The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations
Open accessAbstract
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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- 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)
- 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 · 2017: 4 · 2013: 1
- FWCI
- 3.83
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- 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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