{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T05:43:32Z","timestamp":1778391812175,"version":"3.51.4"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,4,12]],"date-time":"2019-04-12T00:00:00Z","timestamp":1555027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"French National Agency of Research"},{"name":"PORCINET","award":["ANR-09-GENM005"],"award-info":[{"award-number":["ANR-09-GENM005"]}]},{"name":"Digital Agriculture Convergence Lab","award":["ANR-16-CONV-0004"],"award-info":[{"award-number":["ANR-16-CONV-0004"]}]},{"name":"INRA Mathematics and Computer Science Division"},{"name":"INRA Animal Genetics Division"},{"name":"INRA Animal Health Divison"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>In metabolomics, the detection of new biomarkers from Nuclear Magnetic Resonance (NMR) spectra is a promising approach. However, this analysis remains difficult due to the lack of a whole workflow that handles spectra pre-processing, automatic identification and quantification of metabolites and statistical analyses, in a reproducible way.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present ASICS, an R package that contains a complete workflow to analyse spectra from NMR experiments. It contains an automatic approach to identify and quantify metabolites in a complex mixture spectrum and uses the results of the quantification in untargeted and targeted statistical analyses. ASICS was shown to improve the precision of quantification in comparison to existing methods on two independent datasets. In addition, ASICS successfully recovered most metabolites that were found important to explain a two level condition describing the samples by a manual and expert analysis based on bucketing. It also found new relevant metabolites involved in metabolic pathways related to risk factors associated with the condition.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ASICS is distributed as an R package, available on Bioconductor.<\/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\/btz248","type":"journal-article","created":{"date-parts":[[2019,4,8]],"date-time":"2019-04-08T07:16:17Z","timestamp":1554707777000},"page":"4356-4363","source":"Crossref","is-referenced-by-count":73,"title":["ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8166-2281","authenticated-orcid":false,"given":"Ga\u00eblle","family":"Lefort","sequence":"first","affiliation":[{"name":"MIAT, Universit\u00e9 de Toulouse, INRA, Castanet Tolosan , France"},{"name":"GenPhySE, Universit\u00e9 de Toulouse, INRA, ENVT , Castanet Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurence","family":"Liaubet","sequence":"additional","affiliation":[{"name":"GenPhySE, Universit\u00e9 de Toulouse, INRA, ENVT , Castanet Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C\u00e9cile","family":"Canlet","sequence":"additional","affiliation":[{"name":"Toxalim, Universit\u00e9 de Toulouse, INRA, ENVT , INP-Purpan, UPS, Toulouse, France"},{"name":"Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics , Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Tardivel","sequence":"additional","affiliation":[{"name":"Institute of Mathematics, University of Wroclaw , Wroclaw 50-384, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-Christine","family":"P\u00e8re","sequence":"additional","affiliation":[{"name":"PEGASE, INRA, Agrocampus Ouest, Saint-Gilles , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H\u00e9l\u00e8ne","family":"Quesnel","sequence":"additional","affiliation":[{"name":"PEGASE, INRA, Agrocampus Ouest, Saint-Gilles , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alain","family":"Paris","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Mol\u00e9cules de Communication et Adaptation des Microorganismes (MCAM), Mus\u00e9um national d\u2019Histoire naturelle , CNRS, CP54, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathalie","family":"Iannuccelli","sequence":"additional","affiliation":[{"name":"GenPhySE, Universit\u00e9 de Toulouse, INRA, ENVT , Castanet Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathalie","family":"Vialaneix","sequence":"additional","affiliation":[{"name":"MIAT, Universit\u00e9 de Toulouse, INRA, Castanet Tolosan , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1270-1843","authenticated-orcid":false,"given":"R\u00e9mi","family":"Servien","sequence":"additional","affiliation":[{"name":"INTHERES, Universit\u00e9 de Toulouse, INRA , ENVT, Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,4,12]]},"reference":[{"key":"2023062712531967100_btz248-B1","doi-asserted-by":"crossref","first-page":"2692","DOI":"10.1038\/nprot.2007.376","article-title":"Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts","volume":"2","author":"Beckonert","year":"2007","journal-title":"Nat. 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