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 on protein-to-protein interaction graphs.
I am broadly interested in employing techniques from theoretical computer science to study algorithmic problems in computational biology. More specifically, I study combinatorial optimization problems that arise in computational phylogenetics. Currently, I am working on i) designing fast algorithms for the clone tree regression problem and ii) applying the theory of network flows to solve constrained tree coloring problems.
Recent Updates
- (March 2024) The fastBE paper was accepted at RECOMB-CCB 2024 and invited for journal publication.
- (August 2023) The ZCNT paper was published in PLOS Computational Biology.
- (May 2023) Presented my work on the zero agnostic copy number transformation (ZCNT) model at the Banff International Research Station for Mathematical Innovation and Discovery.
- (April 2023) Presented my work on Startle and ZCNT at RECOMB-2023 and the RECOMB-2023 satellite for computational cancer biology.
- (March 2023) Received an Honorable Mention in the NSF GRFP fellowship competition.
Conference Presentations
* denotes joint first authorship.
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
Henri Schmidt, Benjamin J. Raphael
RECOMB Satellite Workshop on Computational Cancer Biology, RECOMB-CCB 2024 [slides].
A zero agnostic model for copy number evolution in cancer
Henri Schmidt, Palash Sashittal, Benjamin J. Raphael
RECOMB Satellite Workshop on Computational Cancer Biology, RECOMB-CCB 2023 [slides].
Best Paper Award
Startle: A star homoplasy approach for CRISPR-Cas9 Lineage Tracing
Henri Schmidt*, Palash Sashittal*, Michelle Chan, Benjamin J. Raphael
International Conference on Research in Computational Molecular Biology, RECOMB 2023 [slides].
Journal Publications
Multi-center integrated analysis of non-coding CRISPR screens
David Yao, Josh Tycko, …, Henri Schmidt, …, Michael C. Bassik, Steven K. Reilly
Nature Methods, 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.
A zero agnostic model for copy number evolution in cancer
Henri Schmidt, Palash Sashittal, Benjamin J. Raphael
PLOS Computational Biology, November 2023.
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.
Preprints
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
bioRxiv, May 3rd, 2022.