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View article: larch: mapping the parsimony-optimal landscape of trees for directed exploration
larch: mapping the parsimony-optimal landscape of trees for directed exploration Open
Phylogenetic inference algorithms for large data sets typically return a single tree. However, there are often many optimal trees, especially when sequence data is closely related. We develop a compact representation of large collections o…
View article: Separating selection from mutation in antibody language models
Separating selection from mutation in antibody language models Open
Antibodies are encoded by nucleotide sequences that are generated by V(D)J recombination and evolve according to mutation and selection processes. Existing antibody language models, however, focus exclusively on antibodies as strings of am…
View article: Thrifty wide-context models of B cell receptor somatic hypermutation
Thrifty wide-context models of B cell receptor somatic hypermutation Open
Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, understanding the selective forces guiding affinity maturation, and under…
View article: A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer–Encoder
A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer–Encoder Open
During affinity maturation, antibodies are selected for their ability to fold and to bind a target antigen between rounds of somatic hypermutation. Previous studies have identified patterns of selection in antibodies using B cell repertoir…
View article: Thrifty wide-context models of B cell receptor somatic hypermutation
Thrifty wide-context models of B cell receptor somatic hypermutation Open
Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, for understanding the selective forces guiding affinity maturation, and f…
View article: Replaying germinal center evolution on a quantified affinity landscape
Replaying germinal center evolution on a quantified affinity landscape Open
Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition between GC B cells drives increased affin…
View article: Thrifty wide-context models of B cell receptor somatic hypermutation
Thrifty wide-context models of B cell receptor somatic hypermutation Open
Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, for understanding the selective forces guiding affinity maturation, and f…
View article: Thrifty wide-context models of B cell receptor somatic hypermutation
Thrifty wide-context models of B cell receptor somatic hypermutation Open
Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, understanding the selective forces guiding affinity maturation, and under…
View article: Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation
Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation Open
The phylogenetic inference package GCtree uses abundance of sampled sequences to improve the performance of parsimony-based inference, using a branching process model. Our previous work showed that GCtree performs competitively on B-cell r…
View article: Thrifty wide-context models of B cell receptor somatic hypermutation
Thrifty wide-context models of B cell receptor somatic hypermutation Open
Somatic hypermutation (SHM) is the diversity-generating process in antibody affinity maturation. Probabilistic models of SHM are needed for analyzing rare mutations, for understanding the selective forces guiding affinity maturation, and f…
View article: The structure of deviations from maximum parsimony for densely-sampled data and applications for clade support estimation
The structure of deviations from maximum parsimony for densely-sampled data and applications for clade support estimation Open
How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has rece…
View article: Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph
Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph Open
In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current Bayesian method…