Ebrahim, Ali

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013) · BMC Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 1,378

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., Ebrahim, A., Palsson, B. O., & Lewis, N. E. (2016) · Nucleic Acids Research

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 938

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

Nagarajan, H., Sahin, M., Nogales, J., Latif, H., Lovley, D. R., Ebrahim, A., & Zengler, K. (2013) · Microbial Cell Factories

Microbial Metabolic Engineering and BioproductionBiofuel production and bioconversion

Cited by 170

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Lloyd, C. J., Ebrahim, A., Yang, L., King, Z. A., Catoiu, E., O’Brien, E. J., Liu, J. K., & Palsson, B. O. (2018) · PLOS Computational Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 167

Multi-omic data integration enables discovery of hidden biological regularities

Ebrahim, A., Brunk, E., Tan, J., O'Brien, E. J., Kim, D., Szubin, R., Lerman, J. A., Lechner, A., Sastry, A., Bordbar, A., et al. (2016) · Nature Communications

Bioinformatics and Genomic NetworksMicrobial Metabolic Engineering and Bioproduction

Cited by 155

Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, A., Famili, I., Feist, A. M., Fleming, R. M., et al. (2015) · Molecular Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 57