Cited by 429Bioinformatics and Genomic NetworksGene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

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The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

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Keenan, Alexandra B., Jenkins, Sherry L., Jagodnik, Kathleen M., Koplev, Simon, He, Edward, Torre, Denis, Wang, Zichen, Dohlman, Anders B., Silverstein, Moshe C., Lachmann, Alexander, Kuleshov, Maxim V., Ma'ayan, Avi, Stathias, Vasileios, Terryn, Raymond, Cooper, Daniel, Forlin, Michele, Koleti, Amar, Vidovic, Dusica, Chung, Caty, Schürer, Stephan C., Vasiliauskas, Jouzas, Pilarczyk, Marcin, Shamsaei, Behrouz, Fazel, Mehdi, Ren, Yan, Niu, Wen, Clark, Nicholas A., White, Shana, Mahi, Naim, Zhang, Lixia, Kouril, Michal, Reichard, John F., Sivaganesan, Siva, Medvedovic, Mario, Meller, Jaroslaw, Koch, Rick J., Birtwistle, Marc R., Iyengar, Ravi, Sobie, Eric A., Azeloglu, Evren U., Kaye, Julia, Osterloh, Jeannette, Haston, Kelly, Kalra, Jaslin, Finkbiener, Steve, Li, Jonathan, Milani, Pamela, Adam, Miriam, Escalante-Chong, Renan, Sachs, Karen, Lenail, Alex, Ramamoorthy, Divya, Fraenkel, Ernest, Daigle, Gavin, Hussain, Uzma, Coye, Alyssa, Rothstein, Jeffrey, Sareen, Dhruv, Ornelas, Loren, Banuelos, Maria, Mandefro, Berhan, Ho, Ritchie, Svendsen, Clive N., Lim, Ryan G., Stocksdale, Jennifer, Casale, Malcolm S., Thompson, Terri G., Wu, Jie, Thompson, Leslie M., Dardov, Victoria, Venkatraman, Vidya, Matlock, Andrea, Van Eyk, Jennifer E., Jaffe, Jacob D., Papanastasiou, Malvina, Subramanian, Aravind, Golub, Todd R., Erickson, Sean D., Fallahi-Sichani, Mohammad, Hafner, Marc, Gray, Nathanael S., Lin, Jia-Ren, Mills, Caitlin E., Muhlich, Jeremy L., Niepel, Mario, Shamu, Caroline E., Williams, Elizabeth H., Wrobel, David, Sorger, Peter K., Heiser, Laura M., Gray, Joe W., Korkola, James E., Mills, Gordon B., LaBarge, Mark, Feiler, Heidi S., Dane, Mark A., Bucher, Elmar, Nederlof, Michel, Sudar, Damir, Gross, Sean, Kilburn, David F., Smith, Rebecca, Devlin, Kaylyn, Margolis, Ron, Derr, Leslie, Lee, Albert, Pillai, Ajay·2018·Cell Systems

DOI 10.1016/j.cels.2017.11.001PMC PMC5799026

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Abstract

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.

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Additional file 4 of Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination
Yang, J. J., Gessner, C. R., Duerksen, J. L., Biber, D., Binder, J., Ozturk, M., Foote, B., McEntire, R., Stirling, K., Ding, Y., et al. (2022) · Figshare · doi:10.6084/m9.figshare.18318355
Additional file 3 of Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination
Yang, J. J., Gessner, C. R., Duerksen, J. L., Biber, D., Binder, J., Ozturk, M., Foote, B., McEntire, R., Stirling, K., Ding, Y., et al. (2022) · Figshare · doi:10.6084/m9.figshare.18318352
Additional file 5 of Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination
Yang, J. J., Gessner, C. R., Duerksen, J. L., Biber, D., Binder, J., Ozturk, M., Foote, B., McEntire, R., Stirling, K., Ding, Y., et al. (2022) · Figshare · doi:10.6084/m9.figshare.18318358
Additional file 2 of Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination
Yang, J. J., Gessner, C. R., Duerksen, J. L., Biber, D., Binder, J., Ozturk, M., Foote, B., McEntire, R., Stirling, K., Ding, Y., et al. (2022) · Figshare · doi:10.6084/m9.figshare.18318349
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Additional file 1 of Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination
Yang, J. J., Gessner, C. R., Duerksen, J. L., Biber, D., Binder, J., Ozturk, M., Foote, B., McEntire, R., Stirling, K., Ding, Y., et al. (2022) · Figshare · doi:10.6084/m9.figshare.18318346

Authors: Keenan, A. B., Jenkins, S. L., Jagodnik, K. M., Koplev, S., He, E., Torre, D., Wang, Z., Dohlman, A. B., Silverstein, M. C., Lachmann, A., Kuleshov, M. V., Ma'ayan, A., Stathias, V., Terryn, R., Cooper, D., Forlin, M., Koleti, A., Vidovic, D., Chung, C., Schürer, S. C., Vasiliauskas, J., Pilarczyk, M., Shamsaei, B., Fazel, M., Ren, Y., Niu, W., Clark, N. A., White, S., Mahi, N., Zhang, L., Kouril, M., Reichard, J. F., Sivaganesan, S., Medvedovic, M., Meller, J., Koch, R. J., Birtwistle, M. R., Iyengar, R., Sobie, E. A., Azeloglu, E. U., Kaye, J., Osterloh, J., Haston, K., Kalra, J., Finkbiener, S., Li, J., Milani, P., Adam, M., Escalante-Chong, R., Sachs, K., Lenail, A., Ramamoorthy, D., Fraenkel, E., Daigle, G., Hussain, U., Coye, A., Rothstein, J., Sareen, D., Ornelas, L., Banuelos, M., Mandefro, B., Ho, R., Svendsen, C. N., Lim, R. G., Stocksdale, J., Casale, M. S., Thompson, T. G., Wu, J., Thompson, L. M., Dardov, V., Venkatraman, V., Matlock, A., Van Eyk, J. E., Jaffe, J. D., Papanastasiou, M., Subramanian, A., Golub, T. R., Erickson, S. D., Fallahi-Sichani, M., Hafner, M., Gray, N. S., Lin, J.-R., Mills, C. E., Muhlich, J. L., Niepel, M., Shamu, C. E., Williams, E. H., Wrobel, D., Sorger, P. K., Heiser, L. M., Gray, J. W., Korkola, J. E., Mills, G. B., LaBarge, M., Feiler, H. S., Dane, M. A., Bucher, E., Nederlof, M., Sudar, D., Gross, S., Kilburn, D. F., Smith, R., Devlin, K., Margolis, R., Derr, L., Lee, A., & Pillai, A.
Affiliations: Icahn School of Medicine at Mount Sinai (US)
University of Miami (US)
University of Cincinnati (US)
University of California, San Francisco (US)
Massachusetts Institute of Technology (US)
Johns Hopkins University (US)
Cedars-Sinai Medical Center (US)
University of California, Irvine (US)
Broad Institute (US)
Harvard University (US)
Oregon Health & Science University (US)
The University of Texas MD Anderson Cancer Center (US)
City Of Hope National Medical Center (US)
National Institutes of Health (US)
ORCID: Jenkins, Sherry L.
Jagodnik, Kathleen M.
Koplev, Simon
He, Edward
Torre, Denis
Wang, Zichen
Dohlman, Anders B.
Silverstein, Moshe C.
Lachmann, Alexander
Kuleshov, Maxim V.
Stathias, Vasileios
Cooper, Daniel
Schürer, Stephan C.
Pilarczyk, Marcin
Shamsaei, Behrouz
Ren, Yan
Clark, Nicholas A.
Mahi, Naim
Zhang, Lixia
Kouril, Michal
Reichard, John F.
Sivaganesan, Siva
Medvedovic, Mario
Birtwistle, Marc R.
Iyengar, Ravi
Sobie, Eric A.
Azeloglu, Evren U.
Kaye, Julia
Osterloh, Jeannette
Kalra, Jaslin
Li, Jonathan
Milani, Pamela
Escalante-Chong, Renan
Ramamoorthy, Divya
Fraenkel, Ernest
Sareen, Dhruv
Ho, Ritchie
Svendsen, Clive N.
Lim, Ryan G.
Stocksdale, Jennifer
Thompson, Terri G.
Wu, Jie
Thompson, Leslie M.
Dardov, Victoria
Venkatraman, Vidya
Matlock, Andrea
Jaffe, Jacob D.
Papanastasiou, Malvina
Subramanian, Aravind
Golub, Todd R.
Hafner, Marc
Gray, Nathanael S.
Lin, Jia-Ren
Mills, Caitlin E.
Muhlich, Jeremy L.
Niepel, Mario
Shamu, Caroline E.
Williams, Elizabeth H.
Sorger, Peter K.
Heiser, Laura M.
Gray, Joe W.
Korkola, James E.
Mills, Gordon B.
LaBarge, Mark
Feiler, Heidi S.
Dane, Mark A.
Bucher, Elmar
Nederlof, Michel
Sudar, Damir
Gross, Sean
Smith, Rebecca
Devlin, Kaylyn
Margolis, Ron
Pillai, Ajay
Venue: Cell Systems
Publisher: Elsevier BV
Published: 2018-01
Volume: 6
Issue: 1
Pages: 13-24
ISSN: 2405-4712 (ISSN-L)
DOI: 10.1016/j.cels.2017.11.001
PMC: PMC5799026
OpenAlex: W2768977980
Cited by: 423
References: 49
Citations by year: 2026: 40 · 2025: 38 · 2024: 40 · 2023: 44 · 2022: 57 · 2021: 51 · 2020: 56 · 2019: 49 · 2018: 41
FWCI: 3.83
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 388 d)
Locations: Cell Systems (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: NIH (U54HL127624, U54HG008098, U54HL127366, U54HG008097, U54NS091046, U54HL127365, U54HG008100)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords: LINCS, chemical perturbation, gene perturbation, transcriptomics, mass spectrometry, cell imaging, data cataloging, data accessibility, data reusability, cancer, heart disease, neurodegenerative diseases, treatment development
MeSH terms: Cataloging, Humans, National Health Programs, National Institutes of Health (U.S.), United States, Gene Library, Information Storage and Retrieval, Computational Biology, Gene Expression Profiling, Systems Biology, Transcriptome, Databases, Chemical

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