C. Schoch

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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Matthew W. Brown, D. Richter, J. Pawlowski, 2018, The Journal of eukaryotic microbiology.

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.

D. Hibbett, J. Stone, J. Rogers, 2004, American journal of botany.

A class-wide phylogenetic assessment of Dothideomycetes

Y. Zhang, M. Grube, J. Spatafora, 2009, Studies in mycology.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

John L. Spouge, Conrad L. Schoch, Vincent Robert, 2012, Proceedings of the National Academy of Sciences.

A five-gene phylogeny of Pezizomycotina.

David Hewitt, Jolanta Miadlikowska, Matthias Schultz, 2006, Mycologia.

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.

David Hewitt, Jolanta Miadlikowska, Damien Ertz, 2009, Systematic biology.

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

A. Salamov, S. Lucas, F. Glaser, 2012, PLoS pathogens.

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

Katalin Molnár, Jolanta Miadlikowska, Arne Thell, 2014, Molecular phylogenetics and evolution.

Sequence-based classification and identification of Fungi

D. Hibbett, P. Kirk, J. Herr, 2016, Mycologia.

Dothideomycete–Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum[W][OA]

James K. Hane, B. Birren, J. Galagan, 2007, The Plant Cell Online.

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Jean, James K. Hane, J. Poulain, 2011, Nature communications.

Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Bernard Henrissat, Scott E. Baker, Mikko Arvas, 2008, Nature Biotechnology.

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

P. Kirk, D. Geiser, G. Cardinali, 2020, IMA Fungus.

The Revised Classification of Eukaryotes

Matthew W. Brown, J. Pawlowski, L. Parfrey, 2012, The Journal of eukaryotic microbiology.

A five-gene phylogeny of Pezizomycotina

D. Geiser, J. Spatafora, D. Hewitt, 2006 .

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Bernard Henrissat, Paul Richardson, Mikko Arvas, 2008, Nature Biotechnology.

A higher-level phylogenetic classification of the Fungi.

Michael Weiss, Robert Bauer, Karl-Henrik Larsson, 2007, Mycological research.

Reconstructing the early evolution of Fungi using a six-gene phylogeny

Kenji Matsuura, Pedro W. Crous, David Hewitt, 2006, Nature.

Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

V. Barbe, C. Cruaud, S. Mangenot, 2014, BMC Genomics.

Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches

Conrad L. Schoch, Bryn T. M. Dentinger, C. Schoch, 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

A multigene phylogeny of the Dothideomycetes using four nuclear loci.

J. Spatafora, C. Schoch, P. Crous, 2006, Mycologia.

Phylogenetic lineages in the Capnodiales Crous

G. S. Hoog, K. Hyde, C. Gueidan, 2010 .

Reply to Kiss: Internal transcribed spacer (ITS) remains the best candidate as a universal DNA barcode marker for Fungi despite imperfections

C. Schoch, K. Seifert, 2012, Proceedings of the National Academy of Sciences.

GenBank

S. Sherry, Kim D. Pruitt, I. Karsch-Mizrachi, 2013, Nucleic Acids Res..

Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Isaac Y. Ho, Nicholas H. Putnam, A. Salamov, 2008, Nature Biotechnology.

Marine fungal lineages in the Hypocreomycetidae.

J. Spatafora, G. Sung, C. Schoch, 2007, Mycological research.

GenBank

S. Sherry, K. Pruitt, I. Karsch-Mizrachi, 2020, Nucleic acids research.

The Cylindrocladium candelabrum species complex includes four distinct mating populations

M. Wingfield, B. Wingfield, C. Schoch, 1999 .

Species Identification in Plant-Associated Prokaryotes and Fungi Using DNA.

C. Schoch, B. Robbertse, P. Inderbitzin, 2020, Phytobiomes journal.

Phylogenetic placement of the ectomycorrhizal genus Cenococcum in Gloniaceae (Dothideomycetes)

J. Spatafora, C. Schoch, E. Boehm, 2012, Mycologia.

Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life

J. Townsend, J. Spatafora, C. Schoch, 2009, Persoonia.

A molecular phylogenetic reappraisal of the Hysteriaceae, Mytilinidiaceae and Gloniaceae (Pleosporomycetidae, Dothideomycetes) with keys to world species

J. Spatafora, C. Schoch, A. Miller, 2009, Studies in mycology.

Detection and Identiﬁcation of Fungi Intimately Associated with the Brown Seaweed Fucus serratus (cid:1) †

J. Spatafora, C. Schoch, J. Kohlmeyer, 2008 .

Detection and Identification of Fungi Intimately Associated with the Brown Seaweed Fucus serratus

J. Spatafora, C. Schoch, J. Kohlmeyer, 2007, Applied and Environmental Microbiology.

The halotolerant fungus Glomerobolus gelineus is a member of the Ostropales.

J. Spatafora, C. Schoch, J. Kohlmeyer, 2006, Mycological research.

Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum.

V. Brover, C. Schoch, B. Robbertse, 2022, Plant disease.

The internal transcribed spacer as a universal DNA barcode marker for fungi

C. Schoch, S. Huhndorf, K. Seifert, 2012 .

Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

V. Barbe, C. Cruaud, S. Mangenot, 2014, BMC Genomics.

Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi).

Andrew W. Wilson, D. Hibbett, K. Matsuura, 2007, Molecular phylogenetics and evolution.

Phylogeny of rock-inhabiting fungi related to Dothideomycetes

J. T. Staley, M. Grube, L. Muggia, 2009, Studies in mycology.

Phylogenetic lineages in the Capnodiales

K. Hyde, C. Gueidan, C. Schoch, 2009, Studies in mycology.

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.

Gianluigi Cardinali, Duong Vu, Walter Gams, 2015, Medical mycology.

A reappraisal of Microthyriaceae

K. Hyde, C. Schoch, P. Chomnunti, 2011, Fungal Diversity.

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences.

R. Henrik Nilsson, Erik Kristiansson, Nils Hallenberg, 2012 .

Database resources of the National Center for Biotechnology Information

Evan Bolton, Mark Johnson, Rebecca Orris, 2017, Nucleic Acids Res..

An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny

J. Rogers, G. Sung, C. Schoch, 2006 .

Pleosporales

K. Hyde, C. Schoch, P. Crous, 2011, Fungal Diversity.

How to publish a new fungal species, or name, version 3.0

P. Kirk, T. May, K. Hyde, 2021, IMA Fungus.

6 Pezizomycotina: Dothideomycetes and Arthoniomycetes

M. Grube, C. Schoch, 2015 .

New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.

Martin Grube, Jolanta Miadlikowska, Erin Tripp, 2006, Mycologia.

A molecular, morphological and ecological re-appraisal of Venturiales―a new order of Dothideomycetes

K. Hyde, C. Schoch, P. Crous, 2011, Fungal Diversity.

An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny.

J. Rogers, G. Sung, C. Schoch, 2006, Mycologia.

A multigene phylogeny of the Dothideomycetes using four nuclear loci

J. Spatafora, C. Schoch, P. Crous, 2006 .

Molecular systematics of the marine Dothideomycetes

J. Spatafora, C. Schoch, E. Jones, 2009, Studies in mycology.

Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): a nuclear rDNA phylogeny.

D. Hibbett, J. Spatafora, C. Schoch, 2006, Molecular phylogenetics and evolution.

The Genera of Fungi: fixing the application of type species of generic names

P. Kirk, J. Guarro, C. Schoch, 2014, IMA fungus.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

R. Henrik Nilsson, Kazuaki Tanaka, Qing Cai, 2014, Database J. Biol. Databases Curation.

Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation

Y. Zhang, J. Spatafora, K. Hyde, 2009, Studies in mycology.

Preserving accuracy in GenBank

Nils Hallenberg, Ning Zhang, Scott E. Baker, 2008 .

NCBI Taxonomy: a comprehensive update on curation, resources and tools

Lu Sun, Detlef D. Leipe, Ilene Karsch-Mizrachi, 2020, Database J. Biol. Databases Curation.

Deletion of all Cochliobolus heterostrophus monofunctional catalase-encoding genes reveals a role for one in sensitivity to oxidative stress but none with a role in virulence.

C. Schoch, B. Robbertse, B. Turgeon, 2003, Molecular plant-microbe interactions : MPMI.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Wen J. Li, Brian Smith-White, Tatiana A. Tatusova, 2015, Nucleic Acids Res..

Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project

Conrad L. Schoch, M. Garbelotto, C. Schoch, 2013, PloS one.

MycoBank gearing up for new horizons

Pedro W. Crous, Gianluigi Cardinali, Linhuan Wu, 2013, IMA fungus.

Testing the phylogenetic utility of Mcm7 in the Ascomycota

C. Schoch, A. Miller, H. Raja, 2011 .

Female Fertility and Single Nucleotide Polymorphism Comparisons in Cylindrocladium pauciramosum.

C. Schoch, P. Crous, S. Koike, 2001, Plant disease.

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

Michael DiCuccio, Stacy Ciufo, Conrad L. Schoch, 2018, International journal of systematic and evolutionary microbiology.

Mycologists' committees strongly support changes to the governance of fungal nomenclature

T. W. May, P. Kirk, R. Lücking, 2017 .

On the evolution of the Hysteriaceae and Mytilinidiaceae (Pleosporomycetidae, Dothideomycetes, Ascomycota) using four nuclear genes.

J. Spatafora, C. Schoch, E. Boehm, 2009, Mycological research.

Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case

Stacy Ciufo, Conrad L. Schoch, Barbara Robbertse, 2017, Database J. Biol. Databases Curation.

Phylogeny of Calonectria and selected hypocrealean genera with cylindrical macroconidia

M. Wingfield, B. Wingfield, C. Schoch, 2000 .

A Saccharomyces cerevisiae mutant defective in the kinesin-like protein Kar3 is sensitive to NaCl-stress

K. Entian, C. Schoch, G. Pretorius, 1997, Current Genetics.

A class-wide phylogenetic assessment of Dothideomycetes Schoch,

Y., M. Grube, G. S. Hoog, 2010 .

An overview of the genus Glyphium and its phylogenetic placement in Patellariales

C. Schoch, E. Boehm, A. Gardiennet, 2015, Mycologia.

New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

M. Grube, B. Büdel, R. Lücking, 2006 .

NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018

Yu. G. Ostapchuk, G. Cochrane, D. Leipe, 2017 .

Fungal taxonomy and sequence-based nomenclature

P. Kirk, D. Geiser, G. Cardinali, 2021, Nature Microbiology.

Species concepts in the Cylindrocladium floridanum and Cy. spathiphylli complexes (Hypocreaceae) based on multi-allelic sequence data, sexual compatibility and morphology.

C. Schoch, P. Crous, J. Kang, 2001, Systematic and applied microbiology.

Phylogenetic relationships of Cylindrocladium pseudogracile and Cylindrocladium rumohrae with morphologically similar ta×a, based on morphology and DNA sequences of internal transcribed spacers and beta-tubulin

C. Schoch, P. Crous, Ji-Chuan Kang, 1999 .

Correction: Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

A. Salamov, S. Lucas, F. Glaser, 2013, PLoS pathogens.

Homologs of ToxB, a host-selective toxin gene from Pyrenophora tritici-repentis, are present in the genome of sister-species Pyrenophora bromi and other members of the Ascomycota.

J. Spatafora, C. Schoch, R. Andrie, 2008, Fungal genetics and biology : FG & B.

A phylogenomic analysis of the Ascomycota.

Conrad L Schoch, Barbara Robbertse, J. Spatafora, 2006, Fungal genetics and biology : FG & B.

The NCBI BioCollections Database.

Ilene Karsch-Mizrachi, Stacy Ciufo, Elena Starchenko, 2019, Database : the journal of biological databases and curation.

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

Eric P. Nawrocki, Beverly A. Underwood, A. Schäffer, 2021, bioRxiv.

A complete inventory of fungal kinesins in representative filamentous ascomycetes.

C. Schoch, O. Yoder, J. Aist, 2003, Fungal genetics and biology : FG & B.

Phylogeny of Calonectria based on comparisons of β-tubulin DNA sequences

M. Wingfield, B. Wingfield, C. Schoch, 2001 .

Recombination in Calonectria morganii and phylogeny with other heterothallic small-spored Calonectria species

B. Wingfield, C. Schoch, P. Crous, 2000 .

A New Root and Crown Rot Disease of Heath in California Caused by Cylindrocladium pauciramosum.

C. Schoch, P. Crous, S. Koike, 1999, Plant Disease.

Cylindrocladium angustatum sp. nov., a new leaf spot pathogen ofTillandsia capitata from Florida, U.S.A.

T. Schubert, C. Schoch, P. Crous, 2000 .

First report of Cylindrocladium root and petiole rot of Spathiphyllum in South Africa

C. Schoch, P. Crous, 1999 .

Xenocylindrocladium guianense andX. subverticillatum, two new species of hyphomycetes from plant debris in the tropics

C. Schoch, P. Crous, C. Decock, 2001 .

Using standard keywords in publications to facilitate updates of new fungal taxonomic names

Pedro W. Crous, M. Catherine Aime, Kevin D. Hyde, 2017 .

Meeting Report: Fungal ITS Workshop (October 2012)

Rob Knight, Laura Wegener Parfrey, Daniel McDonald, 2013, Standards in genomic sciences.

Geographic, climatic, and chemical differentiation in the Hypogymnia imshaugii species complex (Lecanoromycetes, Parmeliaceae) in North America

C. Schoch, J. Miadlikowska, B. McCune, 2011 .

Collection and curation of prokaryotic genome assemblies from type strains at NCBI.

P. Kitts, Michael DiCuccio, C. Schoch, 2023, International journal of systematic and evolutionary microbiology.

Hypogymnia phylogeny, including Cavernularia, reveals biogeographic structure

F. Lutzoni, C. Schoch, J. Miadlikowska, 2011 .

Hypogymnia minilobata (Parmeliaceae), a new lichen from coastal California

C. Schoch, B. McCune, 2009 .

Cylindrocladiella hahajimaensis, a new species of Cylindrocladiella transferred from Verticillium

O. Ovaskainen, J. Bengtsson-Palme, C. Schoch, 2012 .

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

P. Kirk, D. Geiser, G. Cardinali, 2020, IMA Fungus.

Leaf spot on switch grass (Panicum virgatum), symptoms of a new disease caused by Bipolaris oryzae

J. Krupinsky, J. Berdahl, C. Schoch, 2004 .

The NCBI BioCollections Database

Ilene Karsch-Mizrachi, Shobha Sharma, Stacy Ciufo, 2018, Database J. Biol. Databases Curation.

Dolabra nepheliae on rambutan and lychee represents a novel lineage of phytopathogenic Eurotiomycetes

C. Schoch, A. Rossman, L. Keith, 2010, Mycoscience.

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.

D. Hibbett, J. Stone, J. Rogers, 2004, American journal of botany.

The Revised Classification of Eukaryotes

Matthew W. Brown, L. Parfrey, S. Adl, 2012, The Journal of eukaryotic microbiology.

Database resources of the National Center for Biotechnology Information

Gregory D. Schuler, Stephen H. Bryant, David L. Wheeler, 2018, Nucleic acids research.

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Isaac Y. Ho, Nicholas H. Putnam, A. Salamov, 2008, Nature Biotechnology.

Non-commercial Research and Educational Use including without Limitation Use in Instruction at Your Institution, Sending It to Specific Colleagues That You Know, and Providing a Copy to Your Institution's Administrator. All Other Uses, Reproduction and Distribution, including without Limitation Comm

D. Hibbett, J. Rogers, Ning Zhang, 2022 .