Antonis Rokas, Ph.D. - Publications

Affiliations: 
2007- Department of Biological Sciences Vanderbilt University, Nashville, TN 
Area:
evolutionary biology, mycology
Website:
http://www.rokaslab.org

156 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.64
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  0.64
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  0.68
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  0.92
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  0.64
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  0.36
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  0.32
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  0.92
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  0.92
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  0.92
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  0.92
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  0.32
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  0.32
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  0.92
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  0.64
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  0.64
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  0.56
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  0.92
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  0.64
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  0.64
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  0.92
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  0.64
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  0.92
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  0.92
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  0.92
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  0.92
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  0.36
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  0.64
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  0.92
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  0.32
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  0.92
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  0.92
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  0.96
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  0.4
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  0.92
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  0.56
2017 Abbot P, Rokas A. Mammalian pregnancy. Current Biology : Cb. 27: R127-R128. PMID 28222284 DOI: 10.1016/j.cub.2016.10.046  0.32
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  0.36
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  0.92
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  0.92
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  1
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  1
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  0.36
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  0.36
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  1
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  1
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  0.96
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  1
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  1
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  1
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  0.56
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  1
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  0.56
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  0.32
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.56
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2013 Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 497: 327-31. PMID 23657258 DOI: 10.1038/nature12130  1
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  1
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  1
2013 Rokas A. Aspergillus. Current Biology : Cb. 23: R187-8. PMID 23473556 DOI: 10.1016/j.cub.2013.01.021  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez 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  1
2012 Martínez-Barnetche J, Gómez-Barreto RE, Ovilla-Muñoz M, Téllez-Sosa J, García López DE, Dinglasan RR, Ubaida Mohien C, MacCallum RM, Redmond SN, Gibbons JG, Rokas A, Machado CA, Cazares-Raga FE, González-Cerón L, Hernández-Martínez 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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.96
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2008 Rokas A. Genomics. Lining up to avoid bias. Science (New York, N.Y.). 319: 416-7. PMID 18218881 DOI: 10.1126/science.1153156  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2007 Carroll SB. Response [3] Science. 318: 196. DOI: 10.1126/science.318.5848.196  1
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  1
2006 Rokas A, Carroll SB. Bushes in the tree of life. Plos Biology. 4: e352. PMID 17105342 DOI: 10.1371/journal.pbio.0040352  1
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  1
2006 Rokas A. Evolution: different paths to the same end. Nature. 443: 401-2. PMID 17006502 DOI: 10.1038/443401a  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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: 10.1080/10635150309311  1
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  1
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  1
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  1
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  1
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  1
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  1
2002 Rokas A. Sexual selection driving spider diversification Trends in Ecology and Evolution. 17: 304.  1
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  1
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  1
2001 Rokas A. Evolutionary biology meets genomics. Trends in Ecology & Evolution. 16: 15-16. PMID 11146135  1
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  1
2001 Rokas A. Selfish element wars in a wasp battleground Trends in Ecology and Evolution. 16: 277.  1
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  1
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  1
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  1
2000 Rokas A. Wolbachia as a speciation agent Trends in Ecology and Evolution. 15: 44-45. DOI: 10.1016/S0169-5347(99)01783-8  1
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  1
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