Publications

• Michelli F Oliveira, Juan P Romero, Meii Chung, Stephen Williams, Andrew D Gottscho, Anushka Gupta, Susan E Pilipauskas, Syrus Mohabbat, Nandhini Raman, David Sukovich, David Patterson, Visium HD Development Team, Sarah EB Taylor, “High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer”, Nature Genetics 2025. [Paper] [Preprint]
  As a part of “Visium HD Development Team”, that built the product demonstrated in the paper.

• Amanda Janesick, Robert Shelansky, Andrew D Gottscho, Florian Wagner, Stephen R Williams, Morgane Rouault, Ghezal Beliakoff, Carolyn A Morrison, Michelli F Oliveira, Jordan T Sicherman, Andrew Kohlway, Jawad Abousoud, Tingsheng Yu Drennon, Seayar H Mohabbat, 10x Development Teams, Sarah EB Taylor, “High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis” Nature Communications 2023. [Paper] [Preprint]
  As a part of “10x Development Teams”, that built the product demonstrated in the paper.

• Tri Dao, Govinda M Kamath, Vasilis Syrgkanis, and Lester Mackey, “Knowledge Distillation as Semiparametric Inference”, ICLR 2021. [Preprint]

• Govinda M Kamath^*, Tavor Baharav^*, Ilan Shomorony, “Adaptive Learning of Rank-One Models for Efficient Pairwise Sequence Alignment”, NeurIPS 2020. [Paper] [Preprint] [Analysis].
  ^* co-first authors

• Tavor Baharav^*, Govinda M Kamath^*, David N Tse, and Ilan Shomorony, “Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments”, Cell Patterns 1.6. [Paper] [Preprint] [Analysis]
  ^* co-first authors

• Tara Basu Trivedi, Ron Boger, Govinda M Kamath, Georgios Evangelopoulos, Jamie Cate, Jennifer Doudna, and Jack Hidary, “crispr2vec: Machine Learning Model Predicts Off-Target Cuts of CRISPR systems”, [Preprint]

• Jesse M. Zhang, Govinda M. Kamath, David N. Tse, “Valid post-clustering differential analysis for single-cell RNA-Seq”, RECOMB 2019, Cell Systems. [Cell Systems] [Preprint] [Analysis]

• Vivek Bagaria^*, Tavor Baharav^*, Govinda M. Kamath^*, David N. Tse, “Bandit-Based Monte Carlo Optimization for Nearest Neighbors”, IEEE Journal on Selected Areas in Information Theory. [Paper]
  ^* co-first authors

• Vivek Bagaria^*, Govinda M. Kamath^*, David N. Tse, “Adaptive Monte-Carlo Optimization”, [Preprint] [Analysis]
  ^* co-first authors

• Vivek Bagaria^*, Govinda M. Kamath^*, Vasilis Ntranos^*, Martin J. Zhang^*, and David N. Tse. “Medoids in almost linear time via multi-armed bandits”, AISTATS-2018. Also presented at NIPS workshop for learning interactions from complex data. [Paper] [Preprint] [Analysis]
  ^* co-first authors

• Govinda M.Kamath^*, Ilan Shomorony^*, Fei Xia^*, Thomas A. Courtade, and David N. Tse. “HINGE: long-read assembly achieves optimal repeat resolution”, Genome research 27, no. 5 (2017): 747-756. [Paper] [Preprint] [Code] [Analysis] [Press Coverage]
  ^* co-first authors

• Yuxin Chen, Govinda M. Kamath, Changho Suh, and David N. Tse, “Community Recovery in Graphs with Locality”, ICML 2015. [Paper] [Preprint]

• Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Govinda M. Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Douglas Carmean, Georg Seelig, Luis Ceze, Karin Strauss, “Scaling up DNA data storage and random access retrieval”, Nature Biotechnology. [Paper] [Preprint]
  This was a large project that I was a part of as an intern at MSR, Redmond. My work was mainly in analysing the data, modelling and characterising the storage channel.

• Ilan Shomorony, Govinda M. Kamath, Fei Xia, Thomas A. Courtade, and David N. Tse, “Partial Assembly: A Rate-Distortion Perspective””, ISIT- 2016. [Paper] [Preprint]

• Jesse Zhang and Govinda M. Kamath, “Learning the Language of the Genome using RNNs”, CS224d Project. [Technical Report]

• Vasilis Ntranos^*, Govinda M. Kamaths^*, Jesse Zhang^*, Lior Pachter and David N. Tse, “Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts”, Genome Biology special issue on single cell omics. [Paper] [Preprint] [Analysis]
  ^* co-first authors

• Govinda M. Kamath, Eren Sasoglu, and David Tse. “Optimal Haplotype Assembly from High-Throughput Mate Pair Reads”, ISIT-2015. [Paper] [Preprint]

• Govinda M. Kamath, Narayanamoorthy Prakash, Lalitha Vadlamani, and P Vijay Kumar. “Codes With Local Regeneration and Erasure Correction””. IEEE Transactions of Information Theory June 2014. Earlier version published in ISIT 2013. [Journal Version] [Conference Version] [Preprint]

• Govinda M. Kamath, Narayanamoorthy Prakash, Lalitha Vadlamani, P. Vijay Kumar, Natalia Silberstein, Ankit S. Rawat, O. Ozan Koyluoglu, and Sriram Vishwanath, “Explicit MBR All-Symbol Locality Codes”. ISIT 2013. [Paper] [Preprint]

• Narayanamoorthy Prakash, Govinda M. Kamath, Lalitha Vadlamani, and P Vijay Kumar. “Optimal Linear Codes with a Local-Error-Correction Property”. ISIT 2012. [Paper] [Preprint]

• Govinda M. Kamath and P Vijay Kumar. “Regenerating codes: a reformulated storage-bandwidth trade-off and a new construction.” in Proceedings. of the National Conference on Communication 2012 (NCC 2012), IIT Kharagpur, India. [Paper]

• Lalitha Vadlamani, Narayanamoorthy Prakash, Govinda M. Kamath, and P Vijay Kumar. ‘‘On t-designs and bounds relating query complexity to error resilience in locally correctable codes.’’ in Proceedings. of the National Conference on Communication 2012 (NCC 2012), IIT Kharagpur, India. [Paper]