ArticleMolecular biology and evolution2018
Using Genotype Abundance to Improve Phylogenetic Inference.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Article
- Clonal dynamics of germinal center refueling by secondary immunization.bioRxiv : the preprint server for biology · 2026Article
- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.PLoS computational biology · 2025Article
- Nucleotide context models outperform protein language models for predicting antibody affinity maturation.bioRxiv : the preprint server for biology · 2025Article
- Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.Bioinformatics (Oxford, England) · 2025Article
- Clonal expansion and diversification of germinal center and memory B cell responses to booster immunization in primates.Cell reports · 2025Article
- AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees.Bioinformatics (Oxford, England) · 2025Article
- Clonal Expansion and Diversification of Germinal Center and Memory B Cell Responses to Booster Immunization in Primates.bioRxiv : the preprint server for biology · 2025Article
- Article
- Article
- Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Affinity maturation of antibody responses is mediated by differential plasma cell proliferation.Science (New York, N.Y.) · 2025Article
- Affinity maturation of antibody responses is mediated by differential plasma cell proliferation.bioRxiv : the preprint server for biology · 2024Article
- New generalized metric based on branch length distance to compare B cell lineage trees.Algorithms for molecular biology : AMB · 2024Article
- Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data.Cell genomics · 2024Article
- Covalent penicillin-protein conjugates elicit anti-drug antibodies that are clonally and functionally restricted.Nature communications · 2024Article
- Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.Molecular biology and evolution · 2024Article
- Ultrapotent Broadly Neutralizing Human-llama Bispecific Antibodies against HIV-1.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Protocol for fast clonal family inference and analysis from large-scale B cell receptor repertoire sequencing data.STAR protocols · 2024Article
- Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this article, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.