Govinda M. Kamath

10x Genomics

Pleasanton, California

I am a research scientist at 10x Genomics in California, where I design and ship algorithms and machine learning systems for single-cell RNA-seq and spatial transcriptomics. My work spans various aspects of product development — from framing the problem and defining success metrics, to training and shipping the models that process the data, to optimizing the products alongside biologists and manufacturing teams.

Before joining 10x, I was a postdoctoral fellow at the Microsoft Research New England Lab with Lester Mackey, and I received my PhD from Stanford’s Information Systems Lab, advised by David Tse. Earlier, I earned a master’s in Electrical Communication Engineering from the Indian Institute of Science with P. Vijay Kumar.

A common thread through my work is designing and deploying scalable machine learning algorithms to solve real problems — and proving that they work — with problems often coming from computational genomics. More about my past research and publications. I also enjoy writing code in Rust.

news

Oct 08, 2025	Our paper on automated cell-type annotation for single-cell RNA-seq — the algorithm behind Cell Ranger — is now on bioRxiv.
Jun 20, 2025	Nucleus segmentation on visium HD (which I worked on) released.
Jun 05, 2025	Our paper on the Visium HD was published in Nature Genetics.
Mar 29, 2024	Visium HD, the spatial transcriptomics platform I mostly worked on launched publicly.
Dec 19, 2023	Our paper highlighting the Xenium platform was published in Nature Communications.
Jul 01, 2021	Joined 10x Genomics as a research scientist, working on algorithms and machine learning for single-cell and spatial genomics.

latest posts

Aug 09, 2026	Reproducible dev environments with Nix and Home Manager

selected publications

bioRxiv

Accelerating scRNA-seq Analysis: Automated cell type annotation using representation learning and vector search

Stephen R. Williams, Fedor Grab, Govinda M. Kamath, Yerdos Ordabayev, Jeff Mellen, Patrick Roelli, Kristian Cibulskis, Erik Lehnert, Fen Xie, Miguel Covarrubias, Nur-Taz Rahman, Timothy Tickle, Emre Erhan, Nicolas Malfroy-Camine, Kevin Lydon, Mehrtash Babadi, and Nigel F. Delaney

bioRxiv, 2025

Describes the automated cell-type annotation algorithm shipped in Cell Ranger.

bioRxiv Bib

@article{williams2025cellannotation,
  title = {Accelerating scRNA-seq Analysis: Automated cell type annotation using representation learning and vector search},
  author = {Williams, Stephen R. and Grab, Fedor and Kamath, Govinda M. and Ordabayev, Yerdos and Mellen, Jeff and Roelli, Patrick and Cibulskis, Kristian and Lehnert, Erik and Xie, Fen and Covarrubias, Miguel and Rahman, Nur-Taz and Tickle, Timothy and Erhan, Emre and Malfroy-Camine, Nicolas and Lydon, Kevin and Babadi, Mehrtash and Delaney, Nigel F.},
  journal = {bioRxiv},
  year = {2025},
  note = {Describes the automated cell-type annotation algorithm shipped in Cell Ranger.}
}

Nat. Genet.

High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer

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, and Sarah E. B. Taylor

Nature Genetics, 2025

As part of the Visium HD Development Team that built the product demonstrated in the paper.

bioRxiv Bib

@article{oliveira2025visiumhd,
  title = {High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer},
  author = {Oliveira, Michelli F. and Romero, Juan P. and Chung, Meii and Williams, Stephen and Gottscho, Andrew D. and Gupta, Anushka and Pilipauskas, Susan E. and Mohabbat, Syrus and Raman, Nandhini and Sukovich, David and Patterson, David and {Visium HD Development Team} and Taylor, Sarah E. B.},
  journal = {Nature Genetics},
  volume = {57},
  number = {6},
  pages = {1512--1523},
  year = {2025},
  url = {https://www.nature.com/articles/s41588-025-02193-3},
  note = {As part of the Visium HD Development Team that built the product demonstrated in the paper.}
}

Nat. Commun.

High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis

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, and Sarah E. B. Taylor

Nature Communications, 2023

As part of the 10x Development Teams that built the products demonstrated in the paper.

bioRxiv Bib

@article{janesick2023tumor,
  title = {High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis},
  author = {Janesick, Amanda and Shelansky, Robert and Gottscho, Andrew D. and Wagner, Florian and Williams, Stephen R. and Rouault, Morgane and Beliakoff, Ghezal and Morrison, Carolyn A. and Oliveira, Michelli F. and Sicherman, Jordan T. and Kohlway, Andrew and Abousoud, Jawad and Drennon, Tingsheng Yu and Mohabbat, Seayar H. and {10x Development Teams} and Taylor, Sarah E. B.},
  journal = {Nature Communications},
  volume = {14},
  year = {2023},
  url = {https://www.nature.com/articles/s41467-023-43458-x},
  note = {As part of the 10x Development Teams that built the products demonstrated in the paper.}
}

NeurIPS

Adaptive Learning of Rank-One Models for Efficient Pairwise Sequence Alignment

Govinda M. Kamath^*, Tavor Baharav^*, and Ilan Shomorony

In Advances in Neural Information Processing Systems, 2020

* Co-first authors

arXiv Bib PDF Code

@inproceedings{kamath2020adaptive,
  title = {Adaptive Learning of Rank-One Models for Efficient Pairwise Sequence Alignment},
  author = {Kamath, Govinda M. and Baharav, Tavor and Shomorony, Ilan},
  booktitle = {Advances in Neural Information Processing Systems},
  volume = {33},
  year = {2020},
  note = {* Co-first authors}
}

Cell Syst.

Valid post-clustering differential analysis for single-cell RNA-Seq

Jesse M. Zhang, Govinda M. Kamath, and David N. Tse

Cell Systems, 2019

Also presented at RECOMB 2019

bioRxiv Bib Code

@article{zhang2019postclustering,
  title = {Valid post-clustering differential analysis for single-cell RNA-Seq},
  author = {Zhang, Jesse M. and Kamath, Govinda M. and Tse, David N.},
  journal = {Cell Systems},
  volume = {9},
  number = {2},
  pages = {137--148},
  year = {2019},
  url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC7202736/},
  note = {Also presented at RECOMB 2019}
}

Genome Res.

HINGE: long-read assembly achieves optimal repeat resolution

Govinda M. Kamath^*, Ilan Shomorony^*, Fei Xia^*, Thomas A. Courtade, and David N. Tse

Genome Research, 2017

* Co-first authors. Press coverage: GenomeWeb

bioRxiv Bib Code

@article{kamath2017hinge,
  title = {HINGE: long-read assembly achieves optimal repeat resolution},
  author = {Kamath, Govinda M. and Shomorony, Ilan and Xia, Fei and Courtade, Thomas A. and Tse, David N.},
  journal = {Genome Research},
  volume = {27},
  number = {5},
  pages = {747--756},
  year = {2017},
  url = {http://genome.cshlp.org/content/27/5/747},
  note = {* Co-first authors. Press coverage: <a href="https://www.genomeweb.com/scan/week-genome-research-29">GenomeWeb</a>}
}

IEEE TIT

Codes With Local Regeneration and Erasure Correction

Govinda M. Kamath, Narayanamoorthy Prakash, Lalitha Vadlamani, and P. Vijay Kumar

IEEE Transactions on Information Theory, 2014

Earlier version published at ISIT 2013

arXiv Bib

@article{kamath2014localregen,
  title = {Codes With Local Regeneration and Erasure Correction},
  author = {Kamath, Govinda M. and Prakash, Narayanamoorthy and Vadlamani, Lalitha and Kumar, P. Vijay},
  journal = {IEEE Transactions on Information Theory},
  volume = {60},
  number = {7},
  pages = {4116--4130},
  year = {2014},
  url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=6846301},
  note = {Earlier version published at ISIT 2013}
}