{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T00:12:25Z","timestamp":1793146345777,"version":"4.5.0"},"reference-count":260,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T00:00:00Z","timestamp":1711411200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular Aspects of Medicine"],"published-print":{"date-parts":[[2024,6]]},"DOI":"10.1016\/j.mam.2024.101269","type":"journal-article","created":{"date-parts":[[2024,3,29]],"date-time":"2024-03-29T00:11:23Z","timestamp":1711671083000},"page":"101269","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":24,"special_numbering":"C","title":["A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics"],"prefix":"10.1016","volume":"97","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9356-7940","authenticated-orcid":false,"given":"Christian","family":"Gr\u00e4tz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martina","family":"Schuster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Brandes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnes S.","family":"Meidert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benedikt","family":"Kirchner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marlene","family":"Reithmair","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustav","family":"Schelling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael W.","family":"Pfaffl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib1","doi-asserted-by":"crossref","first-page":"R18","DOI":"10.1186\/gb-2011-12-2-r18","article-title":"Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries","volume":"12","author":"Aird","year":"2011","journal-title":"Genome Biol."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib2","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1007\/s11060-015-1784-3","article-title":"miRNA contents of cerebrospinal fluid extracellular vesicles in glioblastoma patients","volume":"123","author":"Akers","year":"2015","journal-title":"J. Neuro Oncol."},{"issue":"5","key":"10.1016\/j.mam.2024.101269_bib3","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2023.e16261","article-title":"Combining cell-free RNA with cell-free DNA in liquid biopsy for hematologic and solid tumors","volume":"9","author":"Albitar","year":"2023","journal-title":"Heliyon"},{"issue":"9","key":"10.1016\/j.mam.2024.101269_bib4","doi-asserted-by":"crossref","first-page":"1506","DOI":"10.1101\/gr.121715.111","article-title":"Barcoding bias in high-throughput multiplex sequencing of miRNA","volume":"21","author":"Alon","year":"2011","journal-title":"Genome Res."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib5","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"issue":"9","key":"10.1016\/j.mam.2024.101269_bib6","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1038\/ki.2012.256","article-title":"Comparison of protein, microRNA, and mRNA yields using different methods of urinary exosome isolation for the discovery of kidney disease biomarkers","volume":"82","author":"Alvarez","year":"2012","journal-title":"Kidney Int."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib7","doi-asserted-by":"crossref","first-page":"e77","DOI":"10.1002\/jex2.77","article-title":"Cellular communication through extracellular vesicles and lipid droplets","volume":"2","author":"Amarasinghe","year":"2023","journal-title":"J. Extracellular Biol."},{"issue":"15","key":"10.1016\/j.mam.2024.101269_bib8","doi-asserted-by":"crossref","first-page":"5245","DOI":"10.1158\/0008-5472.CAN-04-0496","article-title":"Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets","volume":"64","author":"Andersen","year":"2004","journal-title":"Cancer Res."},{"key":"10.1016\/j.mam.2024.101269_bib9","first-page":"72","article-title":"Liquid biopsy analysis in cancer diagnostics","author":"Andersson","year":"2020","journal-title":"Mol. Aspect. Med."},{"key":"10.1016\/j.mam.2024.101269_bib10","doi-asserted-by":"crossref","first-page":"31655","DOI":"10.3402\/jev.v5.31655","article-title":"Comparative analysis of EV isolation procedures for miRNAs detection in serum samples","volume":"5","author":"Andreu","year":"2016","journal-title":"J. Extracell. Vesicles"},{"issue":"15","key":"10.1016\/j.mam.2024.101269_bib11","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkx588","article-title":"Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification","volume":"45","author":"Androvic","year":"2017","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib12","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1002\/humu.10221","article-title":"Determination of SMN1 and SMN2 copy number using TaqMan\u2122 technology","volume":"22","author":"Anhuf","year":"2003","journal-title":"Hum. Mutat."},{"issue":"23","key":"10.1016\/j.mam.2024.101269_bib13","first-page":"2526","article-title":"Acute respiratory distress syndrome: the Berlin Definition","volume":"307","author":"Ards Definition Task Force","year":"2012","journal-title":"JAMA"},{"issue":"12","key":"10.1016\/j.mam.2024.101269_bib14","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0145686","article-title":"Isolation of exosomes from blood plasma: qualitative and quantitative comparison of ultracentrifugation and size exclusion chromatography methods","volume":"10","author":"Baranyai","year":"2015","journal-title":"PLoS One"},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib15","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1002\/cem.785","article-title":"Partial least squares for discrimination","volume":"17","author":"Barker","year":"2003","journal-title":"J. Chemometr."},{"key":"10.1016\/j.mam.2024.101269_bib16","doi-asserted-by":"crossref","first-page":"15005","DOI":"10.1038\/nrdp.2015.5","article-title":"Huntington disease","volume":"1","author":"Bates","year":"2015","journal-title":"Nat. Rev. Dis. Prim."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib17","doi-asserted-by":"crossref","DOI":"10.1186\/s13054-020-02950-2","article-title":"Mortality in sepsis and septic shock in Europe, North America and Australia between 2009 and 2019\u2014 results from a systematic review and meta-analysis","volume":"24","author":"Bauer","year":"2020","journal-title":"Crit. Care"},{"key":"10.1016\/j.mam.2024.101269_bib18","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1016\/j.omtn.2020.03.003","article-title":"The promising role of miR-21 as a cancer biomarker and its importance in RNA-based therapeutics","volume":"20","author":"Bautista-S\u00e1nchez","year":"2020","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"10.1016\/j.mam.2024.101269_bib19","first-page":"91","article-title":"Extracellular vesicles as personalized medicine","author":"Beetler","year":"2023","journal-title":"Mol. Aspect. Med."},{"issue":"5","key":"10.1016\/j.mam.2024.101269_bib20","doi-asserted-by":"crossref","DOI":"10.3892\/ijo.2022.5423","article-title":"Isolation and analysis of tumor-derived extracellular vesicles from head and neck squamous cell carcinoma plasma by galectin-based glycan recognition particles","volume":"61","author":"Benecke","year":"2022","journal-title":"Int. J. Oncol."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib21","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. Roy. Stat. Soc. B"},{"key":"10.1016\/j.mam.2024.101269_bib22","series-title":"Biochemistry","author":"Berg","year":"2010"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib23","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.ymeth.2010.01.009","article-title":"Gene expression profiling\u2013Clusters of possibilities","volume":"50","author":"Bergkvist","year":"2010","journal-title":"Methods"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib24","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/s41572-021-00278-x","article-title":"Haemophilia","volume":"7","author":"Berntorp","year":"2021","journal-title":"Nat. Rev. Dis. Prim."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib25","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1067\/mcp.2001.113989","article-title":"Biomarkers and surrogate endpoints: preferred definitions and conceptual framework","volume":"69","year":"2001","journal-title":"Clin. Pharmacol. Ther."},{"issue":"24","key":"10.1016\/j.mam.2024.101269_bib26","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1001\/jama.1993.03510240069035","article-title":"A New simplified acute physiology score (SAPS II) based on a European\/North American multicenter study","volume":"270","author":"Bone","year":"1993","journal-title":"J. Am. Med. Assoc."},{"key":"10.1016\/j.mam.2024.101269_bib27","doi-asserted-by":"crossref","first-page":"1129766","DOI":"10.3389\/fimmu.2023.1129766","article-title":"Extensive blood transcriptome analysis reveals cellular signaling networks activated by circulating glycocalyx components reflecting vascular injury in COVID-19","volume":"14","author":"Borrmann","year":"2023","journal-title":"Front. Immunol."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib28","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s40635-021-00406-7","article-title":"Progranulin signaling in sepsis, community-acquired bacterial pneumonia and COVID-19: a comparative, observational study","volume":"9","author":"Brandes","year":"2021","journal-title":"Intensive Care Med. Exp."},{"key":"10.1016\/j.mam.2024.101269_bib29","doi-asserted-by":"crossref","first-page":"100087","DOI":"10.1016\/j.bdq.2019.100087","article-title":"The emerging role of cell-free DNA as a molecular marker for cancer management","volume":"17","author":"Bronkhorst","year":"2019","journal-title":"Biomol. Detect Quantif"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib30","doi-asserted-by":"crossref","first-page":"e86","DOI":"10.1002\/cphg.86","article-title":"Best practices for Illumina library preparation","volume":"102","author":"Bronner","year":"2019","journal-title":"Curr. Protocols in Hum. Genetics"},{"key":"10.1016\/j.mam.2024.101269_bib31","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinf."},{"issue":"12","key":"10.1016\/j.mam.2024.101269_bib32","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/s41576-020-00296-7","article-title":"Reaching completion for GTEx","volume":"21","author":"Burgess","year":"2020","journal-title":"Nat. Rev. Genet."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib33","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/s41575-019-0245-4","article-title":"Role of oncogenic KRAS in the diagnosis, prognosis and treatment of pancreatic cancer","volume":"17","author":"Buscail","year":"2020","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"issue":"13","key":"10.1016\/j.mam.2024.101269_bib34","doi-asserted-by":"crossref","first-page":"5995","DOI":"10.1093\/nar\/gkw545","article-title":"Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow","volume":"44","author":"Buschmann","year":"2016","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib35","doi-asserted-by":"crossref","first-page":"1481321","DOI":"10.1080\/20013078.2018.1481321","article-title":"Evaluation of serum extracellular vesicle isolation methods for profiling miRNAs by next-generation sequencing","volume":"7","author":"Buschmann","year":"2018","journal-title":"J. Extracell. Vesicles"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib36","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1097\/ALN.0000000000002986","article-title":"Propofol and sevoflurane differentially impact MicroRNAs in circulating extracellular vesicles during colorectal cancer resection: a pilot study","volume":"132","author":"Buschmann","year":"2020","journal-title":"Anesthesiology"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib37","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1373\/clinchem.2008.112797","article-title":"The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments","volume":"55","author":"Bustin","year":"2009","journal-title":"Clin. Chem."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib38","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/s40364-022-00409-w","article-title":"Current challenges and best practices for cell-free long RNA biomarker discovery","volume":"10","author":"Cabus","year":"2022","journal-title":"Biomark. Res."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib39","doi-asserted-by":"crossref","DOI":"10.1186\/s12867-016-0060-1","article-title":"A reliable method for quantification of splice variants using RT-qPCR","volume":"17","author":"Camacho Londo\u00f1o","year":"2016","journal-title":"BMC Mol. Biol."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib40","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1261\/rna.046060.114","article-title":"Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data","volume":"21","author":"Campbell","year":"2015","journal-title":"RNA"},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib41","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1002\/1878-0261.13150","article-title":"Serial monitoring of genomic alterations in circulating tumor cells of ER-positive\/HER2-negative advanced breast cancer: feasibility of precision oncology biomarker detection","volume":"16","author":"Cani","year":"2022","journal-title":"Mol. Oncol."},{"key":"10.1016\/j.mam.2024.101269_bib42","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1186\/1471-2105-12-253","article-title":"Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems","volume":"12","author":"Le Cao","year":"2011","journal-title":"BMC Bioinf."},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib43","doi-asserted-by":"crossref","DOI":"10.1038\/s41419-019-2015-1","article-title":"Pathological alteration and therapeutic implications of sepsis-induced immune cell apoptosis","volume":"10","author":"Cao","year":"2019","journal-title":"Cell Death Dis."},{"key":"10.1016\/j.mam.2024.101269_bib44","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/978-1-4939-7253-1_13","article-title":"Analysis of extracellular vesicles using fluorescence nanoparticle tracking analysis","volume":"1660","author":"Carnell-Morris","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.mam.2024.101269_bib45","doi-asserted-by":"crossref","first-page":"661679","DOI":"10.3389\/fmed.2021.661679","article-title":"Extracellular vesicles: a novel Opportunity for precision Medicine in respiratory diseases","volume":"8","author":"Carnino","year":"2021","journal-title":"Front. Med."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib46","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/ng854","article-title":"Disruption of an SF2\/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1","volume":"30","author":"Cartegni","year":"2002","journal-title":"Nat. Genet."},{"issue":"5","key":"10.1016\/j.mam.2024.101269_bib47","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1093\/bib\/bbv090","article-title":"Transcriptomic and metabolomic data integration","volume":"17","author":"Cavill","year":"2016","journal-title":"Briefings Bioinf."},{"issue":"20","key":"10.1016\/j.mam.2024.101269_bib48","doi-asserted-by":"crossref","first-page":"e179","DOI":"10.1093\/nar\/gni178","article-title":"Real-time quantification of microRNAs by stem-loop RT-PCR","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib49","doi-asserted-by":"crossref","first-page":"e61","DOI":"10.1093\/nar\/gnh055","article-title":"Real-time PCR genotyping using displacing probes","volume":"32","author":"Cheng","year":"2004","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib50","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1653-z","article-title":"MMSplice: modular modeling improves the predictions of genetic variant effects on splicing","volume":"20","author":"Cheng","year":"2019","journal-title":"Genome Biol."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib51","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s12929-019-0502-4","article-title":"Toward characterizing extracellular vesicles at a single-particle level","volume":"26","author":"Chiang","year":"2019","journal-title":"J. Biomed. Sci."},{"issue":"12","key":"10.1016\/j.mam.2024.101269_bib52","doi-asserted-by":"crossref","first-page":"2760","DOI":"10.1111\/j.1582-4934.2011.01274.x","article-title":"Epigenetic inactivation of the hsa-miR-203 in haematological malignancies","volume":"15","author":"Chim","year":"2011","journal-title":"J. Cell Mol. Med."},{"key":"10.1016\/j.mam.2024.101269_bib53","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1146\/annurev-cellbio-101512-122326","article-title":"Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles","volume":"30","author":"Colombo","year":"2014","journal-title":"Annu. Rev. Cell Dev. Biol."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib54","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1111\/bju.14811","article-title":"A four-group urine risk classifier for predicting outcomes in patients with prostate cancer","volume":"124","author":"Connell","year":"2019","journal-title":"BJU Int."},{"key":"10.1016\/j.mam.2024.101269_bib55","series-title":"The Cell: A Molecular Approach","author":"Cooper","year":"2000"},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib56","doi-asserted-by":"crossref","DOI":"10.1002\/jev2.12184","article-title":"Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis","volume":"11","author":"Correll","year":"2022","journal-title":"J. Extracell. Vesicles"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib57","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1590\/S1415-47572004000400025","article-title":"Comparative analysis of clustering methods for gene expression time course data","volume":"27","author":"Costa","year":"2004","journal-title":"Genet. Mol. Biol."},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib58","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1161\/CIRCRESAHA.117.309417","article-title":"Methodological guidelines to study extracellular vesicles","volume":"120","author":"Coumans","year":"2017","journal-title":"Circ. Res."},{"key":"10.1016\/j.mam.2024.101269_bib59","doi-asserted-by":"crossref","DOI":"10.3402\/jev.v3.24858","article-title":"The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling","volume":"3","author":"Van Deun","year":"2014","journal-title":"J. Extracell. Vesicles"},{"issue":"5","key":"10.1016\/j.mam.2024.101269_bib60","doi-asserted-by":"crossref","DOI":"10.1002\/jev2.12315","article-title":"Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics","volume":"12","author":"Dhondt","year":"2023","journal-title":"J. Extracell. Vesicles"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib61","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.yexcr.2014.01.008","article-title":"Library preparation methods for next-generation sequencing: tone down the bias","volume":"322","author":"van Dijk","year":"2014","journal-title":"Exp. Cell Res."},{"issue":"6","key":"10.1016\/j.mam.2024.101269_bib62","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1093\/bib\/bbs046","article-title":"A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis","volume":"14","author":"Dillies","year":"2013","journal-title":"Briefings Bioinf."},{"issue":"16","key":"10.1016\/j.mam.2024.101269_bib63","doi-asserted-by":"crossref","first-page":"e105","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."},{"key":"10.1016\/j.mam.2024.101269_bib64","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.gene.2017.01.019","article-title":"Profiling of human epigenetic regulators using a semi-automated real-time qPCR platform validated by next generation sequencing","volume":"609","author":"Dudakovic","year":"2017","journal-title":"Gene"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib65","doi-asserted-by":"crossref","first-page":"4684","DOI":"10.1038\/ncomms5684","article-title":"Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs","volume":"5","author":"Enroth","year":"2014","journal-title":"Nat. Commun."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib66","doi-asserted-by":"crossref","DOI":"10.1002\/jev2.12043","article-title":"RNA packaging into extracellular vesicles: An orchestra of RNA-binding proteins?","volume":"10","author":"Fabbiano","year":"2020","journal-title":"J. Extracell. Vesicles"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib67","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1186\/1756-0500-4-324","article-title":"Identification of Phosphoglycerate Kinase 1 (PGK1) as a reference gene for quantitative gene expression measurements in human blood RNA","volume":"4","author":"Falkenberg","year":"2011","journal-title":"BMC Res. Notes"},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib68","doi-asserted-by":"crossref","first-page":"1573","DOI":"10.1007\/s00134-012-2682-1","article-title":"The Berlin definition of ARDS: an expanded rationale, justification, and supplementary material","volume":"38","author":"Ferguson","year":"2012","journal-title":"Intensive Care Med."},{"issue":"S8","key":"10.1016\/j.mam.2024.101269_bib69","doi-asserted-by":"crossref","DOI":"10.1186\/s12864-019-5863-2","article-title":"Recurrent miscalling of missense variation from short-read genome sequence data","volume":"20","author":"Field","year":"2019","journal-title":"BMC Genom."},{"key":"10.1016\/j.mam.2024.101269_bib70","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.nbt.2022.03.001","article-title":"Affinity-based isolation of extracellular vesicles by means of single-domain antibodies bound to macroporous methacrylate-based copolymer","volume":"69","author":"Filipovi\u0107","year":"2022","journal-title":"N. Biotech."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib71","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1164\/rccm.201504-0781OC","article-title":"Assessment of global incidence and mortality of hospital-treated sepsis. Current estimates and limitations","volume":"193","author":"Fleischmann","year":"2016","journal-title":"Am. J. Respir. Crit. Care Med."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib72","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1111\/bcpt.13536","article-title":"Are older adults insufficiently included in clinical trials?\u2014an umbrella review","volume":"128","author":"Florisson","year":"2021","journal-title":"Basic Clin. Pharmacol. Toxicol."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib73","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1002\/humu.22033","article-title":"Detecting false-positive signals in exome sequencing","volume":"33","author":"Fuentes Fajardo","year":"2012","journal-title":"Hum. Mutat."},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib74","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1016\/j.tibtech.2020.05.012","article-title":"Technologies and standardization in research on extracellular vesicles","volume":"38","author":"Gandham","year":"2020","journal-title":"Trends Biotechnol."},{"key":"10.1016\/j.mam.2024.101269_bib75","doi-asserted-by":"crossref","first-page":"1100892","DOI":"10.3389\/fbioe.2022.1100892","article-title":"Recent developments in isolating methods for exosomes","volume":"10","author":"Gao","year":"2022","journal-title":"Front. Bioeng. Biotechnol."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib76","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1016\/j.canlet.2008.01.008","article-title":"Free circulating mRNA in plasma from breast cancer patients and clinical outcome","volume":"263","author":"Garcia","year":"2008","journal-title":"Cancer Lett."},{"key":"10.1016\/j.mam.2024.101269_bib77","doi-asserted-by":"crossref","DOI":"10.3402\/jev.v2i0.19671","article-title":"Extracellular vesicle sizing and enumeration by nanoparticle tracking analysis","volume":"2","author":"Gardiner","year":"2013","journal-title":"J. Extracell. Vesicles"},{"issue":"D1","key":"10.1016\/j.mam.2024.101269_bib78","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gkab1028","article-title":"The reactome pathway knowledgebase 2022","volume":"50","author":"Gillespie","year":"2022","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib79","doi-asserted-by":"crossref","DOI":"10.3390\/biom11010041","article-title":"isomiRs-hidden Soldiers in the miRNA regulatory army, and How to find them?","volume":"11","author":"Glogovitis","year":"2020","journal-title":"Biomolecules"},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib80","doi-asserted-by":"crossref","first-page":"386","DOI":"10.3390\/life12030386","article-title":"Obtaining reliable RT-qPCR Results in molecular diagnostics\u2014MIQE Goals and Pitfalls for transcriptional biomarker discovery","volume":"12","author":"Gr\u00e4tz","year":"2022","journal-title":"Life"},{"issue":"18","key":"10.1016\/j.mam.2024.101269_bib81","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1056\/NEJMoa2002032","article-title":"Clinical characteristics of coronavirus disease 2019 in China","volume":"382","author":"Guan","year":"2020","journal-title":"N. Engl. J. Med."},{"issue":"35","key":"10.1016\/j.mam.2024.101269_bib82","doi-asserted-by":"crossref","first-page":"37043","DOI":"10.18632\/oncotarget.6158","article-title":"Altered microRNA profiles in cerebrospinal fluid exosome in Parkinson disease and Alzheimer disease","volume":"6","author":"Gui","year":"2015","journal-title":"Oncotarget"},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib83","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.thromres.2013.11.010","article-title":"Improved circulating microparticle analysis in acid-citrate dextrose (ACD) anticoagulant tube","volume":"133","author":"Gy\u00f6rgy","year":"2014","journal-title":"Thromb. Res."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib84","doi-asserted-by":"crossref","DOI":"10.1186\/s13195-020-00636-z","article-title":"The dynamics of biomarkers across the clinical spectrum of Alzheimer's disease","volume":"12","author":"Hadjichrysanthou","year":"2020","journal-title":"Alzheimer's Res. Ther."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib85","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/s41572-019-0111-2","article-title":"Breast cancer","volume":"5","author":"Harbeck","year":"2019","journal-title":"Nat. Rev. Dis. Prim."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib86","doi-asserted-by":"crossref","first-page":"6271","DOI":"10.1038\/s41598-020-62801-6","article-title":"RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method","volume":"10","author":"Harrington","year":"2020","journal-title":"Sci. Rep."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib87","article-title":"Extracellular vesicle quantification and characterization: common methods and emerging approaches","volume":"6","author":"Hartjes","year":"2019","journal-title":"Bioengineering (Basel)"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib88","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1073\/pnas.1916312117","article-title":"Clarifying the effect of library batch on extracellular RNA sequencing","volume":"117","author":"Hartl","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.mam.2024.101269_bib89","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1007\/978-1-4939-7614-0_23","article-title":"Rapid and easy protocol for quantification of next-generation sequencing libraries","author":"Hawkins","year":"2018","journal-title":"Methods Mol. Biol."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib90","doi-asserted-by":"crossref","first-page":"R19","DOI":"10.1186\/gb-2007-8-2-r19","article-title":"qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data","volume":"8","author":"Hellemans","year":"2007","journal-title":"Genome Biol."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib91","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/s12864-018-4585-1","article-title":"Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction","volume":"19","author":"Herbert","year":"2018","journal-title":"BMC Genom."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib92","doi-asserted-by":"crossref","first-page":"1670935","DOI":"10.1080\/20013078.2019.1670935","article-title":"Transcriptomic profiling of cell-free and vesicular microRNAs from matched arterial and venous sera","volume":"8","author":"Hermann","year":"2019","journal-title":"J. Extracell. Vesicles"},{"issue":"20","key":"10.1016\/j.mam.2024.101269_bib93","doi-asserted-by":"crossref","first-page":"12054","DOI":"10.1111\/jcmm.15837","article-title":"Diagnostic potential of circulating cell-free microRNAs for community-acquired pneumonia and pneumonia-related sepsis","volume":"24","author":"Hermann","year":"2020","journal-title":"J. Cell Mol. Med."},{"issue":"S1","key":"10.1016\/j.mam.2024.101269_bib94","doi-asserted-by":"crossref","first-page":"S105","DOI":"10.2105\/AJPH.2009.162982","article-title":"Disparate inclusion of older adults in clinical trials: priorities and opportunities for policy and practice change","volume":"100","author":"Herrera","year":"2010","journal-title":"Am. J. Publ. Health"},{"key":"10.1016\/j.mam.2024.101269_bib95","doi-asserted-by":"crossref","first-page":"729061","DOI":"10.3389\/fcell.2021.729061","article-title":"Detection of atherosclerosis by small RNA-sequencing analysis of extracellular vesicle enriched serum samples","volume":"9","author":"Hildebrandt","year":"2021","journal-title":"Front. Cell Dev. Biol."},{"issue":"15","key":"10.1016\/j.mam.2024.101269_bib96","doi-asserted-by":"crossref","first-page":"167070","DOI":"10.1016\/j.jmb.2021.167070","article-title":"miREV: an online Database and Tool to uncover potential reference RNAs and Biomarkers in small-RNA sequencing data Sets from extracellular vesicles enriched samples","volume":"433","author":"Hildebrandt","year":"2021","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.mam.2024.101269_bib97","doi-asserted-by":"crossref","DOI":"10.3402\/jev.v2i0.22859","article-title":"ISEV position paper: extracellular vesicle RNA analysis and bioinformatics","volume":"2","author":"Hill","year":"2013","journal-title":"J. Extracell. Vesicles"},{"issue":"16","key":"10.1016\/j.mam.2024.101269_bib98","doi-asserted-by":"crossref","first-page":"7276","DOI":"10.1073\/pnas.88.16.7276","article-title":"Detection of specific polymerase chain reaction product by utilizing the 5'\u2013--3' exonuclease activity of Thermus aquaticus DNA polymerase","volume":"88","author":"Holland","year":"1991","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"5","key":"10.1016\/j.mam.2024.101269_bib99","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.2214\/AJR.20.22969","article-title":"Radiology perspective of coronavirus disease 2019 (COVID-19): lessons from severe acute respiratory syndrome and Middle East respiratory syndrome","volume":"214","author":"Hosseiny","year":"2020","journal-title":"AJR Am. J. Roentgenol."},{"issue":"11","key":"10.1016\/j.mam.2024.101269_bib100","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1016\/j.humimm.2021.02.012","article-title":"Next-generation sequencing technologies: An overview","volume":"82","author":"Hu","year":"2021","journal-title":"Hum. Immunol."},{"key":"10.1016\/j.mam.2024.101269_bib101","doi-asserted-by":"crossref","DOI":"10.3389\/fragi.2021.797040","article-title":"Gene expression analysis reveals age and ethnicity signatures between young and old adults in human PBMC","volume":"2","author":"Hu","year":"2022","journal-title":"Front. Aging"},{"issue":"D1","key":"10.1016\/j.mam.2024.101269_bib102","first-page":"D148","article-title":"miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database","volume":"48","author":"Huang","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mam.2024.101269_bib103","doi-asserted-by":"crossref","DOI":"10.1002\/0471142905.hg0210s56","article-title":"Genotyping using the TaqMan assay","author":"Hui","year":"2008","journal-title":"Curr. Protoc. Hum. Genet."},{"issue":"2\u20133","key":"10.1016\/j.mam.2024.101269_bib104","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/0166-0934(88)90101-2","article-title":"Pipetting errors in viral titrations: a useful approach","volume":"22","author":"Husson-van Vliet","year":"1988","journal-title":"J. Virol Methods"},{"key":"10.1016\/j.mam.2024.101269_bib105","unstructured":"Illumina. Best practices for library.Illumina. Best practices for library quantification. [cited 2023, September 26th]; Available from:: https:\/\/knowledge.illumina.com\/library-preparation\/general\/library-preparation-general-reference_material-list\/000003750."},{"key":"10.1016\/j.mam.2024.101269_bib106","unstructured":"Illumina. Considerations for RNA Seq Illumina. Considerations for RNA Seq read length and coverage. [cited 2023, September 26th]; Available from:: https:\/\/knowledge.illumina.com\/library-preparation\/rna-library-prep\/library-preparation-rna-library-prep-reference_material-list\/000001243."},{"key":"10.1016\/j.mam.2024.101269_bib107","unstructured":"Illumina. Library quantification and quality Illumina. Library quantification and quality control quick reference guide. [cited 2023, September 26th]; Available from:: https:\/\/knowledge.illumina.com\/library-preparation\/general\/library-preparation-general-reference_material-list\/000001247."},{"key":"10.1016\/j.mam.2024.101269_bib108","unstructured":"Illumina. Technol. Spotlight Illumina. Technol. Spotlight: Illumina\u00ae Sequencing. Available from:: https:\/\/www.illumina.com\/documents\/products\/techspotlights\/techspotlight_sequencing.pdf."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib109","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.cell.2018.12.015","article-title":"Predicting splicing from primary sequence with deep learning","volume":"176","author":"Jaganathan","year":"2019","journal-title":"Cell"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib110","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1186\/s12864-020-07304-4","article-title":"Comparative evaluation for the globin gene depletion methods for mRNA sequencing using the whole blood-derived total RNAs","volume":"21","author":"Jang","year":"2020","journal-title":"BMC Genom."},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib111","doi-asserted-by":"crossref","first-page":"1649","DOI":"10.1161\/CIRCRESAHA.117.310752","article-title":"Extracellular vesicles in cardiovascular disease: potential applications in diagnosis, prognosis, and epidemiology","volume":"120","author":"Jansen","year":"2017","journal-title":"Circ. Res."},{"issue":"19","key":"10.1016\/j.mam.2024.101269_bib112","doi-asserted-by":"crossref","first-page":"9412","DOI":"10.1016\/S0021-9258(18)48095-7","article-title":"Vesicle formation during reticulocyte maturation. Association of plasma membrane activities with released vesicles (exosomes)","volume":"262","author":"Johnstone","year":"1987","journal-title":"J. Biol. Chem."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib113","doi-asserted-by":"crossref","first-page":"170","DOI":"10.3390\/ijms17020170","article-title":"Focus on extracellular vesicles: introducing the next small big thing","volume":"17","author":"Kalra","year":"2016","journal-title":"Int. J. Mol. Sci."},{"issue":"D1","key":"10.1016\/j.mam.2024.101269_bib114","doi-asserted-by":"crossref","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res."},{"issue":"17","key":"10.1016\/j.mam.2024.101269_bib115","doi-asserted-by":"crossref","first-page":"1629","DOI":"10.1056\/NEJMoa1415236","article-title":"Systemic inflammatory response syndrome criteria in defining severe sepsis","volume":"372","author":"Kaukonen","year":"2015","journal-title":"N. Engl. J. Med."},{"issue":"23","key":"10.1016\/j.mam.2024.101269_bib116","doi-asserted-by":"crossref","first-page":"6097","DOI":"10.1158\/0008-5472.CAN-12-3232","article-title":"Why your new cancer biomarker may never work: recurrent patterns and remarkable diversity in biomarker failures","volume":"72","author":"Kern","year":"2012","journal-title":"Cancer Res."},{"key":"10.1016\/j.mam.2024.101269_bib117","author":"Kirchner"},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib118","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0229606","article-title":"Postprandial transfer of colostral extracellular vesicles and their protein and miRNA cargo in neonatal calves","volume":"15","author":"Kirchner","year":"2020","journal-title":"PLoS One"},{"key":"10.1016\/j.mam.2024.101269_bib119","author":"Kirchner"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib120","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1038\/nmeth.1778","article-title":"Counting absolute numbers of molecules using unique molecular identifiers","volume":"9","author":"Kivioja","year":"2012","journal-title":"Nat. Methods"},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib121","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1097\/00003246-198510000-00009","article-title":"Apache II: a severity of disease classification system","volume":"13","author":"Knaus","year":"1985","journal-title":"Crit. Care Med."},{"key":"10.1016\/j.mam.2024.101269_bib122","doi-asserted-by":"crossref","first-page":"8545347","DOI":"10.1155\/2018\/8545347","article-title":"Isolation of extracellular vesicles: general methodologies and latest trends","volume":"2018","author":"Konoshenko","year":"2018","journal-title":"BioMed Res. Int."},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib123","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1093\/bioinformatics\/btm091","article-title":"Enhancements and modifications of primer design program Primer3","volume":"23","author":"Koressaar","year":"2007","journal-title":"Bioinformatics"},{"issue":"11","key":"10.1016\/j.mam.2024.101269_bib124","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1093\/bioinformatics\/bty036","article-title":"Primer3_masker: integrating masking of template sequence with primer design software","volume":"34","author":"Koressaar","year":"2018","journal-title":"Bioinformatics"},{"issue":"14","key":"10.1016\/j.mam.2024.101269_bib125","doi-asserted-by":"crossref","first-page":"3607","DOI":"10.1016\/S0040-4020(98)00094-5","article-title":"LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition","volume":"54","author":"Koshkin","year":"1998","journal-title":"Tetrahedron"},{"issue":"5","key":"10.1016\/j.mam.2024.101269_bib126","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nmeth.2918","article-title":"Large-scale de novo DNA synthesis: technologies and applications","volume":"11","author":"Kosuri","year":"2014","journal-title":"Nat. Methods"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib127","doi-asserted-by":"crossref","first-page":"1560808","DOI":"10.1080\/20013078.2018.1560808","article-title":"TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images","volume":"8","author":"Kotrbov\u00e1","year":"2019","journal-title":"J. Extracell. Vesicles"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib128","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/bioinformatics\/btt703","article-title":"Causal analysis approaches in ingenuity pathway analysis","volume":"30","author":"Kramer","year":"2014","journal-title":"Bioinformatics"},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib129","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1093\/bjd\/ljad137","article-title":"Validation of a microRNA liquid biopsy assay for diagnosis and risk stratification of invasive cutaneous melanoma","volume":"189","author":"Van Laar","year":"2023","journal-title":"Br. J. Dermatol."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib130","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1080\/15476286.2018.1564465","article-title":"Balancing yield, purity and practicality: a modified differential ultracentrifugation protocol for efficient isolation of small extracellular vesicles from human serum","volume":"16","author":"Langevin","year":"2019","journal-title":"RNA Biol."},{"key":"10.1016\/j.mam.2024.101269_bib131","doi-asserted-by":"crossref","first-page":"26533","DOI":"10.3402\/jev.v4.26533","article-title":"Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium","volume":"4","author":"Laurent","year":"2015","journal-title":"J. Extracell. Vesicles"},{"key":"10.1016\/j.mam.2024.101269_bib132","doi-asserted-by":"crossref","first-page":"3141","DOI":"10.2147\/IJN.S303391","article-title":"Analysis of amount, size, protein Phenotype and molecular Content of circulating extracellular vesicles identifies new Biomarkers in multiple myeloma","volume":"16","author":"Laurenzana","year":"2021","journal-title":"Int. J. Nanomed."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib133","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.canlet.2012.10.040","article-title":"Analyzing the cancer methylome through targeted bisulfite sequencing","volume":"340","author":"Lee","year":"2013","journal-title":"Cancer Lett."},{"key":"10.1016\/j.mam.2024.101269_bib134","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1146\/annurev.pharmtox.41.1.347","article-title":"Use of biomarkers and surrogate endpoints in drug development and regulatory decision making: criteria, validation, strategies","volume":"41","author":"Lesko","year":"2001","journal-title":"Annu. Rev. Pharmacol. Toxicol."},{"issue":"14","key":"10.1016\/j.mam.2024.101269_bib135","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1093\/hmg\/ddg180","article-title":"A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly","volume":"12","author":"Lettice","year":"2003","journal-title":"Hum. Mol. Genet."},{"issue":"8","key":"10.1016\/j.mam.2024.101269_bib136","first-page":"1828","article-title":"The blood genome-wide DNA methylation analysis reveals novel epigenetic changes in human heart failure","volume":"21","author":"Li","year":"2017","journal-title":"Eur. Rev. Med. Pharmacol. Sci."},{"key":"10.1016\/j.mam.2024.101269_bib137","doi-asserted-by":"crossref","first-page":"6757","DOI":"10.2147\/CMAR.S169406","article-title":"MALAT1: a potential biomarker in cancer","volume":"10","author":"Li","year":"2018","journal-title":"Cancer Manag. Res."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib138","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s12943-022-01499-8","article-title":"A signature of saliva-derived exosomal small RNAs as predicting biomarker for esophageal carcinoma: a multicenter prospective study","volume":"21","author":"Li","year":"2022","journal-title":"Mol. Cancer"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib139","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1515\/chem-2022-0139","article-title":"Comparison of the yield and purity of plasma exosomes extracted by ultracentrifugation, precipitation, and membrane-based approaches","volume":"20","author":"Li","year":"2022","journal-title":"Open Chem."},{"issue":"6","key":"10.1016\/j.mam.2024.101269_bib140","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1039\/D2NA00959E","article-title":"The potential role of serum extracellular vesicle derived small RNAs in AML research as non-invasive biomarker","volume":"5","author":"Li","year":"2023","journal-title":"Nanoscale Adv."},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib141","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1038\/nmeth0709-474","article-title":"Limitations and possibilities of small RNA digital gene expression profiling","volume":"6","author":"Linsen","year":"2009","journal-title":"Nat. Methods"},{"issue":"5","key":"10.1016\/j.mam.2024.101269_bib142","doi-asserted-by":"crossref","first-page":"551","DOI":"10.2353\/jmoldx.2006.060021","article-title":"Effects of globin mRNA reduction methods on gene expression profiles from whole blood","volume":"8","author":"Liu","year":"2006","journal-title":"J. Mol. Diagn."},{"issue":"24","key":"10.1016\/j.mam.2024.101269_bib143","doi-asserted-by":"crossref","first-page":"7123","DOI":"10.1007\/s00216-022-04253-7","article-title":"Current status and outlook of advances in exosome isolation","volume":"414","author":"Liu","year":"2022","journal-title":"Anal. Bioanal. Chem."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib144","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib145","doi-asserted-by":"crossref","first-page":"26913","DOI":"10.3402\/jev.v3.26913","article-title":"Minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles","volume":"3","author":"L\u00f6tvall","year":"2014","journal-title":"J. Extracell. Vesicles"},{"key":"10.1016\/j.mam.2024.101269_bib146","doi-asserted-by":"crossref","first-page":"27031","DOI":"10.3402\/jev.v4.27031","article-title":"Optimized exosome isolation protocol for cell culture supernatant and human plasma","volume":"4","author":"Lobb","year":"2015","journal-title":"J. Extracell. Vesicles"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib147","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1093\/ckj\/sfs160","article-title":"The RIFLE and AKIN classifications for acute kidney injury: a critical and comprehensive review","volume":"6","author":"Lopes","year":"2013","journal-title":"Clin. Kidney J."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib148","doi-asserted-by":"crossref","DOI":"10.1186\/s12920-015-0109-x","article-title":"Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing","volume":"8","author":"Lopez","year":"2015","journal-title":"BMC Med. Genom."},{"issue":"12","key":"10.1016\/j.mam.2024.101269_bib149","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib150","article-title":"Alternative splicing in alzheimer's disease","volume":"2","author":"Love","year":"2015","journal-title":"J. Parkinson\u2019s Dis. Alzheimer's Dis."},{"issue":"6","key":"10.1016\/j.mam.2024.101269_bib151","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1002\/sam.11638","article-title":"Nonparametric clustering of RNA-sequencing data","volume":"16","author":"Lozano","year":"2023","journal-title":"Stat. Anal. Data Min.: The ASA Data Sci. J."},{"key":"10.1016\/j.mam.2024.101269_bib152","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.jconrel.2014.12.041","article-title":"Possibilities and limitations of current technologies for quantification of biological extracellular vesicles and synthetic mimics","volume":"200","author":"Maas","year":"2015","journal-title":"J. Contr. Release"},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib153","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1038\/nrcardio.2011.208","article-title":"Systems-based approaches to cardiovascular disease","volume":"9","author":"Maclellan","year":"2012","journal-title":"Nat. Rev. Cardiol."},{"issue":"7\u20138","key":"10.1016\/j.mam.2024.101269_bib154","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1159\/000478018","article-title":"Liquid biopsy: current status and future perspectives","volume":"40","author":"Mader","year":"2017","journal-title":"Oncol. Res. Treat."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib155","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41418-018-0246-9","article-title":"Mutant p53 as a guardian of the cancer cell","volume":"26","author":"Mantovani","year":"2019","journal-title":"Cell Death Differ."},{"key":"10.1016\/j.mam.2024.101269_bib156","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/978-1-4939-3652-6_11","article-title":"Protocols for exosome isolation and RNA profiling","author":"Marqu\u00e9s-Garc\u00eda","year":"2016","journal-title":"Methods Mol. Biol."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib157","doi-asserted-by":"crossref","first-page":"1286095","DOI":"10.1080\/20013078.2017.1286095","article-title":"Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper","volume":"6","author":"Mateescu","year":"2017","journal-title":"J. Extracell. Vesicles"},{"issue":"6472","key":"10.1016\/j.mam.2024.101269_bib158","doi-asserted-by":"crossref","DOI":"10.1126\/science.aav1741","article-title":"The biochemical basis of microRNA targeting efficacy","volume":"366","author":"McGeary","year":"2019","journal-title":"Science"},{"issue":"5287","key":"10.1016\/j.mam.2024.101269_bib159","doi-asserted-by":"crossref","first-page":"784028","DOI":"10.3389\/fimmu.2021.784028","article-title":"Extracellular vesicle associated miRNAs regulate signaling pathways involved in COVID-19 pneumonia and the progression to severe acute respiratory corona virus-2 syndrome","volume":"12","author":"Meidert","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.mam.2024.101269_bib160","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.cca.2019.01.011","article-title":"Ki-67 protein as a tumour proliferation marker","volume":"491","author":"Menon","year":"2019","journal-title":"Clin. Chim. Acta"},{"issue":"6","key":"10.1016\/j.mam.2024.101269_bib161","doi-asserted-by":"crossref","first-page":"R64","DOI":"10.1186\/gb-2009-10-6-r64","article-title":"A novel and universal method for microRNA RT-qPCR data normalization","volume":"10","author":"Mestdagh","year":"2009","journal-title":"Genome Biol."},{"issue":"12","key":"10.1016\/j.mam.2024.101269_bib162","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1007\/s00018-019-03071-y","article-title":"Extracellular vesicle isolation methods: rising impact of size-exclusion chromatography","volume":"76","author":"Mongui\u00f3-Tortajada","year":"2019","journal-title":"Cell. Mol. Life Sci."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib163","doi-asserted-by":"crossref","first-page":"1878","DOI":"10.1038\/s41598-017-01731-2","article-title":"Labeling extracellular vesicles for nanoscale flow cytometry","volume":"7","author":"Morales-Kastresana","year":"2017","journal-title":"Sci. Rep."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib164","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1534\/g3.118.200714","article-title":"Evolution of the highly repetitive PEVK region of titin across mammals","volume":"9","author":"Muenzen","year":"2019","journal-title":"G3 (Bethesda)"},{"key":"10.1016\/j.mam.2024.101269_bib165","doi-asserted-by":"crossref","first-page":"100089","DOI":"10.1016\/j.bdq.2019.100089","article-title":"Comparing small urinary extracellular vesicle purification methods with a view to RNA sequencing-Enabling robust and non-invasive biomarker research","volume":"17","author":"Mussack","year":"2019","journal-title":"Biomol. Detect Quantif"},{"key":"10.1016\/j.mam.2024.101269_bib166","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/978-1-4939-9833-3_3","article-title":"MIQE-compliant Validation of MicroRNA biomarker signatures Established by small RNA sequencing","author":"Mussack","year":"2020","journal-title":"Methods Mol. Biol."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib167","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1002\/ajh.26078","article-title":"On the trail of blood doping\u2014microRNA fingerprints to monitor autologous blood transfusions in vivo","volume":"96","author":"Mussack","year":"2021","journal-title":"Am. J. Hematol."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib168","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nrm.2017.125","article-title":"Shedding light on the cell biology of extracellular vesicles","volume":"19","author":"van Niel","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.mam.2024.101269_bib169","article-title":"Good practice guide for the application of quantitative PCR","author":"Nolan","year":"2013","journal-title":"LGC"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib170","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/j.nano.2015.01.003","article-title":"Ultrafiltration with size-exclusion liquid chromatography for high yield isolation of extracellular vesicles preserving intact biophysical and functional properties","volume":"11","author":"Nordin","year":"2015","journal-title":"Nanomedicine"},{"key":"10.1016\/j.mam.2024.101269_bib171","doi-asserted-by":"crossref","DOI":"10.3389\/fendo.2018.00402","article-title":"Overview of MicroRNA biogenesis, Mechanisms of actions, and circulation","volume":"9","author":"O'Brien","year":"2018","journal-title":"Front. Endocrinol."},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib172","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1517\/14656566.1.7.1399","article-title":"Prostate-specific antigen","volume":"1","author":"Ornstein","year":"2000","journal-title":"Expet Opin. Pharmacother."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib173","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/(SICI)1097-0282(1997)44:3<217::AID-BIP3>3.0.CO;2-Y","article-title":"Predicting sequence-dependent melting stability of short duplex DNA oligomers","volume":"44","author":"Owczarzy","year":"1997","journal-title":"Biopolymers"},{"issue":"12","key":"10.1016\/j.mam.2024.101269_bib174","doi-asserted-by":"crossref","first-page":"3537","DOI":"10.1021\/bi034621r","article-title":"Effects of sodium ions on DNA duplex Oligomers: improved predictions of melting temperatures","volume":"43","author":"Owczarzy","year":"2004","journal-title":"Biochemistry"},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib175","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41580-020-0251-y","article-title":"RNA delivery by extracellular vesicles in mammalian cells and its applications","volume":"21","author":"O Brien","year":"2020","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib176","article-title":"Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels","volume":"20","author":"O Grady","year":"2022","journal-title":"BMC Biol."},{"key":"10.1016\/j.mam.2024.101269_bib177","doi-asserted-by":"crossref","first-page":"108010","DOI":"10.1016\/j.diabres.2020.108010","article-title":"The profiles of microRNAs from urinary extracellular vesicles (EVs) prepared by various isolation methods and their correlation with serum EV microRNAs","volume":"160","author":"Park","year":"2020","journal-title":"Diabetes Res. Clin. Pract."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib178","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1158\/1535-7163.MCT-14-0983","article-title":"PD-L1 Expression as a predictive Biomarker in cancer immunotherapy","volume":"14","author":"Patel","year":"2015","journal-title":"Mol. Cancer Therapeut."},{"issue":"18","key":"10.1016\/j.mam.2024.101269_bib179","doi-asserted-by":"crossref","first-page":"10639","DOI":"10.3390\/ijms231810639","article-title":"Salivary Exosomal miRNA-1307-5p predicts disease Aggressiveness and poor Prognosis in oral squamous cell carcinoma patients","volume":"23","author":"Patel","year":"2022","journal-title":"Int. J. Mol. Sci."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib180","doi-asserted-by":"crossref","first-page":"373","DOI":"10.3233\/CBM-201651","article-title":"Isolation of extracellular vesicle with different precipitation-based methods exerts a tremendous impact on the biomarker analysis for clinical plasma samples","volume":"29","author":"Peng","year":"2020","journal-title":"Cancer Biomarkers"},{"issue":"9","key":"10.1016\/j.mam.2024.101269_bib181","doi-asserted-by":"crossref","first-page":"e45","DOI":"10.1093\/nar\/29.9.e45","article-title":"A new mathematical model for relative quantification in real-time RT-PCR","volume":"29","author":"Pfaffl","year":"2001","journal-title":"Nucleic Acids Res."},{"issue":"D1","key":"10.1016\/j.mam.2024.101269_bib182","first-page":"D845","article-title":"The DisGeNET knowledge platform for disease genomics: 2019 update","volume":"48","author":"Pinero","year":"2020","journal-title":"Nucleic Acids Res."},{"issue":"12","key":"10.1016\/j.mam.2024.101269_bib183","doi-asserted-by":"crossref","first-page":"4476","DOI":"10.3390\/ijms21124476","article-title":"Changes in DNA Methylation and gene Expression of Insulin and obesity-related gene PIK3R1 after roux-en-Y gastric bypass","volume":"21","author":"Pinhel","year":"2020","journal-title":"Int. J. Mol. Sci."},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib184","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1111\/jth.12602","article-title":"Particle size distribution of exosomes and microvesicles determined by transmission electron microscopy, flow cytometry, nanoparticle tracking analysis, and resistive pulse sensing","volume":"12","author":"van der Pol","year":"2014","journal-title":"J. Thromb. Haemostasis"},{"issue":"6","key":"10.1016\/j.mam.2024.101269_bib185","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1159\/000499337","article-title":"Liquid biopsy: general concepts","volume":"63","author":"Poulet","year":"2019","journal-title":"Acta Cytol."},{"issue":"5","key":"10.1016\/j.mam.2024.101269_bib186","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0196913","article-title":"Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens","volume":"13","author":"Prendergast","year":"2018","journal-title":"PLoS One"},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib187","doi-asserted-by":"crossref","first-page":"4134","DOI":"10.1007\/s12035-020-02011-3","article-title":"Variability in cerebrospinal fluid MicroRNAs through life","volume":"57","author":"Prieto-Fern\u00e1ndez","year":"2020","journal-title":"Mol. Neurobiol."},{"key":"10.1016\/j.mam.2024.101269_bib188","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.ejca.2020.12.023","article-title":"Clinical practice guidelines for BRCA1 and BRCA2 genetic testing","volume":"146","author":"Pujol","year":"2021","journal-title":"Eur. J. Cancer"},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib189","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1093\/nar\/gkt1021","article-title":"Biases in small RNA deep sequencing data","volume":"42","author":"Raabe","year":"2014","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib190","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1016\/j.bbrc.2003.11.177","article-title":"Guideline to reference gene selection for quantitative real-time PCR","volume":"313","author":"Radonic","year":"2004","journal-title":"Biochem. Biophys. Res. Commun."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib191","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1164\/rccm.201304-0801ED","article-title":"Early recognition and treatment of severe sepsis","volume":"188","author":"Ramar","year":"2013","journal-title":"Am. J. Respir. Crit. Care Med."},{"issue":"11","key":"10.1016\/j.mam.2024.101269_bib192","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1261\/rna.2148705","article-title":"Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs","volume":"11","author":"Raymond","year":"2005","journal-title":"RNA"},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib193","doi-asserted-by":"crossref","first-page":"2403","DOI":"10.1111\/jcmm.13162","article-title":"Cellular and extracellular miRNAs are blood-compartment-specific diagnostic targets in sepsis","volume":"21","author":"Reithmair","year":"2017","journal-title":"J. Cell Mol. Med."},{"key":"10.1016\/j.mam.2024.101269_bib194","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/978-1-0716-2341-1_9","article-title":"Isolation and characterization of urinary extracellular vesicles for MicroRNA biomarker signature development with reference to MISEV compliance","author":"Reithmair","year":"2022","journal-title":"Methods Mol. Biol."},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib195","doi-asserted-by":"crossref","first-page":"7727","DOI":"10.18632\/oncotarget.3115","article-title":"TP53 intron 1 hotspot rearrangements are specific to sporadic osteosarcoma and can cause Li-Fraumeni syndrome","volume":"6","author":"Ribi","year":"2015","journal-title":"Oncotarget"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib196","doi-asserted-by":"crossref","first-page":"1555419","DOI":"10.1080\/20013078.2018.1555419","article-title":"Quality of extracellular vesicle images by transmission electron microscopy is operator and protocol dependent","volume":"8","author":"Rikkert","year":"2019","journal-title":"J. Extracell. Vesicles"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib197","doi-asserted-by":"crossref","first-page":"24067","DOI":"10.1038\/srep24067","article-title":"Comparison of DNA quantification Methods for next generation sequencing","volume":"6","author":"Robin","year":"2016","journal-title":"Sci. Rep."},{"issue":"6","key":"10.1016\/j.mam.2024.101269_bib198","doi-asserted-by":"crossref","first-page":"101182","DOI":"10.1016\/j.isci.2020.101182","article-title":"Profiling extracellular long RNA transcriptome in human plasma and extracellular vesicles for biomarker discovery","volume":"23","author":"Rodosthenous","year":"2020","journal-title":"iScience"},{"key":"10.1016\/j.mam.2024.101269_bib199","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/978-1-4939-2365-6_3","article-title":"Design of primers and probes for quantitative real-time PCR methods","author":"Rodr\u00edguez","year":"2015","journal-title":"Methods Mol. Biol."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib200","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1373\/clinchem.2017.278978","article-title":"Comparison of generic fluorescent markers for detection of extracellular vesicles by flow cytometry","volume":"64","author":"de Rond","year":"2018","journal-title":"Clin. Chem."},{"issue":"9","key":"10.1016\/j.mam.2024.101269_bib201","doi-asserted-by":"crossref","DOI":"10.3390\/cells9091955","article-title":"Methods for separation and characterization of extracellular vesicles: results of a worldwide survey performed by the ISEV rigor and standardization subcommittee","volume":"9","author":"Royo","year":"2020","journal-title":"Cells"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib202","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1073\/pnas.95.4.1460","article-title":"A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor\u2009thermodynamics","volume":"95","author":"Santalucia","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib203","doi-asserted-by":"crossref","first-page":"e43","DOI":"10.1093\/nar\/gnh040","article-title":"A high-throughput method to monitor the expression of microRNA precursors","volume":"32","author":"Schmittgen","year":"2004","journal-title":"Nucleic Acids Res."},{"issue":"7347","key":"10.1016\/j.mam.2024.101269_bib204","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature10098","article-title":"Global quantification of mammalian gene expression control","volume":"473","author":"Schwanh\u00e4usser","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.mam.2024.101269_bib205","doi-asserted-by":"crossref","first-page":"100728","DOI":"10.1016\/j.drup.2020.100728","article-title":"The role of alternative splicing in cancer: from oncogenesis to drug resistance","volume":"53","author":"Sciarrillo","year":"2020","journal-title":"Drug Resist. Updates"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib206","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.jmoldx.2019.08.006","article-title":"Using R and Bioconductor in clinical Genomics and transcriptomics","volume":"22","author":"Sepulveda","year":"2020","journal-title":"J. Mol. Diagn."},{"issue":"8","key":"10.1016\/j.mam.2024.101269_bib207","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1001\/jama.2016.0288","article-title":"Assessment of clinical criteria for sepsis: for the third international consensus definitions for sepsis and septic shock (Sepsis-3)","volume":"315","author":"Seymour","year":"2016","journal-title":"JAMA"},{"issue":"7\u20138","key":"10.1016\/j.mam.2024.101269_bib208","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1177\/1947601912460547","article-title":"KRAS testing: a Tool for the Implementation of personalized medicine","volume":"3","author":"Shackelford","year":"2012","journal-title":"Genes Cancer"},{"issue":"8","key":"10.1016\/j.mam.2024.101269_bib209","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1001\/jama.2016.0289","article-title":"Developing a new definition and assessing new clinical criteria for septic shock: for the third international consensus definitions for sepsis and septic shock (Sepsis-3)","volume":"315","author":"Shankar-Hari","year":"2016","journal-title":"JAMA"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib210","doi-asserted-by":"crossref","first-page":"519","DOI":"10.2144\/000112010","article-title":"Facile means for quantifying microRNA expression by real-time PCR","volume":"39","author":"Shi","year":"2005","journal-title":"Biotechniques"},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib211","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0091041","article-title":"Variation in RNA-seq transcriptome Profiles of peripheral whole Blood from healthy Individuals with and without globin depletion","volume":"9","author":"Shin","year":"2014","journal-title":"PLoS One"},{"issue":"18","key":"10.1016\/j.mam.2024.101269_bib212","doi-asserted-by":"crossref","DOI":"10.3390\/ijms21186466","article-title":"A Review of exosomal isolation methods: is size exclusion Chromatography the best option?","volume":"21","author":"Sidhom","year":"2020","journal-title":"Int. J. Mol. Sci."},{"issue":"6","key":"10.1016\/j.mam.2024.101269_bib213","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1111\/his.14877","article-title":"Digital image analysis and assisted reading of the HER2 score display reduced concordance: pitfalls in the categorisation of HER2-low breast cancer","volume":"82","author":"Sode","year":"2023","journal-title":"Histopathology"},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib214","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/ng1955","article-title":"Common genetic variants account for differences in gene expression among ethnic groups","volume":"39","author":"Spielman","year":"2007","journal-title":"Nat. Genet."},{"issue":"9","key":"10.1016\/j.mam.2024.101269_bib215","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0107259","article-title":"Optimization of extraction of circulating RNAs from plasma \u2013 enabling small RNA sequencing","volume":"9","author":"Spornraft","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.mam.2024.101269_bib216","doi-asserted-by":"crossref","first-page":"122604","DOI":"10.1016\/j.jchromb.2021.122604","article-title":"Isolation of extracellular vesicles with combined enrichment methods","volume":"1169","author":"Stam","year":"2021","journal-title":"J. Chromatogr., B: Anal. Technol. Biomed. Life Sci."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib217","first-page":"357","article-title":"Identification of splice variants and isoforms in transcriptomics and proteomics. Annual review of biomedical data science","volume":"6","author":"Su","year":"2023"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib218","doi-asserted-by":"crossref","DOI":"10.1186\/s12864-015-2044-9","article-title":"MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection","volume":"16","author":"Sun","year":"2015","journal-title":"BMC Genom."},{"issue":"9","key":"10.1016\/j.mam.2024.101269_bib219","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1007\/s00535-023-02024-4","article-title":"Current status of molecular diagnostic approaches using liquid biopsy","volume":"58","author":"Takahashi","year":"2023","journal-title":"J. Gastroenterol."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib220","doi-asserted-by":"crossref","first-page":"834","DOI":"10.3892\/ijmm.2017.3080","article-title":"Comparison of isolation methods of exosomes and exosomal RNA from cell culture medium and serum","volume":"40","author":"Tang","year":"2017","journal-title":"Int. J. Mol. Med."},{"key":"10.1016\/j.mam.2024.101269_bib221","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.70725","article-title":"Framework for rapid comparison of extracellular vesicle isolation methods","volume":"10","author":"Ter-Ovanesyan","year":"2021","journal-title":"Elife"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib222","doi-asserted-by":"crossref","first-page":"12295","DOI":"10.1038\/s41598-019-48181-6","article-title":"Improved methods for fluorescent labeling and detection of single extracellular vesicles using nanoparticle tracking analysis","volume":"9","author":"Thane","year":"2019","journal-title":"Sci. Rep."},{"issue":"W1","key":"10.1016\/j.mam.2024.101269_bib223","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","year":"2022","journal-title":"Nucleic Acids Res."},{"issue":"7793","key":"10.1016\/j.mam.2024.101269_bib224","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/s41586-020-1969-6","article-title":"Pan-cancer analysis of whole genomes","volume":"578","year":"2020","journal-title":"Nature"},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib225","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1158\/1078-0432.CCR-17-2664","article-title":"Clinical significance of PD-l1+ exosomes in plasma of head and neck cancer patients","volume":"24","author":"Theodoraki","year":"2018","journal-title":"Clin. Cancer Res."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib226","doi-asserted-by":"crossref","first-page":"1535750","DOI":"10.1080\/20013078.2018.1535750","article-title":"Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines","volume":"7","author":"Thery","year":"2018","journal-title":"J. Extracell. Vesicles"},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib227","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1002\/bmb.20461","article-title":"Real-time PCR (qPCR) primer design using free online software","volume":"39","author":"Thornton","year":"2011","journal-title":"Biochem. Mol. Biol. Educ."},{"key":"10.1016\/j.mam.2024.101269_bib228","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1007\/978-1-4939-2365-6_13","article-title":"Rapid and simple method of qPCR primer design","author":"Thornton","year":"2015","journal-title":"Methods Mol. Biol."},{"issue":"11","key":"10.1016\/j.mam.2024.101269_bib229","doi-asserted-by":"crossref","DOI":"10.1002\/jev2.12140","article-title":"Formation of a protein corona on the surface of extracellular vesicles in blood plasma","volume":"10","author":"T\u00f3th","year":"2021","journal-title":"J. Extracell. Vesicles"},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib230","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1056\/NEJM197102182840703","article-title":"Hemoglobin components in patients with diabetes mellitus","volume":"284","author":"Trivelli","year":"1971","journal-title":"N. Engl. J. Med."},{"issue":"6220","key":"10.1016\/j.mam.2024.101269_bib231","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Proteomics. Tissue-based map of the human proteome","volume":"347","author":"Uhlen","year":"2015","journal-title":"Science"},{"issue":"15","key":"10.1016\/j.mam.2024.101269_bib232","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1093\/nar\/gks596","article-title":"Primer3\u2013new capabilities and interfaces","volume":"40","author":"Untergasser","year":"2012","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib233","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1101\/gr.266551.120","article-title":"Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA","volume":"31","author":"Vaisvila","year":"2021","journal-title":"Genome Res."},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib234","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2002-3-7-research0034","article-title":"Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes","volume":"3","author":"Vandesompele","year":"2002","journal-title":"Genome Biol."},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib235","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1007\/BF01709751","article-title":"The SOFA (Sepsis-related organ failure assessment) score to describe organ dysfunction\/failure. On behalf of the working Group on sepsis-related Problems of the European Society of intensive care medicine","volume":"22","author":"Vincent","year":"1996","journal-title":"Intensive Care Med."},{"key":"10.1016\/j.mam.2024.101269_bib236","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.semcancer.2022.12.008","article-title":"Status quo of Extracellular Vesicle isolation and detection methods for clinical utility","volume":"88","author":"Visan","year":"2023","journal-title":"Semin. Cancer Biol."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib237","first-page":"266","article-title":"Analysis of one-step and two-step real-time RT-PCR using SuperScript III","volume":"16","author":"Wacker","year":"2005","journal-title":"J. Biomol. Tech."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib238","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-73350-3","article-title":"Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples","volume":"10","author":"Wagner","year":"2020","journal-title":"Sci. Rep."},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib239","article-title":"Integrated analysis of DNA methylation profiling and gene expression profiling identifies novel markers in lung cancer in Xuanwei, China","volume":"13","author":"Wang","year":"2018","journal-title":"PLoS One"},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib240","doi-asserted-by":"crossref","DOI":"10.1002\/jev2.12404","article-title":"Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches","volume":"13","author":"Welsh","year":"2024","journal-title":"J. Extracell. Vesicles"},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib241","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1177\/193229680900300306","article-title":"A review of the challenge in measuring hemoglobin A1c","volume":"3","author":"Weykamp","year":"2009","journal-title":"J. Diabetes Sci. Technol."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib242","doi-asserted-by":"crossref","DOI":"10.1002\/jev2.12207","article-title":"A functional corona around extracellular vesicles enhances angiogenesis, skin regeneration and immunomodulation","volume":"11","author":"Wolf","year":"2022","journal-title":"J. Extracell. Vesicles"},{"issue":"8","key":"10.1016\/j.mam.2024.101269_bib243","doi-asserted-by":"crossref","first-page":"2512","DOI":"10.1158\/1078-0432.CCR-05-2572","article-title":"Reduced plasma RNA integrity in nasopharyngeal carcinoma patients","volume":"12","author":"Wong","year":"2006","journal-title":"Clin. Cancer Res."},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib244","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1007\/s11306-012-0482-9","article-title":"Translational biomarker discovery in clinical metabolomics: an introductory tutorial","volume":"9","author":"Xia","year":"2013","journal-title":"Metabolomics"},{"issue":"2","key":"10.1016\/j.mam.2024.101269_bib245","first-page":"115","article-title":"Principles and problems of exosome isolation from biological fluids","volume":"16","author":"Yakubovich","year":"2022","journal-title":"Biochem. (Mosc) Suppl. Ser. A Membr. Cell Biol."},{"key":"10.1016\/j.mam.2024.101269_bib246","doi-asserted-by":"crossref","first-page":"27066","DOI":"10.3402\/jev.v4.27066","article-title":"Biological properties of extracellular vesicles and their physiological functions","volume":"4","author":"Yanez-Mo","year":"2015","journal-title":"J. Extracell. Vesicles"},{"issue":"8","key":"10.1016\/j.mam.2024.101269_bib247","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.7150\/thno.41580","article-title":"Progress, opportunity, and perspective on exosome isolation - efforts for efficient exosome-based theranostics","volume":"10","author":"Yang","year":"2020","journal-title":"Theranostics"},{"issue":"12","key":"10.1016\/j.mam.2024.101269_bib248","doi-asserted-by":"crossref","DOI":"10.1002\/adbi.202000203","article-title":"Bead-based extracellular vesicle analysis using flow cytometry","volume":"4","author":"Yang","year":"2020","journal-title":"Adv. Biosyst."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib249","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1186\/1471-2105-13-134","article-title":"Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction","volume":"13","author":"Ye","year":"2012","journal-title":"BMC Bioinf."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib250","article-title":"Co-isolation of extracellular vesicles and high-density lipoproteins using density gradient ultracentrifugation","author":"Yuana","year":"2014","journal-title":"J. Extracell. Vesicles"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib251","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-69799-x","article-title":"Expression profiling of human milk derived exosomal microRNAs and their targets in HIV-1 infected mothers","volume":"10","author":"Zahoor","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.mam.2024.101269_bib252","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/1471-2407-13-206","article-title":"Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection","volume":"13","author":"Zapparoli","year":"2013","journal-title":"BMC Cancer"},{"key":"10.1016\/j.mam.2024.101269_bib253","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.ymeth.2015.05.028","article-title":"Integrated isolation and quantitative analysis of exosome shuttled proteins and nucleic acids using immunocapture approaches","volume":"87","author":"Zarovni","year":"2015","journal-title":"Methods"},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib254","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-022-02664-4","article-title":"Predicting RNA splicing from DNA sequence using Pangolin","volume":"23","author":"Zeng","year":"2022","journal-title":"Genome Biol."},{"issue":"4","key":"10.1016\/j.mam.2024.101269_bib255","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1101\/pdb.top074476","article-title":"Strategies for isolation of exosomes","volume":"2015","author":"Zeringer","year":"2015","journal-title":"Cold Spring Harb. Protoc."},{"issue":"1","key":"10.1016\/j.mam.2024.101269_bib256","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1186\/s12859-019-3028-6","article-title":"Influence of batch effect correction methods on drug induced differential gene expression profiles","volume":"20","author":"Zhou","year":"2019","journal-title":"BMC Bioinf."},{"issue":"10229","key":"10.1016\/j.mam.2024.101269_bib257","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1016\/S0140-6736(20)30566-3","article-title":"Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study","volume":"395","author":"Zhou","year":"2020","journal-title":"Lancet"},{"issue":"10","key":"10.1016\/j.mam.2024.101269_bib258","doi-asserted-by":"crossref","first-page":"4901","DOI":"10.1021\/acs.jproteome.1c00549","article-title":"Column-based technology for CD9-HPLC immunoaffinity isolation of serum extracellular vesicles","volume":"20","author":"Zhu","year":"2021","journal-title":"J. Proteome Res."},{"issue":"7","key":"10.1016\/j.mam.2024.101269_bib259","doi-asserted-by":"crossref","first-page":"e54","DOI":"10.1093\/nar\/gkr1263","article-title":"Structural bias in T4 RNA ligase-mediated 3'-adapter ligation","volume":"40","author":"Zhuang","year":"2012","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.mam.2024.101269_bib260","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1369\/0022155414564219","article-title":"Human saliva-derived exosomes","volume":"63","author":"Zlotogorski-Hurvitz","year":"2015","journal-title":"J. Histochem. Cytochem."}],"container-title":["Molecular Aspects of Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0098299724000281?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0098299724000281?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,5,25]],"date-time":"2024-05-25T01:05:11Z","timestamp":1716599111000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0098299724000281"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6]]},"references-count":260,"alternative-id":["S0098299724000281"],"URL":"https:\/\/doi.org\/10.1016\/j.mam.2024.101269","relation":{},"ISSN":["0098-2997"],"issn-type":[{"value":"0098-2997","type":"print"}],"subject":[],"published":{"date-parts":[[2024,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics","name":"articletitle","label":"Article Title"},{"value":"Molecular Aspects of Medicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mam.2024.101269","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Authors. Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"101269"}}