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Jean Fan
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Fast, sensitive and accurate integration of single-cell data with Harmony
I Korsunsky, N Millard, J Fan, K Slowikowski, F Zhang, K Wei, ...
Nature methods 16 (12), 1289-1296, 2019
42982019
RNA velocity of single cells
G La Manno, R Soldatov, A Zeisel, E Braun, H Hochgerner, V Petukhov, ...
Nature 560 (7719), 494-498, 2018
30172018
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
BB Lake, S Chen, BC Sos, J Fan, GE Kaeser, YC Yung, TE Duong, D Gao, ...
Nature biotechnology 36 (1), 70-80, 2018
8622018
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression
C Xia, J Fan, G Emanuel, J Hao, X Zhuang
Proceedings of the National Academy of Sciences 116 (39), 19490-19499, 2019
5462019
Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition
JA Burger, DA Landau, A Taylor-Weiner, I Bozic, H Zhang, K Sarosiek, ...
Nature communications 7 (1), 11589, 2016
3832016
Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia
DA Landau, K Clement, MJ Ziller, P Boyle, J Fan, H Gu, K Stevenson, ...
Cancer cell 26 (6), 813-825, 2014
3822014
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis
J Fan, N Salathia, R Liu, GE Kaeser, YC Yung, JL Herman, F Kaper, ...
Nature methods 13 (3), 241-244, 2016
3782016
Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex
X Zhang, MH Chen, X Wu, A Kodani, J Fan, R Doan, M Ozawa, J Ma, ...
Cell 166 (5), 1147-1162. e15, 2016
3202016
Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma
T Hara, R Chanoch-Myers, ND Mathewson, C Myskiw, L Atta, L Bussema, ...
Cancer Cell 39 (6), 779-792. e11, 2021
3182021
Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia
L Wang, AN Brooks, J Fan, Y Wan, R Gambe, S Li, S Hergert, S Yin, ...
Cancer Cell 30 (5), 750-763, 2016
2212016
Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
J Fan, HO Lee, S Lee, D Ryu, S Lee, C Xue, SJ Kim, K Kim, N Barkas, ...
Genome research 28 (8), 1217-1227, 2018
2152018
Clonal decomposition and dna replication states defined by scaled single-cell genome sequencing
E Laks, A McPherson, H Zahn, D Lai, A Steif, J Brimhall, J Biele, B Wang, ...
Cell 179 (5), 1207-1221. e22, 2019
1962019
Single-cell transcriptomics in cancer: Computational challenges and opportunities
J Fan, K Slowikowski, F Zhang
Experimental & Molecular Medicine 52 (9), 1452-1465, 2020
1532020
Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions
KM Girskis, AB Stergachis, EM DeGennaro, RN Doan, X Qian, ...
Neuron 109 (20), 3239-3251. e7, 2021
1022021
Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data
BF Miller, F Huang, L Atta, A Sahoo, J Fan
Nature communications 13 (1), 2339, 2022
1012022
A murine model of chronic lymphocytic leukemia based on B cell-restricted expression of Sf3b1 mutation and Atm deletion
S Yin, RG Gambe, J Sun, AZ Martinez, ZJ Cartun, FFD Regis, Y Wan, ...
Cancer cell 35 (2), 283-296. e5, 2019
962019
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities
BF Miller, D Bambah-Mukku, C Dulac, X Zhuang, J Fan
Genome research 31 (10), 1843-1855, 2021
942021
Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
L Wang, J Fan, JM Francis, G Georghiou, S Hergert, S Li, R Gambe, ...
Genome research 27 (8), 1300-1311, 2017
872017
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
S Jain, L Pei, JM Spraggins, M Angelo, JP Carson, N Gehlenborg, F Ginty, ...
Nature cell biology 25 (8), 1089-1100, 2023
502023
Computational challenges and opportunities in spatially resolved transcriptomic data analysis
L Atta, J Fan
Nature Communications 12 (1), 5283, 2021
452021
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