PUBLICATIONS (ORCID | GOOGLE SCHOLAR)
We are committed to open access. If you find a manuscript that we have co-authored but is not available here, please contact us directly and we will be happy to send you an electronic copy.* Denotes equal contribution
^ Denotes corresponding author
JEFworks lab trainees are underlined
Spatial organization of the transcriptome in individual neurons
Guiping Wang, Cheen-Euong Ang, Jean Fan, Andrew Wang, Jeffrey R. Moffitt, Xiaowei Zhuang

Paper: bioRxiv
Single-cell transcriptomics in cancer - computational challenges and opportunities
Jean Fan^, Kamil Slowkikowski, Fan Zhang

Paper: Nature Experimental and Molecular Medicine. Sept 15, 2020, doi.org:10.1038/s12276-020-0422-0 | Pubmed | PDF
Fast, sensitive and accurate integration of single-cell data with Harmony
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-ru Loh, and Soumya Raychaudhuri

Paper: Nature Methods. November 18, 2019. doi:10.1038/s41592-019-0619-0 | Pubmed | PDF
Relevant code:
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression
Chenglong Xia*, Jean Fan*, George Emanuel*, Junjie Hao, and Xiaowei Zhuang

Paper: PNAS. Sept 9, 2019, doi:10.1073/pnas.1912459116 | Pubmed | PDF
A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion
Shanye Yin, Rutendo G. Gambe, Jing Sun, Aina Zurita Martinez, Zachary J.Cartun, Fara Faye D.Regis, Youzhong Wan, Jean Fan, Angela N.Brooks, Sarah E. M. Herman, Elisaten Hacken, AmaroTaylor-Weiner, Laura Z. Rassenti, Emanuela M. Ghia, Thomas J. Kipps, Esther A. Obeng, Carrie L. Cibulskis, Donna Neuberg, Dean R.Campagna, Mark D. Fleming, Benjamin L. Ebert, Adrian Wiestner, Ignaty Leshchiner, James A. DeCaprio, Gad Getz, Robin Reed, Ruben D. Carrasco, Catherine J. Wu, Lili Wang

Paper: Cancer Cell. Feb 11, 2019. doi:10.1016/j.ccell.2018.12.013 | Pubmed | PDF
RNA velocity of single cells
Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E Kastriti, Peter Lönnerberg, Alessandro Furlan, Jean Fan, Lars E Borm, Zehua Liu, David van Bruggen, Jimin Guo, Xiaoling He, Roger Barker, Erik Sundström, Gonçalo Castelo-Branco, Patrick Cramer, Igor Adameyko, Sten Linnarsson, Peter V Kharchenko

Paper: Nature. August 8, 2018. doi:10.1038/s41586-018-0414-6 | Pubmed | PDF
Relevant code:
Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Jean Fan*, Hae-Ock Lee*, Soohyun Lee, Da-eun Ryu, Semin Lee, Catherine Xue, Seok Jin Kim, Kihyun Kim, Nikolas Barkas, Peter J Park, Woong-Yang Park and Peter V Kharchenko

Paper: Genome Research. June 13, 2018. doi:10.1101/gr.228080.117 | Pubmed | PDF
Relevant code:
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
Blue B Lake*, Song Chen*, Brandon C Sos*, Jean Fan*, Gwendolyn E Kaeser, Yun C Yung, Thu E Duong, Derek Gao, Jerold Chun, Peter V Kharchenko, Kun Zhang

Paper: Nature Biotechnology. December 11, 2017. doi:10.1038/nbt.4038 | PDF
Relevant code:
Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
Lili Wang*, Jean Fan*, Joshua M. Francis, George Georghiou, Sarah Hergert, Shuqiang Li, Rutendo Gambe, Chensheng W. Zhou, Chunxiao Yang, Sheng Xiao, Paola Dal Cin, Michaela Bowden, Dylan Kotliar, Sachet A. Shukla, Jennifer R. Brown, Donna Neuberg, Dario R. Alessi, Cheng-Zhong Zhang, Peter V. Kharchenko, Kenneth J. Livak, Catherine J. Wu

Paper: Genome Research. May 22, 2017. doi/10.1101/gr.217331.116 | Pubmed | PDF
Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia
Lili Wang*, Angela N. Brooks*, Jean Fan*, Youzhong Wan*, Rutendo Gambe, Shuqiang Li, Sarah Hergert, Shanye Yin, Samuel S. Freeman, Joshua Z. Levin, Lin Fan, Michael Seiler, Silvia Buonamici, Peter G. Smith, Kevin F. Chau, Carrie L. Cibulskis, Wandi Zhang, Laura Z. Rassenti, Emanuela M. Ghia, Thomas J. Kipps, Stacey Fernandes, Donald B. Bloch, Dylan Kotliar, Dan A. Landau, Sachet A. Shukla, Jon C. Aster, Robin Reed, David S. DeLuca, Jennifer R. Brown, Donna Neuberg, Gad Getz, Kenneth J. Livak, Matthew M. Meyerson, Peter V. Kharchenko, Catherine J. Wu

Paper: Cancer Cell. November 3, 2016. doi.org/10.1016/j.ccell.2016.10.005 | Pubmed | PDF
Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex
Xiaochang Zhang, Ming Hui Chen, Xuebing Wu, Andrew Kodani, Jean Fan, Ryan Doan, Manabu Ozawa, Jacqueline Ma, Nobuaki Yoshida, Jeremy F. Reiter, Douglas L. Black, Peter V. Kharchenko, Phillip A. Sharp, Christopher A. Walsh

Paper: Cell. August 25, 2016. doi.org/10.1016/j.cell.2016.07.025 | Pubmed | PDF
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Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition
Jan A. Burger*, Dan A. Landau*, Amaro Taylor-Weiner*, Ivana Bozic*, Huidan Zhang*, Kristopher Sarosiek, Lili Wang, Chip Stewart, Jean Fan, Julia Hoellenriegel, Mariela Sivina, Adrian M. Dubuc, Cameron Fraser, Yulong Han, Shuqiang Li, Kenneth J. Livak, Lihua Zou, Youzhong Wan, Sergej Konoplev, Carrie Sougnez, Jennifer R. Brown, Lynne V. Abruzzo, Scott L. Carter, Michael J. Keating, Matthew S. Davids, William G. Wierda, Kristian Cibulskis, Thorsten Zenz, Lillian Werner, Paola Dal Cin, Peter Kharchencko, Donna Neuberg, Hagop Kantarjian, Eric Lander, Stacey Gabriel, Susan O’Brien, Anthony Letai, David A. Weitz, Martin A. Nowak, Gad Getz, Catherine J. Wu

Paper: Nature Communications. May 20, 2016. doi:10.1038/ncomms11589 | Pubmed | PDF
Relevant code:
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis
Jean Fan, Neeraj Salathia, Rui Liu, Gwendolyn E Kaeser, Yun C Yung, Joseph L Herman, Fiona Kaper, Jian-Bing Fan, Kun Zhang, Jerold Chun, Peter V Kharchenko

Paper: Nature Methods. Jan 18, 2016. doi:10.1038/nmeth.3734 | Pubmed | PDF
Relevant code:
Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia
Dan A. Landau*, Kendell Clement*, Michael J. Ziller, Patrick Boyle, Jean Fan, Hongcang Gu, Kristen Stevenson, Carrie Sougnez, Lili Wang, Shuqiang Li, Dylan Kotliar, Wandi Zhang, Mahmoud Ghandi, Levi Garraway, Stacey M. Fernandes, Kenneth J. Livak, Stacey Gabriel, Andreas Gnirke, Eric S. Lander, Jennifer R. Brown, Donna Neuberg, Peter V. Kharchenko, Nir Hacohen, Gad Getz, Alexander Meissner, Catherine J. Wu

Paper: Cancer Cell. Dec 8, 2014. doi:10.1016/j.ccell.2014.10.012 | Pubmed | PDF