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A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we introduce \u2018soft windowing\u2019, a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype\u2013phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The method is freely available in the R package SmoothWin, available on CRAN http:\/\/CRAN.R-project.org\/package=SmoothWin.<\/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\/btz744","type":"journal-article","created":{"date-parts":[[2019,10,4]],"date-time":"2019-10-04T07:38:11Z","timestamp":1570174691000},"page":"1492-1500","source":"Crossref","is-referenced-by-count":10,"title":["Soft windowing application to improve analysis of high-throughput phenotyping data"],"prefix":"10.1093","volume":"36","author":[{"given":"Hamed","family":"Haselimashhadi","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2796-5123","authenticated-orcid":false,"given":"Jeremy C","family":"Mason","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Violeta","family":"Munoz-Fuentes","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Federico","family":"L\u00f3pez-G\u00f3mez","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Kolawole","family":"Babalola","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Elif F","family":"Acar","sequence":"additional","affiliation":[{"name":"The Centre for Phenogenomics"},{"name":"The Hospital for Sick Children , Toronto, Canada"},{"name":"Department of Statistics, University of Manitoba , Winnipeg, MB R3T 2N2 Canada"}]},{"given":"Vivek","family":"Kumar","sequence":"additional","affiliation":[{"name":"The Jackson Laboratory , Bar Harbor, ME 04609, USA"}]},{"given":"Jacqui","family":"White","sequence":"additional","affiliation":[{"name":"The Jackson Laboratory , Bar Harbor, ME 04609, USA"}]},{"given":"Ann M","family":"Flenniken","sequence":"additional","affiliation":[{"name":"The Centre for Phenogenomics"},{"name":"Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital , Toronto, Canada"}]},{"given":"Ruairidh","family":"King","sequence":"additional","affiliation":[{"name":"MRC Harwell Institute , Harwell OX11 0RD, UK"}]},{"given":"Ewan","family":"Straiton","sequence":"additional","affiliation":[{"name":"MRC Harwell Institute , Harwell OX11 0RD, UK"}]},{"given":"John Richard","family":"Seavitt","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Angelina","family":"Gaspero","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Arturo","family":"Garza","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Audrey E","family":"Christianson","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Chih-Wei","family":"Hsu","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Corey L","family":"Reynolds","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8750-6933","authenticated-orcid":false,"given":"Denise G","family":"Lanza","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Isabel","family":"Lorenzo","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Jennie R","family":"Green","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Juan J","family":"Gallegos","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Ritu","family":"Bohat","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Rodney C","family":"Samaco","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Surabi","family":"Veeraragavan","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Jong Kyoung","family":"Kim","sequence":"additional","affiliation":[{"name":"Daegu Gyeongbuk Institute of Science & Technology (DGIST) , Daegu, Korea"}]},{"given":"Gregor","family":"Miller","sequence":"additional","affiliation":[{"name":"Helmholtz Center Munich , Neuherberg, Germany"}]},{"given":"Helmult","family":"Fuchs","sequence":"additional","affiliation":[{"name":"Helmholtz Center Munich , Neuherberg, Germany"}]},{"given":"Lillian","family":"Garrett","sequence":"additional","affiliation":[{"name":"Helmholtz Center Munich , Neuherberg, Germany"}]},{"given":"Lore","family":"Becker","sequence":"additional","affiliation":[{"name":"Helmholtz Center Munich , Neuherberg, Germany"}]},{"given":"Yeon Kyung","family":"Kang","sequence":"additional","affiliation":[{"name":"Korea Mouse Phenotyping Center (KMPC) , Korea"}]},{"given":"David","family":"Clary","sequence":"additional","affiliation":[{"name":"Mouse Biology Program, University of California Davis , Davis, CA, USA"}]},{"given":"Soo Young","family":"Cho","sequence":"additional","affiliation":[{"name":"National Cancer Center (NCC) & Korea Mouse Phenotyping Center (KMPC) , Korea"}]},{"given":"Masaru","family":"Tamura","sequence":"additional","affiliation":[{"name":"RIKEN BioResource Research Center , Tsukuba, Japan"}]},{"given":"Nobuhiko","family":"Tanaka","sequence":"additional","affiliation":[{"name":"RIKEN BioResource Research Center , Tsukuba, Japan"}]},{"given":"Kyung Dong","family":"Soo","sequence":"additional","affiliation":[{"name":"Seoul National University & Korea Mouse Phenotyping Center (KMPC) , Korea"}]},{"given":"Alexandr","family":"Bezginov","sequence":"additional","affiliation":[{"name":"The Centre for Phenogenomics"},{"name":"The Hospital for Sick Children , Toronto, Canada"}]},{"given":"Ghina Bou","family":"About","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Marie-France","family":"Champy","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Laurent","family":"Vasseur","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Sophie","family":"Leblanc","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Hamid","family":"Meziane","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Mohammed","family":"Selloum","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Patrick T","family":"Reilly","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Nadine","family":"Spielmann","sequence":"additional","affiliation":[{"name":"Helmholtz Center Munich , Neuherberg, Germany"}]},{"given":"Holger","family":"Maier","sequence":"additional","affiliation":[{"name":"Helmholtz Center Munich , Neuherberg, Germany"}]},{"given":"Valerie","family":"Gailus-Durner","sequence":"additional","affiliation":[{"name":"Helmholtz Center Munich , Neuherberg, Germany"}]},{"given":"Tania","family":"Sorg","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Masuya","family":"Hiroshi","sequence":"additional","affiliation":[{"name":"RIKEN BioResource Research Center , Tsukuba, Japan"}]},{"given":"Obata","family":"Yuichi","sequence":"additional","affiliation":[{"name":"RIKEN BioResource Research Center , Tsukuba, Japan"}]},{"given":"Jason D","family":"Heaney","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Mary E","family":"Dickinson","sequence":"additional","affiliation":[{"name":"Baylor College of Medicine , Houston, TX, USA"}]},{"given":"Wurst","family":"Wolfgang","sequence":"additional","affiliation":[{"name":"Institute of Developmental Genetics , Helmholtz Centre Munich, Munich, Germany"}]},{"given":"Glauco P","family":"Tocchini-Valentini","sequence":"additional","affiliation":[{"name":"CNR EMMA Monterotondo , Italy"}]},{"given":"Kevin C Kent","family":"Lloyd","sequence":"additional","affiliation":[{"name":"Mouse Biology Program, University of California Davis , Davis, CA, USA"}]},{"given":"Colin","family":"McKerlie","sequence":"additional","affiliation":[{"name":"The Centre for Phenogenomics"},{"name":"The Hospital for Sick Children , Toronto, Canada"}]},{"given":"Je Kyung","family":"Seong","sequence":"additional","affiliation":[{"name":"Seoul National University & Korea Mouse Phenotyping Center (KMPC) , Korea"}]},{"given":"Herault","family":"Yann","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Strasbourg , CNRS, INSERM, Institut de G\u00e9n\u00e9tique, Biologie Mol\u00e9culaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404 Illkirch, France"}]},{"given":"Martin Hrab\u00e9","family":"de Angelis","sequence":"additional","affiliation":[{"name":"Helmholtz Center Munich , Neuherberg, Germany"}]},{"given":"Steve D M","family":"Brown","sequence":"additional","affiliation":[{"name":"MRC Harwell Institute , Harwell OX11 0RD, UK"}]},{"given":"Damian","family":"Smedley","sequence":"additional","affiliation":[{"name":"William Harvey Research Institute, Charterhouse Square Barts and the London School of Medicine and Dentistry Queen Mary University of London , London EC1M 6BQ, UK"}]},{"given":"Paul","family":"Flicek","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Ann-Marie","family":"Mallon","sequence":"additional","affiliation":[{"name":"MRC Harwell Institute , Harwell OX11 0RD, UK"}]},{"given":"Helen","family":"Parkinson","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Terrence F","family":"Meehan","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome 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