RNA-Seq gene expression estimation with read mapping uncertainty. - Bo Li 015; Victor Ruotti; Ron M. Stewart; James A. Thomson; Colin N. Dewey (Bioinform., 2010)

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. - Bo Li 015; Colin N. Dewey (BMC Bioinform., 2011)

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. - Dongjun Chung; Pei Fen Kuan; Bo Li 015; Rajendran Sanalkumar; Kun Liang 001; Emery H. Bresnick; Colin N. Dewey; Sündüz Keles (PLoS Comput. Biol., 2011)

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. - Xin Zeng; Bo Li 015; Rene Welch; Constanza Rojo; Ye Zheng; Colin N. Dewey; Sündüz Keles (PLoS Comput. Biol., 2015)

Metrics for rapid quality control in RNA structure probing experiments. - Krishna Choudhary; Nathan P. Shih; Fei Deng; Mirko Ledda; Bo Li 015; Sharon Aviran (Bioinform., 2016)

Decoding human fetal liver haematopoiesis. - Dorin-Mirel Popescu; Rachel A. Botting; Emily Stephenson; Kile Green; Simone Webb; Laura Jardine; Emily F. Calderbank; Krzysztof Polanski; Issac Goh; Mirjana Efremova; Meghan Acres; Daniel Maunder; et al. (Nat., 2019)