Anne E. Carpenter

Biochemistry, Genetics and Molecular BiologyEngineeringComputer 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 1%percentile

5.6Author DataRank

Indexed papers

4in 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 4 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 98 papers — median percentile 81. Top paper: “Opportunities and obstacles for deep learning in biology and medicine”.

Opportunities and obstacles for deep learning in biology and medicine

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/142760

N/A

11.2DataRank · unranked

310 citations

Daniel S. Himmelstein, Brett K. Beaulieu‐Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way +31 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

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

BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology

Molecular Neurodegeneration(2020)10.1186/s13024-020-00387-3

N/A

1.6DataRank · unranked

89 citations

Vladislav Petyuk, Charles C. White, Galina Marsh, Yiyi Ma, Hans‐Ulrich Klein +14 more

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic

PLoS Computational Biology(2022)10.1371/journal.pcbi.1009888

N/A

1.5DataRank · unranked

57 citations

Shantanu Singh, Anne E. Carpenter, Gregory P. Way, Yuen Ler Chow

Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.3c01834

N/A

1.4DataRank · unranked

45 citations

Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender +2 more

Developing open-source software for bioimage analysis: opportunities and challenges

F1000Research(2021)10.12688/f1000research.52531.1

N/A

1.3DataRank · unranked

37 citations

Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase +1 more

A field guide to cultivating computational biology

PLOS Biology(2021)10.1371/journal.pbio.3001419

N/A

1.3DataRank · unranked

22 citations

Casey S. Greene, Piero Carninci, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley +11 more

CellProfiler 4: improvements in speed, utility and usability

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

N/A

1.2DataRank · unranked

2242 citations

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

Opportunities and obstacles for deep learning in biology and medicine

Journal of The Royal Society Interface(2018)10.1098/rsif.2017.0387

N/A

1.2DataRank · unranked

2203 citations

Daniel S. Himmelstein, Brett K. Beaulieu‐Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way +31 more

Deciphering the impact of genomic variation on function

Nature(2024)10.1038/s41586-024-07510-0

N/A

1.1DataRank · unranked

89 citations

Jesse M. Engreitz, Heather A. Lawson, Harinder Singh, Lea M. Starita, Gary C. Hon +95 more

Predicting cell health phenotypes using image-based morphology profiling

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.08.193938

N/A

0.952DataRank · unranked

21 citations

Maria Kost‐Alimova, Tsukasa Shibue, William F. Harrington, Stanley Gill, Federica Piccioni +7 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

Image-based profiling for drug discovery: due for a machine-learning upgrade?

Nature Reviews Drug Discovery(2020)10.1038/s41573-020-00117-w

N/A

0.909DataRank · unranked

427 citations

Hugo Ceulemans, Justin D. Boyd, Anne E. Carpenter, Srinivas Niranj Chandrasekaran

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

Cytometry Part A(2019)10.1002/cyto.a.23863

N/A

0.870DataRank · unranked

330 citations

Jonathan Roth, James W. Fairman, Tim Becker, Kyle W. Karhohs, Matthieu Broisin +7 more

Reconstructing cell cycle and disease progression using deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/081364

N/A

0.869DataRank · unranked

21 citations

Niklas D. Köhler, Thomas Blasi, Andrew Filby, Anne E. Carpenter, Paul Rees +4 more

Label-free cell cycle analysis for high-throughput imaging flow cytometry

Nature Communications(2016)10.1038/ncomms10256

N/A

0.863DataRank · unranked

315 citations

Holger Hennig, Huw D. Summers, Fabian Joachim Theis, Joana Cerveira, James O. Patterson +5 more

Reconstructing cell cycle and disease progression using deep learning

Nature Communications(2017)10.1038/s41467-017-00623-3

N/A

0.858DataRank · unranked

304 citations

Niklas D. Köhler, Thomas Blasi, Andrew Filby, Anne E. Carpenter, Paul Rees +3 more

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

Cell Systems(2020)10.1016/j.cels.2020.04.003

N/A

0.848DataRank · unranked

284 citations

Ábel Szkalisity, Tímea Tóth, Ervin Tasnádi, Csaba Molnár, Botond Mathe +20 more

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

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

Predicting reprogramming-related gene expression from cell morphology in human induced pluripotent stem cells

Molecular Biology of the Cell(2023)10.1091/mbc.e22-06-0215

N/A

0.741DataRank · unranked

14 citations

Mitsuru Negishi, Yuta Murakami, Shunsuke Tominaga, Yasushi Shiraishi, Anne E. Carpenter +3 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

Predicting compound activity from phenotypic profiles and chemical structures

Nature Communications(2023)10.1038/s41467-023-37570-1

N/A

0.705DataRank · unranked

109 citations

Tim Becker, Kevin Yang, Péter Horváth, Vlado Dančík, Bridget K. Wagner +5 more

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

Cell Painting: a decade of discovery and innovation in cellular imaging

Nature Methods(2024)10.1038/s41592-024-02528-8

N/A

0.686DataRank · unranked

96 citations

Maria‐Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras‐Puigvert, Nigel Greene +3 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

Label‐Free Leukemia Monitoring by Computer Vision

Cytometry Part A(2020)10.1002/cyto.a.23987

N/A

0.614DataRank · unranked

59 citations

Marian Case, Dino Mašić, Holger Hennig, Claire McQuin, Juan Carlos Caicedo +11 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

ImageJ and CellProfiler: Complements in Open‐Source Bioimage Analysis

Current Protocols(2021)10.1002/cpz1.89

N/A

0.568DataRank · unranked

43 citations

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

Reference compounds for characterizing cellular injury in high-content cellular morphology assays

Nature Communications(2023)10.1038/s41467-023-36829-x

N/A

0.564DataRank · unranked

42 citations

Bruce K. Hua, Beth E. Zucconi, Shawn D. Nelson, Shantanu Singh, Anne E. Carpenter +21 more

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

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

N/A

0.561DataRank · unranked

41 citations

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

Virtual screening for small-molecule pathway regulators by image-profile matching

Cell Systems(2022)10.1016/j.cels.2022.08.003

N/A

0.553DataRank · unranked

39 citations

Ashley M. Fuller, Ceryl Tan, Jonathan T. Goldstein, Deepsing Syangtan, Amos Gutnick +25 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

0.546DataRank · unranked

37 citations

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

Inter-laboratory automation of the in vitro micronucleus assay using imaging flow cytometry and deep learning

Archives of Toxicology(2021)10.1007/s00204-021-03113-0

N/A

0.542DataRank · unranked

36 citations

Jatin R. Verma, Benjamin J. Rees, Danielle S G Harte, Qiellor Haxhiraj, Claire M. Barnes +15 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

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

Cell Metabolism(2023)10.1016/j.cmet.2023.03.018

N/A

0.529DataRank · unranked

33 citations

Juliana Coraor, Choah Kim, Eriene-Heidi Sidhom, Matthew Brown, Jamie L. Marshall +33 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

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

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/335216

N/A

0.470DataRank · unranked

22 citations

Jonathan Roth, James W. Fairman, Tim Becker, Kyle W. Karhohs, Matthieu Broisin +7 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

Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry

New Phytologist(2023)10.1111/nph.19186

N/A

0.464DataRank · unranked

21 citations

Ann Power, Dan Barber, Richard Tennant, Richard T. Jones, Gunhee Lee +10 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

0.449DataRank · unranked

19 citations

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

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

0.406DataRank · unranked

14 citations

Dhara Liyanage, Yu Han, Kathryn B. Hebert, Ruifan Pei, Gregory P. Way +8 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-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly

eLife(2023)10.7554/elife.80168

N/A

0.385DataRank · unranked

12 citations

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

Virtual screening for small molecule pathway regulators by image profile matching

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.29.454377

N/A

0.367DataRank · unranked

6 citations

Ashley M. Fuller, Ceryl Tan, Jonathan T. Goldstein, Deepsing Syangtan, Amos Gutnick +25 more

Cell Painting predicts impact of lung cancer variants

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.18.469171

N/A

0.330DataRank · unranked

8 citations

John Arévalo, Federica Piccioni, Mark‐Anthony Bray, Cathy L Hartland, Xiaoyun Wu +6 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

The OASIS Consortium: integrating multi-omics technologies to transform chemical safety assessment

Toxicological Sciences(2025)10.1093/toxsci/kfaf128

N/A

0.312DataRank · unranked

7 citations

Andreas Bender, Jaime H. Cheah, Chrissy Crute, Deidre A. Dalmas, Jessica Ewald +11 more

Learning Molecular Representation in a Cell

PubMed(2024)10.48550/arxiv.2406.12056

N/A

0.312DataRank · unranked

7 citations

Srijit Seal, John Arévalo, Zhenwen Liang, Anne E. Carpenter, Meng Jiang +2 more

Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.15.562398

Top 54%

0.310DataRank

Top 54%6 citations

Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender +2 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

Step Forward Cross Validation for Bioactivity Prediction: Out of Distribution Validation in Drug Discovery

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.02.601740

N/A

0.269DataRank · unranked

5 citations

Michele Vendruscolo, Anne E. Carpenter, Shantanu Singh, Andreas Bender, Srijit Seal +1 more

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

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

arXiv (Cornell University)(2024)10.48550/arxiv.2405.02767

N/A

0.165DataRank · unranked

2 citations

Maria‐Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras‐Puigvert, Nigel Greene +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

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.19.529127

N/A

0.118DataRank · unranked

1 citations

Juliana Coraor, Choah Kim, Eriene-Heidi Sidhom, Matthew Brown, Jamie L. Marshall +33 more

Identifying and targeting abnormal mitochondrial localization associated with psychosis

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

N/A

0.104DataRank · unranked

1 citations

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

Reference compounds for characterizing cellular injury in high-content cellular morphology assays

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.12.499781

N/A

0.104DataRank · unranked

1 citations

Bruce K. Hua, Beth E. Zucconi, Shawn D. Nelson, Shantanu Singh, Anne E. Carpenter +21 more

Image-based profiling: a powerful and challenging new data type

Biocomputing 2022(2021)10.1142/9789811250477_0038

N/A

0.104DataRank · unranked

1 citations

Hannah Spitzer, Philip Burnham, Arjun Raj, Shantanu Singh, Anne E. Carpenter +2 more

A field guide to cultivating computational biology

arXiv (Cornell University)(2021)10.48550/arxiv.2104.11364

N/A

0.104DataRank · unranked

1 citations

Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley +9 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

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

Progress and new challenges in image-based profiling.

Molecular Systems Biology(2025)10.1038/s44320-026-00197-7

N/A

0.104DataRank · unranked

1 citations

John A. Peters, Jesko Wagner, Rebecca E. Graham, Zhenghao Chen, Brian Feng +17 more

Keras R-CNN: library for cell detection in biological images using deep neural networks

BMC Bioinformatics(2020)10.1186/s12859-020-03635-x

N/A

0DataRank · unranked

82 citations

Allen Goodman, Deepali Ravel, Stefanie Costa Pinto Lopes, Gabriel W. Rangel, Odailton Amaral Nery +10 more

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

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

Small molecule bioactivity benchmarks are often well-predicted by counting cells

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.27.650853

N/A

0DataRank · unranked

4 citations

William Dee, Adit Shah, Andrew Zhang, Katherine Titterton, Ángel Alexander Cabrera +8 more

Evaluating batch correction methods for image-based cell profiling

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.15.558001

N/A

0DataRank · unranked

23 citations

Ellen Su, Robert van Dijk, Anne E. Carpenter, Shantanu Singh, John Arévalo

From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability

Molecular Biology of the Cell(2024)10.1091/mbc.e23-08-0298

N/A

0DataRank · unranked

24 citations

Jordi Carreras‐Puigvert, Shantanu Singh, Anne E. Carpenter, Ola Spjuth, Andreas Bender +1 more

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning

PLoS Computational Biology(2024)10.1371/journal.pcbi.1012547

N/A

0DataRank · unranked

8 citations

John Arévalo, Mehrtash Babadi, Anne E. Carpenter, Shantanu Singh, Robert van Dijk

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.04.592531

N/A

0DataRank · unranked

22 citations

Maria‐Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras‐Puigvert, Nigel Greene +3 more

A versatile information retrieval framework for evaluating profile strength and similarity

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.01.587631

N/A

0DataRank · unranked

15 citations

John Arévalo, Erik Serrano, Loan Vulliard, Hillary Tsang, Michael Bornholdt +7 more

Harnessing the power of microscopy images to accelerate drug discovery: what are the possibilities?

Expert Opinion on Drug Discovery(2020)10.1080/17460441.2020.1743675

N/A

0DataRank · unranked

14 citations

Myles Fennell, Anne E. Carpenter, Justin D. Boyd

Improved Detection of Drug-Induced Liver Injury by Integrating Predicted in vivo and in vitro Data

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.10.575128

N/A

0DataRank · unranked

6 citations

Dominic P. Williams, Layla Hosseini-Gerami, Manas Mahale, Anne E. Carpenter, Ola Spjuth +2 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

Discovery of New Anti-Schistosomal Hits by Integration of QSAR-Based Virtual Screening and High Content Screening

INDIGO (University of Illinois at Chicago)(2020)10.17615/q7zj-hs71

N/A

0DataRank · unranked

0 citations

Walter César Góes Valente, João M. Rezende-Neto, Nicholas Furnham, Ana C. M. de Almeida, Floriano Paes Silva +11 more

The new era of quantitative cell imaging—challenges and opportunities

Molecular Cell(2022)10.1016/j.molcel.2021.12.024

N/A

0DataRank · unranked

55 citations

Anne E. Carpenter, Emma Lundberg, Anne L. Plant, Rick Horwitz, Neda Bagheri

MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction

arXiv (Cornell University)(2024)10.48550/arxiv.2406.08649

N/A

0DataRank · unranked

0 citations

Ellen Su, Anne E. Carpenter, Shantanu Singh, John Arévalo

A versatile information retrieval framework for evaluating profile strength and similarity

Nature Communications(2025)10.1038/s41467-025-60306-2

N/A

0DataRank · unranked

18 citations

John Arévalo, Erik Serrano, Loan Vulliard, Hillary Tsang, Michael Bornholdt +7 more

Genes in human obesity loci are causal obesity genes in C. elegans

PLoS Genetics(2021)10.1371/journal.pgen.1009736

N/A

0DataRank · unranked

32 citations

Jordan N. Reed, Chenyu Yang, Noel Higgason, Leila Rayyan, Carolina Wählby +4 more

Predicting gene expression from cell morphology in human induced pluripotent stem cells

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.19.488786

N/A

0DataRank · unranked

8 citations

Mitsuru Negishi, Yuta Murakami, Shunsuke Tominaga, Yasushi Shiraishi, Anne E. Carpenter +3 more

nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome

Nature Methods(2025)10.1038/s41592-025-02861-6

N/A

0DataRank · unranked

11 citations

Grant Ongo, Nathaniel Robichaud, Jinglin Kong, Woojong Rho, Ivan Teahulos +27 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

In vitro neutrophil migration is associated with inhaled corticosteroid treatment and serum cytokines in pediatric asthma

Frontiers in Pharmacology(2022)10.3389/fphar.2022.1021317

N/A

0DataRank · unranked

1 citations

Markus Weckmann, Anna Wohlers, Adan Chari Jirmo, Ruth Grychtol, Isabell Ricklefs +16 more

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.14.567038

N/A

0DataRank · unranked

5 citations

John Arévalo, Mehrtash Babadi, Anne E. Carpenter, Shantanu Singh, Robert van Dijk

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

Predicting compound activity from phenotypic profiles and chemical structures

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.15.422887

N/A

0DataRank · unranked

24 citations

Tim Becker, Kevin Yang, Péter Horváth, Vlado Dančík, Bridget K. Wagner +5 more

Bridging Domain and Data

Patterns(2020)10.1016/j.patter.2020.100064

N/A

0DataRank · unranked

2 citations

Anne E. Carpenter

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

Anne E. Carpenter

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