Stajich Laboratory for Fungal Evolutionary Genomics

I am interested in the process and mechanisms of evolution. I study this primarily in fungi using comparative, computational, and experimental tools. We utilize genome and RNA sequencing, sequence analysis, molecular evolution, and phylogenetics, and molecular biology tools to explore the functions of genes or genomic regions identified by analyses to be involved in processes we study.

Most of our work is focused in the zygomycete and zoosporic chytrid fungi (fungi that move!). We also have collaborative projects and interests in Aspergillus, Fusarium, Coccidioides, and Clavispora lusitaniae. The lab is increasingly moving towards questions that relate to symbioses with new projects on fungal-bacteria antagonism and on the biological symbioses that occur among fungi, algae, bacteria in desert Biological crusts. I also have a new interest in extremophile fungi and working on projects to understand the halophilic Hortaea werneckii and endolithic Antarctic fungi through genome sequencing and laboratory experiments.

I am involved in several fungal genome projects including co-leading the 1000 fungal genomes project with the JGI and the ZyGoLife project.

My interests are also in the evolution of multicellular forms and regulation of development in fungi. I think understanding how differential gene regulation is established can help learn more about the mechanisms of cell type differentiation. We are also studying the cell wall to understand how innovations in the cell wall and dimorphism impact interactions between pathogenic fungi and hosts they infect. These different projects seek to provide new insight into the big picture of how the complexity of life evolved and how host and pathogen interactions co-evolved.

To address this work we also need tools to sift and mine the gigantic datasets that genomics can produce. In the past I focused on building tools for comparative and computational analyses of genomes including work on the BioPerl and Gbrowse projects and the development of open source software for bioinformatics and life sciences research through the Open Bioinformatics Foundation.


I am a paid consultant for Michroma and on the Scientific Advisory Board of Sincarne. I have served as a paid consultant in the past for Zymergen, Trace Genomics, Triton Algae, and Indigo Ag.


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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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


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
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
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
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
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
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
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
Extremophilic and extremotolerant fungi.
Cene Gostinčar, Jason E Stajich, Nina Gunde-Cimerman
Current biology : CB  ·  24 Jul 2023  ·  pmid:37490857
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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


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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
Fungi are key players in extreme ecosystems.
Claudia Coleine, Jason E Stajich, Laura Selbmann
Trends in ecology & evolution  ·  01 Mar 2022  ·  pmid:35246323
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
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
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


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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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


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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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


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
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
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
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
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
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
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
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
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
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
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
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
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
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
FGMP: assessing fungal genome completeness.
Ousmane H Cissé, Jason E Stajich
BMC bioinformatics  ·  15 Apr 2019  ·  pmid:30987585
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
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
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
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
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
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
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


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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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


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
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
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
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
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
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
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
Fungal Genomes and Insights into the Evolution of the Kingdom.
Jason E Stajich
Microbiology spectrum  ·  01 Jul 2017  ·  pmid:28820125
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
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
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
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


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
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
Fungal Evolution: Mucor and Phycomyces See Double.
Jason E Stajich
Current biology : CB  ·  22 Aug 2016  ·  pmid:27554660
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
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
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
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


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
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
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
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
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
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
Twenty-first century mycology: a diverse, collaborative, and highly relevant science.
Peter Kennedy, Jason Stajich
The New phytologist  ·  01 Jan 2015  ·  pmid:25427217


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
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
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
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
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
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


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
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
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
Toward genome-enabled mycology.
David S Hibbett, Jason E Stajich, Joseph W Spatafora
Mycologia  ·  08 Aug 2013  ·  pmid:23928422
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
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
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
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
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
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
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
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
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


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
Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis.
John Abramyan, Jason E Stajich
mBio  ·  19 Jun 2012  ·  pmid:22718849
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


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
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
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
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


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
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
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
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
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
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
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
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
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
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
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


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
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
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


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
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
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
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


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
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
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
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
An Introduction to BioPerl.
Jason E Stajich
Methods in molecular biology (Clifton, N.J.)  ·  01 Jan 2007  ·  pmid:18287711


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
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
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
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
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
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
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
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
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
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
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


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
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
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
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


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
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


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
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


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
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


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

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