Ratul Chowdhury

Title(s):

Office

Information

∎ Links
Chowdhury Lab Website Chowdhury lab is a part of the Nanovaccine Institute (5th Floor) Publications // Media-coverage // Patents (see here)

∎ Education 
PhD, Chemical Engineering, 2019, Penn State University.
BE, Chemical Engineering, 2013, Jadavpur University, India

∎ Experience
Postdoctoral Fellow, Harvard Program in Therapeutic Sciences, 2020-2022, Harvard Medical School

∎ Interest Areas
→ Computational protein design, Protein dynamics
→ Hybrid optimization with ML and integer-programming
→ Structure-guided metabolic engineering
→ Tailoring enzyme activity
→ Channel protein for separations
→ Antibody design
→ Bio-inspired material design for green chemistry
→ Bio-based separation of rare-earth elements (lanthanides)

∎ Teaching
F22// CHE310 (Computational Methods in Chemical Engg.)
F23// CHE440 (Biomed. Appln in Chemical Engg.)
S24// CHE310 (Computational Methods in Chemical Engg.)
F24// CHE440 (Biomed. Appln in Chemical Engg.)
F24// HONS 3210-4 (Machine Learning for Protein Biology)

Publications

↳ Papers (See on Website)
↳ Google Scholar (Chowdhury)

( * – as corresponding author )

* 2024 // Computational and Structural Biotechnology Journal — Dey, S. et. al

Identification and biophysical characterization of epitope atlas of Porcine Reproductive and Respiratory Syndrome Virus

Article 

2024 // Biotechnology and Bioengineering — Ferdous S. et. al

Reinforcement learning-guided control strategies for CAR T-cell activation and expansion

 Article 

2024 // ACS Nano — Uthaman, S. et. al

Inhibiting the cGAS-STING Pathway in Ulcerative Colitis with Programmable Micelles

 Article 

* 2024 // ICASSP 2024 — Lin J. et. al

Distributed Stochastic Contextual Bandits for Protein Drug Interaction

 Article 

2023 // Iscience — Chowdhury, N.B. et. al

A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation

 Article 

* 2023 // Cell Systems — Samineni, L. et. al

Protein engineering of pores for separation, sensing, and sequencing

 Article 

2023 // Journal of Experimental Botany — Choi, S. et. al

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass

 Article 

2023 // Metabolic Engineering — Jindra, M. et. al

Evaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acids

 Article 

* 2023 // Frontiers in Bioeng. and Biotech — Chowdhury, R.

Advances in protein structure, function, and design

 Article 

2021 // Nature Biotechnology — Chowdhury,R. + Bouatta,N. + Biswas,S. et. al

Single-sequence protein structure prediction using language models from deep learning

 Article   Nature News |ScienceMag | Forbes AI

2022 // Proteins — Boorla,VS. + Chowdhury,R. et. al

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)

 Article

2022 // NPJ Clear Water — Samineni, L. et. al

Effective pathogen removal in sustainable natural fiber Moringa filters

 Article

2022 // Applied & Environmental Microbiology — Oh,C. + Chowdhury,R. et. al

Inactivation mechanism and efficacy of grape seed extract for Human Norovirus surrogate

 Article

2021 // Genome Medicine — Patiño-Galindo, J. et. al

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

 Article   The Scientist

2021 // Nature Nanotechnology — Zeng, H. et. al

Foldamer-based ultrapermeable and highly selective artificial water channels that exclude protons

 Article   ScienMag | SciTech Daily

2021 // PNAS — Chen, C. et. al

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2

 Article   News18 | LabRoots

2020 // Computational and Structural Biotechnology Journal — Chowdhury, R. + Boorla, VS. et. al

Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity

 Article   ScienceDaily

2020 // Structure — Chowdhury, R. et. al

IPRO+/−: Computational Protein Design Tool Allowing for Insertions and Deletions

 Article 

2020 // Nature Nanotechnology — Song, W. et. al

Artificial water channels enable fast and selective water permeation through water-wire networks

 Article   Nature | UT Austin | Water Canada

2020 // Protein Engineering, Design and Selection — Wang, Z. et. al

Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid

 Article

2020 // Nature Materials — Tu, YM. et. al

Rapid fabrication of precise high-throughput filters from membrane protein nanosheets

 Article   Technology Networks | Science Daily



...................................... publications older than 2020 not included ...........................

Primary Strategic Research Area

Engineered Medicine

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