{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,3]],"date-time":"2026-05-03T05:14:55Z","timestamp":1777785295036,"version":"3.51.4"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2016,1]]},"DOI":"10.1186\/s12864-015-2295-5","type":"journal-article","created":{"date-parts":[[2016,1,11]],"date-time":"2016-01-11T10:02:21Z","timestamp":1452506541000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes"],"prefix":"10.1186","volume":"17","author":[{"given":"Naoki","family":"Nariai","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaname","family":"Kojima","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takahiro","family":"Mimori","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yosuke","family":"Kawai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masao","family":"Nagasaki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,1,11]]},"reference":[{"key":"2295_CR1","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/190372a0","volume":"190","author":"MF Lyon","year":"1961","unstructured":"Lyon MF. Gene action in the X-chromosome of the mouse (Mus musculus L). Nature. 1961; 190:372\u20133.","journal-title":"Nature"},{"key":"2295_CR2","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.tig.2004.01.001","volume":"20","author":"JC Knight","year":"2004","unstructured":"Knight JC. Allele-specific gene expression uncovered. Trends Genet. 2004; 20:113\u20136.","journal-title":"Trends Genet"},{"key":"2295_CR3","doi-asserted-by":"crossref","first-page":"R255","DOI":"10.1093\/hmg\/ddh227","volume":"13","author":"PR Buckland","year":"2004","unstructured":"Buckland PR. Allele-specific gene expression differences in humans. Hum Mol Genet. 2004; 13:R255\u201360. Spec No 2.","journal-title":"Hum Mol Genet"},{"key":"2295_CR4","doi-asserted-by":"crossref","first-page":"3345","DOI":"10.1038\/onc.2009.194","volume":"28","author":"Chapelle de la","year":"2009","unstructured":"de la Chapelle A. Genetic predisposition to human disease: allele-specific expression and low-penetrance regulatory loci. Oncogene. 2009; 28:3345\u20138.","journal-title":"Oncogene"},{"key":"2295_CR5","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/nature01434","volume":"422","author":"EE Schadt","year":"2003","unstructured":"Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, et al. Genetics of gene expression surveyed in maize, mouse and man. Nature. 2003; 422:297\u2013302.","journal-title":"Nature"},{"key":"2295_CR6","doi-asserted-by":"crossref","first-page":"6175","DOI":"10.1126\/science.1246949","volume":"343","author":"BP Fairfax","year":"2014","unstructured":"Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, et al. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science. 2014; 343:6175.","journal-title":"Science"},{"key":"2295_CR7","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","volume":"5","author":"A Mortazavi","year":"2008","unstructured":"Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008; 5:621\u20138.","journal-title":"Nat Methods"},{"key":"2295_CR8","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/bioinformatics\/btp692","volume":"26","author":"B Li","year":"2010","unstructured":"Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 2010; 26:493\u2013500.","journal-title":"Bioinformatics"},{"key":"2295_CR9","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1093\/bioinformatics\/bts260","volume":"28","author":"P Glaus","year":"2012","unstructured":"Glaus P, Honkela A, Rattray M. Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics. 2012; 28:1721\u201328.","journal-title":"Bioinformatics"},{"key":"2295_CR10","doi-asserted-by":"crossref","first-page":"2292","DOI":"10.1093\/bioinformatics\/btt381","volume":"29","author":"N Nariai","year":"2013","unstructured":"Nariai N, Hirose O, Kojima K, Nagasaki M. TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. Bioinformatics. 2013; 29:2292\u20139.","journal-title":"Bioinformatics"},{"key":"2295_CR11","doi-asserted-by":"crossref","first-page":"3207","DOI":"10.1093\/bioinformatics\/btp579","volume":"25","author":"JF Degner","year":"2009","unstructured":"Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009; 25:3207\u201312.","journal-title":"Bioinformatics"},{"key":"2295_CR12","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1101\/gr.119784.110","volume":"10","author":"DA Skelly","year":"2011","unstructured":"Skelly DA, Johansson M, Madeoy J, Wakefield J, Akey JM. A flexible Bayesian method for detecting allelic imbalance in RNA-seq data. Genome Res. 2011; 10:1728\u201337.","journal-title":"Genome Res"},{"key":"2295_CR13","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1186\/1471-2164-15-920","volume":"15","author":"LG Le\u00f3n-Novelo","year":"2014","unstructured":"Le\u00f3n-Novelo LG, McIntyre LM, Fear JM, Graze RM. A flexible Bayesian method for detecting allelic imbalance in RNA-seq data. BMC Genomics. 2014; 15:920.","journal-title":"BMC Genomics"},{"key":"2295_CR14","doi-asserted-by":"crossref","first-page":"e127","DOI":"10.1093\/nar\/gks425","volume":"40","author":"RV Satya","year":"2012","unstructured":"Satya RV, Zavaljevski N, Reifman J. A new strategy to reduce allelic bias in RNA-Seq readmapping. Nucleic Acids Res. 2012; 40:e127.","journal-title":"Nucleic Acids Res"},{"key":"2295_CR15","doi-asserted-by":"crossref","unstructured":"van de Geijn B, McVicker G, Gilad Y, Pritchard JK. WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods. 2015; 12(11):1061\u20133. doi: dx.doi.org\/10.1038\/nmeth.3582 . Epub 2015 Sep 14.","DOI":"10.1038\/nmeth.3582"},{"key":"2295_CR16","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/msb.2011.54","volume":"7","author":"J Rozowsky","year":"2011","unstructured":"Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, et al. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011; 7:522.","journal-title":"Mol Syst Biol"},{"key":"2295_CR17","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1101\/gr.161034.113","volume":"24","author":"GK Marinov","year":"2014","unstructured":"Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, et al. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res. 2014; 24:496\u2013510.","journal-title":"Genome Res"},{"key":"2295_CR18","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btp113","volume":"25","author":"H Jiang","year":"2009","unstructured":"Jiang H, Wong WH. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics. 2009; 25:1026\u201332.","journal-title":"Bioinformatics"},{"key":"2295_CR19","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9:357\u20139.","journal-title":"Nat Methods"},{"key":"2295_CR20","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1101\/gr.8.3.175","volume":"8","author":"B Ewing","year":"1998","unstructured":"Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998; 8:175\u201385.","journal-title":"Genome Res"},{"key":"2295_CR21","volume-title":"Proceedings of the Fifteenth conference on Uncertainty in artificial intelligence","author":"H Attias","year":"1999","unstructured":"Attias H. Inferring parameters and structure of latent variable models by variational bayes. In: Proceedings of the Fifteenth conference on Uncertainty in artificial intelligence. San Francisco, CA, USA: Morgan Kaufmann Publishers Inc.: 1999. p. 21\u201330. http:\/\/dl.acm.org\/citation.cfm?id=2073799 ."},{"key":"2295_CR22","volume-title":"Pattern Recognition and Machine Learning","author":"CM Bishop","year":"2006","unstructured":"Bishop CM. Pattern Recognition and Machine Learning. New York, NY, USA: Springer Science + Business Media, LLC; 2006."},{"issue":"(Suppl 10","key":"2295_CR23","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/1471-2164-15-S10-S5","volume":"15","author":"N Nariai","year":"2014","unstructured":"Nariai N, Kojima K, Mimori T, Sato Y, Kawai Y, Yamaguchi-Kabata Y, et al. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads. BMC Genomics. 2014; 15((Suppl 10)):S5.","journal-title":"BMC Genomics"},{"key":"2295_CR24","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12:323.","journal-title":"BMC Bioinformatics"},{"key":"2295_CR25","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C Trapnell","year":"2010","unstructured":"Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28:511\u20135.","journal-title":"Nat Biotechnol"},{"key":"2295_CR26","doi-asserted-by":"crossref","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","volume":"4","author":"BT Sherman","year":"2003","unstructured":"Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, et al. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol. 2003; 4:P3.","journal-title":"Genome Biol"},{"issue":"1","key":"2295_CR27","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","volume":"31","author":"B Boeckmann","year":"2003","unstructured":"Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003; 31(1):365\u201370.","journal-title":"Nucleic Acids Res"},{"key":"2295_CR28","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000; 25:25\u20139.","journal-title":"Nat Genet"},{"key":"2295_CR29","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1126\/science.1184655","volume":"328","author":"R McDaniell","year":"2010","unstructured":"McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science. 2010; 328:235\u20139.","journal-title":"Science"},{"key":"2295_CR30","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1101\/gr.131201.111","volume":"22","author":"TE Reddy","year":"2012","unstructured":"Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, et al. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res. 2012; 22:860\u20139.","journal-title":"Genome Res"},{"key":"2295_CR31","doi-asserted-by":"crossref","first-page":"9869","DOI":"10.1073\/pnas.1400447111","volume":"111","author":"H Tilgner","year":"2014","unstructured":"Tilgner H, Grubert F, Sharon D, Snyder MP. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci U S A. 2014; 111:9869\u201374.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2295_CR32","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1016\/j.cell.2012.02.009","volume":"148","author":"R Chen","year":"2012","unstructured":"Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012; 148:1293\u20131307.","journal-title":"Cell"},{"issue":"10","key":"2295_CR33","first-page":"e10005291728","volume":"5","author":"BN Howie","year":"2009","unstructured":"Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009; 5(10):e10005291728\u201337.","journal-title":"PLoS Genet"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-015-2295-5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T03:25:58Z","timestamp":1498274758000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.biomedcentral.com\/1471-2164\/17\/S1\/2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1]]},"references-count":33,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2016,1]]}},"alternative-id":["2295"],"URL":"https:\/\/doi.org\/10.1186\/s12864-015-2295-5","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,1]]},"article-number":"2"}}