antonis Rokas, Thodoris Danis

Regulation of gliotoxin biosynthesis and protection in Aspergillus species

PLoS Genetics(2022)10.1371/journal.pgen.1009965

N/A

0DataRank · unranked

37 citations

Ana Cristina Colabardini, Maísa Moraes, Maria Augusta Crivelente Horta, Sonja L. Knowles, Huzefa A. Raja +12 more

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

Science Advances(2022)10.1126/sciadv.abn0105

N/A

0DataRank · unranked

30 citations

Megan Phillips, Feng Yang, Swapneeta S. Date, Todd R. Graham, Judith Berman +3 more

Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum

Current Biology(2022)10.1016/j.cub.2022.10.025

N/A

0DataRank · unranked

30 citations

Hongyue Liu, Jacob L. Steenwyk, Abigail L. LaBella, Marie‐Claire Harrison, Marizeth Groenewald +6 more

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

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2200551119

N/A

0DataRank · unranked

22 citations

Abigail L. LaBella, Mingjian Shi, Antonis Rokas, John A. Capra, Jane F. Ferguson +3 more

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

Environmental Microbiology(2022)10.1111/1462-2920.16311

N/A

0DataRank · unranked

10 citations

Yang Li, Yun Chen, Xue‐Xin Chen, Jianhua Huang, Antonis Rokas +2 more

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

mBio(2022)10.1128/mbio.03297-21

N/A

0DataRank · unranked

11 citations

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

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

PLoS Genetics(2022)10.1371/journal.pgen.1010494

N/A

0DataRank · unranked

10 citations

Abigail L. LaBella, John A. Capra, Antonis Rokas, Abin Abraham

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.22.517304

N/A

0DataRank · unranked

4 citations

Charu Balamurugan, Huzefa A. Raja, Carla Gonçalves, N. Li, Frank N. Martin +8 more

Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.23.485522

N/A

0DataRank · unranked

1 citations

Jacob L. Steenwyk, Matthew E. Mead, Luciano H. B. dos Santos, Shu Zhao, John G. Gibbons +5 more

Codon optimization, not gene content, predicts XYL ose metabolism in budding yeasts

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.10.495693

N/A

0DataRank · unranked

1 citations

Kaitlin J. Fisher, Abigail L. LaBella, Taylor A. Meyer, Dana A. Opulente, John F. Wolters +3 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.23.505037

N/A

0DataRank · unranked

1 citations

E. Anne Hatmaker, Abigail L. LaBella, Antonis Rokas, Miya B. Hugaboom

Lack of universal mutational biases in a fungal phylum

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.29.486229

N/A

0DataRank · unranked

0 citations

Jacob L. Steenwyk, Antonis Rokas, Qianhui Zheng

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

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.08.491080

N/A

0DataRank · unranked

0 citations

Abigail L. LaBella, John A. Capra, Antonis Rokas, Abin Abraham

Aspergillus fumigatus FhdA transcription factor is important for mitochondrial activity and codon usage regulation during the caspofungin paradoxical effect

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.21.492902

N/A

0DataRank · unranked

0 citations

Norman van Rhijn, Abigail L. LaBella, Clara Valero, Fang Wang, Lauren Dineen +4 more

Genomic and phenotypic trait variation of the opportunistic human pathogen Aspergillus flavus and its non-pathogenic close relatives

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.12.499845

N/A

0DataRank · unranked

0 citations

Manuel Rangel‐Grimaldo, Huzefa A. Raja, Hadi Pourhadi, Sonja L. Knowles, Kevin K. Fuller +7 more

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

Nature Genetics(2023)10.1038/s41588-023-01343-9

N/A

0DataRank · unranked

100 citations

Christopher Flatley, Valgerður Steinthórsdóttir, Marc Vaudel, Julius Juodakis, Jing Chen +80 more

Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts

Molecular Biology and Evolution(2023)10.1093/molbev/msad111

N/A

0DataRank · unranked

35 citations

Kaitlin J. Fisher, Abigail L. LaBella, Taylor A. Meyer, Dana A. Opulente, John F. Wolters +3 more

The cell morphological diversity of Saccharomycotina yeasts

FEMS Yeast Research(2023)10.1093/femsyr/foad055

N/A

0DataRank · unranked

27 citations

Marizeth Groenewald, Amanda Beth Hulfachor, Gideon Kpurubu, Rene Huerta, Chris Todd Hittinger +2 more

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

PLoS Pathogens(2023)10.1371/journal.ppat.1011704

N/A

0DataRank · unranked

14 citations

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

The dawn of relaxed phylogenetics

(2023)10.1371/journal.pbio.3001998

N/A

0DataRank · unranked

6 citations

Antonis Rokas, Jacob L. Steenwyk

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

Microbiology Spectrum(2023)10.1128/spectrum.05128-22

N/A

0DataRank · unranked

6 citations

Patrícia Alves de Castro, Jacob L. Steenwyk, Jean‐Pierre Gangneux, Martin Hoenigl, Juergen Prattes +13 more

A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae

Genetics(2023)10.1093/genetics/iyad076

N/A

0DataRank · unranked

3 citations

Tristen H. Gittens, David I. Gonzalez, E. Anne Hatmaker, Simcha Plotkin, Mason Engle +8 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.03.547508

N/A

0DataRank · unranked

11 citations

S E Knowles, Rafael Wesley Bastos, Charu Balamurugan, David C. Rinker, Matthew E. Mead +16 more

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

Bioinformatics(2023)10.1093/bioinformatics/btad037

N/A

0DataRank · unranked

8 citations

Abigail L. LaBella, Mary Lauren Benton, Antonis Rokas, John A. Capra, Abin Abraham

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.12.557468

N/A

0DataRank · unranked

4 citations

Allison S. Walker, Antonis Rokas, Olivia L. Riedling

Saccharomycotina yeasts defy longstanding macroecological patterns

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.29.555417

N/A

0DataRank · unranked

2 citations

Marie‐Claire Harrison, Dana A. Opulente, Abigail L. LaBella, John F. Wolters, Xiaofan Zhou +6 more

The evolution of gestation length in eutherian mammals

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.22.563491

N/A

0DataRank · unranked

2 citations

Antonis Rokas, Thodoris Danis

The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.17.524442

N/A

0DataRank · unranked

1 citations

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

Mitochondrial Genome Diversity across the Subphylum Saccharomycotina

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.28.551029

N/A

0DataRank · unranked

1 citations

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

Functional and evolutionary integration of a fungal gene with a bacterial operon

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.21.568075

N/A

0DataRank · unranked

1 citations

Kyle T. David, John F. Wolters, Steven D. Karlen, Carla Gonçalves, Dana A. Opulente +7 more

A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.20.533556

N/A

0DataRank · unranked

0 citations

Tristen H. Gittens, David I. Gonzalez, E. Anne Hatmaker, Simcha Plotkin, Mason Engle +8 more

A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.22.553365

N/A

0DataRank · unranked

0 citations

Camila Figueiredo Pinzan, Patrícia Alves de Castro, Norman van Rhijn, Kayleigh Earle, Hong Liu +22 more

A phylogenetic approach to explore the Aspergillus fumigatus conidial surface-associated proteome and its role in pathogenesis

Research Square(2023)10.21203/rs.3.rs-3306535/v1

N/A

0DataRank · unranked

0 citations

Clara Valero, Camila Figueiredo Pinzan, Patrícia de Castro, Norman van Rhijn, Kayleigh Earle +21 more

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

Microbiology Spectrum(2024)10.1128/spectrum.03400-23

N/A

0DataRank · unranked

37 citations

Allison S. Walker, Antonis Rokas, Olivia L. Riedling

A taxon-rich and genome-scale phylogeny of Opisthokonta

PLoS Biology(2024)10.1371/journal.pbio.3002794

N/A

0DataRank · unranked

29 citations

Jacob L. Steenwyk, Xiaofan Zhou, Darrin T. Schultz, Kevin M. Kocot, Xing‐Xing Shen +3 more

Machine learning enables identification of an alternative yeast galactose utilization pathway

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2315314121

N/A

0DataRank · unranked

28 citations

Emily J. Ubbelohde, Abigail L. LaBella, Dana A. Opulente, John F. Wolters, Xiaofan Zhou +5 more

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

Nature Microbiology(2024)10.1038/s41564-024-01782-y

N/A

0DataRank · unranked

24 citations

Clara Valero, Patrícia Alves de Castro, Jefferson Luiz da Silva, Kayleigh Earle, Hong Liu +28 more

The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics

Systematic Biology(2024)10.1093/sysbio/syae031

N/A

0DataRank · unranked

15 citations

Xiaofan Zhou, Yuanning Li, Chris Todd Hittinger, Ronghui Pan, Jinyan Huang +5 more

Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework

Yeast(2024)10.1002/yea.3981

N/A

0DataRank · unranked

14 citations

Dana A. Opulente, John F. Wolters, Xing‐Xing Shen, Xiaofan Zhou, Marizeth Groenewald +4 more

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

Communications Biology(2024)10.1038/s42003-024-06756-8

N/A

0DataRank · unranked

10 citations

Thomas J. C. Sauters, Karin Steffen, Adiyantara Gumilang, Huzefa A. Raja, Manuel Rangel‐Grimaldo +9 more

Saccharomycotina yeasts defy long-standing macroecological patterns

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2316031121

N/A

0DataRank · unranked

13 citations

Marie‐Claire Harrison, Dana A. Opulente, Abigail L. LaBella, John F. Wolters, Xiaofan Zhou +6 more

PhyKIT: A Multitool for Phylogenomics

Current Protocols(2024)10.1002/cpz1.70016

N/A

0DataRank · unranked

12 citations

Gemma I. Martínez‐Redondo, Thomas J. Buida, Emile Gluck‐Thaler, Xing‐Xing Shen, Toni Gabaldón +3 more

Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication

iScience(2024)10.1016/j.isci.2024.108987

N/A

0DataRank · unranked

9 citations

Francisca Paraíso, Yu‐Ching Liu, Savitree Limtong, Sasitorn Jindamorakot, Lene Jespersen +8 more

Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters

Molecular Biology and Evolution(2024)10.1093/molbev/msae228

N/A

0DataRank · unranked

8 citations

Xiaofan Zhou, Antonis Rokas, Chris Todd Hittinger, Johnathan G. Crandall

Convergent reductive evolution in bee-associated lactic acid bacteria

Applied and Environmental Microbiology(2024)10.1128/aem.01257-24

N/A

0DataRank · unranked

7 citations

Marie‐Claire Harrison, Antonis Rokas, Carla Gonçalves, Ana Pontes

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

G3 Genes Genomes Genetics(2024)10.1093/g3journal/jkae091

N/A

0DataRank · unranked

4 citations

Jacob L. Steenwyk, Antonis Rokas, Alec Brown

Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon

Molecular Biology and Evolution(2024)10.1093/molbev/msae045

N/A

0DataRank · unranked

5 citations

Kyle T. David, John F. Wolters, Steven D. Karlen, Carla Gonçalves, Dana A. Opulente +7 more

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

Fungal Genetics and Biology(2024)10.1016/j.fgb.2023.103862

N/A

0DataRank · unranked

4 citations

Megan N. Biango‐Daniels, Jacob L. Steenwyk, Antonis Rokas, Nicolas L. Louw, Robert Nardella +2 more

The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi

G3 Genes Genomes Genetics(2024)10.1093/g3journal/jkae063

N/A

0DataRank · unranked

2 citations

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

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

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.05.597512

N/A

0DataRank · unranked

7 citations

Yonglin Li, Yonglin Li, Hongyue Liu, Jacob L. Steenwyk, Kyle T. David +17 more

Global patterns of species diversity and distribution in the biomedically and biotechnologically important fungal genus Aspergillus

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.29.626055

N/A

0DataRank · unranked

4 citations

Kyle T. David, Antonis Rokas, Olivia L. Riedling

Pathogenicity is associated with population structure in a fungal pathogen of humans

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.05.602241

N/A

0DataRank · unranked

3 citations

Amelia E. Barber, Milton T. Drott, Thomas J. C. Sauters, Ana Alastruey‐Izquierdo, Dea Garcia‐Hermoso +3 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.08.583994

N/A

0DataRank · unranked

1 citations

Thomas J. C. Sauters, Karin Steffen, Adiyantara Gumilang, Huzefa A. Raja, Manuel Rangel‐Grimaldo +9 more

Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.22.604484

N/A

0DataRank · unranked

1 citations

Joshua G. Schraiber, Johnathan G. Crandall, Abigail L. LaBella, Dana A. Opulente, Marie‐Claire Harrison +8 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.08.574724

N/A

0DataRank · unranked

0 citations

Jacob L. Steenwyk, Antonis Rokas, Alec Brown

Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework

KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences)(2024)10.22541/au.172114831.13001516/v1

N/A

0DataRank · unranked

0 citations

Dana A. Opulente, John F. Wolters, Xing‐Xing Shen, Xiaofan Zhou, Marizeth Goenewald +4 more

Specialization restricts the evolutionary paths available to yeast sugar transporters

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.22.604696

N/A

0DataRank · unranked

0 citations

Xiaofan Zhou, Antonis Rokas, Chris Todd Hittinger, Johnathan G. Crandall

Patterns and mechanisms of fungal genome plasticity

Current Biology(2025)10.1016/j.cub.2025.04.003

N/A

0DataRank · unranked

21 citations

Antonis Rokas, Thomas J. C. Sauters

Population structure in a fungal human pathogen is potentially linked to pathogenicity

Nature Communications(2025)10.1038/s41467-025-62777-9

N/A

0DataRank · unranked

9 citations

Amelia E. Barber, Milton T. Drott, Thomas J. C. Sauters, Adiyantara Gumilang, Ana Alastruey‐Izquierdo +7 more

Machine learning reveals genes impacting oxidative stress resistance across yeasts

Nature Communications(2025)10.1038/s41467-025-60189-3

N/A

0DataRank · unranked

7 citations

Linda C. Horianopoulos, Logan Elkin, Kenia Segura Abá, Drew Jordahl, Katherine A. Overmyer +6 more

Running a genetic stop sign accelerates oxygen metabolism and energy production in horses

Science(2025)10.1126/science.adr8589

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0DataRank · unranked

5 citations

Xin Chen, Zhenhua Xu, Nadir H Dbouk, A. A. Bose, David Carmona-Berrio +14 more

Global patterns of diversity and distribution in Aspergillus fungi are driven by human and environmental influences

Current Biology(2025)10.1016/j.cub.2025.07.081

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0DataRank · unranked

5 citations

Kyle T. David, Antonis Rokas, Olivia L. Riedling

Stable Hypermutators Revealed by the Genomic Landscape of Genes Involved in Genome Stability Among Yeast Species

Molecular Biology and Evolution(2025)10.1093/molbev/msaf285

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0DataRank · unranked

3 citations

Jacob L. Steenwyk, David C. Rinker, Dana A. Opulente, Abigail L. LaBella, Marie‐Claire Harrison +8 more

Use their names: there are no basal, lower, or early diverging fungi

Mycologia(2025)10.1080/00275514.2025.2460003

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0DataRank · unranked

5 citations

Antonis Rokas, Timothy Y. James

Aspergillus fumigatus mitogenomes and their influence on azole-resistant and -susceptible populations

npj Antimicrobials and Resistance(2025)10.1038/s44259-025-00083-6

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0DataRank · unranked

5 citations

Laís Pontes, Johanna Rhodes, Jacob L. Steenwyk, Ling Lü, Thaila Fernanda dos Reis +3 more

Machine-Readable Structural Information Is Essential for Natural Products Research

Journal of Natural Products(2025)10.1021/acs.jnatprod.5c00836

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0DataRank · unranked

2 citations

Nicholas H. Oberlies, Antonis Rokas, Karin Steffen

Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies

Integrative and Comparative Biology(2025)10.1093/icb/icaf037

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0DataRank · unranked

1 citations

Chris Todd Hittinger, Hongmei Li‐Byarlay, Antonis Rokas, Timothy B. Sackton, Robert L. Unckless +1 more

Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.09.653161

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0DataRank · unranked

4 citations

David C. Rinker, Abigail L. LaBella, Dana A. Opulente, John F. Wolters, Xiaofan Zhou +5 more

Ancient co-option of LTR retrotransposons as yeast centromeres

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.25.647736

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0DataRank · unranked

3 citations

Luciana Lazar‐Stefanita, Lyam Baudry, Aleksandra Wudzinska, Xiaofan Zhou, Antonis Rokas +4 more

Discovery of additional ancient genome duplications in yeasts

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.31.673279

N/A

0DataRank · unranked

2 citations

Linda C. Horianopoulos, Carla Gonçalves, Jacob L. Steenwyk, Ana Pontes, Paula Gonçalves +4 more

Genomic factors limiting the diversity of Saccharomycotina plant pathogens

G3 Genes Genomes Genetics(2025)10.1093/g3journal/jkaf184

N/A

0DataRank · unranked

0 citations

Caroline West, Dana A. Opulente, Marie‐Claire Harrison, John F. Wolters, Xing‐Xing Shen +6 more

The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.26.690719

N/A

0DataRank · unranked

0 citations

Marie‐Claire Harrison, Thodoris Danis, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas +1 more

Toward a Fully Resolved Fungal Tree of Life

Annual Review of Microbiology(2020)10.1146/annurev-micro-022020-051835

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0DataRank · unranked

261 citations

Jason Stajich, Chris Todd Hittinger, Antonis Rokas, Timothy Y. James

Gliotoxin, a Known Virulence Factor in the Major Human Pathogen Aspergillus fumigatus, Is Also Biosynthesized by Its Nonpathogenic Relative Aspergillus fischeri

mBio(2020)10.1128/mbio.03361-19

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0DataRank · unranked

52 citations

Matthew E. Mead, Lilian Pereira Silva, Huzefa A. Raja, Jacob L. Steenwyk, Gustavo H. Goldman +3 more

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

eLife(2020)10.7554/elife.58343

N/A

0DataRank · unranked

34 citations

Sam Mesiano, Ortal Tamam, Abigail L. LaBella, Ge Zhang, Louis J. Muglia +1 more

Repeated horizontal gene transfer of GAL actose metabolism genes violates Dollo’s law of irreversible loss

Genetics(2020)10.1093/genetics/iyaa012

N/A

0DataRank · unranked

29 citations

Jacek Kominek, Dana A. Opulente, Xing‐Xing Shen, Abigail L. LaBella, Xiaofan Zhou +6 more

Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements

Microbiology Resource Announcements(2020)10.1128/mra.00763-20

N/A

0DataRank · unranked

3 citations

David A. Baltrus, Vincent M. Bruno, John J. Dennehy, Steven R. Gill, Julia A. Maresca +11 more

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

medRxiv(2020)10.1101/2020.07.15.20154864

N/A

0DataRank · unranked

11 citations

Brian L. Le, Idit Kosti, Péter Straub, Digna R. Velez-Edwards, Lea K. Davis +7 more

Rooting the animal tree of life

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.27.357798

N/A

0DataRank · unranked

6 citations

Xing‐Xing Shen, Benjamin Evans, Casey W. Dunn, Antonis Rokas, Yuanning Li

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.06.371971

N/A

0DataRank · unranked

4 citations

Matthew E. Mead, Patrícia Alves de Castro, Clara Valero, André Damásio, Renato Santos +12 more

Repeated horizontal gene transfer of GAL actose metabolism genes violates Dollo’s law of irreversible loss

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.22.216101

N/A

0DataRank · unranked

2 citations

Jacek Kominek, Dana A. Opulente, Xing‐Xing Shen, Abigail L. LaBella, Xiaofan Zhou +6 more

Biosynthetic gene clusters, secondary metabolite profiles, and cards of virulence in the closest nonpathogenic relatives of Aspergillus fumigatus

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.09.033902

N/A

0DataRank · unranked

1 citations

Matthew E. Mead, Sonja L. Knowles, Huzefa A. Raja, Christopher D. Roberts, Oliver Bader +5 more

The influence of evolutionary history on human health and disease

Nature Reviews Genetics(2021)10.1038/s41576-020-00305-9

N/A

0DataRank · unranked

305 citations

Abin Abraham, Abigail L. LaBella, Patrick Abbot, Antonis Rokas, John A. Capra +1 more

Aspergillus fumigatus Acetate Utilization Impacts Virulence Traits and Pathogenicity

mBio(2021)10.1128/mbio.01682-21

N/A

0DataRank · unranked

28 citations

Patrícia Alves de Castro, Lilian Pereira Silva, Clara Valero, Thaila Fernanda dos Reis, Raquel Saborano +15 more

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

Genetics(2021)10.1093/genetics/iyab183

N/A

0DataRank · unranked

25 citations

Fang Wang, Zhiqiang Dong, Lakhansing Pardeshi, Marina Campos Rocha, Jonas Henrique Costa +10 more

Examining Signatures of Natural Selection in Antifungal Resistance Genes Across Aspergillus Fungi

Frontiers in Fungal Biology(2021)10.3389/ffunb.2021.723051

N/A

0DataRank · unranked

8 citations

Matthew E. Mead, Jacob L. Steenwyk, Olga Rivero-Menéndez, Ana Alastruey‐Izquierdo, Gustavo H. Goldman +2 more

Regulation of gliotoxin biosynthesis and protection in Aspergillus species

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.16.456458

N/A

0DataRank · unranked

1 citations

Ana Cristina Colabardini, Maísa Moraes, Maria Augusta Crivelente Horta, Sonja L. Knowles, Huzefa A. Raja +12 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.30.466607

N/A

0DataRank · unranked

1 citations

Dayna Goltz, Thomas J. Buida, Yuanning Li, Xing‐Xing Shen, Antonis Rokas +1 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.01.433394

N/A

0DataRank · unranked

0 citations

Jacob L. Steenwyk, Lilian Pereira Silva, Patrícia Alves de Castro, Nauman Saeed, Falk Hillmann +3 more

Resistance-guided mining of bacterial genotoxins defines a family of DNA glycosylases

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.29.466481

N/A

0DataRank · unranked

0 citations

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

Extensive sequence divergence of non-coding regions between Aspergillus fumigatus , a major fungal pathogen of humans, and its relatives

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.26.465918

N/A

0DataRank · unranked

0 citations

Matthew E. Mead, Jacob L. Steenwyk, Gustavo H. Goldman, Antonis Rokas, Alec Brown

Evolution of the human pathogenic lifestyle in fungi

Nature Microbiology(2022)10.1038/s41564-022-01112-0

N/A

0DataRank · unranked

229 citations

Antonis Rokas

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

Genetics(2022)10.1093/genetics/iyac079

N/A

0DataRank · unranked

42 citations

Thomas J. Buida, Carla Gonçalves, Dayna Goltz, Grace Morales, Matthew E. Mead +7 more

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

BMC Medicine(2022)10.1186/s12916-022-02522-x

N/A

0DataRank · unranked

37 citations

Brian L. Le, Idit Kosti, Péter Straub, Digna Velez-Edwards, Lea K. Davis +7 more

Antonis Rokas

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