Publication Types

 

Journal Covers

Research Articles
  1. Gibbons, J. G., Klich, M. A. and A. Rokas (2009). Developing highly conserved microsatellite markers: a case study in the filamentous fungal genus Aspergillus. Mol. Ecol. Resources: in press.

  2. Salichos, L. and A. Rokas (2009). The diversity and evolution of circadian clock proteins in fungi. Mycologia: in press.

  3. 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.

  4. Rokas, A. and P. Abbot (2009). Harnessing genomics for evolutionary insights. Trends Ecol. Evol. 24: 192-200.

  5. 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.

  6. Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends Genet. (Genome Analysis section) 25: 60-63.

  7. Rokas, A. (2008). The molecular origins of multicellular transitions. Curr. Opin. Genet. Dev. 18: 472-478.

  8. Rokas, A. (2008). The origins of multicellularity and the early history of the genetic toolkit for animal development. Ann. Rev. Genet. 42: 235-251.

  9. Rokas, A., and S. B. Carroll (2008). Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol.25: 1943-1953.

  10. 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. F1000 Factor 3.0

  11. 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. F1000 Factor 6.0

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Rokas, A. and S. B. Carroll (2006). Bushes in the Tree of Life. PLOS Biology: 4: e352.

  18. 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. F1000 Factor 3.0

  19. 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. Commentary in Nature F1000 Factor 8.0

  20. Rokas, A., D. Krueger and S. B. Carroll (2005). Animal evolution and the molecular signature of radiations compressed in time. Science 310: 1933-1938. F1000 Factor 6.0

  21. 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.

  22. 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. Commentary in Heredity

  23. 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.(* These authors contributed equally to this work) Commentary in Nature | F1000 Factor 9.8

  24. Rokas, A., E. Ladoukakis, and E. Zouros (2003). Animal mitochondrial DNA recombination revisited. Trends Ecol. Evol. 18: 411-417.

  25. 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.

  26. 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.

  27. 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. (* These authors contributed equally to this work) F1000 Factor 3.0

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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.

  33. 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.

  34. 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.

  35. Rokas, A. and P. W. H. Holland (2000). Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15: 454-459.

  36. 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.

  37. 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.
Book Chapters
  1. Rokas, A. and S. Chatzimanolis (2008). From gene-scale to genome-scale phylogenetics; the data flood in but the challenges remain. In “Phylogenomics”, W. J. Murphy (Ed.), Methods in Molecular Biology series, Humana Press, pp. 1-12.

  2. Geiser, D. M., R. A. Samson, J. Varga, A. Rokas and 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., and R. A. Sampson (Eds.), Wageningen Academic Publishers, pp. 17-32.

  3. Rokas, A. and 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. and G. H. Goldman (Eds.), CRC Press, pp. 43-55.

  4. Atkinson, R. J., A. Rokas and 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", S. Weiss and N. Ferrand (Eds.), Springer Netherlands, pp. 127-151.

  5. Stone, G. N., R. J. Atkinson, G. Brown, A. Rokas and G. Csoka (2003). The population geenetic consequences of range expansion: oak gallwasps as a model system. In: "Genes in the Environment", R. S. Hails, J. E. Beringer and H. C. J. Godfray (Eds.), Blackwell and the British Ecological Society, pp. 46-62.
Commentaries and Book Reviews
  1. Rokas, A. 2008. Lining up to avoid bias. Science 319: 416-417.
  2. Rokas, A. and C. T. Hittinger. 2007. Transcriptional rewiring: The proof is in the eating. Curr. Biol. 17: R626-R628.
  3. Rokas, A. 2006. Genomics and the tree of life. Science 313: 1897-1898.
  4. Rokas, A. 2006. Different paths to the same end. Nature 443: 401-402.
  5. 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.
  6. Rokas, A. 2002. Sexual selection driving spider diversification. Trends Ecol. Evol. 17: 304.
  7. Rokas, A. 2001. Getting it right for the wrong reason. Trends Ecol. Evol. 16: 668.
  8. 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.
  9. Rokas, A. 2001. Selfish element wars in a wasp battleground. Trends. Ecol. Evol. 16: 277.
  10. Rokas, A. and 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.
  11. Rokas, A. 2001. Evolutionary biology meets genomics. Trends Ecol. Evol. 16: 15-16.
  12. Rokas, A. and G. McVean. 2000. A Bayesian guide to tree felling. Trends Ecol. Evol. 15: 396.
  13. Cook, J. M. and 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.
  14. Rokas, A. 2000. Bacteria altering reproduction in gall wasps or what happens if you don't take your antibiotics! Cecidology 15: 2-7.
  15. Rokas, A. 2000. Wolbachia as a speciation agent. Trends Ecol. Evol. 15: 44-45.