Publications

Computational Genomics

Integrated analysis of multimodal single-cell data
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P Mimitou, Jaison Jain, Avi Srivastava, Tim Stuart, Lamar M Fleming, Bertrand Yeung, Angela J Rogers, Juliana M McElrath, Catherine A Blish, Raphael Gottardo, Peter Smibert, Rahul Satija
Cell (2021)
Seurat R package

Vargas: heuristic-free alignment for assessing linear and graph read aligners
Charlotte A Darby, Ravi Gaddipati, Michael C Schatz, Ben Langmead
Bioinformatics (2020)
Vargas software

scHLAcount: allele-specific HLA expression from single-cell gene expression data
Charlotte A Darby, Michael J T Stubbington, Patrick J Marks, Álvaro Martínez Barrio, Ian T Fiddes
Bioinformatics (2020)
scHLAcount software

Clonal hematopoiesis before, during, and after human spaceflight
Nuria Mencia-Trinchant, Matthew J MacKay, Christopher Chin, Ebrahim Afshinnekoo, Jonathan Foox, Cem Meydan, Daniel Butler, Christopher Mozsary, Nicholas A Vernice, Charlotte Darby, Michael C Schatz, Susan M Bailey, Ari M Melnick, Monica L Guzman, Kelly Bolton, Lior Z Braunstein, Francine Garrett-Bakelman, Ross L Levine, Duane C Hassane, Christopher E Mason
Cell Reports (2020)
Seurat R package

Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads
Charlotte A Darby, James R Fitch, Patrick J Brennan, Benjamin J Kelly, Natalie Bir, Vincent Magrini, Jeffrey Leonard, Catherine E Cottrell, Julie M Gastier-Foster, Richard K Wilson, Elaine R Mardis, Peter White, Ben Langmead, Michael C Schatz
iScience (2019)
Best Paper Award, RECOMB-Seq 2019
Samovar software

Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Fritz J Sedlazeck, Hayan Lee, Charlotte A Darby, Michael C Schatz
Nature Reviews Genetics (2018)

LRSim: a linked-reads simulator generating insights for better genome partitioning
Ruibang Luo, Fritz J Sedlazeck, Charlotte A Darby, Stephen M Kelly, Michael C Schatz
Computational and structural biotechnology journal (2017)
LRSim software

Phylogenetics

Xenolog classification
Charlotte A Darby, Maureen Stolzer, Patrick J Ropp, Daniel Barker, Dannie Durand
Bioinformatics (2017) Notung software

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