Beth A. Cimini

Biochemistry, Genetics and Molecular Biology

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 1%percentile

5.2Author 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.

Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations

Nature Methods(2024)10.1038/s41592-024-02241-6

Top 8%

2.7DataRank

Top 8%124 citations

Beth A. Cimini, Amy Goodale, Lisa Miller, Maria Kost‐Alimova, Nasim Jamali +18 more

Papers

Driven by 62 papers — median percentile 88. Top paper: “Metrics reloaded: recommendations for image analysis validation”.

Metrics reloaded: recommendations for image analysis validation

Nature Methods(2024)10.1038/s41592-023-02151-z

N/A

9.2DataRank · unranked

411 citations

Annika Reinke, Patrick Godau, Minu D. Tizabi, Florian Buettner, Evangelia Christodoulou +68 more

OME-Zarr: a cloud-optimized bioimaging file format with international community support

Histochemistry and Cell Biology(2023)10.1007/s00418-023-02209-1

N/A

2.8DataRank · unranked

123 citations

Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva Maxfield Brown +64 more

Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations

Nature Methods(2024)10.1038/s41592-024-02241-6

Top 8%

2.7DataRank

Top 8%124 citations

Beth A. Cimini, Amy Goodale, Lisa Miller, Maria Kost‐Alimova, Nasim Jamali +18 more

PyImageJ: A library for integrating ImageJ and Python

Nature Methods(2022)10.1038/s41592-022-01655-4

N/A

1.9DataRank · unranked

54 citations

Mark Hiner, Edward L. Evans, Michael A. Pinkert, Alice Lucas, Anne E. Carpenter +3 more

Community-developed checklists for publishing images and image analyses

Nature Methods(2023)10.1038/s41592-023-01987-9

N/A

1.9DataRank · unranked

80 citations

Michael S. Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof +49 more

Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.05.475090

Top 12%

1.8DataRank

Top 12%51 citations

Beth A. Cimini, Amy Goodale, Lisa Miller, Maria Kost‐Alimova, Nasim Jamali +18 more

A biologist’s guide to planning and performing quantitative bioimaging experiments

PLoS Biology(2023)10.1371/journal.pbio.3002167

N/A

0.995DataRank · unranked

31 citations

Barbara Diaz‐Rohrer, Pina Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor +11 more

Smart microscopes of the future

Nature Methods(2023)10.1038/s41592-023-01912-0

N/A

0.929DataRank · unranked

31 citations

Beth A. Cimini, Kevin W. Eliceiri, Anne E. Carpenter

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.08.459417

Top 25%

0.790DataRank

Top 25%19 citations

Juan C. Caicedo, Beth A. Cimini, Anne E. Carpenter, Shantanu Singh, Marzieh Haghighi

Understanding metric-related pitfalls in image analysis validation

Nature Methods(2024)10.1038/s41592-023-02150-0

N/A

0.783DataRank · unranked

184 citations

Minu D. Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Ali Emre Kavur +65 more

Optimizing the Cell Painting assay for image-based profiling

Nature Protocols(2023)10.1038/s41596-023-00840-9

N/A

0.763DataRank · unranked

161 citations

Srinivas Niranj Chandrasekaran, Maria Kost‐Alimova, Lisa Miller, Amy Goodale, Briana Fritchman +30 more

Morphology and gene expression profiling provide complementary information for mapping cell state

Cell Systems(2022)10.1016/j.cels.2022.10.001

N/A

0.737DataRank · unranked

135 citations

Ted Natoli, Adeniyi Adeboye, Lev Litichevskiy, Andrew X. Yang, Xiaodong Lü +15 more

High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations

Nature Methods(2022)10.1038/s41592-022-01667-0

N/A

0.713DataRank · unranked

115 citations

Juan Carlos Caicedo, Beth A. Cimini, Anne E. Carpenter, Shantanu Singh, Marzieh Haghighi

Learning representations for image-based profiling of perturbations

Nature Communications(2024)10.1038/s41467-024-45999-1

N/A

0.702DataRank · unranked

107 citations

Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman +9 more

CellProfiler 4: Improvements in Speed, Utility and Usability

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.30.450416

N/A

0.673DataRank · unranked

88 citations

Madison J. Swain-Bowden, Alice Lucas, Anne E. Carpenter, Beth A. Cimini, Allen Goodman +1 more

Metrics reloaded: Recommendations for image analysis validation

arXiv (Cornell University)(2022)10.48550/arxiv.2206.01653

N/A

0.621DataRank · unranked

62 citations

Annika Reinke, Patrick Godau, Minu D. Tizabi, Florian Buettner, Evangelia Christodoulou +69 more

Pervasive mislocalization of pathogenic coding variants underlying human disorders

Cell(2024)10.1016/j.cell.2024.09.003

N/A

0.609DataRank · unranked

57 citations

Marzieh Haghighi, Shahan Haider, Chloe Reno, Zhen‐Yuan Lin, Dmitri Segal +24 more

High-dimensional phenotyping to define the genetic basis of cellular morphology

Nature Communications(2024)10.1038/s41467-023-44045-w

N/A

0.598DataRank · unranked

53 citations

Jatin Arora, Samira Asgari, Beth A. Cimini, Ajay Nadig, Emily Peirent +14 more

Learning representations for image-based profiling of perturbations

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.12.503783

N/A

0.574DataRank · unranked

45 citations

Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman +9 more

Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler

Cell Genomics(2023)10.1016/j.xgen.2023.100346

N/A

0.557DataRank · unranked

40 citations

Sophie Strobel, Josep M. Mercader, Hesam Dashti, Felipe R. C. dos Santos, Phil Kubitz +31 more

Reproducible image-based profiling with Pycytominer

PubMed(2023)10.48550/arxiv.2311.13417

N/A

0.538DataRank · unranked

18 citations

Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern +23 more

Morphology and gene expression profiling provide complementary information for mapping cell state

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.21.465335

N/A

0.515DataRank · unranked

30 citations

Ted Natoli, Adeniyi Adeboye, Lev Litichevskiy, Andrew X. Yang, Xiaodong Lü +15 more

High-content microscopy reveals a morphological signature of bortezomib resistance

eLife(2023)10.7554/elife.91362

N/A

0.477DataRank · unranked

23 citations

Adi Y. Berman, David R. Stirling, Beth A. Cimini, Yu Han, Shantanu Singh +4 more

Assessing the performance of the Cell Painting assay across different imaging systems

Cytometry Part A(2023)10.1002/cyto.a.24786

N/A

0.470DataRank · unranked

22 citations

Nasim Jamali, Hamdah Shafqat Abbasi, Kenneth A. Giuliano, Mai Hagimoto, Kevin Jan +12 more

Interpreting Image‐based Profiles using Similarity Clustering and Single‐Cell Visualization

Current Protocols(2023)10.1002/cpz1.713

N/A

0.470DataRank · unranked

22 citations

Mário Costa Cruz, Marzieh Haghighi, Marcelo Bispo de Jesus, Shantanu Singh, Anne E. Carpenter +2 more

The crucial role of bioimage analysts in scientific research and publication

Journal of Cell Science(2024)10.1242/jcs.262322

N/A

0.425DataRank · unranked

16 citations

Peter Bankhead, Rocco D’Antuono, Elnaz Fazeli, Julia Fernández-Rodrı́guez, Caterina Fuster-Barceló +28 more

Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.17.452050

N/A

0.416DataRank · unranked

15 citations

Sophie Strobel, Josep M. Mercader, Hesam Dashti, Alina Ainbinder, Julius Honecker +27 more

Morphological map of under- and overexpression of genes in human cells

Nature Methods(2025)10.1038/s41592-025-02753-9

N/A

0.385DataRank · unranked

12 citations

Eric Alix, John Arévalo, Adriana Borowa, Patrick J. Byrne, William G Charles +51 more

High-dimensional phenotyping to define the genetic basis of cellular morphology

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.09.522731

N/A

0.312DataRank · unranked

7 citations

Jatin Arora, Samira Asgari, Beth A. Cimini, Emily Peirent, Dhara Liyanage +12 more

Community-developed checklists for publishing images and image analysis

arXiv (Cornell University)(2023)10.48550/arxiv.2302.07005

N/A

0.292DataRank · unranked

6 citations

Michael S. Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof +49 more

Enabling Global Image Data Sharing in the Life Sciences

arXiv (Cornell University)(2024)10.48550/arxiv.2401.13023

N/A

0.282DataRank · unranked

5 citations

Sreenivas Bhattiprolu, Boerner, Katy, Beth A. Cimini, Lucy Collinson, Jan Ellenberg +18 more

2020 BioImage Analysis Survey: Community experiences and needs for the future

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.16.456498

N/A

0.269DataRank · unranked

5 citations

Ellen T. A. Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini, Nasim Jamali

Alternate dyes for image-based profiling assays

SLAS DISCOVERY(2025)10.1016/j.slasd.2025.100268

N/A

0.208DataRank · unranked

3 citations

Patrick J. Byrne, Alán F. Muñoz, John Arévalo, Anne E. Carpenter, Shantanu Singh +3 more

High-content microscopy reveals a morphological signature of bortezomib resistance

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.02.539137

N/A

0.165DataRank · unranked

2 citations

Adi Y. Berman, David R. Stirling, Beth A. Cimini, Yu Han, Shantanu Singh +4 more

Alternate dyes for image-based profiling assays

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.19.639058

N/A

0.104DataRank · unranked

1 citations

Patrick J. Byrne, Alán F. Muñoz, John Arévalo, Anne E. Carpenter, Shantanu Singh +3 more

HSBP7 Rescue of a Titin Cardiomyopathy Identified by Morphological Profiling

Research Square(2024)10.21203/rs.3.rs-4558927/v1

N/A

0.104DataRank · unranked

1 citations

Ruifan Pei, Elizabeth M. Brydon, Elizabeth Lee, Matthew C. Hill, Nasim Jamali +14 more

Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging

Communications Biology(2021)10.1038/s42003-021-02276-x

N/A

0DataRank · unranked

19 citations

Alison O’Neil, Hamdah Shafqat Abbasi, Beth A. Cimini, Anne E. Carpenter, Lee L. Rubin +2 more

2020 BioImage Analysis Survey: Community experiences and needs for the future

Biological Imaging(2021)10.1017/s2633903x21000039

N/A

0DataRank · unranked

24 citations

Ellen T. A. Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini, Nasim Jamali

ImageJ and CellProfiler: Complements in Open‐Source Bioimage Analysis

Current Protocols(2021)10.1002/cpz1.89

N/A

0DataRank · unranked

42 citations

Beth A. Cimini, Anna H. Klemm, Carolina Wählby, Anne E. Carpenter, Kevin W. Eliceiri +1 more

Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin

Nature Communications(2021)10.1038/s41467-021-26571-7

N/A

0DataRank · unranked

99 citations

Tushar Kamath, Courtney M. Mazur, Fatemeh Mirzamohammadi, Daniel Rotter, Hironori Hojo +24 more

CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis

Bioinformatics(2021)10.1093/bioinformatics/btab634

N/A

0DataRank · unranked

141 citations

Anne E Carpenter, Beth A. Cimini, David R Stirling

CellProfiler 4: improvements in speed, utility and usability

BMC Bioinformatics(2021)10.1186/s12859-021-04344-9

N/A

0DataRank · unranked

2215 citations

Madison J. Swain-Bowden, Alice Lucas, Anne E. Carpenter, Beth A. Cimini, Allen Goodman +1 more

Cell Painting Gallery: an open resource for image-based profiling

Nature Methods(2024)10.1038/s41592-024-02399-z

N/A

0DataRank · unranked

40 citations

Ankur Kumar, John Arévalo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh +1 more

Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.12.148155

N/A

0DataRank · unranked

3 citations

Karen Perez de Arce, Beth A. Cimini, Eike‐Christian Wamhoff, Shantanu Singh, Jeffrey R. Cottrell +3 more

Building momentum through networks: Bioimaging across the Americas

Journal of Microscopy(2024)10.1111/jmi.13318

N/A

0DataRank · unranked

5 citations

Rodrigo Escobedo García, Celina Terán Ramírez, Ysa Pakowski, Yuriney Abonza, Nikki Bialy +57 more

A mouse model of TB-associated lung fibrosis reveals persistent inflammatory macrophage populations during treatment

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.04.597479

N/A

0DataRank · unranked

0 citations

Threnesan Naidoo, Yuming Liu, Shatavisha Dasgupta, Neha Jain, Jennie Ruelas Castillo +7 more

Building momentum through networks: Bioimaging across the Americas

White Rose Research Online (University of Leeds, The University of Sheffield, University of York)(2024)10.17615/00ds-2x60

N/A

0DataRank · unranked

0 citations

Yael Hernandez Guadarrama, Aurélie Cleret‐Buhot, Caroline Miller, Víctor Abonza, Antje Keppler +57 more

Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion

Nature Communications(2025)10.1038/s41467-025-61547-x

N/A

0DataRank · unranked

13 citations

Dhara Liyanage, Yu Han, Kathryn B. Hebert, Ruifan Pei, Gregory P. Way +8 more

Molecular Diversity of Glutamatergic and GABAergic Synapses from Multiplexed Fluorescence Imaging

eNeuro(2020)10.1523/eneuro.0286-20.2020

N/A

0DataRank · unranked

17 citations

Karen Perez de Arce, Beth A. Cimini, Eike‐Christian Wamhoff, Shantanu Singh, Jeffrey R. Cottrell +3 more

Inflammatory Macrophages Associate With Tissue Injury and Fibrosis in a Mouse Model of Tuberculosis

The Journal of Infectious Diseases(2025)10.1093/infdis/jiaf361

N/A

0DataRank · unranked

1 citations

Jennie Ruelas Castillo, Threnesan Naidoo, Yuming Liu, Shatavisha Dasgupta, Neha Jain +7 more

Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.22.634152

N/A

0DataRank · unranked

10 citations

Katherine Titterton, Alex Bäuerle, Alex Beatson, Daniil A. Boiko, Ángel Alexander Cabrera +12 more

Identifying and targeting abnormal mitochondrial localization associated with psychosis

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.08.676630

N/A

0DataRank · unranked

1 citations

Donna L. McPhie, Mohammad Hossein Rohban, Erin Weisbart, David J. Logan, Kyle W. Karhohs +8 more

Rare missense variants of the leukocyte common antigen related receptor (LAR) display reduced activity in transcellular adhesion and synapse formation

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.16.638491

N/A

0DataRank · unranked

0 citations

Nicolas Chofflet, Deniz Bicer, Sune Skeldal, Jinjie Duan, Benjamin Feller +16 more

A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes

Nature Metabolism(2023)10.1038/s42255-023-00807-w

N/A

0DataRank · unranked

37 citations

Samantha Laber, Nicholas A. Sinnott-Armstrong, Débora R. Sobreira, Sophie Strobel, Thiago M. Batista +21 more

Rare missense variants of the leukocyte common antigen related receptor (LAR) display reduced activity in transcellular adhesion and synapse formation

Research Square(2025)10.21203/rs.3.rs-5928514/v1

N/A

0DataRank · unranked

0 citations

Nicolas Chofflet, Deniz Bicer, Jinjie Duan, Benjamin Feller, Joachim Vilstrup +16 more

Improved tracking via cell region fingerprints

Nature Methods(2022)10.1038/s41592-022-01525-z

N/A

0DataRank · unranked

1 citations

Beth A. Cimini

Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale

Nature Methods(2023)10.1038/s41592-023-01918-8

N/A

0DataRank · unranked

13 citations

Beth A. Cimini, Erin Weisbart

High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly

eLife(2023)10.7554/elife.80168

N/A

0DataRank · unranked

12 citations

Gizem Rizki, Anna Nathanson, Jenny A. Klein, Darina Trendafilova, Sara G. Susco +10 more

The Twenty Questions of bioimage object analysis

Nature Methods(2023)10.1038/s41592-023-01919-7

N/A

0DataRank · unranked

6 citations

Kevin W. Eliceiri, Beth A. Cimini

Moving beyond the desktop: prospects for practical bioimage analysis via the web

Frontiers in Bioinformatics(2023)10.3389/fbinf.2023.1233748

N/A

0DataRank · unranked

7 citations

Kevin W. Eliceiri, Beth A. Cimini, Wei Ouyang

Assessing the performance of the Cell Painting assay across different imaging systems

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.15.528711

N/A

0DataRank · unranked

9 citations

Nasim Jamali, Hamdah Shafqat Abbasi, Kenneth A. Giuliano, Mai Hagimoto, Kevin Jan +12 more

Pervasive mislocalization of pathogenic coding variants underlying human disorders

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.05.556368

N/A

0DataRank · unranked

9 citations

Marzieh Haghighi, Shahan Haider, Zhen‐Yuan Lin, Dmitri Segal, Chloe Reno +18 more

Beth A. Cimini

Indexed papers

Top data-sharing exemplar

Papers