Daniel E. Hoffmann

The paper introduces cellmig, a Bayesian tool for quantifying cell migration velocity with uncertainty, improving reproducibility and biological insight in high-throughput assays.

The paper analyzes TCR repertoires in melanoma tumors and sentinel lymph nodes to reveal distinct clonal architectures and shared antigen recognition patterns.

This paper introduces ClustIRR, a framework for analyzing T cell receptor repertoire structure and dynamics with uncertainty quantification, demonstrating its application in antigen challenge, cancer immunotherapy, and V(D)J recombination biases.

BARMIX quantifies treatment resistance in gastrointestinal stromal tumor cell mixtures using barcoded experiments and probabilistic modeling, accurately reflecting clinical resistance patterns.

This study shows that heparan sulfate (HS) is critical for integrin-mediated cell-matrix interactions and regulates glycosaminoglycan (GAG) synthesis through YAP signaling in chondrocytes.

This study evaluates multiplet rates in scRNA-seq data and shows that existing detection methods are insufficient, leading to distorted clustering and annotation.

scBubbletree provides a scalable visualization method for scRNA-seq data by clustering cells into bubbles on dendrograms, enabling quantitative assessment and biological interpretation.

The paper improves statistical model accuracy in animal research to increase information gain per animal, showing benefits for small sample sizes.

The paper introduces a Bayesian regression model to detect HLA-associated mutations by integrating multiple sources of information, improving detection performance over existing methods.

This study compares transcriptomes from SARS-CoV-2, SARS-CoV, and MERS-CoV infections to investigate alternative entry routes and innate immune responses.

The paper investigates epigenetic mechanisms driving cell state transitions in chondrocytes by analyzing histone modifications and gene expression during differentiation.

This study investigates the role of Atoh8 in chondrocyte proliferation and differentiation during endochondral bone development using mouse models.

The paper introduces an eco-evolutionary model showing that trade-offs between replication rate and competitive ability lead to structured communities with high diversity through self-organization.