Li B - Search Results

1

Evaluation of de novo transcriptome assemblies from RNA-Seq data.

Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Li B, et al. Genome Biol. 2014 Dec 21;15(12):553. doi: 10.1186/s13059-014-0553-5. Genome Biol. 2014. PMID: 25608678 Free PMC article.

2

RNA-Seq gene expression estimation with read mapping uncertainty.

Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. Li B, et al. Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18. Bioinformatics. 2010. PMID: 20022975 Free PMC article.

3

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Li B, Dewey CN. Li B, et al. BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323. BMC Bioinformatics. 2011. PMID: 21816040 Free PMC article.

4

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

Haas BJ, 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, Regev A. Haas BJ, et al. Among authors: li b. Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. Nat Protoc. 2013. PMID: 23845962 Free PMC article.

5

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.

Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keleş S. Zeng X, et al. Among authors: li b. PLoS Comput Biol. 2015 Oct 20;11(10):e1004491. doi: 10.1371/journal.pcbi.1004491. eCollection 2015 Oct. PLoS Comput Biol. 2015. PMID: 26484757 Free PMC article.

6

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.

Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Haas BJ, et al. Among authors: li b. Genome Biol. 2019 Oct 21;20(1):213. doi: 10.1186/s13059-019-1842-9. Genome Biol. 2019. PMID: 31639029 Free PMC article.

7

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, Keleş S. Chung D, et al. Among authors: li b. PLoS Comput Biol. 2011 Jul;7(7):e1002111. doi: 10.1371/journal.pcbi.1002111. Epub 2011 Jul 14. PLoS Comput Biol. 2011. PMID: 21779159 Free PMC article.

8

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq.

Li B, Gould J, Yang Y, Sarkizova S, Tabaka M, Ashenberg O, Rosen Y, Slyper M, Kowalczyk MS, Villani AC, Tickle T, Hacohen N, Rozenblatt-Rosen O, Regev A. Li B, et al. Nat Methods. 2020 Aug;17(8):793-798. doi: 10.1038/s41592-020-0905-x. Epub 2020 Jul 27. Nat Methods. 2020. PMID: 32719530 Free PMC article.

9

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.

Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. Slyper M, et al. Among authors: li b. Nat Med. 2020 May;26(5):792-802. doi: 10.1038/s41591-020-0844-1. Epub 2020 May 11. Nat Med. 2020. PMID: 32405060 Free PMC article.

10

The Diagnostic Value of the Modified STdmax/MET Criterion in Treadmill Exercise Electrocardiographic Test for Coronary Artery Disease in an Aged Population.

Li H, Li B, Cao Z, Zhang P, Gao L, Wang Y. Li H, et al. Among authors: li b. Altern Ther Health Med. 2024 May 3:AT10034. Online ahead of print. Altern Ther Health Med. 2024. PMID: 38702161

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