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Bo Li - Publications

Affiliations: 
2013- University of California, Berkeley, Berkeley, CA, United States 
Area:
Bioinformatics, RNA, Sequencing
Website:
http://bli25ucb.github.io/
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Liu XF, Luo JJ, Li TY, Chen H, Liu JY, Li B, Dou L, Fu ZX. Characterization and phylogenetic analysis of the complete chloroplast genome of (Asteraceae, Cardueae). Mitochondrial Dna. Part B, Resources. 8: 1268-1272. PMID 38188437 DOI: 10.1080/23802359.2023.2281704  0.371
2022 Guo Z, Li B, Du J, Shen F, Zhao Y, Deng Y, Kuang Z, Tao Y, Wan M, Lu X, Wang D, Wang Y, Han Y, Wei J, Li L, et al. LettuceGDB: the community database for lettuce genetics and omics. Plant Communications. 100425. PMID 35964156 DOI: 10.1016/j.xplc.2022.100425  0.318
2022 Wang L, Li B, Jiang J, Tong X. The complete mitochondrial genomes of (Ephemeroptera: Ephemeridae) and phylogenetic analysis. Mitochondrial Dna. Part B, Resources. 7: 461-463. PMID 35295906 DOI: 10.1080/23802359.2022.2044401  0.315
2021 Lozano R, Booth GT, Omar BY, Li B, Buckler ES, Lis JT, Del Carpio DP, Jannink JL. RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants. G3 (Bethesda, Md.). PMID 34499719 DOI: 10.1093/g3journal/jkab273  0.335
2020 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. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Nature Methods. PMID 32719530 DOI: 10.1038/S41592-020-0905-X  0.364
2020 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, ... ... Li B, et al. Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nature Medicine. PMID 32587393 DOI: 10.1038/S41591-020-0976-3  0.335
2020 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, ... ... Li B, et al. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nature Medicine. 26: 792-802. PMID 32405060 DOI: 10.1038/S41591-020-0844-1  0.328
2020 Lavaert M, Liang KL, Vandamme N, Park JE, Roels J, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Vandekerckhove B, Leclercq G, et al. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Immunity. PMID 32304633 DOI: 10.1016/J.Immuni.2020.03.019  0.311
2019 Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biology. 20: 213. PMID 31639029 DOI: 10.1186/S13059-019-1842-9  0.418
2019 Gaublomme JT, Li B, McCabe C, Knecht A, Yang Y, Drokhlyansky E, Van Wittenberghe N, Waldman J, Dionne D, Nguyen L, De Jager PL, Yeung B, Zhao X, Habib N, Rozenblatt-Rosen O, et al. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. Nature Communications. 10: 2907. PMID 31266958 DOI: 10.1038/S41467-019-10756-2  0.331
2019 Zheng YY, Sheng SD, Hui TY, Yue C, Sun JM, Guo D, Guo SL, Li BJ, Xue HL, Wang ZY, Bai WL. An Integrated Analysis of Cashmere Fineness lncRNAs in Cashmere Goats. Genes. 10. PMID 30987022 DOI: 10.3390/genes10040266  0.3
2019 Natarajan KN, Miao Z, Jiang M, Huang X, Zhou H, Xie J, Wang C, Qin S, Zhao Z, Wu L, Yang N, Li B, Hou Y, Liu S, Teichmann SA. Comparative analysis of sequencing technologies for single-cell transcriptomics. Genome Biology. 20: 70. PMID 30961669 DOI: 10.1186/S13059-019-1676-5  0.326
2019 Ouspenskaia T, Law TE, Clauser KR, Klaeger S, Keskin DB, Li B, Christian E, Chow YT, Le PM, Gould J, Ji Z, Zhang W, Bachireddy P, Sarkizova S, Hacohen N, et al. Abstract 566: Neoantigens from translated unannotated open reading frames in cancer Cancer Research. 79: 566-566. DOI: 10.1158/1538-7445.Am2019-566  0.314
2017 Li B. The complete mitochondrial genome of (Siluriformes, Sisoridae, ): genome characterization and phylogenetic analysis. Mitochondrial Dna. Part B, Resources. 2: 259-260. PMID 33473791 DOI: 10.1080/23802359.2017.1307701  0.304
2017 Li B, Tambe A, Aviran S, Pachter L. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Systems. PMID 28501650 DOI: 10.1016/J.Cels.2017.04.007  0.715
2017 Li B, Brinks E, Franz CMAP, Cho GS. Draft Genome Sequence of Staphylococcus fleurettii Strain MBTS-1 Isolated from Cucumber. Genome Announcements. 5. PMID 28495782 DOI: 10.1128/genomeA.00335-17  0.303
2017 Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, Borm TJ, Ohyanagi H, Mineta K, Michell CT, Saber N, Kharbatia NM, Rupper RR, Sharp AR, Dally N, Boughton BA, et al. The genome of Chenopodium quinoa. Nature. 1-6. PMID 28178233 DOI: 10.1038/Nature21370  0.309
2016 Choudhary K, Shih NP, Deng F, Ledda M, Li B, Aviran S. Metrics for rapid quality control in RNA structure probing experiments. Bioinformatics (Oxford, England). PMID 27497441 DOI: 10.1093/Bioinformatics/Btw501  0.354
2016 Master RR, Li B, Li F. The complete mitochondrial genome of Japanese Marsh Warbler, Locustella pryeri Mitochondrial Dna. 27: 373-374. DOI: 10.3109/19401736.2014.895992  0.315
2016 Wang Z, Morris JS, Holmes CC, Ahn J, Li B, Lu W, Tang X, Wistuba II, Wang W. Abstract 2413: Cell type-specific deconvolution of heterogeneous tumor samples with immune infiltration using expression data Cancer Research. 76: 2413-2413. DOI: 10.1158/1538-7445.Am2016-2413  0.305
2015 Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keleş S. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. Plos Computational Biology. 11: e1004491. PMID 26484757 DOI: 10.1371/Journal.Pcbi.1004491  0.728
2015 Cao H, Wu H, Luo R, Huang S, Sun Y, Tong X, Xie Y, Liu B, Yang H, Zheng H, Li J, Li B, Wang Y, Yang F, Sun P, et al. De novo assembly of a haplotype-resolved human genome. Nature Biotechnology. 33: 617-22. PMID 26006006 DOI: 10.1038/Nbt.3200  0.301
2014 Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology. 15: 553. PMID 25608678 DOI: 10.1186/S13059-014-0553-5  0.725
2014 Master RR, Li B, Li F. The complete mitochondrial genome of Japanese Marsh Warbler, Locustella pryeri. Mitochondrial Dna. Part a, Dna Mapping, Sequencing, and Analysis. 27: 373-4. PMID 24617481 DOI: 10.3109/19401736.2014.895992  0.307
2013 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, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols. 8: 1494-512. PMID 23845962 DOI: 10.1038/Nprot.2013.084  0.749
2013 Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C, Chen C, Zhang W, Sun S, Liao Y, Zhang X, et al. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications. 4: 1595. PMID 23481403 DOI: 10.1038/Ncomms2596  0.303
2011 Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Bmc Bioinformatics. 12: 323. PMID 21816040 DOI: 10.1186/1471-2105-12-323  0.76
2011 Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, KeleÅŸ S. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. Plos Computational Biology. 7: e1002111. PMID 21779159 DOI: 10.1371/Journal.Pcbi.1002111  0.738
2010 Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics (Oxford, England). 26: 493-500. PMID 20022975 DOI: 10.1093/Bioinformatics/Btp692  0.736
2010 Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, et al. The sequence and de novo assembly of the giant panda genome. Nature. 463: 311-7. PMID 20010809 DOI: 10.1038/Nature08696  0.307
2004 Xiao M, Gao J, Wang W, Wang Y, Chen J, Chen J, Li B. Specific interaction between the classical swine fever virus NS5B protein and the viral genome. European Journal of Biochemistry. 271: 3888-96. PMID 15373834 DOI: 10.1111/j.1432-1033.2004.04325.x  0.302
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