Javier Tabima Restrepo

Article in Refereed Journal

The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing

NAR Genomics and Bioinformatics

June

●

2023

Robert Drewell

,

Tayla Cormier

,

Jacob Steenwyk

,

James St. Denis

,

Javier Tabima Restrepo

,

Jacqueline Dresch

,

Denis Larochelle

Article in Refereed Journal

The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing

NAR Genomics and Bioinformatics

●

2023

Robert Drewell

,

Tayla Cormier

,

Jacob Steenwyk

,

James St. Denis

,

Javier Tabima Restrepo

,

Jacqueline Dresch

,

Denis Larochelle

Presentations

Fungal species and populations in a genomic perspective

University of Georgia Plant Pathology Seminar series

●

University of Georgia

April

●

2023

Sponsored by Universidad del Rosario

Javier Tabima Restrepo

Article in Refereed Journal

Genetic diversity and aggressiveness of Fusarium virguliforme isolates across the Midwestern United States

Phytopathology

●

2021

●

Issue #ja

Rodrigo Olarte

,

Rebecca Hall

,

Javier Tabima

,

Dean Malvick

,

Kathryn Bushley

Article in Refereed Journal

Identity and pathogenicity of fungi associated with root, crown and vascular symptoms related to winter squash yield decline

Plant Disease

●

2021

●

Issue #ja

Hannah Rivedal

,

Javier Tabima

,

Alexandra Stone

,

Ken Johnson

Article in Refereed Journal

"Spatial genetic structure of the insect-vectored conifer pathogen Leptographium wageneri suggests long distance gene flow among Douglas-fir plantations in western Oregon

Frontiers in Forests and Global Change

Spring

●

2021

Patrick Bennett

,

Javier Tabima Restrepo

,

Anna Leon

,

John Browning

,

Michael Wingfield

,

Jared LeBoldus

Article in Refereed Journal

The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

BMC microbiology

●

2021

●

Vol. 21

●

Issue #1

Nathaly Benavides

,

Alejandro Alvarez

,

Mario Arrieta-Ortiz

,

Luis Rodriguez-R

,

David Botero

,

Javier Tabima

,

Luisa Castiblanco

,

Cesar Trujillo

,

Silvia Restrepo

,

Adriana Bernal

Article in Refereed Journal

Molecular phylogenomics and population structure of Phytophthora pluvialis

Phytopathology

●

2021

●

Vol. 111

●

Issue #1

Javier Tabima

,

Lilah Gonen

,

Mireia G'omez-Gallego

,

Preeti Panda

,

Niklaus Gr"unwald

,

Everett Hansen

,

Rebecca McDougal

,

Jared LeBoldus

,

Nari Williams

Article in Refereed Journal

QTL Analysis of Adult Plant Resistance to Stripe Rust in a Winter Wheat Recombinant Inbred Population

Plants

March

●

2021

●

Vol. 10

●

Issue #3

Kali Brandt

,

Xianming Chen

,

Javier Tabima Restrepo

,

Deven See

,

Kelly Vining

,

Robert Zemetra

Article in Refereed Journal

Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus

G3

●

2020

Javier Tabima

,

Ian Trautman

,

Ying Chang

,

Yan Wang

,

Stephen Mondo

,

Asaf Salamov

,

Igor Grigoriev

,

Jason Stajich

,

Joseph Spatafora

Article in Refereed Journal

Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races

Frontiers in Microbiology

●

2020

●

Vol. 11

Thomas Adams

,

Andrew Armitage

,

Maria Sobczyk

,

Helen Bates

,

Javier Tabima

,

Brent Kronmiller

,

Brett Tyler

,

Niklaus Gr"unwald

,

Jim Dunwell

,

Charlotte Nellist

,

others

Article in Refereed Journal

Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva

Molecular Plant-Microbe Interactions

●

2020

●

Vol. 33

●

Issue #2

J Tabima

,

K Sondreli

,

S Keri"o

,

N Feau

,

M Sakalidis

,

R Hamelin

,

J LeBoldus

Article in Refereed Journal

From genomes to forest management--tackling invasive Phytophthora species in the era of genomics

Canadian Journal of Plant Pathology

●

2020

●

Vol. 42

●

Issue #1

S Keri"o

,

H Daniels

,

M G'omez-Gallego

,

J Tabima

,

R Lenz

,

K Sondreli

,

NJ Gr"unwald

,

N Williams

,

R Mcdougal

,

J LeBoldus

Article in Refereed Journal

Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving

G3 (Bethesda, Md.), 10 (9)

●

2020

Javier Tabima

,

Ian Trautman

,

Ying Chang

Article in Refereed Journal

Molecular phylogenomics and population structure of Phytophthora pluvialis

Phytopathology

●

2020

●

Issue #ja

Javier Tabima

,

Lilah Gonen

,

Mireia G\'omez-Gallego

,

Preeti Panda

,

Niklaus Gr\"unwald

,

Rebecca McDougal

,

Everett Hansen

,

Jared Leboldus

,

Nari Williams

Article in Refereed Journal

Genome-wide increased copy number is associated with emergence of dominant clones of the Irish potato famine pathogen Phytophthora infestans

MBio

●

2020

●

Vol. 11

●

Issue #3

Brian Knaus

,

Javier Tabima

,

Shankar Shakya

,

Howard Judelson

,

Niklaus Gr\"unwald

Article in Refereed Journal

Unexpected conservation and global transmission of agrobacterial virulence plasmids

Science

●

2020

●

Vol. 368

●

Issue #6495

Alexandra Weisberg

,

Edward Davis

,

Javier Tabima

,

Michael Belcher

,

Marilyn Miller

,

Chih-Horng Kuo

,

Joyce Loper

,

Niklaus Gr\"unwald

,

Melodie Putnam

,

Jeff Chang

Other Scholarly or Creative Work

Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorum. MBio 10: e02452-18

●

2019

A Dale

,

N Feau

,

S Everhart

,

B Dhillon

,

B Wong

,

J Sheppard

,

G Bilodeau

,

A Brar

,

J Tabima

,

D Shen

,

others

Article in Refereed Journal

Designing a Socio-Cultural Approach for Teaching and Learning Computational Thinking

Nordic Journal of Digital Literacy

●

2019

●

Vol. 15

●

Issue #02

Francisco Buitrago-Fl'orez

,

Giovanna Danies

,

Javier Tabima

,

Silvia Restrepo

,

Carola Hern'andez

Article in Refereed Journal

Genome-wide increased copy number is associated with emergence of super-fit clones of the Irish potato famine pathogen Phytophthora infestans

BioRxiv

●

2019

Brian Knaus

,

Javier Tabima

,

Shankar Shakya

,

Howard Judelson

,

Niklaus Gr"unwald

Article in Refereed Journal

Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorum

MBio

●

2019

●

Vol. 10

●

Issue #2

Angela Dale

,

Nicolas Feau

,

Sydney Everhart

,

Braham Dhillon

,

Barbara Wong

,

Julie Sheppard

,

Guillaume Bilodeau

,

Avneet Brar

,

Javier Tabima

,

Danyu Shen

,

others

Article in Refereed Journal

effectR: An expandable R package to predict candidate RxLR and CRN effectors in oomycetes using motif searches

Molecular Plant-Microbe Interactions

●

2019

●

Vol. 32

●

Issue #9

Javier Tabima

,

Niklaus Gr"unwald

Article in Refereed Journal

effectR: An expandable R package to predict candidate effectors

BioRxiv

●

2018

Javier Tabima

,

Niklaus Gr"unwald

Papers Published - Conference Proceedings

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

Brian Knaus

,

Javier Tabima

,

Shankar Shakya

,

Howard Judelson

,

Niklaus Grunwald

Article in Refereed Journal

Evolution of the US biological select agent Rathayibacter toxicus

MBio

●

2018

●

Vol. 9

●

Issue #4

Edward Davis

,

Javier Tabima

,

Alexandra Weisberg

,

Lucas Lopes

,

Michele Wiseman

,

Michael Wiseman

,

Tal Pupko

,

Michael Belcher

,

Aaron Sechler

,

Matt Tancos

,

others

Article in Refereed Journal

Populations of Phytophthora rubi show little differentiation and high rates of migration among states in the Western United States

Molecular Plant-Microbe Interactions

●

2018

●

Vol. 31

●

Issue #6

Javier Tabima

,

Michael Coffey

,

Inga Zazada

,

Niklaus Gr"unwald

Article in Refereed Journal

Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia

Persoonia: Molecular Phylogeny and Evolution of Fungi

●

2018

●

Vol. 41

M Mideros

,

D Turissini

,

N Guayaz'an

,

H Ibarra-Avila

,

G Danies

,

M C'ardenas

,

K Myers

,

J Tabima

,

E Goss

,

A Bernal

,

others

Article in Refereed Journal

Genetic diversity of Phytophthora pluvialis, a pathogen of conifers, in New Zealand and the west coast of the United States of America

Plant Pathology

●

2018

●

Vol. 67

●

Issue #5

S Brar

,

J Tabima

,

R McDougal

,

P-Y Dupont

,

N Feau

,

R Hamelin

,

P Panda

,

J LeBoldus

,

NJ Gr"unwald

,

E Hansen

,

others

Papers Published - Conference Proceedings

Population Genomics in R
2017 APS Annual Meeting

●

2017

Niklaus Grunwald

,

Steve Klosterman

,

Brian Knaus

,

Javier Tabima

Article in Refereed Journal

Whole genome sequences of the raspberry and strawberry pathogens Phytophthora rubi and P. fragariae

Molecular Plant-Microbe Interactions

●

2017

●

Vol. 30

●

Issue #10

Javier Tabima

,

Brent Kronmiller

,

Caroline Press

,

Brett Tyler

,

Inga Zasada

,

Niklaus Gr"unwald

Papers Published - Conference Proceedings

Searching for genomic signatures of host jumping onto raspberry and strawberry in two Phytophthora sister taxa
PHYTOPATHOLOGY

●

2016

●

Vol. 106

●

Issue #12

J Tabima

,

B Kronmiller

,

B Knaus

,

C Press

,

I Zasada

,

B Tyler

,

N Grunwald

,

D Shen

Papers Published - Conference Proceedings

What is a clone? Rethinking the ancestry of US clonal lineages of Phytophthora infestans using whole genome sequences
PHYTOPATHOLOGY

●

2016

●

Vol. 106

●

Issue #12

B Knaus

,

J Tabima

,

Z Kamvar

,

C Davis

,

H Judelson

,

N Grunwald

Article in Refereed Journal

Ecological speciation within the Phytophthora genus

bioRxiv

●

2016

Maria Mideros

,

David Turissini

,

Natalia Guayazan

,

Giovanna Danies

,

Martha Cardenas

,

Kevin Myers

,

Javier Tabima

,

Erica Goss

,

Adriana Bernal

,

Luz Lagos

,

others

Article in Refereed Journal

A Covert Operation by a Plant Pathogen

Cell host & microbe

●

2016

●

Vol. 20

●

Issue #4

Jeff Chang

,

Javier Tabima

Article in Refereed Journal

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

Phytopathology

●

2016

●

Vol. 106

●

Issue #11

B Knaus

,

J Tabima

,

C Davis

,

H Judelson

,

NJ Gr"unwald

Article in Refereed Journal

Microbe-ID: an open source toolbox for microbial genotyping and species identification

PeerJ

●

2016

●

Vol. 4

Javier Tabima

,

Sydney Everhart

,

Meredith Larsen

,

Alexandra Weisberg

,

Zhian Kamvar

,

Matthew Tancos

,

Christine Smart

,

Jeff Chang

,

Niklaus Gr"unwald

Article in Refereed Journal

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria

PeerJ

●

2016

●

Vol. 4

II, Davis

,

Alexandra Weisberg

,

Javier Tabima

,

Niklaus Grunwald

,

Jeff Chang

Article in Refereed Journal

Evolutionary history of the group formerly known as protists using a phylogenomics approach

Revista de la Academia Colombiana de Ciencias Exactas, F'isicas y Naturales

●

2016

●

Vol. 40

●

Issue #154

Silvia Restrepo

,

Juan Enciso

,

Javier Tabima

,

Diego Ria~no-Pach'on

Article in Refereed Journal

Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, P hytophthora infestans

Journal of Applied Microbiology

●

2016

●

Vol. 120

●

Issue #4

Z Hansen

,

B Knaus

,

J Tabima

,

C Press

,

H Judelson

,

NJ Gr"unwald

,

Christine Smart

Article in Refereed Journal

SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high-resolution melt analysis

Plant Disease

●

2016

●

Vol. 100

●

Issue #7

Zachariah Hansen

,

Brian Knaus

,

Javier Tabima

,

Caroline Press

,

Howard Judelson

,

Niklaus Gr"unwald

,

Christine Smart

Article in Refereed Journal

Five new species of entomopathogenic fungi from the Amazon and evolution of neotropical Ophiocordyceps

Fungal Biology

●

2015

●

Vol. 119

●

Issue #10

Tatiana Sanjuan

,

Ana Franco-Molano

,

Ryan Kepler

,

Joseph Spatafora

,

Javier Tabima

,

A'ida Vasco-Palacios

,

Silvia Restrepo

Article in Refereed Journal

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.

PeerJ

March

●

2014

Z Kamvar

,

J Tabima

,

NJ Gr"unwald

Article in Refereed Journal

Poppr: an R package for genetic analysis of populations with clonal or partially clonal reproduction

●

2014

Zhian Kamvar

,

Javier Tabima

,

Niklaus Gr"unwald

Papers Published - Conference Proceedings

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

M Cristancho

,

W Giraldo

,

J Tabima

,

D Botero

,

D Ria~no

,

S Restrepo

,

A Gait'an

,

others

Other Scholarly or Creative Work

Polyphasic characterization of Colletotrichum sp. Isolates from tree tomato and mango crops in Cundinamarca and Tolima, Colombia

●

2014

Mendoza, Calder'on

,

others

Article in Refereed Journal

Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

Frontiers in plant science

●

2014

●

Vol. 5

Marco Cristancho

,

David Botero-Rozo

,

William Giraldo

,

Javier Tabima

,

Diego Ria~no-Pach'on

,

Carolina Escobar

,

Yomara Rozo

,

Luis Rivera

,

Andr'es Dur'an

,

Silvia Restrepo

,

others

Chapters In Books

Chapter: Phytophthora ramorum

Published by Springer, Berlin, Heidelberg

●

2014

Sydney Everhart

,

Javier Tabima

,

Niklaus Gr"unwald

Article in Refereed Journal

Speciation in fungal and oomycete plant pathogens

Annual review of phytopathology

●

2014

●

Vol. 52

Silvia Restrepo

,

Javier Tabima

,

Maria Mideros

,

Niklaus Gr"unwald

,

Daniel Matute

Article in Refereed Journal

Pathogenicity, fungicide resistance, and genetic variability of Phytophthora rubi isolates from raspberry (Rubus idaeus) in the western United States

Plant Disease

●

2014

●

Vol. 98

●

Issue #12

Jane Stewart

,

Duncan Kroese

,

Javier Tabima

,

Meredith Larsen

,

Valerie Fieland

,

Caroline Press

,

Inga Zasada

,

Niklaus Gr"unwald

Article in Refereed Journal

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes

Proceedings of the National Academy of Sciences

●

2014

●

Vol. 111

●

Issue #24

Erica Goss

,

Javier Tabima

,

David Cooke

,

Silvia Restrepo

,

William Fry

,

Gregory Forbes

,

Valerie Fieland

,

Martha Cardenas

,

Niklaus Gr"unwald

Article in Refereed Journal

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

PeerJ

●

2014

●

Vol. 2

Zhian Kamvar

,

Javier Tabima

,

Niklaus Gr"unwald

Article in Refereed Journal

Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto)

Mycologia

●

2014

●

Vol. 106

●

Issue #2

Tatiana Sanjuan

,

Javier Tabima

,

Silvia Restrepo

,

Thomas Laessoe

,

Joseph Spatafora

,

Ana Franco-Molano

Chapters In Books

Chapter: Application of genome studies of coffee rust

Published by Springer, Cham

●

2014

Marco Cristancho

,

William Giraldo

,

David Botero

,

Javier Tabima

,

Diana Ortiz

,

Alejandro Peralta

,

'Alvaro Gait'an

,

Silvia Restrepo

,

Diego Ria~no

Article in Refereed Journal

The poppr R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

Phytopathology

●

2013

●

Vol. 103

●

Issue #6

Zhian Kamvar

,

J Tabima

,

Niklaus Gr"unwald

Article in Refereed Journal

Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. manihotis strain CIO151

PloS one

●

2013

●

Vol. 8

●

Issue #11

Mario Arrieta-Ortiz

,

Luis Rodr'iguez-R

,

Alvaro Perez-Quintero

,

Lucie Poulin

,

Ana D'iaz

,

Nathalia Rojas

,

Cesar Trujillo

,

Mariana Benavides

,

Rebecca Bart

,

Jens Boch

,

others

Article in Refereed Journal

Seborrheic dermatitis: predisposing factors and ITS2 secondary structure for Malassezia phylogenic analysis

Medical Mycology

●

2013

●

Vol. 51

●

Issue #8

Yulien Amado

,

Anelvi Pati~no-Uzc'ategui

,

Maria Garc'ia

,

Javier Tabima

,

Adriana Motta

,

Martha C'ardenas

,

Adriana Bernal

,

Silvia Restrepo

,

Adriana Celis

Article in Refereed Journal

Fusarium species associated to onychomycoses in Colombia.

F1000Research

●

2012

●

Vol. 3

Marcela Guevara

,

Angela Mu~noz

,

Yulien Amado

,

Laura Bocanegra

,

Leticia Sopo

,

Adriana Motta

,

Maria Garc'ia

,

Javier Tabima

,

Silvia Restrepo

,

Adriana Celis

Papers Published - Conference Proceedings

Morphological characterization of Colletotrichum species isolated from mango and tree tomato in Cundinamarca and Tolima, Colombia
Phytopathology

●

2012

●

Vol. 102

●

Issue #7

C Calder'on

,

M C'ardenas

,

S Restrepo

,

P Jim'enez

Papers Published - Conference Proceedings

The dynamics of evolution in Phytopththora infestans as told by phylogeographical approaches
PHYTOPATHOLOGY

●

2012

●

Vol. 102

●

Issue #7

J Tabima

,

M Mideros

,

A Bernal

,

P Jimenez

,

D Riano-Pachon

,

N Grunwald

,

S Restrepo

Article in Refereed Journal

Phytophthora infestans population structure: A worldwide scale

Acta Biol'ogica Colombiana

●

2012

●

Vol. 17

●

Issue #2

Martha Cardenas

,

Giovanna Danies

,

Javier Tabima

,

Adriana Bernal

,

Silvia Restrepo

Article in Refereed Journal

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)

Plant Pathology

●

2012

●

Vol. 61

●

Issue #2

M C'ardenas

,

J Tabima

,

W Fry

,

NJ Gr"unwald

,

A Bernal

,

S Restrepo

Article in Refereed Journal

First report of Phytophthora infestans causing late blight on Solanum viarum in Colombia

Plant Disease

●

2011

●

Vol. 95

●

Issue #7

ME C'ardenas

,

E Medina

,

J Tabima

,

A Vargas

,

C Lopera

,

A Bernal

,

S Restrepo

Article in Refereed Journal

Virulence gene expression in Malassezia spp from individuals with seborrheic dermatitis

Journal of investigative dermatology

●

2011

●

Vol. 131

MfLipl Mg13326

Article in Refereed Journal

Phylogeography and molecular epidemiology of Papaya ringspot virus

Virus research

●

2011

●

Vol. 159

●

Issue #2

XA Castillo

,

G Fermin

,

J Tabima

,

Y Rojas

,

P Tennant

,

M Fuchs

,

R Sierra

,

A Bernal

,

S Restrepo

Article in Refereed Journal

Tolypocladamide H and the Proposed Tolypocladamide NRPS in Tolypocladium Species

Journal of Natural Products

Richard Tehan

,

Rheannon Blount

,

Ryan Goold

,

Daphne Mattos

,

Nicolas Spatafora

,

Javier Tabima

,

Romina Gazis

,

Chengshu Wang

,

Jane Ishmael

,

Joseph Spatafora

,

Kerry McPhail

Article in Refereed Journal

Pathogenicity and phylogenetic relationships of fungi associated with root, crown and vascular symptoms related to winter squash yield decline

Plant Disease

Hannah Rivedal

,

Alexandra Stone

,

Javier Tabima

,

Kenneth Johnson

Article in Refereed Journal

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--

Javier Tabima

,

Silvia Restrepo

,

Thomas Laessoe

,

Joseph Spatafora

,

Ana Franco-Molano

Javier Tabima Restrepo

Affiliated Department(s)

Scholarly and Creative Works

Awards & Grants