Publications

* Equal contributors

# Co-senior authors

† Correspondence

Li Lab members are highlighted in bold.

E. L. Bao, S. K. Nandakumar, X. Liao, A. G. Bick, J. Karjalainen, M. Tabaka, O. I. Gan, A. S. Havulinna, T. T. J. Kiiskinen, C. A. Lareau, A. L. de Lapuente Portilla, B. Li, C. Emdin, V. Codd, C. P. Nelson, C. J. Walker, C. Churchhouse, A. de la Chapelle, D. E. Klein, B. Nilsson, P. W. F. Wilson, K. Cho, S. Pyarajan, J. M. Gaziano, N. J. Samani, FinnGen, 23andMe Research Team, A. Regev, A. Palotie, B. M. Neale, J. E. Dick, P. Natarajan, C. J. O’Donnell, M. J. Daly, M. Milyavsky, S. Kathiresan, V. G. Sankaran† (2020). Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells. Nature.

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B. Li†, J. Gould, Y. Yang, S. Sarkizova, M. Tabaka, O. Ashenberg, Y. Rosen, M. Slyper, M. S. Kowalczyk, A.-C. Villani, T. L. Tickle, N. Hacohen, O. Rozenblatt-Rosen†, A. Regev† (2020). Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq. Nature Methods.

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T. Ouspenskaia*, T. Law*, K. R. Clauser*, S. Klaeger*, S. Sarkizova, F. Aguet, B. Li, E. Christian, B. A. Knisbacher, P. M. Le, C. R. Hartigan, H. Keshishian, A. Apffel, G. Oliveira, W. Zhang, Y. T. Chow, Z. Ji, I. Jungreis, S. A. Shukla, P. Bachireddy, M. Kellis, G. Getz, N. Hacohen, D. B. Keskin#, S. A. Carr#, C. J. Wu#†, A. Regev#† (2020). Thousands of Novel Unannotated Proteins Expand the MHC I Immunopeptidome in Cancer. bioRxiv.

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M. Slyper*, C. B. M. Porter*, O. Ashenberg*, J. Waldman, E. Drokhlyansky, I. Wakiro, C. Smillie, G. Smith-Rosario, J. Wu, D. Dionne, S. Vigneau, J. Jané-Valbuena, T. L. Tickle, S. Napolitano, M. Su, A. G. Patel, A. Karlstrom, S. Gritsch, M. Nomura, A. Waghray, S. H. Gohil, A. M. Tsankov, L. Jerby-Arnon, O. Cohen, J. Klughammer, Y. Rosen, J. Gould, L. Nguyen, M. Hofree, P. J. Tramontozzi, B. Li, C. J. Wu, B. Izar, R. Haq, F. S. Hodi, C. H. Yoon, A. N. Hata, S. J. Baker, M. L. Suvà, R. Bueno, E. H. Stover, M. R. Clay, M. A. Dyer, N. B. Collins, U. A. Matulonis, N. Wagle, B. E. Johnson, A. Rotem, O. Rozenblatt-Rosen O†, A. Regev† (2020). A Single-Cell and Single-Nucleus RNA-Seq Toolbox for Fresh and Frozen Human Tumors. Nature Medicine.

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P. Sen, A. R. Wilkie, F. Ji, Y. Yang, I. J. Taylor, M. Velazquez-Palafox, E. A. H. Vanni, J. M. Pesola, R. Fernandez, H. Chen, L. M. Morsett, E. R. Abels, M. Piper, R. J. Lane, S. E. Hickman, T. K. Means, E. S. Rosenberg, R. I. Sadreyev, B. Li, D. M. Coen, J. A. Fishman, J. El Khoury (2020). Linking Indirect Effects of Cytomegalovirus in Transplantation to Modulation of Monocyte Innate Immune Function. Science Advances.

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M. Lavaert, K. L. Liang, N. Vandamme, J. E. Park, J. Roels, M. S. Kowalczyk, B. Li, O. Ashenberg, M. Tabaka, D. Dionne, T. L. Tickle, M. Slyper, O. Rozenblatt-Rosen, B. Vandekerckhove, G. Leclercq, A. Regev, P. Van Vlierberghe, M. Guilliams, S. A. Teichmann, Y. Saeys, T. Taghon (2020). Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Immunity.

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B. J. Haas†, A. Dobin, B. Li, N. Stransky, N. Pochet, A. Regev (2019). Accuracy Assessment of Fusion Transcript Detection via Read-Mapping and De Novo Fusion Transcript Assembly-based Methods. Genome Biology.

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D. M. Popescu*, R. A. Botting*, E. Stephenson*, K. Green, S. Webb, L. Jardine, E. F. Calderbank, K. Polanski, I. Goh, M. Efremova, M. Acres, D. Maunder, P. Vegh, Y. Gitton, J. E. Park, R. Vento-Tormo, Z. Miao, D. Dixon, R. Rowell, D. McDonald, J. Fletcher, E. Poyner, G. Reynolds, M. Mather, C. Moldovan, L. Mamanova, F. Greig, M. D. Young, K. B. Meyer, S. Lisgo, J. Bacardit, A. Fuller, B. Millar, B. Innes, S. Lindsay, M. J. T. Stubbington, M. S. Kowalczyk, B. Li, O. Ashenberg, M. Tabaka, D. Dionne, T. L. Tickle, M. Slyper, O. Rozenblatt-Rosen, A. Filby, P. Carey, A. C. Villani, A. Roy, A. Regev, A. Chédotal, I. Roberts, B. Göttgens, S. Behjati, E. Laurenti†, S. A. Teichmann†, M. Haniffa† (2019). Decoding Human Fetal Liver Haematopoiesis. Nature.

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J. T. Gaublomme*†, B. Li*, C. McCabe, A. Knecht, Y. Yang, E. Drokhlyansky, N. Van Wittenberghe, J. Waldman, D. Dionne, L. Nguyen, P. De Jager, B. Yeung, X. Zhao, N. Habib, O. Rozenblatt-Rosen†, A. Regev† (2019). Nuclei Multiplexing with Barcoded Antibodies for Single-Nucleus Genomics. Nature Communications.

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B. 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.

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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.

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X. Zeng, B. Li, R. Welch, C. Rojo, Y. Zheng, C. N. Dewey, S. Keleş (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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B. 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, B. 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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B. 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. Keleş (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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B. Li, V. Ruotti, R. M. Stewart, J. A. Thomson, C. N. Dewey (2010). RNA-Seq Gene Expression Estimation with Read Mapping Uncertainty. Bioinformatics.

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