{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:22Z","timestamp":1772138062832,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2023,11,28]],"date-time":"2023-11-28T00:00:00Z","timestamp":1701129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"CONAHCyT","award":["FORDECYT-PRONACES\/425859\/2020"],"award-info":[{"award-number":["FORDECYT-PRONACES\/425859\/2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Microbiota data encounters challenges arising from technical noise and the curse of dimensionality, which affect the reliability of scientific findings. Furthermore, abundance matrices exhibit a zero-inflated distribution due to biological and technical influences. Consequently, there is a growing demand for advanced algorithms that can effectively recover missing taxa while also considering the preservation of data structure.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present mb-PHENIX, an open-source algorithm developed in Python that recovers taxa abundances from the noisy and sparse microbiota data. Our method infers the missing information of\u00a0count matrix (in 16S microbiota and shotgun studies) by applying imputation via diffusion with\u00a0supervised Uniform Manifold Approximation Projection (sUMAP) space as initialization. Our hybrid machine learning approach allows to denoise microbiota data, revealing differential abundance microbes among study groups where traditional abundance analysis fails.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The mb-PHENIX algorithm is available at https:\/\/github.com\/resendislab\/mb-PHENIX. An easy-to-use implementation is available on Google Colab (see GitHub).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad706","type":"journal-article","created":{"date-parts":[[2023,11,28]],"date-time":"2023-11-28T15:13:21Z","timestamp":1701184401000},"source":"Crossref","is-referenced-by-count":4,"title":["mb-PHENIX: diffusion and supervised uniform manifold approximation for denoizing microbiota data"],"prefix":"10.1093","volume":"39","author":[{"given":"Cristian","family":"Padron-Manrique","sequence":"first","affiliation":[{"name":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"},{"name":"Programa de Doctorado en Ciencias Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"}]},{"given":"Aar\u00f3n","family":"V\u00e1zquez-Jim\u00e9nez","sequence":"additional","affiliation":[{"name":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"}]},{"given":"Diego Armando","family":"Esquivel-Hernandez","sequence":"additional","affiliation":[{"name":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"}]},{"given":"Yoscelina Estrella","family":"Martinez Lopez","sequence":"additional","affiliation":[{"name":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"},{"name":"Programa de Doctorado en Ciencias M\u00e9dicas, Odontol\u00f3gicas y de la Salud, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"}]},{"given":"Daniel","family":"Neri-Rosario","sequence":"additional","affiliation":[{"name":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"},{"name":"Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"}]},{"given":"Jean Paul","family":"S\u00e1nchez-Casta\u00f1eda","sequence":"additional","affiliation":[{"name":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"},{"name":"Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"}]},{"given":"David","family":"Giron-Villalobos","sequence":"additional","affiliation":[{"name":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"},{"name":"Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5220-541X","authenticated-orcid":false,"given":"Osbaldo","family":"Resendis-Antonio","sequence":"additional","affiliation":[{"name":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"},{"name":"Coordinaci\u00f3n de la Investigaci\u00f3n Cient\u00edfica\u2014Red de Apoyo a la Investigaci\u00f3n\u2014Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"}]}],"member":"286","published-online":{"date-parts":[[2023,11,28]]},"reference":[{"key":"2023120620362782200_btad706-B1","doi-asserted-by":"crossref","first-page":"e0069121","DOI":"10.1128\/mSystems.00691-21","article-title":"Uniform manifold approximation and projection (UMAP) reveals composite patterns and resolves visualization artifacts in microbiome 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