Stajich Laboratory for Fungal Evolutionary Genomics

Research

Research in the Stajich lab encompass a variety of topics from Evolution, Genomics, Mycology, Microbiology, and Bioinformatics.

All

2024

A Cluster of Diutina catenulata Funguria in Patients with Coronavirus Disease 2019 (COVID-19) Hospitalized in a Tertiary Reference Hospital from Rio de Janeiro, Brazil.
A Cluster of Diutina catenulata Funguria in Patients with Coronavirus Disease 2019 (COVID-19) Hospitalized in a Tertiary Reference Hospital from Rio de Janeiro, Brazil.
Rodrigo Almeida-Paes, Marcus de Melo Teixeira, Fernanda Alves de Oliveira, Marcos de Abreu Almeida, Fernando Almeida-Silva, …, Jason E Stajich, Beatriz Grinsztejn, Valdilea Gonçalves Veloso, Andrea d’Avila Freitas, Rosely Maria Zancopé-Oliveira
Current microbiology  ·  03 Sep 2024  ·  pmid:39223407
fungal-pathogen diutina covid-19 population-genomics
Giant transposons promote strain heterogeneity in a major fungal pathogen.
Giant transposons promote strain heterogeneity in a major fungal pathogen.
Emile Gluck-Thaler, Adrian Forsythe, Charles Puerner, Jason E Stajich, Daniel Croll, Robert A Cramer, Aaron A Vogan
bioRxiv : the preprint server for biology  ·  28 Jun 2024  ·  pmid:38979181
starship transposons repetitive-elements aspergillus-fumigatus
Description of new micro-colonial fungi species
Description of new micro-colonial fungi species
Tania Kurbessoian, Sarah A Ahmed, Yu Quan, Sybren de Hoog, Jason E Stajich
bioRxiv : the preprint server for biology  ·  20 Jun 2024  ·  pmid:38915581
taxonomy black-fungi genome
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic
Sara C D Carpenter, Adam J Bogdanove, Bhuwan Abbot, Jason E Stajich, Jessie K Uehling, Brian Lovett, Matt T Kasson, Morgan E Carter
Microbial genomics  ·  01 Jun 2024  ·  pmid:38860878
bacterial-fungal-interactions zygomycete mucoromycotina
Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility.
Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility.
Atul Munish Chander, Marcus de Melo Teixeira, Nitin K Singh, Michael P Williams, Ceth W Parker, …, Jason E Stajich, Tamas Torok, Scott Tighe, Christopher E Mason, Kasthuri Venkateswaran
Scientific reports  ·  28 May 2024  ·  pmid:38806503
black-yeast knufia fungi space-fungi
Study of fungal cell wall evolution through its monosaccharide composition: An insight into fungal species interacting with plants.
Study of fungal cell wall evolution through its monosaccharide composition: An insight into fungal species interacting with plants.
Sara I Yugueros, Jorge Peláez, Jason E Stajich, María Fuertes-Rabanal, Andrea Sánchez-Vallet, Asier Largo-Gosens, Hugo Mélida
Cell surface (Amsterdam, Netherlands)  ·  25 May 2024  ·  pmid:38873189
cell-wall fungi comparative
Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in
Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in
Jason E Stajich, Brian Lovett, Emily Lee, Angie M Macias, Ann E Hajek, Benjamin L de Bivort, Matt T Kasson, Henrik H De Fine Licht, Carolyn Elya
eLife  ·  20 May 2024  ·  pmid:38767950
entomophthora big-genome nanopore transposon zoopagomycota zygomycete
Epidemiological, clinical, and genomic landscape of coccidioidomycosis in northeastern Brazil.
Epidemiological, clinical, and genomic landscape of coccidioidomycosis in northeastern Brazil.
Kelsen Dantas Eulálio, Daniel R Kollath, Liline Maria Soares Martins, Antonio de Deus Filho, Maria do Amparo Salmito Cavalcanti, …, Eduardo Bagagli, Maria Sueli Soares Felipe, Bridget M Barker, Luciana Trilles, Marcus de Melo Teixeira
Nature communications  ·  12 Apr 2024  ·  pmid:38609393
coccidioidomycosis coccidioides brazil
An endogenous DNA virus in an amphibian-killing fungus associated with pathogen genotype and virulence.
An endogenous DNA virus in an amphibian-killing fungus associated with pathogen genotype and virulence.
Rebecca A Clemons, Mark N Yacoub, Evelyn Faust, L Felipe Toledo, Thomas S Jenkinson, …, D Rabern Simmons, Erik Kalinka, Lillian K Fritz-Laylin, Timothy Y James, Jason E Stajich
Current biology : CB  ·  14 Mar 2024  ·  pmid:38490202
batrachochytrium mycovirus genome frog virulence
Tracing histoplasmosis genomic epidemiology and species occurrence across the USA.
Tracing histoplasmosis genomic epidemiology and species occurrence across the USA.
Bernardo Guerra Tenório, Daniel R Kollath, Lalitha Gade, Anastasia P Litvintseva, Tom Chiller, …, Jason E Stajich, Daniel R Matute, Andrew S Hanzlicek, Bridget M Barker, Marcus de Melo Teixeira
Emerging microbes & infections  ·  11 Mar 2024  ·  pmid:38465644
histoplasma
Class-wide genomic tendency throughout specific extremes in black fungi
Class-wide genomic tendency throughout specific extremes in black fungi
Claudia Coleine, Tania Kurbessoian, Giulia Calia, Manuel Delgado-Baquerizo, Alessandro Cestaro, …, Nicola Segata, Claudio Donati, Jason E. Stajich, Sybren de Hoog, Laura Selbmann
Fungal Diversity  ·  26 Feb 2024  ·  doi:10.1007/s13225-024-00533-y
black-yeast
Draft genome sequence of a black yeast fungus <i>Exophiala xenobiotica</i> isolated from La Brea Tar Pits
Draft genome sequence of a black yeast fungus Exophiala xenobiotica isolated from La Brea Tar Pits
Tania Kurbessoian, Danielle Stevenson, Renata Haro, Samantha Ying, Jason E. Stajich
Microbiology Resource Announcements  ·  15 Feb 2024  ·  doi:10.1128/mra.00913-23
exophiala black-yeast genome genome-announcement
Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria.
Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria.
Lluvia Vargas-Gastélum, Alexander S Romer, Marjan Ghotbi, Jason W Dallas, N Reed Alexander, …, Leila Shadmani, Joseph W Spatafora, Jason E Stajich, Javier F Tabima, Donald M Walker
mSphere  ·  13 Feb 2024  ·  pmid:38349154
herptile microbiome network its 16s amplicon bacterial-fungal-interactions
Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert.
Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert.
Thuy M Nguyen, Nuttapon Pombubpa, Marcel Huntemann, Alicia Clum, Brian Foster, …, Miranda Harmon-Smith, Emiley A Eloe-Fadrosh, Nicole Pietrasiak, Jason E Stajich, Erik F Y Hom
Microbiology resource announcements  ·  08 Feb 2024  ·  pmid:38329355
biocrust biological-crust metagenome
Morphological and phylogenetic resolution of <i>Conoideocrella luteorostrata</i> (Hypocreales, Clavicipitaceae), a potential biocontrol fungus for Fiorinia externa in United States Christmas tree production areas
Morphological and phylogenetic resolution of Conoideocrella luteorostrata (Hypocreales, Clavicipitaceae), a potential biocontrol fungus for Fiorinia externa in United States Christmas tree production areas
Brian Lovett, Hana Barrett, Angie M Macias, Jason E Stajich, Lindsay R Kasson, Matt T Kasson
Mycologia  ·  26 Jan 2024  ·  pmid:38275281
conoideocrella biocontrol clavicipitaceae
Comparative genomics reveals intra and inter species variation in the pathogenic fungus<i>Batrachochytrium dendrobatidis</i>
Comparative genomics reveals intra and inter species variation in the pathogenic fungusBatrachochytrium dendrobatidis
Mark N. Yacoub, Jason E. Stajich
Cold Spring Harbor Laboratory  ·  25 Jan 2024  ·  doi:10.1101/2024.01.24.576925
batrachochytrium comparative-genomics pangenome
Haplotype phased genome of ‘Fairchild’ mandarin highlights influence of local chromatin state on gene expression
Haplotype phased genome of ‘Fairchild’ mandarin highlights influence of local chromatin state on gene expression
Isaac A. Diaz, Talieh Ostovar, Jinfeng Chen, Sarah Saddoris, Robert J. Schmitz, Susan R. Wessler, Jason Stajich, Danelle K. Seymour
Cold Spring Harbor Laboratory  ·  24 Jan 2024  ·  doi:10.1101/2024.01.20.575729
citrus genome transposable-elements
Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability.
Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability.
Claudia Coleine, Davide Albanese, Angelique E Ray, Manuel Delgado-Baquerizo, Jason E Stajich, …, Susannah Tringe, Christa Pennacchio, Belinda C Ferrari, Claudio Donati, Laura Selbmann
The Science of the total environment  ·  19 Jan 2024  ·  pmid:38244622
antarctica metagenome
Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting.
Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting.
Thuy M Nguyen, Nuttapon Pombubpa, Marcel Huntemann, Alicia Clum, Brian Foster, …, Miranda Harmon-Smith, Emiley A Eloe-Fadrosh, Nicole Pietrasiak, Jason E Stajich, Erik F Y Hom
Microbiology resource announcements  ·  08 Jan 2024  ·  pmid:38189307
extremophile antarctica bacteria
Large DNA viruses in early diverging fungal genomes are relics of past and present infections
Large DNA viruses in early diverging fungal genomes are relics of past and present infections
Jillian M. Myers, Frederik Schulz, Saleh Rahimlou, Kevin R. Amses, D. Rabern Simmons, Jason E. Stajich, Timothy Y. James
Cold Spring Harbor Laboratory  ·  05 Jan 2024  ·  doi:10.1101/2024.01.04.574182
mycovirus ncldv chytrid fungi

2023

Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus.
Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus.
Hung-Che Lin, Guillermo Vidal-Diez de Ulzurrun, Sheng-An Chen, Ching-Ting Yang, Rebecca J Tay, …, Siou-Ying Lin, Yu-Chu Chang, Jason E Stajich, Erich M Schwarz, Yen-Ping Hsueh
PLoS biology  ·  21 Nov 2023  ·  pmid:37988381
nematode-trapping-fungi genomics transcriptome arthrobotrys
The reference genome assembly of the bright cobblestone lichen, Acarospora socialis.
The reference genome assembly of the bright cobblestone lichen, Acarospora socialis.
Julia N Adams, Merly Escalona, Mohan P A Marimuthu, Colin W Fairbairn, Eric Beraut, William Seligmann, Oanh Nguyen, Noravit Chumchim, Jason E Stajich
The Journal of heredity  ·  15 Nov 2023  ·  pmid:37740386
acarospora genome ccgp
Evaluation of Different Gene Prediction Tools in Coccidioides immitis
Evaluation of Different Gene Prediction Tools in Coccidioides immitis
Theo N. Kirkland, Sinem Beyhan, Jason E. Stajich
Journal of Fungi  ·  09 Nov 2023  ·  doi:10.3390/jof9111094
coccidioides onygenales rna-seq gene-prediction
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.
Sara C. D. Carpenter, Adam J. Bogdanove, Bhuwan Abbot, Jason Eric Stajich, Jessie Uehling, Brian Lovett, Matt T Kasson, Morgan E Carter
Cold Spring Harbor Laboratory  ·  16 Oct 2023  ·  doi:10.1101/2023.10.16.562584
zygomycete fungi bacterial-fungi-interactions
Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters.
Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters.
Cassandra L Ettinger, Jessica Wu-Woods, Tania Kurbessoian, Dylan J Brown, Inaiara de Souza Pacheco, …, Linda L Walling, Peter W Atkinson, Frank J Byrne, Richard Redak, Jason E Stajich
mSphere  ·  06 Oct 2023  ·  pmid:37800904
sharpshooter microbiome insect host-microbe
Genomic characterization and radiation tolerance of <i>Naganishia kalamii</i> sp. nov. and <i>Cystobasidium onofrii</i> sp. nov. from Mars 2020 mission assembly facilities.
Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities.
Patrick Leo, Marcus de Melo Texeira, Atul M Chander, Nitin K Singh, Anna C Simpson, Andrey Yurkov, Fathi Karouia, Jason E Stajich, Christopher E Mason, Kasthuri Venkateswaran
IMA fungus  ·  11 Aug 2023  ·  pmid:37568226
naganishia cystobasidium space-fungi iss mars-2020
Genomes and transcriptomes help unravel the complex life cycle of the blastoclad fungus, <i>Coelomomyces lativittatus</i>, an obligate parasite of mosquitoes and microcrustaceans.
Genomes and transcriptomes help unravel the complex life cycle of the blastoclad fungus, Coelomomyces lativittatus, an obligate parasite of mosquitoes and microcrustaceans.
Cassandra L Ettinger, Talieh Ostovar, Mark Yacoub, Steven Ahrendt, Robert H Hice, Brian A Federici, Jason E Stajich
Mycologia  ·  26 Jul 2023  ·  pmid:37494633
chytrid blastocladiomycota coelomomyces mosquito-pathogen rna-seq transcriptomics
Extremophilic and extremotolerant fungi.
Extremophilic and extremotolerant fungi.
Cene Gostinčar, Jason E Stajich, Nina Gunde-Cimerman
Current biology : CB  ·  24 Jul 2023  ·  pmid:37490857
extremophile review
Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?
Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?
Andrii P Gryganskyi, Jacob Golan, Anna Muszewska, Alexander Idnurm, Somayeh Dolatabadi, …, Nicole Reynolds, Timothy Y James, Igor V Grigoriev, Joseph W Spatafora, Jason E Stajich
Microorganisms  ·  18 Jul 2023  ·  pmid:37513002
zygolife genome
Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung
Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung
Daniel Murante, Elora G. Demers, Tania Kurbessoian, Marina Ruzic, Alix Ashare, Jason E. Stajich, Deborah A. Hogan
mBio  ·  11 Jul 2023  ·  doi:10.1128/mbio.01171-23
candida clavispora cystic-fibrosis
Patterns and determinants of the global herbivorous mycobiome.
Patterns and determinants of the global herbivorous mycobiome.
Casey H Meili, Adrienne L Jones, Alex X Arreola, Jeffrey Habel, Carrie J Pratt, …, Joan A Edwards, Sumit Singh Dagar, Andrew P Foote, Noha H Youssef, Mostafa S Elshahed
Nature communications  ·  26 Jun 2023  ·  pmid:37365172
herbivore microbiome chytrid neocallimastigomycota anaerobic-gut-fungi agf
Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits.
Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits.
Zsolt Merényi, Krisztina Krizsán, Neha Sahu, Xiao-Bin Liu, Balázs Bálint, Jason E Stajich, Joseph W Spatafora, László G Nagy
Nature ecology & evolution  ·  22 Jun 2023  ·  pmid:37349567
fungi taxonomy genomics comparative-genomics evolution 1kfg 1000-fungal-genomes
In host evolution of <i>Exophiala dermatitidis</i> in cystic fibrosis lung micro-environment
In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment
Tania Kurbessoian, Daniel Murante, Alex Crocker, Deborah A Hogan, Jason E Stajich
G3: Genes, Genomes, Genetics  ·  09 Jun 2023  ·  doi:10.1093/g3journal/jkad126
cystic-fibrosis exophiala population-genomics
Genome Sequence of <i>Lichtheimia ornata</i>, an Emerging Opportunistic Mucorales Pathogen
Genome Sequence of Lichtheimia ornata, an Emerging Opportunistic Mucorales Pathogen
Terrance Shea, Jason T Mohabir, Tania Kurbessoian, Brittany Berdy, James Fontaine, Andreas Gnirke, Jonathan Livny, Jason E Stajich, Christina A Cuomo
Microbiology resource announcements  ·  08 Jun 2023  ·  pmid:37289095
lichtheimia mucoromycotina
Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert
Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert
Frederick A. Hansen, Darren K. James, John P. Anderson, Christy S. Meredith, Andrew J. Dominguez, Nuttapon Pombubpa, Jason E. Stajich, Adriana L. Romero-Olivares, Shawn W. Salley, Nicole Pietrasiak
Frontiers in Microbiology  ·  07 Jun 2023  ·  doi:10.3389/fmicb.2023.1135800
mycobiome microbiome aridlands desert chihuahuan-desert soil-health biological-crusts
Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability
Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability
Cassandra L. Ettinger, Morgan Saunders, Laura Selbmann, Manuel Delgado-Baquerizo, Claudio Donati, …, Susannah Tringe, Christa Pennacchio, Tijana G. del Rio, Jason E. Stajich, Claudia Coleine
Microbiome  ·  08 May 2023  ·  doi:10.1186/s40168-023-01554-6
virus antarctica metagenome
Identification of the Neoaspergillic Acid Biosynthesis Gene Cluster by Establishing an <i>In Vitro</i> CRISPR-Ribonucleoprotein Genetic System in <i>Aspergillus melleus</i>
Identification of the Neoaspergillic Acid Biosynthesis Gene Cluster by Establishing an In Vitro CRISPR-Ribonucleoprotein Genetic System in Aspergillus melleus
Bo Yuan, Michelle F Grau, Ramiro Mendonça Murata, Tamas Torok, Kasthuri Venkateswaran, Jason E Stajich, Clay C C Wang
ACS omega  ·  01 May 2023  ·  pmid:37214671
asperigillus secondary-metabolism crispr
Genome Sequence and Assembly of 18 Fusarium Isolates from Florida Citrus under High Huanglongbing Disease Pressure and California Citrus under Low Huanglongbing Disease Pressure.
Genome Sequence and Assembly of 18 Fusarium Isolates from Florida Citrus under High Huanglongbing Disease Pressure and California Citrus under Low Huanglongbing Disease Pressure.
Tania Kurbessoian, Gretchen Heimlich-Villalta, Nichole Ginnan, Flavia Campos Vieira, Philippe E Rolshausen, M Caroline Roper, Jason E Stajich
Microbiology resource announcements  ·  12 Apr 2023  ·  pmid:37042758
fusarium citrus genome-announcement
Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors.
Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors.
Yan Wang, Ying Chang, Jericho Ortañez, Jesús F Peña, Derreck Carter-House, …, Mi Yan, Kerrie Barry, Igor V Grigoriev, Joseph W Spatafora, Jason E Stajich
Genome biology and evolution  ·  06 Apr 2023  ·  pmid:36930540
zygolife zygomycete genome
Microbiome diversity, composition and assembly in a California citrus orchard
Microbiome diversity, composition and assembly in a California citrus orchard
MengYuan Xi, Elizabeth Deyett, Jason E. Stajich, Ashraf El-Kereamy, M. Caroline Roper, Philippe E. Rolshausen
Frontiers in Microbiology  ·  22 Feb 2023  ·  doi:10.3389/fmicb.2023.1100590
citrus microbiome mycobiome
Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists.
Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists.
Xiuping Liu, Lu Lyu, Jiaqian Li, Biswarup Sen, Mohan Bai, Jason E Stajich, Jackie L Collier, Guangyi Wang
Microbiology spectrum  ·  06 Feb 2023  ·  pmid:36744882
labyrinthulomycetes
Phylogenomic analysis of the Neocallimastigomycota: proposal of <i>Caecomycetaceae</i> fam. nov., <i>Piromycetaceae</i> fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae
Phylogenomic analysis of the Neocallimastigomycota: proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae
Radwa A Hanafy, Yan Wang, Jason E Stajich, Carrie J Pratt, Noha H Youssef, Mostafa S Elshahed
International journal of systematic and evolutionary microbiology  ·  01 Feb 2023  ·  pmid:36827202
agf rumen-fungi neocallimastigomycota
Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi.
Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi.
Nicole K Reynolds, Jason E Stajich, Gerald L Benny, Kerrie Barry, Stephen Mondo, …, Igor V Grigoriev, Hsiao-Man Ho, Pedro W Crous, Joseph W Spatafora, Matthew E Smith
Genome biology and evolution  ·  04 Jan 2023  ·  pmid:36617272
kickxellomycotina genomes zygolife mycoparasite
<i>Botrytis cinerea</i>small RNAs are associated with tomato AGO1 and silence tomato defense-related target genes supporting cross-kingdom RNAi
Botrytis cinereasmall RNAs are associated with tomato AGO1 and silence tomato defense-related target genes supporting cross-kingdom RNAi
Baoye He, Qiang Cai, Arne Weiberg, Wei Li, An-Po Cheng, Shouqiang Ouyang, Katherine Borkovich, Jason Stajich, Cei Abreu-Goodger, Hailing Jin
Cold Spring Harbor Laboratory  ·  02 Jan 2023  ·  doi:10.1101/2022.12.30.522274
smallrna tomato botrytis-cinerea gene-silencing

2022

Description and Genome Characterization of Three Novel Fungal Strains Isolated from Mars 2020 Mission-Associated Spacecraft Assembly Facility Surfaces—Recommendations for Two New Genera and One Species
Description and Genome Characterization of Three Novel Fungal Strains Isolated from Mars 2020 Mission-Associated Spacecraft Assembly Facility Surfaces—Recommendations for Two New Genera and One Species
Atul Munish Chander, Marcus de Melo Teixeira, Nitin K. Singh, Michael P. Williams, Anna C. Simpson, …, Ceth W. Parker, Jason E. Stajich, Christopher E. Mason, Tamas Torok, Kasthuri Venkateswaran
Journal of Fungi  ·  23 Dec 2022  ·  doi:10.3390/jof9010031
iss taxonomy space-fungi ascomycota genome nanopore
Cataloging Viral Diversity from Nonaxenic Terrestrial Cyanobacteria Cultures
Cataloging Viral Diversity from Nonaxenic Terrestrial Cyanobacteria Cultures
Cassandra L. Ettinger, Sudipto R. Paul, Neptali Flores, Ryan D. Ward, Nicole Pietrasiak, Jason E. Stajich
Cold Spring Harbor Laboratory  ·  14 Dec 2022  ·  doi:10.1101/2022.12.14.520320
cyanobacteria metagenome virus genome-announcement
A single fungal strain was the unexpected cause of a mass aspergillosis outbreak in the world’s largest and only flightless parrot
A single fungal strain was the unexpected cause of a mass aspergillosis outbreak in the world’s largest and only flightless parrot
David J. Winter, Bevan S. Weir, Travis Glare, Johanna Rhodes, John Perrott, Matthew C. Fisher, Jason E. Stajich, Andrew Digby, Peter K. Dearden, Murray P. Cox
iScience  ·  01 Dec 2022  ·  doi:10.1016/j.isci.2022.105470
kakapo population-genomics outbreak avian
The pan-genome of <i>Aspergillus fumigatus</i> provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination
Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich
PLOS Biology  ·  17 Nov 2022  ·  doi:10.1371/journal.pbio.3001890
aspergillus population-genomics pangenome
The future of fungi: threats and opportunities.
The future of fungi: threats and opportunities.
Nicola T Case, Judith Berman, David S Blehert, Robert A Cramer, Christina Cuomo, …, John W Taylor, Dawn Thompson, Gerard D Wright, Joseph Heitman, Leah E Cowen
G3 (Bethesda, Md.)  ·  04 Nov 2022  ·  pmid:36179219
review cifar future-of-fungi bwf
Transcriptome and population structure of glassy-winged sharpshooters (Homalodisca vitripennis) with varying insecticide resistance in southern California.
Transcriptome and population structure of glassy-winged sharpshooters (Homalodisca vitripennis) with varying insecticide resistance in southern California.
Cassandra L Ettinger, Frank J Byrne, Inaiara de Souza Pacheco, Dylan J Brown, Linda L Walling, Peter W Atkinson, Richard A Redak, Jason E Stajich
BMC genomics  ·  22 Oct 2022  ·  pmid:36273137
gwss resistance glassy-winged-sharpshooter genomics rna-seq
Manipulation of the Global Regulator <i>mcrA</i> Upregulates Secondary Metabolite Production in <i>Aspergillus wentii</i> Using CRISPR-Cas9 with In Vitro Assembled Ribonucleoproteins
Manipulation of the Global Regulator mcrA Upregulates Secondary Metabolite Production in Aspergillus wentii Using CRISPR-Cas9 with In Vitro Assembled Ribonucleoproteins
Bo Yuan, Nancy P Keller, Berl R Oakley, Jason E Stajich, Clay C C Wang
ACS chemical biology  ·  05 Oct 2022  ·  pmid:36197945
aspergillus secondary-metabolism crispr bgc mcra
Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions.
Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions.
Lian Narunsky-Haziza, Gregory D Sepich-Poore, Ilana Livyatan, Omer Asraf, Cameron Martino, …, Amir Bashan, Austin D Swafford, Yitzhak Pilpel, Rob Knight, Ravid Straussman
Cell  ·  29 Sep 2022  ·  pmid:36179670
mycobiome cancer metagenomics
Single nucleotide polymorphisms and chromosomal copy number variation may impact the <i>Sporothrix brasiliensis</i> antifungal susceptibility and sporotrichosis clinical outcomes.
Single nucleotide polymorphisms and chromosomal copy number variation may impact the Sporothrix brasiliensis antifungal susceptibility and sporotrichosis clinical outcomes.
Marcus M Teixeira, Rodrigo Almeida-Paes, Andréa R Bernardes-Engemann, André M Nicola, Priscila M de Macedo, …, Dayvison F S Freitas, Bridget M Barker, Daniel R Matute, Jason E Stajich, Rosely M Zancopé-Oliveira
Fungal genetics and biology : FG & B  ·  21 Sep 2022  ·  pmid:36152775
sporothrix resistance antifungal azole cnv
Diploid-dominant life cycles characterize the early evolution of Fungi.
Diploid-dominant life cycles characterize the early evolution of Fungi.
Kevin R Amses, D Rabern Simmons, Joyce E Longcore, Stephen J Mondo, Kensuke Seto, …, Nicolas E Buchler, Igor V Grigoriev, Joseph W Spatafora, Jason E Stajich, Timothy Y James
Proceedings of the National Academy of Sciences of the United States of America  ·  29 Aug 2022  ·  pmid:36037379
chytrid genome-evolution ploidy phylogenomics
Metagenome-Assembled Genomes of Bacteria Associated with <i>Massospora cicadina</i> Fungal Plugs from Infected Brood VIII Periodical Cicadas.
Metagenome-Assembled Genomes of Bacteria Associated with Massospora cicadina Fungal Plugs from Infected Brood VIII Periodical Cicadas.
Cassandra L Ettinger, Brian Lovett, Matt T Kasson, Jason E Stajich
Microbiology resource announcements  ·  29 Aug 2022  ·  pmid:36036588
massospora genome zoopagomycota entomophthomycotina metagenome
An Improved 1.5-Gigabase Draft Assembly of <i>Massospora cicadina</i> (Zoopagomycota), an Obligate Fungal Parasite of 13- and 17-Year Cicadas.
An Improved 1.5-Gigabase Draft Assembly of Massospora cicadina (Zoopagomycota), an Obligate Fungal Parasite of 13- and 17-Year Cicadas.
Jason E Stajich, Brian Lovett, Cassandra L Ettinger, Derreck A Carter-House, Tania Kurbessoian, Matt T Kasson
Microbiology resource announcements  ·  29 Aug 2022  ·  pmid:36036589
massospora genome zoopagomycota entomophthomycotina
Comparative Genomics Reveals that Metabolism Underlies Evolution of Entomopathogenicity in Bee-loving <i>Ascosphaera spp.</i> Fungi
Comparative Genomics Reveals that Metabolism Underlies Evolution of Entomopathogenicity in Bee-loving Ascosphaera spp. Fungi
J J Maccaro, J F Moreira Salgado, E Klinger, M P Argueta Guzmán, L Ngor, J E Stajich, Q S McFrederick
Journal of invertebrate pathology  ·  03 Aug 2022  ·  pmid:35933037
ascosphaera chalk-brood-disease bee insect-fungal-interactions genomics
Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies
Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies
Ying Chang, Yan Wang, Stephen Mondo, Steven Ahrendt, William Andreopoulos, …, Matthew E. Smith, Adrian Tsang, Igor V. Grigoriev, Jason E. Stajich, Joseph W. Spatafora
iScience  ·  01 Aug 2022  ·  doi:10.1016/j.isci.2022.104840
zygomycete secretome mucoromycota zoopagomycota comparative-genomics
The Early Terrestrial Fungal Lineage of Conidiobolus - Transition from Saprotroph to Parasitic Lifestyle
The Early Terrestrial Fungal Lineage of Conidiobolus - Transition from Saprotroph to Parasitic Lifestyle
Andrii P Gryganskyi, Yong Nie, Ann E Hajek, Kathie T Hodge, Xiao-Yong Liu, …, Liudmyla Kava, Antonina Vuek, Rytas Vilgalys, Bo Huang, Jason E Stajich
Journal of fungi (Basel, Switzerland)  ·  28 Jul 2022  ·  pmid:36012777
The International Space Station Environment Triggers Molecular Responses in <i>Aspergillus niger</i>
The International Space Station Environment Triggers Molecular Responses in Aspergillus niger
Adriana Blachowicz, Jillian Romsdahl, Abby J Chiang, Sawyer Masonjones, Markus Kalkum, Jason E Stajich, Tamas Torok, Clay C C Wang, Kasthuri Venkateswaran
Frontiers in microbiology  ·  30 Jun 2022  ·  pmid:35847112
aspergillus proteomics metabolomics iss space-fungi
Landscape Topography and Regional Drought Alters Dust Microbiomes in the Sierra Nevada of California.
Landscape Topography and Regional Drought Alters Dust Microbiomes in the Sierra Nevada of California.
Mia R Maltz, Chelsea J Carey, Hannah L Freund, Jon K Botthoff, Stephen C Hart, …, Molly Blakowski, Nicholas C Dove, Morgan E Barnes, Nuttapon Pombubpa, Emma L Aronson
Frontiers in microbiology  ·  28 Jun 2022  ·  pmid:35836417
amplicon-metabarcoding its 16s dust
The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA.
The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA.
Jason T Ladner, Jonathan M Palmer, Cassandra L Ettinger, Jason E Stajich, Terence M Farrell, …, Becki Lawson, Steven J Price, Anne G Stengle, Daniel A Grear, Jeffrey M Lorch
PLoS biology  ·  23 Jun 2022  ·  pmid:35737674
snake-fungal-disease onygenales ophidiomyces population-genetics wildlife-disease
Metagenome-Assembled Genomes of Bacterial Symbionts Associated with Insecticide-Resistant and -Susceptible Individuals of the Glassy-Winged Sharpshooter (Homalodisca vitripennis).
Metagenome-Assembled Genomes of Bacterial Symbionts Associated with Insecticide-Resistant and -Susceptible Individuals of the Glassy-Winged Sharpshooter (Homalodisca vitripennis).
Cassandra L Ettinger, Frank J Byrne, Richard A Redak, Jason E Stajich
Microbiology resource announcements  ·  16 Jun 2022  ·  pmid:35708345
gwss sharpshooter metagenome bacteria metagenome-assembled-genome insecticide-resistance
Avian-associated <i>Aspergillus fumigatus</i> displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events
Avian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events
Lotus A Lofgren, Jeffrey M Lorch, Robert A Cramer, David S Blehert, Brenda M Berlowski-Zier, Megan E Winzeler, Cecilia Gutierrez-Perez, Nicole E Kordana, Jason E Stajich
G3 (Bethesda, Md.)  ·  06 May 2022  ·  pmid:35377435
aspergillus-fumigatus avian antifungal population-genomics
Early branching arbuscular mycorrhizal fungus <i>Paraglomus occultum</i> carries a small and repeat-poor genome compared to relatives in the Glomeromycotina
Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina
Mathu Malar C, Yan Wang, Jason E. Stajich, Vasilis Kokkoris, Matthew Villeneuve-Laroche, Gokalp Yildirir, Nicolas Corradi
Microbial Genomics  ·  26 Apr 2022  ·  doi:10.1099/mgen.0.000810
amf zygomycete glomeromycota
Efficient CRISPR/Cas9-mediated genome modification of the glassy-winged sharpshooter <i>Homalodisca vitripennis</i> (Germar)
Efficient CRISPR/Cas9-mediated genome modification of the glassy-winged sharpshooter Homalodisca vitripennis (Germar)
Inaiara de Souza Pacheco, Anna-Louise A Doss, Beatriz G Vindiola, Dylan J Brown, Cassandra L Ettinger, Jason E Stajich, Richard A Redak, Linda L Walling, Peter W Atkinson
Scientific reports  ·  19 Apr 2022  ·  pmid:35440677
gwss sharpshooter insect crispr/cas9
A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain Silveira
A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain Silveira
Marcus de Melo Teixeira, Jason E Stajich, Jason W Sahl, George R Thompson, Rachel B Brem, Claire A Dubin, Austin V Blackmon, Heather L Mead, Paul Keim, Bridget M Barker
G3 (Bethesda, Md.)  ·  04 Apr 2022  ·  pmid:35137016
coccidioides coccidioides-posadasii genome pacbio assembly annotation
Rocks support a distinctive and consistent mycobiome across contrasting dry regions of Earth.
Rocks support a distinctive and consistent mycobiome across contrasting dry regions of Earth.
Claudia Coleine, Manuel Delgado-Baquerizo, Davide Albanese, Brajesh K Singh, Jason E Stajich, Laura Selbmann, Eleonora Egidi
FEMS microbiology ecology  ·  31 Mar 2022  ·  pmid:35298630
extremophile rock-mycobiome fungi
Fungi are key players in extreme ecosystems.
Fungi are key players in extreme ecosystems.
Claudia Coleine, Jason E Stajich, Laura Selbmann
Trends in ecology & evolution  ·  01 Mar 2022  ·  pmid:35246323
extremophile fungi review
Exploring Space via Astromycology A Report on the CIFAR Programs Earth 4D and Fungal Kingdom Inaugural Joint Meeting
Exploring Space via Astromycology A Report on the CIFAR Programs Earth 4D and Fungal Kingdom Inaugural Joint Meeting
Nicola T Case, Min Song, Avery H Fulford, Heather V Graham, Victoria J Orphan, …, Arturo Casadevall, John Mustard, Joseph Heitman, Barbara Sherwood Lollar, Leah E Cowen
Astrobiology  ·  23 Feb 2022  ·  pmid:35196462
meetings reports space-fungi extremophile earth4d fungal-kingdom cifar
Decoding Transcription Regulatory Mechanisms Associated with <i>Coccidioides immitis</i> Phase Transition Using Total RNA
Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA
Sascha H Duttke, Sinem Beyhan, Rajendra Singh, Sonya Neal, Suganya Viriyakosol, Joshua Fierer, Theo N Kirkland, Jason E Stajich, Christopher Benner, Aaron F Carlin
mSystems  ·  25 Jan 2022  ·  pmid:35076277
coccidioides development phase-transition mycelia spherule rna-seq
Genomic Characterization of <i>Parengyodontium torokii</i> sp. nov., a Biofilm-Forming Fungus Isolated from Mars 2020 Assembly Facility
Genomic Characterization of Parengyodontium torokii sp. nov., a Biofilm-Forming Fungus Isolated from Mars 2020 Assembly Facility
Ceth W Parker, Marcus de Melo Teixeira, Nitin K Singh, Huzefa A Raja, Kristof B Cank, …, Nicholas H Oberlies, Bridget M Barker, Jason E Stajich, Christopher E Mason, Kasthuri Venkateswaran
Journal of fungi (Basel, Switzerland)  ·  09 Jan 2022  ·  pmid:35050006
biofilm taxonomy space-fungi ascomycota

2021

Host Lung Environment Limits Aspergillus fumigatus Germination through an SskA-Dependent Signaling Response
Host Lung Environment Limits Aspergillus fumigatus Germination through an SskA-Dependent Signaling Response
Marina E. Kirkland, McKenzie Stannard, Caitlin H. Kowalski, Dallas Mould, Alayna Caffrey-Carr, …, Brandon S. Ross, Lotus A. Lofgren, Jason E. Stajich, Robert A. Cramer, Joshua J. Obar
mSphere  ·  22 Dec 2021  ·  doi:10.1128/msphere.00922-21
aspergillus-fumigatus experimental-evolution
Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples
Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples
Nicole K. Reynolds, Michelle A. Jusino, Jason E. Stajich, Matthew E. Smith
Molecular Ecology Resources  ·  10 Nov 2021  ·  doi:10.1111/1755-0998.13540
zoopagomycota its molecular-ecology systematics early-diverging-fungi
Crowdsourced analysis of fungal growth and branching on microfluidic platforms
Crowdsourced analysis of fungal growth and branching on microfluidic platforms
Alex Hopke, Alex Mela, Felix Ellett, Derreck Carter-House, Jesús F. Peña, …, David Breslauer, Hiral Shah, Bryan R. Coad, Michelle Momany, Daniel Irimia
PLOS ONE  ·  29 Sep 2021  ·  doi:10.1371/journal.pone.0257823
fungus-olympics growth zygolife aspergillus
Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease.
Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease.
Cassandra L Ettinger, Frank J Byrne, Matthew A Collin, Derreck Carter-House, Linda L Walling, Peter W Atkinson, Rick A Redak, Jason E Stajich
G3 (Bethesda, Md.)  ·  27 Sep 2021  ·  pmid:34568917
gwss sharpshooter insect genome nanopore
Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic <i>Fusarium</i> that Includes the <i>Fusarium solani</i> Species Complex
Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex
David M Geiser, Abdullah M S Al-Hatmi, Takayuki Aoki, Tsutomu Arie, Virgilio Balmas, …, Latiffah Zakaria, Hao Zhang, Ning Zhang, Sean X Zhang, Xue Zhang
Phytopathology  ·  09 Sep 2021  ·  pmid:33200960
phylogenomics fusarium
Seven Years at High Salinity—Experimental Evolution of the Extremely Halotolerant Black Yeast Hortaea werneckii
Seven Years at High Salinity—Experimental Evolution of the Extremely Halotolerant Black Yeast Hortaea werneckii
Cene Gostinčar, Jason E. Stajich, Anja Kejžar, Sunita Sinha, Corey Nislow, Metka Lenassi, Nina Gunde-Cimerman
Journal of Fungi  ·  04 Sep 2021  ·  doi:10.3390/jof7090723
hortaea experimental-evolution salinity halotolerance population-genomics
Aspergillus fumigatus In-Host HOG Pathway Mutation for Cystic Fibrosis Lung Microenvironment Persistence
Aspergillus fumigatus In-Host HOG Pathway Mutation for Cystic Fibrosis Lung Microenvironment Persistence
Brandon S. Ross, Lotus A. Lofgren, Alix Ashare, Jason E. Stajich, Robert A. Cramer
mBio  ·  31 Aug 2021  ·  doi:10.1128/mBio.02153-21
aspergillus-fumigatus population-genomics aspergillus cystic-fibrosis
Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii.
Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii.
Marcus de Melo Teixeira, B Franz Lang, Daniel R Matute, Jason E Stajich, Bridget M Barker
G3 (Bethesda, Md.)  ·  14 Jul 2021  ·  pmid:33871031
coccidioides onygenales genomics mitogenome
Diploidy within a Haploid Genus of Entomopathogenic Fungi.
Diploidy within a Haploid Genus of Entomopathogenic Fungi.
Knud Nor Nielsen, João Felipe Moreira Salgado, Myrsini Eirini Natsopoulou, Thea Kristensen, Jason E Stajich, Henrik H De Fine Licht
Genome biology and evolution  ·  06 Jul 2021  ·  pmid:34247231
insect-fungal-interactions ascomycota genome ploidy
Amplicon Sequencing of Rock-Inhabiting Microbial Communities from Joshua Tree National Park, USA.
Amplicon Sequencing of Rock-Inhabiting Microbial Communities from Joshua Tree National Park, USA.
Claudia Coleine, Laura Selbmann, Nuttapon Pombubpa, Jason E Stajich
Microbiology resource announcements  ·  24 Jun 2021  ·  pmid:34165331
amplicon its endoliths fungi joshua-tree aridlands
Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria
Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria
Ryan D. Ward, Jason E. Stajich, Jeffrey R. Johansen, Marcel Huntemann, Alicia Clum, …, Natalia N. Ivanova, Nikos C. Kyrpides, Nicole Shapiro, Emiley A. Eloe-Fadrosh, Nicole Pietrasiak
Microbiology Resource Announcements  ·  03 Jun 2021  ·  doi:10.1128/MRA.00258-21
cyanobacteria metagenomics aridlands genome-announcement
High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534.
High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534.
Jason E Stajich, Andrea L Vu, Howard S Judelson, Gregory M Vogel, Michael A Gore, …, Nicholas Devitt, Jennifer Jacobi, Joann Mudge, Kurt H Lamour, Christine D Smart
Microbiology resource announcements  ·  27 May 2021  ·  pmid:34042486
genome phytophthora
Three species of <i>Trimmatothelopsis</i> (Acarosporaceae) from Europe and North America
Three species of Trimmatothelopsis (Acarosporaceae) from Europe and North America
Kerry Knudsen, Jana Kocourková, Eva Hodková, J. N. Adams, Y. Wang
The Bryologist  ·  14 May 2021  ·  doi:10.1639/0007-2745-124.2.271
lichen systematics taxonomy
Transcriptional Analysis of <i>Coccidioides immitis</i> Mycelia and Spherules by RNA Sequencing
Transcriptional Analysis of Coccidioides immitis Mycelia and Spherules by RNA Sequencing
Aaron F Carlin, Sinem Beyhan, Jesús F Peña, Jason E Stajich, Suganya Viriyakosol, Joshua Fierer, Theo N Kirkland
Journal of fungi (Basel, Switzerland)  ·  07 May 2021  ·  pmid:34067070
coccidioides onygenales rna-seq
Balancing Positive and Negative Selection - <i>In Vivo</i> Evolution of <i>Candida lusitaniae</i> MRR1
Balancing Positive and Negative Selection - In Vivo Evolution of Candida lusitaniae MRR1
Elora G Demers, Jason E Stajich, Alix Ashare, Patricia Occhipinti, Deborah A Hogan
mBio  ·  30 Mar 2021  ·  pmid:33785623
candida clavispora-lusitaniae drug-resistance
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture.
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture.
Alex Rajewski, Derreck Carter-House, Jason Stajich, Amy Litt
BMC genomics  ·  22 Mar 2021  ·  pmid:33752605
datura plant-genomics genome
Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages.
Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages.
Davide Albanese, Claudia Coleine, Omar Rota-Stabelli, Silvano Onofri, Susannah G Tringe, Jason E Stajich, Laura Selbmann, Claudio Donati
Microbiome  ·  19 Mar 2021  ·  pmid:33741058
metagenomics antarctica endoliths genome mag
Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus
Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus
Donatella Tesei, Abby J Chiang, Markus Kalkum, Jason E Stajich, Ganesh Babu Malli Mohan, Katja Sterflinger, Kasthuri Venkateswaran
Frontiers in genetics  ·  18 Mar 2021  ·  pmid:33815472
black-yeast knufia
Culture-Dependent and Amplicon Sequencing Approaches Reveal Diversity and Distribution of Black Fungi in Antarctic Cryptoendolithic Communities.
Culture-Dependent and Amplicon Sequencing Approaches Reveal Diversity and Distribution of Black Fungi in Antarctic Cryptoendolithic Communities.
Laura Selbmann, Gerardo A Stoppiello, Silvano Onofri, Jason E Stajich, Claudia Coleine
Journal of fungi (Basel, Switzerland)  ·  16 Mar 2021  ·  pmid:33809619
antarctica endoliths amplicon fungi
Genomic insights into the host specific adaptation of the Pneumocystis genus.
Genomic insights into the host specific adaptation of the Pneumocystis genus.
Ousmane H Cissé, Liang Ma, John P Dekker, Pavel P Khil, Jung-Ho Youn, …, Nathan S Upham, Jason E Stajich, Christina A Cuomo, Melanie T Cushion, Joseph A Kovacs
Communications biology  ·  08 Mar 2021  ·  pmid:33686174
pneumocystis comparative-genomics
Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins.
Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins.
Thomas Hollin, Lukasz Jaroszewski, Jason E Stajich, Adam Godzik, Karine G Le Roch
Microbial genomics  ·  03 Mar 2021  ·  pmid:33656416
apicomplexian rna-binding evolution
A genome-scale phylogeny of the kingdom Fungi.
A genome-scale phylogeny of the kingdom Fungi.
Yuanning Li, Jacob L Steenwyk, Ying Chang, Yan Wang, Timothy Y James, …, Marizeth Groenewald, Casey W Dunn, Chris Todd Hittinger, Xing-Xing Shen, Antonis Rokas
Current biology : CB  ·  18 Feb 2021  ·  pmid:33607033
fungi phylogenomics systematics evolution
Aspergillus fumigatus Strain-Specific Conidia Lung Persistence Causes an Allergic Broncho-Pulmonary Aspergillosis-Like Disease Phenotype.
Aspergillus fumigatus Strain-Specific Conidia Lung Persistence Causes an Allergic Broncho-Pulmonary Aspergillosis-Like Disease Phenotype.
Jane T Jones, Ko-Wei Liu, Xi Wang, Caitlin H Kowalski, Brandon S Ross, …, Tobias M Hohl, Lotus A Lofgren, Jason E Stajich, Joshua J Obar, Robert A Cramer
mSphere  ·  17 Feb 2021  ·  pmid:33597172
aspergillus-fumigatus cystic-fibrosis
A Heterogeneously Expressed Gene Family Modulates the Biofilm Architecture and Hypoxic Growth of <i>Aspergillus fumigatus</i>
A Heterogeneously Expressed Gene Family Modulates the Biofilm Architecture and Hypoxic Growth of Aspergillus fumigatus
Caitlin H Kowalski, Kaesi A Morelli, Jason E Stajich, Carey D Nadell, Robert A Cramer
mBio  ·  16 Feb 2021  ·  pmid:33593969
aspergillus-fumigatus biofilm rna-seq
The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis.
The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis.
Mathu Malar C, Manuela Krüger, Claudia Krüger, Yan Wang, Jason E Stajich, …, Gokalp Yildirir, Matthew Villeneuve-Laroche, Christophe Roux, Pierre-Marc Delaux, Nicolas Corradi
Current biology : CB  ·  15 Feb 2021  ·  pmid:33592192
geosiphon amf zygomycete genome comparative-genomics
Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains.
Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains.
Guillermo Vidal-Diez de Ulzurrun, Yi-Yun Lee, Jason E Stajich, Erich M Schwarz, Yen-Ping Hsueh
G3 (Bethesda, Md.)  ·  09 Feb 2021  ·  pmid:33585863
genome pleurotus
Genome sequence of the oyster mushroom Pleurotus ostreatus strain PC9.
Genome sequence of the oyster mushroom Pleurotus ostreatus strain PC9.
Yi-Yun Lee, Guillermo Vidal-Diez de Ulzurrun, Erich M Schwarz, Jason E Stajich, Yen-Ping Hsueh
G3 (Bethesda, Md.)  ·  09 Feb 2021  ·  pmid:33585864
genome pleurotus
Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi.
Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi.
Lotus A Lofgren, Nhu H Nguyen, Rytas Vilgalys, Joske Ruytinx, Hui-Ling Liao, …, Hyunsoo Na, Kerrie Barry, Igor V Grigoriev, Jason E Stajich, Peter G Kennedy
The New phytologist  ·  06 Feb 2021  ·  pmid:33355923
suillus basidomycota comparative-genomics phylogenomics
Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi.
Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi.
Ying Chang, D’Ann Rochon, Satoshi Sekimoto, Yan Wang, Mansi Chovatia, Laura Sandor, Asaf Salamov, Igor V Grigoriev, Jason E Stajich, Joseph W Spatafora
Scientific reports  ·  05 Feb 2021  ·  pmid:33547391
fungi phylogenomics zygomycete chytrid evolution metagenomics genome

2020

Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.
Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.
Laura Selbmann, Zsigmond Benkő, Claudia Coleine, Sybren de Hoog, Claudio Donati, …, Vania A Vicente, Emanuel M Souza, Polona Zalar, Allison K Walker, Jason E Stajich
Life (Basel, Switzerland)  ·  19 Dec 2020  ·  pmid:33352712
black-yeast review
A novel <i>Sporothrix brasiliensis</i> genomic variant in Midwestern Brazil evidence for an older and wider sporotrichosis epidemic
A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil evidence for an older and wider sporotrichosis epidemic
João Eudes Filho, Isabele Barbieri Dos Santos, Carmélia Matos Santiago Reis, José Salvatore Leister Patané, Verenice Paredes, …, Daniel R Matute, Bridget M Barker, Maria Sueli Soares Felipe, Marcus de Melo Teixeira, André Moraes Nicola
Emerging microbes & infections  ·  01 Dec 2020  ·  pmid:33155518
sporothrix genome comparative-genomics
Beyond the extremes: Rocks as ultimate refuge for fungi in drylands.
Beyond the extremes: Rocks as ultimate refuge for fungi in drylands.
Claudia Coleine, Jason E Stajich, Asunción de Los Ríos, Laura Selbmann
Mycologia  ·  24 Nov 2020  ·  pmid:33232202
endoliths review fungi rock
Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa.
Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa.
Alexander J Carrillo, Ilva E Cabrera, Marko J Spasojevic, Patrick Schacht, Jason E Stajich, Katherine A Borkovich
BMC genomics  ·  02 Nov 2020  ·  pmid:33138786
neurospora phenotype
Belowground impacts of alpine woody encroachment are determined by plant traits, local climate, and soil conditions.
Belowground impacts of alpine woody encroachment are determined by plant traits, local climate, and soil conditions.
Courtney G Collins, Marko J Spasojevic, Concepción L Alados, Emma L Aronson, Juan C Benavides, …, Hannah B Shulman, Jason E Stajich, Alexia Stokes, Sören E Weber, Jeffrey M Diez
Global change biology  ·  08 Oct 2020  ·  pmid:32902066
soil-microbiome its 16s amplicon environmental-microbiology
Genomic diversity generated by a transposable element burst in a rice recombinant inbred population.
Genomic diversity generated by a transposable element burst in a rice recombinant inbred population.
Jinfeng Chen, Lu Lu, Sofia M C Robb, Matthew Collin, Yutaka Okumoto, Jason E Stajich, Susan R Wessler
Proceedings of the National Academy of Sciences of the United States of America  ·  05 Oct 2020  ·  pmid:33020276
rice transposon mping
No to
No to
Kerry O’Donnell, Abdullah M S Al-Hatmi, Takayuki Aoki, Balázs Brankovics, José F Cano-Lira, …, Brian L Wickes, Nathan P Wiederhold, Michael J Wingfield, Ning Zhang, Sean X Zhang
mSphere  ·  16 Sep 2020  ·  pmid:32938701
fusarium phylogeny taxonomy systematics
Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics.
Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics.
Natalie Vandepol, Julian Liber, Alessandro Desirò, Hyunsoo Na, Megan Kennedy, …, Igor V Grigoriev, Andrew N Miller, Kerry O’Donnell, Jason E Stajich, Gregory Bonito
Fungal diversity  ·  16 Sep 2020  ·  pmid:33364917
genome zygomycete mortierellaceae phylogenomics
Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses.
Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses.
J M Myers, A E Bonds, R A Clemons, N A Thapa, D R Simmons, …, Y Chang, L M Corrochano, A Gryganskyi, I V Grigoriev, T Y James
mBio  ·  08 Sep 2020  ·  pmid:32900807
mycovirus chytrid zygomycete virus
Best Practices for Successfully Writing and Publishing a Genome Announcement in <i>Microbiology Resource Announcements</i>
Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements
Julie C Dunning Hotopp, David A Baltrus, Vincent M Bruno, John J Dennehy, Steven R Gill, …, Simon Roux, Jason E Stajich, Kenneth M Stedman, Frank J Stewart, J Cameron Thrash
Microbiology resource announcements  ·  03 Sep 2020  ·  pmid:32883786
review mra
Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont,
Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont,
Javier F Tabima, Ian A Trautman, Ying Chang, Yan Wang, Stephen Mondo, Alan Kuo, Asaf Salamov, Igor V Grigoriev, Jason E Stajich, Joseph W Spatafora
G3 (Bethesda, Md.)  ·  02 Sep 2020  ·  pmid:32727924
phylogenomics basidiobolus hgt fungi zygomycete
Insights into dryland biocrust microbiome: geography, soil depth and crust type affect biocrust microbial communities and networks in Mojave Desert, USA.
Insights into dryland biocrust microbiome: geography, soil depth and crust type affect biocrust microbial communities and networks in Mojave Desert, USA.
Nuttapon Pombubpa, Nicole Pietrasiak, Paul De Ley, Jason E Stajich
FEMS microbiology ecology  ·  01 Sep 2020  ·  pmid:32573682
amplicon its 16s fungi aridlands biological-crust biocrust
Toward a Fully Resolved Fungal Tree of Life.
Toward a Fully Resolved Fungal Tree of Life.
Timothy Y James, Jason E Stajich, Chris Todd Hittinger, Antonis Rokas
Annual review of microbiology  ·  13 Jul 2020  ·  pmid:32660385
review fungi phylogeny phylogenomics
Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling three Representative Locations of the Victoria Land.
Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling three Representative Locations of the Victoria Land.
Claudia Coleine, Nuttapon Pombubpa, Laura Zucconi, Silvano Onofri, Benedetta Turchetti, Pietro Buzzini, Jason E Stajich, Laura Selbmann
Microorganisms  ·  23 Jun 2020  ·  pmid:32585947
amplicon culture antarctica endoliths
Behavioral betrayal: How select fungal parasites enlist living insects to do their bidding.
Behavioral betrayal: How select fungal parasites enlist living insects to do their bidding.
Brian Lovett, Angie Macias, Jason E Stajich, John Cooley, Jørgen Eilenberg, Henrik H de Fine Licht, Matt T Kasson
PLoS pathogens  ·  18 Jun 2020  ·  pmid:32555716
insect-fungal-interactions review zygomycete entomophthomycotina
Evolutionary relationships among
Evolutionary relationships among
Angie M Macias, David M Geiser, Jason E Stajich, Piotr Łukasik, Claudio Veloso, DeAnna C Bublitz, Matthew C Berger, Greg R Boyce, Kathie Hodge, Matt T Kasson
Mycologia  ·  15 May 2020  ·  pmid:32412847
massospora insect-fungal-interactions zygomycete systematics entomophthomycotina
Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture.
Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture.
Matthew C Fisher, Sarah J Gurr, Christina A Cuomo, David S Blehert, Hailing Jin, …, John W Taylor, Gerard D Wright, Joseph Heitman, Arturo Casadevall, Leah E Cowen
mBio  ·  05 May 2020  ·  pmid:32371596
review fungi disease wildlife-disease
Draft Genome Sequence of the Yeast <i>Rhodotorula sp.</i> strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica
Draft Genome Sequence of the Yeast Rhodotorula sp. strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica
Claudia Coleine, Sawyer Masonjones, Silvano Onofri, Laura Selbmann, Jason E Stajich
Microbiology resource announcements  ·  02 Apr 2020  ·  pmid:32241854
genome rhodotorula antarctica
Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi.
Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi.
Ching-Ting Yang, Guillermo Vidal-Diez de Ulzurrun, A Pedro Gonçalves, Hung-Che Lin, Ching-Wen Chang, …, Cheng-Kuo Lai, Isheng J Tsai, Frank C Schroeder, Jason E Stajich, Yen-Ping Hsueh
Proceedings of the National Academy of Sciences of the United States of America  ·  11 Mar 2020  ·  pmid:32161129
nematode-trapping-fungi arthrobotrys genome population-genomics
Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.
Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.
Claudia Coleine, Davide Albanese, Silvano Onofri, Susannah G Tringe, Christa Pennacchio, Claudio Donati, Jason E Stajich, Laura Selbmann
Microbiology resource announcements  ·  05 Mar 2020  ·  pmid:32139564
metagenomics endoliths antarctica
Endolithic Fungal Species Markers for Harshest Conditions in the McMurdo Dry Valleys, Antarctica.
Endolithic Fungal Species Markers for Harshest Conditions in the McMurdo Dry Valleys, Antarctica.
Claudia Coleine, Nuttapon Pombubpa, Laura Zucconi, Silvano Onofri, Jason E Stajich, Laura Selbmann
Life (Basel, Switzerland)  ·  06 Feb 2020  ·  pmid:32041249
antarctica endoliths fungi amplicon
Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus.
Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus.
Claudia Coleine, Sawyer Masonjones, Katja Sterflinger, Silvano Onofri, Laura Selbmann, Jason E Stajich
Fungal biology  ·  31 Jan 2020  ·  pmid:32389308
friedmannomyces black-yeast antarctica genome
The monophyletic Sarcogyne canadensis–wheeleri clade, a newly recognized group sister to the European Acarospora glaucocarpa group
The monophyletic Sarcogyne canadensis–wheeleri clade, a newly recognized group sister to the European Acarospora glaucocarpa group
Kerry Knudsen, Julia N. Adams, Jana Kocourková, Yan Wang, Jericho Ortañez, Jason E. Stajich
The Bryologist  ·  13 Jan 2020  ·  doi:10.1639/0007-2745-123.1.011
lichen acarospora sarcogyne taxonomy
Airborne fungi spores distribution in various locations in Lagos, Nigeria.
Airborne fungi spores distribution in various locations in Lagos, Nigeria.
Adeyinka Odebode, Adedotun Adekunle, Jason Stajich, Peter Adeonipekun
Environmental monitoring and assessment  ·  03 Jan 2020  ·  pmid:31900675
africa spore fungi

2019

Probe-Based Multiplex Real-Time PCR as a Diagnostic Tool to Distinguish Distinct Fungal Symbionts Associated With
Probe-Based Multiplex Real-Time PCR as a Diagnostic Tool to Distinguish Distinct Fungal Symbionts Associated With
Joseph D Carrillo, Joey S Mayorquin, Jason E Stajich, Akif Eskalen
Plant disease  ·  23 Oct 2019  ·  pmid:31647694
fusarium plant-pathology tool
Reproduction and Dispersal of Biological Soil Crust Organisms
Reproduction and Dispersal of Biological Soil Crust Organisms
Steven D. Warren, Larry L. Clair, Lloyd R. Stark, Louise A. Lewis, Nuttapon Pombubpa, Tania Kurbessoian, Jason E. Stajich, Zachary T. Aanderud
Frontiers in Ecology and Evolution  ·  04 Oct 2019  ·  doi:10.3389/fevo.2019.00344
aridlands review microbes biological-crusts
Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between <i>Mortierella elongata</i> and <i>Burkholderia</i> Include Metabolite Exchange
Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange
Jessie K Uehling, Matthew R Entler, Hannah R Meredith, Larry J Millet, Collin M Timm, …, Scott T Retterer, Joseph W Spatafora, Jason E Stajich, Timothy J Tschaplinski, Rytas J Vilgalys
Frontiers in microbiology  ·  01 Oct 2019  ·  pmid:31632357
zygomycete tool bacteria-fungi-interactions
Fungal biofilm morphology impacts hypoxia fitness and disease progression.
Fungal biofilm morphology impacts hypoxia fitness and disease progression.
Caitlin H Kowalski, Joshua D Kerkaert, Ko-Wei Liu, Matthew C Bond, Raimo Hartmann, Carey D Nadell, Jason E Stajich, Robert A Cramer
Nature microbiology  ·  23 Sep 2019  ·  pmid:31548684
aspergillus-fumigatus biofilm disease hypoxia
Members of the Euwallacea fornicatus species complex exhibit promiscuous mutualism with ambrosia fungi in Taiwan.
Members of the Euwallacea fornicatus species complex exhibit promiscuous mutualism with ambrosia fungi in Taiwan.
Joseph D Carrillo, Paul F Rugman-Jones, Deena Husein, Jason E Stajich, Matt T Kasson, Daniel Carrillo, Richard Stouthamer, Akif Eskalen
Fungal genetics and biology : FG & B  ·  10 Sep 2019  ·  pmid:31518652
fusarium avocado plant-pathology
Future-Proofing Your <i>Microbiology Resource Announcements</i> Genome Assembly for Reproducibility and Clarity
Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity
David A Baltrus, Christina A Cuomo, John J Dennehy, Julie C Dunning Hotopp, Julia A Maresca, Irene L G Newton, David A Rasko, Antonis Rokas, Simon Roux, Jason E Stajich
Microbiology resource announcements  ·  05 Sep 2019  ·  pmid:31488541
review mra
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes.
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes.
Yan Wang, Noha H Youssef, Matthew Brian Couger, Radwa A Hanafy, Mostafa S Elshahed, Jason E Stajich
mSystems  ·  27 Aug 2019  ·  pmid:31455637
hgt systematics agf neocallimastigomycota transcriptome
Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities.
Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities.
Claudia Coleine, Jason E Stajich, Nuttapon Pombubpa, Laura Zucconi, Silvano Onofri, Fabiana Canini, Laura Selbmann
Environmental microbiology reports  ·  26 Aug 2019  ·  pmid:31393667
antarctica amplicon its 16s
Improved Reference Genome Sequence of <i>Coccidioides immitis</i> Strain WA_211, Isolated in Washington State
Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State
Marcus de Melo Teixeira, Bridget Marie Barker, Jason E Stajich
Microbiology resource announcements  ·  15 Aug 2019  ·  pmid:31416856
genome coccidioides
Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage.
Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage.
Chelsea L Murphy, Noha H Youssef, Radwa A Hanafy, M B Couger, Jason E Stajich, …, Sumit S Dagar, Gareth W Griffith, Ibrahim F Farag, T M Callaghan, Mostafa S Elshahed
Applied and environmental microbiology  ·  18 Jul 2019  ·  pmid:31126947
hgt neocallimastigomycota agf
Diversity and function of fungi associated with the fungivorous millipede, <i>Brachycybe lecontii</i>
Diversity and function of fungi associated with the fungivorous millipede, Brachycybe lecontii
Angie M Macias, Paul E Marek, Ember M Morrissey, Michael S Brewer, Dylan P G Short, …, Rita V M Rio, Daniel G Panaccione, Victoria Wong, Tappey H Jones, Matt T Kasson
Fungal ecology  ·  09 Jul 2019  ·  pmid:31871487
millipede culture-based zygomycete
Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens.
Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens.
Greg R Boyce, Emile Gluck-Thaler, Jason C Slot, Jason E Stajich, William J Davis, …, Dylan P G Short, Teiya Kijimoto, Dan Mozgai, Nidia Arguedas, Matt T Kasson
Fungal ecology  ·  24 Jun 2019  ·  pmid:31768192
massospora zygomycete genome insect-fungal-interactions
Proteomic and Metabolomic Characteristics of Extremophilic Fungi Under Simulated Mars Conditions.
Proteomic and Metabolomic Characteristics of Extremophilic Fungi Under Simulated Mars Conditions.
Adriana Blachowicz, Abby J Chiang, Andreas Elsaesser, Markus Kalkum, Pascale Ehrenfreund, Jason E Stajich, Tamas Torok, Clay C C Wang, Kasthuri Venkateswaran
Frontiers in microbiology  ·  15 May 2019  ·  pmid:31156574
proteomics black-yeast extremophile
Draft Genome Sequence of an Antarctic Isolate of the Black Yeast Fungus <i>Exophiala mesophila</i>
Draft Genome Sequence of an Antarctic Isolate of the Black Yeast Fungus Exophiala mesophila
Claudia Coleine, Laura Selbmann, Sawyer Masonjones, Silvano Onofri, Laura Zucconi, Jason E Stajich
Microbiology resource announcements  ·  09 May 2019  ·  pmid:31072892
exophiala extremophile antarctica
FGMP: assessing fungal genome completeness.
FGMP: assessing fungal genome completeness.
Ousmane H Cissé, Jason E Stajich
BMC bioinformatics  ·  15 Apr 2019  ·  pmid:30987585
tool genomics
Fungi in the Marine Environment: Open Questions and Unsolved Problems.
Fungi in the Marine Environment: Open Questions and Unsolved Problems.
Anthony Amend, Gaetan Burgaud, Michael Cunliffe, Virginia P Edgcomb, Cassandra L Ettinger, …, Jason Stajich, José Vargas-Muñiz, Allison K Walker, Oded Yarden, Amy S Gladfelter
mBio  ·  05 Mar 2019  ·  pmid:30837337
review marine-fungi chytrid marine-microbiology
Diversity of cytosine methylation across the fungal tree of life.
Diversity of cytosine methylation across the fungal tree of life.
Adam J Bewick, Brigitte T Hofmeister, Rob A Powers, Stephen J Mondo, Igor V Grigoriev, Timothy Y James, Jason E Stajich, Robert J Schmitz
Nature ecology & evolution  ·  18 Feb 2019  ·  pmid:30778188
epigenetics fungi 5mc methylation
Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice.
Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice.
Jinfeng Chen, Lu Lu, Jazmine Benjamin, Stephanie Diaz, C Nathan Hancock, Jason E Stajich, Susan R Wessler
Nature communications  ·  07 Feb 2019  ·  pmid:30733435
transposon rice mping
Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2).
Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2).
Barbara Valent, Mark Farman, Yukio Tosa, Dominik Begerow, Elisabeth Fournier, …, Jason E Stajich, Nicholas J Talbot, Ryohei Terauchi, Didier Tharreau, Ning Zhang
Molecular plant pathology  ·  01 Feb 2019  ·  pmid:30697917
systematics pyricularia wheat-blast
Genome Sequence of a Lethal Vascular Wilt Fungus, Verticillium nonalfalfae, a Biological Control Used Against the Invasive Ailanthus altissima.
Genome Sequence of a Lethal Vascular Wilt Fungus, Verticillium nonalfalfae, a Biological Control Used Against the Invasive Ailanthus altissima.
Matt T Kasson, Lindsay R Kasson, Kristen L Wickert, Donald D Davis, Jason E Stajich
Microbiology resource announcements  ·  24 Jan 2019  ·  pmid:30701257
verticllium genome genome-announcement
Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota.
Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota.
Ying Chang, Alessandro Desirò, Hyunsoo Na, Laura Sandor, Anna Lipzen, …, Francis M Martin, Jason E Stajich, Matthew E Smith, Gregory Bonito, Joseph W Spatafora
The New phytologist  ·  12 Jan 2019  ·  pmid:30485448
phylogenomics systematics zygomycete endogone
Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).
Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).
William J Davis, Kevin R Amses, Gerald L Benny, Derreck Carter-House, Ying Chang, Igor Grigoriev, Matthew E Smith, Joseph W Spatafora, Jason E Stajich, Timothy Y James
Molecular phylogenetics and evolution  ·  11 Jan 2019  ·  pmid:30639767
zoopagales zoopagomycota zygomycete phylogenomics systematics

2018

International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulans.
International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulans.
Jillian Romsdahl, Adriana Blachowicz, Abby J Chiang, Yi-Ming Chiang, Sawyer Masonjones, …, Fathi Karouia, Markus Kalkum, Jason E Stajich, Kasthuri Venkateswaran, Clay C C Wang
Applied microbiology and biotechnology  ·  12 Dec 2018  ·  pmid:30539259
aspergillus-nidulans proteomics space-fungi iss
Evolution of drug resistance in an antifungal-naive chronic
Evolution of drug resistance in an antifungal-naive chronic
Elora G Demers, Amy R Biermann, Sawyer Masonjones, Alex W Crocker, Alix Ashare, Jason E Stajich, Deborah A Hogan
Proceedings of the National Academy of Sciences of the United States of America  ·  02 Nov 2018  ·  pmid:30389707
candida clavispora-lusitaniae drug-resistance
Parasitoid Jewel Wasp Mounts Multipronged Neurochemical Attack to Hijack a Host Brain.
Parasitoid Jewel Wasp Mounts Multipronged Neurochemical Attack to Hijack a Host Brain.
Ryan Arvidson, Maayan Kaiser, Sang Soo Lee, Jean-Paul Urenda, Christopher Dail, …, Cebrina Nolan, Songqin Pan, Jason E Stajich, Frederic Libersat, Michael E Adams
Molecular & cellular proteomics : MCP  ·  06 Oct 2018  ·  pmid:30293061
insect rna-seq venom
Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases.
Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases.
Jonathan A Arnesen, Joanna Małagocka, Andrii Gryganskyi, Igor V Grigoriev, Kerstin Voigt, Jason E Stajich, Henrik H De Fine Licht
G3 (Bethesda, Md.)  ·  03 Oct 2018  ·  pmid:30111619
entomophthomycotina protease entomopthora-muscae
Characterization of Aspergillus niger Isolated from the International Space Station.
Characterization of Aspergillus niger Isolated from the International Space Station.
Jillian Romsdahl, Adriana Blachowicz, Abby J Chiang, Nitin Singh, Jason E Stajich, Markus Kalkum, Kasthuri Venkateswaran, Clay C C Wang
mSystems  ·  18 Sep 2018  ·  pmid:30246146
aspergillus-niger population-genomics iss space-fungi
Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis.
Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis.
Zhiquan Song, Jason E Stajich, Yunxuan Xie, Xianhua Liu, Yaodong He, Jinfeng Chen, Glenn R Hicks, Guangyi Wang
BMC genomics  ·  17 Jul 2018  ·  pmid:30016947
genome thraustochytrid comparative-genomics
Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes.
Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes.
Claudia Coleine, Jason E Stajich, Laura Zucconi, Silvano Onofri, Nuttapon Pombubpa, Eleonora Egidi, Ashley Franks, Pietro Buzzini, Laura Selbmann
Frontiers in microbiology  ·  29 Jun 2018  ·  pmid:30008702
antarctica its fungi endoliths
Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities.
Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities.
Claudia Coleine, Laura Zucconi, Silvano Onofri, Nuttapon Pombubpa, Jason E Stajich, Laura Selbmann
Life (Basel, Switzerland)  ·  02 Jun 2018  ·  pmid:29865244
antarctica fungi its
Phylogenetic and Phylogenomic Definition of <i>Rhizopus</i> Species
Phylogenetic and Phylogenomic Definition of Rhizopus Species
Andrii P Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, …, G Sybren de Hoog, Matthew E Smith, Joseph Heitman, Rytas Vilgalys, Jason E Stajich
G3 (Bethesda, Md.)  ·  31 May 2018  ·  pmid:29674435
rhizopus systematics phylogenomics
Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast.
Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast.
Cene Gostinčar, Jason E Stajich, Jerneja Zupančič, Polona Zalar, Nina Gunde-Cimerman
BMC genomics  ·  15 May 2018  ·  pmid:29764372
population-genomics black-yeast extremophile halotolerance hortaea
Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis.
Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis.
Yan Wang, Matt Stata, Wei Wang, Jason E Stajich, Merlin M White, Jean-Marc Moncalvo
mBio  ·  15 May 2018  ·  pmid:29764946
comparative-genomics insect-fungal-interactions symbiosis
Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient.
Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient.
Courtney G Collins, Jason E Stajich, Sören E Weber, Nuttapon Pombubpa, Jeffrey M Diez
Molecular ecology  ·  10 May 2018  ·  pmid:29675967
its molecular-ecology soil-microbiome
Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen
Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen
Ousmane H Cissé, Liang Ma, Da Wei Huang, Pavel P Khil, John P Dekker, …, Vanessa Hirsch, Richard A Lempicki, Jason E Stajich, Christina A Cuomo, Joseph A Kovacs
mBio  ·  08 May 2018  ·  pmid:29739910
pneumocystis comparative-genomics
Two Novel Fungal Symbionts Fusarium kuroshium sp. nov. and Graphium kuroshium sp. nov. of Kuroshio Shot Hole Borer (Euwallacea sp. nr. fornicatus) Cause Fusarium Dieback on Woody Host Species in California.
Two Novel Fungal Symbionts Fusarium kuroshium sp. nov. and Graphium kuroshium sp. nov. of Kuroshio Shot Hole Borer (Euwallacea sp. nr. fornicatus) Cause Fusarium Dieback on Woody Host Species in California.
Francis Na, Joseph D Carrillo, Joey S Mayorquin, Cedric Ndinga-Muniania, Jason E Stajich, Richard Stouthamer, Yin-Tse Huang, Yu-Ting Lin, Chi-Yu Chen, Akif Eskalen
Plant disease  ·  02 Apr 2018  ·  pmid:30673440
fusarium-kuroshium avocado afc
Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi.
Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi.
Denis Beaudet, Eric C H Chen, Stephanie Mathieu, Gokalp Yildirir, Steve Ndikumana, Yolande Dalpé, Sylvie Séguin, Laurent Farinelli, Jason E Stajich, Nicolas Corradi
DNA research : an international journal for rapid publication of reports on genes and genomes  ·  01 Apr 2018  ·  pmid:29211832
amf transcriptome phylogenomics scrna-seq
Analysis of Transposable Elements in Coccidioides Species.
Analysis of Transposable Elements in Coccidioides Species.
Theo N Kirkland, Anna Muszewska, Jason E Stajich
Journal of fungi (Basel, Switzerland)  ·  19 Jan 2018  ·  pmid:29371508
coccidioides transposon
Comparative genomic analysis of the 'pseudofungus'
Comparative genomic analysis of the 'pseudofungus'
Guy Leonard, Aurélie Labarre, David S Milner, Adam Monier, Darren Soanes, …, Konrad Paszkiewicz, Matthew W Brown, Neil Hall, Bill Wickstead, Thomas A Richards
Open biology  ·  01 Jan 2018  ·  pmid:29321239
thraustochytrid comparative-genomics

2017

Tracking the genome-wide outcomes of a transposable element burst over decades of amplification.
Tracking the genome-wide outcomes of a transposable element burst over decades of amplification.
Lu Lu, Jinfeng Chen, Sofia M C Robb, Yutaka Okumoto, Jason E Stajich, Susan R Wessler
Proceedings of the National Academy of Sciences of the United States of America  ·  20 Nov 2017  ·  pmid:29158416
transposon rice mping
Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions.
Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions.
Sang-Youl Park, Melissa A Scranton, Jason E Stajich, Ashley Yee, Linda L Walling
PloS one  ·  12 Oct 2017  ·  pmid:29023459
m18-aspartyl-aminopeptidases dap molecular-evolution
Microbial associates of the southern mole cricket (Scapteriscus borellii) are highly pathogenic.
Microbial associates of the southern mole cricket (Scapteriscus borellii) are highly pathogenic.
Sudarshan K Aryal, Derreck Carter-House, Jason E Stajich, Adler R Dillman
Journal of invertebrate pathology  ·  12 Sep 2017  ·  pmid:28916147
symbiosis insect-bacteria-interactions insect-fungal-interactions mole-cricket
The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies.
The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies.
Joseph W Spatafora, M Catherine Aime, Igor V Grigoriev, Francis Martin, Jason E Stajich, Meredith Blackwell
Microbiology spectrum  ·  01 Sep 2017  ·  pmid:28917057
review systematics fungi
Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.
Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.
Terry J Torres-Cruz, Terri L Billingsley Tobias, Maryam Almatruk, Cedar N Hesse, Cheryl R Kuske, …, Gregory Bonito, Jason E Stajich, Christopher Dunlap, A Elizabeth Arnold, Andrea Porras-Alfaro
Mycologia  ·  08 Aug 2017  ·  pmid:28876195
bifiguratus mucoromycotina comparative-genomics
Draft Genome Sequences of the Antarctic Endolithic Fungi <i>Rachicladosporium antarcticum</i> CCFEE 5527 and <i>Rachicladosporium</i> sp. CCFEE 5018
Draft Genome Sequences of the Antarctic Endolithic Fungi Rachicladosporium antarcticum CCFEE 5527 and Rachicladosporium sp. CCFEE 5018
Claudia Coleine, Sawyer Masonjones, Laura Selbmann, Laura Zucconi, Silvano Onofri, Claudia Pacelli, Jason E Stajich
Genome announcements  ·  06 Jul 2017  ·  pmid:28684563
rachicladosporium genome antarctica
Insight into the Recent Genome Duplication of the Halophilic Yeast
Insight into the Recent Genome Duplication of the Halophilic Yeast
Sunita Sinha, Stephane Flibotte, Mauricio Neira, Sean Formby, Ana Plemenitaš, Nina Gunde Cimerman, Metka Lenassi, Cene Gostinčar, Jason E Stajich, Corey Nislow
G3 (Bethesda, Md.)  ·  05 Jul 2017  ·  pmid:28500048
hortaea black-yeast genome extremophile halotolerance
Fungal Genomes and Insights into the Evolution of the Kingdom.
Fungal Genomes and Insights into the Evolution of the Kingdom.
Jason E Stajich
Microbiology spectrum  ·  01 Jul 2017  ·  pmid:28820125
review genomics fungi
Widespread adenine N6-methylation of active genes in fungi.
Widespread adenine N6-methylation of active genes in fungi.
Stephen J Mondo, Richard O Dannebaum, Rita C Kuo, Katherine B Louie, Adam J Bewick, …, Michelle A O’Malley, Jason E Stajich, Joseph W Spatafora, Axel Visel, Igor V Grigoriev
Nature genetics  ·  08 May 2017  ·  pmid:28481340
n6-methylation 6ma fungi
Exploring the binding properties and structural stability of an opsin in the chytrid
Exploring the binding properties and structural stability of an opsin in the chytrid
Steven R Ahrendt, Edgar Mauricio Medina, Chia-En A Chang, Jason E Stajich
PeerJ  ·  27 Apr 2017  ·  pmid:28462022
spizellomyces opsin molecular-modeling
Innovation and constraint leading to complex multicellularity in the Ascomycota.
Innovation and constraint leading to complex multicellularity in the Ascomycota.
Tu Anh Nguyen, Ousmane H Cissé, Jie Yun Wong, Peng Zheng, David Hewitt, Minou Nowrousian, Jason E Stajich, Gregory Jedd
Nature communications  ·  08 Feb 2017  ·  pmid:28176784
multicellularity ascomycota neolecta comparative-genomics
RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing.
RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing.
Jinfeng Chen, Travis R Wrightsman, Susan R Wessler, Jason E Stajich
PeerJ  ·  26 Jan 2017  ·  pmid:28149701
tool transposon

2016

PCR Multiplexes Discriminate Fusarium Symbionts of Invasive Euwallacea Ambrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States.
PCR Multiplexes Discriminate Fusarium Symbionts of Invasive Euwallacea Ambrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States.
Dylan P G Short, Kerry O’Donnell, Jason E Stajich, Jiri Hulcr, Teiya Kijimoto, …, Akif Eskalen, Shannon C Lynch, Anthony I Cognato, Miriam F Cooperband, Matthew T Kasson
Plant disease  ·  01 Nov 2016  ·  pmid:30682305
fusarium ambrosia-beetle pcr
A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.
A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.
Joseph W Spatafora, Ying Chang, Gerald L Benny, Katy Lazarus, Matthew E Smith, …, Thomas N Taylor, Jessie Uehling, Rytas Vilgalys, Merlin M White, Jason E Stajich
Mycologia  ·  01 Sep 2016  ·  pmid:27738200
zygomycete phylogenomics systematics phylogenetics genome
Fungal Evolution: Mucor and Phycomyces See Double.
Fungal Evolution: Mucor and Phycomyces See Double.
Jason E Stajich
Current biology : CB  ·  22 Aug 2016  ·  pmid:27554660
review mucor phycomyces
Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles.
Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles.
Raúl Castanera, Leticia López-Varas, Alessandra Borgognone, Kurt LaButti, Alla Lapidus, …, Gúmer Pérez, Antonio G Pisabarro, Igor V Grigoriev, Jason E Stajich, Lucía Ramírez
PLoS genetics  ·  13 Jun 2016  ·  pmid:27294409
transposon pleurotus
Deacetylation of Fungal Exopolysaccharide Mediates Adhesion and Biofilm Formation.
Deacetylation of Fungal Exopolysaccharide Mediates Adhesion and Biofilm Formation.
Mark J Lee, Alexander M Geller, Natalie C Bamford, Hong Liu, Fabrice N Gravelat, …, Evgeny Vinogradov, Jason E Stajich, Scott G Filler, P Lynne Howell, Donald C Sheppard
mBio  ·  05 Apr 2016  ·  pmid:27048799
aspergillus gag biofilm
Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture.
Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture.
Tom J B de Man, Jason E Stajich, Christian P Kubicek, Clotilde Teiling, Komal Chenthamara, …, Seth M Barribeau, Brooke A Bozick, Garret Suen, Cameron R Currie, Nicole M Gerardo
Proceedings of the National Academy of Sciences of the United States of America  ·  14 Mar 2016  ·  pmid:26976598
escovopsis genome symbiosis mycoparasite
Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).
Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).
Jana M U’Ren, Jolanta Miadlikowska, Naupaka B Zimmerman, François Lutzoni, Jason E Stajich, A Elizabeth Arnold
Molecular phylogenetics and evolution  ·  20 Feb 2016  ·  pmid:26903035
xylariaceae endophyte

2015

Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar.
Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar.
Michelle Momany, Antonio Di Pietro, William G Alexander, Bridget M Barker, Omar S Harb, …, Francis Martin, J Chris Pires, Jason E Stajich, Bart P H J Thomma, Sarah Unruh
G3 (Bethesda, Md.)  ·  01 Dec 2015  ·  pmid:27034999
social-media meeting-report review
Cellular Subcompartments through Cytoplasmic Streaming.
Cellular Subcompartments through Cytoplasmic Streaming.
Laurent Pieuchot, Julian Lai, Rachel Ann Loh, Fong Yew Leong, Keng-Hwee Chiam, Jason Stajich, Gregory Jedd
Developmental cell  ·  24 Aug 2015  ·  pmid:26305593
neurospora cytoplasmic-streaming
Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon.
Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon.
Yizhou Wang, Kristina M Smith, John W Taylor, Michael Freitag, Jason E Stajich
G3 (Bethesda, Md.)  ·  23 Jun 2015  ·  pmid:26109355
small-rna transposon neurospora msud
Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis.
Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis.
Peng Liu, Jason E Stajich
Fungal genetics and biology : FG & B  ·  25 Mar 2015  ·  pmid:25819009
cbm18 batrachochytrium
The low information content of <i>Neurospora</i> splicing signals: implications for RNA splicing and intron origin
The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin
Richard A. Collins, Jason E. Stajich, Deborah J. Field, Joan E. Olive, Diane M. DeAbreu
RNA  ·  24 Mar 2015  ·  doi:10.1261/rna.047985.114
neurospora intron splicing
Analysis of the Candida albicans Phosphoproteome.
Analysis of the Candida albicans Phosphoproteome.
S D Willger, Z Liu, R A Olarte, M E Adamo, J E Stajich, L C Myers, A N Kettenbach, D A Hogan
Eukaryotic cell  ·  06 Mar 2015  ·  pmid:25750214
candida-albicans phosphoproteome
Twenty-first century mycology: a diverse, collaborative, and highly relevant science.
Twenty-first century mycology: a diverse, collaborative, and highly relevant science.
Peter Kennedy, Jason Stajich
The New phytologist  ·  01 Jan 2015  ·  pmid:25427217
meeting-report

2014

Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis.
Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis.
Marcus M Teixeira, Luiz G P de Almeida, Paula Kubitschek-Barreira, Fernanda L Alves, Erika S Kioshima, …, Sandro R Almeida, Jason E Stajich, Leila M Lopes-Bezerra, Ana T R Vasconcelos, Maria S S Felipe
BMC genomics  ·  29 Oct 2014  ·  pmid:25351875
sporothrix genome
MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum.
MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum.
Shouqiang Ouyang, Gyungsoon Park, Hagop S Atamian, Cliff S Han, Jason E Stajich, Isgouhi Kaloshian, Katherine A Borkovich
PLoS pathogens  ·  16 Oct 2014  ·  pmid:25330340
microrna fusarium tomato
Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches.
Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches.
Hugo Mélida, Divya Sain, Jason E Stajich, Vincent Bulone
Environmental microbiology  ·  22 Sep 2014  ·  pmid:25143134
cell-wall mucoromycotina phylogenomics
Evolutionary histories of soil fungi are reflected in their large-scale biogeography.
Evolutionary histories of soil fungi are reflected in their large-scale biogeography.
Kathleen K Treseder, Mia R Maltz, Bradford A Hawkins, Noah Fierer, Jason E Stajich, Krista L McGuire
Ecology letters  ·  09 Jun 2014  ·  pmid:24912000
soil-fungi phylogeny
Literature-based gene curation and proposed genetic nomenclature for cryptococcus.
Literature-based gene curation and proposed genetic nomenclature for cryptococcus.
Diane O Inglis, Marek S Skrzypek, Edward Liaw, Venkatesh Moktali, Gavin Sherlock, Jason E Stajich
Eukaryotic cell  ·  09 May 2014  ·  pmid:24813190
cryptococcus annotation curation
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
Guilhem Janbon, Kate L Ormerod, Damien Paulet, Edmond J Byrnes, Vikas Yadav, …, Kaustuv Sanyal, Joseph Heitman, James A Fraser, Christina A Cuomo, Fred S Dietrich
PLoS genetics  ·  17 Apr 2014  ·  pmid:24743168
cryptococcus genome rna-seq microevolution

2013

Evolutionary origins and diversification of proteobacterial mutualists.
Evolutionary origins and diversification of proteobacterial mutualists.
Joel L Sachs, Ryan G Skophammer, Nidhanjali Bansal, Jason E Stajich
Proceedings. Biological sciences  ·  27 Nov 2013  ·  pmid:24285193
symbiosis proteobacteria mutalism evolution
MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.
MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.
Elizabeth M Glass, Yekaterina Dribinsky, Pelin Yilmaz, Hal Levin, Robert Van Pelt, …, Mitch Sogin, Jason Stajich, Rob Knight, Folker Meyer, Lynn M Schriml
The ISME journal  ·  24 Oct 2013  ·  pmid:24152717
genomic-standards built-environment mixs-be
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.
Stefanie Traeger, Florian Altegoer, Michael Freitag, Toni Gabaldon, Frank Kempken, Abhishek Kumar, Marina Marcet-Houben, Stefanie Pöggeler, Jason E Stajich, Minou Nowrousian
PLoS genetics  ·  19 Sep 2013  ·  pmid:24068976
pyronema genome
Toward genome-enabled mycology.
Toward genome-enabled mycology.
David S Hibbett, Jason E Stajich, Joseph W Spatafora
Mycologia  ·  08 Aug 2013  ·  pmid:23928422
review mycology
Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia.
Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia.
Timothy Y James, Adrian Pelin, Linda Bonen, Steven Ahrendt, Divya Sain, Nicolas Corradi, Jason E Stajich
Current biology : CB  ·  08 Aug 2013  ·  pmid:23932404
cryptomycota genome rozella phylogenomics
Sequential utilization of hosts from different fly families by genetically distinct, sympatric populations within the Entomophthora muscae species complex.
Sequential utilization of hosts from different fly families by genetically distinct, sympatric populations within the Entomophthora muscae species complex.
Andrii P Gryganskyi, Richard A Humber, Jason E Stajich, Bradley Mullens, Iryna M Anishchenko, Rytas Vilgalys
PloS one  ·  08 Aug 2013  ·  pmid:23951101
entomophthora-muscae insect-fungal-interactions fly
Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus.
Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus.
Anastasia Gioti, Jason E Stajich, Hanna Johannesson
Evolution; international journal of organic evolution  ·  05 Aug 2013  ·  pmid:24299411
neurospora selfing
The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice.
The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice.
Sofia M C Robb, Lu Lu, Elizabeth Valencia, James M Burnette, Yutaka Okumoto, Susan R Wessler, Jason E Stajich
G3 (Bethesda, Md.)  ·  21 Jun 2013  ·  pmid:23576519
transposon tool
Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data.
Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data.
Erica Bree Rosenblum, Timothy Y James, Kelly R Zamudio, Thomas J Poorten, Dan Ilut, …, Silvia Restrepo, Sandra Victoria Flechas, Lee Berger, Cheryl J Briggs, Jason E Stajich
Proceedings of the National Academy of Sciences of the United States of America  ·  06 May 2013  ·  pmid:23650365
batrachochytrium population-genomics
Meeting report: fungal its workshop (october 2012).
Meeting report: fungal its workshop (october 2012).
Scott T Bates, Steven Ahrendt, Holly M Bik, Thomas D Bruns, J Gregory Caporaso, …, Conrad Schoch, James Scott, D Lee Taylor, Laura Wegener Parfrey, Jason E Stajich
Standards in genomic sciences  ·  15 Apr 2013  ·  pmid:23961317
meeting-report
Regional control of histone H3 lysine 27 methylation in Neurospora.
Regional control of histone H3 lysine 27 methylation in Neurospora.
Kirsty Jamieson, Michael R Rountree, Zachary A Lewis, Jason E Stajich, Eric U Selker
Proceedings of the National Academy of Sciences of the United States of America  ·  25 Mar 2013  ·  pmid:23530226
histone neurospora h3k27me
5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea.
5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea.
Chi Keung Cheng, Chun Hang Au, Sarah K Wilke, Jason E Stajich, Miriam E Zolan, Patricia J Pukkila, Hoi Shan Kwan
BMC genomics  ·  20 Mar 2013  ·  pmid:23514374
coprinus coprinopsis 5-sage transcriptome
Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.
Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.
Anastasia Gioti, Björn Nystedt, Wenjun Li, Jun Xu, Anna Andersson, …, Carol A Munro, Piet W J de Groot, Geraldine Butler, Joseph Heitman, Annika Scheynius
mBio  ·  22 Jan 2013  ·  pmid:23341551
malassezia genome

2012

Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi.
Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi.
Kristiina Nygren, Andreas Wallberg, Nicklas Samils, Jason E Stajich, Jeffrey P Townsend, Magnus Karlsson, Hanna Johannesson
BMC evolutionary biology  ·  27 Nov 2012  ·  pmid:23186325
neurospora sexual-reproduction est
Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis.
Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis.
John Abramyan, Jason E Stajich
mBio  ·  19 Jun 2012  ·  pmid:22718849
cbm18 batrachochytrium
Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements.
Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements.
Anastasia Gioti, Alexandra A Mushegian, Rebecka Strandberg, Jason E Stajich, Hanna Johannesson
Molecular biology and evolution  ·  15 May 2012  ·  pmid:22593224
neurospora mating transposon

2011

FungiDB: an integrated functional genomics database for fungi.
FungiDB: an integrated functional genomics database for fungi.
Jason E Stajich, Todd Harris, Brian P Brunk, John Brestelli, Steve Fischer, …, Wei Li, Vishal Nayak, Deborah F Pinney, Chris J Stoeckert, David S Roos
Nucleic acids research  ·  07 Nov 2011  ·  pmid:22064857
fungidb tool database
Genomic transition to pathogenicity in chytrid fungi.
Genomic transition to pathogenicity in chytrid fungi.
Suzanne Joneson, Jason E Stajich, Shin-Han Shiu, Erica Bree Rosenblum
PLoS pathogens  ·  03 Nov 2011  ·  pmid:22072962
chytrid genome batrachochytrium homolaphlyctis
Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.
Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.
Christopher E Ellison, Jason E Stajich, David J Jacobson, Donald O Natvig, Alla Lapidus, …, Andrea Aerts, Robert Riley, Erika A Lindquist, Igor V Grigoriev, John W Taylor
Genetics  ·  12 Jul 2011  ·  pmid:21750257
neurospora selfing genome sex-chromosome
Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.
Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.
C A D’Souza, J W Kronstad, G Taylor, R Warren, M Yuen, …, S Jones, R Holt, B W Birren, J E Galagan, C A Cuomo
mBio  ·  08 Feb 2011  ·  pmid:21304167
cryptococcus genome

2010

A molecular perspective: biology of the emerging pathogen Batrachochytrium dendrobatidis.
A molecular perspective: biology of the emerging pathogen Batrachochytrium dendrobatidis.
Erica Bree Rosenblum, Matthew C Fisher, Timothy Y James, Jason E Stajich, Joyce E Longcore, Lydia R Gentry, Thomas J Poorten
Diseases of aquatic organisms  ·  01 Nov 2010  ·  pmid:21268975
batrachochytrium review
Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution.
Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution.
Claire Burns, Jason E Stajich, Andreas Rechtsteiner, Lorna Casselton, Sean E Hanlon, …, Allen C Gathman, Walt W Lilly, Jason D Lieb, Miriam E Zolan, Patricia J Pukkila
PLoS genetics  ·  23 Sep 2010  ·  pmid:20885784
meiosis transcriptome coprinus coprinopsis
Using the Generic Synteny Browser (GBrowse_syn).
Using the Generic Synteny Browser (GBrowse_syn).
Sheldon J McKay, Ismael A Vergara, Jason E Stajich
Current protocols in bioinformatics  ·  01 Sep 2010  ·  pmid:20836076
gbrowse tool
Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex.
Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex.
Kristina M Smith, Gencer Sancar, Rigzin Dekhang, Christopher M Sullivan, Shaojie Li, …, James C Carrington, Jason E Stajich, Deborah Bell-Pedersen, Michael Brunner, Michael Freitag
Eukaryotic cell  ·  30 Jul 2010  ·  pmid:20675579
neurospora chip-seq white-collar-complex circadian-clock
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire.
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire.
C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, …, Ronald P De Vries, Sophien Kamoun, Mark Yandell, Ned Tisserat, C Robin Buell
Genome biology  ·  13 Jul 2010  ·  pmid:20626842
pythium genome
Genome sequence of the model mushroom Schizophyllum commune.
Genome sequence of the model mushroom Schizophyllum commune.
Robin A Ohm, Jan F de Jong, Luis G Lugones, Andrea Aerts, Erika Kothe, …, Francis W M R Schwarze, Patricia A vanKuyk, J Stephen Horton, Igor V Grigoriev, Han A B Wösten
Nature biotechnology  ·  11 Jul 2010  ·  pmid:20622885
schizophyllum genome
Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora.
Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora.
Rebecka Strandberg, Kristiina Nygren, Audrius Menkis, Timothy Y James, Lotta Wik, Jason E Stajich, Hanna Johannesson
Fungal genetics and biology : FG & B  ·  01 Jul 2010  ·  pmid:20601044
neurospora heterothallic homothallic
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).
Jason E Stajich, Sarah K Wilke, Dag Ahrén, Chun Hang Au, Bruce W Birren, …, Rajesh Velagapudi, Todd J Vision, Qiandong Zeng, Miriam E Zolan, Patricia J Pukkila
Proceedings of the National Academy of Sciences of the United States of America  ·  14 Jun 2010  ·  pmid:20547848
coprinopsis coprinus genome multicellularity
Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.
Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.
Daniel E Neafsey, Bridget M Barker, Thomas J Sharpton, Jason E Stajich, Daniel J Park, …, Garry T Cole, Bruce W Birren, Matthew R Henn, John W Taylor, Steven D Rounsley
Genome research  ·  01 Jun 2010  ·  pmid:20516208
coccidioides genome population-genomics transposon
De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.
De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.
Minou Nowrousian, Jason E Stajich, Meiling Chu, Ines Engh, Eric Espagne, …, Stephan Seiler, Kristina M Smith, Denise Zickler, Ulrich Kück, Michael Freitag
PLoS genetics  ·  08 Apr 2010  ·  pmid:20386741
sordaria genome
The deadly chytrid fungus: a story of an emerging pathogen.
The deadly chytrid fungus: a story of an emerging pathogen.
Erica Bree Rosenblum, Jamie Voyles, Thomas J Poorten, Jason E Stajich
PLoS pathogens  ·  29 Jan 2010  ·  pmid:20126439
batrachochytrium review

2009

The fungi.
The fungi.
Jason E Stajich, Mary L Berbee, Meredith Blackwell, David S Hibbett, Timothy Y James, Joseph W Spatafora, John W Taylor
Current biology : CB  ·  29 Sep 2009  ·  pmid:19788875
review mycology
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.
Thomas J Sharpton, Jason E Stajich, Steven D Rounsley, Malcolm J Gardner, Jennifer R Wortman, …, Theo N Kirkland, Garry T Cole, Matthew R Henn, Bruce W Birren, John W Taylor
Genome research  ·  28 Aug 2009  ·  pmid:19717792
coccidioides genome
Proteomic and phenotypic profiling of the amphibian pathogen Batrachochytrium dendrobatidis shows that genotype is linked to virulence.
Proteomic and phenotypic profiling of the amphibian pathogen Batrachochytrium dendrobatidis shows that genotype is linked to virulence.
Matthew C Fisher, Jaime Bosch, Zhikang Yin, David A Stead, Janet Walker, …, Alistair J P Brown, Louise A Walker, Neil A R Gow, Jason E Stajich, Trenton W J Garner
Molecular ecology  ·  01 Feb 2009  ·  pmid:19161465
batrachochytrium proteomics virulence

2008

Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence.
Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence.
Jerome C Regier, Jeffrey W Shultz, Austen R D Ganley, April Hussey, Diane Shi, …, Andreas Zwick, Jason E Stajich, Michael P Cummings, Joel W Martin, Clifford W Cunningham
Systematic biology  ·  01 Dec 2008  ·  pmid:19085333
arthropod phylogeny
Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis.
Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis.
Erica Bree Rosenblum, Jason E Stajich, Nicole Maddox, Michael B Eisen
Proceedings of the National Academy of Sciences of the United States of America  ·  13 Oct 2008  ·  pmid:18852473
batrachochytrium gene-expression
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.
F Martin, A Aerts, D Ahrén, A Brun, E G J Danchin, …, I R Sanders, J E Stajich, A Tunlid, G Tuskan, I V Grigoriev
Nature  ·  06 Mar 2008  ·  pmid:18322534
laccaria genome
Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans.
Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans.
Guanggan Hu, Iris Liu, Anita Sham, Jason E Stajich, Fred S Dietrich, James W Kronstad
Genome biology  ·  22 Feb 2008  ·  pmid:18294377
cryptococcus

2007

An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea.
An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea.
Walt W Lilly, Jason E Stajich, Patricia J Pukkila, Sarah K Wilke, Noriko Inoguchi, Allen C Gathman
Mycological research  ·  14 Dec 2007  ·  pmid:18313909
coprinus coprinopsis metallopeptidases
Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii.
Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii.
James A Fraser, Jason E Stajich, Eric J Tarcha, Garry T Cole, Diane O Inglis, Anita Sil, Joseph Heitman
Eukaryotic cell  ·  02 Mar 2007  ·  pmid:17337636
mating-type-locus histoplasma coccidioides
Evolution of budding yeast prion-determinant sequences across diverse fungi.
Evolution of budding yeast prion-determinant sequences across diverse fungi.
Luke B Harrison, Zhan Yu, Jason E Stajich, Fred S Dietrich, Paul M Harrison
Journal of molecular biology  ·  03 Feb 2007  ·  pmid:17320905
prion fungi comparative-genomics
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors.
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors.
Jason E Stajich, Fred S Dietrich, Scott W Roy
Genome biology  ·  01 Jan 2007  ·  pmid:17949488
intron fungi
An Introduction to BioPerl.
An Introduction to BioPerl.
Jason E Stajich
Methods in molecular biology (Clifton, N.J.)  ·  01 Jan 2007  ·  pmid:18287711
bioperl tool

2006

The evolution of mammalian gene families.
The evolution of mammalian gene families.
Jeffery P Demuth, Tijl De Bie, Jason E Stajich, Nello Cristianini, Matthew W Hahn
PloS one  ·  20 Dec 2006  ·  pmid:17183716
gene-family-evolution
BASC: an integrated bioinformatics system for Brassica research.
BASC: an integrated bioinformatics system for Brassica research.
Timothy A Erwin, Erica G Jewell, Christopher G Love, Geraldine A C Lim, Xi Li, …, Emmanuel Mongin, Elia Stupka, Bruce Ross, German Spangenberg, David Edwards
Nucleic acids research  ·  05 Dec 2006  ·  pmid:17148473
tool database
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.
David A Fitzpatrick, Mary E Logue, Jason E Stajich, Geraldine Butler
BMC evolutionary biology  ·  22 Nov 2006  ·  pmid:17121679
fungi phylogeny phylogenomics
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.
Jörg Kämper, Regine Kahmann, Michael Bölker, Li-Jun Ma, Thomas Brefort, …, David B Jaffe, Sarah Calvo, Chad Nusbaum, James Galagan, Bruce W Birren
Nature  ·  02 Nov 2006  ·  pmid:17080091
ustilago genome
Reconstructing the early evolution of Fungi using a six-gene phylogeny.
Reconstructing the early evolution of Fungi using a six-gene phylogeny.
Timothy Y James, Frank Kauff, Conrad L Schoch, P Brandon Matheny, Valérie Hofstetter, …, David S Hibbett, François Lutzoni, David J McLaughlin, Joseph W Spatafora, Rytas Vilgalys
Nature  ·  19 Oct 2006  ·  pmid:17051209
phylogeny mycology fungi
The Cryptococcus neoformans catalase gene family and its role in antioxidant defense.
The Cryptococcus neoformans catalase gene family and its role in antioxidant defense.
Steven S Giles, Jason E Stajich, Connie Nichols, Quincy D Gerrald, J Andrew Alspaugh, Fred Dietrich, John R Perfect
Eukaryotic cell  ·  01 Sep 2006  ·  pmid:16963629
cryptococcus catalase
Open source tools and toolkits for bioinformatics: significance, and where are we?
Open source tools and toolkits for bioinformatics: significance, and where are we?
Jason E Stajich, Hilmar Lapp
Briefings in bioinformatics  ·  09 Aug 2006  ·  pmid:16899494
tool review
Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus.
Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus.
Robert A Cramer, Jason E Stajich, Yvonne Yamanaka, Fred S Dietrich, William J Steinbach, John R Perfect
Gene  ·  21 Jul 2006  ·  pmid:16962256
aspergillus-fumigatus nrps
Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans.
Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans.
Jason E Stajich, Fred S Dietrich
Eukaryotic cell  ·  01 May 2006  ·  pmid:16682456
intron cryptococcus
Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins.
Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins.
Jay R Hesselberth, John P Miller, Anna Golob, Jason E Stajich, Gregory A Michaud, Stanley Fields
Genome biology  ·  10 Apr 2006  ·  pmid:16606443
saccharomyces ww-domain
Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species.
Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species.
Avril Coghlan, Jason E Stajich, Todd W Harris
Methods in molecular biology (Clifton, N.J.)  ·  01 Jan 2006  ·  pmid:16988423
comparative-genomics caenorhabditis

2005

Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak.
Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak.
James A Fraser, Steven S Giles, Emily C Wenink, Scarlett G Geunes-Boyer, Jo Rae Wright, …, Andria Allen, Jason E Stajich, Fred S Dietrich, John R Perfect, Joseph Heitman
Nature  ·  09 Oct 2005  ·  pmid:16222245
cryptococcus
Likelihoods from summary statistics: recent divergence between species.
Likelihoods from summary statistics: recent divergence between species.
Scotland C Leman, Yuguo Chen, Jason E Stajich, Mohamed A F Noor, Marcy K Uyenoyama
Genetics  ·  02 Sep 2005  ·  pmid:16143628
population-genetics
Estimating the tempo and mode of gene family evolution from comparative genomic data.
Estimating the tempo and mode of gene family evolution from comparative genomic data.
Matthew W Hahn, Tijl De Bie, Jason E Stajich, Chi Nguyen, Nello Cristianini
Genome research  ·  01 Aug 2005  ·  pmid:16077014
gene-family-evolution tool
Investigating hookworm genomes by comparative analysis of two Ancylostoma species.
Investigating hookworm genomes by comparative analysis of two Ancylostoma species.
Makedonka Mitreva, James P McCarter, Prema Arasu, John Hawdon, John Martin, …, Jason E Stajich, Wadim Kapulkin, Sandra W Clifton, Robert H Waterston, Richard K Wilson
BMC genomics  ·  26 Apr 2005  ·  pmid:15854223
hookworm comparative-genomics

2004

Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray.
Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray.
Peter R Kraus, Marie-Josée Boily, Steven S Giles, Jason E Stajich, Andria Allen, Gary M Cox, Fred S Dietrich, John R Perfect, Joseph Heitman
Eukaryotic cell  ·  01 Oct 2004  ·  pmid:15470254
cryptococcus gene-expression
Disentangling the effects of demography and selection in human history.
Disentangling the effects of demography and selection in human history.
Jason E Stajich, Matthew W Hahn
Molecular biology and evolution  ·  08 Sep 2004  ·  pmid:15356276
population-genetics tool abo human-genetics

2003

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.
Lincoln D Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R Brent, …, C Wei, David Willey, Richard K Wilson, Richard Durbin, Robert H Waterston
PLoS biology  ·  17 Nov 2003  ·  pmid:14624247
caenorhabditis genome
The effects of selection against spurious transcription factor binding sites.
The effects of selection against spurious transcription factor binding sites.
Matthew W Hahn, Jason E Stajich, Gregory A Wray
Molecular biology and evolution  ·  25 Apr 2003  ·  pmid:12716998
tool comparative-genomics

2002

The generic genome browser: a building block for a model organism system database.
The generic genome browser: a building block for a model organism system database.
Lincoln D Stein, Christopher Mungall, ShengQiang Shu, Michael Caudy, Marco Mangone, …, Elizabeth Nickerson, Jason E Stajich, Todd W Harris, Adrian Arva, Suzanna Lewis
Genome research  ·  01 Oct 2002  ·  pmid:12368253
tool gbrowse
The Bioperl toolkit: Perl modules for the life sciences.
The Bioperl toolkit: Perl modules for the life sciences.
Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, …, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson, Ewan Birney
Genome research  ·  01 Oct 2002  ·  pmid:12368254
bioperl tool

2001

Ganglioside-induced differentiation-associated protein-1 is mutant in Charcot-Marie-Tooth disease type 4A/8q21.
Ganglioside-induced differentiation-associated protein-1 is mutant in Charcot-Marie-Tooth disease type 4A/8q21.
Rachel V Baxter, Kamel Ben Othmane, Julie M Rochelle, Jason E Stajich, Christine Hulette, …, S Bel, Judy E Stenger, John R Gilbert, Margaret A Pericak-Vance, Jeffery M Vance
Nature genetics  ·  17 Dec 2001  ·  pmid:11743579
human-genetics cmt