{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:40:44Z","timestamp":1761864044472,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,11,28]],"date-time":"2019-11-28T00:00:00Z","timestamp":1574899200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Translational Research Institute for Space Health"},{"DOI":"10.13039\/100000104","name":"National Aeronautics and Space Administration","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000104","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000104","name":"NASA","doi-asserted-by":"publisher","award":["NNX16AO69A"],"award-info":[{"award-number":["NNX16AO69A"]}],"id":[{"id":"10.13039\/100000104","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>PyIOmica is an open-source Python package focusing on integrating longitudinal multiple omics datasets, characterizing and categorizing temporal trends. The package includes multiple bioinformatics tools including data normalization, annotation, categorization, visualization and enrichment analysis for gene ontology terms and pathways. Additionally, the package includes an implementation of visibility graphs to visualize time series as networks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PyIOmica is implemented as a Python package (pyiomica), available for download and installation through the Python Package Index (https:\/\/pypi.python.org\/pypi\/pyiomica), and can be deployed using the Python import function following installation. PyIOmica has been tested on Mac OS X, Unix\/Linux and Microsoft Windows. The application is distributed under an MIT license. Source code for each release is also available for download on Zenodo (https:\/\/doi.org\/10.5281\/zenodo.3548040).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz896","type":"journal-article","created":{"date-parts":[[2019,11,26]],"date-time":"2019-11-26T20:13:37Z","timestamp":1574799217000},"page":"2306-2307","source":"Crossref","is-referenced-by-count":12,"title":["PyIOmica: longitudinal omics analysis and trend identification"],"prefix":"10.1093","volume":"36","author":[{"given":"Sergii","family":"Domanskyi","sequence":"first","affiliation":[{"name":"Department of Physics and Astronomy , East Lansing, MI 48824, USA"}]},{"given":"Carlo","family":"Piermarocchi","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy , East Lansing, MI 48824, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9083-1216","authenticated-orcid":false,"given":"George I","family":"Mias","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy , East Lansing, MI 48824, USA"},{"name":"Department of Biochemistry and Molecular Biology , East Lansing, MI 48824, USA"},{"name":"Institute for Quantitative Health Science and Engineering, Michigan State University , East Lansing, MI 48824, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,11,28]]},"reference":[{"key":"2023062300072370600_btz896-B1","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"44","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023062300072370600_btz896-B2","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1016\/j.cell.2012.02.009","article-title":"Personal omics profiling reveals dynamic molecular and medical phenotypes","volume":"148","author":"Chen","year":"2012","journal-title":"Cell"},{"key":"2023062300072370600_btz896-B3","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2023062300072370600_btz896-B4","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1186\/s12859-014-0396-9","article-title":"Pathomx: an interactive workflow-based tool for the analysis of metabolomic data","volume":"15","author":"Fitzpatrick","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023062300072370600_btz896-B5","doi-asserted-by":"crossref","first-page":"6436","DOI":"10.1126\/science.aau8650","article-title":"The NASA Twins Study: a multidimensional analysis of a year-long human spaceflight","volume":"364","author":"Garrett-Bakelman","year":"2019","journal-title":"Science"},{"key":"2023062300072370600_btz896-B6","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"2023062300072370600_btz896-B7","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/s12859-018-2134-1","article-title":"SECIMTools: a suite of metabolomics data analysis tools","volume":"19","author":"Kirpich","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023062300072370600_btz896-B8","doi-asserted-by":"crossref","first-page":"4972","DOI":"10.1073\/pnas.0709247105","article-title":"From time series to complex networks: the visibility graph","volume":"105","author":"Lacasa","year":"2008","journal-title":"Proc. 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