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Mohamed Embaby, PhD

Animal Scientist · Ruminant Nutrition & Agricultural AI

[email protected] Davis, California Google Scholar ORCID LinkedIn

Profile

Animal scientist and ruminant nutritionist studying enteric methane and rumen fermentation, and co-developing deep-learning tools that quantify livestock greenhouse-gas emissions from optical gas imaging. Postdoctoral fellow at the CLEAR Center, UC Davis; Fulbright scholar; co-investigator on USDA-NIFA projects bridging animal science and artificial intelligence.

Present Appointment

2025 - nowPostdoctoral Fellow - CLEAR Center (Clarity & Leadership for Environmental Awareness and Research), University of California, Davis

Previous Appointments

2024 - 2025Postdoctoral Fellow, Department of Animal Science - Southern Illinois University, Carbondale
2015 - 2023Research Assistant, Animal-Nutrition Laboratory, Dairy Science Dept. - National Research Centre, Egypt
2009 - 2015Statistician, Centre of Social & Demographic Studies - Central Agency for Public Mobilization and Statistics (CAPMAS), Egypt
ConsultancyConsultant, Civil-Registration & Vital-Statistics - League of Arab States

Education

2024PhD, Agricultural Sciences - Southern Illinois University, Carbondale. Dissertation: Effect of bromoform on enteric methane and rumen fermentation characteristics.
2018M.Sc., Animal Science - Southern Illinois University, Carbondale. Thesis: Effects of unconventional plant oils and rumen adaptation on methane-gas emission and rumen fermentation characteristics.
2014M.Sc., Geoinformation in Environmental Management - Mediterranean Agronomic Institute of Chania (MAICH), Greece
DiplomaInternational Diploma, GIS for Development - EPHE, Sorbonne, Paris
2008B.Sc., Agriculture (Animal Production) - Fayoum University, Egypt

Grants

Honors & Awards

Publications

Peer-reviewed journal articles

  1. Embaby, M.G., Sarker, T.T., AbuGhazaleh, A., & Ahmed, K.R. (2025). Optical gas imaging and deep learning for quantifying enteric methane emissions from rumen fermentation in vitro. IET Image Processing, 19(1), e13327.
  2. Lakhssassi, N., El Baze, A., Knizia, D., …, Embaby, M.G., …, Shi, H. (2024). A sucrose-binding protein and β-conglycinins regulate soybean seed protein content and control multiple seed traits. Plant Physiology, 196(2), 1298-1321.
  3. Knizia, D., Bellaloui, N., Yuan, J., …, Embaby, M., …, Meksem, K. (2023). Quantitative trait loci and candidate genes that control seed-sugar contents in the soybean 'Forrest' × 'Williams 82' RIL population. Plants, 12(19), 3498.
  4. Sufyan, A., Ahmad, N., Shahzad, F., Embaby, M.G., AbuGhazaleh, A., & Khan, N.A. (2022). Improving the nutritional value and digestibility of wheat straw, rice straw, and corn cob through solid-state fermentation using different Pleurotus species. Journal of the Science of Food and Agriculture, 102(6), 2445-2453.
  5. Lakhssassi, N., Lopes-Caitar, V.S., Knizia, D., …, Embaby, M.G., … (2021). TILLING-by-Sequencing+ reveals the role of novel fatty-acid desaturases (GmFAD2-2s) in increasing soybean seed oleic-acid content. Cells, 10(5), 1245.
  6. Lakhssassi, N., Zhou, Z., Cullen, M.A., …, Embaby, M.G., …, Neves, L.G. (2021). TILLING-by-Sequencing+ to decipher the oil-biosynthesis pathway in soybeans. International Journal of Molecular Sciences, 22(8), 4219.
  7. Zhou, Z., Lakhssassi, N., Knizia, D., …, Embaby, M.G., … (2021). Genome-wide identification and analysis of the soybean acyl-ACP thioesterase gene family reveals the role of GmFAT. Theoretical and Applied Genetics, 134(11), 3611-3623.
  8. Lakhssassi, N., Zhou, Z., Liu, S., …, Embaby, M.G., … (2020). Soybean TILLING-by-Sequencing+ reveals the role of novel GmSACPD members in unsaturated fatty-acid biosynthesis while maintaining healthy nodules. Journal of Experimental Botany, 71(22), 6969-6987.
  9. Aboragah, A., Embaby, M., Günal, M., & AbuGhazaleh, A. (2020). Effect of alkaline and sonication pretreatments on the rumen degradability of date-palm seeds. Tropical Animal Health and Production, 52(2), 771-776.
  10. Alghamdi, F., Embaby, M.G., Günal, M., & AbuGhazaleh, A. (2020). Analysis of the omega-3 fatty-acid content in commercial omega-3 supplements in Arab Gulf countries. American Journal of Animal and Veterinary Sciences, 15(4).
  11. Embaby, M.G., Günal, M., & AbuGhazaleh, A. (2019). Effect of unconventional oils on in vitro rumen methane production and fermentation. Ciencia e Investigación Agraria, 46(3), 276-285.
  12. Embaby, M.G., Günal, M., & Amer, A. (2019). Effect of rumen-culture adaptation to Origanum vulgare L. essential oil on rumen methane and fermentation. American Journal of Animal and Veterinary Sciences, 14(3), 169-190.
  13. Alani, M.F., Embaby, M.G., Joshi, P., Pahariya, P., & Choudhary, R. (2025). Effects of packaging materials and ventilation placement on strawberry shelf-life. International Journal on Food, Agriculture and Natural Resources, 6(2), 8-14.

Conference proceedings & abstracts

  1. Sarker, T.T., Embaby, M., Islam, T., AbuGhazaleh, A., & Ahmed, K.R. (2025). GasTwinFormer: A hybrid vision transformer for livestock methane-emission segmentation and dietary classification in optical gas imaging. Proc. IEEE/CVF ICCV, 2787-2796.
  2. Sarker, T.T., Embaby, M.G., Ahmed, K.R., & AbuGhazaleh, A. (2024). Gasformer: A transformer-based architecture for segmenting methane emissions from livestock in optical gas imaging. Proc. IEEE/CVF CVPR, 5489-5497.
  3. Islam, T., Sarker, T.T., Embaby, M., Ahmed, K.R., & AbuGhazaleh, A. (2025). CarboFormer: A lightweight semantic-segmentation architecture for efficient CO₂ detection using optical gas imaging. Int. Symposium on Visual Computing (ISVC), 3-15.
  4. Embaby, M., Handlos, G., & AbuGhazaleh, A. (2025). The effect of adding different levels of bromoform on enteric methane and rumen fermentation using a continuous-culture system in vitro. Journal of Animal Science, 103(Suppl. 3), 636-637.
  5. Grey, K.R., Embaby, M., Handlos, G., & AbuGhazaleh, A. (2024). The effect of the partial inclusion of non-forage fiber sources (NFFS) on methane production and rumen fermentation. Journal of Animal Science, 102(Suppl. 3), 777.
  6. Bien, R.A., Kaplan, D., Embaby, M., …, Nair, J. (2023). Effects of strategic blending of food-industry by-products with canola meal on in vitro and in situ fermentation and nutrient degradation. Journal of Animal Science, 101.
  7. Kaplan, D., Bien, R.A., Embaby, M., …, Nair, J. (2023). Effects of inoculation of alfalfa hay with Pediococcus pentosaceus and α-amylase on hay temperature, microbial ecology, nutrient composition, and feed value. Journal of Animal Science, 101(Suppl. 3), 385-386.
  8. Lakhssassi, N., Caitar, V., Knizia, D., …, Embaby, M., … (2022). An alternative fatty-acid pathway involving novel GmFAD2-2 members to increase seed oleic acid in soybeans. Plant & Animal Genome XXIX Conference.
  9. Lakhssassi, N., Zhou, Z., Cullen, M.A., …, Embaby, M.G., Meksem, K. (2020). TILLING by target-exome-capture sequencing as a new and effective platform for gene functional analysis. Plant & Animal Genome XXVIII Conference.
  10. Aboragah, A., Embaby, M., & AbuGhazaleh, A. (2019). The effect of ultrasound processing and exogenous cellulase supplementation on the ruminal degradability of palm date. Journal of Dairy Science, 102 (Suppl.), 375.
  11. Aboragah, A., Embaby, M., & AbuGhazaleh, A. (2019). The rumen degradability of palm-date seeds treated with sodium hydroxide and ultrasound processing. Journal of Dairy Science, 102 (Suppl.), 228.

Preprints

  1. Islam, T., Sarker, T.T., Embaby, M., Ahmed, K.R., & AbuGhazaleh, A. (2026). FUME: Fused Unified Multi-Gas Emission Network for livestock rumen-acidosis detection. arXiv:2601.08205.
  2. Islam, T., Lakhssassi, A., Sarker, T.T., Embaby, M., Ahmed, K.R., & AbuGhazaleh, A. (2026). TRACE: Thermal Recognition Attentive-Framework for CO₂ emissions from livestock. arXiv:2604.09648.
  3. Islam, T., Sarker, T.T., Embaby, M.G., Ahmed, K.R., & AbuGhazaleh, A. (2025). CarboNeXT and CarboFormer: Dual semantic-segmentation architectures for detecting and quantifying CO₂ emissions using optical gas imaging. arXiv:2506.05360.

Theses

  1. Embaby, M. (2024). Effect of bromoform on enteric methane and rumen fermentation characteristics. PhD Dissertation, Southern Illinois University Carbondale.
  2. Embaby, M. (2018). Effects of unconventional plant oils and rumen adaptation on methane-gas emission and rumen fermentation characteristics. M.Sc. Thesis, Southern Illinois University Carbondale.

Laboratory Techniques

Gas chromatography (CH₄, VFA, fatty acids)LECO protein analyzerAtomic absorption ANKOM RF · Daisy incubatorFiber & fat-extraction systemsIn vitro batch culture In vitro continuous cultureProtein / fiber / VFA / ammonia analysisDNA extraction PCRBasic microbiology

Selected Conferences & Training

Curriculum vitae · Mohamed Embaby, PhD · last updated