89 citations · 255 across the 26 of their papers we have counts for
31 papers
Automatic differentiation is no panacea for phylogenetic gradient computation
Mathieu Fourment, Christiaan J. Swanepoel, Jared G. Galloway +4
Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily…
Inference of B cell clonal families using heavy/light chain pairing information
Duncan K. Ralph, Frederick A. Matsen
Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large…
Lack of evidence for a substantial rate of templated mutagenesis in B cell diversification
Julia Fukuyama, Branden J Olson, Frederick A Matsen
B cell receptor sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major…
Using B cell receptor lineage structures to predict affinity
Duncan K. Ralph, Frederick A. Matsen
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic fo…
Estimation of cell lineage trees by maximum-likelihood phylogenetics
Jean Feng, William S DeWitt, Aaron McKenna +3
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, th…
On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model
Lam Si Tung Ho, Vu Dinh, Frederick A. Matsen +1
Maximum likelihood estimators are used extensively to estimate unknown parameters of stochastic trait evolution models on phylogenetic trees. Although the MLE has been proven to co…