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

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

doi:10.1016/j.cels.2017.11.001

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

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

Research output: Contribution to journal › Review article › peer-review

254 Scopus citations

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. 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.

Original language	English (US)
Pages (from-to)	13-24
Number of pages	12
Journal	Cell Systems
Volume	6
Issue number	1
DOIs	https://doi.org/10.1016/j.cels.2017.11.001
State	Published - Jan 24 2018

Keywords

BD2K
L1000
MCF10A
MEMA
P100
data integration
lincsprogram
lincsproject
systems biology
systems pharmacology

ASJC Scopus subject areas

Pathology and Forensic Medicine
Histology
Cell Biology

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10.1016/j.cels.2017.11.001

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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., ... Pillai, A. (2018). The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems, 6(1), 13-24. https://doi.org/10.1016/j.cels.2017.11.001

Keenan, AB, Jenkins, SL, Jagodnik, KM, Koplev, S, He, E, Torre, D, Wang, Z, Dohlman, AB, Silverstein, MC, Lachmann, A, Kuleshov, MV, Ma'ayan, A, Stathias, V, Terryn, R, Cooper, D, Forlin, M, Koleti, A, Vidovic, D, Chung, C, Schürer, SC, Vasiliauskas, J, Pilarczyk, M, Shamsaei, B, Fazel, M, Ren, Y, Niu, W, Clark, NA, White, S, Mahi, N, Zhang, L, Kouril, M, Reichard, JF, Sivaganesan, S, Medvedovic, M, Meller, J, Koch, RJ, Birtwistle, MR, Iyengar, R, Sobie, EA, Azeloglu, EU, 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, CN, Lim, RG, Stocksdale, J, Casale, MS, Thompson, TG, Wu, J, Thompson, LM, Dardov, V, Venkatraman, V, Matlock, A, Van Eyk, JE, Jaffe, JD, Papanastasiou, M, Subramanian, A, Golub, TR, Erickson, SD, Fallahi-Sichani, M, Hafner, M, Gray, NS, Lin, JR, Mills, CE, Muhlich, JL, Niepel, M, Shamu, CE, Williams, EH, Wrobel, D, Sorger, PK, Heiser, LM, Gray, JW, Korkola, JE , Mills, GB, LaBarge, M, Feiler, HS, Dane, MA, Bucher, E, Nederlof, M, Sudar, D, Gross, S, Kilburn, DF, Smith, R, Devlin, K, Margolis, R, Derr, L, Lee, A & Pillai, A 2018, 'The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations', Cell Systems, vol. 6, no. 1, pp. 13-24. https://doi.org/10.1016/j.cels.2017.11.001

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

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. 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.",

keywords = "BD2K, L1000, MCF10A, MEMA, P100, data integration, lincsprogram, lincsproject, systems biology, systems pharmacology",

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

note = "Publisher Copyright: {\textcopyright} 2017 Elsevier Inc.",

year = "2018",

month = jan,

day = "24",

doi = "10.1016/j.cels.2017.11.001",

language = "English (US)",

volume = "6",

pages = "13--24",

journal = "Cell Systems",

issn = "2405-4712",

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TY - JOUR

T1 - The Library of Integrated Network-Based Cellular Signatures NIH Program

T2 - System-Level Cataloging of Human Cells Response to Perturbations

AU - Keenan, Alexandra B.

AU - Jenkins, Sherry L.

AU - Jagodnik, Kathleen M.

AU - Koplev, Simon

AU - He, Edward

AU - Torre, Denis

AU - Wang, Zichen

AU - Dohlman, Anders B.

AU - Silverstein, Moshe C.

AU - Lachmann, Alexander

AU - Kuleshov, Maxim V.

AU - Ma'ayan, Avi

AU - Stathias, Vasileios

AU - Terryn, Raymond

AU - Cooper, Daniel

AU - Forlin, Michele

AU - Koleti, Amar

AU - Vidovic, Dusica

AU - Chung, Caty

AU - Schürer, Stephan C.

AU - Vasiliauskas, Jouzas

AU - Pilarczyk, Marcin

AU - Shamsaei, Behrouz

AU - Fazel, Mehdi

AU - Ren, Yan

AU - Niu, Wen

AU - Clark, Nicholas A.

AU - White, Shana

AU - Mahi, Naim

AU - Zhang, Lixia

AU - Kouril, Michal

AU - Reichard, John F.

AU - Sivaganesan, Siva

AU - Medvedovic, Mario

AU - Meller, Jaroslaw

AU - Koch, Rick J.

AU - Birtwistle, Marc R.

AU - Iyengar, Ravi

AU - Sobie, Eric A.

AU - Azeloglu, Evren U.

AU - Kaye, Julia

AU - Osterloh, Jeannette

AU - Haston, Kelly

AU - Kalra, Jaslin

AU - Finkbiener, Steve

AU - Li, Jonathan

AU - Milani, Pamela

AU - Adam, Miriam

AU - Escalante-Chong, Renan

AU - Sachs, Karen

AU - Lenail, Alex

AU - Ramamoorthy, Divya

AU - Fraenkel, Ernest

AU - Daigle, Gavin

AU - Hussain, Uzma

AU - Coye, Alyssa

AU - Rothstein, Jeffrey

AU - Sareen, Dhruv

AU - Ornelas, Loren

AU - Banuelos, Maria

AU - Mandefro, Berhan

AU - Ho, Ritchie

AU - Svendsen, Clive N.

AU - Lim, Ryan G.

AU - Stocksdale, Jennifer

AU - Casale, Malcolm S.

AU - Thompson, Terri G.

AU - Wu, Jie

AU - Thompson, Leslie M.

AU - Dardov, Victoria

AU - Venkatraman, Vidya

AU - Matlock, Andrea

AU - Van Eyk, Jennifer E.

AU - Jaffe, Jacob D.

AU - Papanastasiou, Malvina

AU - Subramanian, Aravind

AU - Golub, Todd R.

AU - Erickson, Sean D.

AU - Fallahi-Sichani, Mohammad

AU - Hafner, Marc

AU - Gray, Nathanael S.

AU - Lin, Jia Ren

AU - Mills, Caitlin E.

AU - Muhlich, Jeremy L.

AU - Niepel, Mario

AU - Shamu, Caroline E.

AU - Williams, Elizabeth H.

AU - Wrobel, David

AU - Sorger, Peter K.

AU - Heiser, Laura M.

AU - Gray, Joe W.

AU - Korkola, James E.

AU - Mills, Gordon B.

AU - LaBarge, Mark

AU - Feiler, Heidi S.

AU - Dane, Mark A.

AU - Bucher, Elmar

AU - Nederlof, Michel

AU - Sudar, Damir

AU - Gross, Sean

AU - Kilburn, David F.

AU - Smith, Rebecca

AU - Devlin, Kaylyn

AU - Margolis, Ron

AU - Derr, Leslie

AU - Lee, Albert

AU - Pillai, Ajay

PY - 2018/1/24

Y1 - 2018/1/24

N2 - 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. 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.

AB - 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. 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.

KW - BD2K

KW - L1000

KW - MCF10A

KW - MEMA

KW - P100

KW - data integration

KW - lincsprogram

KW - lincsproject

KW - systems biology

KW - systems pharmacology

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UR - http://www.scopus.com/inward/citedby.url?scp=85036553710&partnerID=8YFLogxK

U2 - 10.1016/j.cels.2017.11.001

DO - 10.1016/j.cels.2017.11.001

M3 - Review article

C2 - 29199020

AN - SCOPUS:85036553710

SN - 2405-4712

VL - 6

SP - 13

EP - 24

JO - Cell Systems

JF - Cell Systems

IS - 1

ER -

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

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Keywords

ASJC Scopus subject areas

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