Ali Ebrahim
Ali Ebrahim
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COBRApy: constraints-based reconstruction and analysis for python
A Ebrahim, JA Lerman, BO Palsson, DR Hyduke
BMC systems biology 7 (1), 74, 2013
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
ZA King, J Lu, A Dräger, P Miller, S Federowicz, JA Lerman, A Ebrahim, ...
Nucleic acids research 44 (D1), D515-D522, 2016
Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways
ZA King, A Dräger, A Ebrahim, N Sonnenschein, NE Lewis, BO Palsson
PLoS computational biology 11 (8), e1004321, 2015
Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium
RA LaCroix, TE Sandberg, EJ O'Brien, J Utrilla, A Ebrahim, GI Guzman, ...
Applied and environmental microbiology 81 (1), 17-30, 2015
Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii
H Nagarajan, M Sahin, J Nogales, H Latif, DR Lovley, A Ebrahim, ...
Microbial cell factories 12 (1), 118, 2013
Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations
TE Sandberg, M Pedersen, RA LaCroix, A Ebrahim, M Bonde, ...
Molecular biology and evolution 31 (10), 2647-2662, 2014
Multi-omic data integration enables discovery of hidden biological regularities
A Ebrahim, E Brunk, J Tan, EJ O'brien, D Kim, R Szubin, JA Lerman, ...
Nature Communications 7, 13091, 2016
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
BJ Schmidt, A Ebrahim, TO Metz, JN Adkins, BØ Palsson, DR Hyduke
Bioinformatics 29 (22), 2900-2908, 2013
COBRAme: A computational framework for genome-scale models of metabolism and gene expression
CJ Lloyd, A Ebrahim, L Yang, ZA King, E Catoiu, EJ O’Brien, JK Liu, ...
PLoS computational biology 14 (7), e1006302, 2018
Sulfide-driven microbial electrosynthesis
Y Gong, A Ebrahim, AM Feist, M Embree, T Zhang, D Lovley, K Zengler
Environmental science & technology 47 (1), 568-573, 2012
Electrical detection of TATA binding protein at DNA-modified microelectrodes
AA Gorodetsky, A Ebrahim, JK Barton
Journal of the American Chemical Society 130 (10), 2924-2925, 2008
Model-driven discovery of underground metabolic functions in Escherichia coli
GI Guzmán, J Utrilla, S Nurk, E Brunk, JM Monk, A Ebrahim, BO Palsson, ...
Proceedings of the National Academy of Sciences 112 (3), 929-934, 2015
Determining the control circuitry of redox metabolism at the genome-scale
S Federowicz, D Kim, A Ebrahim, J Lerman, H Nagarajan, B Cho, ...
PLoS genetics 10 (4), e1004264, 2014
solveME: fast and reliable solution of nonlinear ME models
L Yang, D Ma, A Ebrahim, CJ Lloyd, MA Saunders, BO Palsson
BMC bioinformatics 17 (1), 391, 2016
Do genome‐scale models need exact solvers or clearer standards?
A Ebrahim, E Almaas, E Bauer, A Bordbar, AP Burgard, RL Chang, ...
Molecular systems biology 11 (10), 2015
Minimal metabolic pathway structure is consistent with associated biomolecular interactions
A Bordbar, H Nagarajan, NE Lewis, H Latif, A Ebrahim, S Federowicz, ...
Molecular systems biology 10 (7), 2014
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
JK Liu, C Lloyd, M Al-Bassam, A Ebrahim, JN Kim, C Olson, A Aksenov, ...
PLoS computational biology 15 (3), e1006848, 2019
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
L Yang, J Tan, EJ O’Brien, JM Monk, D Kim, HJ Li, P Charusanti, ...
Proceedings of the National Academy of Sciences 112 (34), 10810-10815, 2015
DynamicME: Dynamic simulation and refinement of integrated models of metabolism and protein expression
L Yang, A Ebrahim, CJ Lloyd, MA Saunders, BO Palsson
BMC systems biology 13 (1), 2, 2019
Principles of proteome allocation are revealed using proteomic data and genome-scale models
L Yang, JT Yurkovich, CJ Lloyd, A Ebrahim, MA Saunders, BO Palsson
Scientific reports 6, 36734, 2016
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