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.
@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.}}
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.
@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.}}
Spatial Transcriptomic Profiling of the Tumor Microenvironment at Single-Cell-Scale Resolution Using Visium HD 3’
Anuj Patel, Debashish Chitnis, Josh Gu, Anushka Gupta, Marco Serra, Zixue Ma, Monica Nagendran, Joey Arthur, Govinda M. Kamath, David Sukovich, Sean Osinski, and Augusto M. Tentori
@article{patel2025visiumhd,title={Spatial Transcriptomic Profiling of the Tumor Microenvironment at Single-Cell-Scale Resolution Using Visium HD 3'},author={Patel, Anuj and Chitnis, Debashish and Gu, Josh and Gupta, Anushka and Serra, Marco and Ma, Zixue and Nagendran, Monica and Arthur, Joey and Kamath, Govinda M. and Sukovich, David and Osinski, Sean and Tentori, Augusto M.},journal={Journal of Molecular Diagnostics},volume={27},number={11},year={2025}}
Visium HD 3’ enables unbiased whole transcriptome spatial profiling of tumor microenvironment in fresh frozen cancer tissues at single cell-scale resolution
Debashish Chitnis, Marco Serra, Josh Gu, Anushka Gupta, Nancy Conejo, Aarushi Kalaimani, Govinda M. Kamath, Zixue Ma, Monica Nagendran, Joey Arthur, Julia Cowen, Anuj Patel, David Sukovich, and Augusto M. Tentori
@article{chitnis2025abstract,title={Visium HD 3' enables unbiased whole transcriptome spatial profiling of tumor microenvironment in fresh frozen cancer tissues at single cell-scale resolution},author={Chitnis, Debashish and Serra, Marco and Gu, Josh and Gupta, Anushka and Conejo, Nancy and Kalaimani, Aarushi and Kamath, Govinda M. and Ma, Zixue and Nagendran, Monica and Arthur, Joey and Cowen, Julia and Patel, Anuj and Sukovich, David and Tentori, Augusto M.},journal={Cancer Research},volume={85},number={8 Supplement},pages={5301},year={2025},doi={10.1158/1538-7445.am2025-5301},note={AACR 2025 conference abstract}}
@misc{williams2024patent,title={Reference free spot deconvolution in spatial transcriptomics},author={Williams, Stephen R. and Kamath, Govinda M. and Arthur, Joey G.},year={2024},url={https://patents.google.com/patent/US20240287599A1/en},note={US Patent Application US20240287599A1}}
Whole transcriptome spatial profiling of the tumor microenvironment in FFPE, fresh frozen, and fixed frozen tissues
Jun Chiang, Naishitha Anaparthy, Nancy Conejo, Monica Nagendran, David Sukovich, David Patterson, Lauren Gutgesell, Govinda M. Kamath, and Augusto M. Tentori
@article{chiang2024abstract,title={Whole transcriptome spatial profiling of the tumor microenvironment in FFPE, fresh frozen, and fixed frozen tissues},author={Chiang, Jun and Anaparthy, Naishitha and Conejo, Nancy and Nagendran, Monica and Sukovich, David and Patterson, David and Gutgesell, Lauren and Kamath, Govinda M. and Tentori, Augusto M.},journal={Journal for ImmunoTherapy of Cancer},volume={12},number={Suppl 2},pages={A1376},year={2024},doi={10.1136/jitc-2024-sitc2024.1376},note={SITC 2024 conference abstract}}
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.
@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.}}
Spatially resolved whole-transcriptome analysis with simultaneous highly multiplexed immune cell epitope detection in multiple cancer tissues
Anushka Gupta, Stephen Williams, Lauren Gutgasell, Benton Veire, Ace Santiago, Hardeep Singh, Rena Chan, Alex Hermes, Govinda M. Kamath, Anuj Patel, and David Sukovich
@article{gupta2023abstract,title={Spatially resolved whole-transcriptome analysis with simultaneous highly multiplexed immune cell epitope detection in multiple cancer tissues},author={Gupta, Anushka and Williams, Stephen and Gutgasell, Lauren and Veire, Benton and Santiago, Ace and Singh, Hardeep and Chan, Rena and Hermes, Alex and Kamath, Govinda M. and Patel, Anuj and Sukovich, David},journal={The Journal of Immunology},volume={210},number={1 Supplement},pages={251.04},year={2023},doi={10.4049/jimmunol.210.Supp.251.04},note={AAI 2023 conference abstract}}
Application of spatially resolved transcriptomics to screen multiple tumor biospecimens using tissue microarrays
Syrus Mohabbat, Hardeep Singh, Stephen R. Williams, Lauren M. M. Gutgesell, David J. Sukovich, Govinda M. Kamath, Hanyoup Kim, Amanda Janesick, Robert Shelansky, Ghezal Beliakoff, Augusto M. Tentori, Albert Kim, Cedric R. Uytingco, and Sarah E. B. Taylor
@article{mohabbat2023abstract,title={Application of spatially resolved transcriptomics to screen multiple tumor biospecimens using tissue microarrays},author={Mohabbat, Syrus and Singh, Hardeep and Williams, Stephen R. and Gutgesell, Lauren M. M. and Sukovich, David J. and Kamath, Govinda M. and Kim, Hanyoup and Janesick, Amanda and Shelansky, Robert and Beliakoff, Ghezal and Tentori, Augusto M. and Kim, Albert and Uytingco, Cedric R. and Taylor, Sarah E. B.},journal={Cancer Research},volume={83},number={7 Supplement},pages={4708},year={2023},doi={10.1158/1538-7445.AM2023-4708},note={AACR 2023 conference abstract}}
@inproceedings{dao2021distillation,title={Knowledge Distillation as Semiparametric Inference},author={Dao, Tri and Kamath, Govinda M. and Syrgkanis, Vasilis and Mackey, Lester},booktitle={International Conference on Learning Representations},year={2021},url={https://openreview.net/forum?id=m4UCf24r0Y}}
@article{bagaria2021bandit,title={Bandit-Based Monte Carlo Optimization for Nearest Neighbors},author={Bagaria, Vivek and Baharav, Tavor and Kamath, Govinda M. and Tse, David N.},journal={IEEE Journal on Selected Areas in Information Theory},volume={2},number={2},pages={599--614},year={2021},url={https://ieeexplore.ieee.org/document/9420755},note={* Co-first authors}}
Michal Sheffer, Emily Lowry, Nicky Beelen, Minasri Borah, Suha Naffar-Abu Amara, Chris C. Mader, Jennifer A. Roth, Aviad Tsherniak, Samuel S. Freeman, Olga Dashevsky, Sara Gandolfi, Samantha Bender, Jordan G. Bryan, Cong Zhu, Li Wang, Ifrah Tariq, Govinda M. Kamath, Ricardo De Matos Simoes, Eugen Dhimolea, Channing Yu, Yiguo Hu, Olli Dufva, Marios Giannakis, Vasilis Syrgkanis, Ernest Fraenkel, Todd Golub, Rizwan Romee, Satu Mustjoki, Aedin C. Culhane, Lotte Wieten, and Constantine S. Mitsiades
@article{sheffer2021nkg,title={Genome-scale screens identify factors regulating tumor cell responses to natural killer cells},author={Sheffer, Michal and Lowry, Emily and Beelen, Nicky and Borah, Minasri and Amara, Suha Naffar-Abu and Mader, Chris C. and Roth, Jennifer A. and Tsherniak, Aviad and Freeman, Samuel S. and Dashevsky, Olga and Gandolfi, Sara and Bender, Samantha and Bryan, Jordan G. and Zhu, Cong and Wang, Li and Tariq, Ifrah and Kamath, Govinda M. and Simoes, Ricardo De Matos and Dhimolea, Eugen and Yu, Channing and Hu, Yiguo and Dufva, Olli and Giannakis, Marios and Syrgkanis, Vasilis and Fraenkel, Ernest and Golub, Todd and Romee, Rizwan and Mustjoki, Satu and Culhane, Aedin C. and Wieten, Lotte and Mitsiades, Constantine S.},journal={Nature Genetics},volume={53},number={8},pages={1196--1206},year={2021},doi={10.1038/s41588-021-00889-w}}
@inproceedings{shomorony2021sketching,title={Sketching and sequence alignment: A rate-distortion perspective},author={Shomorony, Ilan and Kamath, Govinda M.},booktitle={IEEE International Symposium on Information Theory},pages={3308--3313},year={2021},doi={10.1109/isit45174.2021.9518131}}
@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}}
@article{baharav2020spectral,title={Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments},author={Baharav, Tavor and Kamath, Govinda M. and Tse, David N. and Shomorony, Ilan},journal={Cell Patterns},volume={1},number={6},pages={100083},year={2020},note={* Co-first authors}}
@article{trivedi2020crispr2vec,title={crispr2vec: Machine Learning Model Predicts Off-Target Cuts of CRISPR systems},author={Trivedi, Tara Basu and Boger, Ron and Kamath, Govinda M. and Evangelopoulos, Georgios and Cate, Jamie and Doudna, Jennifer and Hidary, Jack},journal={bioRxiv},year={2020},}
@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}}
@misc{wang2019pos,title={Proof-of-Stake Longest Chain Protocols Revisited},author={Wang, Xintong and Kamath, Govinda M. and Bagaria, Vivek and Kannan, Sreeram and Oh, Sewoong and Tse, David N. and Viswanath, Pramod},journal={arXiv preprint arXiv:1910.02218},year={2019},}
@phdthesis{kamath2019thesis,title={Almost Linear Time Algorithms for Problems of Computational Genomics},author={Kamath, Govinda M.},school={Stanford University},year={2019}}
@article{bagaria2018amco,title={Adaptive Monte-Carlo Optimization},author={Bagaria, Vivek and Kamath, Govinda M. and Tse, David N.},journal={arXiv preprint arXiv:1805.08321},year={2018},note={* Co-first authors}}
@inproceedings{bagaria2018medoids,title={Medoids in almost linear time via multi-armed bandits},author={Bagaria, Vivek and Kamath, Govinda M. and Ntranos, Vasilis and Zhang, Martin J. and Tse, David N.},booktitle={International Conference on Artificial Intelligence and Statistics},series={Proceedings of Machine Learning Research},volume={84},pages={520--528},year={2018},note={* Co-first authors}}
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, and Karin Strauss
Nature Biotechnology, 2018
Work done as an intern at Microsoft Research, Redmond: data analysis, modeling, and characterization of the storage channel.
@article{organick2018dnastorage,title={Random access in large-scale DNA data storage},author={Organick, Lee and Dumas Ang, Siena and Chen, Yuan-Jyue and Lopez, Randolph and Yekhanin, Sergey and Makarychev, Konstantin and Racz, Miklos Z. and Kamath, Govinda M. and Gopalan, Parikshit and Nguyen, Bichlien and Takahashi, Christopher and Newman, Sharon and Parker, Hsing-Yeh and Rashtchian, Cyrus and Stewart, Kendall and Gupta, Gagan and Carlson, Robert and Mulligan, John and Carmean, Douglas and Seelig, Georg and Ceze, Luis and Strauss, Karin},journal={Nature Biotechnology},volume={36},number={3},pages={242--248},year={2018},url={https://pubmed.ncbi.nlm.nih.gov/29457795/},note={Work done as an intern at Microsoft Research, Redmond: data analysis, modeling, and characterization of the storage channel.}}
@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>}}
@inproceedings{chen2016community,title={Community Recovery in Graphs with Locality},author={Chen, Yuxin and Kamath, Govinda M. and Suh, Changho and Tse, David N.},booktitle={International Conference on Machine Learning},series={Proceedings of Machine Learning Research},volume={48},pages={373--381},year={2016},}
@inproceedings{shomorony2016partial,title={Partial Assembly: A Rate-Distortion Perspective},author={Shomorony, Ilan and Kamath, Govinda M. and Xia, Fei and Courtade, Thomas A. and Tse, David N.},booktitle={IEEE International Symposium on Information Theory},year={2016},url={http://ieeexplore.ieee.org/document/7541609/},}
@article{ntranos2016tcc,title={Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts},author={Ntranos, Vasilis and Kamath, Govinda M. and Zhang, Jesse and Pachter, Lior and Tse, David N.},journal={Genome Biology},volume={17},pages={144},year={2016},url={https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0970-8},note={* Co-first authors}}
@techreport{zhang2015rnn,title={Learning the Language of the Genome using RNNs},author={Zhang, Jesse and Kamath, Govinda M.},institution={Stanford University, CS224d Course Project},year={2015},}
@inproceedings{kamath2015haplotype,title={Optimal Haplotype Assembly from High-Throughput Mate Pair Reads},author={Kamath, Govinda M. and Sasoglu, Eren and Tse, David N.},booktitle={IEEE International Symposium on Information Theory},year={2015},url={http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7282588},}
@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}}
Govinda M. Kamath, Narayanamoorthy Prakash, Lalitha Vadlamani, P. Vijay Kumar, Natalia Silberstein, Ankit S. Rawat, O. Ozan Koyluoglu, and Sriram Vishwanath
In IEEE International Symposium on Information Theory, 2013
@inproceedings{kamath2013mbr,title={Explicit MBR All-Symbol Locality Codes},author={Kamath, Govinda M. and Prakash, Narayanamoorthy and Vadlamani, Lalitha and Kumar, P. Vijay and Silberstein, Natalia and Rawat, Ankit S. and Koyluoglu, O. Ozan and Vishwanath, Sriram},booktitle={IEEE International Symposium on Information Theory},year={2013},url={http://ieeexplore.ieee.org/document/6620277/},}
@inproceedings{prakash2012optimal,title={Optimal Linear Codes with a Local-Error-Correction Property},author={Prakash, Narayanamoorthy and Kamath, Govinda M. and Vadlamani, Lalitha and Kumar, P. Vijay},booktitle={IEEE International Symposium on Information Theory},year={2012},url={http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=6284028},}
@inproceedings{kamath2012regenerating,title={Regenerating codes: a reformulated storage-bandwidth trade-off and a new construction},author={Kamath, Govinda M. and Kumar, P. Vijay},booktitle={National Conference on Communications},year={2012},url={http://ieeexplore.ieee.org/document/6176911/}}
@inproceedings{vadlamani2012tdesigns,title={On t-designs and bounds relating query complexity to error resilience in locally correctable codes},author={Vadlamani, Lalitha and Prakash, Narayanamoorthy and Kamath, Govinda M. and Kumar, P. Vijay},booktitle={National Conference on Communications},year={2012},url={https://ieeexplore.ieee.org/abstract/document/6176752/}}