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1
Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
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Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

PloS one, 2015-07, Vol.10 (7), p.e0132628-e0132628 [Peer Reviewed Journal]

COPYRIGHT 2015 Public Library of Science ;COPYRIGHT 2015 Public Library of Science ;2015 Gordon et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2015 Gordon et al 2015 Gordon et al ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0132628 ;PMID: 26177194

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2
PhycoCosm, a comparative algal genomics resource
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PhycoCosm, a comparative algal genomics resource

Nucleic acids research, 2021-01, Vol.49 (D1), p.D1004-D1011 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021 ;The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkaa898 ;PMID: 33104790

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3
Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution
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Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution

Molecular biology and evolution, 2022-02, Vol.39 (2) [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2022 ;The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. ;COPYRIGHT 2022 Oxford University Press ;ISSN: 0737-4038 ;EISSN: 1537-1719 ;DOI: 10.1093/molbev/msab372 ;PMID: 35060603

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4
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
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The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

Nucleic acids research, 2014-01, Vol.42 (Database issue), p.D26-D31 [Peer Reviewed Journal]

The Author(s) 2013. Published by Oxford University Press. 2013 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkt1069 ;PMID: 24225321

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5
Genome-wide role of codon usage on transcription and identification of potential regulators
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Genome-wide role of codon usage on transcription and identification of potential regulators

Proceedings of the National Academy of Sciences - PNAS, 2021-02, Vol.118 (6) [Peer Reviewed Journal]

2021 ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.2022590118 ;PMID: 33526697

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6
Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles
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Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

PLoS genetics, 2016-06, Vol.12 (6), p.e1006108-e1006108 [Peer Reviewed Journal]

COPYRIGHT 2016 Public Library of Science ;COPYRIGHT 2016 Public Library of Science ;2016 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet 12(6): e1006108. doi:10.1371/journal.pgen.1006108 ;2016 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet 12(6): e1006108. doi:10.1371/journal.pgen.1006108 ;ISSN: 1553-7404 ;ISSN: 1553-7390 ;EISSN: 1553-7404 ;DOI: 10.1371/journal.pgen.1006108 ;PMID: 27294409

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7
MycoCosm portal: gearing up for 1000 fungal genomes
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MycoCosm portal: gearing up for 1000 fungal genomes

Nucleic acids research, 2014-01, Vol.42 (Database issue), p.D699-D704 [Peer Reviewed Journal]

Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US. 2013 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkt1183 ;PMID: 24297253

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8
The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis
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The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis

Proceedings of the National Academy of Sciences - PNAS, 2022-01, Vol.119 (3) [Peer Reviewed Journal]

Copyright © 2022 the Author(s). Published by PNAS. ;Copyright National Academy of Sciences Jan 18, 2022 ;Attribution - NonCommercial - NoDerivatives ;Copyright © 2022 the Author(s). Published by PNAS. 2022 ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.2103527119 ;PMID: 35012977

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9
Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress
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Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

PLoS biology, 2017-12, Vol.15 (12), p.e2004050-e2004050 [Peer Reviewed Journal]

2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, et al. (2017) Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol 15(12): e2004050. https://doi.org/10.1371/journal.pbio.2004050 ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, et al. (2017) Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol 15(12): e2004050. https://doi.org/10.1371/journal.pbio.2004050 ;ISSN: 1545-7885 ;ISSN: 1544-9173 ;EISSN: 1545-7885 ;DOI: 10.1371/journal.pbio.2004050 ;PMID: 29240790

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10
Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts
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Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

PLoS genetics, 2018-04, Vol.14 (4), p.e1007322-e1007322 [Peer Reviewed Journal]

COPYRIGHT 2018 Public Library of Science ;COPYRIGHT 2018 Public Library of Science ;2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: from its plant-associated hosts. PLoS Genet 14(4): e1007322. https://doi.org/10.1371/journal.pgen.1007322 ;Attribution ;2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: from its plant-associated hosts. PLoS Genet 14(4): e1007322. https://doi.org/10.1371/journal.pgen.1007322 ;ISSN: 1553-7404 ;ISSN: 1553-7390 ;EISSN: 1553-7404 ;DOI: 10.1371/journal.pgen.1007322 ;PMID: 29630596

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11
Genetic determinants of endophytism in the Arabidopsis root mycobiome
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Genetic determinants of endophytism in the Arabidopsis root mycobiome

Nature communications, 2021-12, Vol.12 (1), p.7227-15, Article 7227 [Peer Reviewed Journal]

2021. The Author(s). ;The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Distributed under a Creative Commons Attribution 4.0 International License ;The Author(s) 2021 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-021-27479-y ;PMID: 34893598

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12
Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
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Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

Scientific reports, 2018-04, Vol.8 (1), p.6321-13, Article 6321 [Peer Reviewed Journal]

2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Attribution ;The Author(s) 2018 ;ISSN: 2045-2322 ;EISSN: 2045-2322 ;DOI: 10.1038/s41598-018-24686-4 ;PMID: 29679020

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13
Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes
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Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Nucleic acids research, 2023-07, Vol.51 (W1), p.W108-W114 [Peer Reviewed Journal]

The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. 2023 ;The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkad385 ;PMID: 37216585

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14
Genome-reconstruction for eukaryotes from complex natural microbial communities
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Genome-reconstruction for eukaryotes from complex natural microbial communities

Genome research, 2018-04, Vol.28 (4), p.569-580 [Peer Reviewed Journal]

2018 West et al.; Published by Cold Spring Harbor Laboratory Press. ;Copyright Cold Spring Harbor Laboratory Press Apr 2018 ;2018 ;ISSN: 1088-9051 ;EISSN: 1549-5469 ;DOI: 10.1101/gr.228429.117 ;PMID: 29496730

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15
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi
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The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi

Molecular biology and evolution, 2020-10, Vol.37 (10), p.2838-2856 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2020 ;The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. ;ISSN: 0737-4038 ;EISSN: 1537-1719 ;DOI: 10.1093/molbev/msaa122 ;PMID: 32421770

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16
FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation
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FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation

Bioinformatics (Oxford, England), 2017-09, Vol.33 (18), p.2936-2937 [Peer Reviewed Journal]

The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btx353 ;PMID: 28582481

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17
Trichoderma : the genomics of opportunistic success
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Trichoderma : the genomics of opportunistic success

Nature reviews. Microbiology, 2011-10, Vol.9 (10), p.749-759 [Peer Reviewed Journal]

COPYRIGHT 2011 Nature Publishing Group ;Copyright Nature Publishing Group Oct 2011 ;ISSN: 1740-1526 ;EISSN: 1740-1534 ;DOI: 10.1038/nrmicro2637 ;PMID: 21921934

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18
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
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Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Proceedings of the National Academy of Sciences - PNAS, 2014-07, Vol.111 (27), p.9923-9928 [Peer Reviewed Journal]

copyright © 1993—2008 National Academy of Sciences of the United States of America ;Copyright National Academy of Sciences Jul 8, 2014 ;Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.1400592111 ;PMID: 24958869

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19
Early Diverging Fungus Mucor circinelloides Lacks Centromeric Histone CENP-A and Displays a Mosaic of Point and Regional Centromeres
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Early Diverging Fungus Mucor circinelloides Lacks Centromeric Histone CENP-A and Displays a Mosaic of Point and Regional Centromeres

Current biology, 2019-11, Vol.29 (22), p.3791-3802.e6 [Peer Reviewed Journal]

2019 The Authors ;Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved. ;ISSN: 0960-9822 ;EISSN: 1879-0445 ;DOI: 10.1016/j.cub.2019.09.024 ;PMID: 31679929

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20
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
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Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The ISME Journal, 2021-02, Vol.15 (2), p.421-434 [Peer Reviewed Journal]

The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Distributed under a Creative Commons Attribution 4.0 International License ;The Author(s) 2020 ;ISSN: 1751-7362 ;EISSN: 1751-7370 ;DOI: 10.1038/s41396-020-00769-x ;PMID: 32929206

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