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List of works by Jason E. Stajich

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea

scientific article

A chromosomal-level reference genome of the widely utilized <i>Coccidioides posadasii</i> laboratory strain “Silveira”

scientific article published in 2022

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

scientific article

A molecular perspective: biology of the emerging pathogen Batrachochytrium dendrobatidis

scientific article

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

scientific article (publication date: September 2016)

Airborne fungi spores distribution in various locations in Lagos, Nigeria

scientific article published on 03 January 2020

Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities

scientific article published on 26 August 2019

Amplicon Sequencing of Rock-Inhabiting Microbial Communities from Joshua Tree National Park, USA

publication published on 24 June 2021

An Improved 1.5-Gigabase Draft Assembly of Massospora cicadina (Zoopagomycota), an Obligate Fungal Parasite of 13- and 17-Year Cicadas

An Introduction to BioPerl

scientific article

An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea.

scientific article published on 14 December 2007

Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi

scientific article

Analysis of Transposable Elements in Coccidioides Species

scientific article

Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution

scientific article published in September 2010

Analysis of the Candida albicans Phosphoproteome

scientific article published on 6 March 2015

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation

scientific article

Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes

scientific article published on 29 June 2018

Avian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events

scientific article published on 01 May 2022

BASC: an integrated bioinformatics system for Brassica research

scientific article published on 5 December 2006

Behavioral betrayal: How select fungal parasites enlist living insects to do their bidding

scientific article published on 18 June 2020

Belowground Impacts of Alpine Woody Encroachment are determined by Plant Traits, Local Climate and Soil Conditions

scientific article published on 09 September 2020

Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements ⬇️

scientific article published on 03 September 2020

Beyond the extremes: Rocks as ultimate refuge for fungi in drylands

scientific article published on 24 November 2020

Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.

scientific article published on 8 August 2017

Cellular Subcompartments through Cytoplasmic Streaming

scientific article published on August 2015

Characterization of Aspergillus niger Isolated from the International Space Station

Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis

scientific article published on 25 March 2015

Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions.

scientific article published on 12 October 2017

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis.

scientific article

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

scientific article

Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins.

scientific article

Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis

scientific article published on 17 July 2018

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

scientific article

Comparative genomic analysis of fungal genomes reveals intron-rich ancestors

scientific article published in 2007

Comparative genomic analysis of the 'pseudofungus' Hyphochytrium catenoides.

scientific article published in January 2018

Comparative genomics and divergence time estimation of the anaerobic fungi in herbivorous mammals

Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species.

scientific article published on January 2006

Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis.

scientific article

Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans

scientific article published on 22 February 2008

Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data

scientific article (publication date: 4 June 2013)

Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora

article

Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota).

scientific article

Culture-Dependent and Amplicon Sequencing Approaches Reveal Diversity and Distribution of Black Fungi in Antarctic Cryptoendolithic Communities

scientific article published on 16 March 2021

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture

scientific article published in 2021

De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis

scientific article

Deacetylation of Fungal Exopolysaccharide Mediates Adhesion and Biofilm Formation

scientific article published on 5 April 2016

Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches

scientific article

Decoding Transcription Regulatory Mechanisms Associated with <i>Coccidioides immitis</i> Phase Transition Using Total RNA

scientific article published on 25 January 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

scientific article published in 2022

Disentangling the effects of demography and selection in human history

scientific article

Diversity and function of fungi associated with the fungivorous millipede, Brachycybe lecontii

scientific article published on 09 July 2019

Diversity of cytosine methylation across the fungal tree of life

scientific article published on 18 February 2019

Draft Genome Sequence of an Antarctic Isolate of the Black Yeast Fungus

scientific article published on 09 May 2019

Draft Genome Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica

scientific article published on 02 April 2020

Draft Genome Sequences of the Antarctic Endolithic Fungi Rachicladosporium antarcticum CCFEE 5527 and Rachicladosporium sp. CCFEE 5018.

scientific article

Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases

scientific article published on 03 October 2018

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon

scientific article

Erratum for Myers et al., "Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses"

scientific article published on 15 December 2020

Estimating the tempo and mode of gene family evolution from comparative genomic data

scientific article

Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans

scientific article published on May 2006

Evolution of Budding Yeast Prion-determinant Sequences Across Diverse Fungi

scientific article published on 03 February 2007

Evolution of drug resistance in an antifungal-naive chronic infection

article published in the Proceedings of the National Academy of Sciences of the United States of America

Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii

scientific article published on 2 March 2007

Evolutionary histories of soil fungi are reflected in their large-scale biogeography

scientific article

Evolutionary origins and diversification of proteobacterial mutualists

scientific article (publication date: 22 January 2014)

Evolutionary relationships among Massospora spp. (Entomophthorales), obligate pathogens of cicadas

scientific article published on 15 May 2020

Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

scientific article

FGMP: assessing fungal genome completeness

FGMP: assessing fungal genome completeness and gene content

article

Faculty of 1000 evaluation for De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient

Fungal Evolution: Mucor and Phycomyces See Double

scientific article published in August 2016

Fungal Genomes and Insights into the Evolution of the Kingdom

scientific article

Fungal biofilm morphology impacts hypoxia fitness and disease progression

scientific article published on 23 September 2019

Fungi in the Marine Environment: Open Questions and Unsolved Problems

scientific article published on 05 March 2019

FungiDB: an integrated functional genomics database for fungi

scientific article published on 7 November 2011

Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity

scientific article published on 05 September 2019

Ganglioside-induced differentiation-associated protein-1 is mutant in Charcot-Marie-Tooth disease type 4A/8q21

scientific article (publication date: 2002)

Genome Sequence of a Lethal Vascular Wilt Fungus, Verticillium nonalfalfae, a Biological Control Used Against the Invasive Ailanthus altissima ⬇️

scientific article published on 24 January 2019

Genome sequence of the model mushroom Schizophyllum commune

scientific article

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

scientific article

Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.

scientific article

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

scientific article published on 11 January 2019

Genomic Characterization of Parengyodontium torokii sp. nov., a Biofilm-Forming Fungus Isolated from Mars 2020 Assembly Facility

scholarly article published in 2022

Genomic diversity generated by a transposable element burst in a rice recombinant inbred population

scientific article published on 05 October 2020

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast.

scientific article published on 15 May 2018

Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis

scientific article published on 22 January 2013

Genomic insights into the host specific adaptation of the Pneumocystis genus

scientific article published on 08 March 2021

Genomic transition to pathogenicity in chytrid fungi

scientific article

Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis

scholarly article

Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage

article

Horizontal gene transfer as an indispensible driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage: Entire supplementary document

article

Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins.

scientific article

Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray

scientific article published on October 2004

Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State

scientific article published on 15 August 2019

Innovation and constraint leading to complex multicellularity in the Ascomycota.

scientific article published on 08 February 2017

Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure

scientific article

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

scientific article

International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulans

scientific article published on 12 December 2018

Investigating hookworm genomes by comparative analysis of two Ancylostoma species ⬇️

scientific article

Likelihoods from summary statistics: recent divergence between species.

scientific article

Literature-based gene curation and proposed genetic nomenclature for cryptococcus

scientific article

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

scientific article

Manipulation of the Global Regulator mcrA Upregulates Secondary Metabolite Production in Aspergillus wentii Using CRISPR-Cas9 with In Vitro Assembled Ribonucleoproteins

Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma

scientific article

Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar

scientific article

Meeting report: fungal its workshop (october 2012).

scientific article published on 15 April 2013

Members of the Euwallacea fornicatus species complex exhibit promiscuous mutualism with ambrosia fungi in Taiwan

scientific article published on 10 September 2019

Metagenome-Assembled Genomes of Bacteria Associated with Massospora cicadina Fungal Plugs from Infected Brood VIII Periodical Cicadas

scientific article published in 2022

Metagenome-Assembled Genomes of Bacterial Symbionts Associated with Insecticide-Resistant and -Susceptible Individuals of the Glassy-Winged Sharpshooter (Homalodisca vitripennis)

scientific article published in 2022

Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities

scientific article published on 05 March 2020

MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum

scientific article

Microbial associates of the southern mole cricket (Scapteriscus borellii) are highly pathogenic

scientific article published on 12 September 2017

Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange

scientific article published on 01 October 2019

Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes

scientific article published on 27 August 2019

Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi

scientific article published on 11 March 2020

Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus

scientific article published on 5 August 2013

No to Neocosmospora: Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium

scientific article published on 16 September 2020

Open source tools and toolkits for bioinformatics: significance, and where are we?

scientific article

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

scientific article published on 01 November 2016

Parasitoid Jewel Wasp Mounts Multi-Pronged Neurochemical Attack to Hijack a Host Brain

scientific article published on 06 October 2018

Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus

scientific article published on 31 January 2020

Phylogenetic and Phylogenomic Definition of Rhizopus Species.

scientific article

Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

scientific article published on 17 November 2020

Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus

scientific article published on 21 July 2006

Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota

scientific article published on 12 January 2019

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

scientific article

Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.

scientific article published in 2024

Proteomic and Metabolomic Characteristics of Extremophilic Fungi Under Simulated Mars Conditions

scientific article published on 15 May 2019

Proteomic and phenotypic profiling of the amphibian pathogen Batrachochytrium dendrobatidis shows that genotype is linked to virulence.

scientific article

Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al . (MPP 20:2)

scientific article published on 01 February 2019

Regional control of histone H3 lysine 27 methylation in Neurospora

scientific article published on 25 March 2013

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

scientific article

Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence

scientific article published on December 2008

Rocks support a distinctive and consistent mycobiome across contrasting dry regions of Earth

scientific article published in 2022

Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak

scientific article published in Nature

Sequential utilization of hosts from different fly families by genetically distinct, sympatric populations within the Entomophthora muscae species complex

scientific article

Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia

scientific article published on 8 August 2013

Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES

scientific article published on 19 December 2020

Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient

scientific article published on 10 May 2018

Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture

scientific article published on 14 March 2016

Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis.

scientific article published on 19 June 2012

Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities

scientific article published on 02 June 2018

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

scientific article published on 08 September 2020

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

article

The Bioperl toolkit: Perl modules for the life sciences

scientific article

The Cryptococcus neoformans catalase gene family and its role in antioxidant defense

scientific article

The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies

scientific article published in September 2017

The deadly chytrid fungus: a story of an emerging pathogen

scientific article

The effects of selection against spurious transcription factor binding sites

scientific article published on 25 April 2003

The evolution of mammalian gene families

scientific article published in 2006

The fungi

scientific article (publication date: 29 September 2009)

The future of fungi: threats and opportunities

scientific article published on 4 November 2022

The generic genome browser: a building block for a model organism system database

scientific article

The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution

scientific article

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

scientific article

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

scientific article published in November 2003

The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin.

scientific article published on 24 March 2015

The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice

scientific article published on 21 June 2013

Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture

scientific article published on 05 May 2020

Toward genome-enabled mycology

scientific article published on 08 August 2013

Tracking the genome-wide outcomes of a transposable element burst over decades of amplification

scientific article published on 20 November 2017

Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice

scientific article published in Nature Communications

Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex

scientific article (publication date: October 2010)

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

scientific article published on 13 June 2016

Twenty-first century mycology: a diverse, collaborative, and highly relevant science

scientific article published in January 2015

Two key events associated with a transposable element burst occurred during rice domestication

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

scientific article published on 02 April 2018

Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi

scientific article

Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling three Representative Locations of the Victoria Land

scientific article published on 23 June 2020

Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements

scientific article published on 15 May 2012

Using the Generic Synteny Browser (GBrowse_syn)

scientific article

Widespread adenine N6-methylation of active genes in fungi.

scientific article

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