Author
Simons Foundation
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
5 papers
Recent·Most cited
Tymor Hamamsy, James T. Morton, Daniel Berenberg…·Richard Bonneau
TM-Vec predicts structural similarity from sequence pairs to detect remote homologs, outperforming sequence alignment methods and matching structure-based alignment performance.
Claudia Skok Gibbs, Christopher A. Jackson, Giuseppe-Antonio Saldi…·Richard Bonneau
The paper introduces Inferelator 3.0, a tool for inferring gene regulatory networks from single-cell data, showing improved performance on yeast and mouse brain datasets.
Anders W. Rasmussen, Tarmo Äijö, Mariano I. Gabitto…·Richard Bonneau
CRISPR-Decryptr analyzes noncoding CRISPR screens to infer regulatory elements by accounting for experimental design and validating on published data.
Mariano I. Gabitto, Anders W. Rasmussen, Orly L. Wapinski…·Richard Bonneau
The paper introduces ChromA, a Bayesian method for analyzing ATAC-seq data to annotate chromatin accessibility, improving cell type identification and correcting biases in single-cell data.
Xi Xian Chen, Bowen Yu, Nicholas John Carriero…·Richard Bonneau
Mocap predicts transcription factor binding sites using chromatin accessibility and genomic features, outperforming existing methods for new TF-cell-type combinations.