I am a PhD candidate in Computer Science at Princeton University. I am very fortunate to be advised by Ben Raphael. Prior to working with Ben Raphael, I completed a Bachelor of Science in Math and Computer Science at Tufts University, where I worked with Lenore Cowen designing algorithms for protein-to-protein interaction networks.
Currently, my research employs techniques from combinatorial and convex optimization to study problems in biology and machine learning. For example, I applied linear and convex optimization techniques to large-scale phylogenetic problems in cancer evolution (fastBE) and ancestral reconstruction (tree labeling polytope). More recently, I have applied similar tools to design approximation algorithms for low-rank optimal transport.
Recent Updates
- (July 2025) I presented our work fastppm at ISMB 2025.
- (January 2025) Our preprint Fast tumor phylogeny regression via tree-structured dual dynamic programming is now available on bioRxiv.
- (December 2024) The tree labeling polytope manuscript was accepted for presentation at RECOMB2025.
- (December 2024) The fastBE manuscript was published in PLoS Computational Biology.
- (September 2024) Attended the ICERM workshop regarding Current Methods and Open Problems in Mathematical and Statistical Phylogenetics.
Journal Publications
* denotes joint first authorship; author order is rearranged with permission from co-authors.
† denotes additional conference presentation.
Inferring cell differentiation maps from lineage tracing data†
Palash Sashittal*, Richard Y. Zhang*, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael
In Press at Nature Methods, September, 2025. Presented at RECOMB 2025.
A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints
Kiril Kuzmin, Henri Schmidt, Maryam Kafi Kang, Sagi Snir, Benjamin J. Raphael, Pavel Skums
Nature Communications, Volume 16, August 2025.
Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML†
Gillian Chu*, Uyen Mai*, Henri Schmidt, and Benjamin J. Raphael
Genome Biology, Volume 26, July 2025. Presented at RECOMB 2025.
Fast tumor phylogeny regression via tree-structured dual dynamic programming†
Henri Schmidt*, Yuanyuan Qi*, Benjamin J. Raphael,and Mohammed El-Kebir
Bioinformatics, Volume 41, July 2025. Presented at ISMB 2025. [slides]
Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
Henri Schmidt*, Minsi Zhang*, Haralambos Mourelatos, Francisco J. Sánchez-Rivera, Scott W. Lowe, Andrea Ventura, Christina S. Leslie, Yuri Pritykin
Genome Biology, Volume 26, Article 41, February 26, 2025.
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors†
Henri Schmidt and Benjamin J. Raphael
PLoS Computational Biology, Volume 20, Issue 12, December 2024. Presented at RECOMB-CCB. [slides]
Multi-center integrated analysis of non-coding CRISPR screens
David Yao, Josh Tycko, …, Henri Schmidt, …, Michael C. Bassik, Steven K. Reilly
Nature Methods, Volume 21, Issue 4, Pages 723-734, February 2024.
Startle: A star homoplasy approach for CRISPR-Cas9 Lineage Tracing†
Henri Schmidt*, Palash Sashittal*, Michelle Chan, and Benjamin J. Raphael
Cell Systems, Volume 14, Issue 12, December 2023, Pages 1113-1121. Presented at RECOMB 2023. [slides]
A zero agnostic model for copy number evolution in cancer†
Henri Schmidt, Palash Sashittal, and Benjamin J. Raphael
PLoS Computational Biology, Volume 19, Issue 11, November 2023. Best paper at RECOMB-CCB. [slides]
GLIDER: function prediction from GLIDE-based neighborhoods
Kapil Devkota, Henri Schmidt, Matt Werenski, James M Murphy, Mert Erden, Victor Arsenescu, Lenore J. Cowen
Bioinformatics, Volume 38, Issue 13, July 2022, Pages 3395-3406.
Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants
Francisco J. Sánchez-Rivera, Bianca J. Diaz, Edward R. Kastenhuber, Henri Schmidt, …, Scott W. Lowe, Lukas Dow
Nature biotechnology, Volume 40, Issue 6, June 2022, Pages 862-873.
Conference Papers
The tree labeling polytope: a unified approach to ancestral reconstruction problems
Henri Schmidt and Benjamin J. Raphael
bioRxiv, February 19th, 2025. Presented at RECOMB 2025. [slides]
Manuscripts in preparation
Transport clustering: solving low-rank optimal transport via clustering
Henri Schmidt*, Peter Halmos*, and Benjamin J. Raphael
Under review at ICLR 2026.
LAML-Pro: Joint maximum likelihood inference of cell genotypes and cell lineage trees
Gillian Chu*, Henri Schmidt*, and Benjamin J. Raphael
In submission at RECOMB 2026.
Genetic mechanisms of resistance to targeted KRAS inhibition
Bianca J Diaz*, Max Kops*, Sara Bernardo*, Henri Schmidt*, …, Lukas E. Dow
bioRxiv, August 2025.