Academic Employment

• 2017.07 — present        Postdoctoral associate at Regev Lab, Broad Institute of MIT and Harvard
• 2013.08 — 2017.06        Postdoctoral researcher at Pachter Lab, University of California at Berkeley

Education

• 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

Research

I'm a computational biologist working on single cell RNA-Seq data analysis. I use statistics and machine learning extensively in my research.

Publications

* Equal contributors

• Gaublomme JT*, Li B*, McCabe C, Knecht A, Drokhlyansky E, Van Wittenberghe N, Waldman J, Dionne D, Nguyen L, De Jager P, Yeung B, Zhao X, Habib N, Rozenblatt-Rosen O and Regev A. (2018). Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. bioRxiv, 10.1101/476036.


• Li B, Tambe A, Aviran S and Pachter L. (2017). PROBer provides a general toolkit for analyzing sequencing-based toeprinting assays. Cell Systems, 4(5), 568-574.


• 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, 32(23), 3575-3583.


• 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.

Software

• 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.

Miscellaneous

• Manubot: a piece of open-source software that automates the process of collating, formatting and publishing a scientific paper. Each time an author creates a version of the manuscript, the software logs that event on the Bitcoin blockchain.


• Sciencematters EUREKA: Using a peer-review platform called Eureka, ScienceMatters offering its triple-blind peer-review process through a publishing platform that uses the Ethereum blockchain (as well as the prevailing many other projects).


• ARTiFACTS: provides a forum in which researchers can upload almost anything that they deem worth sharing, with each file logged to a blockchain.