Comparative Genomic Analysis of Ochratoxin A Biosynthetic Cluster in Producing Fungi: New Evidence of a Cyclase Gene Involvement

by Massimo Ferrara, Antonia Gallo, Giancarlo Perrone, Donato Magistà, Scott E. Baker, Scott E. Baker
Published 2020-12-01

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

by Kevin McCluskey, Scott E. Baker
Published 2017-04-01

Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica

by Kyle R. Pomraning, Erin L. Bredeweg, Scott E. Baker, Aaron P. Mitchell
Published 2017-02-01

Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospo...

by William R. Cannon, Jeremy D. Zucker, Douglas J. Baxter, Neeraj Kumar, Scott E. Baker, Jennifer M. Hurley, Jay C. Dunlap
Published 2018-05-01

A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable.

by Laure M C Leynaud-Kieffer, Samuel C Curran, Irene Kim, Jon K Magnuson, John M Gladden, Scott E Baker, Blake A Simmons
Published 2019-01-01

Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of...

by Christa Ivanova, Jonas Ramoni, Thiziri Aouam, Alexa Frischmann, Bernhard Seiboth, Scott E. Baker, Stéphane Le Crom, Sophie Lemoine, Antoine Margeot, Frédérique Bidard
Published 2017-09-01

Identification of a Classical Mutant in the Industrial Host Aspergillus niger by Systems Genetics: LaeA Is Required for Citric Acid Production and Regulates the Formation of Some S...

by Jing Niu, Mark Arentshorst, P. Deepa S. Nair, Ziyu Dai, Scott E. Baker, Jens C. Frisvad, Kristian F. Nielsen, Peter J. Punt, Arthur F.J. Ram
Published 2016-01-01

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

by Joonhoon Kim, Joonhoon Kim, Joonhoon Kim, Samuel T. Coradetti, Samuel T. Coradetti, Young-Mo Kim, Young-Mo Kim, Yuqian Gao, Yuqian Gao, Junko Yaegashi, Junko Yaegashi, Jeremy D. Zucker, Jeremy D. Zucker, Nathalie Munoz, Nathalie Munoz, Erika M. Zink, Kristin E. Burnum-Johnson, Kristin E. Burnum-Johnson, Scott E. Baker, Scott E. Baker, Scott E. Baker, Blake A. Simmons, Blake A. Simmons, Blake A. Simmons, Jeffrey M. Skerker, John M. Gladden, John M. Gladden, John M. Gladden, Jon K. Magnuson, Jon K. Magnuson, Jon K. Magnuson
Published 2021-01-01

Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis.

by Kyle R Pomraning, Siwei Wei, Sue A Karagiosis, Young-Mo Kim, Alice C Dohnalkova, Bruce W Arey, Erin L Bredeweg, Galya Orr, Thomas O Metz, Scott E Baker
Published 2015-01-01

Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans

by Claire Khosravi, Evy Battaglia, Roland S. Kun, Sacha Dalhuijsen, Jaap Visser, María Victoria Aguilar-Pontes, Miaomiao Zhou, Heino M. Heyman, Young-Mo Kim, Scott E. Baker, Ronald P. de Vries
Published 2018-03-01

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica

by Eduard J. Kerkhoven, Young-Mo Kim, Siwei Wei, Carrie D. Nicora, Thomas L. Fillmore, Samuel O. Purvine, Bobbie-Jo Webb-Robertson, Richard D. Smith, Scott E. Baker, Thomas O. Metz, Jens Nielsen, Sang Yup Lee
Published 2017-06-01

Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica

by Kyle R. Pomraning, Erin L. Bredeweg, Eduard J. Kerkhoven, Kerrie Barry, Sajeet Haridas, Hope Hundley, Kurt LaButti, Anna Lipzen, Mi Yan, Jon K. Magnuson, Blake A. Simmons, Igor V. Grigoriev, Jens Nielsen, Scott E. Baker
Published 2018-12-01

Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

by Tania Chroumpi, Mao Peng, Lye Meng Markillie, Hugh D. Mitchell, Carrie D. Nicora, Chelsea M. Hutchinson, Vanessa Paurus, Nikola Tolic, Chaevien S. Clendinen, Galya Orr, Scott E. Baker, Miia R. Mäkelä, Miia R. Mäkelä, Ronald P. de Vries
Published 2021-03-01

Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger.

by Saori Amaike Campen, Jed Lynn, Stephanie J Sibert, Sneha Srikrishnan, Pallavi Phatale, Taya Feldman, Joel M Guenther, Jennifer Hiras, Yvette Thuy An Tran, Steven W Singer, Paul D Adams, Kenneth L Sale, Blake A Simmons, Scott E Baker, Jon K Magnuson, John M Gladden
Published 2017-01-01

High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440

by Yuqian Gao, Yuqian Gao, Thomas L. Fillmore, Nathalie Munoz, Nathalie Munoz, Gayle J. Bentley, Gayle J. Bentley, Christopher W. Johnson, Christopher W. Johnson, Joonhoon Kim, Joonhoon Kim, Jamie A. Meadows, Jamie A. Meadows, Jeremy D. Zucker, Jeremy D. Zucker, Meagan C. Burnet, Meagan C. Burnet, Anna K. Lipton, Anna K. Lipton, Aivett Bilbao, Aivett Bilbao, Daniel J. Orton, Young-Mo Kim, Young-Mo Kim, Ronald J. Moore, Errol W. Robinson, Errol W. Robinson, Scott E. Baker, Scott E. Baker, Bobbie-Jo M. Webb-Robertson, Bobbie-Jo M. Webb-Robertson, Adam M. Guss, Adam M. Guss, John M. Gladden, John M. Gladden, Gregg T. Beckham, Gregg T. Beckham, Jon K. Magnuson, Jon K. Magnuson, Kristin E. Burnum-Johnson, Kristin E. Burnum-Johnson
Published 2020-12-01

Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

by Kyle R. Pomraning, Ziyu Dai, Nathalie Munoz, Young-Mo Kim, Yuqian Gao, Shuang Deng, Joonhoon Kim, Joonhoon Kim, Beth A. Hofstad, Marie S. Swita, Teresa Lemmon, James R. Collett, Ellen A. Panisko, Bobbie-Jo M. Webb-Robertson, Jeremy D. Zucker, Carrie D. Nicora, Henrique De Paoli, Scott E. Baker, Kristin E. Burnum-Johnson, Nathan J. Hillson, Jon K. Magnuson, Jon K. Magnuson
Published 2021-04-01

Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.

by Bradford J Condon, Yueqiang Leng, Dongliang Wu, Kathryn E Bushley, Robin A Ohm, Robert Otillar, Joel Martin, Wendy Schackwitz, Jane Grimwood, NurAinizzati MohdZainudin, Chunsheng Xue, Rui Wang, Viola A Manning, Braham Dhillon, Zheng Jin Tu, Brian J Steffenson, Asaf Salamov, Hui Sun, Steve Lowry, Kurt LaButti, James Han, Alex Copeland, Erika Lindquist, Kerrie Barry, Jeremy Schmutz, Scott E Baker, Lynda M Ciuffetti, Igor V Grigoriev, Shaobin Zhong, B Gillian Turgeon
Published 2013-01-01

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