Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning

by Harrison Ho, Mansi Chovatia, Rob Egan, Guifen He, Yuko Yoshinaga, Ivan Liachko, Ronan O’Malley, Zhong Wang
Published 2023-09-01

Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete <i>Clavariopsis aquatica</i>

by Felix Heeger, Elizabeth C. Bourne, Christian Wurzbacher, Elisabeth Funke, Anna Lipzen, Guifen He, Vivian Ng, Igor V. Grigoriev, Dietmar Schlosser, Michael T. Monaghan
Published 2021-10-01

Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network

by Claire Khosravi, Joanna E. Kowalczyk, Tania Chroumpi, Evy Battaglia, Maria-Victoria Aguilar Pontes, Mao Peng, Ad Wiebenga, Vivian Ng, Anna Lipzen, Guifen He, Diane Bauer, Igor V. Grigoriev, Ronald P. de Vries
Published 2019-11-01

Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales)

by Andrew S. Urquhart, Stephen J. Mondo, Miia R. Mäkelä, James K. Hane, James K. Hane, Ad Wiebenga, Guifen He, Sirma Mihaltcheva, Jasmyn Pangilinan, Anna Lipzen, Kerrie Barry, Ronald P. de Vries, Igor V. Grigoriev, Alexander Idnurm
Published 2018-12-01

Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

by Jingcheng Zhang, Nan Shen, Chuang Li, Xingjie Xiang, Gaolei Liu, Ying Gui, Sean Patev, David S. Hibbett, Kerrie Barry, William Andreopoulos, Anna Lipzen, Robert Riley, Guifen He, Mi Yan, Igor V. Grigoriev, Hoi Shan Kwan, Man Kit Cheung, Yinbing Bian, Yang Xiao
Published 2022-05-01

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate l...

by Jennifer L. Brown, Candice L. Swift, Stephen J. Mondo, Susanna Seppala, Asaf Salamov, Vasanth Singan, Bernard Henrissat, Elodie Drula, John K. Henske, Samantha Lee, Kurt LaButti, Guifen He, Mi Yan, Kerrie Barry, Igor V. Grigoriev, Michelle A. O’Malley
Published 2021-12-01

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

by Marc W. Van Goethem, Andrew R. Osborn, Benjamin P. Bowen, Peter F. Andeer, Tami L. Swenson, Alicia Clum, Robert Riley, Guifen He, Maxim Koriabine, Laura Sandor, Mi Yan, Chris G. Daum, Yuko Yoshinaga, Thulani P. Makhalanyane, Ferran Garcia-Pichel, Axel Visel, Len A. Pennacchio, Ronan C. O’Malley, Trent R. Northen
Published 2021-11-01

Genome sequencing of Porostereum spadiceum to study the degradation of levofloxacin

by Amal Ben Ayed, Imen Akrout, Karima Staita, Quentin Albert, Stéphane Greff, Charlotte Simmler, Steven Ahrendt, Kurt LaButti, Anna Lipzen, Guifen He, Emily Savage, Jean Armengaud, Mélodie Kielbasa, David Navarro, Elodie Drula, Annick Turbé-Doan, Emmanuel Bertrand, Anne Lomascolo, Delphine Chaduli, Craig B. Faulds, Mohamed Chamkha, Amina Maalej, Kerrie Barry, Igor V. Grigoriev, Francis Martin, Héla Zouari-Mechichi, Giuliano Sciara, Tahar Mechichi, Eric Record
Published 2024-01-01

Corrigendum to “Genome sequencing of Porostereum spadiceum to study the degradation of levofloxacin” [Ecotoxicol. Environ. Saf. 270 (2024) 115808]

by Amal Ben Ayed, Imen Akrout, Karima Staita, Quentin Albert, Stéphane Greff, Charlotte Simmler, Steven Ahrendt, Kurt LaButti, Anna Lipzen, Guifen He, Emily Savage, Jean Armengaud, Mélodie Kielbasa, David Navarro, Elodie Drula, Annick Turbé-Doan, Emmanuel Bertrand, Anne Lomascolo, Delphine Chaduli, Craig B. Faulds, Mohamed Chamkha, Amina Maalej, Kerrie Barry, Igor V. Grigoriev, Francis Martin, Héla Zouari-Mechichi, Giuliano Sciara, Tahar Mechichi, Eric Record
Published 2024-06-01

A comparative genomics study of 23 Aspergillus species from section Flavi

by Inge Kjærbølling, Tammi Vesth, Jens C. Frisvad, Jane L. Nybo, Sebastian Theobald, Sara Kildgaard, Thomas Isbrandt Petersen, Alan Kuo, Atsushi Sato, Ellen K. Lyhne, Martin E. Kogle, Ad Wiebenga, Roland S. Kun, Ronnie J. M. Lubbers, Miia R. Mäkelä, Kerrie Barry, Mansi Chovatia, Alicia Clum, Chris Daum, Sajeet Haridas, Guifen He, Kurt LaButti, Anna Lipzen, Stephen Mondo, Jasmyn Pangilinan, Robert Riley, Asaf Salamov, Blake A. Simmons, Jon K. Magnuson, Bernard Henrissat, Uffe H. Mortensen, Thomas O. Larsen, Ronald P. de Vries, Igor V. Grigoriev, Masayuki Machida, Scott E. Baker, Mikael R. Andersen
Published 2020-02-01