Ali Ebrahim

5.1k citations

28 papers · 3.0k indexed · 2 hit papers · h-index 19

Impact in

Molecular Biology top 2%
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Enzyme Catalysis and Immobilization
- Metabolomics and Mass Spectrometry Studies
- Viral Infectious Diseases and Gene Expression in Insects
Biomedical Engineering top 5%
- Biofuel production and bioconversion

Papers in ⓘ

Molecular Biology 21
- Microbial Metabolic Engineering and Bioproduction 18
- Gene Regulatory Network Analysis 9
- Bioinformatics and Genomic Networks 8
- Enzyme Catalysis and Immobilization 3
- Metabolomics and Mass Spectrometry Studies 2
Biomedical Engineering 6
- Biofuel production and bioconversion 5

Co-authors: Bernhard Ø. Palsson (18 shared papers)Joshua A. Lerman (4 shared papers)Daniel R. Hyduke (2 shared papers)Zachary A. King (3 shared papers)Nathan E. Lewis (3 shared papers)Andreas Dräger (3 shared papers)Stephen Federowicz (4 shared papers)Adam M. Feist (5 shared papers)
Journals: PLoS Computational Biology (4 papers)BMC Systems Biology (2 papers)Proceedings of the National Academy of Sciences (2 papers)Scientific Reports (1 paper)Journal of the American Chemical Society (1 paper)
Partner nations: United States Denmark Germany

In The Last Decade

Ali Ebrahim

28 papers receiving 3.0k citations

Hit Papers

align trajectories log scale

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models 2015 · 586 citations

Peers

Countries citing papers authored by Ali Ebrahim

Since Specialization

Citations

This map shows the geographic impact of Ali Ebrahim's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Ali Ebrahim with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Ali Ebrahim more than expected).

Fields of papers citing papers by Ali Ebrahim

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Ali Ebrahim. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Ali Ebrahim. The network helps show where Ali Ebrahim may publish in the future.

Co-authors

The 25 scholars most cited alongside Ali Ebrahim, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Ali Ebrahim Line = papers co-authored together Ali Ebrahim links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

Showing the 20 most-cited of 28 papers — load more, or switch the sort, to bring in the rest.

#	Work
1	COBRApy: COnstraints-Based Reconstruction and Analysis for Python BMC Systems Biology ·Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson, Daniel R. Hyduke Hit paper breakdown →	2013	841
2	BiGG Models: A platform for integrating, standardizing and sharing genome-scale models Nucleic Acids Research ·Zachary A. King, Justin S. Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard Ø. Palsson, Nathan E. Lewis Hit paper breakdown →	2015	586
3	Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways PLoS Computational Biology ·Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard Ø. Palsson	2015	247
4	Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium Applied and Environmental Microbiology ·Ryan A. LaCroix, Troy E. Sandberg, Edward J. O’Brien, José Utrilla, Ali Ebrahim, Gabriela I. Guzmán, Richard Szubin, Bernhard Ø. Palsson, Adam M. Feist	2014	192
5	Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii Microbial Cell Factories ·Harish Nagarajan, Merve Şahin, Juan Nogales, Haythem Latif, Derek R. Lovley, Ali Ebrahim, Karsten Zengler	2013	134
6	Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations Molecular Biology and Evolution ·Troy E. Sandberg, Margit Pedersen, Ryan A. LaCroix, Ali Ebrahim, Mads Bonde, Markus J. Herrgård, Bernhard Ø. Palsson, Morten Otto Alexander Sommer, Adam M. Feist	2014	127
7	Multi-omic data integration enables discovery of hidden biological regularities Nature Communications ·Ali Ebrahim, Elizabeth Brunk, Justin Tan, Edward J. O’Brien, Donghyuk Kim, Richard Szubin, Joshua A. Lerman, Anna Lechner, Anand V. Sastry, Aarash Bordbar, Adam M. Feist, Bernhard Ø. Palsson	2016	119
8	COBRAme: A computational framework for genome-scale models of metabolism and gene expression PLoS Computational Biology ·Colton J. Lloyd, Ali Ebrahim, Laurence Yang, Zachary A. King, Edward Catoiu, Edward J. O’Brien, Joanne K. Liu, Bernhard Ø. Palsson	2018	107
9	GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data Bioinformatics ·Brian J. Schmidt, Ali Ebrahim, Thomas Metz, Joshua Adkins, Bernhard Ø. Palsson, Daniel R. Hyduke	2013	93
10	Sulfide-Driven Microbial Electrosynthesis Environmental Science & Technology ·Yuehang Gong, Ali Ebrahim, Adam M. Feist, Mallory Embree, Tian Zhang, Derek R. Lovley, Karsten Zengler	2012	86
11	Electrical Detection of TATA Binding Protein at DNA-Modified Microelectrodes Journal of the American Chemical Society ·Alon A. Gorodetsky, Ali Ebrahim, Jacqueline K. Barton	2008	77
12	Model-driven discovery of underground metabolic functions in Escherichia coli Proceedings of the National Academy of Sciences ·Gabriela I. Guzmán, José Utrilla, Sergey Nurk, Elizabeth Brunk, Jonathan M. Monk, Ali Ebrahim, Bernhard Ø. Palsson, Adam M. Feist	2015	76
13	Determining the Control Circuitry of Redox Metabolism at the Genome-Scale PLoS Genetics ·Stephen Federowicz, Donghyuk Kim, Ali Ebrahim, Joshua A. Lerman, Harish Nagarajan, Byung-kwan Cho, Karsten Zengler, Bernhard Ø. Palsson	2014	53
14	Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen PLoS Computational Biology ·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	2019	49
15	DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression BMC Systems Biology ·Laurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard Ø. Palsson	2019	44
16	solveME: fast and reliable solution of nonlinear ME models BMC Bioinformatics ·Laurence Yang, Ding Ma, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard Ø. Palsson	2016	35
17	Minimal metabolic pathway structure is consistent with associated biomolecular interactions Molecular Systems Biology ·Aarash Bordbar, Harish Nagarajan, Nathan E. Lewis, Haythem Latif, Ali Ebrahim, Stephen Federowicz, Jan Schellenberger, Bernhard Ø. Palsson	2014	33
18	Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data Proceedings of the National Academy of Sciences ·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, Andreas Dräger, Alex Thomas, Yuekai Sun, Michael A. Saunders, Bernhard Ø. Palsson	2015	31
19	Principles of proteome allocation are revealed using proteomic data and genome-scale models Scientific Reports ·Laurence Yang, James T. Yurkovich, Colton J. Lloyd, Ali Ebrahim, Michael A. Saunders, Bernhard Ø. Palsson	2016	26
20	ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions PLoS ONE ·Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, José Utrilla, Karsten Zengler, Bernhard Ø. Palsson	2018	14

About Ali Ebrahim

Ali Ebrahim is a scholar working on Molecular Biology, Biomedical Engineering, Genetics, Obstetrics and Gynecology and Surgery, having authored 28 papers that have together received 3.0k indexed citations. Recurring topics across this work include Microbial Metabolic Engineering and Bioproduction (18 papers), Gene Regulatory Network Analysis (9 papers), Bioinformatics and Genomic Networks (8 papers), Biofuel production and bioconversion (5 papers), Enzyme Catalysis and Immobilization (3 papers), Bacterial Genetics and Biotechnology (2 papers), Pregnancy and preeclampsia studies (2 papers) and Metabolomics and Mass Spectrometry Studies (2 papers). The work is most often cited by research in Molecular Biology (2.6k citations), Biomedical Engineering (956 citations), Genetics (387 citations), Renewable Energy, Sustainability and the Environment (165 citations) and Environmental Engineering (133 citations). Ali Ebrahim has collaborated with scholars based in United States, Denmark and Germany. Frequent co-authors include Bernhard Ø. Palsson, Joshua A. Lerman, Daniel R. Hyduke, Zachary A. King, Nathan E. Lewis, Andreas Dräger, Stephen Federowicz, Adam M. Feist, Philip Miller and Edward J. O’Brien. Their work appears in journals such as PLoS Computational Biology, BMC Systems Biology, Proceedings of the National Academy of Sciences, Scientific Reports and Journal of the American Chemical Society.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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