AliMohammadEbrahimMD

PubMed

• 33 citations
  Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
  Joanne K. Liu, Colton J. Lloyd, Mahmoud M. Al-Bassam, Ali Ebrahim, Ji-Nu Kim, Connor A. Olson, Alexander A. Aksenov, Pieter C. Dorrestein, Karsten Zengler> ;Plos Computational Biology. 2019 Mar 7
• 27 citations
  DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression.
  Laurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson> ;BMC Systems Biology. 2019 Jan 9
• 77 citations
  COBRAme: A computational framework for genome-scale models of metabolism and gene expression
  Colton J. Lloyd, Ali Ebrahim, Laurence Yang, Zachary A. King, Edward Catoiu, Edward J. O’Brien, Joanne K. Liu, Bernhard O. Palsson> ;Plos Computational Biology. 2018 Jul 5
• 31 citations
  Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
  Laurence Yang, Justin Tan, Edward J. O’Brien, Jonathan M. Monk, Donghyuk Kim, Howard J. Li, Pep Charusanti, Ali Ebrahim, Colton J. Lloyd, James T. Yurkovich, Bin Du, A...> ;Proceedings of the National Academy of Sciences of the United States of America. 2015 Aug 25
• 156 citations
  Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium
  Ryan A. LaCroix, Troy E. Sandberg, Edward J. O’Brien, José Utrilla, Ali Ebrahim, Gabriela I. Guzman, Richard Szubin, Bernhard O. Palsson, Adam M. Feist> ;Applied and Environmental Microbiology. 2015 Jan 1
• 112 citations
  Evolution of Escherichia coli to 42°C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations
  Troy E. Sandberg, Margit Pedersen, Ryan A. LaCroix, Ali Ebrahim, Mads Bonde, Markus J. Herrgård, Bernhard O. Palsson, Morten Otto Alexander Sommer, Adam M. Feist> ;Molecular Biology and Evolution. 2014 Oct 1
• 30 citations
  Minimal metabolic pathway structure is consistent with associated biomolecular interactions
  Aarash Bordbar, Harish Nagarajan, Nathan E. Lewis, Haythem Latif, Ali Ebrahim, Stephen Federowicz, Jan Schellenberger, Bernhard O. Palsson> ;Molecular Systems Biology. 2014 Jul 1
• 49 citations
  Determining the control circuitry of redox metabolism at the genome-scale.
  Stephen Federowicz, Donghyuk Kim, Ali Ebrahim, Joshua A. Lerman, Harish Nagarajan, Byung-Kwan Cho, Karsten Zengler, Bernhard O. Palsson> ;Plos Genetics. 2014 Apr 3
• 100 citations
  Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii
  Harish Nagarajan, Merve Sahin, Juan Nogales, Haythem Latif, Derek R. Lovley, Ali Ebrahim, Karsten Zengler> ;Microbial Cell Factories. 2013 Nov 25
• 641 citations
  COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
  Ali Ebrahim, Joshua A. Lerman, Bernhard O. Palsson, Daniel R. Hyduke> ;BMC Systems Biology. 2013 Aug 8
• 48 citations
  Sulfide-Driven Microbial Electrosynthesis
  Yanming Gong, Ali Ebrahim, Adam M. Feist, Mallory Embree, Tian Zhang, Derek R. Lovley, Karsten Zengler> ;Environmental Science & Technology. 2013 Jan 2
• Join now to see all

Journal Articles

• COBRAme: A Computational Framework for Genome-Scale Models of Metabolism and Gene Expression  
  Ali Ebrahim, Ali Ebrahim, PLoS One