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Javier is an Assistant Professor of Genomics at the Department of Biology of Clark University. His lab is interested in identifying the patterns of genomic evolution of fungal species and populations, especially focused on the evolution, systematics, and genomics of secondary metabolism of the genus Basidiobolus.
The Tabima lab uses a multidisciplinary approach of integrating tools and concepts from evolutionary theory, computational biology, genomics, genetics, and plant pathology/mycology in order to study these phenomena, as well as to create computational and molecular tools for the rapid identification of species, populations, genes of interest and molecular patterns of fungal evolution.
Affiliated Department(s)
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Scholarly and Creative Works
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The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing
Published in NAR Genomics and Bioinformatics
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2023
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Fungal species and populations in a genomic perspective
University of Georgia Plant Pathology Seminar series
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University of Georgia
April
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2023
Sponsored by University of Georgia
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Fungal and oomycete populations and the boundaries of species
Seminar Series: University of Richmond
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University of Richmond, VA
February
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2023
Sponsored by University of Richmond, VA
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First report of Pyricularia oryzae causing gray leaf spot of perennial ryegrass (Lolium perenne L.) in Oregon
Published in Plant Health Progress
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2023
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Issue #ja
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Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer
Published in Molecular Plant-Microbe Interactions
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2023
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Vol. 36
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Issue #1
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Fungal and oomycete populations and the boundaries of species
Seminar Series: Plant Pathology department
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Penn State University
October
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2022
Sponsored by Penn State University
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Evolution and epidemiology of global populations of nursery-associated Agrobacterium
Published in Ecological genetics
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2022
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Vol. 20
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Swedish University of Agricultural Sciences (SLU, Sveriges lantbruksuniversitet)
Invited Seminar Series
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Murfreesboro, Tennessee
February
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2022
Sponsored by Middle Tennessee State University
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Genome Sequence of Estuarine Synechococcus sp. NB0720_010
Published in Microbiology Resource Announcements
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2022
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The intricacies of the genome of a small, gut associated fungus: Basidiobolus (Basidiobolaceae, Zoopagomycota)
Invited Seminar Series
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Uppsala, Sweden
November
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2021
Sponsored by Swedish University of Agricultural Sciences (SLU, Sveriges lantbruksuniversitet)
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The intricacies of the genome of a small, gut associated fungus: Basidiobolus (Basidiobolaceae, Zoopagomycota)
Winter Bioinformatics School
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Bogota, Colombia
November
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2021
Sponsored by Universidad del Rosario
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Genetic diversity and aggressiveness of Fusarium virguliforme isolates across the Midwestern United States
Published in Phytopathology
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2021
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Issue #ja
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Identity and pathogenicity of fungi associated with root, crown and vascular symptoms related to winter squash yield decline
Published in Plant Disease
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2021
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Issue #ja
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"Spatial genetic structure of the insect-vectored conifer pathogen Leptographium wageneri suggests long distance gene flow among Douglas-fir plantations in western Oregon
Published in Frontiers in Forests and Global Change
Spring
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2021
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The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility
Published in BMC microbiology
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2021
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Vol. 21
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Issue #1
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Molecular phylogenomics and population structure of Phytophthora pluvialis
Published in Phytopathology
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2021
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Vol. 111
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Issue #1
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Published in Plants
March
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2021
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Vol. 10
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Issue #3
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Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus
Published in G3
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2020
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Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races
Published in Frontiers in Microbiology
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2020
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Vol. 11
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Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva
Published in Molecular Plant-Microbe Interactions
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2020
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Vol. 33
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Issue #2
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From genomes to forest management--tackling invasive Phytophthora species in the era of genomics
Published in Canadian Journal of Plant Pathology
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2020
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Vol. 42
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Issue #1
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Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving
Published in G3 (Bethesda, Md.), 10 (9)
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2020
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Molecular phylogenomics and population structure of Phytophthora pluvialis
Published in Phytopathology
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2020
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Issue #ja
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Genome-wide increased copy number is associated with emergence of dominant clones of the Irish potato famine pathogen Phytophthora infestans
Published in MBio
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2020
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Vol. 11
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Issue #3
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Unexpected conservation and global transmission of agrobacterial virulence plasmids
Published in Science
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2020
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Vol. 368
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Issue #6495
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Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorum. MBio 10: e02452-18
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2019
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Designing a Socio-Cultural Approach for Teaching and Learning Computational Thinking
Published in Nordic Journal of Digital Literacy
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2019
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Vol. 15
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Issue #02
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Genome-wide increased copy number is associated with emergence of super-fit clones of the Irish potato famine pathogen Phytophthora infestans
Published in BioRxiv
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2019
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Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorum
Published in MBio
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2019
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Vol. 10
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Issue #2
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effectR: An expandable R package to predict candidate RxLR and CRN effectors in oomycetes using motif searches
Published in Molecular Plant-Microbe Interactions
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2019
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Vol. 32
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Issue #9
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effectR: An expandable R package to predict candidate effectors
Published in BioRxiv
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2018
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Copy number variation appears increased in clonal lineages over sexual lineages of Phytophthora infestans
International Congress of Plant Pathology (ICPP) 2018: Plant Health in A Global Economy●
2018
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Evolution of the US biological select agent Rathayibacter toxicus
Published in MBio
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2018
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Vol. 9
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Issue #4
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Populations of Phytophthora rubi show little differentiation and high rates of migration among states in the Western United States
Published in Molecular Plant-Microbe Interactions
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2018
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Vol. 31
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Issue #6
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Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia
Published in Persoonia: Molecular Phylogeny and Evolution of Fungi
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2018
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Vol. 41
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Genetic diversity of Phytophthora pluvialis, a pathogen of conifers, in New Zealand and the west coast of the United States of America
Published in Plant Pathology
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2018
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Vol. 67
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Issue #5
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Population Genomics in R
2017 APS Annual Meeting●
2017
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Whole genome sequences of the raspberry and strawberry pathogens Phytophthora rubi and P. fragariae
Published in Molecular Plant-Microbe Interactions
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2017
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Vol. 30
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Issue #10
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Searching for genomic signatures of host jumping onto raspberry and strawberry in two Phytophthora sister taxa
PHYTOPATHOLOGY●
2016
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Vol. 106
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Issue #12
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What is a clone? Rethinking the ancestry of US clonal lineages of Phytophthora infestans using whole genome sequences
PHYTOPATHOLOGY●
2016
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Vol. 106
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Issue #12
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Ecological speciation within the Phytophthora genus
Published in bioRxiv
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2016
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A Covert Operation by a Plant Pathogen
Published in Cell host & microbe
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2016
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Vol. 20
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Issue #4
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Genomic analyses of dominant US clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other US lineages
Published in Phytopathology
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2016
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Vol. 106
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Issue #11
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Microbe-ID: an open source toolbox for microbial genotyping and species identification
Published in PeerJ
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2016
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Vol. 4
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Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria
Published in PeerJ
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2016
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Vol. 4
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Evolutionary history of the group formerly known as protists using a phylogenomics approach
Published in Revista de la Academia Colombiana de Ciencias Exactas, F'isicas y Naturales
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2016
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Vol. 40
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Issue #154
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Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, P hytophthora infestans
Published in Journal of Applied Microbiology
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2016
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Vol. 120
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Issue #4
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SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high-resolution melt analysis
Published in Plant Disease
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2016
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Vol. 100
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Issue #7
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Five new species of entomopathogenic fungi from the Amazon and evolution of neotropical Ophiocordyceps
Published in Fungal Biology
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2015
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Vol. 119
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Issue #10
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Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.
Published in PeerJ
March
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2014
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Poppr: an R package for genetic analysis of populations with clonal or partially clonal reproduction
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2014
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Identification of pathogenesis-related proteins in the coffee rust, Hemileia vastatrix.
25th International Conference on Coffee Science, ASIC 2014, Armenia, Colombia, 8-13 September 2014●
2014
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Polyphasic characterization of Colletotrichum sp. Isolates from tree tomato and mango crops in Cundinamarca and Tolima, Colombia
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2014
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Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales
Published in Frontiers in plant science
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2014
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Vol. 5
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Chapter: Phytophthora ramorumPublished by Springer, Berlin, Heidelberg
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2014
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Speciation in fungal and oomycete plant pathogens
Published in Annual review of phytopathology
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2014
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Vol. 52
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Pathogenicity, fungicide resistance, and genetic variability of Phytophthora rubi isolates from raspberry (Rubus idaeus) in the western United States
Published in Plant Disease
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2014
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Vol. 98
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Issue #12
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The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes
Published in Proceedings of the National Academy of Sciences
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2014
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Vol. 111
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Issue #24
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Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction
Published in PeerJ
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2014
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Vol. 2
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Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto)
Published in Mycologia
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2014
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Vol. 106
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Issue #2
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Chapter: Application of genome studies of coffee rustPublished by Springer, Cham
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2014
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The poppr R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
Published in Phytopathology
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2013
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Vol. 103
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Issue #6
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Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. manihotis strain CIO151
Published in PloS one
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2013
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Vol. 8
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Issue #11
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Seborrheic dermatitis: predisposing factors and ITS2 secondary structure for Malassezia phylogenic analysis
Published in Medical Mycology
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2013
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Vol. 51
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Issue #8
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Fusarium species associated to onychomycoses in Colombia.
Published in F1000Research
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2012
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Vol. 3
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Morphological characterization of Colletotrichum species isolated from mango and tree tomato in Cundinamarca and Tolima, Colombia
Phytopathology●
2012
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Vol. 102
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Issue #7
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The dynamics of evolution in Phytopththora infestans as told by phylogeographical approaches
PHYTOPATHOLOGY●
2012
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Vol. 102
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Issue #7
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Phytophthora infestans population structure: A worldwide scale
Published in Acta Biol'ogica Colombiana
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2012
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Vol. 17
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Issue #2
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Defining species boundaries in the genus Phytophthora: the case of Phytophthora andina A response to ‘Phytophthora andina sp. nov., a newly identified heterothallic pathogen of solanaceous hosts in the Andean highlands’(Oliva et al., 2010)
Published in Plant Pathology
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2012
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Vol. 61
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Issue #2
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First report of Phytophthora infestans causing late blight on Solanum viarum in Colombia
Published in Plant Disease
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2011
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Vol. 95
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Issue #7
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Virulence gene expression in Malassezia spp from individuals with seborrheic dermatitis
Published in Journal of investigative dermatology
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2011
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Vol. 131
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Phylogeography and molecular epidemiology of Papaya ringspot virus
Published in Virus research
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2011
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Vol. 159
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Issue #2
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A novel natural product reservoir: secondary metabolite extracts from a zygomycete, Basidiobolus meristosporus, show selective antibacterial activity.
Published in TBD
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Tolypocladamide H and the Proposed Tolypocladamide NRPS in Tolypocladium Species
Published in Journal of Natural Products
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Pathogenicity and phylogenetic relationships of fungi associated with root, crown and vascular symptoms related to winter squash yield decline
Published in Plant Disease
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Genome-wide analysis of vernalization requirements in a winter wheat recombinant inbred population
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Short title: Amazonian Cordyceps of Orthopterida Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto) Tatiana Sanjuan Laboratorio de Taxonom'ia y Ecolog'ia de Hongos, Universidad de Antioquia, calle 67 No. 53--
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Awards & Grants
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Using the study of urban impacts on water quality, frogs, and microbial communities in Worcester waterways to integrate student research, classroom learning, and local STEM outreach.
Clark University
Feb. 1, 2022 - Dec. 31, 2022
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Diversity and richness of an understudied Filamentous Fungal Genus (Basidiobolus) Associated with Amphibian Gastrointestinal Tracts.
Clark University
Mar. 1, 2023
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How the mushroom lost its gills: phylogenomics and population genetics of a morphological innovation in the fungal genus Lentinus
National Science Foundation
Jun. 1, 2023
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The Evolutionary Dynamics of a Filamentous Fungal Genus (Basidiobolus) Associated with Amphibian Gastrointestinal Tracts
National Science Foundation
Jun. 1, 2023
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Investigating epigenetic nucleic acid methylation in Dictyostelium slime mold
Clark University
Mar. 3, 2022
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The Evolutionary Dynamics of a Filamentous Fungal Genus (Basidiobolus) Associated with Amphibian Gastrointestinal Tracts
National Science Foundation
May. 24, 2022
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