TheBioMLClinic

TheBioMLClinic

TheBioMLClinic

Unsolved Problems

Unsolved Problems

Unsolved Problems

Capsid Fitness and Manufacturability

→ Simon Pacouret, …, Fatma Elzahraa Eid, Andrew Barry, Yujia Alina Chan, Ken Chan, Benjamin Deverman. A Modular Capsid Engineering Platform to Confer Neutralizing Antibody Evasion to CNS and muscle targeted AAVs. ASGCT, 2026.


→ Benjamin Deverman, Simon Pacouret, Fatma Elzahraa Eid. Engineered viral capsids with increased stability and methods of use thereof. US Patent App, 18/950,128, 2025.


→ Benjamin Deverman, Fatma Elzahraa Eid, Ken Chan. Adeno-associated viral vectors and uses thereof. US Patent App, 18/940,565, 2025.


→ Ken Chan, Benjamin Deverman, Fatma Elzahraa Eid. Adeno-associated viral vectors and uses thereof. US Patent App, 18/834,583, 2025.


→ Fatma Elzahraa Eid, Albert T Chen, Ken Y Chan, …, Benjamin E Deverman. Systematic multi-trait AAV capsid engineering for efficient gene delivery. Nature Communications, 2024.


→ Fatma Elzahraa Eid, Albert Chen, Ken Chan, Qin Huang, …, Benjamin E Deverman. The Machine Learning-Guided Fit4Function Platform Quantitatively Profiles the Biodistribution of Peptide-Modified AAV Capsids after a Single Round of Screening in Macaque. ASGCT, 2023.


→ Simon Pacouret, Fatma Elzahraa Eid, William Donahoe, Ken Y Chan, Jason Wu, Qingxia Zheng, Casey Keyes, Pamela Brauer, Albert Chen, Yujia A Chan, Benjamin Deverman. Development of Stabilized AAV Capsids for Vector Engineering. ASGCT, 2023.


→ Fatma Elzahraa Eid, Ken Y Chan, Albert T Chen, Qin Huang, …, Benjamin E Deverman. Fit4Function: A Machine Learning-Guided Approach for Systematic Multi-Trait AAV Capsid Engineering. ASGCT, 2022.


→ Fatma Elzahraa Eid, Ken Chan, Albert T Chen, Isabelle G Tobey, Qin Huang, Qingxia Zheng, Yujia Alina Chan, Ben Deverman. Machine Learning-Accelerated AAV Engineering through the Generation of Production-Fit Capsid Libraries. ASGCT, 2021.


→ Benjamin Deverman, Fatma Elzahraa Eid, Ken Chan. Machine learning accelerated protein engineering through fitness prediction. US Patent App, 17/244,774, 2021.


Receptor-Mediated and Targeted Discovery

→ Fatma Elzahraa Eid. ReceptorFit: Receptor-informed, programmable design of AAV capsid insertion peptides. ASGCT, 2026.


→ Ken Chan, Chin-Yen Lin, Simon Pacouret, Qin Huang, …, Fatma Elzahraa Eid, Jarrett Rios, Yujia Alina Chan, Benjamin Deverman. Second Generation Human Transferrin Receptor Targeted AAV Capsids With Enhanced CNS Tropisms and Liver Detargeting In Vivo. ASGCT, 2025.


→ Benjamin Deverman, Qin Huang, Ken Chan, Andrew Barry, Fatma Elzahraa Eid. AAV capsids that enable CNS-wide gene delivery through interactions with the transferrin receptor. US Patent App, 19/020,432, 2025.


→ Benjamin Deverman, Qin Huang, Ken Chan, Andrew Barry, Fatma Elzahraa Eid. AAV capsids that enable CNS-wide gene delivery through interactions with the transferrin receptor. US Patent App, 63/621,839, 2025.


→ Qin Huang, Ken Y Chan, …, Fatma Elzahraa Eid, Yujia A Chan, Benjamin E Deverman. An AAV capsid reprogrammed to bind human transferrin receptor mediates brain-wide gene delivery. Science, 2024.


→ Ken Y Chan, Qin Huang, …, Fatma Elzahraa Eid, Yujia A Chan, Benjamin E Deverman. Second Generation AAV Capsids Reprogrammed to Bind Human Transferrin Receptor are Targeted to the Brain and De-Targeted from the Liver in Human TFRC Knock-In Mice. ASGCT, 2024.


→ Nuria Roxana Botticello-Romero, Jason Wu, Qin Huang, Thomas Beddow, Ken Y Chan, Pamela Brauer, Fatma Elzahraa Eid, Alina Chan, Benjamin E Deverman. Human CA4-Targeting AAV Capsids Efficiently Transduce the CNS in Humanized Mice. ASGCT, 2024.


→ Qin Huang, Albert T Chen, Ken Y Chan, …, Fatma Elzahraa Eid, …, Benjamin E Deverman. Targeting AAV vectors to the central nervous system by engineering capsid–receptor interactions that enable crossing of the blood–brain barrier. PLoS biology, 2023.


→ Andrew J Barry, Fatma Elzahraa Eid, Ken Y Chan, Qin Huang, Jencilin Johnston, Benjamin E Deverman. Generative Networks Create Novel Receptor Targeted AAVs with Only 1,200 Training Examples. ASGCT, 2023.


→ Ken Y Chan, Qin Huang, …, Fatma Elzahraa Eid, Yujia A Chan, Benjamin E Deverman. AAV-Mediated CNS-Wide Gene Delivery via a De Novo Engineered Capsid-Human Receptor Interaction. ASGCT, 2023.


→ Qin Huang, Albert T Chen, Ken Y Chan, …, Fatma Elzahraa Eid, …, Benjamin E Deverman. Targeting AAV vectors to the CNS via de novo engineered capsid-receptor interactions. bioRxiv, 2022.

Multi-Trait Engineering

→ Fatma Elzahraa Eid, Albert T Chen, Ken Y Chan, …, Benjamin E Deverman. Systematic multi-trait AAV capsid engineering for efficient gene delivery. Nature Communications, 2024.


→ Fatma Elzahraa Eid, Ken Y Chan, Albert T Chen, Qin Huang, …, Benjamin E Deverman. Fit4Function: A Machine Learning-Guided Approach for Systematic Multi-Trait AAV Capsid Engineering. ASGCT, 2022.


AAV immunogenicity

→ Simon Pacouret, Ken Chan, …, Fatma Elzahraa Eid, Andrew Barry, Yujia Alina Chan, Benjamin Deverman. Antibody-evading AAV capsids compatible with CNS and muscle-targeting modifications. ASGCT, 2025.


→ Simon Pacouret, …, Fatma Elzahraa Eid, Andrew J Barry, Yujia A Chan, Ken Y Chan, Benjamin E Deverman. Engineering Human CNS Receptor-Targeted Capsids for Improved Antibody Evasion. ASGCT, 2024.


→ Simon Pacouret, Ken Y Chan, Fatma Elzahraa Eid, …, Benjamin E Deverman. Developing Blood-Brain Barrier-Crossing AAV9 Variants with Reduced Sensitivity to Neutralizing Antibodies. ASGCT, 2023.


ML for Protein Applications

→ Fatma Elzahraa Eid, Mahmoud ElHefnawi, Lenwood S Heath. DeNovo: virus-host sequence-based protein–protein interaction prediction. Bioinformatics, 2015.


→ Junjie Zhu, Fatma Elzahraa Eid, Lu Tong, Wan Zhao, Wei Wang, Lenwood S Heath, Le Kang, Feng Cui. Characterization of protein–protein interactions between rice viruses and vector insects. Insect Science, 2021.

Auditing bioML for Generalization

→ Fatma Elzahraa Eid, Haitham A Elmarakeby, Yujia Alina Chan, …, Lenwood S Heath, Kasper Lage. Systematic auditing is essential to debiasing machine learning in biology. Communications biology, Nature Publishing Group, 2021.


Current Programs


→ Transferability Across Species

→ Dual-loop and Long-length/ High-Burden Capsid Engineering

→ Multi-trait/ Cross-species AAV Engineering from Disjoint Screens

→ Affordable AAV-ML from Hisotrical and Noisy Screens



→ Transferability Across Species

→ Dual-loop and Long-length/ High-Burden Capsid Engineering

→ Multi-trait/ Cross-species AAV Engineering from Disjoint Screens

→ Affordable AAV-ML from Hisotrical and Noisy Screens


→ Learn More


→ Learn More