{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T22:06:10Z","timestamp":1762898770749},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput screening (HTS) is an important method in drug discovery in which the activities of a large number of candidate chemicals or genetic materials are rapidly evaluated. Data are usually obtained by measurements on samples in microwell plates and are often subjected to artefacts that can bias the result selection. We report here a novel edge effect correction algorithm suitable for RNA interference (RNAi) screening, because its normalization does not rely on the entire dataset and takes into account the specificities of such a screening process. The proposed method is able to estimate the edge effects for each assay plate individually using the data from a single control column based on diffusion model, and thus targeting a specific but recurrent well-known HTS artefact. This method was first developed and validated using control plates and was then applied to the correction of experimental data generated during a genome-wide siRNA screen aimed at studying HIV\u2013host interactions. The proposed algorithm was able to correct the edge effect biasing the control data and thus improve assay quality and, consequently, the hit-selection step.<\/jats:p>\n               <jats:p>Contact: \u00a0dorvalt@ip-korea.org; jean-philippe.carralot@roche.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr648","type":"journal-article","created":{"date-parts":[[2011,11,27]],"date-time":"2011-11-27T01:27:48Z","timestamp":1322357268000},"page":"261-268","source":"Crossref","is-referenced-by-count":19,"title":["A novel specific edge effect correction method for RNA interference screenings"],"prefix":"10.1093","volume":"28","author":[{"given":"Jean-Philippe","family":"Carralot","sequence":"first","affiliation":[{"name":"1 Biology of Intracellular Pathogens, Inserm Avenir Team, 2Cellular Differentiation, 3Cell Biology of Retroviruses, 4Image Mining, Institut Pasteur Korea, Seongnam-si, Korea, 5Chemical Genomics of Intracellular Mycobacteria, Inserm U1019, CNRS UMR8204, Institut Pasteur of Lille, France and 6Functional Morphometry, Institut Pasteur Korea, Seongnam-si, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arnaud","family":"Ogier","sequence":"additional","affiliation":[{"name":"1 Biology of Intracellular Pathogens, Inserm Avenir Team, 2Cellular Differentiation, 3Cell Biology of Retroviruses, 4Image Mining, Institut Pasteur Korea, Seongnam-si, Korea, 5Chemical Genomics of Intracellular Mycobacteria, Inserm U1019, CNRS UMR8204, Institut Pasteur of Lille, France and 6Functional Morphometry, Institut Pasteur Korea, Seongnam-si, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Annette","family":"Boese","sequence":"additional","affiliation":[{"name":"1 Biology of Intracellular Pathogens, Inserm Avenir Team, 2Cellular Differentiation, 3Cell Biology of Retroviruses, 4Image Mining, Institut Pasteur Korea, Seongnam-si, Korea, 5Chemical Genomics of Intracellular Mycobacteria, Inserm U1019, CNRS UMR8204, Institut Pasteur of Lille, France and 6Functional Morphometry, Institut Pasteur Korea, Seongnam-si, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Auguste","family":"Genovesio","sequence":"additional","affiliation":[{"name":"1 Biology of Intracellular Pathogens, Inserm Avenir Team, 2Cellular Differentiation, 3Cell Biology of Retroviruses, 4Image Mining, Institut Pasteur Korea, Seongnam-si, Korea, 5Chemical Genomics of Intracellular Mycobacteria, Inserm U1019, CNRS UMR8204, Institut Pasteur of Lille, France and 6Functional Morphometry, Institut Pasteur Korea, Seongnam-si, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Priscille","family":"Brodin","sequence":"additional","affiliation":[{"name":"1 Biology of Intracellular Pathogens, Inserm Avenir Team, 2Cellular Differentiation, 3Cell Biology of Retroviruses, 4Image Mining, Institut Pasteur Korea, Seongnam-si, Korea, 5Chemical Genomics of Intracellular Mycobacteria, Inserm U1019, CNRS UMR8204, Institut Pasteur of Lille, France and 6Functional Morphometry, Institut Pasteur Korea, Seongnam-si, Korea"},{"name":"1 Biology of Intracellular Pathogens, Inserm Avenir Team, 2Cellular Differentiation, 3Cell Biology of Retroviruses, 4Image Mining, Institut Pasteur Korea, Seongnam-si, Korea, 5Chemical Genomics of Intracellular Mycobacteria, Inserm U1019, CNRS UMR8204, Institut Pasteur of Lille, France and 6Functional Morphometry, Institut Pasteur Korea, Seongnam-si, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Sommer","sequence":"additional","affiliation":[{"name":"1 Biology of Intracellular Pathogens, Inserm Avenir Team, 2Cellular Differentiation, 3Cell Biology of Retroviruses, 4Image Mining, Institut Pasteur Korea, Seongnam-si, Korea, 5Chemical Genomics of Intracellular Mycobacteria, Inserm U1019, CNRS UMR8204, Institut Pasteur of Lille, France and 6Functional Morphometry, Institut Pasteur Korea, Seongnam-si, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thierry","family":"Dorval","sequence":"additional","affiliation":[{"name":"1 Biology of Intracellular Pathogens, Inserm Avenir Team, 2Cellular Differentiation, 3Cell Biology of Retroviruses, 4Image Mining, Institut Pasteur Korea, Seongnam-si, Korea, 5Chemical Genomics of Intracellular Mycobacteria, Inserm U1019, CNRS UMR8204, Institut Pasteur of Lille, France and 6Functional Morphometry, Institut Pasteur Korea, Seongnam-si, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,11,26]]},"reference":[{"key":"2023012511501377800_B1","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/nmeth.1351","article-title":"Statistical methods for analysis of highthroughput rna interference screens","volume":"6","author":"Birmingham","year":"2009","journal-title":"Nat. Methods"},{"key":"2023012511501377800_B2","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1177\/1087057103258285","article-title":"Improved statistical methods for hit selection in high-throughput screening","volume":"8","author":"Brideau","year":"2003","journal-title":"J. Biomol. Screen."},{"key":"2023012511501377800_B3","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1147\/rd.112.0215","article-title":"On the partial difference equations of mathematical physics","volume":"11","author":"Courant","year":"1967","journal-title":"IBM J. Res. Development"},{"key":"2023012511501377800_B4","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1471-2105-12-25","article-title":"Systematic error detection in experimental high-throughput screening","volume":"12","author":"Dragiev","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012511501377800_B5","first-page":"535","article-title":"Comprehensive analysis of high-throughput screening data","volume-title":"Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series","author":"Heyse","year":"2002"},{"key":"2023012511501377800_B6","doi-asserted-by":"crossref","DOI":"10.1002\/3527609326","volume-title":"High-Throughput Screening in Drug Discovery.","author":"H\u00fcser","year":"2006"},{"key":"2023012511501377800_B7","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1177\/1087057105276989","article-title":"Statistical analysis of systematic errors in high-throughput screening","volume":"10","author":"Kevorkov","year":"2005","journal-title":"J. Biomol. Screen."},{"key":"2023012511501377800_B8","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1177\/1087057103256465","article-title":"A simple technique for reducing edge effect in cell-based assays","volume":"8","author":"Lundholt","year":"2003","journal-title":"J. Biomol. Screen."},{"key":"2023012511501377800_B9","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1093\/bioinformatics\/btl126","article-title":"Hts-corrector: software for the statistical analysis and correction of experimental high-throughput screening data","volume":"22","author":"Makarenkov","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012511501377800_B10","doi-asserted-by":"crossref","first-page":"1648","DOI":"10.1093\/bioinformatics\/btm145","article-title":"An efficient method for the detection and elimination of systematic error in high-throughput screening","volume":"23","author":"Makarenkov","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012511501377800_B11","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/nbt1186","article-title":"Statistical practice in high-throughput screening data analysis","volume":"24","author":"Malo","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"2023012511501377800_B12","doi-asserted-by":"crossref","first-page":"2245","DOI":"10.1038\/nprot.2007.250","article-title":"Design and implementation of high-throughput RNAi screens in cultured Drosophila cells","volume":"2","author":"Ramadan","year":"2007","journal-title":"Nat. Protoc."},{"key":"2023012511501377800_B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1177\/1087057110389039","article-title":"Identifying actives from hts data sets: practical approaches for the selection of an appropriate hts data-processing method and quality control review","volume":"16","author":"Shun","year":"2011","journal-title":"J. Biomol. Screen."},{"key":"2023012511501377800_B14","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1177\/1087057108317062","article-title":"Novel analytic criteria and effective plate designs for quality control in genome-scale RNAi screens","volume":"13","author":"Zhang","year":"2008","journal-title":"J. Biomol. Screen."},{"key":"2023012511501377800_B15","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511973888","volume-title":"Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-Scale RNAi Research.","author":"Zhang","year":"2011"},{"key":"2023012511501377800_B16","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."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/2\/261\/48869390\/bioinformatics_28_2_261.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/2\/261\/48869390\/bioinformatics_28_2_261.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:51:45Z","timestamp":1674647505000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/2\/261\/199160"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,26]]},"references-count":16,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2012,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr648","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,1,15]]},"published":{"date-parts":[[2011,11,26]]}}}