Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM.

by Jonathan M Dreyfuss, Jeremy D Zucker, Heather M Hood, Linda R Ocasio, Matthew S Sachs, James E Galagan
Published 2013-01-01

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

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

by Richard Allen White, Eric M. Bottos, Taniya Roy Chowdhury, Jeremy D. Zucker, Colin J. Brislawn, Carrie D. Nicora, Sarah J. Fansler, Kurt R. Glaesemann, Kevin Glass, Janet K. Jansson, Morgan Langille
Published 2016-06-01

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

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

by Jonathan R Karr, Alex H Williams, Jeremy D Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, DREAM8 Parameter Estimation Challenge Consortium, Simon Wilkinson, Brandon A Allgood, Brian M Bot, Bruce R Hoff, Michael R Kellen, Markus W Covert, Gustavo A Stolovitzky, Pablo Meyer
Published 2015-05-01

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