Engineering at the limits of complexity with molecular-scale parts
DESIGNING PROTEINS WITH REDUCED TCELL EPITOPES THROUGH POLICY OPTIMIZATION
Ponnapati, M., Sinha, S., Lynch, B., Boyden, E.S. and Jacobson, J., 2025. Designing proteins with reduced T-cell epitopes through policy optimization. bioRxiv, pp.2025-09.
Accelerating Protein Molecular Dynamics Simulation with DeepJump
Costa, A.D.S., Ponnapati, M., Rubin, D., Smidt, T. and Jacobson, J., 2025. Accelerating Protein Molecular Dynamics Simulation with DeepJump. arXiv preprint arXiv:2509.13294.
CAMP: COMBINATORIAL ENGINEERING OF PROTEINS
Ponnapati, M., Sinha, S., Lynch, B., Boyden, E. and JACOBSON, J., CAMP: COMBINATORIAL ENGINEERING OF PROTEINS. In ICLR 2025 Workshop on Generative and Experimental Perspectives for Biomolecular Design.
RiboGen: RNA Sequence and Structure Co-Generation with Equivariant MultiFlow
Rubin, D., Costa, A. dos S., Ponnapati, M., & Jacobson, J. (2025). RiboGen: RNA Sequence and Structure Co-Generation with Equivariant Multiflow. AI for Nucleic Acids Workshop at ICLR 2025. Best Paper Award.
Design of a water-soluble transmembrane receptor kinase with intact molecular function by QTY code
Li, M., Tang, H., Qing, R. et al. Design of a water-soluble transmembrane receptor kinase with intact molecular function by QTY code. Nat Commun 15, 4293 (2024). https://doi.org/10.1038/s41467-024-48513-9
Study of glutamate transporters and their AF2 predicted water-soluble QTY variants and uncovering the natural mutations L->Q, I->T, F->Y,
Karago ̈l A, Karago ̈l T, Smorodina E, Zhang S (2024) Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F- >Y and Q->L, T->I and Y->F. PLoS ONE 19(4): e0289644.
Study of serotonin, dopamine, norepinephrine transporters and their AF2 predicted water-soluble QTY variants and uncovering natural mutation
Structural bioinformatics studies of six human ABC transporters and their AlphaFold2- predicted water-soluble QTY variants
QRB Discov. 2024 Jan 19;5:e1. doi: 10.1017/qrd.2024.2. PMID: 38577032; PMCID: PMC10988169.
Scalable biomimetic sensing system with membrane receptor dual-monolayer probe and graphene transistor arrays
Rui Qing, et al. "Scalable biomimetic sensing system with membrane receptor dual-monolayer probe and graphene transistor arrays." Science Advances. DOI: 10.1126/sciadv.adf1402
How to Grow (Almost) Anything: a Hybrid Distance Learning Model for Global Laboratory-Based Synthetic Biology Education
Perry, Eyal, et al. "How to grow (almost) anything: a hybrid distance learning model for global laboratory-based synthetic biology education." Nature Biotechnology (2022): 1-6.
Distillation of Language Model Semantics to Folded Three-Dimensional Protein Structures
Learning on knowledge graph dynamics provides an early warning of impactful research
Weis, J.W., Jacobson, J.M. Learning on knowledge graph dynamics provides an early warning of impactful research. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-00907-6
Non-full-length Water-Soluble CXCR4QTY and CCR5QTY Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Recepto
Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions
Chatterjee, P., Ponnapati, M., Kramme, C. et al. Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions. Commun Biol 3, 715 (2020). https://doi.org/10.1038/s42003-020-01470-7
A Cas9 with PAM recognition for adenine dinucleotides
An engineered ScCas9 with broad PAM range and high specificity and activity
QTY code designed thermostable and water-soluble chimeric chemokine receptors with tunable ligand affinity
Rui Qing, Qiuyi Han, Michael Skuhersky, Haeyoon Chung, Myriam Badr, View ORCID ProfileThomas Schubert, and Shuguang Zhang. PNAS first published November 27, 2019 (https://doi.org/10.1073/pnas.1909026116). Edited by Alan R. Fersht, University of Cambridge, Cambridge, United Kingdom, and approved October 30, 2019 (received for review May 24, 2019).
Minimal PAM specificity of a highly similar SpCas9 ortholog
Minimal PAM specificity of a highly similar SpCas9 ortholog
Chimeric CRISPR guides enhance Cas9 target specificity
Noah Jakimo, Pranam Chatterjee, Joseph M. Jacobson. Chimeric CRISPR guides enhance Cas9 target specificity, doi: https://doi.org/10.1101/147686
Genomic nucleic acid memory storage with directed endonucleases
Jakimo, N. "Genomic nucleic acid memory storage with directed endonuclease"
Language & tools for context-aware biology
Fracchia, C. "Language & tools for context-aware biology"
Exploration of Methods for Many-Site Genome Editing with MAGE
Sterling, B. "Exploration of Methods for Many-Site Genome Editing with MAGE"
Photoelectrochemical Synthesis of Low-Cost DNA Microarrays
Chow, B. "Photoelectrochemical Synthesis of Low-Cost DNA Microarrays"
Growing Machines
Griffith, S. "Growing Machines"
Nanostructure Fabrication by Electron and Ion Beam Patterning of Nanoparticles
Kong, D. "Nanostructure Fabrication by Electron and Ion Beam Patterning of Nanoparticles"
Printed Inorganic Transistors
Ridley, B. "Printed Inorganic Transistors"
The Design of a Molecular Assembly Line Based on Biological Molecules
Chow, B. "The Design of a Molecular Assembly Line Based on Biological Molecules"
Reverse-QTY code design of active human serum albumin self-assembled amphiphilic nanoparticles for effective anti-tumor drug doxorubicin...
Run Meng, Shilei Hao, Changfa Sun, Zongkun Hou, Yao Hou, Lili Wang, Peiying Deng, Jia Deng, Yaying Yang, Haijian Xia, Bochu Wang, Rui Qing, Shuguang Zhang. "Reverse-QTY code design of active human serum albumin self-assembled amphiphilic nanoparticles for effective anti-tumor drug doxorubicin release in mice." PNAS.