{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T17:00:56Z","timestamp":1768755656119,"version":"3.49.0"},"reference-count":33,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T00:00:00Z","timestamp":1759104000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001835","name":"Maastricht University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001835","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Genomics"],"published-print":{"date-parts":[[2025,11]]},"DOI":"10.1016\/j.ygeno.2025.111122","type":"journal-article","created":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T00:31:22Z","timestamp":1759797082000},"page":"111122","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["A bioinformatics pipeline for identifying homoplasmic and heteroplasmic mitochondrial DNA SNVs in single-cell RNA-Seq datasets"],"prefix":"10.1016","volume":"117","author":[{"given":"Zhiling","family":"Guan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Lindsey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rick","family":"Kamps","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hubert J.M.","family":"Smeets","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.ygeno.2025.111122_bb0005","author":"Mitochondrial diseases | Nature Reviews Disease Primers"},{"issue":"12","key":"10.1016\/j.ygeno.2025.111122_bb0010","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1038\/nrg3275","article-title":"Human mitochondrial DNA: roles of inherited and somatic mutations","volume":"13","author":"Schon","year":"2012","journal-title":"Nat. Rev. Genet."},{"issue":"1","key":"10.1016\/j.ygeno.2025.111122_bb0015","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.cell.2015.08.067","article-title":"Mitochondrial DNA variation in human radiation and disease","volume":"163","author":"Wallace","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.ygeno.2025.111122_bb0020","author":"The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease | Nature Reviews Genetics"},{"issue":"9","key":"10.1016\/j.ygeno.2025.111122_bb0025","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1080\/14737159.2023.2241365","article-title":"Enhanced mitochondrial genome analysis: bioinformatic and long-read sequencing advances and their diagnostic implications","volume":"23","author":"Macken","year":"2023","journal-title":"Expert. Rev. Mol. Diagn."},{"key":"10.1016\/j.ygeno.2025.111122_bb0030","author":"Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics - ScienceDirect"},{"key":"10.1016\/j.ygeno.2025.111122_bb0035","author":"MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data - PMC"},{"issue":"1","key":"10.1016\/j.ygeno.2025.111122_bb0040","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-28845-0","article-title":"MQuad enables clonal substructure discovery using single cell mitochondrial variants","volume":"13","author":"Kwok","year":"2022","journal-title":"Nat. Commun."},{"issue":"1","key":"10.1016\/j.ygeno.2025.111122_bb0045","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-30230-w","article-title":"Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines","volume":"13","author":"Ramazzotti","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ygeno.2025.111122_bb0050","author":"Biology | Free Full-Text | Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing"},{"issue":"6182","key":"10.1016\/j.ygeno.2025.111122_bb0085","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1126\/science.1251110","article-title":"High-resolution genomic analysis of human mitochondrial RNA sequence variation","volume":"344","author":"Hodgkinson","year":"2014","journal-title":"Science"},{"issue":"1","key":"10.1016\/j.ygeno.2025.111122_bb0090","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42003-020-0879-3","article-title":"Analysis of mitochondrial m1A\/G RNA modification reveals links to nuclear genetic variants and associated disease processes","volume":"3","author":"Ali","year":"2020","journal-title":"Commun. Biol."},{"issue":"1","key":"10.1016\/j.ygeno.2025.111122_bb0060","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1186\/1471-2164-13-666","article-title":"The effect of strand bias in Illumina short-read sequencing data","volume":"13","author":"Guo","year":"2012","journal-title":"BMC Genomics"},{"issue":"16","key":"10.1016\/j.ygeno.2025.111122_bb0065","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkn425","article-title":"Substantial biases in ultra-short read data sets from high-throughput DNA sequencing","volume":"36","author":"Dohm","year":"2008","journal-title":"Nucleic Acids Res."},{"issue":"6","key":"10.1016\/j.ygeno.2025.111122_bb0070","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/s41576-022-00559-5","article-title":"Navigating the pitfalls of mapping DNA and RNA modifications","volume":"24","author":"Kong","year":"2023","journal-title":"Nat. Rev. Genet."},{"issue":"1","key":"10.1016\/j.ygeno.2025.111122_bb0075","doi-asserted-by":"crossref","first-page":"4079","DOI":"10.1038\/s41467-019-11713-9","article-title":"Accurate detection of m6A RNA modifications in native RNA sequences","volume":"10","author":"Liu","year":"2019","journal-title":"Nat. Commun."},{"issue":"8","key":"10.1016\/j.ygeno.2025.111122_bb0080","doi-asserted-by":"crossref","first-page":"2461","DOI":"10.1093\/nar\/gkp093","article-title":"Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications","volume":"37","author":"Ebhardt","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2025.111122_bb0095","doi-asserted-by":"crossref","first-page":"851","DOI":"10.3389\/fonc.2019.00851","article-title":"Standardization of sequencing coverage depth in NGS: recommendation for detection of clonal and subclonal mutations in cancer diagnostics","volume":"9","author":"Petrackova","year":"2019","journal-title":"Front. Oncol."},{"key":"10.1016\/j.ygeno.2025.111122_bb0100","author":"Helix Mitochondrial Database | Helix"},{"issue":"47","key":"10.1016\/j.ygeno.2025.111122_bb0105","doi-asserted-by":"crossref","first-page":"17074","DOI":"10.1021\/jacs.7b07914","article-title":"Fingerprints of modified RNA bases from deep sequencing profiles","volume":"139","author":"Kietrys","year":"2017","journal-title":"J. Am. Chem. Soc."},{"issue":"2","key":"10.1016\/j.ygeno.2025.111122_bb0110","doi-asserted-by":"crossref","DOI":"10.1002\/wrna.1753","article-title":"The emergent role of mitochondrial RNA modifications in metabolic alterations","volume":"14","author":"Boughanem","year":"2023","journal-title":"WIREs RNA"},{"issue":"1","key":"10.1016\/j.ygeno.2025.111122_bb0115","doi-asserted-by":"crossref","first-page":"4269","DOI":"10.1038\/s41467-020-18068-6","article-title":"Complete chemical structures of human mitochondrial tRNAs","volume":"11","author":"Suzuki","year":"2020","journal-title":"Nat. Commun."},{"issue":"7","key":"10.1016\/j.ygeno.2025.111122_bb0120","doi-asserted-by":"crossref","DOI":"10.1038\/s41587-022-01210-8","article-title":"Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations","volume":"40","author":"Miller","year":"2022","journal-title":"Nat. Biotechnol."},{"issue":"4","key":"10.1016\/j.ygeno.2025.111122_bb0125","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1016\/j.cell.2011.06.051","article-title":"The human mitochondrial transcriptome","volume":"146","author":"Mercer","year":"2011","journal-title":"Cell"},{"issue":"2","key":"10.1016\/j.ygeno.2025.111122_bb0130","article-title":"A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data","volume":"4","author":"Battle","year":"2022","journal-title":"NAR Genom. Bioinforma"},{"issue":"1","key":"10.1016\/j.ygeno.2025.111122_bb0135","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nprot.2014.006","article-title":"Full-length RNA-seq from single cells using Smart-seq2","volume":"9","author":"Picelli","year":"2014","journal-title":"Nat. Protoc."},{"issue":"2","key":"10.1016\/j.ygeno.2025.111122_bb0140","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/nmeth.2772","article-title":"Quantitative single-cell RNA-seq with unique molecular identifiers","volume":"11","author":"Islam","year":"2014","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ygeno.2025.111122_bb0145","doi-asserted-by":"crossref","first-page":"2718","DOI":"10.1038\/s41598-017-02727-8","article-title":"A high-throughput assay for quantitative measurement of PCR errors","volume":"7","author":"Shagin","year":"2017","journal-title":"Sci. Rep."},{"issue":"2","key":"10.1016\/j.ygeno.2025.111122_bb0150","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.mrgentox.2012.02.006","article-title":"The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation","volume":"744","author":"Guo","year":"2012","journal-title":"Mutat. Res."},{"key":"10.1016\/j.ygeno.2025.111122_bb0155","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.ymeth.2018.10.011","article-title":"Misincorporation signatures for detecting modifications in mRNA: Not as simple as it sounds","volume":"156","author":"Sas-Chen","year":"2019","journal-title":"Methods"},{"key":"10.1016\/j.ygeno.2025.111122_bb0160","first-page":"1","article-title":"All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies","author":"Oberdoeffer","year":"2024","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"4","key":"10.1016\/j.ygeno.2025.111122_bb0165","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1016\/j.cell.2016.03.023","article-title":"Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos","volume":"165","author":"Petropoulos","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.ygeno.2025.111122_bb0170","author":"Chromium Single Cell V(D)J Reagent Kits User Guide (v1.1 Chemistry) with Feature Barcoding technology for Cell Surface Protein - Official 10x Genomics Support"}],"container-title":["Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754325001387?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754325001387?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T01:37:15Z","timestamp":1768700235000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0888754325001387"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11]]},"references-count":33,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,11]]}},"alternative-id":["S0888754325001387"],"URL":"https:\/\/doi.org\/10.1016\/j.ygeno.2025.111122","relation":{},"ISSN":["0888-7543"],"issn-type":[{"value":"0888-7543","type":"print"}],"subject":[],"published":{"date-parts":[[2025,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A bioinformatics pipeline for identifying homoplasmic and heteroplasmic mitochondrial DNA SNVs in single-cell RNA-Seq datasets","name":"articletitle","label":"Article Title"},{"value":"Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ygeno.2025.111122","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"111122"}}