Match tier
Listed
Presence
Current · Arkansas
Last published
2026
Sources
OpenAlex · ORCID
Refreshed
2026-10-05
Biography and Research Information
OverviewAI-generated summary
Ibrahim Farag's research focuses on microbial ecology and evolution, particularly investigating the diversity and function of microbial communities in various ecosystems. His work often employs genome-resolved metagenomics to uncover the genetic makeup and evolutionary trajectories of bacteria and archaea, including those from challenging environments like groundwater and marine sediments. Farag has published on novel phyla, such as "Sifarchaeota," and explored the genomic characteristics that facilitate animal associations in Candidate Phyla Radiation bacteria.
His research extends to understanding microbial roles in biogeochemical cycles, such as sulfur cycling and methane oxidation. Farag also investigates specific microbial lineages, including "Candidatus Patescibacteria" and *Leptothrix ochracea*, examining their metabolic capabilities and evolutionary adaptations. Additionally, his publication record includes studies on the impact of dietary supplements on animal physiology, indicating a breadth of research interests that intersect with environmental microbiology and animal science.
Metrics
- h-index: 20
- Publications: 103
- Citations: 2,344
Positions
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Postdoctoral ScholarUniversity of Delaware School of Marine Science and Policy ORCID
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Postdoctoral ScholarUniversity of Arkansas for Medical Sciences ORCID
Selected Publications
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ColiFormer: A Transformer-Based Codon Optimization Model Balancing Multiple Objectives for Enhanced E. coli Gene Expression (2026)
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ColiFormer: A Transformer-Based Codon Optimization Model Balancing Multiple Objectives for Enhanced E. coli Gene Expression (2025)
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Metagenomics elucidates how biogenic methanogenesis may increase in CO 2 -injected petroleum wells (2025)
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Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments (2025)
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Correction for Tothero et al., “ Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon” (2024)
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Identifying potential introduced and natural sources of pollution in Delaware watersheds (2024)
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Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon (2024)
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Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments (2024)
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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) (2024)
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TAMING THE UNCULTURED: MODELING MICROBIAL LIFE UNDER VERY LOW REDOX POTENTIAL IN THE SUBSURFACE AND DEEP-SEA BIOSPHERE (2023)
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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) (2023)
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Reference library for microbial source tracking in the mid-Atlantic United States (2023)
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Comparative Study for FABP7, TPD52L1, NCOA7, GJA1, and ASF1A mRNA Expressions in Four Chicken Breeds and Their Relationship with Carcass Traits (2023)
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Association of Genetic Polymorphisms of POU1F1 Gene on Twin Production in Egyptian Sheep and Goats (2022)
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Taming the uncultured: Modeling microbial life under very low redox potential in the subsurface and deep-sea biosphere (2022)
Collaboration Network
Top Collaborators
Amr Badr
26 shared publications
- A Nested Genetic Algorithm for feature selection in high-dimensional cancer Microarray datasets
- Arabic document layout analysis
- Towards a Spiking Neural P Systems OS
- A Hybrid Artificial Immune Genetic Algorithm with Fuzzy Rules for Breast Cancer Diagnosis
- An Auto-Recommender Based Intelligent E-Learning System
Showing 5 of 26 shared publications
Jennifer F. Biddle
University of Delaware (US)
15 shared publications
- Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments
- “ Sifarchaeota ,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy
- Occurrence, Diversity, and Genomes of “ Candidatus 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
Showing 5 of 15 shared publications
Noha H. Youssef
Oklahoma State University (US)
12 shared publications
- In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)
- Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)
- Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’
- Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage
- Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)
Showing 5 of 12 shared publications
Mostafa S. Elshahed
Oklahoma State University (US)
12 shared publications
- Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)
- Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’
- Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage
- Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)
- The Wood–Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1)
Showing 5 of 12 shared publications
Mohammad Nassef
11 shared publications
- A Nested Genetic Algorithm for feature selection in high-dimensional cancer Microarray datasets
- Multistage feature selection approach for high-dimensional cancer data
- Fractional canny edge detection for biomedical applications
- Fractional edge detection based on genetic algorithm
- Radiographic Images Fractional Edge Detection Based on Genetic Algorithm
Showing 5 of 11 shared publications
Rui Zhao
Massachusetts Institute of Technology (US)
8 shared publications
- Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments
- “ Sifarchaeota ,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy
- Occurrence, Diversity, and Genomes of “ Candidatus 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
- “Sifarchaeota” a novel Asgard phylum capable of polysaccharide degradation and anaerobic methylotrophy
Showing 5 of 8 shared publications
Christine He
Innovative Genomics Institute (US)
7 shared publications
- Clades of huge phages from across Earth’s ecosystems
- Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
- Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog
- Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria
- Clades of huge phage from across Earth’s ecosystems
Showing 5 of 7 shared publications
Emad Nabil
Cairo University (EG)
6 shared publications
- A Novel Neural Network Method for Face Recognition With a Single Sample Per Person
- A Hybrid Artificial Immune Genetic Algorithm with Fuzzy Rules for Breast Cancer Diagnosis
- An Immuno-Genetic Hybrid Algorithm
- A MEMBRANE-IMMUNE ALGORITHM FOR SOLVING THE MULTIPLE 0/1 KNAPSACK PROBLEM
- A P system design using clonal selection algorithm
Showing 5 of 6 shared publications
Ray Keren
University of California, Berkeley (US)
6 shared publications
- Clades of huge phages from across Earth’s ecosystems
- 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
- Clades of huge phage from across Earth’s ecosystems
- Huge and variable diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
Showing 5 of 6 shared publications
Sabrina Beckmann
Oklahoma State University Oklahoma City (US)
6 shared publications
- Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean
- Evidence for an expanded repertoire of electron acceptors for the anaerobic oxidation of methane in authigenic carbonates in the Atlantic and Pacific Ocean
- Nitrate dependent anaerobic oxidation of methane drives the carbon cycle in authigenic carbonates along the Atlantic and Pacific Margin
- 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
Showing 5 of 6 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
C. Ryan Hahn
Oklahoma State University (US)
5 shared publications
- Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality
- Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics
- Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities
- 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
Yuki Amano
Japan Atomic Energy Agency (JP)
5 shared publications
- Clades of huge phages from across Earth’s ecosystems
- Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog
- Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria
- Clades of huge phage from across Earth’s ecosystems
- Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria
Chelsea L. Murphy
Oklahoma State University (US)
5 shared publications
- Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage
- Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality
- Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage
- 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
Jillian F. Banfield
Planetary Science Institute (US)
5 shared publications
- Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
- Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog
- Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria
- Huge and variable 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 CPR bacteria
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