A5093063061- Genomics and Phylogenetic Studies
- Evolution and Paleontology Studies
- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Single-cell and spatial transcriptomics
- Immune Cell Function and Interaction
- Chronic Lymphocytic Leukemia Research
- T-cell and B-cell Immunology
Fred Hutch Cancer Center
2023-2025
Howard Hughes Medical Institute
2025
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2024-2025
The phylogenetic inference package GCtree uses abundance of sampled sequences to improve the performance parsimony-based inference, using a branching process model. Our previous work showed that performs competitively on B-cell receptor data, compared with other similar tools. In this article, we describe recent enhancements GCtree, including an efficient tree storage data structure discovers additional diversity parsimonious trees negligible computational cost. We also suite new objective...
Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, understanding selective forces guiding maturation, and underlying biochemical process. High throughput data offers potential to develop fit on relevant sets. In this paper we model using modern frameworks. We motivated by recent work suggesting importance a wider context SHM, however, assigning an independent rate each k-mer...
Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, understanding selective forces guiding maturation, and underlying biochemical process. High throughput data offers potential to develop fit on relevant sets. In this paper we model using modern frameworks. We motivated by recent work suggesting importance a wider context SHM, however, assigning an independent rate each k-mer...
Abstract In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current methods do scale large sets. Furthermore, sets with relatively low signal one cannot even store every good individually, especially when trees are required bifurcating. this paper, we develop novel object called “history subpartition directed acyclic graph” (or sDAG”...
Abstract Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, understanding selective forces guiding maturation, and underlying biochemical process. High throughput data offers potential to develop fit on relevant sets. In this paper we model using modern frameworks. We motivated by recent work suggesting importance a wider context SHM, however, assigning an independent rate each...
Why do phylogenetic algorithms fail when they return incorrect answers? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest criterion. Understanding MP recently gained relevance regime of extremely dense sampling, where each virus sample commonly differs by zero or one mutation from another previously sampled virus. Although recent research shows that evolutionary histories this are close to being maximally parsimonious, structure their...
In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current methods do scale large sets. Furthermore, sets with relatively low signal one cannot even store every good individually, especially when trees are required bifurcating. this paper, we develop novel object called "history subpartition directed acyclic graph" (or sDAG" short)...