Biography and Research Information
OverviewAI-generated summary
Ibrahim Farag's research investigates microbial communities, focusing on their diversity, evolution, and ecological roles, particularly within challenging environments. His work has explored the symbiotic relationships between bacteria and archaea in groundwater ecosystems, revealing site-specific diversity patterns. Farag has also studied microbial communities in environments analogous to early Earth, examining sulfur cycling and the evolution of microbial life. His research extends to the evolutionary trajectories of specific bacterial groups, such as the Candidate Phyla Radiation (CPR) bacteria, and their association with animals. He has also characterized novel phyla, like the "Sifarchaeota," identified in sediment samples and shown to possess unique metabolic capabilities, including polysaccharide degradation and anaerobic methylotrophy.
Further investigations by Farag include the occurrence and genomes of "Candidatus Patescibacteria" in marine sediments and the metabolic potential of specific bacteria, such as *Leptothrix ochracea*, for mixotrophic growth on iron and carbon. His work also contributes to understanding microbial roles in biogeochemical cycles, such as the anaerobic oxidation of methane in oceanic carbonates. Farag has also published on the impact of dietary supplements on animal growth and biochemical parameters, indicating a breadth of research interests that include applied aspects of microbial and nutritional science. With a significant publication record, including 103 publications and 2,337 citations, Farag is recognized as a highly cited researcher.
Metrics
- h-index: 20
- Publications: 103
- Citations: 2,344
Selected Publications
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ColiFormer: A Transformer-Based Codon Optimization Model Balancing Multiple Objectives for Enhanced <i>E. coli</i> Gene Expression (2025)
Collaboration Network
Top Collaborators
Jennifer F. Biddle
University of Delaware (US)
9 shared publications
- “ <i>Sifarchaeota</i> ,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy
- Occurrence, Diversity, and Genomes of “ <i>Candidatus</i> Patescibacteria” along the Early Diagenesis of Marine Sediments
- Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean
- Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments
- Reference library for microbial source tracking in the mid-Atlantic United States
Showing 5 of 9 shared publications
Malique Bowen
University of Delaware (US)
6 shared publications
- Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments
- Reference library for microbial source tracking in the mid-Atlantic United States
- Identifying potential introduced and natural sources of pollution in Delaware watersheds
- Taming the uncultured: Modeling microbial life under very low redox potential in the subsurface and deep-sea biosphere
- Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments
Showing 5 of 6 shared publications
Sabrina Beckmann
Oklahoma State University Oklahoma City (US)
4 shared publications
- Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean
- Taming the uncultured: Modeling microbial life under very low redox potential in the subsurface and deep-sea biosphere
- TAMING THE UNCULTURED: MODELING MICROBIAL LIFE UNDER VERY LOW REDOX POTENTIAL IN THE SUBSURFACE AND DEEP-SEA BIOSPHERE
- TAMING THE UNCULTURED: MODELING MICROBIAL LIFE UNDER VERY LOW REDOX POTENTIAL IN THE SUBSURFACE AND DEEP-SEA BIOSPHERE
Dalia Aboelhassan
National Research Centre (EG)
4 shared publications
- Impact of Spirulina platensis as a Dietary Supplement on Growth Performance, Blood Biochemical Parameters, and Expression of Growth-Related Genes in Nile Tilapia (Oreochromis niloticus)
- Comparative Study for FABP7, TPD52L1, NCOA7, GJA1, and ASF1A mRNA Expressions in Four Chicken Breeds and Their Relationship with Carcass Traits
- Effect of ethanolic extract of Fagonia cretica on BPA induced genotoxicity and histopathology in brain and testis tissues of rats
- Nutritional Effect of Using a Bioactive Mixture (Lemon, Onion and Garlic) on Growth Performances, Feed Utilization, Immune Status and Gene Expression of Nile tilapia (Oreochromis niloticus)
Christine He
University of California, Berkeley (US)
3 shared publications
- Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
- Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria
- Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria
Ray Keren
University of California, Berkeley (US)
3 shared publications
- Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
- Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria
- Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria
Jillian F. Banfield
University of California, Berkeley (US)
3 shared publications
- Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
- Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria
- Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria
Rui Zhao
University of Delaware (US)
3 shared publications
- “ <i>Sifarchaeota</i> ,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy
- Occurrence, Diversity, and Genomes of “ <i>Candidatus</i> Patescibacteria” along the Early Diagenesis of Marine Sediments
- Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean
Nancy G. Prouty
United States Geological Survey (US)
3 shared publications
- Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean
- Taming the uncultured: Modeling microbial life under very low redox potential in the subsurface and deep-sea biosphere
- TAMING THE UNCULTURED: MODELING MICROBIAL LIFE UNDER VERY LOW REDOX POTENTIAL IN THE SUBSURFACE AND DEEP-SEA BIOSPHERE
C. Ryan Hahn
Oklahoma State University (US)
3 shared publications
- Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality
- Microbial diversity and sulfur cycling in an early earth analogue: From ancient novelty to modern commonality
- Microbial diversity in an early earth analogue: From ancient novelty to modern commonality
Chelsea L. Murphy
Oklahoma State University (US)
3 shared publications
- Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality
- Microbial diversity and sulfur cycling in an early earth analogue: From ancient novelty to modern commonality
- Microbial diversity in an early earth analogue: From ancient novelty to modern commonality
Mircea Podar
University of Tennessee at Knoxville (US)
3 shared publications
- Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality
- Microbial diversity and sulfur cycling in an early earth analogue: From ancient novelty to modern commonality
- Microbial diversity in an early earth analogue: From ancient novelty to modern commonality
Mostafa S. Elshahed
Oklahoma State University (US)
3 shared publications
- Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality
- Microbial diversity and sulfur cycling in an early earth analogue: From ancient novelty to modern commonality
- Microbial diversity in an early earth analogue: From ancient novelty to modern commonality
Noha H. Youssef
Oklahoma State University (US)
3 shared publications
- Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality
- Microbial diversity and sulfur cycling in an early earth analogue: From ancient novelty to modern commonality
- Microbial diversity in an early earth analogue: From ancient novelty to modern commonality
Inas S. Ghaly
3 shared publications
- Impact of Spirulina platensis as a Dietary Supplement on Growth Performance, Blood Biochemical Parameters, and Expression of Growth-Related Genes in Nile Tilapia (Oreochromis niloticus)
- Comparative Study for FABP7, TPD52L1, NCOA7, GJA1, and ASF1A mRNA Expressions in Four Chicken Breeds and Their Relationship with Carcass Traits
- Effect of ethanolic extract of Fagonia cretica on BPA induced genotoxicity and histopathology in brain and testis tissues of rats
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