Jean Fan

Also affiliated with Johns Hopkins University, Office of Technology Transfer, Johns Hopkins Medicine, Johns Hopkins University – Nanjing University Center for Chinese and American Studies

Biochemistry, Genetics and Molecular BiologyMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 3%percentile

1.2Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage

Nature Methods(2025)10.1038/s41592-024-02563-5

Top 25%

0.802DataRank

Top 25%33 citations

Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo, Rahul Satija, Sarah A. Teichmann +95 more

Papers

Driven by 38 papers — median percentile 65. Top paper: “Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data”.

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

Nature Communications(2022)10.1038/s41467-022-30033-z

N/A

5.1DataRank · unranked

244 citations

Feiyang Huang, Lyla Atta, Arpan Sahoo, Jean Fan, Brendan Miller

Single-cell transcriptomics in cancer: computational challenges and opportunities

Experimental & Molecular Medicine(2020)10.1038/s12276-020-0422-0

N/A

4.9DataRank · unranked

198 citations

Kamil Slowikowski, Fan Zhang, Jean Fan

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

Nature Methods(2019)10.1038/s41592-019-0619-0

N/A

1.4DataRank · unranked

10108 citations

Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei +6 more

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

Cancer Cell(2021)10.1016/j.ccell.2021.05.002

N/A

0.953DataRank · unranked

575 citations

Rony Chanoch-Myers, Nathan D. Mathewson, Chad Myskiw, Lyla Atta, Lillian Bussema +17 more

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

Science(2021)10.1126/science.aax2656

N/A

0.902DataRank · unranked

408 citations

Daniel R. Goodwin, Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Evan R. Daugharthy +164 more

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage

Nature Methods(2025)10.1038/s41592-024-02563-5

Top 25%

0.802DataRank

Top 25%33 citations

Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo, Rahul Satija, Sarah A. Teichmann +95 more

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

Genome Research(2021)10.1101/gr.271288.120

N/A

0.801DataRank · unranked

207 citations

Dhananjay Bambah-Mukku, Catherine Dulac, Xiaowei Zhuang, Jean Fan, Brendan Miller

Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

Nature Neuroscience(2024)10.1038/s41593-024-01806-0

N/A

0.691DataRank · unranked

29 citations

Gonçalo Castelo-Branco, Fei Chen, Simone Codeluppi, M. Ryan Corces, Jean Fan +26 more

A model for decoding resistance in precision oncology: acquired resistance to FGFR inhibitors in cholangiocarcinoma

Annals of Oncology(2024)10.1016/j.annonc.2024.12.011

N/A

0.538DataRank · unranked

35 citations

Daniel DiToro, Francesco Facchinetti, E Martin, P. Peng, Islam Baiev +50 more

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.27.587041

Top 45%

0.407DataRank

Top 45%9 citations

Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo, Rahul Satija, Sarah A. Teichmann +16 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.30.555624

N/A

0.269DataRank · unranked

5 citations

Kalen Clifton, Manjari Anant, Gohta Aihara, Jean Fan, Lyla Atta

Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling

10.7554/elife.107070.1

N/A

0.208DataRank · unranked

3 citations

Hyun Joo Ji, Steven L. Salzberg, Jean Fan, Caleb Hallinan

Characterizing cell-type spatial relationships across length scales in spatially resolved omics data

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.05.560733

N/A

0.165DataRank · unranked

2 citations

Brendan F. Miller, Maigan A. Brusko, Gohta Aihara, Lyla Atta, Manjari Anant +5 more

Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

Nature Neuroscience(2024)10.1038/s41593-024-01858-2

N/A

0.118DataRank · unranked

1 citations

Gonçalo Castelo-Branco, Fei Chen, Simone Codeluppi, M. Ryan Corces, Jean Fan +26 more

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

Cancer Cell(2025)10.1016/j.ccell.2025.05.007

N/A

0.110DataRank · unranked

1 citations

Rony Chanoch-Myers, Nathan D. Mathewson, Chad Myskiw, Lyla Atta, Lillian Bussema +17 more

Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections

Nature Communications(2024)10.1038/s41467-024-47883-4

N/A

0DataRank · unranked

7 citations

Alain Trouvé, Laurent Younès, Michael Kunst, Lydia Ng, Hongkui Zeng +7 more

Single-cell morphology encodes functional subtypes of senescence in aging human dermal fibroblasts

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.10.593637

N/A

0DataRank · unranked

4 citations

Nicolas C. Macaluso, Chanhong Min, Yukang Li, Anshika Agrawal, Aaron Winston +8 more

Single-cell morphology encodes functional subtypes of senescence in aging human dermal fibroblasts

Science Advances(2025)10.1126/sciadv.ads1875

N/A

0DataRank · unranked

13 citations

Nicolas C. Macaluso, Yukang Li, Anshika Agrawal, Aaron Winston, Lauren Pan +9 more

Characterizing cell-type spatial relationships across length scales in spatially resolved omics data

Nature Communications(2025)10.1038/s41467-024-55700-1

N/A

0DataRank · unranked

10 citations

Brendan F. Miller, Maigan A. Brusko, Gohta Aihara, Lyla Atta, Manjari Anant +5 more

Exploring endothelial cell environments across organs in spatially resolved omics data

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.23.678129

N/A

0DataRank · unranked

3 citations

Jodie Jepson, Roy Chen, Elizabeth Maier, Bruce W. Herr, Aleix Puig-Barbe +24 more

Evidence of off-target probe binding affecting 10x Genomics Xenium gene panels compromise accuracy of spatial transcriptomic profiling

eLife(2025)10.7554/elife.107070

N/A

0DataRank · unranked

2 citations

Hyun Joo Ji, Edmund Tsou, Steven L. Salzberg, Jean Fan, Caleb Hallinan

Impact of Data Quality on Deep Learning Prediction of Spatial Transcriptomics from Histology Images

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.04.674228

N/A

0DataRank · unranked

0 citations

Calixto‐Hope G. Lucas, Jean Fan, Caleb Hallinan

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.18.695193

N/A

0DataRank · unranked

0 citations

Caleb Hallinan, Roujin An, Kalen Clifton, Jean Fan, Dee Velazquez

Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys

Scientific Reports(2023)10.1038/s41598-023-48213-2

N/A

0DataRank · unranked

15 citations

Kyungho Lee, Kathleen Noller, Emily K.W. Lo, Brendan Miller, Hyun Jun Jung +9 more

TAMI-12. CANCER-IMMUNE CELL INTERACTIONS DRIVE TRANSITIONS TO MESENCHYMAL-LIKE STATES IN GLIOBLASTOMA

Neuro-Oncology(2021)10.1093/neuonc/noab196.796

N/A

0DataRank · unranked

0 citations

Rony Chanoch-Myers, Chad Myskiw, Lyla Atta, Lillian Bussema, Alissa Greenwald +17 more

Spatial organization of the transcriptome in individual neurons

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.07.414060

N/A

0DataRank · unranked

36 citations

Cheen Euong Ang, Jean Fan, Andrew Wang, Jeffrey R. Moffitt, Xiaowei Zhuang +1 more

Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions

Neuron(2021)10.1016/j.neuron.2021.08.005

N/A

0DataRank · unranked

209 citations

Andrew B. Stergachis, Ellen M. DeGennaro, Ryan N. Doan, Xuyu Qian, Matthew B. Johnson +20 more

Computational challenges and opportunities in spatially resolved transcriptomic data analysis

Nature Communications(2021)10.1038/s41467-021-25557-9

N/A

0DataRank · unranked

81 citations

Jean Fan, Lyla Atta

VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories

Bioinformatics(2021)10.1093/bioinformatics/btab653

N/A

0DataRank · unranked

22 citations

Arpan Sahoo, Jean Fan, Lyla Atta

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.15.448381

N/A

0DataRank · unranked

15 citations

Feiyang Huang, Lyla Atta, Arpan Sahoo, Jean Fan, Brendan F. Miller

Single-cell analysis reveals immune dysfunction from the earliest stages of CLL that can be reversed by ibrutinib

Blood(2022)10.1182/blood.2021013926

N/A

0DataRank · unranked

18 citations

Yuzhou Evelyn Tong, Camilla K. Lemvigh, Nicoletta Cieri, Shuqiang Li, Erin M. Parry +17 more

STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping

Nature Communications(2023)10.1038/s41467-023-43915-7

N/A

0DataRank · unranked

141 citations

Manjari Anant, Gohta Aihara, Lyla Atta, Osagie K. Aimiuwu, Justus M. Kebschull +4 more

Soluble PD-L1 reprograms blood monocytes to prevent cerebral edema and facilitate recovery after ischemic stroke

Brain Behavior and Immunity(2023)10.1016/j.bbi.2023.12.007

N/A

0DataRank · unranked

34 citations

Ryan P. Lee, Eli Yazigi, Lyla Atta, James Feghali, Ayush Pant +23 more

OTME-7. Cancer - immune cell interactions drive transitions to mesenchymal-like state in glioblastoma

Neuro-Oncology Advances(2021)10.1093/noajnl/vdab070.058

N/A

0DataRank · unranked

0 citations

Rony Chanoch-Myers, Chad Myskiw, Lyla Atta, Lillian Bussema, Gabriela S. Kinker +17 more

Alignment of spatial transcriptomics data using diffeomorphic metric mapping

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.11.534630

N/A

0DataRank · unranked

13 citations

Manjari Anant, Gohta Aihara, Lyla Atta, Osagie K. Aimiuwu, Justus M. Kebschull +4 more

First-In-Human Phase I Study of Tinengotinib (TT-00420), a Multiple Kinase Inhibitor, as a Single Agent in Patients With Advanced Solid Tumors

The Oncologist(2024)10.1093/oncolo/oyad338

N/A

0DataRank · unranked

27 citations

Binghe Xu, Ecaterina E. Dumbrava, Siqing Fu, Daniel D. Karp, Funda Meric‐Bernstam +20 more

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

Genome biology(2024)10.1186/s13059-024-03303-w

N/A

0DataRank · unranked

24 citations

Kalen Clifton, Manjari Anant, Gohta Aihara, Jean Fan, Lyla Atta

SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis

Bioinformatics(2024)10.1093/bioinformatics/btae412

N/A

0DataRank · unranked

10 citations

Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan Miller +4 more

Jean Fan

Indexed papers

Top data-sharing exemplar

Papers