Henri Schmidt

LAML-Pro: Maximum Likelihood Inference of Cell Genotypes and Cell Lineage Trees

LAML-Pro jointly infers cell genotypes and lineage trees from lineage tracing data, improving accuracy by correcting genotype errors and producing more spatially coherent trees.

The tree labeling polytope: a unified approach to ancestral reconstruction problems

This paper introduces a polyhedral framework for ancestral reconstruction in phylogenetic trees, enabling efficient algorithms with additional constraints and improved performance on real datasets.

POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets

POTTR identifies recurrent mutation trajectories in cancer and development using posets, resolving uncertainty in phylogenies and discovering significant new patterns.

Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data using Backbone Trees

Sapling infers and summarizes tumor phylogenies from bulk data using backbone trees, demonstrating high-quality results on simulated and real data.

Inferring Cell Differentiation Dynamics with Unobserved Progenitors

The paper introduces TROUPE, a framework to infer cell differentiation dynamics from lineage trees, allowing for unobserved progenitor types and providing better rate estimates than existing methods.

Inferring cell differentiation maps from lineage tracing data

The paper introduces Carta, an algorithm that infers cell differentiation maps from single-cell lineage tracing data, showing improved accuracy over existing methods in simulated and real data.

Genetic mechanisms of resistance to targeted KRAS inhibition

This study identifies genetic mechanisms of resistance to KRAS inhibitors by using CRISPR screens to find resistance mutations and signaling rewiring in NSCLC.

Fast tumor phylogeny regression via tree-structured dual dynamic programming

The paper introduces fastppm, a fast tool for solving the regression problem in tumor phylogeny reconstruction, achieving significant speedups and accuracy improvements.

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2

GuideScan2 constructs high-specificity CRISPR gRNA databases and enables design of allele-specific gRNAs, reducing off-target effects in gene essentiality screens.

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors

This paper introduces fastBE, a method for phylogenetic reconstruction from bulk DNA sequencing data that improves accuracy and scalability over existing approaches.

Startle: a star homoplasy approach for CRISPR-Cas9 lineage tracing

Startle is a method for inferring CRISPR-Cas9 lineage trees using a star homoplasy model, showing improved accuracy on simulated and real datasets.

A zero-agnostic model for copy number evolution in cancer

The paper introduces a zero-agnostic copy number transformation model and develops an algorithm for inferring copy number phylogenies, showing improved performance on simulated and real data.

Multi-center integrated analysis of non-coding CRISPR screens

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.