Publications

Nitya Thakkar*, Merzu Belete*, Indu Khatri, Meijian Guan, Yu Sun, Anantharaman Muthuswamy, Iris Kolder, Han Si, David Soong, Brandon W Higgs, Lauren K Brady, James Zou, Sriram Sridhar (2026). Integrated histopathology–transcriptomic biomarker enhances survival prediction in HNSCC patients treated with immunotherapy. Translational Oncology.

DOI

Nitya Thakkar, Rajita Patil, Rebecca Levy-Gantt, Yulin Hswen, Monica Agrawal, James Zou, Irene Y Chen (2026). Characterization of menopause onset and associated disease risks using large-scale electronic health records. medRxiv.

DOI

Nitya Thakkar, Mert Yuksekgonul, Jake Silberg, Animesh Garg, Nanyun Peng, Fei Sha, Rose Yu, Carl Vondrick, James Zou (2026). A large-scale randomized study of large language model feedback in peer review. Nature Machine Intelligence.

Code DOI

Suchen Zheng*, Nitya Thakkar*, Hannah L. Harris, Megan Zhang, Susanna Liu, Mark Gerstein, Erez Lieberman Aiden, Jordan Rowley, William Stafford Noble, Gamze Gürsoy, Ritambhara Singh (2024). Predicting A/B compartments from histone modifications using deep learning. iScience, 27(5).

Code DOI

Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Alex X. Lu, Nicolo Fusi, Ava P. Amini, Kevin K. Yang (2023). Protein generation with evolutionary diffusion: sequence is all you need. eLife.

Code DOI

Nitya Thakkar, Ritambhara Singh (2023). Using Graph Neural Networks to Model the Glioblastoma Free Energy Landscape. Honors Thesis.

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