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Wordle made from abstracts of articles published between 1999 and 2017 

Preprint Articles

  1. Lind, A. L., J. H. Wisecaver, C. Lameiras, F. Rodrigues, G. H. Goldman, & A. Rokas (2017). Drivers of genetic diversity in secondary metabolic gene clusters in a fungal population. PDF
    Preprint on BioRxiv server
  2. Zhou, X., X.-X. Shen, C. T. Hittinger, & A. Rokas (2017). Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. PDF
  3. Preprint on BioRxiv server

  4. Moon, J. M., D. M. Aronoff, J. A. Capra, P. Abbot, & A. Rokas (2017). Genes involved in human sialic acid biology do not harbor signatures of recent positive selection. PDF
    Preprint on BioRxiv server
  5. Rinker, D. C., X. Zhou, R. J. Pitts, P. L. Jones, A. Rokas, & L. J. Zwiebel (2015). RNAseq in the mosquito maxillary palp: a little antennal RNA goes a long way. PDF
    Preprint on BioRxiv server

Research Articles

  1. Wu, M.-Y., M. E. Mead, S.-C. Kim, A. Rokas, & J.-H. Yu (2017). WetA bridges cellular and chemical development in Aspergillus flavus. PLoS ONE: in press.
  2. Zhao, L., X. Zhou, A. Rokas, & R. D. Cone (2017). Functional variants of the melanocortin-4 receptor associated with the Odontoceti and Mysticeti suborders of cetaceans. Sci. Rep.: in press.
  3. Fidler, A. L., C. E. Darris, S. V. Chetyrkin, V. K. Pedchenko, S. P. Boudko, K. L. Brown, W. G. Jerome, J. K. Hudson, A. Rokas, & B. G. Hudson (2017). Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues. eLife 6: e24176. PDF
  4. Wisecaver, J. H., A. T. Borowsky, V. Tzin, G. Jander, D. J. Kliebenstein, & A. Rokas (2017). A global co-expression network approach for connecting genes to specialized metabolic pathways in plants. The Plant Cell 29: 944–959. PDF
    Commentary in The Plant Cell
  5. Shen, X.-X., C. T. Hittinger, & A. Rokas (2017). Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecol. Evol. 1: 0126. PDF
    The story behind the paper in Nature Ecology & Evolution blog
  6. Steenwyk, J. & A. Rokas (2017). Extensive copy number variation in fermentation-related genes among Saccharomyces cerevisiae wine strains. G3 7: 1475-1485. PDF
  7. Ortiz, J. F. & A. Rokas (2017). CTDGFinder: A novel homology-based algorithm for identifying closely spaced clusters of tandemly duplicated genes. Mol. Biol. Evol. 34: 215-229. PDF
    Download CTDGFinder
  8. Lind, A. L., T. Satterlee, T. D. Smith, A. M. Calvo, & A. Rokas (2016). Regulation of secondary metabolism by the Velvet complex is temperature-responsive in Aspergillus. G3 6: 4023-4033. PDF
  9. Shen, X.-X., X. Zhou, J. Kominek, C. P. Kurtzman, C. T. Hittinger, & A. Rokas (2016). Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 6: 3927-3939. PDF
  10. Zhou, X., D. Peris, C. T. Hittinger, & A. Rokas (2016). in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies. G3 6: 3655-3662. PDF
    Download iWGS
  11. Shen, X.-X., L. Salichos, & A. Rokas (2016). A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference. Genome Biol. Evol. 8: 2565–2580. PDF
  12. Riley, R., S. Haridas, K. H. Wolfe, M. R. Lopes, C. T. Hittinger, M. Göker, A. Salamov, J. H. Wisecaver, T. M. Long, C. H. Calvey, A. L. Aerts, K. Barry, C. Choi, A Clum, A. Y. Coughlan, S. Deshpande, A. P. Douglass, S. J. Hanson, H.-P. Klenk, K. LaButti, A. Lapidus, E. Lindquist, A. Lipzen, J. P. Meier-Kolthoff, R. A. Ohm, R. P. Otillar, J. Pangilinan, Y. Peng, A. Rokas, C. A. Rosa, C. Scheuner, A. A. Sibirny, J. C. Slot, J. B. Stielow, H. Sun, C. P. Kurtzman, M. Blackwell, I. V. Grigoriev, & T. W. Jeffries (2016). Comparative genomics of biotechnologically important yeasts. Proc. Natl. Acad. Sci. USA 113: 9882–9887. PDF
  13. Ackerman IV, W. E., I. A. Buhimschi, H. R. Eidem, D. C. Rinker, A. Rokas, K. Rood, G. Zhao, T. L. Summerfield, M. B. Landon, & C. S. Buhimschi (2016). Comprehensive RNA profiling of villous trophoblast and decidua basalis in pregnancies complicated by preterm birth following intra-amniotic infection. Placenta 44: 23-33. PDF
  14. Wisecaver, J. H., W. G. Alexander, S. B. King, C. T. Hittinger, & A. Rokas (2016). Dynamic evolution of nitric oxide detoxifying flavohemoglobins, a family of single-protein metabolic modules in bacteria and eukaryotes. Mol. Biol. Evol. 33: 1979–1987. PDF
  15. Eidem, H. R., D. C. Rinker, W. E. Ackerman IV, I. A. Buhimschi, C. S. Buhimschi, C. Dunn-Fletcher, S. G. Kallapur, M. Pavlicev, L. J. Muglia, P. Abbot, & A. Rokas (2016). Comparing human and macaque placental transcriptomes to disentangle preterm birth pathology from gestational age effects. Placenta 41: 74-82. PDF
  16. Alexander, W. G., J. H. Wisecaver, A. Rokas, & C. T. Hittinger (2016). Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proc. Natl. Acad. Sci. USA 113: 4116–4121. PDF
  17. Kobert, K., L. Salichos, A. Rokas, & A. Stamatakis (2016). Computing the Internode Certainty and related measures from partial gene trees. Mol. Biol. Evol. 33: 1606-1617. PDF
  18. Staehlin, B. M., J. G. Gibbons, A. Rokas, T. V. O’Halloran, & J. C. Slot (2016). Evolution of a heavy metal homeostasis/resistance island reflects increasing copper stress in Enterobacteria. Genome Biol. Evol. 8: 811-826. PDF
  19. Kim, M., B. A. Cooper, R. Venkat, J. B. Phillips, H. R. Eidem, J. Hirbo, S. Nutakki, S. M. Williams, L. J. Muglia, J. A. Capra, K. Petren, P. Abbot, A. Rokas, & K. L. McGary (2016). 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 Res. 44, Database issue: D908-916. PDF
    OggiScienza article
    Science Daily article
  20. Wang, Y., X. Zhou, D. Yang, & A. Rokas (2015). A genome-scale investigation of incongruence in Culicidae mosquitoes. Genome Biol. Evol. 7: 3463-3471. PDF
  21. Hirbo, J., H. R. Eidem, A. Rokas, & P. Abbot (2015). Integrating diverse types of genomic data to identify genes that underlie adverse pregnancy phenotypes. PLoS ONE 10: e0144155. PDF
  22. Hittinger, C. T., A. Rokas, F.-Y. Bai, T. Boekhout, P. Gonçalves, T. W. Jeffries, J. Kominek, M.-A. Lachance, D. Libkind, C. A. Rosa, J. P. Sampaio, & C. P. Kurtzman (2015). Genomics and the making of yeast biodiversity. Curr. Opin. Genet. Dev. 35: 100–109. PDF
  23. Zhou, X., A. Rokas, S. L. Berger, J. Liebig, A. Ray, & L. J. Zwiebel (2015). Chemoreceptor evolution in Hymenoptera and its implications for the evolution of eusociality. Genome Biol. Evol. 7: 2407-2416. PDF
  24. Phillips, J. B., P. Abbot, & A. Rokas (2015). Is preterm birth a human-specific syndrome? Evol. Med. Public Health 2015: 136-148. PDF
  25. Eidem, H. R., W. E. Ackerman IV, K. L. McGary, P. Abbot, & A. Rokas (2015). Gestational tissue transcriptomics in term and preterm human pregnancies: A systematic review and meta-analysis. BMC Med. Genomics 8: 27. PDF
  26. Lind, A. L., J. H. Wisecaver, T. D. Smith, X. Feng, A. M. Calvo, & A. Rokas (2015). Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus. PLoS Genet. 11: e1005096. PDF
    Aspergillus fumigatus data in FungiDB
    Aspergillus nidulans data in FungiDB
  27. Wisecaver, J. H., & A. Rokas (2015). Fungal metabolic gene clusters – caravans traveling across genomes and environments. Front. Microbiol. 6: 161. PDF
  28. Eidem, H. R.*, K. L. McGary*, & A. Rokas (2015). Shared selective pressures on fungal and human metabolic pathways lead to divergent yet analogous genetic responses. Mol. Biol. Evol. 32: 1449–1455. (*Equal contributors) PDF
  29. Elmore, M. H.*, K. L. McGary*, J. H. Wisecaver, J. C. Slot, D. M. Geiser, S. Sink, K. O’Donnell, & A. Rokas (2015). Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. Genome Biol. Evol. 7: 789-800. (*Equal contributors) PDF
  30. Neafsey, D. E., R. M. Waterhouse, 117 other authors including X. Zhou, D. C. Rinker, A. Rokas and L. J. Zwiebel, & N. J. Besansky (2015). Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science 347: 43. PDF
    Commentary in Science
    Commentary in Nature Genetics
  31. Wisecaver, J. H.*, J. C. Slot*, & A. Rokas (2014). The evolution of fungal metabolic pathways. PLoS Genet. 10: e1004816. (*Equal contributors) PDF
  32. Zhou, X.*, D. C. Rinker*, R. J. Pitts, A. Rokas, and L. J. Zwiebel (2014). Divergent and conserved elements comprise the chemoreceptive repertoire of the non-blood feeding mosquito Toxorhynchites amboinensis. Genome Biol. Evol. 6: 2883-2896. (*Equal contributors) PDF
  33. Polzin, K. and A. Rokas (2014). Evaluating rare amino acid substitutions (RGC_CAMs) in a yeast model clade. PLoS ONE 9: e92213. PDF
    Retrieve scripts and data
  34. Salichos, L., A. Stamatakis, and A. Rokas (2014). Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol. Evol. 31: 1261-1271. PDF
  35. Zhou, X. and A. Rokas (2014). Prevention, diagnosis, and treatment of high throughput sequencing data pathologies. Mol. Ecol. 23: 1679-1700. PDF
  36. Soria, P. S.*, K. L. McGary*, and A. Rokas (2014). Functional divergence for every paralog. Mol. Biol. Evol. 31: 984-992. (*Equal contributors) PDF
  37. Greene, G. H., K. L. McGary, A. Rokas, and J. C. Slot (2014). Ecology drives the distribution of specialized tyrosine metabolism modules in fungi. Genome Biol. Evol. 6: 121-132. PDF
  38. Samuels, D. C., C. Li, B. Li, Z. Song, E. Torstenson, H. B. Clay, A. Rokas, T. Thornton-Wells, J. H. Moore, T. Hughes, R. Hoffman, J. L. Haines, D. G. Murdock, D. P. Mortlock, and S. M. Williams (2013). Recurrent tissue-specific mtDNA mutations are common in humans. PLoS Genetics 9: e1003929. PDF
  39. Rinker, D. C.*, X. Zhou*, R. J. Pitts, The AGC Consortium, A. Rokas, and L. J. Zwiebel (2013). Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. BMC Genomics 14: 749. (*Equal contributors) PDF
  40. Dhingra, S., A. L. Lind, H-C. Lin, Y. Tang, A. Rokas, and A. M. Calvo (2013). The fumagillin gene cluster, an example of hundreds of genes under veA control in Aspergillus fumigatus. PLoS ONE 8: e77147. PDF
  41. Campbell, M. A., M. Staats, J. L. A. van Kan, A. Rokas, and J. C. Slot (2013). Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia 105: 1126–1134. PDF
  42. McGary, K. L., J. C. Slot, and A. Rokas (2013). The physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds. Proc. Natl. Acad. Sci. USA 110: 11481–11486. PDF
  43. Predazzi, I. M., A. Rokas, A. Deinard, N. Schnetz-Boutaud, N. D. Williams, W. S. Bush, A. Tacconelli, K. Friedrich, S. Fazio, G. Novelli, J. L. Haines, G. Sirugo, and S. M. Williams (2013). Putting pleiotropy and selection into context defines a new paradigm for interpreting genetic data. Circ. Cardiovasc. Genet. 6: 299-307. PDF
  44. Salichos, L., and A. Rokas (2013). Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331. PDF
    Retrieve data
    Wired article
  45. Rinker, D. C., R. J. Pitts, X. Zhou, E. Suh, A. Rokas, and L. J. Zwiebel (2013). Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in the malaria vector mosquito Anopheles gambiae. Proc. Natl. Acad. Sci. USA 110: 8260-8265. PDF
    Cover article
  46. Bradshaw, R. E., J. C. Slot, G. G. Moore, P. Chettri, P. J. G. M. de Wit, K. C. Ehrlich, A. R. D. Ganley, M. A. Olson, A Rokas, I. Carbone, and M. P. Cox (2013). Fragmentation of an aflatoxin-like gene cluster in a forest pathogen. New Phytol. 198: 525–535. PDF
  47. Xu, Y., P. Ma, P. Shah, A. Rokas, Y. Liu, and C. H. Johnson (2013). Non-optimal codon usage is a post-transcriptional mechanism to achieve conditionality of circadian clock function. Nature 495: 116-120. PDF
    Commentary in Nature
    Commentary in Nature Reviews Microbiology
  48. Adhikary, S., M. C. Cato, K. L. McGary, A. Rokas, and B. F. Eichman (2013). Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. DNA Repair 12: 196-204. PDF
  49. Muszkieta, L., A. Beauvais, V. Pähtz, J. G. Gibbons, V. A. Leberre, R. Beau, K. Shibuya, A. Rokas, J. M. Francois, O. Kniemeyyer, A. A. Brakhage, and J.-P. Latge (2013). Investigation of Aspergillus fumigatus biofilm formation by various “omics” approaches. Front. Microbiol. 4: 13. PDF
  50. Ubaida Mohien, C., D. R. Colquhoun, D. K. Mathias, J. G. Gibbons, J. S. Armistead, M. del Carmen-Rodriguez, M. H. Rodriguez, N. J. Edwards, J. Hartler, G. G. Thallinger, D. R. Graham, J. Martinez-Barnetche, A. Rokas, and R. R. Dinglasan (2013). A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Mol. Cell. Proteomics 12: 120-131. PDF
    Science Daily article
  51. Gibbons, J. G., and A. Rokas (2013). The function and evolution of the Aspergillus genome. Trends Microbiol. 21: 14-22. PDF
  52. Rokas, A., J. G. Gibbons, X. Zhou, A. Beauvais, and J.-P. Latge (2012). The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. Ann. N. Y. Acad. Sci. 1273: 25-34. PDF
  53. Elmore, M. H.*, J. G. Gibbons*, and A. Rokas (2012). Assessing the genome-wide effect of promoter region tandem repeat natural variation on gene expression. G3 2: 1643-1649. (*Equal contributors) PDF
  54. Zhou, X.*, J. D. Slone*, A. Rokas, S. L. Berger, J. Liebig, A. Ray, D. Reinberg, and L. J. Zwiebel (2012). Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding. PLoS Genet. 8: e1002930. (*Equal contributors) PDF
    New York Times article
  55. League, G. P., J. C. Slot, and A. Rokas (2012). The ASP3 locus in Saccharomyces cerevisiae originated by horizontal gene transfer from Wickerhamomyces. FEMS Yeast Res. 12: 859-863. PDF
  56. Zhang, H., A. Rokas, and J. C. Slot (2012). Two different secondary metabolism gene clusters occupied the same ancestral locus in fungal dermatophytes of the Arthrodermataceae. PLoS ONE 7: e41903. PDF
    Blogs: The Mycelium Connection
  57. Gibbons, J. G., L. Salichos, J. C. Slot, D. C. Rinker, K. L. McGary, J. G. King, M. A. Klich, D. L. Tabb, W. H. McDonald, and A. Rokas (2012). The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Curr. Biol. 22: 1403-1409. PDF
    Retrieve sequence alignment data
    Dataset of the Week, The Global Proteome Machine
    Scientific American podcast
    Aspergillus website
    A Schooner of Science
    Small Things Considered
    Biotechniques article
    Science Daily article
  58. Stergiopoulos, I., Y. A. I. Kourmpetis, J. C. Slot, F. T. Bakker, P. J. G. M. De Wit, and A. Rokas (2012). In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins. Mol. Biol. Evol. 29: 3371-3384. PDF
  59. Floudas, D., M. Binder, 68 other authors including A. Rokas and J. C. Slot, and D. S. Hibbett (2012). The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719. PDF
    Commentary in Science
    Scientific American article
  60. Martínez-Barnetche, J., R. E. Gómez-Barreto, M. Ovilla-Muñoz, J. Téllez-Sosa, D. E. García López, R. R. Dinglasan, C. Ubaida-Mohien, R. M. MacCallum, S. N. Redmond, J. G. Gibbons, A.Rokas, C. A. Machado, F. Cazares-Raga, L. González-Cerón, S. Hernández-Martínez, and M. H. Rodríguez López (2012). Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. BMC Genomics 13: 207. PDF
  61. Wei, C., L. Salichos, C. M. Wittgrove, A. Rokas, and J. G. Patton (2012). Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA 18: 915-929. PDF
  62. Campbell, M. A., A. Rokas, and J. C. Slot (2012). Horizontal transfer and death of a fungal secondary metabolic gene cluster. Genome Biol. Evol. 4: 289-293. PDF
  63. Klaassen,C. H. W.*, J. G. Gibbons*, N. D. Fedorova, J. F. Meis, and A. Rokas (2012). Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus. Mol. Ecol. 21: 57-70. (*Equal contributors) PDF
  64. Gibbons, J. G., A. Beauvais, R. Beau, K. L. McGary, J.-P. Latge, and A. Rokas (2012). Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Euk. Cell 11: 68-78. PDF
    Cover article
    Spotlight
  65. Rokas, A. (2011). Phylogenetic analysis of protein sequence data using the Randomized Axelerated Maximum Likelihood (RAxML) program. Curr. Prot. Mol. Biol. 96:19.11.1-19.11.14. PDF
  66. Pitts, R. J.*, D. C Rinker*, P. L. Jones*, A. Rokas, and L. J. Zwiebel (2011). Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding. BMC Genomics 12: 271. (*Equal contributors) PDF
  67. Scannell, D. R., O. A. Zill, A. Rokas, C. Payen, M. J. Dunham, M. B. Eisen, J. Rine, M. Johnston, C. T. Hittinger (2011). The awesome power of yeast evolutionary genetics: New genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3 1: 11-25. PDF
    Retrieve data
    Science Daily article
  68. Salichos, L., and A. Rokas (2011). Evaluating ortholog prediction algorithms in a yeast model clade. PLoS ONE 6: e18755. PDF
    Retrieve cRBH script
  69. Slot, J. C. and A. Rokas (2011). Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr. Biol. 21: 134-139. PDF

    Cover article
    Video abstract
    Commentary in Current Biology
    Athens News article
    Sminton Science comic
    Science Daily article
  70. Kent, B. N., L. Salichos, J. G. Gibbons, A. Rokas, I. L. G. Newton, M. E. Clark, and S. R. Bordenstein (2011). Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol. Evol. 3: 209-218. PDF
    Cover article
  71. Carnahan, R. H.*, A. Rokas*, E. A. Gaucher, and A. B. Reynolds (2010). The molecular evolution of the p120-catenin subfamily and its functional associations. PLoS ONE 5: e15747. (*Equal contributors) PDF
  72. Slot, J. C. and A. Rokas (2010). Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc. Natl. Acad. Sci. USA 107: 10136-10141. PDF
  73. Hittinger, C. T., P. Gonçalves, J. P. Sampaio, J. Dover, M. Johnston and A. Rokas (2010). Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464: 54-58. PDF
    Commentary in Nature Reviews Genetics
    Science Daily article
  74. Salichos, L. and A. Rokas (2010). The diversity and evolution of circadian clock proteins in fungi. Mycologia 102: 269-278. PDF
  75. Gibbons, J. G., M. A. Klich and A. Rokas (2010). Developing highly conserved microsatellite markers: a case study in the filamentous fungal genus Aspergillus. Mol. Ecol. Resources 10: 404-408.
    Summary article: PDF
    Full article: PDF
  76. Hittinger, C. T., M. Johnston, J. T. Tossberg and A. Rokas (2010). Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc. Natl. Acad. Sci. USA 107: 1476-1481. PDF
    Biotechniques article
    UCD advocate article
  77. Gibbons, J. G., E. Janson, C. T. Hittinger, M. Johnston, P. Abbot and A. Rokas (2009).
    Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol. Biol. Evol. 26: 2731-2744. PDF
  78. Rokas, A. and P. Abbot (2009). Harnessing genomics for evolutionary insights. Trends Ecol. Evol. 24: 192-200. PDF
  79. Gibbons, J. G. and A. Rokas (2009). Comparative and functional characterization of intragenic tandem repeats in ten Aspergillus genomes. Mol. Biol. Evol. 26: 591-602. PDF
  80. Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends Genet. (Genome Analysis section) 25: 60-63. PDF
  81. Rokas, A. (2008). The molecular origins of multicellular transitions. Curr. Opin. Genet. Dev. 18: 472-478. PDF
  82. Rokas, A. (2008). The origins of multicellularity and the early history of the genetic toolkit for animal development. Ann. Rev. Genet. 42: 235-251. PDF
  83. Rokas, A., and S. B. Carroll (2008). Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol.25: 1943-1953. PDF
  84. Mathee, K., G. Narasimhan, C. Valdes, X. Qiu, J. M. Matewish, M. Koehrsen, A. Rokas, C. N. Yandava, R. Engels, E. Zeng, R. Olavarietta, M. Doud, R. S. Smith, P. Montgomery, J. R. White, P. A. Godfrey, C. Kodira, B. Birren, J. E. Galagan, and S. Lory (2008). Dynamics of Pseudomonas aeruginosa genome evolution. Proc. Natl. Acad. Sci. USA 105: 3100-3105. PDF
  85. King, N., M. J. Westbrook, S. L. Young, A. Kuo, M. Abedin, J. Chapman, S. Fairclough, U. Hellsten, Y. Isogai, I. Letunic, M. Marr, D. Pincus, N. Putnam, A. Rokas, K. J. Wright, R. Zuzow, W. Dirks, M. Good, D. Goodstein, D. Lemons, W. Li, J. Lyons, A. Morris, S. Nichols, D. J. Richter, A. Salamov, JGI Sequencing, P. Bork, W. A. Lim, G. Manning, W. T. Miller, W. McGinnis, H. Shapiro, R. Tjian, I. V. Grigoriev, and D. Rokhsar (2008). The genome of the choanoflagellate Monosiga brevicollis and the origins of metazoan multicellularity. Nature 451: 783-788.PDF
  86. Stone, G. N., R. J. Atkinson, A. Rokas, J.-L.Nieves-Aldrey, G. Melika, Z. Acs, G. Csóka, A. Hayward, R. Bailey, C. Buckee and G. A. T. McVean (2008). Evidence for widespread cryptic sexual generations in apparently purely asexual Andricus gallwasps. Mol. Ecol. 17: 652-665. PDF
    Cover article
  87. Rokas, A., G. Payne, N.D. Fedorova, S.E. Baker, M. Machida, J. Yu, D. R. Georgianna, R. A. Dean, D. Bhatnagar, T.E. Cleveland, J.R. Wortman, R. Maiti, V. Joardar, P. Amedeo, D.W. Denning and W.C. Nierman (2007). What can comparative genomics tell us about species concepts in the genus Aspergillus? Studies in Mycology 59: 11-17. PDF
  88. Stone, G. N., R. J. Challis, R. J. Atkinson, G. Csóka, A. Hayward, G. Melika, S. Mutun, S. Preuss, A. Rokas, E. Sadeghi, and K. Schönrogge (2007). The phylogeographic clade trade: Tracing the impact of human-mediated dispersal on the colonisation of northern Europe by the oak gallwasp Andricus kollari. Mol. Ecol. 16: 2768-2781. PDF
  89. Challis, R. J., S. Mutun, J.-L. Nieves-Aldrey, S. Preuss, A. Rokas, A. Aebi, E. Sadeghi, M. Tavakoli, and G. N. Stone (2007). Longitudinal range expansion and cryptic eastern species in the western Palaearctic oak gallwasp Andricus coriarius. Mol. Ecol. 16: 2103-2114. PDF
  90. Ane, C., B. Larget, D. A. Baum, S. D. Smith, and Rokas, A. (2007). Bayesian estimation of concordance among gene trees. Mol. Biol. Evol.: 24: 412-426. PDF
  91. Rokas, A. and S. B. Carroll (2006). Bushes in the Tree of Life. PLOS Biology: 4: e352. PDF
  92. Jeong, S., A. Rokas and S. B. Carroll (2006). Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution. Cell 125: 1387-1399. PDF
  93. Prud’homme, B., N. Gompel, A. Rokas, V. A. Kassner, T. M. Williams, S.-D. Yeh, J. R. True and S. B. Carroll (2006). Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440: 1050-1053. PDF

    Commentary in Nature
    Science Daily article
  94. Rokas, A., D. Krueger and S. B. Carroll (2005). Animal evolution and the molecular signature of radiations compressed in time. Science 310: 1933-1938. PDF

    Science Daily article
  95. Rokas, A. and S. B. Carroll (2005). More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22: 1337-1344. PDF
    Retrieve data
  96. Hittinger, C. T., A. Rokas and S. B. Carroll (2004). Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc. Natl. Acad. Sci. USA 101: 14144-14149. PDF
    Commentary in Heredity
    HHMI Bulletin article
    Science Daily article
  97. Rokas, A.*, B. L. Williams*, N. King and S. B. Carroll (2003). Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804. (*Equal contributors) PDF

    Retrieve data
    Commentary in Nature
    Milwaukee Journal Sentinel article
  98. Rokas, A., E. Ladoukakis, and E. Zouros (2003). Animal mitochondrial DNA recombination revisited. Trends Ecol. Evol. 18: 411-417. PDF
  99. Rokas, A., R. J. Atkinson, L. W. I. Webster and G. N. Stone (2003). Out of Anatolia: Longitudinal gradients in genetic diversity support a Turkish origin for a circum-mediterranean oak gallwasp Andricus quercustozae. Mol. Ecol. 12: 2153-2174. PDF
  100. Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas and K. Winka (2003). Comparing bootstrap and posterior probability values in the four taxon case. Syst. Biol. 52: 477-487. PDF
  101. Rokas, A.*, N. King*, J. R. Finnerty and S. B. Carroll (2003). Conflicting phylogenetic signals at the base of the metazoan tree. Devel. Evol. 5: 346-359. (*Equal contributors) PDF

    Cover article
  102. Rokas, A., G. Melika, Y. Abe, J.-L. Nieves-Aldrey, J. M. Cook and G. N. Stone (2003). Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera: Cynipidae: Cynipini) using mitochondrial sequence data. Mol. Phylog. Evol. 26: 36-45. PDF
  103. Cook, J. M., A. Rokas, M. Pagel and G. N. Stone (2002). Evolutionary shifts between host oak species and host plant organs in Andricus gallwasps. Evolution 56: 1821-1830. PDF
  104. Rokas, A., R. J. Atkinson, J.-L. Nieves-Aldrey, S. A. West and G. N. Stone (2002).
    The incidence and diversity of Wolbachia in gallwasps (Hymenoptera; Cynipidae) on oak. Mol. Ecol. 11: 1815-1829. PDF
  105. Rokas, A., J. A. A. Nylander, F. Ronquist and G. N. Stone (2002). A maximum likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae); implications for insect phylogenetic studies. Mol. Phylog. Evol. 22: 206-219. PDF
  106. Stone, G. N., R. J. Atkinson, G. Brown and A. Rokas (2002). The population genetic consequences of range expansion: a review of pattern and process, and the value of oak gallwasps as a model system. Biodiversity Science: 10: 80-97. PDF
  107. Rokas, A., R. J. Atkinson, G. S. Brown, S. A. West and G. N. Stone (2001). Understanding patterns of genetic variation in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep? Heredity 87: 294-304. PDF
  108. Stone, G. N., R. J. Atkinson, A. Rokas, G. Csoka and J.-L. Nieves-Aldrey (2001). Differential success in northwards range expansion between ecotypes of the marble gallwasp Andricus kollari: a tale of two refugia. Mol. Ecol. 10: 761-778. PDF
  109. Rokas, A. and P. W. H. Holland (2000). Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15: 454-459. PDF
    Cover article
  110. Averof, M., A. Rokas, K. H. Wolfe and P. M. Sharp (2000). Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287: 1283-1286. PDF
  111. Rokas, A., J. Kathirithamby and P. W. H. Holland (1999). Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera. Insect Mol. Biol. 8: 527-530. PDF

Edited Volumes

  1. Rokas, A., & P. S. Soltis, Eds. (2015). Special issue on Genomes and Evolution.
    Curr. Opin. Genet. Dev., volume 35: 1-126.
    PDF


Book Chapters

  1. Rokas, A. (2016). Systematics in the age of genomics. In “Next Generation Systematics“, Olson P. D., J. Hughes, & J. A. Cotton (Eds.), Cambridge University Press, pp. 219-228.
  2. Rokas, A. & S. Chatzimanolis (2008). From gene-scale to genome-scale phylogenetics; the data flood in but the challenges remain. In “Phylogenomics“, Murphy, W. J. (Ed.), Methods in Molecular Biology series, Humana Press, pp. 1-12.
  3. Geiser, D. M., R. A. Samson, J. Varga, A. Rokas, & S. M. Witiak (2008). A review of molecular phylogenetics in Aspergillus, and prospects for a robust genus-wide phylogeny. In “Aspergillus in the genomics era“, Varga, J. & R. A. Sampson (Eds.), Wageningen Academic Publishers, pp. 17-32.
  4. Rokas, A. & J. E. Galagan (2007). The Aspergillus nidulans genome and comparative analysis with other Aspergilli. In “The Aspergilli: Genomics, Medical Applications, Biotechnology, and Research Methods”, Osmani, S. A. & G. H. Goldman (Eds.), CRC Press, pp. 43-55.
  5. Atkinson, R. J., A. Rokas, & G. N. Stone (2007). Longitudinal patterns in species richness and genetic diversity in European oaks and oak gallwasps. In: “Phylogeography in southern European refugia: Evolutionary Perspectives on the origins and conservation of European Biodiversity“, Weiss S. & N. Ferrand (Eds.), Springer Netherlands, pp. 127-151.
  6. Stone, G. N., R. J. Atkinson, G. Brown, A. Rokas, & G. Csoka (2003). The population geenetic consequences of range expansion: oak gallwasps as a model system. In: “Genes in the Environment“, Hails R. S., J. E. Beringer, & H. C. J. Godfray (Eds.), Blackwell and the British Ecological Society, pp. 46-62.

Commentaries and Book Reviews

  1. Shropshire, J. D. & A. Rokas (2017). Heredity: The gene family that cheats Mendel. eLife 6: e28567. PDF
  2. Abbot, P. & A. Rokas (2017). Mammalian pregnancy. Curr. Biol. 27: R127-R128. PDF
  3. Rokas, A. (2013). My oldest sister is a sea walnut? Science 342: 1327-1329. PDF
  4. Rokas, A. (2013). Aspergillus. Curr. Biol. 23: R187-R188. PDF
  5. Rokas, A. (2008). Lining up to avoid bias. Science 319: 416-417. PDF
  6. Rokas, A. & C. T. Hittinger (2007). Transcriptional rewiring: The proof is in the eating. Curr. Biol. 17: R626-R628. PDF
  7. Rokas, A. (2006). Genomics and the tree of life. Science 313: 1897-1898. PDF
  8. Rokas, A. (2006). Different paths to the same end. Nature 443: 401-402. PDF
  9. Rokas, A. (2004). What determines the direction of evolutionary change? Book Review of: Biased Embryos and Evolution by W. Arthur, Cambridge University Press, 2004. Trends Ecol. Evol. 19: 287-288.
  10. Rokas, A. (2002). Sexual selection driving spider diversification. Trends Ecol. Evol. 17: 304.
  11. Rokas, A. (2001). Getting it right for the wrong reason. Trends Ecol. Evol. 16: 668.
  12. Rokas, A. (2001). What is a character? Book Review of: The Character Concept in Evolutionary Biology by G. P. Wagner (Ed.), Academic Press, 2000. Trends Ecol. Evol. 16: 590.
  13. Rokas, A. (2001). Selfish element wars in a wasp battleground. Trends. Ecol. Evol. 16: 277.
  14. Rokas, A. & D. Charlesworth (2001). Book Review of: Molecular Evolution and Phylogenetics by M. Nei and S. Kumar, Oxford University Press, 2000. Genet. Res. 77: 117-119.
  15. Rokas, A. (2001). Evolutionary biology meets genomics. Trends Ecol. Evol. 16: 15-16.
  16. Rokas, A. & G. McVean (2000). A Bayesian guide to tree felling. Trends Ecol. Evol. 15: 396.
  17. Cook, J. M. & A. Rokas (2000). Influential passengers come of age, 1st International Wolbachia Conference, Orthodox Academy, Kolymbari, Crete, Greece, 7-12 June 2000. Trends Genet. 16: 378-379.
  18. Rokas, A. (2000). Bacteria altering reproduction in gall wasps or what happens if you don’t take your antibiotics! Cecidology 15: 2-7.
  19. Rokas, A. (2000). Wolbachia as a speciation agent. Trends Ecol. Evol. 15: 44-45. PDF