Ziv Bar‐Joseph

Also affiliated with Digital Science (United States), Sanofi (United States), European Biomass Association, Carnegie Mellon University

Biochemistry, Genetics and Molecular BiologyComputer Science

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 100%percentile

0Author DataRank

Indexed papers

1in 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 1 indexed paper 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.

A unified analysis of atlas single cell data

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.06.503038

Top 100%

0DataRank

Top 100%0 citations

Nam D. Nguyen, Matthew Ruffalo, Ziv Bar‐Joseph, Hao Chen

Papers

Driven by 52 papers — median percentile 0. Top paper: “SCS: cell segmentation for high-resolution spatial transcriptomics”.

SCS: cell segmentation for high-resolution spatial transcriptomics

Nature Methods(2023)10.1038/s41592-023-01939-3

N/A

2.9DataRank · unranked

96 citations

Dongshunyi Li, Ziv Bar‐Joseph, Hao Chen

Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

Nature Cell Biology(2023)10.1038/s41556-023-01194-w

N/A

2.3DataRank · unranked

175 citations

Liming Pei, Jeffrey M. Spraggins, Michael Angelo, James P. Carson, Nils Gehlenborg +95 more

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

Nature Aging(2022)10.1038/s43587-022-00326-5

N/A

2.1DataRank · unranked

128 citations

Patty J. Lee, Christopher C. Benz, Philip D. Blood, Katy Börner, Judith Campisi +93 more

GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data

Genome biology(2020)10.1186/s13059-020-02214-w

N/A

0.794DataRank · unranked

198 citations

Ziv Bar‐Joseph, Ye Yuan

Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors

Cell stem cell(2020)10.1016/j.stem.2019.12.009

N/A

0.766DataRank · unranked

164 citations

Jun Ding, Carlos Villacorta-Martín, Michael J. Herriges, Anjali Jacob, Marall Vedaie +18 more

Spatial mapping of cellular senescence: emerging challenges and opportunities

Nature Aging(2023)10.1038/s43587-023-00446-6

N/A

0.729DataRank · unranked

128 citations

Akos A. Gerencser, Ana L. Mora, Andrew C. Nelson, Anru R. Zhang, Anthony B. Lagnado +40 more

Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data

mSystems(2021)10.1128/msystems.01105-20

N/A

0.624DataRank · unranked

63 citations

Jose Lugo-Martinez, Natalia Bourguignon, Kalai Mathee, Betiana Lerner, Ziv Bar‐Joseph +2 more

Identifying signaling genes in spatial single-cell expression data

Bioinformatics(2020)10.1093/bioinformatics/btaa769

N/A

0.614DataRank · unranked

59 citations

Jun Ding, Ziv Bar‐Joseph, Dongshunyi Li

Supervised Adversarial Alignment of Single-Cell RNA-seq Data

Journal of Computational Biology(2021)10.1089/cmb.2020.0439

N/A

0.538DataRank · unranked

35 citations

Haohan Wang, Amir Alavi, Eric P. Xing, Ziv Bar‐Joseph, Songwei Ge

Analysis of time-series regulatory networks

Current Opinion in Systems Biology(2020)10.1016/j.coisb.2020.07.005

N/A

0.442DataRank · unranked

18 citations

Ziv Bar‐Joseph, Jun Ding

Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.15.545118

N/A

0.442DataRank · unranked

18 citations

Amir Alavi, Qi Song, Rayna Schoenberger, Kamyar Keshavarz F., Ryan LeGraw +12 more

Computational tools for analyzing single-cell data in pluripotent cell differentiation studies

Cell Reports Methods(2021)10.1016/j.crmeth.2021.100087

N/A

0.373DataRank · unranked

11 citations

Amir Alavi, Mo R. Ebrahimkhani, Ziv Bar‐Joseph, Jun Ding

scDOT: optimal transport for mapping senescent cells in spatial transcriptomics

Genome biology(2024)10.1186/s13059-024-03426-0

N/A

0.330DataRank · unranked

8 citations

Lorena Rosas, Timur O. Khaliullin, Peiran Jiang, Euxhen Hasanaj, José Antonio Ovando-Ricárdez +13 more

Recovering single-cell expression profiles from spatial transcriptomics with scResolve

Cell Reports Methods(2024)10.1016/j.crmeth.2024.100864

N/A

0.292DataRank · unranked

6 citations

Young Je Lee, José Antonio Ovando-Ricárdez, Lorena Rosas, Mauricio Rojas, Ana L. Mora +3 more

Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.01.127589

N/A

0.292DataRank · unranked

6 citations

Jose Lugo-Martinez, Ye Yuan, Jessie Huang, Adam J. Hume, Ellen L. Suder +4 more

Iterative point set registration for aligning scRNA-seq data

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007939

N/A

0.269DataRank · unranked

5 citations

Ziv Bar‐Joseph, Amir Alavi

UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation

Journal of Computational Biology(2022)10.1089/cmb.2022.0251

N/A

0.241DataRank · unranked

4 citations

Jun Ding, Ziv Bar‐Joseph, Dongshunyi Li

scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.18.572269

N/A

0.104DataRank · unranked

1 citations

Young Je Lee, Jose A. Ovando, Lorena Rosas, Mauricio Rojas, Ana L. Mora +3 more

CINS: Cell Interaction Network inference from Single cell expression data

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010468

N/A

0DataRank · unranked

10 citations

Carlos Cosme, Taylor Adams, Jonas C. Schupp, Koji Sakamoto, Nikos Xylourgidis +5 more

Unsupervised cell functional annotation for single-cell RNA-seq

Genome Research(2022)10.1101/gr.276609.122

N/A

0DataRank · unranked

10 citations

Jun Ding, Ziv Bar‐Joseph, Dongshunyi Li

NIH SenNet Consortium: Mapping Senescent Cells in the Human Body to Understand Health and Disease

Preprints.org(2022)10.20944/preprints202207.0160.v1

N/A

0DataRank · unranked

1 citations

Philip D. Blood, Katy Börner, Judith Campisi, Feng Chen, Heike E. Daldrup‐Link +38 more

A unified analysis of atlas single cell data

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.06.503038

Top 100%

0DataRank

Top 100%0 citations

Nam D. Nguyen, Matthew Ruffalo, Ziv Bar‐Joseph, Hao Chen

NIH SenNet Consortium: Mapping Senescent Cells in the Human Body to Understand Health and Disease

Preprints.org(2022)10.20944/preprints202207.0160.v2

N/A

0DataRank · unranked

0 citations

Philip D. Blood, Katy Börner, Judith Campisi, Feng Chen, Heike E. Daldrup‐Link +38 more

Modelling post-implantation human development to yolk sac blood emergence

Nature(2023)10.1038/s41586-023-06914-8

N/A

0DataRank · unranked

74 citations

Qi Song, Kamyar Keshavarz F., Amir Alavi, Rayna Schoenberger, Ryan LeGraw +12 more

Using single cell atlas data to reconstruct regulatory networks

Nucleic Acids Research(2023)10.1093/nar/gkad053

N/A

0DataRank · unranked

17 citations

Matthew Ruffalo, Ziv Bar‐Joseph, Qi Song

Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis

Bioinformatics(2023)10.1093/bioinformatics/btad245

N/A

0DataRank · unranked

17 citations

Alexandro E. Trevino, Honesty Kim, Matthew Ruffalo, H. Blaize D’Angio, Ryan Preska +4 more

Predicting lung aging using scRNA-Seq data

PLoS Computational Biology(2024)10.1371/journal.pcbi.1012632

N/A

0DataRank · unranked

2 citations

A Singh, John E. McDonough, Taylor Adams, Robin Vos, Ruben De Man +10 more

Integrating patients in time series clinical transcriptomics data

Bioinformatics(2024)10.1093/bioinformatics/btae241

N/A

0DataRank · unranked

3 citations

Sachin Mathur, Ziv Bar‐Joseph, Euxhen Hasanaj

Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework

Genome Research(2024)10.1101/gr.278960.124

N/A

0DataRank · unranked

19 citations

Marcus H. Stoiber, Ziv Bar‐Joseph, Carl Kingsford, Haotian Teng

Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.06.574484

N/A

0DataRank · unranked

5 citations

Marcus H. Stoiber, Ziv Bar‐Joseph, Carl Kingsford, Haotian Teng

Using spatial proteomics to enhance cell type assignments in histology images

Cell Reports Methods(2025)10.1016/j.crmeth.2025.101204

N/A

0DataRank · unranked

3 citations

Aaron T. Mayer, Alexandro E. Trevino, Ziv Bar‐Joseph, Monica T. Dayao

Recovering time-varying networks from single-cell data

Bioinformatics(2025)10.1093/bioinformatics/btaf210

N/A

0DataRank · unranked

2 citations

Barnabás Póczos, Ziv Bar‐Joseph, Euxhen Hasanaj

Predicting lung aging using scRNA-Seq data

UNC Libraries(2025)10.17615/ka9b-3z04

N/A

0DataRank · unranked

0 citations

Vanaudenaerde B.M, Ceulemans L.J, Naftali Kaminski, Jonas C. Schupp, Vos R +10 more

A unified analysis of atlas single-cell data

Genome Research(2025)10.1101/gr.279631.124

N/A

0DataRank · unranked

0 citations

Nam D. Nguyen, Matt Ruffalo, Ziv Bar‐Joseph, Hao Chen

Characterizing Cellular Heterogeneity and Transcriptomic Features of Senotype Using Deep Graph Representation Learning

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.01.662364

N/A

0DataRank · unranked

0 citations

Hao Cheng, Ahmed Ghobashi, Natalia Vanegas-Avendano, Chen Hu, Jesús Rodríguez +20 more

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

Nature Communications(2020)10.1038/s41467-020-16821-5

N/A

0DataRank · unranked

86 citations

Chieh Hubert Lin, Ziv Bar‐Joseph, Hamim Zafar

Inferring TF activation order in time series scRNA-Seq studies

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007644

N/A

0DataRank · unranked

15 citations

Jun Ding, Ziv Bar‐Joseph, Chieh Hubert Lin

Identifying signaling genes in spatial single cell expression data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.27.221465

N/A

0DataRank · unranked

6 citations

Jun Ding, Ziv Bar‐Joseph, Dongshunyi Li

Iterative point set registration for aligning scRNA-seq data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.13.093948

N/A

0DataRank · unranked

0 citations

Ziv Bar‐Joseph, Amir Alavi

Clustering spatial transcriptomics data

Bioinformatics(2021)10.1093/bioinformatics/btab704

N/A

0DataRank · unranked

63 citations

Ye Yuan, Ziv Bar‐Joseph, Haotian Teng

Deep learning of gene relationships from single cell time-course expression data

Briefings in Bioinformatics(2021)10.1093/bib/bbab142

N/A

0DataRank · unranked

41 citations

Ziv Bar‐Joseph, Ye Yuan

CINS: Cell Interaction Network inference from Single cell expression data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.22.432206

N/A

0DataRank · unranked

4 citations

Carlos Cosme, Taylor Adams, Jonas C. Schupp, Koji Sakamoto, Nikos Xylourgidis +4 more

Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.28.454054

N/A

0DataRank · unranked

4 citations

Jeremy J. Velazquez, Jun Ding, Joshua Hislop, Mo R. Ebrahimkhani, Ziv Bar‐Joseph +1 more

Cellar: Interactive single cell data annotation tool

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.19.436162

N/A

0DataRank · unranked

3 citations

Jingtao Wang, Arjun Sarathi, Jun Ding, Ziv Bar‐Joseph, Euxhen Hasanaj

Unsupervised cell functional annotation for single-cell RNA-Seq

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.20.469410

N/A

0DataRank · unranked

2 citations

Jun Ding, Ziv Bar‐Joseph, Dongshunyi Li

Temporal modelling using single-cell transcriptomics

Nature Reviews Genetics(2022)10.1038/s41576-021-00444-7

N/A

0DataRank · unranked

217 citations

Nadav Sharon, Ziv Bar‐Joseph, Jun Ding

De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids

Nature Methods(2022)10.1038/s41592-022-01583-3

N/A

0DataRank · unranked

68 citations

Connor Wiegand, Wen Liu, Catherine McCormick, K. Ravikumar, Amir Alavi +13 more

Interactive single-cell data analysis using Cellar

Nature Communications(2022)10.1038/s41467-022-29744-0

N/A

0DataRank · unranked

35 citations

Jingtao Wang, Arjun Sarathi, Jun Ding, Ziv Bar‐Joseph, Euxhen Hasanaj

Membrane marker selection for segmenting single cell spatial proteomics data

Nature Communications(2022)10.1038/s41467-022-29667-w

N/A

0DataRank · unranked

25 citations

Maigan A. Brusko, Clive Wasserfall, Ziv Bar‐Joseph, Monica T. Dayao

TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data

Genome biology(2022)10.1186/s13059-022-02629-7

N/A

0DataRank · unranked

21 citations

Jeremy J. Velazquez, Jun Ding, Joshua Hislop, Mo R. Ebrahimkhani, Ziv Bar‐Joseph +1 more

Multiset multicover methods for discriminative marker selection

Cell Reports Methods(2022)10.1016/j.crmeth.2022.100332

N/A

0DataRank · unranked

8 citations

Amir Alavi, Anupam Gupta, Barnabás Póczos, Ziv Bar‐Joseph, Euxhen Hasanaj

scSTEM: clustering pseudotime ordered single-cell data

Genome biology(2022)10.1186/s13059-022-02716-9

N/A

0DataRank · unranked

9 citations

Jingtao Wang, Ziv Bar‐Joseph, Qi Song

Ziv Bar‐Joseph

Indexed papers

Top data-sharing exemplar

Papers