| COBRApy: constraints-based reconstruction and analysis for python A Ebrahim, JA Lerman, BO Palsson, DR Hyduke BMC systems biology 7 (1), 74, 2013 | 1238 | 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 | 947 | 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 | 401 | 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 | 261 | 2015 |
| 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 | 185 | 2014 |
| 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 | 181 | 2013 |
| 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 | 171 | 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 | 165 | 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 | 156 | 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 | 116 | 2012 |
| 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 | 111 | 2015 |
| 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 | 110 | 2008 |
| 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 | 84 | 2014 |
| 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 | 64 | 2015 |
| 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 | 59 | 2016 |
| 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 | 57 | 2014 |
| 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 | 55 | 2019 |
| 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 | 54 | 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 | 46 | 2015 |
| 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 | 44 | 2016 |
Joshua A. LermanDirector of Computation, Bota BiosciencesVerified email at bota.bio
