{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:17:00Z","timestamp":1787962620135,"version":"build-2784847793"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,7,26]],"date-time":"2026-07-26T00:00:00Z","timestamp":1785024000000},"content-version":"vor","delay-in-days":206,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2014Next Generation EU","award":["CN00000013"],"award-info":[{"award-number":["CN00000013"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Inferring gene networks from single-cell RNA sequencing data is challenging due to high sparsity, dimensionality, and technical noise. Current pipelines lack the multi-dataset integration and comprehensive post-processing analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>scGraphVerse is an R package that integrates multiple algorithms (GENIE3, GRNBoost2, ZILGM, PCzinb, and JRF) with extensive evaluation and visualization tools. Its modular workflow supports early, late, and joint integration strategies for multi-dataset analysis, providing standardized input\/output interfaces and biological interpretation tools, including community detection, pathway enrichment, and literature mining. Benchmarking on simulated data showed model-based methods (PCzinb and ZILGM) perform well with limited sample sizes, while JRF performs best as the network size and dataset numbers increase. A PBMC case study demonstrates JRF\u2019s ability to identify literature-supported regulatory communities across donors.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The package is available in Bioconductor 3.22 at https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/scGraphVerse.html. Code and examples: https:\/\/github.com\/ngsFC\/scGV_analysis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbag208","type":"journal-article","created":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T11:39:40Z","timestamp":1784979580000},"source":"Crossref","is-referenced-by-count":0,"title":["scGraphVerse: a modular workflow for single-cell gene network inference"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0329-0870","authenticated-orcid":false,"given":"Francesco","family":"Cecere","sequence":"first","affiliation":[{"name":"Institute of Genetics and Biophysics, \u201cAdriano Buzzati-Traverso\u201d, Consiglio Nazionale delle Ricerche (CNR) , Napoli, 80131,","place":["Italy"]},{"name":"UOS Laboratori di Ricerca e Biobanca, UOC Ricerca Clinica e Traslazionale, AORN Santobono-Pausilipon IRCCS , Naples, 80129,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3022-3411","authenticated-orcid":false,"given":"Daniela","family":"De Canditiis","sequence":"additional","affiliation":[{"name":"Istituto per le Applicazioni del Calcolo \u201cMauro Picone\u201d, Consiglio Nazionale delle Ricerche (CNR) , Rome, 00185,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4636-3969","authenticated-orcid":false,"given":"Annamaria","family":"Carissimo","sequence":"additional","affiliation":[{"name":"Istituto per le Applicazioni del Calcolo \u201cMauro Picone\u201d, Consiglio Nazionale delle Ricerche (CNR) , Napoli, 80131,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Angelini","sequence":"additional","affiliation":[{"name":"Istituto per le Applicazioni del Calcolo \u201cMauro Picone\u201d, Consiglio Nazionale delle Ricerche (CNR) , Napoli, 80131,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,25]]},"reference":[{"key":"2026082819313946100_vbag208-B1","author":"Allaire","year":"2023"},{"key":"2026082819313946100_vbag208-B2","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s41592-019-0654-x","article-title":"Orchestrating single-cell analysis with bioconductor","volume":"17","author":"Amezquita","year":"2020","journal-title":"Nat Methods"},{"key":"2026082819313946100_vbag208-B3","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1038\/s41576-023-00618-5","article-title":"Gene regulatory network inference in the era of single-cell multi-omics","volume":"24","author":"Badia-I Mompel","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2026082819313946100_vbag208-B4","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1186\/s12859-018-2217-z","article-title":"Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data","volume":"19","author":"Chen","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2026082819313946100_vbag208-B5","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s12864-019-6413-7","article-title":"The advantages of the Matthews correlation coefficient (mcc) over f1 score and accuracy in binary classification evaluation","volume":"21","author":"Chicco","year":"2020","journal-title":"BMC Genomics"},{"key":"2026082819313946100_vbag208-B6","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"InterJournal, Complex Syst"},{"key":"2026082819313946100_vbag208-B7","first-page":"293","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"41","author":"Hao","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2026082819313946100_vbag208-B8","doi-asserted-by":"publisher","author":"Hawkins","year":"2024","DOI":"10.1101\/2024.04.19.590243"},{"key":"2026082819313946100_vbag208-B9","doi-asserted-by":"crossref","first-page":"bbaf470","DOI":"10.1093\/bib\/bbaf470","article-title":"Machine learning methods for gene regulatory network inference","volume":"26","author":"Hegde","year":"2025","journal-title":"Brief Bioinform"},{"key":"2026082819313946100_vbag208-B10","doi-asserted-by":"crossref","first-page":"e12776","DOI":"10.1371\/journal.pone.0012776","article-title":"Inferring regulatory networks from expression data using tree-based methods","volume":"5","author":"Huynh-Thu","year":"2010","journal-title":"PLoS One"},{"key":"2026082819313946100_vbag208-B11","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/s41540-023-00312-6","article-title":"Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data","volume":"9","author":"Kim","year":"2023","journal-title":"NPJ Syst Biol Appl"},{"key":"2026082819313946100_vbag208-B12","doi-asserted-by":"publisher","first-page":"3634","DOI":"10.1038\/s41467-024-47712-8","article-title":"Identifying tumor type and cell type-specific gene expression alterations in pediatric Central nervous system tumors","volume":"15","author":"Lee","year":"2024","journal-title":"Nat Commun"},{"key":"2026082819313946100_vbag208-B13","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1093\/bioinformatics\/bty916","article-title":"Grnboost2 and Arboreto: efficient and scalable inference of gene regulatory networks","volume":"35","author":"Moerman","year":"2019","journal-title":"Bioinformatics"},{"key":"2026082819313946100_vbag208-B14","author":"Morgan","year":"2025"},{"key":"2026082819313946100_vbag208-B15","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780199206650.001.0001","volume-title":"Networks: An Introduction","author":"Newman","year":"2010"},{"key":"2026082819313946100_vbag208-B16","doi-asserted-by":"crossref","first-page":"2555","DOI":"10.1214\/23-AOAS1732","article-title":"Structure learning for zero-inflated counts with an application to single-cell RNA sequencing data","volume":"17","author":"Nguyen","year":"2023","journal-title":"Ann Appl Stat"},{"key":"2026082819313946100_vbag208-B17","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1002\/sam.11536","article-title":"Negative binomial graphical model with excess zeros","volume":"14","author":"Park","year":"2021","journal-title":"Stat Anal"},{"key":"2026082819313946100_vbag208-B18","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1021\/acs.jproteome.5b00925","article-title":"New method for joint network analysis reveals common and different coexpression patterns among genes and proteins in breast cancer","volume":"15","author":"Petralia","year":"2016","journal-title":"J Proteome Res"},{"key":"2026082819313946100_vbag208-B19","doi-asserted-by":"crossref","first-page":"292","DOI":"10.32614\/RJ-2021-040","article-title":"Robustness in network (robin): an r package for comparison and validation of communities","volume":"13","author":"Policastro","year":"2021","journal-title":"R J"},{"key":"2026082819313946100_vbag208-B20","first-page":"1517","article-title":"Inet for network integration","volume":"40","author":"Policastro","year":"2025","journal-title":"Comput Stat"},{"key":"2026082819313946100_vbag208-B21","doi-asserted-by":"crossref","first-page":"vbaf184","DOI":"10.1093\/bioadv\/vbaf184","article-title":"robin2: accelerating single-cell data clustering evaluation","volume":"5","author":"Policastro","year":"2025","journal-title":"Bioinform Adv"},{"key":"2026082819313946100_vbag208-B22","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/s41592-019-0690-6","article-title":"Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data","volume":"17","author":"Pratapa","year":"2020","journal-title":"Nat Methods"},{"key":"2026082819313946100_vbag208-B23","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/j.ipm.2009.03.002","article-title":"A systematic analysis of performance measures for classification tasks","volume":"45","author":"Sokolova","year":"2009","journal-title":"Inf Process Manag"},{"key":"2026082819313946100_vbag208-B24","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The string database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026082819313946100_vbag208-B25","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat Biotechnol"},{"key":"2026082819313946100_vbag208-B26","doi-asserted-by":"crossref","first-page":"520","DOI":"10.32614\/RJ-2017-058","article-title":"Rentrez: an r package for the ncbi eutils api","volume":"9","author":"Winter","year":"2017","journal-title":"R J"},{"key":"2026082819313946100_vbag208-B27","doi-asserted-by":"crossref","first-page":"3292","DOI":"10.1038\/s41596-024-01020-z","article-title":"Using clusterprofiler to characterize multiomics data","volume":"19","author":"Xu","year":"2024","journal-title":"Nat Protoc"},{"key":"2026082819313946100_vbag208-B28","first-page":"100722","article-title":"Thirteen years of clusterprofiler","volume":"5","author":"Yu","year":"2024","journal-title":"Innovation (Camb)"}],"container-title":["Bioinformatics Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/advance-article-pdf\/doi\/10.1093\/bioadv\/vbag208\/70111089\/vbag208.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/6\/1\/vbag208\/70111089\/vbag208.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/6\/1\/vbag208\/70111089\/vbag208.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T23:31:45Z","timestamp":1787959905000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article\/doi\/10.1093\/bioadv\/vbag208\/8742102"}},"subtitle":[],"editor":[{"given":"Ana\u00efs","family":"Baudot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/bioadv\/vbag208","relation":{},"ISSN":["2635-0041"],"issn-type":[{"value":"2635-0041","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"vbag208"}}