Antonis Rokas

Antonis Rokas

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Antonis Rokas

Publications by authors named "Antonis Rokas"

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Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation.

Bioessays 2019 Sep 2;41(9):e1900072. Epub 2019 Aug 2.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.

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http://dx.doi.org/10.1002/bies.201900072DOI Listing
September 2019

Future-Proofing Your Genome Assembly for Reproducibility and Clarity.

Microbiol Resour Announc 2019 Sep 5;8(36). Epub 2019 Sep 5.

Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA.

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http://dx.doi.org/10.1128/MRA.00954-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728651PMC
September 2019

Draft Genome Sequence of the Griseofulvin-Producing Fungus Xylaria flabelliformis Strain G536.

Microbiol Resour Announc 2019 Sep 19;8(38). Epub 2019 Sep 19.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA

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http://dx.doi.org/10.1128/MRA.00890-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753274PMC
September 2019

Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues.

G3 (Bethesda) 2019 08 8;9(8):2761-2774. Epub 2019 Aug 8.

Department of Biological Sciences,

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http://dx.doi.org/10.1534/g3.119.400186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686946PMC
August 2019

Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution.

Curr Biol 2019 Aug 25;29(15):2555-2562.e8. Epub 2019 Jul 25.

Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2019.06.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692504PMC
August 2019

Treehouse: a user-friendly application to obtain subtrees from large phylogenies.

BMC Res Notes 2019 Aug 27;12(1):541. Epub 2019 Aug 27.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.

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http://dx.doi.org/10.1186/s13104-019-4577-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6712805PMC
August 2019

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

Syst Biol 2019 Aug 29. Epub 2019 Aug 29.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.

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http://dx.doi.org/10.1093/sysbio/syz058DOI Listing
August 2019

Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism.

Fungal Genet Biol 2019 Jul 3;128:60-73. Epub 2019 Apr 3.

USDA, ARS, US National Poultry Research Center, Toxicology & Mycotoxin Research Unit, Athens, GA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.fgb.2019.04.002DOI Listing
July 2019

A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera and .

MBio 2019 Jul 9;10(4). Epub 2019 Jul 9.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA

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http://dx.doi.org/10.1128/mBio.00925-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747717PMC
July 2019

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

Mol Plant Pathol 2019 Jul 11. Epub 2019 Jul 11.

Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.

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http://dx.doi.org/10.1111/mpp.12848DOI Listing
July 2019

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

PLoS Genet 2019 Jul 31;15(7):e1008304. Epub 2019 Jul 31.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6701816PMC
July 2019

Unearthing fungal chemodiversity and prospects for drug discovery.

Curr Opin Microbiol 2019 May 6;51:22-29. Epub 2019 May 6.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. Electronic address:

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http://dx.doi.org/10.1016/j.mib.2019.03.002DOI Listing
May 2019

Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication.

Evol Med Public Health 2019 17;2019(1):93-103. Epub 2019 May 17.

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA.

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http://dx.doi.org/10.1093/emph/eoz015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592264PMC
May 2019

Eukaryotic Acquisition of a Bacterial Operon.

Cell 2019 Mar 21;176(6):1356-1366.e10. Epub 2019 Feb 21.

Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.01.034DOI Listing
March 2019

Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data.

Int J Mol Sci 2019 Mar 1;20(5). Epub 2019 Mar 1.

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.

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http://dx.doi.org/10.3390/ijms20051072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429444PMC
March 2019

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

Nat Rev Microbiol 2018 12;16(12):731-744

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://www.nature.com/articles/s41579-018-0075-3
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http://dx.doi.org/10.1038/s41579-018-0075-3DOI Listing
December 2018

The power of discussion: Support for women at the fungal Gordon Research Conference.

Fungal Genet Biol 2018 12 24;121:65-67. Epub 2018 Sep 24.

Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10871845183020
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http://dx.doi.org/10.1016/j.fgb.2018.09.007DOI Listing
December 2018

Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases.

Bioessays 2018 11 28;40(11):e1800133. Epub 2018 Sep 28.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA.

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http://doi.wiley.com/10.1002/bies.201800133
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http://dx.doi.org/10.1002/bies.201800133DOI Listing
November 2018

Gene Essentiality Analyzed by Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of .

MBio 2018 10 30;9(5). Epub 2018 Oct 30.

School of Molecular Cell Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel

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http://dx.doi.org/10.1128/mBio.02048-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212825PMC
October 2018

Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth.

PLoS Genet 2018 07 12;14(7):e1007394. Epub 2018 Jul 12.

Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042692PMC
July 2018

Fungal Isocyanide Synthases and Xanthocillin Biosynthesis in Aspergillus fumigatus.

MBio 2018 05 29;9(3). Epub 2018 May 29.

Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA

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http://dx.doi.org/10.1128/mBio.00785-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5974471PMC
May 2018

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

J Cell Sci 2018 04 9;131(7). Epub 2018 Apr 9.

Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, 37232, USA

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http://dx.doi.org/10.1242/jcs.203950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963836PMC
April 2018

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

G3 (Bethesda) 2018 03 28;8(4):1315-1325. Epub 2018 Mar 28.

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA

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http://dx.doi.org/10.1534/g3.118.200035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5873920PMC
March 2018

Factors driving metabolic diversity in the budding yeast subphylum.

BMC Biol 2018 03 2;16(1):26. Epub 2018 Mar 2.

Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1186/s12915-018-0498-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5833115PMC
March 2018

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

mSphere 2018 Mar-Apr;3(2). Epub 2018 Mar 14.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.

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http://dx.doi.org/10.1128/mSphere.00050-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853485PMC
March 2018

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

Mol Biol Evol 2018 02;35(2):486-503

Department of Biological Sciences, Vanderbilt University, Nashville, TN.

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http://dx.doi.org/10.1093/molbev/msx302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850867PMC
February 2018

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

Front Microbiol 2018 22;9:288. Epub 2018 Feb 22.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States.

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http://dx.doi.org/10.3389/fmicb.2018.00288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826948PMC
February 2018

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

EMBO J 2018 01 20;37(1):63-74. Epub 2017 Oct 20.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA

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http://dx.doi.org/10.15252/embj.201797833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753038PMC
January 2018

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

Elife 2018 01 8;7. Epub 2018 Jan 8.

Center for the Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, United States.

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http://dx.doi.org/10.7554/eLife.31150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758111PMC
January 2018

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

PLoS Biol 2017 Nov 17;15(11):e2003583. Epub 2017 Nov 17.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.2003583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711037PMC
November 2017

Embracing Uncertainty in Reconstructing Early Animal Evolution.

Curr Biol 2017 Oct;27(19):R1081-R1088

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2017.08.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679448PMC
October 2017

WetA bridges cellular and chemical development in Aspergillus flavus.

PLoS One 2017 28;12(6):e0179571. Epub 2017 Jun 28.

Departments of Bacteriology and Genetics, University of Wisconsin, Madison, Wisconsin, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0179571PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5489174PMC
September 2017

The transformative potential of an integrative approach to pregnancy.

Placenta 2017 Sep 15;57:204-215. Epub 2017 Jul 15.

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37235, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01434004173065
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http://dx.doi.org/10.1016/j.placenta.2017.07.010DOI Listing
September 2017

LFO1 Is an IsdG Family Heme Oxygenase.

mSphere 2017 Jul-Aug;2(4). Epub 2017 Aug 16.

Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.

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http://dx.doi.org/10.1128/mSphere.00176-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557675PMC
August 2017

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

Sci Rep 2017 07 18;7(1):5684. Epub 2017 Jul 18.

Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.

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http://dx.doi.org/10.1038/s41598-017-05962-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515947PMC
July 2017

The gene family that cheats Mendel.

Elife 2017 06 20;6. Epub 2017 Jun 20.

Department of Biological Sciences, Vanderbilt University, Nashville, United States.

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http://dx.doi.org/10.7554/eLife.28567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478260PMC
June 2017

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

G3 (Bethesda) 2017 05 5;7(5):1475-1485. Epub 2017 May 5.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235

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http://dx.doi.org/10.1534/g3.117.040105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427499PMC
May 2017

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

Elife 2017 04 18;6. Epub 2017 Apr 18.

Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, United States.

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http://dx.doi.org/10.7554/eLife.24176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395295PMC
April 2017

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

Nat Ecol Evol 2017 Apr 10;1(5):126. Epub 2017 Apr 10.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.

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http://www.nature.com/articles/s41559-017-0126
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http://dx.doi.org/10.1038/s41559-017-0126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560076PMC
April 2017

Mammalian pregnancy.

Curr Biol 2017 Feb;27(4):R127-R128

Department of Biological Sciences, Vanderbilt University, VU Station B #351634, Nashville, TN 37235, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2016.10.046DOI Listing
February 2017

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

Mol Biol Evol 2017 01 20;34(1):215-229. Epub 2016 Oct 20.

Department of Biological Sciences, Vanderbilt University, Nashville, TN

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http://dx.doi.org/10.1093/molbev/msw227DOI Listing
January 2017

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

G3 (Bethesda) 2016 12 7;6(12):4023-4033. Epub 2016 Dec 7.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232

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http://g3journal.org/lookup/doi/10.1534/g3.116.033084
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http://dx.doi.org/10.1534/g3.116.033084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5144971PMC
December 2016

Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of Genome Sequencing Studies.

G3 (Bethesda) 2016 Nov 8;6(11):3655-3662. Epub 2016 Nov 8.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235

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http://dx.doi.org/10.1534/g3.116.034249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100864PMC
November 2016

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

Placenta 2016 08 30;44:23-33. Epub 2016 May 30.

Department of Obstetrics and Gynecology, The Ohio State College of Medicine, Columbus, OH, USA. Electronic address:

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http://dx.doi.org/10.1016/j.placenta.2016.05.010DOI Listing
August 2016

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

PLoS One 2015 7;10(12):e0144155. Epub 2015 Dec 7.

Department of Biological Sciences, Vanderbilt University, Box 35164 Station B, Nashville, TN, 37235-1634, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144155PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671692PMC
June 2016

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

Mol Biol Evol 2016 06 25;33(6):1606-17. Epub 2016 Feb 25.

Heidelberg Institute for Theoretical Studies, Heidelberg, Germany Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Postfach 6980, Karlsruhe, 76128, Germany.

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http://dx.doi.org/10.1093/molbev/msw040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868120PMC
June 2016

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

Placenta 2016 05 12;41:74-82. Epub 2016 Mar 12.

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Program in Human Genetics, Vanderbilt University, Nashville, TN 37235, USA. Electronic address:

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http://dx.doi.org/10.1016/j.placenta.2016.03.006DOI Listing
May 2016

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

Proc Natl Acad Sci U S A 2016 Apr 29;113(15):4116-21. Epub 2016 Mar 29.

Laboratory of Genetics, DOE (Department of Energy) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Genome Center of Wisconsin, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706;

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http://dx.doi.org/10.1073/pnas.1517242113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839431PMC
April 2016

Genomics and the making of yeast biodiversity.

Curr Opin Genet Dev 2015 Dec 30;35:100-9. Epub 2015 Nov 30.

Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL, USA.

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http://dx.doi.org/10.1016/j.gde.2015.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771062PMC
December 2015

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

Curr Opin Genet Dev 2015 Dec 9;35:iv-vi. Epub 2015 Dec 9.

Florida Museum of Natural History and the Genetics Institute, University of Florida, Gainesville, FL 32611 USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2015.11.005DOI Listing
December 2015

A Genome-Scale Investigation of Incongruence in Culicidae Mosquitoes.

Genome Biol Evol 2015 Nov 25;7(12):3463-71. Epub 2015 Nov 25.

Department of Biological Sciences, Vanderbilt University

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https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/
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http://dx.doi.org/10.1093/gbe/evv235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700963PMC
November 2015

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

Genome Biol Evol 2015 Aug 12;7(8):2407-16. Epub 2015 Aug 12.

Department of Biological Sciences, Vanderbilt University

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http://dx.doi.org/10.1093/gbe/evv149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4558866PMC
August 2015

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

Mol Biol Evol 2015 Jun 12;32(6):1449-55. Epub 2015 Feb 12.

Department of Biological Sciences, Vanderbilt University

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http://dx.doi.org/10.1093/molbev/msv034DOI Listing
June 2015

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

BMC Med Genomics 2015 Jun 5;8:27. Epub 2015 Jun 5.

Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, USA.

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http://dx.doi.org/10.1186/s12920-015-0099-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456776PMC
June 2015

Is preterm birth a human-specific syndrome?

Evol Med Public Health 2015 Jun 14;2015(1):136-48. Epub 2015 Jun 14.

Department of Biological Sciences, Vanderbilt University, VU Station B 35-1364, Nashville, TN 37235, USA

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http://dx.doi.org/10.1093/emph/eov010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493222PMC
June 2015

Fungal metabolic gene clusters-caravans traveling across genomes and environments.

Front Microbiol 2015 3;6:161. Epub 2015 Mar 3.

Department of Biological Sciences, Vanderbilt University Nashville, TN, USA.

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http://dx.doi.org/10.3389/fmicb.2015.00161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4347624PMC
March 2015

Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus.

PLoS Genet 2015 Mar 18;11(3):e1005096. Epub 2015 Mar 18.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364702PMC
March 2015

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Authors:
Daniel E Neafsey Robert M Waterhouse Mohammad R Abai Sergey S Aganezov Max A Alekseyev James E Allen James Amon Bruno Arcà Peter Arensburger Gleb Artemov Lauren A Assour Hamidreza Basseri Aaron Berlin Bruce W Birren Stephanie A Blandin Andrew I Brockman Thomas R Burkot Austin Burt Clara S Chan Cedric Chauve Joanna C Chiu Mikkel Christensen Carlo Costantini Victoria L M Davidson Elena Deligianni Tania Dottorini Vicky Dritsou Stacey B Gabriel Wamdaogo M Guelbeogo Andrew B Hall Mira V Han Thaung Hlaing Daniel S T Hughes Adam M Jenkins Xiaofang Jiang Irwin Jungreis Evdoxia G Kakani Maryam Kamali Petri Kemppainen Ryan C Kennedy Ioannis K Kirmitzoglou Lizette L Koekemoer Njoroge Laban Nicholas Langridge Mara K N Lawniczak Manolis Lirakis Neil F Lobo Ernesto Lowy Robert M MacCallum Chunhong Mao Gareth Maslen Charles Mbogo Jenny McCarthy Kristin Michel Sara N Mitchell Wendy Moore Katherine A Murphy Anastasia N Naumenko Tony Nolan Eva M Novoa Samantha O'Loughlin Chioma Oringanje Mohammad A Oshaghi Nazzy Pakpour Philippos A Papathanos Ashley N Peery Michael Povelones Anil Prakash David P Price Ashok Rajaraman Lisa J Reimer David C Rinker Antonis Rokas Tanya L Russell N'Fale Sagnon Maria V Sharakhova Terrance Shea Felipe A Simão Frederic Simard Michel A Slotman Pradya Somboon Vladimir Stegniy Claudio J Struchiner Gregg W C Thomas Marta Tojo Pantelis Topalis José M C Tubio Maria F Unger John Vontas Catherine Walton Craig S Wilding Judith H Willis Yi-Chieh Wu Guiyun Yan Evgeny M Zdobnov Xiaofan Zhou Flaminia Catteruccia George K Christophides Frank H Collins Robert S Cornman Andrea Crisanti Martin J Donnelly Scott J Emrich Michael C Fontaine William Gelbart Matthew W Hahn Immo A Hansen Paul I Howell Fotis C Kafatos Manolis Kellis Daniel Lawson Christos Louis Shirley Luckhart Marc A T Muskavitch José M Ribeiro Michael A Riehle Igor V Sharakhov Zhijian Tu Laurence J Zwiebel Nora J Besansky

Science 2015 Jan 27;347(6217):1258522. Epub 2014 Nov 27.

Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA.

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http://dx.doi.org/10.1126/science.1258522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380271PMC
January 2015

The evolution of fungal metabolic pathways.

PLoS Genet 2014 Dec 4;10(12):e1004816. Epub 2014 Dec 4.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256263PMC
December 2014

Evaluating rare amino acid substitutions (RGC_CAMs) in a yeast model clade.

PLoS One 2014 17;9(3):e92213. Epub 2014 Mar 17.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092213PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956930PMC
November 2014

Divergent and conserved elements comprise the chemoreceptive repertoire of the nonblood-feeding mosquito Toxorhynchites amboinensis.

Genome Biol Evol 2014 Oct 16;6(10):2883-96. Epub 2014 Oct 16.

Department of Biological Sciences, Vanderbilt University Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee Department of Pharmacology, Vanderbilt Brain Institute, Program in Developmental Biology and Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee

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http://dx.doi.org/10.1093/gbe/evu231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224357PMC
October 2014

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

Mycologia 2013 Sep-Oct;105(5):1126-34. Epub 2013 Aug 6.

Vanderbilt University, Department of Biological Sciences, VU Station B 351364, Nashville, Tennessee 37235, and University of Hawaii at Mânoa, Botany Department, 3190 Maile Way, Room 101, Honolulu, Hawaii 96822.

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https://www.tandfonline.com/doi/full/10.3852/12-390
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June 2014

The fumagillin gene cluster, an example of hundreds of genes under veA control in Aspergillus fumigatus.

PLoS One 2013 7;8(10):e77147. Epub 2013 Oct 7.

Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792039PMC
June 2014

Functional divergence for every paralog.

Mol Biol Evol 2014 Apr 21;31(4):984-92. Epub 2014 Jan 21.

Department of Biological Sciences, Vanderbilt University.

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April 2014

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

Mol Ecol 2014 Apr 13;23(7):1679-700. Epub 2014 Mar 13.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.

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http://dx.doi.org/10.1111/mec.12680DOI Listing
April 2014

Ecology drives the distribution of specialized tyrosine metabolism modules in fungi.

Genome Biol Evol 2014 Jan;6(1):121-32

Department of Biological Sciences, Vanderbilt University.

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http://dx.doi.org/10.1093/gbe/evt208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914699PMC
January 2014

Genetics. My oldest sister is a sea walnut?

Authors:
Antonis Rokas

Science 2013 Dec;342(6164):1327-9

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1248424
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December 2013

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

BMC Genomics 2013 Nov 1;14:749. Epub 2013 Nov 1.

Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA.

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http://dx.doi.org/10.1186/1471-2164-14-749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833343PMC
November 2013

Recurrent tissue-specific mtDNA mutations are common in humans.

PLoS Genet 2013 Nov 7;9(11):e1003929. Epub 2013 Nov 7.

Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820769PMC
November 2013

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

Proc Natl Acad Sci U S A 2013 Jul 24;110(28):11481-6. Epub 2013 Jun 24.

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.

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http://dx.doi.org/10.1073/pnas.1304461110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710872PMC
July 2013

Putting pleiotropy and selection into context defines a new paradigm for interpreting genetic data.

Circ Cardiovasc Genet 2013 Jun 24;6(3):299-307. Epub 2013 Apr 24.

Division of Cardiovascular Medicine, Section of Cardiovascular Disease Prevention, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1161/CIRCGENETICS.113.000126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889706PMC
June 2013

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

Proc Natl Acad Sci U S A 2013 May 29;110(20):8260-5. Epub 2013 Apr 29.

Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37235, USA.

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http://dx.doi.org/10.1073/pnas.1302562110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657813PMC
May 2013

Inferring ancient divergences requires genes with strong phylogenetic signals.

Nature 2013 May 8;497(7449):327-31. Epub 2013 May 8.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.

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May 2013