| Year |
Citation |
Score |
| 2024 |
Steenwyk JL, Balamurugan C, Raja HA, Gonçalves C, Li N, Martin F, Berman J, Oberlies NH, Gibbons JG, Goldman GH, Geiser DM, Houbraken J, Hibbett DS, Rokas A. Phylogenomics reveals extensive misidentification of fungal strains from the genus . Microbiology Spectrum. e0398023. PMID 38445873 DOI: 10.1128/spectrum.03980-23 |
0.362 |
|
| 2024 |
Jones RE, Tice AK, Eliáš M, Eme L, Kolísko M, Nenarokov S, Pánek T, Rokas A, Salomaki E, Strassert JFH, Shen XX, Žihala D, Brown MW. Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher. Current Protocols. 4: e969. PMID 38265166 DOI: 10.1002/cpz1.969 |
0.543 |
|
| 2024 |
Brown A, Steenwyk JL, Rokas A. Genome-wide patterns of non-coding sequence variation in the major fungal pathogen . Biorxiv : the Preprint Server For Biology. PMID 38260267 DOI: 10.1101/2024.01.08.574724 |
0.803 |
|
| 2024 |
Ye R, Biango-Daniels M, Steenwyk JL, Rokas A, Louw NL, Nardella R, Wolfe BE. Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genetics and Biology : Fg & B. 171: 103862. PMID 38218228 DOI: 10.1016/j.fgb.2023.103862 |
0.82 |
|
| 2024 |
Riedling O, Walker AS, Rokas A. Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning. Microbiology Spectrum. e0340023. PMID 38193680 DOI: 10.1128/spectrum.03400-23 |
0.537 |
|
| 2024 |
Chavez CM, Groenewald M, Hulfachor AB, Kpurubu G, Huerta R, Hittinger CT, Rokas A. The cell morphological diversity of Saccharomycotina yeasts. Fems Yeast Research. 24. PMID 38142225 DOI: 10.1093/femsyr/foad055 |
0.8 |
|
| 2023 |
Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial genome diversity across the subphylum Saccharomycotina. Frontiers in Microbiology. 14: 1268944. PMID 38075892 DOI: 10.3389/fmicb.2023.1268944 |
0.724 |
|
| 2023 |
Sun L, David KT, Wolters JF, Karlen SD, Gonçalves C, Opulente DA, LaBella AL, Groenewald M, Zhou X, Shen XX, Rokas A, Hittinger CT. Functional and evolutionary integration of a fungal gene with a bacterial operon. Biorxiv : the Preprint Server For Biology. PMID 38045280 DOI: 10.1101/2023.11.21.568075 |
0.827 |
|
| 2023 |
Danis T, Rokas A. The evolution of gestation length in eutherian mammals. Biorxiv : the Preprint Server For Biology. PMID 37961105 DOI: 10.1101/2023.10.22.563491 |
0.485 |
|
| 2023 |
Steenwyk JL, Rokas A, Goldman GH. Know the enemy and know yourself: Addressing cryptic fungal pathogens of humans and beyond. Plos Pathogens. 19: e1011704. PMID 37856485 DOI: 10.1371/journal.ppat.1011704 |
0.784 |
|
| 2023 |
Goldman G, Valero C, Pinzan C, de Castro P, van Rhijn N, Earle K, Liu H, Horta MA, Kniemeyer O, Kruger T, Pschibul A, Coemert D, Heinekamp T, Brakhage A, Steenwyk J, ... Rokas A, et al. A phylogenetic approach to explore the conidial surface-associated proteome and its role in pathogenesis. Research Square. PMID 37790311 DOI: 10.21203/rs.3.rs-3306535/v1 |
0.802 |
|
| 2023 |
Riedling O, Walker AS, Rokas A. Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning. Biorxiv : the Preprint Server For Biology. PMID 37745539 DOI: 10.1101/2023.09.12.557468 |
0.523 |
|
| 2023 |
Gonçalves C, Harrison MC, Steenwyk JL, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Diverse signatures of convergent evolution in cacti-associated yeasts. Biorxiv : the Preprint Server For Biology. PMID 37745407 DOI: 10.1101/2023.09.14.557833 |
0.836 |
|
| 2023 |
David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A. Saccharomycotina yeasts defy longstanding macroecological patterns. Biorxiv : the Preprint Server For Biology. PMID 37693602 DOI: 10.1101/2023.08.29.555417 |
0.799 |
|
| 2023 |
Valero C, Pinzan CF, de Castro PA, van Rhijn N, Earle K, Liu H, Horta MAC, Kniemeyer O, Krüger T, Pschibul A, Coemert DN, Heinekamp T, Brakhage AA, Steenwyk JL, Mead ME, ... Rokas A, et al. A phylogenetic approach to explore the conidial surface-associated proteome and its role in pathogenesis. Biorxiv : the Preprint Server For Biology. PMID 37662192 DOI: 10.1101/2023.08.22.553365 |
0.802 |
|
| 2023 |
Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial Genome Diversity across the Subphylum Saccharomycotina. Biorxiv : the Preprint Server For Biology. PMID 37577532 DOI: 10.1101/2023.07.28.551029 |
0.832 |
|
| 2023 |
Bradshaw MJ, Aime MC, Rokas A, Maust A, Moparthi S, Jellings K, Pane AM, Hendricks D, Pandey B, Li Y, Pfister DH. Extensive intragenomic variation in the internal transcribed spacer region of fungi. Iscience. 26: 107317. PMID 37529098 DOI: 10.1016/j.isci.2023.107317 |
0.78 |
|
| 2023 |
Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, Mead ME, Roberts CD, Raja HA, Li Y, Colabardini AC, de Castro PA, Dos Reis TF, Canóvas D, Sanchez RL, Lagrou K, ... ... Rokas A, et al. Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen. Biorxiv : the Preprint Server For Biology. PMID 37461539 DOI: 10.1101/2023.07.03.547508 |
0.835 |
|
| 2023 |
Hatmaker EA, Schmitz JE, Rokas A. Draft genomes of and isolates from human eye infections. Microbiology Resource Announcements. e0039123. PMID 37458446 DOI: 10.1128/MRA.00391-23 |
0.802 |
|
| 2023 |
Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, ... ... Rokas A, et al. Genomic and ecological factors shaping specialism and generalism across an entire subphylum. Biorxiv : the Preprint Server For Biology. PMID 37425695 DOI: 10.1101/2023.06.19.545611 |
0.824 |
|
| 2023 |
Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nature Reviews. Genetics. PMID 37369847 DOI: 10.1038/s41576-023-00620-x |
0.823 |
|
| 2023 |
Solé-Navais P, Flatley C, Steinthorsdottir V, Vaudel M, Juodakis J, Chen J, Laisk T, LaBella AL, Westergaard D, Bacelis J, Brumpton B, Skotte L, Borges MC, Helgeland Ø, Mahajan A, ... ... Rokas A, et al. Author Correction: Genetic effects on the timing of parturition and links to fetal birth weight. Nature Genetics. PMID 37165137 DOI: 10.1038/s41588-023-01412-z |
0.723 |
|
| 2023 |
Nalabothu RL, Fisher KJ, LaBella AL, Meyer TA, Opulente DA, Wolters JF, Rokas A, Hittinger CT. Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts. Molecular Biology and Evolution. PMID 37154525 DOI: 10.1093/molbev/msad111 |
0.837 |
|
| 2023 |
Ngo K, Gittens TH, Gonzalez DI, Hatmaker EA, Plotkin S, Engle M, Friedman GA, Goldin M, Hoerr RE, Eichman BF, Rokas A, Benton ML, Friedman KL. A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae. Genetics. PMID 37119805 DOI: 10.1093/genetics/iyad076 |
0.785 |
|
| 2023 |
Solé-Navais P, Flatley C, Steinthorsdottir V, Vaudel M, Juodakis J, Chen J, Laisk T, LaBella AL, Westergaard D, Bacelis J, Brumpton B, Skotte L, Borges MC, Helgeland Ø, Mahajan A, ... ... Rokas A, et al. Genetic effects on the timing of parturition and links to fetal birth weight. Nature Genetics. PMID 37012456 DOI: 10.1038/s41588-023-01343-9 |
0.756 |
|
| 2023 |
Ngo K, Gittens TH, Gonzalez DI, Hatmaker EA, Plotkin S, Engle M, Friedman GA, Goldin M, Hoerr RE, Eichman BF, Rokas A, Benton ML, Friedman KL. A comprehensive map of hotspots of de novo telomere addition in . Biorxiv : the Preprint Server For Biology. PMID 36993206 DOI: 10.1101/2023.03.20.533556 |
0.784 |
|
| 2023 |
Mead ME, de Castro PA, Steenwyk JL, Gangneux JP, Hoenigl M, Prattes J, Rautemaa-Richardson R, Guegan H, Moore CB, Lass-Flörl C, Reizine F, Valero C, Van Rhijn N, Bromley MJ, Rokas A, et al. COVID-19-Associated Pulmonary Aspergillosis Isolates Are Genomically Diverse but Similar to Each Other in Their Responses to Infection-Relevant Stresses. Microbiology Spectrum. e0512822. PMID 36946762 DOI: 10.1128/spectrum.05128-22 |
0.813 |
|
| 2023 |
Sierra-Patev S, Min B, Naranjo-Ortiz M, Looney B, Konkel Z, Slot JC, Sakamoto Y, Steenwyk JL, Rokas A, Carro J, Camarero S, Ferreira P, Molpeceres G, Ruiz-Dueñas FJ, Serrano A, et al. A global phylogenomic analysis of the shiitake genus . Proceedings of the National Academy of Sciences of the United States of America. 120: e2214076120. PMID 36848567 DOI: 10.1073/pnas.2214076120 |
0.828 |
|
| 2023 |
Balamurugan C, Steenwyk JL, Goldman GH, Rokas A. The evolution of the gliotoxin biosynthetic gene cluster in fungi. Biorxiv : the Preprint Server For Biology. PMID 36711793 DOI: 10.1101/2023.01.17.524442 |
0.848 |
|
| 2023 |
Steenwyk JL, Rokas A. The dawn of relaxed phylogenetics. Plos Biology. 21: e3001998. PMID 36696649 DOI: 10.1371/journal.pbio.3001998 |
0.799 |
|
| 2023 |
Abraham A, LaBella AL, Benton ML, Rokas A, Capra JA. GSEL: A fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic. Bioinformatics (Oxford, England). PMID 36655767 DOI: 10.1093/bioinformatics/btad037 |
0.788 |
|
| 2022 |
Brown A, Mead ME, Steenwyk JL, Goldman GH, Rokas A. Extensive non-coding sequence divergence between the major human pathogen and its relatives. Frontiers in Fungal Biology. 3. PMID 36866034 DOI: 10.3389/ffunb.2022.802494 |
0.816 |
|
| 2022 |
Liu C, Li Y, Chen Y, Chen XX, Huang J, Rokas A, Shen XX. How has horizontal gene transfer shaped the evolution of insect genomes? Environmental Microbiology. PMID 36511824 DOI: 10.1111/1462-2920.16311 |
0.798 |
|
| 2022 |
Abraham A, LaBella AL, Capra JA, Rokas A. Mosaic patterns of selection in genomic regions associated with diverse human traits. Plos Genetics. 18: e1010494. PMID 36342969 DOI: 10.1371/journal.pgen.1010494 |
0.784 |
|
| 2022 |
Li Y, Liu H, Steenwyk JL, LaBella AL, Harrison MC, Groenewald M, Zhou X, Shen XX, Zhao T, Hittinger CT, Rokas A. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Current Biology : Cb. PMID 36334587 DOI: 10.1016/j.cub.2022.10.025 |
0.841 |
|
| 2022 |
Hatmaker EA, Rangel-Grimaldo M, Raja HA, Pourhadi H, Knowles SL, Fuller K, Adams EM, Lightfoot JD, Bastos RW, Goldman GH, Oberlies NH, Rokas A. Genomic and Phenotypic Trait Variation of the Opportunistic Human Pathogen Aspergillus flavus and Its Close Relatives. Microbiology Spectrum. e0306922. PMID 36318036 DOI: 10.1128/spectrum.03069-22 |
0.819 |
|
| 2022 |
Hugaboom M, Hatmaker EA, LaBella AL, Rokas A. Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi. G3 (Bethesda, Md.). PMID 36305682 DOI: 10.1093/g3journal/jkac285 |
0.826 |
|
| 2022 |
Steenwyk JL, Goltz DC, Buida TJ, Li Y, Shen XX, Rokas A. OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. Plos Biology. 20: e3001827. PMID 36228036 DOI: 10.1371/journal.pbio.3001827 |
0.832 |
|
| 2022 |
Hatmaker EA, Miller DL, Newton I, Rokas A. Draft Genome Sequence of an Aspergillus Strain Isolated from a Honey Bee Pupa. Microbiology Resource Announcements. e0079822. PMID 36194126 DOI: 10.1128/mra.00798-22 |
0.807 |
|
| 2022 |
Abraham A, Le B, Kosti I, Straub P, Velez-Edwards DR, Davis LK, Newton JM, Muglia LJ, Rokas A, Bejan CA, Sirota M, Capra JA. Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth. Bmc Medicine. 20: 333. PMID 36167547 DOI: 10.1186/s12916-022-02522-x |
0.418 |
|
| 2022 |
Colabardini AC, Van Rhijn N, LaBella AL, Valero C, Dineen L, Rokas A, Goldman GH. Aspergillus fumigatus FhdA Transcription Factor Is Important for Mitochondrial Activity and Codon Usage Regulation during the Caspofungin Paradoxical Effect. Antimicrobial Agents and Chemotherapy. e0070122. PMID 35916517 DOI: 10.1128/aac.00701-22 |
0.745 |
|
| 2022 |
Li Y, Liu Z, Liu C, Shi Z, Pang L, Chen C, Chen Y, Pan R, Zhou W, Chen XX, Rokas A, Huang J, Shen XX. HGT is widespread in insects and contributes to male courtship in lepidopterans. Cell. PMID 35853453 DOI: 10.1016/j.cell.2022.06.014 |
0.783 |
|
| 2022 |
Horta MAC, Steenwyk JL, Mead ME, Dos Santos LHB, Zhao S, Gibbons JG, Marcet-Houben M, Gabaldón T, Rokas A, Goldman GH. Examination of Genome-Wide Ortholog Variation in Clinical and Environmental Isolates of the Fungal Pathogen Aspergillus fumigatus. Mbio. e0151922. PMID 35766381 DOI: 10.1128/mbio.01519-22 |
0.818 |
|
| 2022 |
Markowitz RHG, LaBella AL, Shi M, Rokas A, Capra JA, Ferguson JF, Mosley JD, Bordenstein SR. Microbiome-associated human genetic variants impact phenome-wide disease risk. Proceedings of the National Academy of Sciences of the United States of America. 119: e2200551119. PMID 35749358 DOI: 10.1073/pnas.2200551119 |
0.764 |
|
| 2022 |
Steenwyk JL, Buida Iii TJ, Gonçalves C, Goltz DC, Morales G, Mead ME, LaBella AL, Chavez CM, Schmitz JE, Hadjifrangiskou M, Li Y, Rokas A. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Genetics. PMID 35536198 DOI: 10.1093/genetics/iyac079 |
0.817 |
|
| 2022 |
Rokas A. Evolution of the human pathogenic lifestyle in fungi. Nature Microbiology. 7: 607-619. PMID 35508719 DOI: 10.1038/s41564-022-01112-0 |
0.529 |
|
| 2022 |
Steenwyk JL, Phillips MA, Yang F, Date SS, Graham TR, Berman J, Hittinger CT, Rokas A. An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. Science Advances. 8: eabn0105. PMID 35507651 DOI: 10.1126/sciadv.abn0105 |
0.825 |
|
| 2022 |
Bradley NP, Wahl KL, Steenwyk JL, Rokas A, Eichman BF. Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases. Mbio. e0329721. PMID 35311535 DOI: 10.1128/mbio.03297-21 |
0.802 |
|
| 2022 |
de Castro PA, Colabardini AC, Moraes M, Horta MAC, Knowles SL, Raja HA, Oberlies NH, Koyama Y, Ogawa M, Gomi K, Steenwyk JL, Rokas A, Gonçales RA, Duarte-Oliveira C, Carvalho A, et al. Regulation of gliotoxin biosynthesis and protection in Aspergillus species. Plos Genetics. 18: e1009965. PMID 35041649 DOI: 10.1371/journal.pgen.1009965 |
0.823 |
|
| 2021 |
Dos Santos RAC, Mead ME, Steenwyk JL, Rivero-Menéndez O, Alastruey-Izquierdo A, Goldman GH, Rokas A. Examining Signatures of Natural Selection in Antifungal Resistance Genes Across Fungi. Frontiers in Fungal Biology. 2: 723051. PMID 37744093 DOI: 10.3389/ffunb.2021.723051 |
0.8 |
|
| 2021 |
Steenwyk JL, Rokas A. ggpubfigs: Colorblind-Friendly Color Palettes and ggplot2 Graphic System Extensions for Publication-Quality Scientific Figures. Microbiology Resource Announcements. 10: e0087121. PMID 34734767 DOI: 10.1128/MRA.00871-21 |
0.763 |
|
| 2021 |
Colabardini AC, Wang F, Dong Z, Pardeshi L, Rocha MC, Costa JH, Dos Reis TF, Brown A, Jaber QZ, Fridman M, Fill T, Rokas A, Malavazi I, Wong KH, Goldman GH. Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin. Genetics. PMID 34718550 DOI: 10.1093/genetics/iyab183 |
0.806 |
|
| 2021 |
LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. Correction: Variation and selection on codon usage bias across an entire subphylum. Plos Genetics. 17: e1009824. PMID 34570754 DOI: 10.1371/journal.pgen.1009824 |
0.764 |
|
| 2021 |
Phillips MA, Steenwyk JL, Shen XX, Rokas A. Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum. Genome Biology and Evolution. PMID 34554246 DOI: 10.1093/gbe/evab219 |
0.837 |
|
| 2021 |
Steenwyk JL, Rokas A. orthofisher: a broadly applicable tool for automated gene identification and retrieval. G3 (Bethesda, Md.). 11. PMID 34544141 DOI: 10.1093/g3journal/jkab250 |
0.835 |
|
| 2021 |
Harrison MC, LaBella AL, Hittinger CT, Rokas A. The evolution of the GALactose utilization pathway in budding yeasts. Trends in Genetics : Tig. PMID 34538504 DOI: 10.1016/j.tig.2021.08.013 |
0.827 |
|
| 2021 |
Kwon MJ, Steiniger C, Cairns TC, Wisecaver JH, Lind AL, Pohl C, Regner C, Rokas A, Meyer V. Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways. Microbiology Spectrum. e0089821. PMID 34523946 DOI: 10.1128/Spectrum.00898-21 |
0.82 |
|
| 2021 |
Tice AK, Žihala D, Pánek T, Jones RE, Salomaki ED, Nenarokov S, Burki F, Eliáš M, Eme L, Roger AJ, Rokas A, Shen XX, Strassert JFH, Kolísko M, Brown MW. PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. Plos Biology. 19: e3001365. PMID 34358228 DOI: 10.1371/journal.pbio.3001365 |
0.759 |
|
| 2021 |
Ries LNA, Alves de Castro P, Pereira Silva L, Valero C, Dos Reis TF, Saborano R, Duarte IF, Persinoti GF, Steenwyk JL, Rokas A, Almeida F, Costa JH, Fill T, Sze Wah Wong S, Aimanianda V, et al. Aspergillus fumigatus Acetate Utilization Impacts Virulence Traits and Pathogenicity. Mbio. e0168221. PMID 34311583 DOI: 10.1128/mBio.01682-21 |
0.791 |
|
| 2021 |
Steenwyk JL, Mead ME, de Castro PA, Valero C, Damasio A, Dos Santos RAC, Labella AL, Li Y, Knowles SL, Raja HA, Oberlies NH, Zhou X, Cornely OA, Fuchs F, Koehler P, ... ... Rokas A, et al. Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus. Microbiology Spectrum. e0001021. PMID 34106569 DOI: 10.1128/Spectrum.00010-21 |
0.817 |
|
| 2021 |
Li Y, Shen XX, Evans B, Dunn CW, Rokas A. Rooting the animal tree of life. Molecular Biology and Evolution. PMID 34097041 DOI: 10.1093/molbev/msab170 |
0.792 |
|
| 2021 |
Mead ME, Steenwyk JL, Silva LP, de Castro PA, Saeed N, Hillmann F, Goldman GH, Rokas A. An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi. Genetics. PMID 33944921 DOI: 10.1093/genetics/iyab066 |
0.845 |
|
| 2021 |
LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. Signatures of optimal codon usage in metabolic genes inform budding yeast ecology. Plos Biology. 19: e3001185. PMID 33872297 DOI: 10.1371/journal.pbio.3001185 |
0.831 |
|
| 2021 |
Haase MAB, Kominek J, Opulente DA, Shen XX, LaBella AL, Zhou X, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT. Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo's law of irreversible loss. Genetics. 217. PMID 33724406 DOI: 10.1093/genetics/iyaa012 |
0.831 |
|
| 2021 |
Shen XX, Steenwyk JL, Rokas A. Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data. Systematic Biology. PMID 33616672 DOI: 10.1093/sysbio/syab011 |
0.813 |
|
| 2021 |
Li Y, Steenwyk JL, Chang Y, Wang Y, James TY, Stajich JE, Spatafora JW, Groenewald M, Dunn CW, Hittinger CT, Shen XX, Rokas A. A genome-scale phylogeny of the kingdom Fungi. Current Biology : Cb. PMID 33607033 DOI: 10.1016/j.cub.2021.01.074 |
0.838 |
|
| 2021 |
Wu MY, Mead ME, Lee MK, Neuhaus GF, Adpressa DA, Martien JI, Son YE, Moon H, Amador-Noguez D, Han KH, Rokas A, Loesgen S, Yu JH, Park HS. Transcriptomic, Protein-DNA Interaction, and Metabolomic Studies of VosA, VelB, and WetA in Aspergillus nidulans Asexual Spores. Mbio. 12. PMID 33563821 DOI: 10.1128/mBio.03128-20 |
0.787 |
|
| 2021 |
Steenwyk JL, Buida TJ, Labella AL, Li Y, Shen XX, Rokas A. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics (Oxford, England). PMID 33560364 DOI: 10.1093/bioinformatics/btab096 |
0.799 |
|
| 2021 |
Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. The influence of evolutionary history on human health and disease. Nature Reviews. Genetics. PMID 33408383 DOI: 10.1038/s41576-020-00305-9 |
0.766 |
|
| 2020 |
Rokas A, Mesiano S, Tamam O, LaBella A, Zhang G, Muglia L. Developing a theoretical evolutionary framework to solve the mystery of parturition initiation. Elife. 9. PMID 33380346 DOI: 10.7554/eLife.58343 |
0.744 |
|
| 2020 |
Hatmaker EA, Zhou X, Mead ME, Moon H, Yu JH, Rokas A. Revised Transcriptome-Based Gene Annotation for Aspergillus flavus Strain NRRL 3357. Microbiology Resource Announcements. 9. PMID 33273000 DOI: 10.1128/MRA.01155-20 |
0.815 |
|
| 2020 |
Steenwyk JL, Buida TJ, Li Y, Shen XX, Rokas A. ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. Plos Biology. 18: e3001007. PMID 33264284 DOI: 10.1371/journal.pbio.3001007 |
0.796 |
|
| 2020 |
Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nature Communications. 11: 6096. PMID 33257660 DOI: 10.1038/s41467-020-20005-6 |
0.813 |
|
| 2020 |
Li Y, David KT, Shen XX, Steenwyk JL, Halanych KM, Rokas A. Feature frequency profile-based phylogenies are inaccurate. Proceedings of the National Academy of Sciences of the United States of America. PMID 33234569 DOI: 10.1073/pnas.2013143117 |
0.758 |
|
| 2020 |
Steenwyk JL, Mead ME, de Castro PA, Valero C, Damasio A, Dos Santos RAC, Labella AL, Li Y, Knowles SL, Raja HA, Oberlies NH, Zhou X, Cornely OA, Fuchs F, Koehler P, ... ... Rokas A, et al. Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of . Biorxiv : the Preprint Server For Biology. PMID 33173866 DOI: 10.1101/2020.11.06.371971 |
0.825 |
|
| 2020 |
Shen XX, Steenwyk JL, LaBella AL, Opulente DA, Zhou X, Kominek J, Li Y, Groenewald M, Hittinger CT, Rokas A. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Science Advances. 6. PMID 33148650 DOI: 10.1126/sciadv.abd0079 |
0.83 |
|
| 2020 |
Filho APDC, Brancini GTP, de Castro PA, Valero C, Ferreira Filho JA, Silva LP, Rocha MC, Malavazi I, Pontes JGM, Fill T, Silva RN, Almeida F, Steenwyk JL, Rokas A, Dos Reis TF, et al. 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. PMID 33051372 DOI: 10.1128/mBio.02458-20 |
0.806 |
|
| 2020 |
Dos Santos RAC, Rivero-Menendez O, Steenwyk JL, Mead ME, Goldman GH, Alastruey-Izquierdo A, Rokas A. Draft Genome Sequences of Four Section Clinical Strains. Microbiology Resource Announcements. 9. PMID 33004453 DOI: 10.1128/MRA.00856-20 |
0.813 |
|
| 2020 |
Dunning Hotopp JC, Baltrus DA, Bruno VM, Dennehy JJ, Gill SR, Maresca JA, Matthijnssens J, Newton ILG, Putonti C, Rasko DA, Rokas A, Roux S, Stajich JE, Stedman KM, Stewart FJ, et al. Best Practices for Successfully Writing and Publishing a Genome Announcement in . Microbiology Resource Announcements. 9. PMID 32883786 DOI: 10.1128/MRA.00763-20 |
0.455 |
|
| 2020 |
Steenwyk JL, Mead ME, Knowles SL, Raja HA, Roberts CD, Bader O, Houbraken J, Goldman GH, Oberlies NH, Rokas A. Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Species. Genetics. PMID 32817009 DOI: 10.1534/Genetics.120.303549 |
0.839 |
|
| 2020 |
LaBella AL, Abraham A, Pichkar Y, Fong SL, Zhang G, Muglia LJ, Abbot P, Rokas A, Capra JA. Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nature Communications. 11: 3731. PMID 32709900 DOI: 10.1038/S41467-020-17258-6 |
0.773 |
|
| 2020 |
Ries LNA, Pardeshi L, Dong Z, Tan K, Steenwyk JL, Colabardini AC, Ferreira Filho JA, de Castro PA, Silva LP, Preite NW, Almeida F, de Assis LJ, Dos Santos RAC, Bowyer P, Bromley M, ... ... Rokas A, et al. The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence. Plos Pathogens. 16: e1008645. PMID 32667960 DOI: 10.1371/Journal.Ppat.1008645 |
0.81 |
|
| 2020 |
James TY, Stajich JE, Hittinger CT, Rokas A. Toward a Fully Resolved Fungal Tree of Life. Annual Review of Microbiology. PMID 32660385 DOI: 10.1146/Annurev-Micro-022020-051835 |
0.797 |
|
| 2020 |
Steenwyk JL, Lind AL, Ries LNA, Dos Reis TF, Silva LP, Almeida F, Bastos RW, Fraga da Silva TFC, Bonato VLD, Pessoni AM, Rodrigues F, Raja HA, Knowles SL, Oberlies NH, Lagrou K, ... ... Rokas A, et al. Pathogenic Allodiploid Hybrids of Aspergillus Fungi. Current Biology : Cb. PMID 32502407 DOI: 10.1016/J.Cub.2020.04.071 |
0.825 |
|
| 2020 |
Dos Santos RAC, Steenwyk JL, Rivero-Menendez O, Mead ME, Silva LP, Bastos RW, Alastruey-Izquierdo A, Goldman GH, Rokas A. Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens , , and . Frontiers in Genetics. 11: 459. PMID 32477406 DOI: 10.3389/fgene.2020.00459 |
0.831 |
|
| 2020 |
Mead ME, Borowsky AT, Joehnk B, Steenwyk JL, Shen XX, Sil A, Rokas A. 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. PMID 32442273 DOI: 10.1093/Gbe/Evaa107 |
0.845 |
|
| 2020 |
Drott MT, Bastos RW, Rokas A, Ries LNA, Gabaldón T, Goldman GH, Keller NP, Greco C. Diversity of Secondary Metabolism in Aspergillus nidulans Clinical Isolates. Msphere. 5. PMID 32269157 DOI: 10.1128/mSphere.00156-20 |
0.617 |
|
| 2020 |
Bastos RW, Valero C, Silva LP, Schoen T, Drott M, Brauer V, Silva-Rocha R, Lind A, Steenwyk JL, Rokas A, Rodrigues F, Resendiz-Sharpe A, Lagrou K, Marcet-Houben M, Gabaldón T, et al. Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans. Msphere. 5. PMID 32269156 DOI: 10.1128/mSphere.00153-20 |
0.798 |
|
| 2020 |
Rokas A, Mead ME, Steenwyk JL, Oberlies NH, Goldman GH. Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity. Plos Pathogens. 16: e1008315. PMID 32106242 DOI: 10.1371/Journal.Ppat.1008315 |
0.787 |
|
| 2020 |
Knowles SL, Raja HA, Isawi IH, Flores-Bocanegra L, Reggio PH, Pearce CJ, Burdette JE, Rokas A, Oberlies NH. Wheldone: Characterization of a Unique Scaffold from the Coculture of and . Organic Letters. PMID 32096649 DOI: 10.1021/Acs.Orglett.0C00219 |
0.576 |
|
| 2020 |
Knowles SL, Mead ME, Silva LP, Raja HA, Steenwyk JL, Goldman GH, Oberlies NH, Rokas A. Gliotoxin, a Known Virulence Factor in the Major Human Pathogen Aspergillus fumigatus, Is Also Biosynthesized by Its Nonpathogenic Relative . Mbio. 11. PMID 32047138 DOI: 10.1128/Mbio.03361-19 |
0.829 |
|
| 2020 |
Libkind D, Peris D, Cubillos FA, Steenwyk JL, Opulente DA, Langdon QK, Rokas A, Hittinger CT. Into the wild: new yeast genomes from natural environments and new tools for their analysis. Fems Yeast Research. 20. PMID 32009143 DOI: 10.1093/Femsyr/Foaa008 |
0.832 |
|
| 2020 |
Rokas A, Mead ME, Steenwyk JL, Raja HA, Oberlies NH. Biosynthetic gene clusters and the evolution of fungal chemodiversity. Natural Product Reports. PMID 31898704 DOI: 10.1039/C9Np00045C |
0.832 |
|
| 2019 |
Knowles SL, Vu N, Todd DA, Raja HA, Rokas A, Zhang Q, Oberlies NH. Orthogonal Method for Double-Bond Placement via Ozone-Induced Dissociation Mass Spectrometry (OzID-MS). Journal of Natural Products. PMID 31823607 DOI: 10.1021/Acs.Jnatprod.9B00787 |
0.571 |
|
| 2019 |
Bodinaku I, Shaffer J, Connors AB, Steenwyk JL, Biango-Daniels MN, Kastman EK, Rokas A, Robbat A, Wolfe BE. Rapid Phenotypic and Metabolomic Domestication of Wild Molds on Cheese. Mbio. 10. PMID 31615965 DOI: 10.1128/Mbio.02445-19 |
0.809 |
|
| 2019 |
Mead ME, Raja HA, Steenwyk JL, Knowles SL, Oberlies NH, Rokas A. Draft Genome Sequence of the Griseofulvin-Producing Fungus Xylaria flabelliformis Strain G536. Microbiology Resource Announcements. 8. PMID 31537670 DOI: 10.1128/MRA.00890-19 |
0.831 |
|
| 2019 |
Zhou X, Lutteropp S, Czech L, Stamatakis A, von Looz M, Rokas A. Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence. Systematic Biology. PMID 31504977 DOI: 10.1093/Sysbio/Syz058 |
0.669 |
|
| 2019 |
Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A. The impact of natural selection on the evolution and function of placentally expressed galectins. Genome Biology and Evolution. PMID 31504490 DOI: 10.1093/Gbe/Evz183 |
0.819 |
|
| 2019 |
Baltrus DA, Cuomo CA, Dennehy JJ, Dunning Hotopp JC, Maresca JA, Newton ILG, Rasko DA, Rokas A, Roux S, Stajich JE. Future-Proofing Your Genome Assembly for Reproducibility and Clarity. Microbiology Resource Announcements. 8. PMID 31488541 DOI: 10.1128/MRA.00954-19 |
0.522 |
|
| 2019 |
Steenwyk JL, Rokas A. Treehouse: a user-friendly application to obtain subtrees from large phylogenies. Bmc Research Notes. 12: 541. PMID 31455362 DOI: 10.1186/s13104-019-4577-5 |
0.776 |
|
| 2019 |
Dos Reis TF, Silva LP, de Castro PA, do Carmo RA, Marini MM, da Silveira JF, Ferreira BH, Rodrigues F, Lind AL, Rokas A, Goldman GH. The Aspergillus fumigatus Mismatch Repair Homolog Is Important for Virulence and Azole Resistance. Msphere. 4. PMID 31391280 DOI: 10.1128/mSphere.00416-19 |
0.786 |
|
| 2019 |
Moon JM, Capra JA, Abbot P, Rokas A. 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. e1900072. PMID 31373044 DOI: 10.1002/Bies.201900072 |
0.5 |
|
| 2019 |
Labella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. Variation and selection on codon usage bias across an entire subphylum. Plos Genetics. 15: e1008304. PMID 31365533 DOI: 10.1371/Journal.Pgen.1008304 |
0.837 |
|
| 2019 |
Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH. Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution. Current Biology : Cb. PMID 31353182 DOI: 10.1016/J.Cub.2019.06.056 |
0.798 |
|
| 2019 |
Wang M, Fu H, Shen XX, Ruan R, Rokas A, Li H. Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata. Molecular Plant Pathology. PMID 31297970 DOI: 10.1111/Mpp.12848 |
0.839 |
|
| 2019 |
Steenwyk JL, Shen XX, Lind AL, Goldman GH, Rokas A. A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera and . Mbio. 10. PMID 31289177 DOI: 10.1128/Mbio.00925-19 |
0.843 |
|
| 2019 |
Smith SP, Phillips JB, Johnson ML, Abbot P, Capra JA, Rokas A. Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication. Evolution, Medicine, and Public Health. 2019: 93-103. PMID 31263560 DOI: 10.1093/Emph/Eoz015 |
0.793 |
|
| 2019 |
Moon JM, Capra JA, Abbot P, Rokas A. Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. G3 (Bethesda, Md.). PMID 31213516 DOI: 10.1534/G3.119.400186 |
0.519 |
|
| 2019 |
Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Čadež N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT, Rokas A. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. Plos Biology. 17: e3000255. PMID 31112549 DOI: 10.1371/Journal.Pbio.3000255 |
0.819 |
|
| 2019 |
Ries LNA, Steenwyk JL, de Castro PA, de Lima PBA, Almeida F, de Assis LJ, Manfiolli AO, Takahashi-Nakaguchi A, Kusuya Y, Hagiwara D, Takahashi H, Wang X, Obar JJ, Rokas A, Goldman GH. Nutritional Heterogeneity Among Strains Has Consequences for Virulence in a Strain- and Host-Dependent Manner. Frontiers in Microbiology. 10: 854. PMID 31105662 DOI: 10.3389/Fmicb.2019.00854 |
0.804 |
|
| 2019 |
Greco C, Keller NP, Rokas A. Unearthing fungal chemodiversity and prospects for drug discovery. Current Opinion in Microbiology. 51: 22-29. PMID 31071615 DOI: 10.1016/J.Mib.2019.03.002 |
0.532 |
|
| 2019 |
Gao S, Gold SE, Wisecaver JH, Zhang Y, Guo L, Ma LJ, Rokas A, Glenn AE. Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism. Fungal Genetics and Biology : Fg & B. PMID 30953838 DOI: 10.1016/J.Fgb.2019.04.002 |
0.793 |
|
| 2019 |
Knowles SL, Raja HA, Wright AJ, Lee AML, Caesar LK, Cech NB, Mead ME, Steenwyk JL, Ries LNA, Goldman GH, Rokas A, Oberlies NH. Mapping the Fungal Battlefield: Using Chemistry and Deletion Mutants to Monitor Interspecific Chemical Interactions Between Fungi. Frontiers in Microbiology. 10: 285. PMID 30837981 DOI: 10.3389/Fmicb.2019.00285 |
0.786 |
|
| 2019 |
Wang Y, Zhou X, Wang L, Liu X, Yang D, Rokas A. Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. International Journal of Molecular Sciences. 20. PMID 30832228 DOI: 10.3390/Ijms20051072 |
0.781 |
|
| 2019 |
Kominek J, Doering DT, Opulente DA, Shen XX, Zhou X, DeVirgilio J, Hulfachor AB, Groenewald M, Mcgee MA, Karlen SD, Kurtzman CP, Rokas A, Hittinger CT. Eukaryotic Acquisition of a Bacterial Operon. Cell. PMID 30799038 DOI: 10.1016/J.Cell.2019.01.034 |
0.829 |
|
| 2019 |
Mead ME, Knowles SL, Raja HA, Beattie SR, Kowalski CH, Steenwyk JL, Silva LP, Chiaratto J, Ries LNA, Goldman GH, Cramer RA, Oberlies NH, Rokas A. Characterizing the Pathogenic, Genomic, and Chemical Traits of , a Close Relative of the Major Human Fungal Pathogen . Msphere. 4. PMID 30787113 DOI: 10.1128/mSphere.00018-19 |
0.835 |
|
| 2018 |
Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, et al. Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Scientific Data. 5: 3. PMID 30563979 DOI: 10.1038/S41597-018-0004-3 |
0.761 |
|
| 2018 |
Eidem HR, Steenwyk JL, Wisecaver JH, Capra JA, Abbot P, Rokas A. 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: 107. PMID 30453955 DOI: 10.1186/S12920-018-0426-Y |
0.816 |
|
| 2018 |
Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, ... ... Rokas A, et al. Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell. PMID 30415838 DOI: 10.1016/J.Cell.2018.10.023 |
0.839 |
|
| 2018 |
Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, et al. Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Scientific Data. 5: 180219. PMID 30398470 DOI: 10.1038/Sdata.2018.219 |
0.782 |
|
| 2018 |
Segal ES, Gritsenko V, Levitan A, Yadav B, Dror N, Steenwyk JL, Silberberg Y, Mielich K, Rokas A, Gow NAR, Kunze R, Sharan R, Berman J. Gene Essentiality Analyzed by Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of . Mbio. 9. PMID 30377286 DOI: 10.1128/Mbio.02048-18 |
0.843 |
|
| 2018 |
Krause DJ, Kominek J, Opulente DA, Shen XX, Zhou X, Langdon QK, DeVirgilio J, Hulfachor AB, Kurtzman CP, Rokas A, Hittinger CT. 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. PMID 30297402 DOI: 10.1073/Pnas.1806268115 |
0.822 |
|
| 2018 |
Shi R, Shen XX, Rokas A, Eichman BF. Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 30264543 DOI: 10.1002/Bies.201800133 |
0.696 |
|
| 2018 |
Riquelme M, Catherine Aime M, Branco S, Brand A, Brown A, Louise Glass N, Kahmann R, Momany M, Rokas A, Trail F. The Power of Discussion: Support for Women at the Fungal Gordon Research Conference. Fungal Genetics and Biology : Fg & B. PMID 30261275 DOI: 10.1016/J.Fgb.2018.09.007 |
0.415 |
|
| 2018 |
Huusko JM, Karjalainen MK, Graham BE, Zhang G, Farrow EG, Miller NA, Jacobsson B, Eidem HR, Murray JC, Bedell B, Breheny P, Brown NW, Bødker FL, Litterman NK, Jiang PP, ... ... Rokas A, et al. Correction: Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth. Plos Genetics. 14: e1007673. PMID 30212495 DOI: 10.1371/Journal.Pgen.1007673 |
0.782 |
|
| 2018 |
Rokas A, Wisecaver JH, Lind AL. The birth, evolution and death of metabolic gene clusters in fungi. Nature Reviews. Microbiology. PMID 30194403 DOI: 10.1038/S41579-018-0075-3 |
0.831 |
|
| 2018 |
Wu MY, Mead ME, Lee MK, Ostrem Loss EM, Kim SC, Rokas A, Yu JH. Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi. Mbio. 9. PMID 30131357 DOI: 10.1128/mBio.01130-18 |
0.795 |
|
| 2018 |
Huusko JM, Karjalainen MK, Graham BE, Zhang G, Farrow EG, Miller NA, Jacobsson B, Eidem HR, Murray JC, Bedell B, Breheny P, Brown NW, Bødker FL, Litterman NK, Jiang PP, ... ... Rokas A, et al. Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth. Plos Genetics. 14: e1007394. PMID 30001343 DOI: 10.1371/Journal.Pgen.1007394 |
0.803 |
|
| 2018 |
Lim FY, Won TH, Raffa N, Baccile JA, Wisecaver J, Rokas A, Schroeder FC, Keller NP. Fungal Isocyanide Synthases and Xanthocillin Biosynthesis in Aspergillus fumigatus. Mbio. 9. PMID 29844112 DOI: 10.1128/Mbio.00785-18 |
0.539 |
|
| 2018 |
Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature Communications. 9: 1887. PMID 29760453 DOI: 10.1038/S41467-018-04374-7 |
0.814 |
|
| 2018 |
Gonçalves C, Wisecaver JH, Kominek J, Oom MS, Leandro MJ, Shen XX, Opulente DA, Zhou X, Peris D, Kurtzman CP, Hittinger CT, Rokas A, Gonçalves P. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage. Elife. 7. PMID 29648535 DOI: 10.7554/Elife.33034 |
0.816 |
|
| 2018 |
Fidler AL, Boudko SP, Rokas A, Hudson BG. The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution. Journal of Cell Science. 131. PMID 29632050 DOI: 10.1242/Jcs.203950 |
0.782 |
|
| 2018 |
Lind AL, Lim FY, Soukup AA, Keller NP, Rokas A. An LaeA- and BrlA-Dependent Cellular Network Governs Tissue-Specific Secondary Metabolism in the Human Pathogen. Msphere. 3. PMID 29564395 DOI: 10.1128/mSphere.00050-18 |
0.788 |
|
| 2018 |
Steenwyk JL, Rokas A. Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation. Frontiers in Microbiology. 9: 288. PMID 29520259 DOI: 10.3389/fmicb.2018.00288 |
0.818 |
|
| 2018 |
Opulente DA, Rollinson EJ, Bernick-Roehr C, Hulfachor AB, Rokas A, Kurtzman CP, Hittinger CT. Factors driving metabolic diversity in the budding yeast subphylum. Bmc Biology. 16: 26. PMID 29499717 DOI: 10.1186/S12915-018-0498-3 |
0.795 |
|
| 2018 |
Moon JM, Aronoff DM, Capra JA, Abbot P, Rokas A. Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology. G3 (Bethesda, Md.). PMID 29467190 DOI: 10.1534/G3.118.200035 |
0.57 |
|
| 2018 |
Lamm KYB, Johnson ML, Baker Phillips J, Muntifering MB, James JM, Jones HN, Redline RW, Rokas A, Muglia LJ. Inverted formin 2 regulates intracellular trafficking, placentation, and pregnancy outcome. Elife. 7. PMID 29309034 DOI: 10.7554/Elife.31150 |
0.768 |
|
| 2017 |
Zhou X, Shen X, Hittinger CT, Rokas A. Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. Molecular Biology and Evolution. PMID 29177474 DOI: 10.1093/Molbev/Msx302 |
0.804 |
|
| 2017 |
Lind AL, Wisecaver JH, Lameiras C, Wiemann P, Palmer JM, Keller NP, Rodrigues F, Goldman GH, Rokas A. Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species. Plos Biology. 15: e2003583. PMID 29149178 DOI: 10.1371/Journal.Pbio.2003583 |
0.828 |
|
| 2017 |
Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF. Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. The Embo Journal. PMID 29054852 DOI: 10.15252/Embj.201797833 |
0.703 |
|
| 2017 |
King N, Rokas A. Embracing Uncertainty in Reconstructing Early Animal Evolution. Current Biology : Cb. 27: R1081-R1088. PMID 29017048 DOI: 10.1016/J.Cub.2017.08.054 |
0.647 |
|
| 2017 |
Eidem HR, McGary KL, Capra JA, Abbot P, Rokas A. The transformative potential of an integrative approach to pregnancy. Placenta. 57: 204-215. PMID 28864013 DOI: 10.1016/J.Placenta.2017.07.010 |
0.795 |
|
| 2017 |
Shropshire JD, Rokas A. Correction: Heredity: The gene family that cheats Mendel. Elife. 6. PMID 28829287 DOI: 10.7554/eLife.31295 |
0.478 |
|
| 2017 |
Lojek LJ, Farrand AJ, Wisecaver JH, Blaby-Haas CE, Michel BW, Merchant SS, Rokas A, Skaar EP. Chlamydomonas reinhardtii LFO1 Is an IsdG Family Heme Oxygenase. Msphere. 2. PMID 28815214 DOI: 10.1128/mSphere.00176-17 |
0.706 |
|
| 2017 |
Shen XX, Hittinger CT, Rokas A. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology & Evolution. 1: 126. PMID 28812701 DOI: 10.1038/S41559-017-0126 |
0.814 |
|
| 2017 |
Zhao L, Zhou X, Rokas A, Cone RD. Functional variants of the melanocortin-4 receptor associated with the Odontoceti and Mysticeti suborders of cetaceans. Scientific Reports. 7: 5684. PMID 28720755 DOI: 10.1038/S41598-017-05962-1 |
0.679 |
|
| 2017 |
Valsecchi I, Sarikaya Bayram Ö, Wong Sak Hoi J, Muszkieta L, Gibbons J, Prevost MC, Mallet A, Krijnse-Locker J, Ibrahim-Granet O, Mouyna I, Carr P, Bromley M, Aimanianda V, Yu YJ, Rokas A, et al. MybA, a transcription factor involved in conidiation and conidial viability of the human pathogen Aspergillus fumigatus. Molecular Microbiology. PMID 28677124 DOI: 10.1111/Mmi.13744 |
0.798 |
|
| 2017 |
Wu MY, Mead ME, Kim SC, Rokas A, Yu JH. WetA bridges cellular and chemical development in Aspergillus flavus. Plos One. 12: e0179571. PMID 28658268 DOI: 10.1371/Journal.Pone.0179571 |
0.779 |
|
| 2017 |
Shropshire JD, Rokas A. The gene family that cheats Mendel. Elife. 6. PMID 28631611 DOI: 10.7554/eLife.28567 |
0.474 |
|
| 2017 |
Fidler AL, Darris CE, Chetyrkin SV, Pedchenko VK, Boudko SP, Brown KL, Gray Jerome W, Hudson JK, Rokas A, Hudson BG. Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues. Elife. 6. PMID 28418331 DOI: 10.7554/Elife.24176 |
0.789 |
|
| 2017 |
Wisecaver JH, Borowsky AT, Tzin V, Jander G, Kliebenstein DJ, Rokas A. A Global Co-expression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants. The Plant Cell. PMID 28408660 DOI: 10.1105/Tpc.17.00009 |
0.817 |
|
| 2017 |
Steenwyk J, Rokas A. Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains. G3 (Bethesda, Md.). PMID 28292787 DOI: 10.1534/g3.117.040105 |
0.83 |
|
| 2017 |
Abbot P, Rokas A. Mammalian pregnancy. Current Biology : Cb. 27: R127-R128. PMID 28222284 DOI: 10.1016/J.Cub.2016.10.046 |
0.408 |
|
| 2016 |
Ortiz JF, Rokas A. CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes. Molecular Biology and Evolution. PMID 28007975 DOI: 10.1093/molbev/msw227 |
0.752 |
|
| 2016 |
Lind AL, Smith TD, Saterlee T, Calvo AM, Rokas A. Regulation of Secondary Metabolism by the Velvet Complex is Temperature-Responsive in Aspergillus. G3 (Bethesda, Md.). PMID 27694115 DOI: 10.1534/G3.116.033084 |
0.785 |
|
| 2016 |
Shen XX, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data. G3 (Bethesda, Md.). PMID 27672114 DOI: 10.1534/G3.116.034744 |
0.846 |
|
| 2016 |
Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies. G3 (Bethesda, Md.). PMID 27638685 DOI: 10.1534/G3.116.034249 |
0.82 |
|
| 2016 |
Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, ... ... Rokas A, et al. Comparative genomics of biotechnologically important yeasts. Proceedings of the National Academy of Sciences of the United States of America. PMID 27535936 DOI: 10.1073/Pnas.1603941113 |
0.847 |
|
| 2016 |
Shen XX, Salichos L, Rokas A. A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference. Genome Biology and Evolution. PMID 27492233 DOI: 10.1093/Gbe/Evw179 |
0.827 |
|
| 2016 |
Ackerman WE, Buhimschi IA, Eidem HR, Rinker DC, Rokas A, Rood K, Zhao G, Summerfield TL, Landon MB, Buhimschi CS. Comprehensive RNA profiling of villous trophoblast and decidua basalis in pregnancies complicated by preterm birth following intra-amniotic infection. Placenta. 44: 23-33. PMID 27452435 DOI: 10.1016/J.Placenta.2016.05.010 |
0.772 |
|
| 2016 |
Eidem HR, Rinker DC, Ackerman WE, Buhimschi IA, Buhimschi CS, Dunn-Fletcher C, Kallapur SG, Pavličev M, Muglia LJ, Abbot P, Rokas A. Comparing human and macaque placental transcriptomes to disentangle preterm birth pathology from gestational age effects. Placenta. 41: 74-82. PMID 27208410 DOI: 10.1016/J.Placenta.2016.03.006 |
0.788 |
|
| 2016 |
Wisecaver JH, Alexander WG, King SB, Todd Hittinger C, Rokas A. Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes. Molecular Biology and Evolution. PMID 27189567 DOI: 10.1093/Molbev/Msw073 |
0.808 |
|
| 2016 |
Alexander WG, Wisecaver JH, Rokas A, Hittinger CT. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proceedings of the National Academy of Sciences of the United States of America. PMID 27035945 DOI: 10.1073/Pnas.1517242113 |
0.819 |
|
| 2016 |
Kobert K, Salichos L, Rokas A, Stamatakis A. Computing the Internode Certainty and related measures from partial gene trees. Molecular Biology and Evolution. PMID 26915959 DOI: 10.1093/Molbev/Msw040 |
0.78 |
|
| 2016 |
Staehlin BM, Gibbons JG, Rokas A, O'Halloran TV, Slot JC. Evolution of a heavy metal homeostasis/resistance island reflects increasing copper stress in Enterobacteria. Genome Biology and Evolution. PMID 26893455 DOI: 10.1093/Gbe/Evw031 |
0.789 |
|
| 2016 |
Ackerman WE, Jing H, Zhao G, Rokas A, Summerfield T, Wysocki V, Buhimschi CS, Buhimschi IA. 182: Signature placental and kidney-specific transcripts in the urinary misfoldome of women with preeclampsia (PE) American Journal of Obstetrics and Gynecology. 214: S113-S114. DOI: 10.1016/J.Ajog.2015.10.219 |
0.405 |
|
| 2015 |
Rokas A, Soltis PS. Editorial overview: Genomes and evolution: "Seq-ing" answers in life's genomes. Current Opinion in Genetics & Development. PMID 26684354 DOI: 10.1016/J.Gde.2015.11.005 |
0.544 |
|
| 2015 |
Hittinger CT, Rokas A, Bai FY, Boekhout T, Gonçalves P, Jeffries TW, Kominek J, Lachance MA, Libkind D, Rosa CA, Sampaio JP, Kurtzman CP. Genomics and the making of yeast biodiversity. Current Opinion in Genetics & Development. 35: 100-109. PMID 26649756 DOI: 10.1016/J.Gde.2015.10.008 |
0.832 |
|
| 2015 |
Hirbo J, Eidem H, Rokas A, Abbot P. Integrating Diverse Types of Genomic Data to Identify Genes that Underlie Adverse Pregnancy Phenotypes. Plos One. 10: e0144155. PMID 26641094 DOI: 10.1371/Journal.Pone.0144155 |
0.831 |
|
| 2015 |
Wang Y, Zhou X, Yang D, Rokas A. A genome-scale investigation of incongruence in Culicidae mosquitoes. Genome Biology and Evolution. PMID 26608059 DOI: 10.1093/Gbe/Evv235 |
0.807 |
|
| 2015 |
Kim M, Cooper BA, Venkat R, Phillips JB, Eidem HR, Hirbo J, Nutakki S, Williams SM, Muglia LJ, Capra JA, Petren K, Abbot P, Rokas A, McGary KL. GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. Nucleic Acids Research. PMID 26567549 DOI: 10.1093/Nar/Gkv1137 |
0.811 |
|
| 2015 |
Wisecaver JH, Slot JC, Rokas A. Correction: The Evolution of Fungal Metabolic Pathways. Plos Genetics. 11: e1005449. PMID 26378934 DOI: 10.1371/Journal.Pgen.1005449 |
0.796 |
|
| 2015 |
Zhou X, Rokas A, Berger SL, Liebig J, Ray A, Zwiebel LJ. Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality. Genome Biology and Evolution. 7: 2407-16. PMID 26272716 DOI: 10.1093/Gbe/Evv149 |
0.693 |
|
| 2015 |
Phillips JB, Abbot P, Rokas A. Is Preterm Birth a Human-Specific Syndrome? Evolution, Medicine, and Public Health. PMID 26077822 DOI: 10.1093/Emph/Eov010 |
0.699 |
|
| 2015 |
Eidem HR, Ackerman WE, McGary KL, Abbot P, Rokas A. Gestational tissue transcriptomics in term and preterm human pregnancies: a systematic review and meta-analysis. Bmc Medical Genomics. 8: 27. PMID 26044726 DOI: 10.1186/S12920-015-0099-8 |
0.81 |
|
| 2015 |
Lind AL, Wisecaver JH, Smith TD, Feng X, Calvo AM, Rokas A. Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus. Plos Genetics. 11: e1005096. PMID 25786130 DOI: 10.1371/Journal.Pgen.1005096 |
0.828 |
|
| 2015 |
Wisecaver JH, Rokas A. Fungal metabolic gene clusters-caravans traveling across genomes and environments. Frontiers in Microbiology. 6: 161. PMID 25784900 DOI: 10.3389/Fmicb.2015.00161 |
0.788 |
|
| 2015 |
Eidem HR, McGary KL, Rokas A. Shared Selective Pressures on Fungal and Human Metabolic Pathways Lead to Divergent yet Analogous Genetic Responses. Molecular Biology and Evolution. 32: 1449-55. PMID 25681382 DOI: 10.1093/Molbev/Msv034 |
0.81 |
|
| 2015 |
Elmore MH, McGary KL, Wisecaver JH, Slot JC, Geiser DM, Sink S, O'Donnell K, Rokas A. Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. Genome Biology and Evolution. 7: 789-800. PMID 25663439 DOI: 10.1093/Gbe/Evv025 |
0.822 |
|
| 2015 |
Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, ... ... Rokas A, et al. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science (New York, N.Y.). 347: 1258522. PMID 25554792 DOI: 10.1126/Science.1258522 |
0.848 |
|
| 2015 |
Ackerman W, Buhimschi I, Eidem H, Rinker D, Rokas A, Rood K, Zhao G, Summerfield T, Landon M, Buhimschi C. 274: Next generation sequencing (RNA-seq) of the human decidual and placental villous transcriptomes in intra-amniotic infection (IAI) induced preterm birth (PTB) American Journal of Obstetrics and Gynecology. 212: S149-S150. DOI: 10.1016/J.Ajog.2014.10.320 |
0.779 |
|
| 2015 |
Ackerman W, Buhimschi I, Eidem H, Rinker D, Rokas A, Millen KR, Summerfield T, Zhao G, Shellhaas C, Landon M, Buhimschi C. 115: A comprehensive analysis of the human decidual and placental villous transcriptomes in women with preeclampsia (PE) using next generation sequencing (RNA-seq) American Journal of Obstetrics and Gynecology. 212: S75. DOI: 10.1016/J.Ajog.2014.10.161 |
0.781 |
|
| 2015 |
Paulus CG, Potamitis S, Rokas A, Tirado I. Insolvency law as a main pillar of market economy-A critical assessment of the greek insolvency law International Insolvency Review. 24: 1-27. DOI: 10.1002/iir.1229 |
0.384 |
|
| 2014 |
Wisecaver JH, Slot JC, Rokas A. The evolution of fungal metabolic pathways. Plos Genetics. 10: e1004816. PMID 25474404 DOI: 10.1371/Journal.Pgen.1004816 |
0.825 |
|
| 2014 |
Zhou X, Rinker DC, Pitts RJ, Rokas A, Zwiebel LJ. Divergent and conserved elements comprise the chemoreceptive repertoire of the nonblood-feeding mosquito Toxorhynchites amboinensis. Genome Biology and Evolution. 6: 2883-96. PMID 25326137 DOI: 10.1093/Gbe/Evu231 |
0.814 |
|
| 2014 |
Polzin K, Rokas A. Evaluating rare amino acid substitutions (RGC_CAMs) in a yeast model clade. Plos One. 9: e92213. PMID 24637883 DOI: 10.1371/journal.pone.0092213 |
0.462 |
|
| 2014 |
Salichos L, Stamatakis A, Rokas A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Molecular Biology and Evolution. 31: 1261-71. PMID 24509691 DOI: 10.1093/Molbev/Msu061 |
0.756 |
|
| 2014 |
Zhou X, Rokas A. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Molecular Ecology. 23: 1679-700. PMID 24471475 DOI: 10.1111/Mec.12680 |
0.644 |
|
| 2014 |
Soria PS, McGary KL, Rokas A. Functional divergence for every paralog. Molecular Biology and Evolution. 31: 984-92. PMID 24451325 DOI: 10.1093/Molbev/Msu050 |
0.824 |
|
| 2014 |
Greene GH, McGary KL, Rokas A, Slot JC. Ecology drives the distribution of specialized tyrosine metabolism modules in fungi. Genome Biology and Evolution. 6: 121-32. PMID 24391152 DOI: 10.1093/Gbe/Evt208 |
0.821 |
|
| 2013 |
Rokas A. Genetics. My oldest sister is a sea walnut? Science (New York, N.Y.). 342: 1327-9. PMID 24337283 DOI: 10.1126/science.1248424 |
0.449 |
|
| 2013 |
Samuels DC, Li C, Li B, Song Z, Torstenson E, Boyd Clay H, Rokas A, Thornton-Wells TA, Moore JH, Hughes TM, Hoffman RD, Haines JL, Murdock DG, Mortlock DP, Williams SM. Recurrent tissue-specific mtDNA mutations are common in humans. Plos Genetics. 9: e1003929. PMID 24244193 DOI: 10.1371/Journal.Pgen.1003929 |
0.465 |
|
| 2013 |
Rinker DC, Zhou X, Pitts RJ, Rokas A, Zwiebel LJ. Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. Bmc Genomics. 14: 749. PMID 24182346 DOI: 10.1186/1471-2164-14-749 |
0.815 |
|
| 2013 |
Dhingra S, Lind AL, Lin HC, Tang Y, Rokas A, Calvo AM. The fumagillin gene cluster, an example of hundreds of genes under veA control in Aspergillus fumigatus. Plos One. 8: e77147. PMID 24116213 DOI: 10.1371/Journal.Pone.0077147 |
0.811 |
|
| 2013 |
Campbell MA, Staats M, van Kan JA, Rokas A, Slot JC. Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia. 105: 1126-34. PMID 23921237 DOI: 10.3852/12-390 |
0.807 |
|
| 2013 |
McGary KL, Slot JC, Rokas A. Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds. Proceedings of the National Academy of Sciences of the United States of America. 110: 11481-6. PMID 23798424 DOI: 10.1073/Pnas.1304461110 |
0.817 |
|
| 2013 |
Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497: 327-31. PMID 23657258 DOI: 10.1038/Nature12130 |
0.817 |
|
| 2013 |
Rinker DC, Pitts RJ, Zhou X, Suh E, Rokas A, Zwiebel LJ. Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in Anopheles gambiae. Proceedings of the National Academy of Sciences of the United States of America. 110: 8260-5. PMID 23630291 DOI: 10.1073/Pnas.1302562110 |
0.79 |
|
| 2013 |
Predazzi IM, Rokas A, Deinard A, Schnetz-Boutaud N, Williams ND, Bush WS, Tacconelli A, Friedrich K, Fazio S, Novelli G, Haines JL, Sirugo G, Williams SM. Putting pleiotropy and selection into context defines a new paradigm for interpreting genetic data. Circulation. Cardiovascular Genetics. 6: 299-307. PMID 23616601 DOI: 10.1161/Circgenetics.113.000126 |
0.561 |
|
| 2013 |
Rokas A. Aspergillus. Current Biology : Cb. 23: R187-8. PMID 23473556 DOI: 10.1016/j.cub.2013.01.021 |
0.454 |
|
| 2013 |
Bradshaw RE, Slot JC, Moore GG, Chettri P, de Wit PJ, Ehrlich KC, Ganley AR, Olson MA, Rokas A, Carbone I, Cox MP. Fragmentation of an aflatoxin-like gene cluster in a forest pathogen. The New Phytologist. 198: 525-35. PMID 23448391 DOI: 10.1111/Nph.12161 |
0.751 |
|
| 2013 |
Xu Y, Ma P, Shah P, Rokas A, Liu Y, Johnson CH. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature. 495: 116-20. PMID 23417065 DOI: 10.1038/Nature11942 |
0.51 |
|
| 2013 |
Muszkieta L, Beauvais A, Pähtz V, Gibbons JG, Anton Leberre V, Beau R, Shibuya K, Rokas A, Francois JM, Kniemeyer O, Brakhage AA, Latgé JP. Investigation of Aspergillus fumigatus biofilm formation by various "omics" approaches. Frontiers in Microbiology. 4: 13. PMID 23407341 DOI: 10.3389/Fmicb.2013.00013 |
0.795 |
|
| 2013 |
Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF. Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. Dna Repair. 12: 196-204. PMID 23273506 DOI: 10.1016/J.Dnarep.2012.12.001 |
0.77 |
|
| 2013 |
Gibbons JG, Rokas A. The function and evolution of the Aspergillus genome. Trends in Microbiology. 21: 14-22. PMID 23084572 DOI: 10.1016/J.Tim.2012.09.005 |
0.843 |
|
| 2013 |
Ubaida Mohien C, Colquhoun DR, Mathias DK, Gibbons JG, Armistead JS, Rodriguez MC, Rodriguez MH, Edwards NJ, Hartler J, Thallinger GG, Graham DR, Martinez-Barnetche J, Rokas A, Dinglasan RR. A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Molecular & Cellular Proteomics : McP. 12: 120-31. PMID 23082028 DOI: 10.1074/Mcp.M112.019596 |
0.798 |
|
| 2012 |
Elmore MH, Gibbons JG, Rokas A. Assessing the genome-wide effect of promoter region tandem repeat natural variation on gene expression. G3 (Bethesda, Md.). 2: 1643-9. PMID 23275886 DOI: 10.1534/G3.112.004663 |
0.834 |
|
| 2012 |
Rokas A, Gibbons JG, Zhou X, Beauvais A, Latgé JP. The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. Annals of the New York Academy of Sciences. 1273: 25-34. PMID 23230834 DOI: 10.1111/J.1749-6632.2012.06755.X |
0.812 |
|
| 2012 |
Zhou X, Slone JD, Rokas A, Berger SL, Liebig J, Ray A, Reinberg D, Zwiebel LJ. Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding. Plos Genetics. 8: e1002930. PMID 22952454 DOI: 10.1371/Journal.Pgen.1002930 |
0.691 |
|
| 2012 |
Zhang H, Rokas A, Slot JC. Two different secondary metabolism gene clusters occupied the same ancestral locus in fungal dermatophytes of the arthrodermataceae. Plos One. 7: e41903. PMID 22860027 DOI: 10.1371/Journal.Pone.0041903 |
0.783 |
|
| 2012 |
Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Current Biology : Cb. 22: 1403-9. PMID 22795693 DOI: 10.1016/J.Cub.2012.05.033 |
0.823 |
|
| 2012 |
League GP, Slot JC, Rokas A. The ASP3 locus in Saccharomyces cerevisiae originated by horizontal gene transfer from Wickerhamomyces. Fems Yeast Research. 12: 859-63. PMID 22776361 DOI: 10.1111/J.1567-1364.2012.00828.X |
0.766 |
|
| 2012 |
Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, MartÃnez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, ... ... Rokas A, et al. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science (New York, N.Y.). 336: 1715-9. PMID 22745431 DOI: 10.1126/Science.1221748 |
0.796 |
|
| 2012 |
MartÃnez-Barnetche J, Gómez-Barreto RE, Ovilla-Muñoz M, Téllez-Sosa J, GarcÃa López DE, Dinglasan RR, Ubaida Mohien C, MacCallum RM, Redmond SN, Gibbons JG, Rokas A, Machado CA, Cazares-Raga FE, González-Cerón L, Hernández-MartÃnez S, et al. Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. Bmc Genomics. 13: 207. PMID 22646700 DOI: 10.1186/1471-2164-13-207 |
0.821 |
|
| 2012 |
Stergiopoulos I, Kourmpetis YA, Slot JC, Bakker FT, De Wit PJ, Rokas A. In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins. Molecular Biology and Evolution. 29: 3371-84. PMID 22628532 DOI: 10.1093/Molbev/Mss143 |
0.842 |
|
| 2012 |
Wei C, Salichos L, Wittgrove CM, Rokas A, Patton JG. Transcriptome-wide analysis of small RNA expression in early zebrafish development. Rna (New York, N.Y.). 18: 915-29. PMID 22408181 DOI: 10.1261/Rna.029090.111 |
0.746 |
|
| 2012 |
Campbell MA, Rokas A, Slot JC. Horizontal transfer and death of a fungal secondary metabolic gene cluster. Genome Biology and Evolution. 4: 289-93. PMID 22294497 DOI: 10.1093/Gbe/Evs011 |
0.786 |
|
| 2012 |
Klaassen CH, Gibbons JG, Fedorova ND, Meis JF, Rokas A. Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus. Molecular Ecology. 21: 57-70. PMID 22106836 DOI: 10.1111/J.1365-294X.2011.05364.X |
0.799 |
|
| 2012 |
Gibbons JG, Beauvais A, Beau R, McGary KL, Latgé JP, Rokas A. Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryotic Cell. 11: 68-78. PMID 21724936 DOI: 10.1128/Ec.05102-11 |
0.839 |
|
| 2011 |
Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda, Md.). 1: 11-25. PMID 22384314 DOI: 10.1534/G3.111.000273 |
0.828 |
|
| 2011 |
Rokas A. Phylogenetic analysis of protein sequence data using the Randomized Axelerated Maximum Likelihood (RAXML) Program. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit19.11. PMID 21987055 DOI: 10.1002/0471142727.mb1911s96 |
0.508 |
|
| 2011 |
Pitts RJ, Rinker DC, Jones PL, Rokas A, Zwiebel LJ. Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding. Bmc Genomics. 12: 271. PMID 21619637 DOI: 10.1186/1471-2164-12-271 |
0.747 |
|
| 2011 |
Salichos L, Rokas A. Evaluating ortholog prediction algorithms in a yeast model clade. Plos One. 6: e18755. PMID 21533202 DOI: 10.1371/Journal.Pone.0018755 |
0.785 |
|
| 2011 |
Kent BN, Salichos L, Gibbons JG, Rokas A, Newton IL, Clark ME, Bordenstein SR. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biology and Evolution. 3: 209-18. PMID 21292630 DOI: 10.1093/Gbe/Evr007 |
0.835 |
|
| 2011 |
Slot JC, Rokas A. Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Current Biology : Cb. 21: 134-9. PMID 21194949 DOI: 10.1016/J.Cub.2010.12.020 |
0.729 |
|
| 2010 |
An J, Bechet A, Berggren A, Brown SK, Bruford MW, Cai Q, Cassel-Lundhagen A, Cezilly F, Chen SL, Cheng W, Choi SK, Ding XY, Fan Y, Feldheim KA, ... ... Rokas A, et al. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009. Molecular Ecology Resources. 10: 404-8. PMID 21565039 DOI: 10.1111/J.1755-0998.2009.02827.X |
0.802 |
|
| 2010 |
Carnahan RH, Rokas A, Gaucher EA, Reynolds AB. The molecular evolution of the p120-catenin subfamily and its functional associations. Plos One. 5: e15747. PMID 21209830 DOI: 10.1371/Journal.Pone.0015747 |
0.503 |
|
| 2010 |
Slot JC, Rokas A. Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proceedings of the National Academy of Sciences of the United States of America. 107: 10136-41. PMID 20479238 DOI: 10.1073/Pnas.0914418107 |
0.752 |
|
| 2010 |
Salichos L, Rokas A. The diversity and evolution of circadian clock proteins in fungi. Mycologia. 102: 269-78. PMID 20361495 DOI: 10.3852/09-073 |
0.77 |
|
| 2010 |
Hittinger CT, Gonçalves P, Sampaio JP, Dover J, Johnston M, Rokas A. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature. 464: 54-8. PMID 20164837 DOI: 10.1038/Nature08791 |
0.816 |
|
| 2010 |
Hittinger CT, Johnston M, Tossberg JT, Rokas A. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proceedings of the National Academy of Sciences of the United States of America. 107: 1476-81. PMID 20080632 DOI: 10.1073/Pnas.0910449107 |
0.818 |
|
| 2009 |
Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Molecular Biology and Evolution. 26: 2731-44. PMID 19706727 DOI: 10.1093/Molbev/Msp188 |
0.828 |
|
| 2009 |
Rokas A, Abbot P. Harnessing genomics for evolutionary insights. Trends in Ecology & Evolution. 24: 192-200. PMID 19201503 DOI: 10.1016/J.Tree.2008.11.004 |
0.527 |
|
| 2009 |
Rokas A. The effect of domestication on the fungal proteome. Trends in Genetics : Tig. 25: 60-3. PMID 19081651 DOI: 10.1016/j.tig.2008.11.003 |
0.494 |
|
| 2009 |
Gibbons JG, Rokas A. Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes. Molecular Biology and Evolution. 26: 591-602. PMID 19056904 DOI: 10.1093/Molbev/Msn277 |
0.833 |
|
| 2008 |
Rokas A. The origins of multicellularity and the early history of the genetic toolkit for animal development. Annual Review of Genetics. 42: 235-51. PMID 18983257 DOI: 10.1146/annurev.genet.42.110807.091513 |
0.536 |
|
| 2008 |
Rokas A. The molecular origins of multicellular transitions. Current Opinion in Genetics & Development. 18: 472-8. PMID 18926910 DOI: 10.1016/j.gde.2008.09.004 |
0.522 |
|
| 2008 |
Rokas A, Chatzimanolis S. From gene-scale to genome-scale phylogenetics: the data flood in, but the challenges remain. Methods in Molecular Biology (Clifton, N.J.). 422: 1-12. PMID 18629657 DOI: 10.1007/978-1-59745-581-7_1 |
0.573 |
|
| 2008 |
Rokas A, Carroll SB. Frequent and widespread parallel evolution of protein sequences. Molecular Biology and Evolution. 25: 1943-53. PMID 18583353 DOI: 10.1093/molbev/msn143 |
0.637 |
|
| 2008 |
Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, Koehrsen M, Rokas A, Yandava CN, Engels R, Zeng E, Olavarietta R, Doud M, Smith RS, Montgomery P, White JR, et al. Dynamics of Pseudomonas aeruginosa genome evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 3100-5. PMID 18287045 DOI: 10.1073/Pnas.0711982105 |
0.589 |
|
| 2008 |
King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 451: 783-8. PMID 18273011 DOI: 10.1038/Nature06617 |
0.677 |
|
| 2008 |
Rokas A. Genomics. Lining up to avoid bias. Science (New York, N.Y.). 319: 416-7. PMID 18218881 DOI: 10.1126/science.1153156 |
0.504 |
|
| 2008 |
Stone GN, Atkinson RJ, Rokas A, Aldrey JL, Melika G, Acs Z, Csóka G, Hayward A, Bailey R, Buckee C, McVean GA. Evidence for widespread cryptic sexual generations in apparently purely asexual Andricus gallwasps. Molecular Ecology. 17: 652-65. PMID 18086197 DOI: 10.1111/J.1365-294X.2007.03573.X |
0.635 |
|
| 2008 |
Geiser DM, Samson RA, Varga J, Rokas A, Witiak SM. A review of molecular phylogenetics in Aspergillus, and prospects for a robust genus-wide phylogeny Aspergillus in the Genomic Era. 17-32. DOI: 10.3920/978-90-8686-635-9 |
0.487 |
|
| 2007 |
Rokas A, Payne G, Fedorova ND, Baker SE, Machida M, Yu J, Georgianna DR, Dean RA, Bhatnagar D, Cleveland TE, Wortman JR, Maiti R, Joardar V, Amedeo P, Denning DW, et al. What can comparative genomics tell us about species concepts in the genus Aspergillus? Studies in Mycology. 59: 11-7. PMID 18490942 DOI: 10.3114/Sim.2007.59.02 |
0.598 |
|
| 2007 |
Rokas A, Hittinger CT. Transcriptional rewiring: the proof is in the eating. Current Biology : Cb. 17: R626-8. PMID 17714646 DOI: 10.1016/J.Cub.2007.06.025 |
0.779 |
|
| 2007 |
Stone GN, Challis RJ, Atkinson RJ, Csóka G, Hayward A, Melika G, Mutun S, Preuss S, Rokas A, Sadeghi E, Schönrogge K. The phylogeographical clade trade: tracing the impact of human-mediated dispersal on the colonization of northern Europe by the oak gallwasp Andricus kollari. Molecular Ecology. 16: 2768-81. PMID 17594446 DOI: 10.1111/J.1365-294X.2007.03348.X |
0.647 |
|
| 2007 |
Challis RJ, Mutun S, Nieves-Aldrey JL, Preuss S, Rokas A, Aebi A, Sadeghi E, Tavakoli M, Stone GN. Longitudinal range expansion and cryptic eastern species in the western Palaearctic oak gallwasp, Andricus coriarius. Molecular Ecology. 16: 2103-14. PMID 17498235 DOI: 10.1111/J.1365-294X.2006.03210.X |
0.68 |
|
| 2007 |
Ané C, Larget B, Baum DA, Smith SD, Rokas A. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution. 24: 412-26. PMID 17095535 DOI: 10.1093/Molbev/Msl170 |
0.572 |
|
| 2007 |
Atkinson RJ, Rokas A, Stone GN. Longitudinal patterns in species richness and genetic diversity in European oaks and oak gallwasps Phylogeography of Southern European Refugia: Evolutionary Perspectives On the Origins and Conservation of European Biodiversity. 127-151. DOI: 10.1007/1-4020-4904-8_4 |
0.654 |
|
| 2006 |
Rokas A, Carroll SB. Bushes in the tree of life. Plos Biology. 4: e352. PMID 17105342 DOI: 10.1371/journal.pbio.0040352 |
0.579 |
|
| 2006 |
Rokas A. Genomics. Genomics and the tree of life. Science (New York, N.Y.). 313: 1897-9. PMID 17008515 DOI: 10.1126/science.1134490 |
0.539 |
|
| 2006 |
Rokas A. Evolution: different paths to the same end. Nature. 443: 401-2. PMID 17006502 DOI: 10.1038/443401a |
0.447 |
|
| 2006 |
Jeong S, Rokas A, Carroll SB. Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution. Cell. 125: 1387-99. PMID 16814723 DOI: 10.1016/j.cell.2006.04.043 |
0.647 |
|
| 2006 |
Prud'homme B, Gompel N, Rokas A, Kassner VA, Williams TM, Yeh SD, True JR, Carroll SB. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature. 440: 1050-3. PMID 16625197 DOI: 10.1038/Nature04597 |
0.768 |
|
| 2005 |
Rokas A, Krüger D, Carroll SB. Animal evolution and the molecular signature of radiations compressed in time. Science (New York, N.Y.). 310: 1933-8. PMID 16373569 DOI: 10.1126/science.1116759 |
0.642 |
|
| 2005 |
Rokas A, Carroll SB. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Molecular Biology and Evolution. 22: 1337-44. PMID 15746014 DOI: 10.1093/molbev/msi121 |
0.688 |
|
| 2004 |
Hittinger CT, Rokas A, Carroll SB. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proceedings of the National Academy of Sciences of the United States of America. 101: 14144-9. PMID 15381776 DOI: 10.1073/Pnas.0404319101 |
0.849 |
|
| 2004 |
Rokas A. What determines the direction of evolutionary change? Trends in Ecology & Evolution. 19: 287-288. DOI: 10.1016/J.TREE.2004.03.019 |
0.437 |
|
| 2003 |
Rokas A, Williams BL, King N, Carroll SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 425: 798-804. PMID 14574403 DOI: 10.1038/Nature02053 |
0.773 |
|
| 2003 |
Rokas A, Atkinson RJ, Webster L, Csóka G, Stone GN. Out of Anatolia: longitudinal gradients in genetic diversity support an eastern origin for a circum-Mediterranean oak gallwasp Andricus quercustozae. Molecular Ecology. 12: 2153-74. PMID 12859636 DOI: 10.1046/J.1365-294X.2003.01894.X |
0.671 |
|
| 2003 |
Cummings MP, Handley SA, Myers DS, Reed DL, Rokas A, Winka K. Comparing bootstrap and posterior probability values in the four-taxon case. Systematic Biology. 52: 477-87. PMID 12857639 DOI: 10.1080/10635150390218213 |
0.449 |
|
| 2003 |
Rokas A, King N, Finnerty J, Carroll SB. Conflicting phylogenetic signals at the base of the metazoan tree. Evolution & Development. 5: 346-59. PMID 12823451 DOI: 10.1046/J.1525-142X.2003.03042.X |
0.739 |
|
| 2003 |
Rokas A, Melika G, Abe Y, Nieves-Aldrey JL, Cook JM, Stone GN. Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera: Cynipidae: Cynipini) using mitochondrial sequence data. Molecular Phylogenetics and Evolution. 26: 36-45. PMID 12470936 DOI: 10.1016/S1055-7903(02)00329-9 |
0.693 |
|
| 2003 |
Rokas A, Ladoukakis E, Zouros E. Animal mitochondrial DNA recombination revisited Trends in Ecology and Evolution. 18: 411-417. DOI: 10.1016/S0169-5347(03)00125-3 |
0.671 |
|
| 2002 |
Cook JM, Rokas A, Pagel M, Stone GN. Evolutionary shifts between host oak sections and host-plant organs in Andricus gallwasps. Evolution; International Journal of Organic Evolution. 56: 1821-30. PMID 12389727 DOI: 10.1111/J.0014-3820.2002.Tb00196.X |
0.646 |
|
| 2002 |
Rokas A, Atkinson RJ, Nieves-Aldrey JL, West SA, Stone GN. The incidence and diversity of Wolbachia in gallwasps (Hymenoptera; Cynipidae) on oak. Molecular Ecology. 11: 1815-29. PMID 12207731 DOI: 10.1046/J.1365-294X.2002.01556.X |
0.639 |
|
| 2002 |
Rokas A, Nylander JA, Ronquist F, Stone GN. A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae): implications for insect phylogenetic studies. Molecular Phylogenetics and Evolution. 22: 206-19. PMID 11820842 DOI: 10.1006/Mpev.2001.1032 |
0.657 |
|
| 2002 |
Rokas A. Sexual selection driving spider diversification Trends in Ecology and Evolution. 17: 304. |
0.405 |
|
| 2001 |
Rokas A, Atkinson RJ, Brown GS, West SA, Stone GN. Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep? Heredity. 87: 294-304. PMID 11737276 DOI: 10.1046/J.1365-2540.2001.00872.X |
0.645 |
|
| 2001 |
Rokas A. Selfish element wars in a wasp battleground. Trends in Ecology & Evolution. 16: 277. PMID 11369093 |
0.385 |
|
| 2001 |
Stone G, Atkinson R, Rokas A, Csóka G, Nieves-Aldrey JL. Differential success in northwards range expansion between ecotypes of the marble gallwasp Andricus kollari: a tale of two lifecycles. Molecular Ecology. 10: 761-78. PMID 11298986 DOI: 10.1046/J.1365-294X.2001.01211.X |
0.651 |
|
| 2001 |
Rokas A. Evolutionary biology meets genomics. Trends in Ecology & Evolution. 16: 15-16. PMID 11146135 |
0.563 |
|
| 2001 |
Rokas A. Getting it right for the wrong reason Trends in Ecology and Evolution. 16: 668. DOI: 10.1016/S0169-5347(01)02376-X |
0.378 |
|
| 2001 |
Rokas A. What is a character? Trends in Ecology & Evolution. 16: 590. DOI: 10.1016/S0169-5347(01)02301-1 |
0.425 |
|
| 2001 |
Rokas A. Selfish element wars in a wasp battleground Trends in Ecology and Evolution. 16: 277. |
0.385 |
|
| 2000 |
Rokas A, Holland PW. Rare genomic changes as a tool for phylogenetics. Trends in Ecology & Evolution. 15: 454-459. PMID 11050348 DOI: 10.1016/S0169-5347(00)01967-4 |
0.708 |
|
| 2000 |
Cook JM, Rokas A. Influential passengers come of age. 1st International Wolbachia Conference, Orthodox Academy, Kolymbari, Crete, Greece, 7-12 June 2000. Trends in Genetics : Tig. 16: 378-9. PMID 11041802 DOI: 10.1016/S0168-9525(00)02085-0 |
0.397 |
|
| 2000 |
Rokas A, McVean G. A Bayesian guide to tree felling. Trends in Ecology & Evolution. 15: 396. PMID 10998515 |
0.424 |
|
| 2000 |
Averof M, Rokas A, Wolfe KH, Sharp PM. Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science (New York, N.Y.). 287: 1283-6. PMID 10678838 DOI: 10.1126/Science.287.5456.1283 |
0.466 |
|
| 2000 |
Rokas A. Wolbachia as a speciation agent Trends in Ecology and Evolution. 15: 44-45. DOI: 10.1016/S0169-5347(99)01783-8 |
0.394 |
|
| 1999 |
Rokas A, Kathirithamby J, Holland PW. Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera. Insect Molecular Biology. 8: 527-30. PMID 10620047 DOI: 10.1046/J.1365-2583.1999.00149.X |
0.669 |
|
| Show low-probability matches. |
