Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways von King, Zachary A, Dräger, Andreas, Ebrahim, Ali, Sonnenschein, Nikolaus, Lewis, Nathan E, Palsson, Bernhard O

Volltext

Reconstruction of biochemical networks in microorganisms von Palsson, Bernhard Ø, Feist, Adam M, Herrgård, Markus J, Thiele, Ines, Reed, Jennie L

Volltext

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods von Lewis, Nathan E., Nagarajan, Harish, Palsson, Bernhard O.

Volltext

Using Genome-scale Models to Predict Biological Capabilities von O’Brien, Edward J., Monk, Jonathan M., Palsson, Bernhard O.

Volltext

Constraint-based models predict metabolic and associated cellular functions von Bordbar, Aarash, Monk, Jonathan M., King, Zachary A., Palsson, Bernhard O.

Volltext

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli von Palsson, Bernhard Ø, Feist, Adam M

Volltext

Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism von Akbari, Amir, Palsson, Bernhard O

Volltext

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology von Sandberg, Troy E., Salazar, Michael J., Weng, Liam L., Palsson, Bernhard O., Feist, Adam M.

Volltext

Drug off-target effects predicted using structural analysis in the context of a metabolic network model von Chang, Roger L, Xie, Li, Xie, Lei, Bourne, Philip E, Palsson, Bernhard Ø

Volltext

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 von Schellenberger, Jan, Que, Richard, Fleming, Ronan M T, Thiele, Ines, Orth, Jeffrey D, Feist, Adam M, Zielinski, Daniel C, Bordbar, Aarash, Lewis, Nathan E, Rahmanian, Sorena, Kang, Joseph, Hyduke, Daniel R, Palsson, Bernhard Ø

Volltext

Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function von Yang, Jason H., Bhargava, Prerna, McCloskey, Douglas, Mao, Ning, Palsson, Bernhard O., Collins, James J.

Volltext

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments von O'Brien, Edward J, Utrilla, Jose, Palsson, Bernhard O

Volltext

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome von Rychel, Kevin, Sastry, Anand V., Palsson, Bernhard O.

Volltext

COBRApy: COnstraints-Based Reconstruction and Analysis for Python von Ebrahim, Ali, Lerman, Joshua A, Palsson, Bernhard O, Hyduke, Daniel R

Volltext

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol von Lee, Dae-Hee, Palsson, Bernhard Ø

Volltext

The Escherichia coli transcriptome mostly consists of independently regulated modules von Sastry, Anand V., Gao, Ye, Szubin, Richard, Hefner, Ying, Xu, Sibei, Kim, Donghyuk, Choudhary, Kumari Sonal, Yang, Laurence, King, Zachary A., Palsson, Bernhard O.

Volltext

Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655 von Seo, Sang Woo, Kim, Donghyuk, Szubin, Richard, Palsson, Bernhard O.

Volltext

COBRAme: A computational framework for genome-scale models of metabolism and gene expression von Lloyd, Colton J, Ebrahim, Ali, Yang, Laurence, King, Zachary A, Catoiu, Edward, O'Brien, Edward J, Liu, Joanne K, Palsson, Bernhard O

Volltext

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models von Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O.

Volltext

Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli von Seo, Sang Woo, Kim, Donghyuk, Latif, Haythem, O’Brien, Edward J., Szubin, Richard, Palsson, Bernhard O.

Volltext