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Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J Cooper, John P Turner, Dušica Vidović, Michele Forlin, Tanya T Kelley, Alessandro D'Urso, Bryce K Allen, Denis Torre (+17 others)
2017 Nucleic Acids Research  
The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response  ...  In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses.  ...  We acknowledge resources from the Center for Computational Science (University of Miami, FL) for maintaining and administering the production environment and server for the LINCS Data Portal and related  ... 
doi:10.1093/nar/gkx1063 pmid:29140462 pmcid:PMC5753343 fatcat:gkmeiah7h5flxdtlpcd5bf5vxi

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures

2019 Nucleic Acids Research  
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalogue of perturbation-response signatures  ...  The LINCS Data Portal (LDP) has been the primary access point for the compendium of LINCS data and has been widely utilized.  ...  We acknowledge resources from the Center for Computational Science at the University of Miami for maintaining and administering the production environment and server for the LINCS Data Portal and related  ... 
doi:10.1093/nar/gkz1023 pmid:31701147 pmcid:PMC7145650 fatcat:mx256xxvxrfgzbesb6la2fxqne

Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center

Vasileios Stathias, Amar Koleti, Dušica Vidović, Daniel J. Cooper, Kathleen M. Jagodnik, Raymond Terryn, Michele Forlin, Caty Chung, Denis Torre, Nagi Ayad, Mario Medvedovic, Avi Ma'ayan (+2 others)
2018 Scientific Data  
The NIH-funded LINCS Consortium is creating an extensive reference library of cell-based perturbation response signatures and sophisticated informatics tools incorporating a large number of perturbagens  ...  The large volume and variety of data necessitate rigorous data standards and effective data management including modular data processing pipelines and end-user interfaces to facilitate accurate and reliable  ...  Acknowledgements This work was supported by NIH grant U54HL127624 awarded by the National Heart, Lung, and Blood Institute through funds provided by the trans-NIH Library of Integrated Network-based Cellular  ... 
doi:10.1038/sdata.2018.117 pmid:29917015 pmcid:PMC6007090 fatcat:kssix6bcm5eppacpn7fngdwq5q

SigCom LINCS: data and metadata search engine for a million gene expression signatures

John Erol Evangelista, Daniel J B Clarke, Zhuorui Xie, Alexander Lachmann, Minji Jeon, Kerwin Chen, Kathleen M Jagodnik, Sherry L Jenkins, Maxim V Kuleshov, Megan L Wojciechowicz, Stephan C Schürer, Mario Medvedovic (+1 others)
2022 Nucleic Acids Research  
Millions of transcriptome samples were generated by the Library of Integrated Network-based Cellular Signatures (LINCS) program.  ...  In addition, all the data and signatures within SigCom LINCS are available via a well-documented API.  ...  The success and promise of the Connectivity Mapping concept, and the CMAP resource, prompted the NIH to establish the Library of Integrated Network-based Cellular Signatures (LINCS) Common Fund program  ... 
doi:10.1093/nar/gkac328 pmid:35524556 pmcid:PMC9252724 fatcat:7gjogoo6ijd3xki2ihmefprtye

Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks

Aliyu Musa, Shailesh Tripathi, Matthias Dehmer, Olli Yli-Harja, Stuart A. Kauffman, Frank Emmert-Streib
2019 Scientific Reports  
The Library of Integrated Network-based Cellular Signatures (LINCS) is an example for a large-scale genomic data repository providing hundred thousands of high-dimensional gene expression measurements  ...  In this paper, we use LINCS data to construct drug association networks (DANs) representing the relationships between drugs.  ...  The LINCS data API provides a programmatic pipeline to annotations and perturbational signatures in the L1000 dataset via a collection of HTTP-based RESTful web services.  ... 
doi:10.1038/s41598-019-44291-3 pmid:31127155 pmcid:PMC6534546 fatcat:f3s5r62zpzbcxgxu5ixitddobi

Public data and open source tools for multi-assay genomic investigation of disease

Lavanya Kannan, Marcel Ramos, Angela Re, Nehme El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan (+3 others)
2015 Briefings in Bioinformatics  
This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.  ...  Large publicly funded projects have generated extensive and freely available multiassay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent  ...  Combination of drug and genetic perturbations Library of Integrated Network-based Cellular Signals The NIH Library of Integrated Network-based Cellular Signatures (LINCS) project (http://www.lincsproject.org  ... 
doi:10.1093/bib/bbv080 pmid:26463000 pmcid:PMC4945830 fatcat:buqkv6y5dra3jjlco7wdcbvcl4

Cancer Systems Biology: a peek into the future of patient care?

Henrica M. J. Werner, Gordon B. Mills, Prahlad T. Ram
2014 Nature Reviews Clinical Oncology  
To ensure the survival of the organism, millions of signals are sent and received every second between cells, tissues, or organs and the external environment, and they are integrated into responses at  ...  Robust homeostatic mechanisms must be in place to fine-tune responses and, in particular, allow the organism to deal with potentially toxic environmental perturbations, such as those derived from pathogens  ...  Cancer) http://www.standup2cancer.org/ SU2C aims to drive innovative cancer research through interdisciplinary science LINCS (Library of Integrated Network-based Cellular Signatures) http://www.lincsproject.org  ... 
doi:10.1038/nrclinonc.2014.6 pmid:24492837 pmcid:PMC4321721 fatcat:vmme3yi2q5ctfdswbv4rupdsti

Building Concordant Ontologies for Drug Discovery

Hande Küçük-McGinty, Saurabh Metha, Yu Lin, Nooshin Nabizadeh, Vasileios Stathias, Dusica Vidovic, Amar Koleti, Christopher Mader, Jianbin Duan, Ubbo Visser, Stephan C. Schürer
2016 International Conference on Biomedical Ontology  
The three ontologies are built and maintained for three different projects: BAO for the BioAssay Ontology Project, LIFEo for the Library of Integrated Network-Based Cellular Signatures (LINCS) project,  ...  The three ontologies use the same principle architecture that allows for re-use and easy integration of ontology modules and instance data.  ...  LINCS Information FramEwork Ontology (LIFEo) The Library of Integrated Network-Based Cellular Signatures (LINCS) project aims to create a network-based understanding of biology by cataloging changes in  ... 
dblp:conf/icbo/Kucuk-McGintyML16 fatcat:eocm6wzxu5h5xa3je3pgsboxmm

Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action

Yunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng
2017 Biocomputing 2018  
In this work, we develop Mania, a novel method for the scalable integration of large-scale pharmacogenomic data.  ...  A variety of large-scale pharmacogenomic data, such as perturbation experiments and sensitivity profiles, enable the systematical identification of drug mechanism of actions (MoAs), which is a crucial  ...  Acknowledgements: This work was supported in part by the NSF CAREER Award, the Sloan Research Fellowship, and the PhRMA Foundation Award in Informatics.  ... 
doi:10.1142/9789813235533_0005 fatcat:jospa2zilfcsnben4e2p3a6a5u

signatureSearch: environment for gene expression signature searching and functional interpretation

Yuzhu Duan, Daniel S Evans, Richard A Miller, Nicholas J Schork, Steven R Cummings, Thomas Girke
2020 Nucleic Acids Research  
Database matches sharing correlated signatures with the query indicate related cellular responses frequently governed by connected mechanisms, such as drugs mimicking the expression responses of a disease  ...  The signatureSearch software is unique in that it provides access to an integrated environment for GESS/FEA routines that includes several novel search and enrichment methods, efficient data structures  ...  ACKNOWLEDGEMENTS We acknowledge the Bioconductor core team and community for providing valuable input for developing signature-Search and signatureSearchData.  ... 
doi:10.1093/nar/gkaa878 pmid:33068417 fatcat:isizncqzenbbno2npok6keobjy

Drug Repositioning Based on the Reversal of Gene Expression Signatures Identifies TOP2A as a Therapeutic Target for Rectal Cancer

Robson Francisco Carvalho, Luisa Matos do Canto, Sarah Santiloni Cury, Torben Frøstrup Hansen, Lars Henrik Jensen, Silvia Regina Rogatto
2021 Cancers  
Here we combined the gene expression signatures of rectal cancer patients with the reverse drug-induced gene-expression profiles to identify drug repositioning candidates for cancer therapy.  ...  Furthermore, CRISPR-Cas9 and shRNA screenings confirmed that loss-of-function of the TOP2A has the highest efficacy in reducing cellular proliferation.  ...  Acknowledgments: The results shown here are in part based upon data generated by the Genotype-Tissue Expression project (GTEx) (https://gtexportal.org/) and by the TCGA Research Network  ... 
doi:10.3390/cancers13215492 pmid:34771654 pmcid:PMC8583090 fatcat:sobj2dxkabcu3dkmnyhpwvo6pi

Computational Approaches and Pharmacogenomics Data Resources for Drug Repositioning

Fuhai LI
2017 Medical Research Archives  
Comprehensive genomics data analysis revealed the diverse dysfunctional biomarkers of individual cancer patients, which are believed to be responsible for heterogeneous drug response.  ...  Large-scale data sets of cancer patients have been being generated due to the significantly reduced cost of sequencing full genome of individual patients using the Next Generation Sequencing (NGS) technology  ...  Acknowledgements This work was supported partially by the startup funding (to Li) from the Department of Biomedical Informatics, and Translational Data Analytics (TDA), The Ohio State University.  ... 
doi:10.18103/mra.v5i6.1225 fatcat:yebpsd6u6bg35huknuh4fzyvpi

The cellular response to drug perturbation is limited: comparison of large-scale chemogenomic fitness signatures

Marjan Barazandeh, Divya Kriti, Corey Nislow, Guri Giaever
2022 BMC Genomics  
We previously reported that the cellular response to small molecules is limited and can be described by a network of 45 chemogenomic signatures.  ...  Background Chemogenomic profiling is a powerful approach for understanding the genome-wide cellular response to small molecules.  ...  Acknowledgments We thank Nislow-Giaever lab members for their constructive feedback on the website material.  ... 
doi:10.1186/s12864-022-08395-x pmid:35277135 pmcid:PMC8915488 fatcat:prknyu4bx5by5jcm4htstvwckq

Kaleidoscope: A New Bioinformatics Pipeline Web Application for In Silico Hypothesis Exploration of Omics Signatures [article]

Khaled Alganem, Rammohan Shukla, Hunter Eby, Mackenzie Abel, Xiaolu Zhang, William Brett McIntyre, Jiwon Lee, Christy Au-Yeung, Roshanak Asgariroozbehani, Roshni Panda, Sinead M O'Donovan, Adam Funk (+3 others)
2020 bioRxiv   pre-print
This application streamlines the process of in silico data exploration for users and expands the efficient use of these tools to stakeholders without specific bioinformatics expertise.  ...  The application offers access to several omics databases and tools to let users explore research questions in silico.  ...  The Library of Integrated Network-Based Cellular Signatures (LINCS) The LINCS database is a large multi-omics profiling database. For transcriptional datasets, it utilizes the L1000.  ... 
doi:10.1101/2020.05.01.070805 fatcat:cwnmxhi4mba7biiptqpptkbpba

In silico models in drug development: where we are

Janet Piñero, Laura I Furlong, Ferran Sanz
2018 Current opinion in pharmacology (Print)  
and toxicogenomics data are employed to gain mechanistic understanding  Cellular signaling models are mostly used to predict treatment response in cancer.  GSMN models allow easy integration of mechanistic  ...  helping to reduce the costs of drug development.  ...  -JU under grants agreements no. 116030 (TransQST) and no. 777365 (eTRANSAFE), resources of which are composed of financial contribution from the EU-H2020 and EFPIA companies in kind contribution.  ... 
doi:10.1016/j.coph.2018.08.007 pmid:30205360 fatcat:ajiwjzvlxvef7cjznavsz4jbvy
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