Center for RNA Systems Biology
University of California at Berkeley
378F Stanley Hall
Berkeley, CA 94720-3840
Email: bli25 [at] berkeley [dot] edu
- 2013.08 — present        Postdoctoral researcher at Prof. Lior Pachter 's lab
- 2008.09 — 2013.07        Ph.D. in Computer Sciences,   University of Wisconsin-Madison
- 2008.09 — 2010.05        M.S. in Computer Sciences,   University of Wisconsin-Madison
- 2004.09 — 2008.07        B.E. in Computer Science and Engineering (ACM Honor Class),   Shanghai Jiao Tong University
I'm a computational biologist working on RNA-centric systems biology and next-generation sequencing (NGS) data analysis. I use statistics and machine learning extensively in my research.
* Equal contributors
- Li B, Tambe A, Aviran S and Pachter L. (2016). PROBer: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays. Submitted.
- Choudhary K, Shih NP, Deng F, Ledda M, Li B and Aviran S. (2016). Metrics for rapid quality control in RNA structure probing experiments. Bioinformatics, advance online access.
- Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN and Keleʂ S. (2015). Perm-seq: Mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping. PLoS Computational Biology, 11(10):e1004491.
- Li B*, Fillmore N*, Bai Y, Collins M, Thomson JA, Stewart R and Dewey CN. (2014). Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology, 15(12), 553.
- Haas B, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N and Regev A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8), 1494-1512.
- Li B and Dewey CN. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 12:323.
- Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick E, Dewey CN and Keleʂ S. (2011). Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-seq data. PLoS Computational Biology, 7:e1002111.
- Li B, Ruotti V, Stewart RM, Thomson JA and Dewey CN. (2010). RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics, 26(4), 493-500.
- PROBer: A principled and unified probabilistic framework for analyzing sequencing-based 'toeprinting' assays.
- DETONATE(DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation): A de novo transcriptome assembly evaluation package, which contains two components, RSEM-EVAL and REF-EVAL. I developed the RSEM-EVAL component.
- RSEM(RNA-Seq by Expectation-Maximization): Accurate gene and isoform expression levels quantification from RNA-Seq data with or without a reference genome.
- CSEM(ChIP-Seq multi-read allocation using Expectation-Maximization): One of the first ChIP-Seq multi-mapping read allocators. CSEM allows multi-reads to be utilized by peak callers.