{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T01:13:59Z","timestamp":1784337239692,"version":"3.55.0"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,6,9]],"date-time":"2024-06-09T00:00:00Z","timestamp":1717891200000},"content-version":"vor","delay-in-days":160,"URL":"http:\/\/www.nationalarchives.gov.uk\/doc\/open-government-licence\/version\/3\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["203141\/Z\/16\/Z"],"award-info":[{"award-number":["203141\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Oxford Health Biomedical Research Centre"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>EAD workflow is available at https:\/\/isarnassiri.github.io\/scDIV\/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioadv\/vbae085","type":"journal-article","created":{"date-parts":[[2024,6,9]],"date-time":"2024-06-09T05:21:25Z","timestamp":1717910485000},"source":"Crossref","is-referenced-by-count":8,"title":["Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression"],"prefix":"10.1093","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1886-1151","authenticated-orcid":false,"given":"Isar","family":"Nassiri","sequence":"first","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford , Oxford, OX3 7BN, United Kingdom"},{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"},{"name":"Nuffield Department of Clinical Neurosciences, University of Oxford , Oxford, OX3 9DU, United Kingdom"},{"name":"Department of Psychiatry, University of Oxford , Oxford, OX3 7JX, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8928-5054","authenticated-orcid":false,"given":"Andrew J","family":"Kwok","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"},{"name":"Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong SAR, 999077, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aneesha","family":"Bhandari","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine R","family":"Bull","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucy C","family":"Garner","sequence":"additional","affiliation":[{"name":"Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford , Oxford, OX3 9DU, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4307-9161","authenticated-orcid":false,"given":"Paul","family":"Klenerman","sequence":"additional","affiliation":[{"name":"Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford , Oxford, OX3 9DU, United Kingdom"},{"name":"Peter Medawar Building for Pathogen Research, University of Oxford , Oxford, OX1 3SY, United Kingdom"},{"name":"NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital , Oxford, OX3 9DU, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caleb","family":"Webber","sequence":"additional","affiliation":[{"name":"Department of Physiology, Anatomy, Genetics, Oxford Parkinson\u2019s Disease Centre, University of Oxford , Oxford, OX1 3PT, United Kingdom"},{"name":"UK Dementia Research Institute, Cardiff University , Cardiff, CF24 4HQ, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Parkkinen","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford , Oxford, OX3 7BN, United Kingdom"},{"name":"Nuffield Department of Clinical Neurosciences, Oxford Parkinson\u2019s Disease Centre, University of Oxford , Oxford, OX3 9DU, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela W","family":"Lee","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-2226-5757","authenticated-orcid":false,"given":"Yanxia","family":"Wu","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Fairfax","sequence":"additional","affiliation":[{"name":"MRC\u2013Weatherall Institute of Molecular Medicine, University of Oxford , Oxford, OX3 9DS, United Kingdom"},{"name":"Department of Oncology, University of Oxford & Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, OX3 7DQ, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0377-5536","authenticated-orcid":false,"given":"Julian C","family":"Knight","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"},{"name":"Chinese Academy of Medical Science Oxford Institute, University of Oxford , Oxford, OX3 7BN, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Buck","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Piazza","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford , Oxford, OX3 7BN, United Kingdom"},{"name":"Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,6,8]]},"reference":[{"key":"2024062210014277500_vbae085-B1","doi-asserted-by":"crossref","first-page":"4183","DOI":"10.1038\/s41467-020-17876-0","article-title":"A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders","volume":"11","author":"Agarwal","year":"2020","journal-title":"Nat Commun"},{"key":"2024062210014277500_vbae085-B2","doi-asserted-by":"crossref","first-page":"248","DOI":"10.32614\/RJ-2018-051","article-title":"ggplot2 compatible quantile-quantile plots in R","volume":"10","author":"Almeida","year":"2018","journal-title":"R J"},{"key":"2024062210014277500_vbae085-B3","first-page":"564","article-title":"Fatal COVID-19 in a child with persistence of SARS-CoV-2 despite extensive multidisciplinary treatment: a case report","volume":"8","author":"Apostolidou","year":"2021","journal-title":"Children (Basel)"},{"key":"2024062210014277500_vbae085-B4","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1101\/gr.275430.121","article-title":"Applications of single-cell genomics and computational strategies to study common disease and population-level variation","volume":"31","author":"Auerbach","year":"2021","journal-title":"Genome Res"},{"key":"2024062210014277500_vbae085-B5","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":"2024062210014277500_vbae085-B6","doi-asserted-by":"crossref","first-page":"669","DOI":"10.3233\/JAD-160036","article-title":"Dysregulation of elongation factor 1A expression is correlated with synaptic plasticity impairments in Alzheimer\u2019s disease","volume":"54","author":"Beckelman","year":"2016","journal-title":"J Alzheimers Dis"},{"key":"2024062210014277500_vbae085-B7","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1159\/000438925","article-title":"Impaired eukaryotic elongation factor 1A expression in Alzheimer\u2019s disease","volume":"16","author":"Beckelman","year":"2016","journal-title":"Neurodegener Dis"},{"key":"2024062210014277500_vbae085-B8","doi-asserted-by":"crossref","first-page":"2791","DOI":"10.1093\/bioinformatics\/btac213","article-title":"BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data","volume":"38","author":"Boggy","year":"2022","journal-title":"Bioinformatics"},{"key":"2024062210014277500_vbae085-B9","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1016\/j.celrep.2019.10.019","article-title":"Sex differences in the blood transcriptome identify robust changes in immune cell proportions with aging and influenza infection","volume":"29","author":"Bongen","year":"2019","journal-title":"Cell Rep"},{"key":"2024062210014277500_vbae085-B10","doi-asserted-by":"crossref","first-page":"e202301979","DOI":"10.26508\/lsa.202301979","article-title":"Evaluation of genetic demultiplexing of single-cell sequencing data from model species","volume":"6","author":"Cardiello","year":"2023","journal-title":"Life Sci Alliance"},{"key":"2024062210014277500_vbae085-B11","doi-asserted-by":"crossref","first-page":"6077","DOI":"10.1038\/s41467-020-19894-4","article-title":"Muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data","volume":"11","author":"Crowell","year":"2020","journal-title":"Nat Commun"},{"key":"2024062210014277500_vbae085-B12","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1182\/blood-2017-12-821413","article-title":"A single-cell hematopoietic landscape resolves 8 lineage trajectories and defects in kit mutant mice","volume":"131","author":"Dahlin","year":"2018","journal-title":"Blood"},{"key":"2024062210014277500_vbae085-B13","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13073-015-0152-4","article-title":"Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels","volume":"7","author":"Deelen","year":"2015","journal-title":"Genome Med"},{"key":"2024062210014277500_vbae085-B14","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1186\/s13148-019-0730-1","article-title":"Statistical predictions with glmnet","volume":"11","author":"Engebretsen","year":"2019","journal-title":"Clin Epigenetics"},{"key":"2024062210014277500_vbae085-B15","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1038\/ng.2205","article-title":"Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles","volume":"44","author":"Fairfax","year":"2012","journal-title":"Nat Genet"},{"key":"2024062210014277500_vbae085-B16","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/s41591-019-0734-6","article-title":"Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma","volume":"26","author":"Fairfax","year":"2020","journal-title":"Nat Med"},{"key":"2024062210014277500_vbae085-B17","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1177\/0963689718755778","article-title":"Microenvironment imbalance of spinal cord injury","volume":"27","author":"Fan","year":"2018","journal-title":"Cell Transplant"},{"key":"2024062210014277500_vbae085-B18","doi-asserted-by":"crossref","first-page":"891","DOI":"10.3390\/brainsci13060891","article-title":"Neuroanatomical alterations in the CNTNAP2 mouse model of autism spectrum disorder","volume":"13","author":"Gandhi","year":"2023","journal-title":"Brain Sci"},{"key":"2024062210014277500_vbae085-B19","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1038\/s41590-023-01575-1","article-title":"Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity","volume":"24","author":"Garner","year":"2023","journal-title":"Nat Immunol"},{"key":"2024062210014277500_vbae085-B20","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1038\/s41467-019-10756-2","article-title":"Nuclei multiplexing with barcoded antibodies for single-nucleus genomics","volume":"10","author":"Gaublomme","year":"2019","journal-title":"Nat Commun"},{"key":"2024062210014277500_vbae085-B21","doi-asserted-by":"crossref","first-page":"2667","DOI":"10.1038\/s41467-018-05083-x","article-title":"Detection and removal of barcode swapping in single-cell RNA-seq data","volume":"9","author":"Griffiths","year":"2018","journal-title":"Nat Commun"},{"key":"2024062210014277500_vbae085-B22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v028.i04","article-title":"FlexMix version 2: finite mixtures with concomitant variables and varying and constant parameters","volume":"28","author":"Grun","year":"2008","journal-title":"J Stat Soft"},{"key":"2024062210014277500_vbae085-B23","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s13059-019-1699-y","article-title":"CellTag indexing: genetic barcode-based sample multiplexing for single-cell genomics","volume":"20","author":"Guo","year":"2019","journal-title":"Genome Biol"},{"key":"2024062210014277500_vbae085-B24","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1038\/s41588-023-01533-5","article-title":"Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases","volume":"55","author":"Guo","year":"2023","journal-title":"Nat Genet"},{"key":"2024062210014277500_vbae085-B25","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2024062210014277500_vbae085-B26","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/s41592-020-0820-1","article-title":"Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes","volume":"17","author":"Heaton","year":"2020","journal-title":"Nat Methods"},{"key":"2024062210014277500_vbae085-B27","doi-asserted-by":"crossref","first-page":"lqad086","DOI":"10.1093\/nargab\/lqad086","article-title":"Benchmarking single-cell hashtag oligo demultiplexing methods","volume":"5","author":"Howitt","year":"2023","journal-title":"NAR Genom Bioinform"},{"key":"2024062210014277500_vbae085-B28","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/s41592-018-0033-z","article-title":"SAVER: gene expression recovery for single-cell RNA sequencing","volume":"15","author":"Huang","year":"2018","journal-title":"Nat Methods"},{"key":"2024062210014277500_vbae085-B29","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1093\/bioinformatics\/btab358","article-title":"Cellsnp-lite: an efficient tool for genotyping single cells","volume":"37","author":"Huang","year":"2021","journal-title":"Bioinformatics"},{"key":"2024062210014277500_vbae085-B30","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/s13059-019-1865-2","article-title":"Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference","volume":"20","author":"Huang","year":"2019","journal-title":"Genome Biol"},{"key":"2024062210014277500_vbae085-B31","doi-asserted-by":"crossref","first-page":"14430","DOI":"10.1073\/pnas.0700901104","article-title":"Inhibition of the leucine-rich repeat protein LINGO-1 enhances survival, structure, and function of dopaminergic neurons in Parkinson\u2019s disease models","volume":"104","author":"Inoue","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024062210014277500_vbae085-B32","doi-asserted-by":"crossref","first-page":"eadf2359","DOI":"10.1126\/science.adf2359","article-title":"Interindividual variation in human cortical cell type abundance and expression","volume":"382","author":"Johansen","year":"2023","journal-title":"Science"},{"key":"2024062210014277500_vbae085-B33","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1136\/jmedgenet-2020-107111","article-title":"Association between ARID2 and RAS-MAPK pathway in intellectual disability and short stature","volume":"58","author":"Kang","year":"2021","journal-title":"J Med Genet"},{"key":"2024062210014277500_vbae085-B34","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/nbt.4042","article-title":"Multiplexed droplet single-cell RNA-sequencing using natural genetic variation","volume":"36","author":"Kang","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024062210014277500_vbae085-B35","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1038\/s41467-022-30309-4","article-title":"Nuclear oligo hashing improves differential analysis of single-cell RNA-seq","volume":"13","author":"Kim","year":"2022","journal-title":"Nat Commun"},{"key":"2024062210014277500_vbae085-B36","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1038\/s41588-023-01421-y","article-title":"Mapping interindividual dynamics of innate immune response at single-cell resolution","volume":"55","author":"Kumasaka","year":"2023","journal-title":"Nat Genet"},{"key":"2024062210014277500_vbae085-B37","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1038\/s41590-023-01490-5","article-title":"Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis","volume":"24","author":"Kwok","year":"2023","journal-title":"Nat Immunol"},{"key":"2024062210014277500_vbae085-B38","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/s41592-020-0905-x","article-title":"Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq","volume":"17","author":"Li","year":"2020","journal-title":"Nat Methods"},{"key":"2024062210014277500_vbae085-B39","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"2024062210014277500_vbae085-B40","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024062210014277500_vbae085-B41","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/s41588-020-00751-5","article-title":"A cross-platform approach identifies genetic regulators of human metabolism and health","volume":"53","author":"Lotta","year":"2021","journal-title":"Nat Genet"},{"key":"2024062210014277500_vbae085-B42","doi-asserted-by":"crossref","first-page":"1600557","DOI":"10.1002\/mnfr.201600557","article-title":"Addressing the inter-individual variation in response to consumption of plant food bioactives: towards a better understanding of their role in healthy aging and cardiometabolic risk reduction","volume":"61","author":"Manach","year":"2017","journal-title":"Mol Nutr Food Res"},{"key":"2024062210014277500_vbae085-B43","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/bioinformatics\/btw777","article-title":"Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R","volume":"33","author":"McCarthy","year":"2017","journal-title":"Bioinformatics"},{"key":"2024062210014277500_vbae085-B44","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1038\/s41592-019-0433-8","article-title":"MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices","volume":"16","author":"McGinnis","year":"2019","journal-title":"Nat Methods"},{"key":"2024062210014277500_vbae085-B45","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1186\/s12918-016-0349-1","article-title":"DGCA: a comprehensive R package for differential gene correlation analysis","volume":"10","author":"McKenzie","year":"2016","journal-title":"BMC Syst Biol"},{"key":"2024062210014277500_vbae085-B46","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/s41380-021-01060-x","article-title":"Neurobiology of ARID1B haploinsufficiency related to neurodevelopmental and psychiatric disorders","volume":"27","author":"Moffat","year":"2022","journal-title":"Mol Psychiatry"},{"key":"2024062210014277500_vbae085-B47","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41593-022-01222-2","article-title":"Insights into Alzheimer\u2019s disease from single-cell genomic approaches","volume":"26","author":"Murdock","year":"2023","journal-title":"Nat Neurosci"},{"key":"2024062210014277500_vbae085-B48","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1186\/s12864-023-09447-6","article-title":"scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data","volume":"24","author":"Nassiri","year":"2023","journal-title":"BMC Genomics"},{"key":"2024062210014277500_vbae085-B49","doi-asserted-by":"crossref","first-page":"e116","DOI":"10.1093\/nar\/gky626","article-title":"Systematic exploration of cell morphological phenotypes associated with a transcriptomic query","volume":"46","author":"Nassiri","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2024062210014277500_vbae085-B50","volume-title":"Genome Biol","author":"Neavin","year":"2024"},{"key":"2024062210014277500_vbae085-B51","doi-asserted-by":"crossref","first-page":"3267","DOI":"10.1038\/s41467-022-30893-5","article-title":"Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure","volume":"13","author":"Oelen","year":"2022","journal-title":"Nat Commun"},{"key":"2024062210014277500_vbae085-B52","doi-asserted-by":"crossref","first-page":"5849","DOI":"10.1038\/s41467-021-26085-2","article-title":"DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data","volume":"12","author":"Ranjan","year":"2021","journal-title":"Nat Commun"},{"key":"2024062210014277500_vbae085-B53","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1016\/j.biopsych.2020.12.023","article-title":"Gene expression imputation across multiple tissue types provides insight into the genetic architecture of frontotemporal dementia and its clinical subtypes","volume":"89","author":"Reus","year":"2021","journal-title":"Biol Psychiatry"},{"key":"2024062210014277500_vbae085-B54","doi-asserted-by":"crossref","first-page":"e12087","DOI":"10.1002\/pul2.12087","article-title":"NEDD9 provides mechanistic insight into the coagulopathy of COVID-19","volume":"12","author":"Rizzo","year":"2022","journal-title":"Pulm Circ"},{"key":"2024062210014277500_vbae085-B55","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1016\/j.biopsych.2023.03.014","article-title":"Loss of CNTNAP2 alters human cortical excitatory neuron differentiation and neural network development","volume":"94","author":"St George-Hyslop","year":"2023","journal-title":"Biol Psychiatry"},{"key":"2024062210014277500_vbae085-B56","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/s13059-018-1603-1","article-title":"Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics","volume":"19","author":"Stoeckius","year":"2018","journal-title":"Genome Biol"},{"key":"2024062210014277500_vbae085-B57","doi-asserted-by":"crossref","first-page":"4658","DOI":"10.7150\/ijbs.73640","article-title":"Structural basis of SARS-CoV-2 and its variants binding to intermediate horseshoe bat ACE2","volume":"18","author":"Tang","year":"2022","journal-title":"Int J Biol Sci"},{"key":"2024062210014277500_vbae085-B58","doi-asserted-by":"crossref","first-page":"11.10.11","DOI":"10.1002\/0471250953.bi1110s43","article-title":"From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline","volume":"43","author":"Van der Auwera","year":"2013","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024062210014277500_vbae085-B59","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41588-018-0089-9","article-title":"Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs","volume":"50","author":"van der Wijst","year":"2018","journal-title":"Nat Genet"},{"key":"2024062210014277500_vbae085-B60","doi-asserted-by":"crossref","first-page":"146","DOI":"10.3390\/biom12010146","article-title":"The role of the lncRNA MALAT1 in neuroprotection against hypoxic\/ischemic injury","volume":"12","author":"Wang","year":"2022","journal-title":"Biomolecules"},{"key":"2024062210014277500_vbae085-B61","doi-asserted-by":"crossref","first-page":"645647","DOI":"10.3389\/fcell.2021.645647","article-title":"Biological function of long non-coding RNA (LncRNA) xist","volume":"9","author":"Wang","year":"2021","journal-title":"Front Cell Dev Biol"},{"key":"2024062210014277500_vbae085-B62","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: computational identification of cell doublets in single-cell transcriptomic data","volume":"8","author":"Wolock","year":"2019","journal-title":"Cell Syst"},{"key":"2024062210014277500_vbae085-B63","first-page":"100141","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"},{"key":"2024062210014277500_vbae085-B64","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1186\/s13059-020-02084-2","article-title":"GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing","volume":"21","author":"Xin","year":"2020","journal-title":"Genome Biol"},{"key":"2024062210014277500_vbae085-B65","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1186\/s13059-019-1852-7","article-title":"Genotype-free demultiplexing of pooled single-cell RNA-seq","volume":"20","author":"Xu","year":"2019","journal-title":"Genome Biol"},{"key":"2024062210014277500_vbae085-B66","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1186\/s13059-021-02544-3","article-title":"Feature selection revisited in the single-cell era","volume":"22","author":"Yang","year":"2021","journal-title":"Genome Biol"},{"key":"2024062210014277500_vbae085-B67","doi-asserted-by":"crossref","first-page":"eabf3041","DOI":"10.1126\/science.abf3041","article-title":"Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease","volume":"376","author":"Yazar","year":"2022","journal-title":"Science"}],"container-title":["Bioinformatics Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/advance-article-pdf\/doi\/10.1093\/bioadv\/vbae085\/58177670\/vbae085.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/4\/1\/vbae085\/58304868\/vbae085.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/4\/1\/vbae085\/58304868\/vbae085.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,22]],"date-time":"2024-06-22T10:03:18Z","timestamp":1719050598000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article\/doi\/10.1093\/bioadv\/vbae085\/7690196"}},"subtitle":[],"editor":[{"given":"Magnus","family":"Rattray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024]]},"references-count":67,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1,5]]}},"URL":"https:\/\/doi.org\/10.1093\/bioadv\/vbae085","relation":{},"ISSN":["2635-0041"],"issn-type":[{"value":"2635-0041","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024]]},"published":{"date-parts":[[2024]]},"article-number":"vbae085"}}