Jean Fan

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 35

Top Venues

bioRxiv : the preprint server for biology

Nature communications

Genome biology

Bioinformatics (Oxford, England)

Johns Hopkins University

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Johns Hopkins University Jul 01 2020

United States

Assistant Professor :: Biomedical Engineering

Harvard University - Jun 30 2020

United States

Post-doc Fellow :: Chemistry and Chemical Biology

Publications

Kaitlin M Stouffer, Alain Trouvé, Laurent Younes, Michael Kunst, Lydia Ng, Hongkui Zeng, Manjari Anant, Jean Fan, Yongsoo Kim, Xiaoyin Chen, Mara C P Rue, Michael I Miller
Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections. Nature communications 15 (1) (2024)
Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F Miller, Rahul Satija, John W Hickey, Jean Fan
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. Bioinformatics (Oxford, England) 40 (7) (2024)
Lyla Atta, Kalen Clifton, Manjari Anant, Gohta Aihara, Jean Fan
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. Genome biology 25 (1) (2024)
Katy Börner, Philip D Blood, Jonathan C Silverstein, Matthew Ruffalo, Sarah A Teichmann, Gloria S Pryhuber, Ravi S Misra, Jeffrey M Purkerson, Jean Fan, John W Hickey, Gesmira Molla, Chuan Xu, Yun Zhang, Griffin M Weber, Yashvardhan Jain, Danial Qaurooni, Yongxin Kong, null null, Andreas Bueckle, Bruce W Herr
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. bioRxiv : the preprint server for biology (2024)
Pratik Kamat, Nicolas C Macaluso, Chanhong Min, Yukang Li, Anshika Agrawal, Aaron Winston, Lauren Pan, Bartholomew Starich, Teasia Stewart, Pei-Hsun Wu, Jean Fan, Jeremy D Walston, Jude M Phillip
Single-cell morphology encodes functional subtypes of senescence in aging human dermal fibroblasts. bioRxiv : the preprint server for biology (2024)
Lyla Atta, Kalen Clifton, Manjari Anant, Gohta Aihara, Jean Fan
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. Genome biology 25 (1) (2024)
Lyla Atta, Kalen Clifton, Manjari Anant, Gohta Aihara, Jean Fan
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. Genome biology 25 (1) (2024)
Lyla Atta, Kalen Clifton, Manjari Anant, Gohta Aihara, Jean Fan
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. Genome biology 25 (1) (2024)
Katy Börner, Philip D Blood, Jonathan C Silverstein, Matthew Ruffalo, Sarah A Teichmann, Gloria S Pryhuber, Ravi S Misra, Jeffrey M Purkerson, Jean Fan, John W Hickey, Gesmira Molla, Chuan Xu, Yun Zhang, Griffin M Weber, Yashvardhan Jain, Danial Qaurooni, Yongxin Kong, null null, Andreas Bueckle, Bruce W Herr
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. bioRxiv : the preprint server for biology (2024)
Pratik Kamat, Nicolas C Macaluso, Chanhong Min, Yukang Li, Anshika Agrawal, Aaron Winston, Lauren Pan, Bartholomew Starich, Teasia Stewart, Pei-Hsun Wu, Jean Fan, Jeremy D Walston, Jude M Phillip
Single-cell morphology encodes functional subtypes of senescence in aging human dermal fibroblasts. bioRxiv : the preprint server for biology (2024)
Katy Börner, Philip D Blood, Jonathan C Silverstein, Matthew Ruffalo, Sarah A Teichmann, Gloria S Pryhuber, Ravi S Misra, Jeffrey M Purkerson, Jean Fan, John W Hickey, Gesmira Molla, Chuan Xu, Yun Zhang, Griffin M Weber, Yashvardhan Jain, Danial Qaurooni, Yongxin Kong, null null, Andreas Bueckle, Bruce W Herr
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. bioRxiv : the preprint server for biology (2024)
Katy Börner, Philip D Blood, Jonathan C Silverstein, Matthew Ruffalo, Sarah A Teichmann, Gloria S Pryhuber, Ravi S Misra, Jeffrey M Purkerson, Jean Fan, John W Hickey, Gesmira Molla, Chuan Xu, Yun Zhang, Griffin M Weber, Yashvardhan Jain, Danial Qaurooni, Yongxin Kong, null null, Andreas Bueckle, Bruce W Herr
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. bioRxiv : the preprint server for biology (2024)
Kaitlin M Stouffer, Alain Trouvé, Laurent Younes, Michael Kunst, Lydia Ng, Hongkui Zeng, Manjari Anant, Jean Fan, Yongsoo Kim, Xiaoyin Chen, Mara C P Rue, Michael I Miller
Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections. Nature communications 15 (1) (2024)
Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F Miller, Rahul Satija, John W Hickey, Jean Fan
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. Bioinformatics (Oxford, England) 40 (7) (2024)
Kaitlin M Stouffer, Alain Trouvé, Laurent Younes, Michael Kunst, Lydia Ng, Hongkui Zeng, Manjari Anant, Jean Fan, Yongsoo Kim, Xiaoyin Chen, Mara C P Rue, Michael I Miller
Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections. Nature communications 15 (1) (2024)
Lyla Atta, Kalen Clifton, Manjari Anant, Gohta Aihara, Jean Fan
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. Genome biology 25 (1) (2024)
Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F Miller, Rahul Satija, John W Hickey, Jean Fan
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. Bioinformatics (Oxford, England) 40 (7) (2024)
Pratik Kamat, Nicolas C Macaluso, Chanhong Min, Yukang Li, Anshika Agrawal, Aaron Winston, Lauren Pan, Bartholomew Starich, Teasia Stewart, Pei-Hsun Wu, Jean Fan, Jeremy D Walston, Jude M Phillip
Single-cell morphology encodes functional subtypes of senescence in aging human dermal fibroblasts. bioRxiv : the preprint server for biology (2024)
Lyla Atta, Kalen Clifton, Manjari Anant, Jean Fan
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. bioRxiv : the preprint server for biology (2023)
Kalen Clifton, Manjari Anant, Osagie K Aimiuwu, Justus M Kebschull, Michael I Miller, Daniel J Tward, Jean Fan
Alignment of spatial transcriptomics data using diffeomorphic metric mapping. bioRxiv : the preprint server for biology (2023)
Kalen Clifton, Manjari Anant, Gohta Aihara, Lyla Atta, Osagie K Aimiuwu, Justus M Kebschull, Michael I Miller, Daniel J Tward, Jean Fan
STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping. Nature communications 14 (1) (2023)
Kalen Clifton, Manjari Anant, Osagie K Aimiuwu, Justus M Kebschull, Michael I Miller, Daniel J Tward, Jean Fan
Alignment of spatial transcriptomics data using diffeomorphic metric mapping. bioRxiv : the preprint server for biology (2023)
Kalen Clifton, Manjari Anant, Osagie K Aimiuwu, Justus M Kebschull, Michael I Miller, Daniel J Tward, Jean Fan
Alignment of spatial transcriptomics data using diffeomorphic metric mapping. bioRxiv : the preprint server for biology (2023)
Kalen Clifton, Manjari Anant, Osagie K Aimiuwu, Justus M Kebschull, Michael I Miller, Daniel J Tward, Jean Fan
Alignment of spatial transcriptomics data using diffeomorphic metric mapping. bioRxiv : the preprint server for biology (2023)
Brendan F Miller, Feiyang Huang, Lyla Atta, Arpan Sahoo, Jean Fan
Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data. Nature communications 13 (1) (2022)
Noelia Purroy, Yuzhou Evelyn Tong, Camilla K Lemvigh, Nicoletta Cieri, Shuqiang Li, Erin M Parry, Wandi Zhang, Laura Z Rassenti, Thomas J Kipps, Susan L Slager, Neil E Kay, Connie Lesnick, Tait D Shanafelt, Paolo Ghia, Lydia Scarfò, Kenneth J Livak, Peter V Kharchenko, Donna S Neuberg, Lars Rønn Olsen, Jean Fan, Satyen H Gohil, Catherine J Wu
Single-cell analysis reveals immune dysfunction from the earliest stages of CLL that can be reversed by ibrutinib. Blood 139 (14) (2022)
Lyla Atta, Jean Fan
Computational challenges and opportunities in spatially resolved transcriptomic data analysis. Nature communications 12 (1) (2021)
Brendan F Miller, Dhananjay Bambah-Mukku, Catherine Dulac, Xiaowei Zhuang, Jean Fan
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities. Genome research 31 (10) (2021)
Jean Fan, Kamil Slowikowski, Fan Zhang
Single-cell transcriptomics in cancer: computational challenges and opportunities. Experimental & molecular medicine 52 (9) (2020)
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri
Fast, sensitive and accurate integration of single-cell data with Harmony. Nature methods 16 (12) (2019)
Chenglong Xia, Jean Fan, George Emanuel, Junjie Hao, Xiaowei Zhuang
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proceedings of the National Academy of Sciences of the United States of America 116 (39) (2019)
Jean Fan, Hae-Ock Lee, Soohyun Lee, Da-Eun Ryu, Semin Lee, Catherine Xue, Seok Jin Kim, Kihyun Kim, Nikolaos Barkas, Peter J Park, Woong-Yang Park, Peter V Kharchenko
Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data. Genome research 28 (8) (2018)
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
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nature biotechnology 36 (1) (2017)
Jan A Burger, Dan A Landau, Amaro Taylor-Weiner, Ivana Bozic, Huidan Zhang, Kristopher A 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 S Neuberg, Hagop Kantarjian, Eric Lander, Stacey Gabriel, Susan O'Brien, Anthony Letai, David A Weitz, Martin A Nowak, Gad Getz, Catherine J Wu
Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition. Nature communications 7 (2016)
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
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nature methods 13 (3) (2016)

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Publication Activity (10 Years)

Top Topics

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Jean Fan