Ruchir Rastogi

I am a fourth year CS Ph.D. student at UC Berkeley, coadvised by Nir Yosef and Nilah Ioannidis. My research lies at the intersection of machine learning and biology. Currently, I work on methods to predict variant effects, understand noncoding genomic sequences, and analyze single-cell sequencing data. This summer, I am working at Microsoft Research in the Health Futures division.

Email: ruchir [underscore] rastogi [at] berkeley [dot] edu

Publications

Critical assessment of missense variant effect predictors on disease-relevant variant data

Ruchir Rastogi, Ryan Chung, Sindy Li, CAGI Annotate All Missense Participants, Predrag Radivojac, Steven Brenner, Nilah Ioannidis

bioRxiv

Characterizing uncertainty in predictions of genomic sequence-to-activity models

Ayesha Bajwa*, Ruchir Rastogi*, Pooja Kathail*, Richard Shuai, Nilah Ioannidis

Machine Learning in Computational Biology (MLCB), 2023

Personal transcriptome variation is poorly explained by current genomic deep learning models

Connie Huang*, Richard Shuai*, Parth Baokar*, Ryan Chung, Ruchir Rastogi, Pooja Kathail, Nilah Ioannidis

Nature Genetics, 2023

Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects

Milind Jagota*, Chengzhong Ye*, Carlos Albors, Ruchir Rastogi, Antoine Koehl, Nilah Ioannidis, Yun S. Song

Genome Biology, 2023

[code]

X-CAP improves pathogenicity prediction of stopgain variants

Ruchir Rastogi, Peter D. Stenson, David N. Cooper, Gill Bejerano

Genome Medicine, 2022

[code]

Descriptive analysis of ICU patient mobilization from depth videos

Ruchir Rastogi*, Laëtitia Shao*, Zaid Nabulsi*, Bingbin Liu, Francesca Rinaldo, Serena Yeung, N. Lance Downing, William Beninati, Arnold Milstein, Li Fei-Fei

NeurIPS Machine Learning for Health (ML4H) Workshop, 2018

Modulation of macrophage functional polarity towards anti-inflammatory phenotype with plasmid DNA delivery in CD44 targeting hyaluronic acid nanoparticles

Thanh-Huyen Tran, Ruchir Rastogi, Juili Shelke, Mansoor M. Amiji

Scientific Reports, 2015