Publications

Dr. Bo Li, A. tambe, S. aviran, L. pachter (2017). PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Systems.
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B. haas, A. dobin, N. stransky, B. li, X. yang, T. tickle, A. bankapur, C. ganote, T. doak, N. pochet, J. sun, C. wu, T. gingeras, A. regev (2017). STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. bioRxiv.
Preprint
K. choudhary, N. p. shih, F. deng, M. ledda, B. li, S. aviran (2016). Metrics for Rapid Quality Control in RNA Structure Probing Experiments. Bioinformatics.
PDF Link
X. zeng, Dr. Bo Li, R. welch, C. rojo, Y. zheng, C. n. dewey, S. keles (2015). Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. PLoS Computational Biology.
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Dr. Alex Johnson
Equal contribution
, Robert ford
Equal contribution
(2015). An example journal article. Journal of Source Themes, 1(1).
PDF Code Dataset Poster Project Slides Source Document Video Preprint
Dr. Bo Li, N. fillmore, Y. bai, M. collins, J. a. thomson, R. stewart, C. n. dewey (2014). Evaluation of de novo Transcriptome Assemblies from RNA-Seq Data. Genome Biology.
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B. haas, A. papanicolaou, M. yassour, M. grabherr, P. d. blood, J. bowden, M. b. couger, D. eccles, Dr. Bo Li, M. lieber, M. d. macmanes, M. ott, J. orvis, N. pochet, F. strozzi, N. weeks, R. westerman, T. william, C. n. dewey, R. henschel, R. d. leduc, N. friedman, A. regev (2013). De novo Transcript Sequence Reconstruction from RNA-seq using the Trinity Platform for Reference Generation and Analysis. Nature Protocols.
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Dr. Alex Johnson
Equal contribution
, Robert ford
Equal contribution
(2013). An example conference paper. In ICW.
PDF Code Dataset Slides Source Document Video PDF DOI
Dr. Bo Li, C. n. dewey (2011). RSEM: Accurate Transcript Quantification from RNA-Seq Data with or without a Reference Genome. BMC Bioinformatics.
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D. chung, P. f. kuan, B. li, R. sanalkumar, K. liang, E. h. bresnick, C. dewey, S. keles (2011). Discoevering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. PLoS Computational Biology.
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