{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T13:02:55Z","timestamp":1769605375019,"version":"3.49.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T00:00:00Z","timestamp":1631059200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["322761"],"award-info":[{"award-number":["322761"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Network analysis is a powerful approach to investigate biological systems. It is often applied to study gene co-expression patterns derived from transcriptomics experiments. Even though co-expression analysis is widely used, there is still a lack of tools that are open and customizable on the basis of different network types and analysis scenarios (e.g. through function accessibility), but are also suitable for novice users by providing complete analysis pipelines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed VOLTA, a Python package suited for complex co-expression network analysis. VOLTA is designed to allow users direct access to the individual functions, while they are also provided with complete analysis pipelines. Moreover, VOLTA offers when possible multiple algorithms applicable to each analytical step (e.g. multiple community detection or clustering algorithms are provided), hence providing the user with the possibility to perform analysis tailored to their needs. This makes VOLTA highly suitable for experienced users who wish to build their own analysis pipelines for a wide range of networks as well as for novice users for which a \u2018plug and play\u2019 system is provided.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The package and used data are available at GitHub: https:\/\/github.com\/fhaive\/VOLTA and 10.5281\/zenodo.5171719.<\/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\/btab642","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T11:46:10Z","timestamp":1631101570000},"page":"4587-4588","source":"Crossref","is-referenced-by-count":8,"title":["VOLTA: adVanced mOLecular neTwork Analysis"],"prefix":"10.1093","volume":"37","author":[{"given":"Alisa","family":"Pavel","sequence":"first","affiliation":[{"name":"Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"},{"name":"BioMediTech Institute, Tampere University , Tampere 33520, Finland"},{"name":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"}]},{"given":"Antonio","family":"Federico","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"},{"name":"BioMediTech Institute, Tampere University , Tampere 33520, Finland"},{"name":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"}]},{"given":"Giusy","family":"del Giudice","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"},{"name":"BioMediTech Institute, Tampere University , Tampere 33520, Finland"},{"name":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"}]},{"given":"Angela","family":"Serra","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"},{"name":"BioMediTech Institute, Tampere University , Tampere 33520, Finland"},{"name":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9195-9003","authenticated-orcid":false,"given":"Dario","family":"Greco","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"},{"name":"BioMediTech Institute, Tampere University , Tampere 33520, Finland"},{"name":"Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University , Tampere 33520, Finland"},{"name":"Institute of Biotechnology, University of Helsinki , Helsinki 00790, Finland"}]}],"member":"286","published-online":{"date-parts":[[2021,9,8]]},"reference":[{"key":"2023061310545584900_btab642-B1","first-page":"575","article-title":"Gene co-expression analysis for functional classification and gene-disease predictions","volume":"19","author":"van Dam","year":"2018","journal-title":"Brief. Bioinf"},{"key":"2023061310545584900_btab642-B2"},{"key":"2023061310545584900_btab642-B3","first-page":"1791","article-title":"Weighted gene co-expression network analysis in biomedicine research","volume":"33","author":"Liu","year":"2017","journal-title":"Sheng Wu Gong Cheng Xue Bao"},{"key":"2023061310545584900_btab642-B4","doi-asserted-by":"crossref","first-page":"2136","DOI":"10.1093\/bioinformatics\/bty063","article-title":"Inform: inference of network response modules","volume":"34","author":"Marwah","year":"2018","journal-title":"Bioinformatics"},{"key":"2023061310545584900_btab642-B5","doi-asserted-by":"crossref","first-page":"W133","DOI":"10.1093\/nar\/gky336","article-title":"CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses","volume":"46","author":"Proost","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023061310545584900_btab642-B6","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1007\/s12012-013-9230-2","article-title":"Mitochondrial cumulative damage induced by mitoxantrone: late onset cardiac energetic impairment","volume":"14","author":"Rossato","year":"2014","journal-title":"Cardiovasc. Toxicol"},{"key":"2023061310545584900_btab642-B7","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1007\/s41109-019-0165-9","article-title":"CDLIB: a python library to extract, compare and evaluate communities from complex networks","volume":"4","author":"Rossetti","year":"2019","journal-title":"Appl. Netw. Sci"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab642\/40351857\/btab642.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/23\/4587\/50579669\/btab642.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/23\/4587\/50579669\/btab642.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T10:56:24Z","timestamp":1686653784000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/23\/4587\/6366543"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,9,8]]},"references-count":7,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2021,12,7]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab642","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,12,1]]},"published":{"date-parts":[[2021,9,8]]}}}