{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T13:07:11Z","timestamp":1762607231574,"version":"3.37.3"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,6,27]],"date-time":"2018-06-27T00:00:00Z","timestamp":1530057600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ruth L. Kirschstein National Research Service Award"},{"DOI":"10.13039\/100009429","name":"NRSA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009429","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Institutional Predoctoral Fellowship","award":["T32GM081739"],"award-info":[{"award-number":["T32GM081739"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Director\u2019s Innovator Award","award":["DP2NS083372"],"award-info":[{"award-number":["DP2NS083372"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["RF1AG056296"],"award-info":[{"award-number":["RF1AG056296"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Missouri Spinal Cord Injury"},{"name":"Disease Research Program"},{"name":"SCIDRP"},{"DOI":"10.13039\/100007625","name":"Cure Alzheimer\u2019s Fund","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100007625","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Presidential Early Career Award for Scientists and Engineers","award":["NSF-1566292","NSF-1564894"],"award-info":[{"award-number":["NSF-1566292","NSF-1564894"]}]},{"name":"Saint Louis University President's Research Fund 2018"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Reprogramming somatic cells into neurons holds great promise to model neuronal development and disease. The efficiency and success rate of neuronal reprogramming, however, may vary between different conversion platforms and cell types, thereby necessitating an unbiased, systematic approach to estimate neuronal identity of converted cells. Recent studies have demonstrated that long genes (&amp;gt;100\u2009kb from transcription start to end) are highly enriched in neurons, which provides an opportunity to identify neurons based on the expression of these long genes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a versatile R package, LONGO, to analyze gene expression based on gene length. We propose a systematic analysis of long gene expression (LGE) with a metric termed the long gene quotient (LQ) that quantifies LGE in RNA-seq or microarray data to validate neuronal identity at the single-cell and population levels. This unique feature of neurons provides an opportunity to utilize measurements of LGE in transcriptome data to quickly and easily distinguish neurons from non-neuronal cells. By combining this conceptual advancement and statistical tool in a user-friendly and interactive software package, we intend to encourage and simplify further investigation into LGE, particularly as it applies to validating and improving neuronal differentiation and reprogramming methodologies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>LONGO is freely available for download at https:\/\/github.com\/biohpc\/longo.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty243","type":"journal-article","created":{"date-parts":[[2018,4,12]],"date-time":"2018-04-12T19:32:51Z","timestamp":1523561571000},"page":"i422-i428","source":"Crossref","is-referenced-by-count":25,"title":["LONGO: an R package for interactive gene length dependent analysis for neuronal identity"],"prefix":"10.1093","volume":"34","author":[{"given":"Matthew J","family":"McCoy","sequence":"first","affiliation":[{"name":"Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, USA"}]},{"given":"Alexander J","family":"Paul","sequence":"additional","affiliation":[{"name":"Program in Bioinformatics & Computational Biology, Saint Louis University, Saint Louis, MO, USA"}]},{"given":"Matheus B","family":"Victor","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, USA"}]},{"given":"Michelle","family":"Richner","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, USA"},{"name":"Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA"}]},{"given":"Harrison W","family":"Gabel","sequence":"additional","affiliation":[{"name":"Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA"}]},{"given":"Haijun","family":"Gong","sequence":"additional","affiliation":[{"name":"Department of Mathematics & Statistics, Saint Louis University, Saint Louis, MO, USA"}]},{"given":"Andrew S","family":"Yoo","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, USA"}]},{"given":"Tae-Hyuk","family":"Ahn","sequence":"additional","affiliation":[{"name":"Program in Bioinformatics & Computational Biology, Saint Louis University, Saint Louis, MO, USA"},{"name":"Department of Computer Science, Saint Louis University, Saint Louis, MO, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,6,27]]},"reference":[{"key":"2023051604341254600_bty243-B1","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.stem.2017.08.002","article-title":"MicroRNAs induce a permissive chromatin environment that enables neuronal subtype-specific reprogramming of adult human fibroblasts","volume":"21","author":"Abernathy","year":"2017","journal-title":"Cell Stem Cell"},{"key":"2023051604341254600_bty243-B2","first-page":"1600","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume-title":"Bioinformatics","author":"Alexa","year":"2006"},{"key":"2023051604341254600_bty243-B3","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1126\/science.1230612","article-title":"The evolutionary landscape of alternative splicing in vertebrate species","volume":"338","author":"Barbosa-Morais","year":"2012","journal-title":"Science"},{"key":"2023051604341254600_bty243-B4","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/j.stem.2015.09.002","article-title":"Rapid conversion of fibroblasts into functional forebrain GABAergic interneurons by direct genetic reprogramming","volume":"17","author":"Colasante","year":"2015","journal-title":"Cell Stem Cell"},{"key":"2023051604341254600_bty243-B5","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/nprot.2009.97","article-title":"Mapping identifiers for the integration of genomic datasets with the R\/Bioconductor package biomaRt","volume":"4","author":"Durinck","year":"2009","journal-title":"Nat. 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