All Stories

  1. Machine learning enables identification of an alternative yeast galactose utilization pathway

    Article • Proceedings of the National Academy of Sciences, April 2024, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  2. Saccharomycotina yeasts defy long-standing macroecological patterns

    Article • Proceedings of the National Academy of Sciences, February 2024, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

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

    Article • PLoS Biology, October 2022, PLOS

    Professor Antonis Rokas

  4. Signatures of optimal codon usage in metabolic genes inform budding yeast ecology

    Article • PLoS Biology, April 2021, PLOS

    Professor Antonis Rokas

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

    Article • PLoS Biology, December 2020, PLOS

    Professor Antonis Rokas

  6. Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity

    Article • PLoS Pathogens, February 2020, PLOS

    Professor Antonis Rokas

  7. Variation and selection on codon usage bias across an entire subphylum

    Article • PLoS Genetics, July 2019, PLOS

    Professor Antonis Rokas

  8. integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth

    Article • BMC Medical Genomics, November 2018, Springer Science + Business Media

    Professor Antonis Rokas

  9. Gene Essentiality Analyzed byIn VivoTransposon Mutagenesis and Machine Learning in a Stable Haploid Isolate ofCandida albicans

    Article • mBio, October 2018, ASM Journals

    Professor Antonis Rokas

  10. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts

    Article • Proceedings of the National Academy of Sciences, October 2018, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  11. The birth, evolution and death of metabolic gene clusters in fungi

    Article • Nature Reviews Microbiology, September 2018, Springer Science + Business Media

    Professor Antonis Rokas

  12. Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi

    Article • mBio, August 2018, ASM Journals

    Professor Antonis Rokas, Prof Jae-Hyuk Yu

  13. A robust phylogenomic timetree for biotechnologically and medically important fungi from Aspergillaceae (Eurotiomycetes, Ascomycota)

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  14. Fungal Isocyanide Synthases and Xanthocillin Biosynthesis inAspergillus fumigatus

    Article • mBio, May 2018, ASM Journals

    Dr nancy p keller, Professor Antonis Rokas

  15. Conservation and Divergence in the Asexual Sporulation Gene Regulatory Network Across a Genus of Filamentous Fungi

    Article • May 2018, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  16. integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth

    Article • April 2018, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  17. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage

    Article • eLife, April 2018, eLife

    Professor Antonis Rokas

  18. The triple helix of collagens – an ancient protein structure that enabled animal multicellularity and tissue evolution

    Article • Journal of Cell Science, April 2018, The Company of Biologists

    Professor Antonis Rokas

  19. Genome wide association analysis identifies genetic variants associated with reproductive variation across domestic dog breeds and uncovers links to domestication

    Article • March 2018, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  20. An LaeA- and BrlA-Dependent Cellular Network Governs Tissue-Specific Secondary Metabolism in the Human PathogenAspergillus fumigatus

    Article • mSphere, March 2018, ASM Journals

    Dr nancy p keller, Professor Antonis Rokas

  21. Factors driving metabolic diversity in the budding yeast subphylum

    Article • BMC Biology, March 2018, Springer Science + Business Media

    Professor Antonis Rokas

  22. Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation

    Article • Frontiers in Microbiology, February 2018, Frontiers

    Professor Antonis Rokas

  23. Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology

    Article • G3 Genes Genomes Genetics, February 2018, Genetics Society of America

    Professor Antonis Rokas

  24. Inverted formin 2 regulates intracellular trafficking, placentation, and pregnancy outcome

    Article • eLife, January 2018, eLife

    Professor Antonis Rokas

  25. Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation

    Article • December 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  26. Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

    Article • Molecular Biology and Evolution, November 2017, Oxford University Press (OUP)

    Professor Antonis Rokas

  27. Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

    Article • PLoS Biology, November 2017, PLOS

    Professor Antonis Rokas

  28. Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage

    Article • November 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  29. Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  30. Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC

    Article • The EMBO Journal, October 2017, EMBO

    Professor Antonis Rokas

  31. Embracing Uncertainty in Reconstructing Early Animal Evolution

    Article • Current Biology, October 2017, Elsevier

    Professor Antonis Rokas

  32. A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus

    Article • September 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  33. The transformative potential of an integrative approach to pregnancy

    Article • Placenta, September 2017, Elsevier

    Professor Antonis Rokas

  34. Correction: Heredity: The gene family that cheats Mendel

    Article • eLife, August 2017, eLife

    Professor Antonis Rokas

  35. Chlamydomonas reinhardtii LFO1 Is an IsdG Family Heme Oxygenase

    Article • mSphere, August 2017, ASM Journals

    Dr Eric P Skaar, Professor Antonis Rokas

  36. Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence

    Article • July 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  37. MybA, a transcription factor involved in conidiation and conidial viability of the human pathogen Aspergillus fumigatus

    Article • Molecular Microbiology, July 2017, Wiley

    Professor Antonis Rokas

  38. Functional variants of the melanocortin-4 receptor associated with the Odontoceti and Mysticeti suborders of cetaceans

    Article • Scientific Reports, July 2017, Nature

    Professor Antonis Rokas

  39. WetA bridges cellular and chemical development in Aspergillus flavus

    Article • PLoS ONE, June 2017, PLOS

    Professor Antonis Rokas, Prof Jae-Hyuk Yu

  40. The gene family that cheats Mendel

    Article • eLife, June 2017, eLife

    Professor Antonis Rokas

  41. Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  42. Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

    Article • May 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  43. Examination of signatures of recent positive selection on genes involved in human sialic acid biology

    Article • May 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  44. Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues

    Article • eLife, April 2017, eLife

    Professor Antonis Rokas

  45. A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants

    Article • The Plant Cell, April 2017, American Society of Plant Biologists (ASPB)

    Professor Antonis Rokas

  46. Contentious relationships in phylogenomic studies can be driven by a handful of genes

    Article • Nature Ecology & Evolution, April 2017, Nature

    Professor Antonis Rokas

  47. Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains

    Article • G3 Genes Genomes Genetics, March 2017, Genetics Society of America

    Professor Antonis Rokas

  48. Extensive Copy Number Variation in Fermentation-Related Genes among Saccharomyces cerevisiae Wine Strains

    Article • February 2017, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  49. Mammalian pregnancy

    Article • Current Biology, February 2017, Elsevier

    Professor Antonis Rokas

  50. A global co-expression network approach for connecting genes to specialized metabolic pathways in plants

    Article • December 2016, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  51. CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes

    Article • Molecular Biology and Evolution, October 2016, Oxford University Press (OUP)

    Professor Antonis Rokas

  52. Regulation of Secondary Metabolism by the Velvet Complex is Temperature-Responsive in Aspergillus

    Article • G3 Genes Genomes Genetics, September 2016, Genetics Society of America

    Professor Antonis Rokas

  53. Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

    Article • G3 Genes Genomes Genetics, September 2016, Genetics Society of America

    Professor Antonis Rokas

  54. in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

    Article • G3 Genes Genomes Genetics, September 2016, Genetics Society of America

    Professor Antonis Rokas

  55. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

    Article • August 2016, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  56. Comparative genomics of biotechnologically important yeasts

    Article • Proceedings of the National Academy of Sciences, August 2016, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  57. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

    Article • Genome Biology and Evolution, August 2016, Oxford University Press (OUP)

    Professor Antonis Rokas

  58. Comprehensive RNA profiling of villous trophoblast and decidua basalis in pregnancies complicated by preterm birth following intra-amniotic infection

    Article • Placenta, August 2016, Elsevier

    Professor Antonis Rokas

  59. A novel homology-based algorithm for the identification of physically linked clusters of paralogous genes

    Article • May 2016, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  60. Comparing human and macaque placental transcriptomes to disentangle preterm birth pathology from gestational age effects

    Article • Placenta, May 2016, Elsevier

    Dr Mihaela Pavlicev, Professor Antonis Rokas

  61. Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes

    Article • Molecular Biology and Evolution, April 2016, Oxford University Press (OUP)

    Professor Antonis Rokas

  62. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides

    Article • Proceedings of the National Academy of Sciences, March 2016, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  63. Computing the Internode Certainty and Related Measures from Partial Gene Trees

    Article • Molecular Biology and Evolution, February 2016, Oxford University Press (OUP)

    Professor Antonis Rokas

  64. Evolution of a heavy metal homeostasis/resistance island reflects increasing copper stress in Enterobacteria

    Article • Genome Biology and Evolution, February 2016, Oxford University Press (OUP)

    Professor Antonis Rokas

  65. 182: Signature placental and kidney-specific transcripts in the urinary misfoldome of women with preeclampsia (PE)

    Article • American Journal of Obstetrics and Gynecology, January 2016, Elsevier

    Professor Antonis Rokas

  66. Integrating Diverse Types of Genomic Data to Identify Genes that Underlie Adverse Pregnancy Phenotypes

    Article • PLoS ONE, December 2015, PLOS

    Professor Antonis Rokas

  67. Editorial overview: Genomes and evolution: “Seq-ing” answers in life's genomes

    Article • Current Opinion in Genetics & Development, December 2015, Elsevier

    Professor Antonis Rokas

  68. Genomics and the making of yeast biodiversity

    Article • Current Opinion in Genetics & Development, December 2015, Elsevier

    Professor Antonis Rokas

  69. A Genome-Scale Investigation of Incongruence in Culicidae Mosquitoes

    Article • Genome Biology and Evolution, November 2015, Oxford University Press (OUP)

    Professor Antonis Rokas

  70. Correction: The Evolution of Fungal Metabolic Pathways

    Article • PLoS Genetics, September 2015, PLOS

    Professor Antonis Rokas

  71. Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality

    Article • Genome Biology and Evolution, August 2015, Oxford University Press (OUP)

    Professor Antonis Rokas

  72. Computing the Internode Certainty and related measures from partial gene trees.

    Article • July 2015, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  73. Gestational tissue transcriptomics in term and preterm human pregnancies: a systematic review and meta-analysis

    Article • BMC Medical Genomics, June 2015, Springer Science + Business Media

    Professor Antonis Rokas

  74. Examining the Evolution of the Regulatory Circuit Controlling Secondary Metabolism and Development in the Fungal Genus Aspergillus

    Article • PLoS Genetics, March 2015, PLOS

    Professor Antonis Rokas

  75. Fungal metabolic gene clusters—caravans traveling across genomes and environments

    Article • Frontiers in Microbiology, March 2015, Frontiers

    Professor Antonis Rokas

  76. Shared Selective Pressures on Fungal and Human Metabolic Pathways Lead to Divergent yet Analogous Genetic Responses

    Article • Molecular Biology and Evolution, February 2015, Oxford University Press (OUP)

    Professor Antonis Rokas

  77. Clustering of Two Genes Putatively Involved in Cyanate Detoxification Evolved Recently and Independently in Multiple Fungal Lineages

    Article • Genome Biology and Evolution, February 2015, Oxford University Press (OUP)

    Professor Antonis Rokas

  78. 274: Next generation sequencing (RNA-seq) of the human decidual and placental villous transcriptomes in intra-amniotic infection (IAI) induced preterm birth (PTB)

    Article • American Journal of Obstetrics and Gynecology, January 2015, Elsevier

    Professor Antonis Rokas

  79. Is preterm birth a human-specific syndrome?

    Article • Evolution Medicine and Public Health, January 2015, Oxford University Press (OUP)

    Professor Antonis Rokas

  80. The Evolution of Fungal Metabolic Pathways

    Article • PLoS Genetics, December 2014, PLOS

    Professor Antonis Rokas

  81. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

    Article • Science, November 2014, American Association for the Advancement of Science

    Professor Antonis Rokas

  82. Divergent and Conserved Elements Comprise the Chemoreceptive Repertoire of the Nonblood-Feeding Mosquito Toxorhynchites amboinensis

    Article • Genome Biology and Evolution, October 2014, Oxford University Press (OUP)

    Professor Antonis Rokas

  83. Evaluating Rare Amino Acid Substitutions (RGC_CAMs) in a Yeast Model Clade

    Article • PLoS ONE, March 2014, PLOS

    Professor Antonis Rokas

  84. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies

    Article • Molecular Ecology, March 2014, Wiley

    Professor Antonis Rokas

  85. Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

    Article • Molecular Biology and Evolution, February 2014, Oxford University Press (OUP)

    Professor Antonis Rokas

  86. Functional Divergence for Every Paralog

    Article • Molecular Biology and Evolution, January 2014, Oxford University Press (OUP)

    Professor Antonis Rokas

  87. Ecology Drives the Distribution of Specialized Tyrosine Metabolism Modules in Fungi

    Article • Genome Biology and Evolution, January 2014, Oxford University Press (OUP)

    Professor Antonis Rokas

  88. My Oldest Sister Is a Sea Walnut?

    Article • Science, December 2013, American Association for the Advancement of Science

    Professor Antonis Rokas

  89. Recurrent Tissue-Specific mtDNA Mutations Are Common in Humans

    Article • PLoS Genetics, November 2013, PLOS

    Professor Antonis Rokas

  90. The Fumagillin Gene Cluster, an Example of Hundreds of Genes under veA Control in Aspergillus fumigatus

    Article • PLoS ONE, October 2013, PLOS

    Professor Antonis Rokas

  91. Repeated loss of an anciently horizontally transferred gene cluster in Botrytis

    Article • Mycologia, September 2013, Taylor & Francis

    Professor Antonis Rokas

  92. Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds

    Article • Proceedings of the National Academy of Sciences, June 2013, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  93. Inferring ancient divergences requires genes with strong phylogenetic signals

    Article • Nature, May 2013, Nature

    Professor Antonis Rokas

  94. Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in Anopheles gambiae

    Article • Proceedings of the National Academy of Sciences, April 2013, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  95. Putting Pleiotropy and Selection Into Context Defines a New Paradigm for Interpreting Genetic Data

    Article • Circulation Cardiovascular Genetics, April 2013, Wolters Kluwer Health

    Professor Antonis Rokas

  96. Fragmentation of an aflatoxin-like gene cluster in a forest pathogen

    Article • New Phytologist, March 2013, Wiley

    Professor Antonis Rokas

  97. Aspergillus

    Article • Current Biology, March 2013, Elsevier

    Professor Antonis Rokas

  98. Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe

    Article • DNA Repair, March 2013, Elsevier

    Professor Antonis Rokas

  99. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

    Article • Nature, February 2013, Nature

    Professor Antonis Rokas

  100. The function and evolution of the Aspergillus genome

    Article • Trends in Microbiology, January 2013, Elsevier

    Professor Antonis Rokas

  101. Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Professor Antonis Rokas

  102. Investigation of Aspergillus fumigatus biofilm formation by various “omics” approaches

    Article • Frontiers in Microbiology, January 2013, Frontiers

    Professor Antonis Rokas

  103. Assessing the Genome-Wide Effect of Promoter Region Tandem Repeat Natural Variation on Gene Expression

    Article • G3 Genes Genomes Genetics, December 2012, Genetics Society of America

    Professor Antonis Rokas

  104. The diverse applications of RNA-seq for functional genomic studies inAspergillus fumigatus

    Article • Annals of the New York Academy of Sciences, December 2012, Wiley

    Professor Antonis Rokas

  105. A Bioinformatics Approach for Integrated Transcriptomic and Proteomic Comparative Analyses of Model and Non-sequenced Anopheline Vectors of Human Malaria Parasites

    Article • Molecular & Cellular Proteomics, October 2012, American Society for Biochemistry & Molecular Biology (ASBMB)

    Professor Antonis Rokas

  106. Phylogenetic and Transcriptomic Analysis of Chemosensory Receptors in a Pair of Divergent Ant Species Reveals Sex-Specific Signatures of Odor Coding

    Article • PLoS Genetics, August 2012, PLOS

    Professor Antonis Rokas

  107. The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae

    Article • Current Biology, August 2012, Elsevier

    Professor Antonis Rokas

  108. TheASP3locus inSaccharomyces cerevisiaeoriginated by horizontal gene transfer fromWickerhamomyces

    Article • FEMS Yeast Research, July 2012, Oxford University Press (OUP)

    Professor Antonis Rokas

  109. Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes of the Arthrodermataceae

    Article • PLoS ONE, July 2012, PLOS

    Professor Antonis Rokas

  110. In Silico Characterization and Molecular Evolutionary Analysis of a Novel Superfamily of Fungal Effector Proteins

    Article • Molecular Biology and Evolution, July 2012, Oxford University Press (OUP)

    Professor Antonis Rokas

  111. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

    Article • Science, June 2012, American Association for the Advancement of Science

    Professor Antonis Rokas

  112. Transcriptome-wide analysis of small RNA expression in early zebrafish development

    Article • RNA, March 2012, Cold Spring Harbor Laboratory Press

    Professor Antonis Rokas

  113. Transcriptome of the adult female malaria mosquito vector Anopheles albimanus

    Article • BMC Genomics, January 2012, Springer Science + Business Media

    Professor Antonis Rokas

  114. Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster

    Article • Genome Biology and Evolution, January 2012, Oxford University Press (OUP)

    Professor Antonis Rokas

  115. Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogenAspergillus fumigatus

    Article • Molecular Ecology, November 2011, Wiley

    Dr Jacques F Meis, Professor Antonis Rokas

  116. Phylogenetic Analysis of Protein Sequence Data Using the Randomized Axelerated Maximum Likelihood (RAXML) Program

    Article • October 2011, Wiley

    Professor Antonis Rokas

  117. Global Transcriptome Changes Underlying Colony Growth in the Opportunistic Human Pathogen Aspergillus fumigatus

    Article • Eukaryotic Cell, July 2011, ASM Journals

    Professor Antonis Rokas

  118. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

    Article • G3 Genes Genomes Genetics, June 2011, Genetics Society of America

    Professor Antonis Rokas

  119. Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding

    Article • BMC Genomics, May 2011, Springer Science + Business Media

    Professor Antonis Rokas

  120. Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

    Article • PLoS ONE, April 2011, PLOS

    Professor Antonis Rokas

  121. Complete Bacteriophage Transfer in a Bacterial Endosymbiont (Wolbachia) Determined by Targeted Genome Capture

    Article • Genome Biology and Evolution, February 2011, Oxford University Press (OUP)

    Professor Antonis Rokas

  122. Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi

    Article • Current Biology, January 2011, Elsevier

    Professor Antonis Rokas

  123. The Molecular Evolution of the p120-Catenin Subfamily and Its Functional Associations

    Article • PLoS ONE, December 2010, PLOS

    Dr Robert H Carnahan, Professor Antonis Rokas

  124. Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi

    Article • Proceedings of the National Academy of Sciences, May 2010, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  125. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009

    Article • Molecular Ecology Resources, March 2010, Wiley

    Professor Antonis Rokas

  126. The diversity and evolution of circadian clock proteins in fungi

    Article • Mycologia, March 2010, Taylor & Francis

    Professor Antonis Rokas

  127. Remarkably ancient balanced polymorphisms in a multi-locus gene network

    Article • Nature, February 2010, Nature

    Professor Antonis Rokas

  128. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

    Article • Proceedings of the National Academy of Sciences, January 2010, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  129. Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics

    Article • Molecular Biology and Evolution, August 2009, Oxford University Press (OUP)

    Professor Antonis Rokas

  130. Harnessing genomics for evolutionary insights

    Article • Trends in Ecology & Evolution, April 2009, Elsevier

    Professor Antonis Rokas

  131. The effect of domestication on the fungal proteome

    Article • Trends in Genetics, February 2009, Elsevier

    Professor Antonis Rokas

  132. Comparative and Functional Characterization of Intragenic Tandem Repeats in 10 Aspergillus Genomes

    Article • Molecular Biology and Evolution, December 2008, Oxford University Press (OUP)

    Professor Antonis Rokas

  133. The Origins of Multicellularity and the Early History of the Genetic Toolkit For Animal Development

    Article • Annual Review of Genetics, December 2008, Annual Reviews

    Professor Antonis Rokas

  134. The molecular origins of multicellular transitions

    Article • Current Opinion in Genetics & Development, December 2008, Elsevier

    Professor Antonis Rokas

  135. Differential success in northwards range expansion between ecotypes of the marble gallwasp Andricuskollari: a tale of two lifecycles

    Article • Molecular Ecology, July 2008, Wiley

    Professor Antonis Rokas

  136. Frequent and Widespread Parallel Evolution of Protein Sequences

    Article • Molecular Biology and Evolution, June 2008, Oxford University Press (OUP)

    Professor Antonis Rokas

  137. Dynamics of Pseudomonas aeruginosa genome evolution

    Article • Proceedings of the National Academy of Sciences, February 2008, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  138. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

    Article • Nature, February 2008, Springer Science + Business Media

    Professor Michael T Marr, Nicole King, Professor Antonis Rokas

  139. GENOMICS: Lining Up to Avoid Bias

    Article • Science, January 2008, American Association for the Advancement of Science

    Professor Antonis Rokas

  140. From Gene-Scale to Genome-Scale Phylogenetics: the Data Flood In, but the Challenges Remain

    Article • January 2008, Springer Science + Business Media

    Professor Antonis Rokas

  141. Evidence for widespread cryptic sexual generations in apparently purely asexual Andricus gallwasps

    Article • Molecular Ecology, December 2007, Wiley

    Professor Antonis Rokas

  142. Aspergillus nidulans Genome and a Comparative Analysis of Genome Evolution in Aspergillus

    Article • December 2007, Taylor & Francis

    Professor Antonis Rokas

  143. Transcriptional Rewiring: The Proof Is in the Eating

    Article • Current Biology, August 2007, Elsevier

    Professor Antonis Rokas

  144. The phylogeographical clade trade: tracing the impact of human-mediated dispersal on the colonization of northern Europe by the oak gallwasp Andricus kollari

    Article • Molecular Ecology, July 2007, Wiley

    Professor Antonis Rokas

  145. Longitudinal range expansion and cryptic eastern species in the western Palaearctic oak gallwasp, Andricus coriarius

    Article • Molecular Ecology, May 2007, Wiley

    Professor Antonis Rokas

  146. What can comparative genomics tell us about species concepts in the genus Aspergillus?

    Article • Studies in Mycology, January 2007, Elsevier

    Professor Antonis Rokas

  147. Bushes in the Tree of Life

    Article • PLoS Biology, November 2006, PLOS

    Professor Antonis Rokas

  148. Bayesian Estimation of Concordance among Gene Trees

    Article • Molecular Biology and Evolution, November 2006, Oxford University Press (OUP)

    Professor Antonis Rokas

  149. GENOMICS: Genomics and the Tree of Life

    Article • Science, September 2006, American Association for the Advancement of Science

    Professor Antonis Rokas

  150. Different paths to the same end

    Article • Nature, September 2006, Nature

    Professor Antonis Rokas

  151. Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution

    Article • Cell, June 2006, Elsevier

    Professor Antonis Rokas

  152. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

    Article • Nature, April 2006, Nature

    Professor Antonis Rokas

  153. Animal Evolution and the Molecular Signature of Radiations Compressed in Time

    Article • Science, December 2005, American Association for the Advancement of Science

    Professor Antonis Rokas

  154. More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

    Article • Molecular Biology and Evolution, March 2005, Oxford University Press (OUP)

    Professor Antonis Rokas

  155. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts

    Article • Proceedings of the National Academy of Sciences, September 2004, Proceedings of the National Academy of Sciences

    Professor Antonis Rokas

  156. What determines the direction of evolutionary change?

    Article • Trends in Ecology & Evolution, June 2004, Elsevier

    Professor Antonis Rokas

  157. Genome-scale approaches to resolving incongruence in molecular phylogenies

    Article • October 2003

    Nicole King, Professor Antonis Rokas

  158. Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case

    Article • Systematic Biology, August 2003, Oxford University Press (OUP)

    Professor Antonis Rokas

  159. Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case

    Article • Systematic Biology, August 2003, Oxford University Press (OUP)

    Professor Antonis Rokas

  160. Out of Anatolia: longitudinal gradients in genetic diversity support an eastern origin for a circum-Mediterranean oak gallwasp Andricus quercustozae

    Article • Molecular Ecology, August 2003, Wiley

    Professor Antonis Rokas

  161. Animal mitochondrial DNA recombination revisited

    Article • Trends in Ecology & Evolution, August 2003, Elsevier

    Professor Antonis Rokas

  162. Conflicting phylogenetic signals at the base of the metazoan tree

    Article • Evolution & Development, June 2003, Wiley

    Nicole King, Professor Antonis Rokas

  163. Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera: Cynipidae: Cynipini) using mitochondrial sequence data

    Article • Molecular Phylogenetics and Evolution, January 2003, Elsevier

    Professor Antonis Rokas

  164. The incidence and diversity of Wolbachia in gallwasps (Hymenoptera; Cynipidae) on oak

    Article • Molecular Ecology, September 2002, Wiley

    Professor Antonis Rokas

  165. EVOLUTIONARY SHIFTS BETWEEN HOST OAK SECTIONS AND HOST-PLANT ORGANS IN ANDRICUS GALLWASPS

    Article • Evolution, September 2002, Wiley

    Professor Antonis Rokas

  166. Sexual selection driving spider diversification

    Article • Trends in Ecology & Evolution, July 2002, Elsevier

    Professor Antonis Rokas

  167. A Maximum-Likelihood Analysis of Eight Phylogenetic Markers in Gallwasps (Hymenoptera: Cynipidae): Implications for Insect Phylogenetic Studies

    Article • Molecular Phylogenetics and Evolution, February 2002, Elsevier

    Professor Antonis Rokas

  168. Getting it right for the wrong reason

    Article • Trends in Ecology & Evolution, December 2001, Elsevier

    Professor Antonis Rokas

  169. What is a character?

    Article • Trends in Ecology & Evolution, October 2001, Elsevier

    Professor Antonis Rokas

  170. Selfish element wars in a wasp battleground

    Article • Trends in Ecology & Evolution, June 2001, Elsevier

    Professor Antonis Rokas

  171. Molecular Evolution and Phylogenetics. By M. Nei and S. Kumar. Oxford University Press. 2000. ISBN: 0-19-513584-9 (hbk); 0-19-513585-7 (pbk). xiv+333 pages. Price: £65 (hbk); £32.50 (pbk).

    Article • Genetics Research, February 2001, Cambridge University Press

    Professor Antonis Rokas

  172. Evolutionary biology meets genomics

    Article • Trends in Ecology & Evolution, January 2001, Elsevier

    Professor Antonis Rokas

  173. Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep?

    Article • Heredity, January 2001, Nature

    Professor Antonis Rokas

  174. Rare genomic changes as a tool for phylogenetics

    Article • Trends in Ecology & Evolution, November 2000, Elsevier

    Professor Antonis Rokas

  175. A Bayesian guide to tree felling

    Article • Trends in Ecology & Evolution, October 2000, Elsevier

    Professor Antonis Rokas

  176. Influential passengers come of age 1st International Wolbachia Conference, Orthodox Academy, Kolymbari, Crete, Greece, 7–12 June 2000

    Article • Trends in Genetics, September 2000, Elsevier

    Professor Antonis Rokas

  177. Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions

    Article • Science, February 2000, American Association for the Advancement of Science

    Professor Antonis Rokas

  178. Wolbachia as a speciation agent

    Article • Trends in Ecology & Evolution, February 2000, Elsevier

    Professor Antonis Rokas

  179. Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera

    Article • Insect Molecular Biology, November 1999, Wiley

    Professor Antonis Rokas

  180. Longitudinal patterns in species richness and genetic diversity in European oaks and oak gallwasps

    Article • Springer Science + Business Media

    Professor Antonis Rokas

  181. Perspective: Systematics in the age of genomics

    Article • Cambridge University Press

    Professor Antonis Rokas