Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Bo Li, Ph.D.

Title
Institution
Department
Address
Phone
Profile Picture

Biography
Shanghai Jiao Tong University, Shanghai, ChinaB.E.07/2008Computer Science and Engineering
University of Wisconsin-Madison, Madison, WIPh.D.07/2013Computer Sciences
University of California, Berkeley, Berkeley, CAPostdoc06/2017Computational Biology
Broad Institute of MIT and Harvard, Cambridge, MAPostdoc04/2019Computational Biology

Overview

Featured Content

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, et al. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021 07; 595(7865):107-113. PMID: 33915569.
    Citations: 12     Fields:    Translation:HumansCells
  2. Bao EL, Nandakumar SK, Liao X, Bick AG, Karjalainen J, Tabaka M, Gan OI, Havulinna AS, Kiiskinen TTJ, Lareau CA, de Lapuente Portilla AL, Li B, Emdin C, Codd V, Nelson CP, Walker CJ, Churchhouse C, de la Chapelle A, Klein DE, Nilsson B, Wilson PWF, Cho K, Pyarajan S, Gaziano JM, Samani NJ, Regev A, Palotie A, Neale BM, Dick JE, Natarajan P, O'Donnell CJ, Daly MJ, Milyavsky M, Kathiresan S, Sankaran VG. Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells. Nature. 2020 10; 586(7831):769-775. PMID: 33057200.
    Citations: 12     Fields:    Translation:HumansCells
  3. 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. Nat Methods. 2020 08; 17(8):793-798. PMID: 32719530.
    Citations: 14     Fields:    
  4. 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. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med. 2020 05; 26(5):792-802. PMID: 32405060.
    Citations: 43     Fields:    Translation:HumansAnimalsCells
  5. Sen P, Wilkie AR, Ji F, Yang Y, Taylor IJ, Velazquez-Palafox M, Vanni EAH, Pesola JM, Fernandez R, Chen H, Morsett LM, Abels ER, Piper M, Lane RJ, Hickman SE, Means TK, Rosenberg ES, Sadreyev RI, Li B, Coen DM, Fishman JA, El Khoury J. Linking indirect effects of cytomegalovirus in transplantation to modulation of monocyte innate immune function. Sci Adv. 2020 Apr; 6(17):eaax9856. PMID: 32494628.
    Citations:    Fields:    
  6. 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, Regev A, Van Vlierberghe P, Guilliams M, Teichmann SA, Saeys Y, Taghon T. Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Immunity. 2020 06 16; 52(6):1088-1104.e6. PMID: 32304633.
    Citations: 15     Fields:    Translation:HumansCells
  7. 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 Biol. 2019 10 21; 20(1):213. PMID: 31639029.
    Citations: 68     Fields:    Translation:Cells
  8. Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M. Decoding human fetal liver haematopoiesis. Nature. 2019 10; 574(7778):365-371. PMID: 31597962.
    Citations: 90     Fields:    Translation:HumansCells
  9. 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, Regev A. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. Nat Commun. 2019 07 02; 10(1):2907. PMID: 31266958.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  10. Li B, Tambe A, Aviran S, Pachter L. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Syst. 2017 05 24; 4(5):568-574.e7. PMID: 28501650.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  11. Choudhary K, Shih NP, Deng F, Ledda M, Li B, Aviran S. Metrics for rapid quality control in RNA structure probing experiments. Bioinformatics. 2016 12 01; 32(23):3575-3583. PMID: 27497441.
    Citations: 9     Fields:    
  12. Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keles S. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. PLoS Comput Biol. 2015 Oct; 11(10):e1004491. PMID: 26484757.
    Citations: 5     Fields:    Translation:HumansCells
  13. 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 Biol. 2014 Dec 21; 15(12):553. PMID: 25608678.
    Citations: 93     Fields:    Translation:Animals
  14. 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. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug; 8(8):1494-512. PMID: 23845962.
    Citations: 2210     Fields:    Translation:AnimalsCells
  15. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011 Aug 04; 12:323. PMID: 21816040.
    Citations: 4887     Fields:    Translation:HumansAnimals
  16. Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, Keles S. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. PLoS Comput Biol. 2011 Jul; 7(7):e1002111. PMID: 21779159.
    Citations: 42     Fields:    Translation:HumansAnimalsCells
  17. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 2010 Feb 15; 26(4):493-500. PMID: 20022975.
    Citations: 444     Fields:    Translation:AnimalsCells
Local representatives can answer questions about the Profiles website or help with editing a profile or issues with profile data. For assistance with this profile: HMS/HSDM faculty should contact contactcatalyst.harvard.edu. For faculty or fellow appointment updates and changes, please ask your appointing department to contact HMS. For fellow personal and demographic information, contact HMS Human Resources at human_resourceshms.harvard.edu. For faculty personal and demographic information, contact HMS Office for Faculty Affairs at facappthms.harvard.edu.
Li's Networks
Click the
Explore
buttons for more information and interactive visualizations!
Concepts (101)
Explore
_
Co-Authors (72)
Explore
_
Similar People (60)
Explore
_
Same Department 
Explore
_
Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.