{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T01:52:09Z","timestamp":1785894729159,"version":"3.56.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,3,2]],"date-time":"2020-03-02T00:00:00Z","timestamp":1583107200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"University of Helsinki and Biocenter Finland"},{"name":"Sigrid Juselius Foundation"},{"name":"Cancer Society of Finland, Academy of Finland","award":["292611"],"award-info":[{"award-number":["292611"]}]},{"name":"Cancer Society of Finland, Academy of Finland","award":["326238"],"award-info":[{"award-number":["326238"]}]},{"name":"Cancer Society of Finland, Academy of Finland","award":["310507"],"award-info":[{"award-number":["310507"]}]},{"name":"Magnus Ehrnrooth Foundation, Biocentrum Helsinki"},{"name":"St. Baldrick\u2019s Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus, HTS data processing requires the use of robust quality control procedures before analysis and interpretation. Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data. Furthermore, Breeze enables a reliable way to identify individual drug sensitivity and resistance patterns in cell lines or patient-derived samples for functional precision medicine applications. The Breeze application provides a complete solution for data quality assessment, dose\u2013response curve fitting and quantification of the drug responses along with interactive visualization of the results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The Breeze application with video tutorial and technical documentation is accessible at https:\/\/breeze.fimm.fi; the R source code is publicly available at https:\/\/github.com\/potdarswapnil\/Breeze under GNU General Public License v3.0.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>swapnil.potdar@helsinki.fi<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa138","type":"journal-article","created":{"date-parts":[[2020,2,26]],"date-time":"2020-02-26T20:18:20Z","timestamp":1582748300000},"page":"3602-3604","source":"Crossref","is-referenced-by-count":101,"title":["Breeze: an integrated quality control and data analysis application for high-throughput drug screening"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2778-6918","authenticated-orcid":false,"given":"Swapnil","family":"Potdar","sequence":"first","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksandr","family":"Ianevski","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"},{"name":"Department of Computer Science , Helsinki Institute for Information Technology (HIIT), Aalto University, FI-02150 Espoo, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John-Patrick","family":"Mpindi","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitrii","family":"Bychkov","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cl\u00e9ment","family":"Fiere","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Ianevski","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bhagwan","family":"Yadav","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krister","family":"Wennerberg","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"},{"name":"Biotech Research & Innovation Centre , University of Copenhagen, 2200 Copenhagen N, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0886-9769","authenticated-orcid":false,"given":"Tero","family":"Aittokallio","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"},{"name":"Department of Computer Science , Helsinki Institute for Information Technology (HIIT), Aalto University, FI-02150 Espoo, Finland"},{"name":"Department of Mathematics and Statistics , University of Turku, FI-20014 Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olli","family":"Kallioniemi","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"},{"name":"Science for Life Laboratory (SciLifeLab) , Department of Oncology and Pathology, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jani","family":"Saarela","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P\u00e4ivi","family":"\u00d6stling","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM) , University of Helsinki, FI-00290 Helsinki, Finland"},{"name":"Science for Life Laboratory (SciLifeLab) , Department of Oncology and Pathology, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,3,2]]},"reference":[{"key":"2023062312021581500_btaa138-B1","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2023062312021581500_btaa138-B2","doi-asserted-by":"crossref","first-page":"R66","DOI":"10.1186\/gb-2006-7-7-r66","article-title":"Analysis of cell-based RNAi screens","volume":"7","author":"Boutros","year":"2006","journal-title":"Genome Biol"},{"key":"2023062312021581500_btaa138-B3","doi-asserted-by":"crossref","first-page":"E260","DOI":"10.1208\/aapsj0902029","article-title":"Appropriate calibration curve fitting in ligand binding assays","volume":"9","author":"Findlay","year":"2007","journal-title":"AAPS J"},{"key":"2023062312021581500_btaa138-B4","doi-asserted-by":"crossref","first-page":"37741","DOI":"10.1038\/srep37741","article-title":"mQC: a heuristic quality-control metric for high-throughput drug combination screening","volume":"6","author":"Chen","year":"2016","journal-title":"Sci. Rep"},{"key":"2023062312021581500_btaa138-B5","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1093\/bioinformatics\/btt718","article-title":"HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data","volume":"30","author":"Fourches","year":"2014","journal-title":"Bioinformatics"},{"key":"2023062312021581500_btaa138-B6","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nature17987","article-title":"Reproducible pharmacogenomic profiling of cancer cell line panels","volume":"533","author":"Haverty","year":"2016","journal-title":"Nature"},{"key":"2023062312021581500_btaa138-B7","doi-asserted-by":"crossref","first-page":"3298","DOI":"10.1016\/j.celrep.2017.11.051","article-title":"Primary patient-derived cancer cells and their potential for personalized cancer patient care","volume":"21","author":"Kodack","year":"2017","journal-title":"Cell Rep"},{"key":"2023062312021581500_btaa138-B8","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/j.cell.2018.03.017","article-title":"Tumor evolution and drug response in patient-derived organoid models of bladder cancer","volume":"173","author":"Lee","year":"2018","journal-title":"Cell"},{"key":"2023062312021581500_btaa138-B9","doi-asserted-by":"crossref","first-page":"3815","DOI":"10.1093\/bioinformatics\/btv455","article-title":"Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data","volume":"31","author":"Mpindi","year":"2015","journal-title":"Bioinformatics"},{"key":"2023062312021581500_btaa138-B10","doi-asserted-by":"crossref","first-page":"E5","DOI":"10.1038\/nature20171","article-title":"Consistency in drug response profiling","volume":"540","author":"Mpindi","year":"2016","journal-title":"Nature"},{"key":"2023062312021581500_btaa138-B11","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nature14119","article-title":"Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation","volume":"519","author":"Pemovska","year":"2015","journal-title":"Nature"},{"key":"2023062312021581500_btaa138-B12","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1158\/2159-8290.CD-13-0350","article-title":"Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia","volume":"3","author":"Pemovska","year":"2013","journal-title":"Cancer Discov"},{"key":"2023062312021581500_btaa138-B13","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/j.eururo.2016.04.019","article-title":"Comprehensive drug testing of patient-derived conditionally reprogrammed cells from castration-resistant prostate cancer","volume":"71","author":"Saeed","year":"2017","journal-title":"Eur. Urol"},{"key":"2023062312021581500_btaa138-B14","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1158\/2159-8290.CD-15-0235","article-title":"Harnessing connectivity in a large-scale small-molecule sensitivity dataset","volume":"5","author":"Seashore-Ludlow","year":"2015","journal-title":"Cancer Discov"},{"key":"2023062312021581500_btaa138-B15","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1093\/bioinformatics\/btv723","article-title":"PharmacoGx: an R package for analysis of large pharmacogenomic datasets","volume":"32","author":"Smirnov","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062312021581500_btaa138-B16","doi-asserted-by":"crossref","first-page":"357","DOI":"10.2307\/2530598","article-title":"Application of the four-parameter logistic model to bioassay: comparison with slope ratio and parallel line models","volume":"34","author":"V\u00f8lund","year":"1978","journal-title":"Biometrics"},{"key":"2023062312021581500_btaa138-B17","doi-asserted-by":"crossref","first-page":"5193","DOI":"10.1038\/srep05193","article-title":"Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies","volume":"4","author":"Yadav","year":"2015","journal-title":"Sci. Rep"},{"key":"2023062312021581500_btaa138-B18","first-page":"D955","article-title":"Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells","volume":"41 (Database issue","author":"Yang","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023062312021581500_btaa138-B19","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1177\/108705719900400206","article-title":"A simple statistical parameter for use in evaluation and validation of high throughput screening assays","volume":"4","author":"Zhang","year":"1999","journal-title":"J. Biomol. Screen"},{"key":"2023062312021581500_btaa138-B20","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1016\/j.ygeno.2006.12.014","article-title":"A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays","volume":"89","author":"Zhang","year":"2007","journal-title":"Genomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa138\/32923764\/btaa138.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/11\/3602\/50670828\/bioinformatics_36_11_3602.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/11\/3602\/50670828\/bioinformatics_36_11_3602.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T21:28:22Z","timestamp":1687642102000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/11\/3602\/5771328"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,3,2]]},"references-count":20,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2020,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa138","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,6]]},"published":{"date-parts":[[2020,3,2]]}}}