Dr Pranam Chatterjee, Ph.D.

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 LT, Pulugurta R, Vure P, Chatterjee P. DPAC: Prediction and Design of Protein-DNA Interactions via Sequence-Based Contrastive Learning. Cold Spring Harbor Laboratory. 2025.
• Peng FZ, Wang C, Chen T, Schussheim B, Vincoff S, Chatterjee P. PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks. Nature methods. 2025 Apr;
• Hong L, Ye T, Wang TZ, Srijay D, Liu H, Zhao L, et al. Programmable protein stabilization with language model-derived peptide guides. Nature communications. 2025 Apr;16(1):3555.
• Patel S, Peng FZ, Fraser K, Friedman AD, Chatterjee P, Yao S. EvoFlow-RNA: Generating and Representing non-coding RNA with a Language Model. Cold Spring Harbor Laboratory. 2025.
• Vincoff S, Goel S, Kholina K, Pulugurta R, Vure P, Chatterjee P. FusOn-pLM: a fusion oncoprotein-specific language model via adjusted rate masking. Nature communications. 2025 Feb;16(1):1436.
• Torres MDT, Chen T, Wan F, Chatterjee P, de la Fuente-Nunez C. Generative latent diffusion language modeling yields anti-infective synthetic peptides. 2025.
• Bhat S, Palepu K, Hong L, Mao J, Ye T, Iyer R, et al. De novo design of peptide binders to conformationally diverse targets with contrastive language modeling. Sci Adv. 2025 Jan 24;11(4):eadr8638.
• Chen T, Chatterjee P. Synergizing sequence and structure representations to predict protein variants. Cell research. 2024 Sep;34(9):597u20138.
• 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.
• 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.
• 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.
• Zhang Y, He P, Hsu A, Chatterjee P. MetaLATTE: Metal Binding Prediction via Multi-Task Learning on Protein Language Model Latents. bioRxiv. 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.
• 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.
• 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.
• 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.
• 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):898u2013907.
• 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):507u201321.
• 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):101670u2013101670.
• 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, Rodru00edguez T, Koseki SRT, et al. An engineered ScCas9 with broad PAM range and high specificity and activity. Nature biotechnology. 2020 Oct;38(10):1154u20138.
• Chatterjee P, Jakimo N, Lee J, Amrani N, Rodru00edguez 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):265u201371.

In The News

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