Publications

Martina Damo, Noah I Hornick, Aarthi Venkat, Ivana William, Kathryn Clulo, Srividhya Venkatesan, Jiaming He, Eric Fagerberg, Jennifer L Loza, Darwin Kwok, others (2023). PD-1 maintains CD8 T cell tolerance towards cutaneous neoantigens. Nature.

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Aarthi Venkat, Dhananjay Bhaskar, Smita Krishnaswamy (2023). Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data. Trends in Immunology.

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Aarthi Venkat, Martina Damo, Nikhil S Joshi, Smita Krishnaswamy (2023). Mapping the gene space at single-cell resolution with gene signal pattern analysis. The Journal of Immunology.

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Alexander Tong, Manik Kuchroo, Shabarni Gupta, Aarthi Venkat, Beatriz Perez San Juan, Laura Rangel, Brandon Zhu, John G Lock, Christine Chaffer, Smita Krishnaswamy (2023). Learning transcriptional and regulatory dynamics driving cancer cell plasticity using neural ODE-based optimal transport. bioRxiv.

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Dhananjay Bhaskar, Sumner Magruder, Edward De Brouwer, Aarthi Venkat, Frederik Wenkel, Guy Wolf, Smita Krishnaswamy (2023). Inferring dynamic regulatory interaction graphs from time series data with perturbations. *LoG Conference 2023.

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Samuel Leone, Aarthi Venkat, Guillaume Huguet, Alexander Tong, Guy Wolf, Smita Krishnaswamy (2023). Graph Fourier MMD for Signals on Graphs. arXiv preprint arXiv:2306.02508.

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Aarthi Venkat, Joyce Chew, Ferran Cardoso Rodriguez, Christopher J Tape, Michael Perlmutter, Smita Krishnaswamy (2023). Directed Scattering for Knowledge Graph-based Cellular Signaling Analysis. arXiv preprint arXiv:2309.07813.

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Matthew Amodio, Scott E Youlten, Aarthi Venkat, Beatriz P San Juan, Christine L Chaffer, Smita Krishnaswamy (2022). Single-cell multi-modal GAN reveals spatial patterns in single-cell data from triple-negative breast cancer. Patterns.

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Cathy C Garcia, Lauren Lawres, Sherry Agabiti, Jaffarguriqbal Singh, Alex Tong, Aarthi Venkat, Daniel B Burkhardt, Rebecca Cardone, Richard G Kibbey, Smita Krishnaswamy, others (2022). Elucidating mechanisms of endocrine-exocrine signaling in obesity-driven pancreatic cancer.. CANCER RESEARCH.

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Yihua Su, Aarthi Venkat, Yadush Yadav, Lisa B Puglisi, Samah J Fodeh (2021). Twitter-based analysis reveals differential COVID-19 concerns across areas with socioeconomic disparities. Computers in Biology and Medicine.

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Jing Xia, Aarthi Venkat, Rachel E Bainbridge, Michael L Reese, Karine G Le Roch, Ferhat Ay, Jon P Boyle (2021). Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants. Genome research.

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Kelli A Connolly, Manik Kuchroo, Aarthi Venkat, Achia Khatun, Jiawei Wang, Ivana William, Noah I Hornick, Brittany L Fitzgerald, Martina Damo, Moujtaba Y Kasmani, others (2021). A reservoir of stem-like CD8+ T cells in the tumor-draining lymph node preserves the ongoing antitumor immune response. Science immunology.

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Evelien M Bunnik, Aarthi Venkat, Jianlin Shao, Kathryn E McGovern, Gayani Batugedara, Danielle Worth, Jacques Prudhomme, Stacey A Lapp, Chiara Andolina, Leila S Ross, others (2019). Comparative 3D genome organization in apicomplexan parasites. Proceedings of the National Academy of Sciences.

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