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 theoretical computer science and operations research to study problems in computational biology. Specifically, I apply these techniques to study phylogenetic optimization problems that arise in cancer evolution and lineage tracing. As an example, my recent work fastBE develops specialized algorithms to enable large-scale phylogenetic reconstruction of tumors using primal-dual methods for solving linear programs.
Recent Updates
- (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.
- (April 2024) The fastBE paper was presented at RECOMB-CCB.
Journal Publications
* denotes joint first authorship; author order is rearranged with permission from co-authors.
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, Benjamin J. Raphael
PLoS Computational Biology, Volume 20, Issue 12, December 2024. [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, Benjamin J. Raphael
Cell Systems, Volume 14, Issue 12, December 2023, Pages 1113-1121. [slides]
A zero agnostic model for copy number evolution in cancer
Henri Schmidt, Palash Sashittal, Benjamin J. Raphael
PLoS Computational Biology, Volume 19, Issue 11, November 2023. [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, Benjamin J. Raphael
bioRxiv, February 19th, 2025. Presented at RECOMB 2025. [slides]
Fast tumor phylogeny regression via tree-structured dual dynamic programming
Henri Schmidt*, Yuanyuan Qi*, Benjamin J. Raphael, Mohammed El-Kebir
bioRxiv, January 27th, 2025. Accepted to Bioinformatics, presenting at ISMB 2025.
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
bioRxiv, September 13th, 2024. Presented at RECOMB 2025.
Manuscripts in preparation
Outbreaks, Metastases and Homomorphisms: Phylogenetic Inference of Migration Histories of Heterogeneous Populations under Evolutionary and Structural Constraints
Kiril Kuzmin, Henri Schmidt, Sagi Snir, Benjamin Raphael, Pavel Skums
Research Square, September 13th, 2024.