Pranam D. Chatterjee

Research Themes

Computational Modeling of Biological Systems, Drug & Gene Delivery, Synthetic & Systems Biology, Tissue Engineering & Regenerative Medicine

Research Interests

Integration of computational and experimental methodologies to design novel proteins for applications in genome editing, targeted protein modulation, and reproductive bioengineering

Education

• Ph.D. Massachusetts Institute of Technology, 2020

Positions

• Assistant Professor of Biomedical Engineering
• Assistant Professor in Biostatistics & Bioinformatics
• Assistant Professor of Computer Science
• Member of the Duke Cancer Institute

Courses Taught

• EGR 393: Research Projects in Engineering
• COMPSCI 590: Advanced Topics in Computer Science
• COMPSCI 394: Research Independent Study
• COMPSCI 393: Research Independent Study
• BME 791: Graduate Independent Study
• BME 789: Internship in Biomedical Engineering
• BME 590: Special Topics in Biomedical Engineering
• BME 494: Projects in Biomedical Engineering (GE)
• BME 493: Projects in Biomedical Engineering (GE)
• BME 390L: Special Topics with a Lab

Publications

• Chen T, Chatterjee P. Synergizing sequence and structure representations to predict protein variants. Cell research. 2024 Sep;34(9):597–8.
• Hong L, Ye T, Wang T, Sri D, Zhao L, Watson R, et al. Programmable Protein Stabilization with Language Model-Derived Peptide Guides. Springer Science and Business Media LLC. 2024.
• Hong L, Ye T, Wang TZ, Srijay D, Zhao L, Watson R, et al. Programmable Protein Stabilization with Language Model-Derived Peptide Guides. In: Res Sq. 2024.
• Vincoff S, Goel S, Kholina K, Pulugurta R, Vure P, Chatterjee P. FusOn-pLM: A Fusion Oncoprotein-Specific Language Model via Focused Probabilistic Masking. 2024.
• Peng Z, Schussheim B, Chatterjee P. PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks. bioRxiv. 2024.
• Chen T, Zhang Y, Chatterjee P. moPPIt:De NovoGeneration of Motif-Specific Binders with Protein Language Models. bioRxiv. 2024.
• Zhang Y, He P, Hsu A, Chatterjee P. MetaLATTE: Metal Binding Prediction via Multi-Task Learning on Protein Language Model Latents. bioRxiv. 2024.
• Chen T, Hong L, Yudistyra V, Vincoff S, Chatterjee P. Generative design of therapeutics that bind and modulate protein states. Current Opinion in Biomedical Engineering. 2023 Dec 1;28.
• Brixi G, Ye T, Hong L, Wang T, Monticello C, Lopez-Barbosa N, et al. SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders. Communications biology. 2023 Oct;6(1):1081.
• Zhao L, Koseki SRT, Silverstein RA, Amrani N, Peng C, Kramme C, et al. PAM-flexible genome editing with an engineered chimeric Cas9. Nature communications. 2023 Oct;14(1):6175.
• Liang S-Q, Liu P, Ponnienselvan K, Suresh S, Chen Z, Kramme C, et al. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nature methods. 2023 Jun;20(6):898–907.
• Koseki S, Hong L, Yudistyra V, Stan T, Tysinger E, Silverstein R, et al. PAM-Flexible Genome Editing with an Engineered Chimeric Cas9. Res Sq. 2023 Mar 7;
• Pierson Smela MD, Kramme CC, Fortuna PRJ, Adams JL, Su R, Dong E, et al. Directed differentiation of human iPSCs to functional ovarian granulosa-like cells via transcription factor overexpression. eLife. 2023 Feb;12:e83291.
• Bhat S, Palepu K, Hong L, Mao J, Ye T, Iyer R, et al. De NovoDesign of Peptide Binders to Conformationally Diverse Targets with Contrastive Language Modeling. bioRxiv. 2023.
• Kobayashi M, Odajima J, Shioda K, Hwang YS, Sasaki K, Chatterjee P, et al. Expanding homogeneous culture of human primordial germ cell-like cells maintaining germline features without serum or feeder layers. Stem Cell Reports. 2022 Mar;17(3):507–21.
• Palepu K, Ponnapati M, Bhat S, Tysinger E, Stan T, Brixi G, et al. Design of Peptide-Based Protein Degraders via Contrastive Deep Learning. bioRxiv. 2022.
• Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, et al. MegaGate: A toxin-less gateway molecular cloning tool. STAR protocols. 2021 Dec;2(4):100907.
• Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, et al. An integrated pipeline for mammalian genetic screening. Cell reports methods. 2021 Oct;1(6):100082.
• Tripathy S, Ponnapati M, Jacobson J, Chatterjee P. Sub-Picomolar Detection of SARS-CoV-2 RBD via Computationally-Optimized Peptide Beacons. bioRxiv. 2021.
• Costa A, Ponnapati M, Jacobson J, Chatterjee P. Distillation of MSA Embeddings to Folded Protein Structures with Graph Transformers. bioRxiv. 2021.
• Qing R, Tao F, Chatterjee P, Yang G, Han Q, Chung H, et al. Non-full-length Water-Soluble CXCR4QTY and CCR5QTY Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Receptors. iScience. 2020 Dec;23(12):101670–101670.
• Chatterjee P, Ponnapati M, Kramme C, Plesa AM, Church GM, Jacobson JM. Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions. Communications biology. 2020 Nov;3(1):715.
• Chatterjee P, Jakimo N, Lee J, Amrani N, Rodríguez T, Koseki SRT, et al. An engineered ScCas9 with broad PAM range and high specificity and activity. Nature biotechnology. 2020 Oct;38(10):1154–8.
• Chatterjee P, Jakimo N, Lee J, Amrani N, Rodríguez T, Koseki SRT, et al. Publisher Correction: An engineered ScCas9 with broad PAM range and high specificity and activity. Nature biotechnology. 2020 Oct;38(10):1212.
• Chatterjee P, Lee J, Nip L, Koseki SRT, Tysinger E, Sontheimer EJ, et al. A Cas9 with PAM recognition for adenine dinucleotides. Nature Communications. 2020 May 18;11(1).
• Chatterjee P, Ponnapati M, Jacobson J. Targeted Intracellular Degradation of SARS-CoV-2 RBD via Computationally-Optimized Peptide Fusions. bioRxiv. 2020.
• Chatterjee P, Ponnapati M, Kramme C, Plesa A, Jacobson J, Church G. Targeted Intracellular Degradation of SARS-CoV-2 via Computationally-Optimized Peptide Fusions. Research Square. 2020.
• Chatterjee P, Jakimo N, Jacobson J. Robust Genome Editing of Single-Base PAM Targets with Engineered ScCas9 Variants. bioRxiv. 2019.
• Chatterjee P, Jakimo N, Jacobson JM. Minimal PAM specificity of a highly similar SpCas9 ortholog. Science advances. 2018 Oct;4(10):eaau0766.
• Jakimo N, Chatterjee P, Nip L, Jacobson J. A Cas9 with Complete PAM Recognition for Adenine Dinucleotides. bioRxiv. 2018.
• Patsoukis N, Bardhan K, Chatterjee P, Sari D, Liu B, Bell LN, et al. PD-1 alters T-cell metabolic reprogramming by inhibiting glycolysis and promoting lipolysis and fatty acid oxidation. Nature communications. 2015 Mar;6:6692.
• Boussiotis VA, Chatterjee P, Li L. Biochemical Signaling of PD-1 on T Cells and Its Functional Implications. The Cancer Journal. 2014 Jul;20(4):265–71.

In The News

• Duke Companies and Faculty Share Ideas with Investors at Triangle Venture Day (Sep 15, 2023 | Duke Today)