Jean Fan

发表

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

Joseph L. Herman, Jian-Bing Fan, P. Kharchenko, 2015, Nature Methods.

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

Joseph L. Herman, Jian-Bing Fan, P. Kharchenko, 2015, bioRxiv.

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

P. Kharchenko, Kun Zhang, Jean Fan, 2017, Nature Biotechnology.

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.

Michael J. Ziller, Shuqiang Li, K. Livak, 2014, Cancer cell.

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

Chenglong Xia, George Emanuel, Xiaowei Zhuang, 2019, Proceedings of the National Academy of Sciences.

HJ-Aggregate Behavior of Crystalline 7,8,15,16-Tetraazaterrylene: Introducing a New Design Paradigm for Organic Materials

F. Spano, D. S. Maxwell, Jean Fan, 2014 .

Differential Pathway Analysis.

Jean Fan, 2019, Methods in molecular biology.

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia.

Jon C. Aster, Donna Neuberg, Angela N. Brooks, 2016, Cancer cell.

Long-term benefits of breast screening

L. Tabár, S. Duffy, B. Viták, 2012 .

RNA velocity of single cells

Erik Sundström, Zehua Liu, Viktor Petukhov, 2018, Nature.

A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion.

Angela N. Brooks, Emanuela M. Ghia, D. Neuberg, 2019, Cancer cell.

Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions

E. M. DeGennaro, M. Greenberg, N. Šestan, 2021, Neuron.

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

Peter J Park, Peter V Kharchenko, Woong-Yang Park, 2018, Genome research.

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia

Donna Neuberg, Kenneth J Livak, Shuqiang Li, 2017, Genome research.

Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition

Shuqiang Li, K. Livak, K. Cibulskis, 2016, Nature Communications.

Transcriptomic Characterization of SF 3 B 1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia

Angela N. Brooks, Emanuela M. Ghia, Shuqiang Li, 2016 .

Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex

Peter V. Kharchenko, Phillip A. Sharp, Nobuaki Yoshida, 2016, Cell.

Spatial organization of the transcriptome in individual neurons

X. Zhuang, Jean Fan, Guiping Wang, 2020, bioRxiv.

Computational challenges and opportunities in spatially resolved transcriptomic data analysis

Jean Fan, Jean Fan, Lyla Atta, 2021, Nature Communications.

Single-cell transcriptomics in cancer: computational challenges and opportunities

Fan Zhang, Kamil Slowikowski, Jean Fan, 2020, Experimental & Molecular Medicine.

Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma.

A. Regev, X. Zhuang, I. Tirosh, 2021, Cancer cell.

VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories

Jean Fan, Lyla Atta, Arpan Sahoo, 2021, Bioinform..

Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data

Jean Fan, Jean Fan, Feiyang Huang, 2021, Nature Communications.

Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities

X. Zhuang, Jean Fan, Dhananjay Bambah-Mukku, 2021, Genome research.

Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

Jean Fan, Lyla Atta, Manjari Anant, 2023, bioRxiv.

Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition

Shuqiang Li, K. Livak, K. Cibulskis, 2016, Nature Communications.

Fast, sensitive, and accurate integration of single cell data with Harmony

Kamil Slowikowski, Soumya Raychaudhuri, Michael Brenner, 2019, Nature Methods.

Single cell biology—a Keystone Symposia report

Samantha A. Morris, Aaron M. Streets, Allon M. Klein, 2021, Annals of the New York Academy of Sciences.

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

Richard A. Moore, Khanh N. Dinh, S. Tavaré, 2019, Cell.

VeloViz: RNA-velocity informed embeddings for visualizing cellular trajectories

Jean Fan, Jean Fan, Lyla Atta, 2021, bioRxiv.

STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping

Justus M. Kebschull, Jean Fan, Michael I. Miller, 2023, Nature communications.

A Universal Method for Crossing Molecular and Atlas Modalities using Simplex-Based Image Varifolds and Quadratic Programming

Kaitlin M. Stouffer, L. Younes, Hongkui Zeng, 2023, bioRxiv.

RNA velocity in single cells

Lars E. Borm, S. Linnarsson, P. Kharchenko, 2017, bioRxiv.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges

Silvio C. E. Tosatto, Hui Ting Grace Yeo, Madeleine P. Ball, 2017, Human mutation.