{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T04:13:29Z","timestamp":1792815209718,"version":"4.5.0"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"7695","license":[{"start":{"date-parts":[[2018,2,28]],"date-time":"2018-02-28T00:00:00Z","timestamp":1519776000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2018,3]]},"DOI":"10.1038\/nature25784","type":"journal-article","created":{"date-parts":[[2018,2,28]],"date-time":"2018-02-28T10:21:34Z","timestamp":1519813294000},"page":"256-259","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":353,"title":["The SMAD2\/3 interactome reveals that TGF\u03b2 controls m6A mRNA methylation in pluripotency"],"prefix":"10.1038","volume":"555","author":[{"given":"Alessandro","family":"Bertero","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro","family":"Madrigal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Osnato","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Ortmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Loukia","family":"Yiangou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juned","family":"Kadiwala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nina C.","family":"Hubner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Igor Ruiz","family":"de los Mozos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Sad\u00e9e","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An-Sofie","family":"Lenaerts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shota","family":"Nakanoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo","family":"Grandy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward","family":"Farnell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jernej","family":"Ule","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hendrik G.","family":"Stunnenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sasha","family":"Mendjan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludovic","family":"Vallier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,2,28]]},"reference":[{"key":"BFnature25784_CR1","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.devcel.2009.02.012","volume":"16","author":"MY Wu","year":"2009","unstructured":"Wu, M. Y. & Hill, C. S. TGF\u03b2 superfamily signaling in embryonic development and homeostasis. Dev. Cell 16, 329\u2013343 (2009)","journal-title":"Dev. Cell"},{"key":"BFnature25784_CR2","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1016\/j.stem.2012.11.001","volume":"11","author":"N Oshimori","year":"2012","unstructured":"Oshimori, N . & Fuchs, E. The harmonies played by TGF\u03b2 in stem cell biology. Cell Stem Cell 11, 751\u2013764 (2012)","journal-title":"Cell Stem Cell"},{"key":"BFnature25784_CR3","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.semcdb.2014.01.009","volume":"32","author":"T Gaarenstroom","year":"2014","unstructured":"Gaarenstroom, T. & Hill, C. S. TGF\u03b2 signaling to chromatin: how SMADs regulate transcription during self-renewal and differentiation. Semin. Cell Dev. Biol. 32, 107\u2013118 (2014)","journal-title":"Semin. Cell Dev. Biol."},{"key":"BFnature25784_CR4","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1016\/j.cell.2015.04.021","volume":"161","author":"H Heyn","year":"2015","unstructured":"Heyn, H. & Esteller, M. An adenine code for DNA: a second life for N6-methyladenine. Cell 161, 710\u2013713 (2015)","journal-title":"Cell"},{"key":"BFnature25784_CR5","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/nrc3603","volume":"13","author":"M Pickup","year":"2013","unstructured":"Pickup, M., Novitskiy, S. & Moses, H. L. The roles of TGF\u03b2 in the tumour microenvironment. Nat. Rev. Cancer 13, 788\u2013799 (2013)","journal-title":"Nat. Rev. Cancer"},{"key":"BFnature25784_CR6","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/j.ydbio.2004.08.031","volume":"275","author":"L Vallier","year":"2004","unstructured":"Vallier, L., Reynolds, D. & Pedersen, R. A. NODAL inhibits differentiation of human embryonic stem cells along the neuroectodermal default pathway. Dev. Biol. 275, 403\u2013421 (2004)","journal-title":"Dev. Biol."},{"key":"BFnature25784_CR7","doi-asserted-by":"publisher","first-page":"4495","DOI":"10.1242\/jcs.02553","volume":"118","author":"L Vallier","year":"2005","unstructured":"Vallier, L., Alexander, M. & Pedersen, R. A. Activin\/NODAL and FGF pathways cooperate to maintain pluripotency of human embryonic stem cells. J. Cell Sci. 118, 4495\u20134509 (2005)","journal-title":"J. Cell Sci."},{"key":"BFnature25784_CR8","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.1242\/dev.01706","volume":"132","author":"D James","year":"2005","unstructured":"James, D., Levine, A. J., Besser, D. & Hemmati-Brivanlou, A. TGF\u03b2\/activin\/NODAL signaling is necessary for the maintenance of pluripotency in human embryonic stem cells. Development 132, 1273\u20131282 (2005)","journal-title":"Development"},{"key":"BFnature25784_CR9","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.ydbio.2007.10.003","volume":"313","author":"JR Smith","year":"2008","unstructured":"Smith, J. R. et al. Inhibition of activin\/NODAL signaling promotes specification of human embryonic stem cells into neuroectoderm. Dev. Biol. 313, 107\u2013117 (2008)","journal-title":"Dev. Biol."},{"key":"BFnature25784_CR10","doi-asserted-by":"publisher","first-page":"702","DOI":"10.1101\/gad.255984.114","volume":"29","author":"A Bertero","year":"2015","unstructured":"Bertero, A. et al. Activin\/NODAL signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark. Genes Dev. 29, 702\u2013717 (2015)","journal-title":"Genes Dev."},{"key":"BFnature25784_CR11","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1038\/nbt1163","volume":"23","author":"KA D\u2019Amour","year":"2005","unstructured":"D\u2019Amour, K. A. et al. Efficient differentiation of human embryonic stem cells to definitive endoderm. Nat. Biotechnol. 23, 1534\u20131541 (2005)","journal-title":"Nat. Biotechnol."},{"key":"BFnature25784_CR12","doi-asserted-by":"publisher","first-page":"2655","DOI":"10.1002\/stem.199","volume":"27","author":"L Vallier","year":"2009","unstructured":"Vallier, L. et al. Signaling pathways controlling pluripotency and early cell fate decisions of human induced pluripotent stem cells. Stem Cells 27, 2655\u20132666 (2009)","journal-title":"Stem Cells"},{"key":"BFnature25784_CR13","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1101\/gad.607311","volume":"25","author":"AK Teo","year":"2011","unstructured":"Teo, A. K. et al. Pluripotency factors regulate definitive endoderm specification through eomesodermin. Genes Dev. 25, 238\u2013250 (2011)","journal-title":"Genes Dev."},{"key":"BFnature25784_CR14","doi-asserted-by":"publisher","first-page":"1651","DOI":"10.1242\/dev.01044","volume":"131","author":"A Kubo","year":"2004","unstructured":"Kubo, A. et al. Development of definitive endoderm from embryonic stem cells in culture. Development 131, 1651\u20131662 (2004)","journal-title":"Development"},{"key":"BFnature25784_CR15","doi-asserted-by":"publisher","first-page":"2037","DOI":"10.1101\/gad.269415.115","volume":"29","author":"S Ke","year":"2015","unstructured":"Ke, S. et al. A majority of m6A residues are in the last exons, allowing the potential for 3\u2032 UTR regulation. Genes Dev. 29, 2037\u20132053 (2015)","journal-title":"Genes Dev."},{"key":"BFnature25784_CR16","doi-asserted-by":"publisher","first-page":"990","DOI":"10.1101\/gad.301036.117","volume":"31","author":"S Ke","year":"2017","unstructured":"Ke, S. et al. m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev. 31, 990\u20131006 (2017)","journal-title":"Genes Dev."},{"key":"BFnature25784_CR17","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1038\/nature11112","volume":"485","author":"D Dominissini","year":"2012","unstructured":"Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201\u2013206 (2012)","journal-title":"Nature"},{"key":"BFnature25784_CR18","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1016\/j.cell.2015.10.012","volume":"163","author":"KD Meyer","year":"2015","unstructured":"Meyer, K. D. et al. 5\u2032 UTR m6A promotes cap-independent translation. Cell 163, 999\u20131010 (2015)","journal-title":"Cell"},{"key":"BFnature25784_CR19","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1016\/j.cell.2012.05.003","volume":"149","author":"KD Meyer","year":"2012","unstructured":"Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3\u2032 UTRs and near stop codons. Cell 149, 1635\u20131646 (2012)","journal-title":"Cell"},{"key":"BFnature25784_CR20","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1038\/nature24678","volume":"552","author":"I Barbieri","year":"2017","unstructured":"Barbieri, I. et al. Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control. Nature 552, 126\u2013131 (2017)","journal-title":"Nature"},{"key":"BFnature25784_CR21","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1038\/nm.4416","volume":"23","author":"LP Vu","year":"2017","unstructured":"Vu, L. P. et al. The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nat. Med. 23, 1369\u20131376 (2017)","journal-title":"Nat. Med."},{"key":"BFnature25784_CR22","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.1126\/science.1261417","volume":"347","author":"S Geula","year":"2015","unstructured":"Geula, S. et al. Stem cells. m6A mRNA methylation facilitates resolution of na\u00efve pluripotency toward differentiation. Science 347, 1002\u20131006 (2015)","journal-title":"Science"},{"key":"BFnature25784_CR23","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1016\/j.stem.2014.09.019","volume":"15","author":"PJ Batista","year":"2014","unstructured":"Batista, P. J. et al. m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15, 707\u2013719 (2014)","journal-title":"Cell Stem Cell"},{"key":"BFnature25784_CR24","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1016\/j.celrep.2014.05.048","volume":"8","author":"S Schwartz","year":"2014","unstructured":"Schwartz, S. et al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5\u2032 sites. Cell Reports 8, 284\u2013296 (2014)","journal-title":"Cell Reports"},{"key":"BFnature25784_CR25","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1038\/nature12730","volume":"505","author":"X Wang","year":"2014","unstructured":"Wang, X. et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117\u2013120 (2014)","journal-title":"Nature"},{"key":"BFnature25784_CR26","doi-asserted-by":"publisher","first-page":"11356","DOI":"10.1093\/nar\/gkx778","volume":"45","author":"M Bartosovic","year":"2017","unstructured":"Bartosovic, M. et al. N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3\u2032-end processing. Nucleic Acids Res. 45, 11356\u201311370 (2017)","journal-title":"Nucleic Acids Res."},{"key":"BFnature25784_CR27","doi-asserted-by":"publisher","first-page":"4405","DOI":"10.1242\/dev.138081","volume":"143","author":"A Bertero","year":"2016","unstructured":"Bertero, A. et al. Optimized inducible shRNA and CRISPR\/Cas9 platforms for in vitro studies of human development using hPSCs. Development 143, 4405\u20134418 (2016)","journal-title":"Development"},{"key":"BFnature25784_CR28","doi-asserted-by":"publisher","first-page":"1339","DOI":"10.1242\/dev.033951","volume":"136","author":"L Vallier","year":"2009","unstructured":"Vallier, L. et al. Activin\/NODAL signalling maintains pluripotency by controlling NANOG expression. Development 136, 1339\u20131349 (2009)","journal-title":"Development"},{"key":"BFnature25784_CR29","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1016\/j.stem.2014.06.006","volume":"15","author":"S Mendjan","year":"2014","unstructured":"Mendjan, S. et al. NANOG and CDX2 pattern distinct subtypes of human mesoderm during exit from pluripotency. Cell Stem Cell 15, 310\u2013325 (2014)","journal-title":"Cell Stem Cell"},{"key":"BFnature25784_CR30","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1002\/stem.666","volume":"29","author":"S Brown","year":"2011","unstructured":"Brown, S. et al. Activin\/NODAL signaling controls divergent transcriptional networks in human embryonic stem cells and in endoderm progenitors. Stem Cells 29, 1176\u20131185 (2011)","journal-title":"Stem Cells"},{"key":"BFnature25784_CR31","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1038\/nature10424","volume":"478","author":"K Yusa","year":"2011","unstructured":"Yusa, K. et al. Targeted gene correction of \u03b11-antitrypsin deficiency in induced pluripotent stem cells. Nature 478, 391\u2013394 (2011)","journal-title":"Nature"},{"key":"BFnature25784_CR32","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1007\/978-1-60761-962-8_3","volume":"690","author":"L Vallier","year":"2011","unstructured":"Vallier, L. Serum-free and feeder-free culture conditions for human embryonic stem cells. Methods Mol. Biol. 690, 57\u201366 (2011)","journal-title":"Methods Mol. Biol."},{"key":"BFnature25784_CR33","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1002\/hep.23506","volume":"51","author":"T Touboul","year":"2010","unstructured":"Touboul, T. et al. Generation of functional hepatocytes from human embryonic stem cells under chemically defined conditions that recapitulate liver development. Hepatology 51, 1754\u20131765 (2010)","journal-title":"Hepatology"},{"key":"BFnature25784_CR34","doi-asserted-by":"publisher","first-page":"e6082","DOI":"10.1371\/journal.pone.0006082","volume":"4","author":"L Vallier","year":"2009","unstructured":"Vallier, L. et al. Early cell fate decisions of human embryonic stem cells and mouse epiblast stem cells are controlled by the same signalling pathways. PLoS One 4, e6082 (2009)","journal-title":"PLoS One"},{"key":"BFnature25784_CR35","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1016\/j.cell.2006.01.040","volume":"124","author":"J Moffat","year":"2006","unstructured":"Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283\u20131298 (2006)","journal-title":"Cell"},{"key":"BFnature25784_CR36","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1016\/j.stemcr.2017.02.016","volume":"8","author":"M Pawlowski","year":"2017","unstructured":"Pawlowski, M. et al. Inducible and deterministic forward programming of human pluripotent stem cells into neurons, skeletal myocytes, and oligodendrocytes. Stem Cell Reports 8, 803\u2013812 (2017)","journal-title":"Stem Cell Reports"},{"key":"BFnature25784_CR37","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1016\/j.ymeth.2010.12.016","volume":"53","author":"NC Hubner","year":"2011","unstructured":"Hubner, N. C. & Mann, M. Extracting gene function from protein-protein interactions using quantitative BAC interactomics (QUBIC). Methods 53, 453\u2013459 (2011)","journal-title":"Methods"},{"key":"BFnature25784_CR38","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.1038\/nprot.2007.261","volume":"2","author":"J Rappsilber","year":"2007","unstructured":"Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896\u20131906 (2007)","journal-title":"Nat. Protoc."},{"key":"BFnature25784_CR39","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1038\/nprot.2009.21","volume":"4","author":"PJ Boersema","year":"2009","unstructured":"Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S. & Heck, A. J. R. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protoc. 4, 484\u2013494 (2009)","journal-title":"Nat. Protoc."},{"key":"BFnature25784_CR40","doi-asserted-by":"publisher","first-page":"1315","DOI":"10.1021\/pr5009515","volume":"14","author":"NC Hubner","year":"2015","unstructured":"Hubner, N. C., Nguyen, L. N., Hornig, N. C. & Stunnenberg, H. G. A quantitative proteomics tool to identify DNA\u2013protein interactions in primary cells or blood. J. Proteome Res. 14, 1315\u20131329 (2015)","journal-title":"J. Proteome Res."},{"key":"BFnature25784_CR41","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/nbt.1511","volume":"26","author":"J Cox","year":"2008","unstructured":"Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367\u20131372 (2008)","journal-title":"Nat. Biotechnol."},{"key":"BFnature25784_CR42","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1083\/jcb.200911091","volume":"189","author":"NC Hubner","year":"2010","unstructured":"Hubner, N. C. et al. Quantitative proteomics combined with BAC transgeneomics reveals in vivo protein interactions. J. Cell Biol. 189, 739\u2013754 (2010)","journal-title":"J. Cell Biol."},{"key":"BFnature25784_CR43","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498\u20132504 (2003)","journal-title":"Genome Res."},{"key":"BFnature25784_CR44","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/1471-2105-14-128","volume":"14","author":"EY Chen","year":"2013","unstructured":"Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013)","journal-title":"BMC Bioinformatics"},{"key":"BFnature25784_CR45","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1038\/nprot.2012.148","volume":"8","author":"D Dominissini","year":"2013","unstructured":"Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N. & Rechavi, G. Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nat. Protoc. 8, 176\u2013189 (2013)","journal-title":"Nat. Protoc."},{"key":"BFnature25784_CR46","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR47","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","volume":"14","author":"D Kim","year":"2013","unstructured":"Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013)","journal-title":"Genome Biol."},{"key":"BFnature25784_CR48","first-page":"1","volume":"PP","author":"X Cui","year":"2015","unstructured":"Cui, X. et al. MeTDiff: a novel differential RNA methylation analysis for MeRIP\u2013seq data. IEEE\/ACM Trans. Comput. Biol. Bioinforma. PP, 1 (2015)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinforma."},{"key":"BFnature25784_CR49","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1186\/gb-2012-13-10-175","volume":"13","author":"Y Saletore","year":"2012","unstructured":"Saletore, Y. et al. The birth of the epitranscriptome: deciphering the function of RNA modifications. Genome Biol. 13, 175 (2012)","journal-title":"Genome Biol."},{"key":"BFnature25784_CR50","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1038\/nmeth.4110","volume":"14","author":"X Li","year":"2017","unstructured":"Li, X., Xiong, X. & Yi, C. Epitranscriptome sequencing technologies: decoding RNA modifications. Nat. Methods 14, 23\u201331 (2017)","journal-title":"Nat. Methods"},{"key":"BFnature25784_CR51","doi-asserted-by":"publisher","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP\u2013seq (MACS). Genome Biol. 9, R137 (2008)","journal-title":"Genome Biol."},{"key":"BFnature25784_CR52","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1093\/bioinformatics\/btw724","volume":"33","author":"P Madrigal","year":"2017","unstructured":"Madrigal, P. fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets. Bioinformatics 33, 746\u2013748 (2017)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR53","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","volume":"28","author":"L Wang","year":"2012","unstructured":"Wang, L., Wang, S. & Li, W. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28, 2184\u20132185 (2012)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR54","doi-asserted-by":"publisher","first-page":"e91","DOI":"10.1093\/nar\/gkx120","volume":"45","author":"B Uyar","year":"2017","unstructured":"Uyar, B. et al. RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. Nucleic Acids Res. 45, e91 (2017)","journal-title":"Nucleic Acids Res."},{"key":"BFnature25784_CR55","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1093\/bioinformatics\/btr261","volume":"27","author":"TL Bailey","year":"2011","unstructured":"Bailey, T. L. DREME: motif discovery in transcription factor ChIP\u2013seq data. Bioinformatics 27, 1653\u20131659 (2011)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR56","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1093\/bioinformatics\/btr020","volume":"27","author":"TA Down","year":"2011","unstructured":"Down, T. A., Piipari, M. & Hubbard, T. J. P. Dalliance: interactive genome viewing on the web. Bioinformatics 27, 889\u2013890 (2011)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR57","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923\u2013930 (2014)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR58","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014)","journal-title":"Genome Biol."},{"key":"BFnature25784_CR59","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","volume":"17","author":"A Conesa","year":"2016","unstructured":"Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 13 (2016)","journal-title":"Genome Biol."},{"key":"BFnature25784_CR60","doi-asserted-by":"publisher","first-page":"2046","DOI":"10.1093\/bioinformatics\/btt343","volume":"29","author":"A Heger","year":"2013","unstructured":"Heger, A., Webber, C., Goodson, M., Ponting, C. P. & Lunter, G. GAT: a simulation framework for testing the association of genomic intervals. Bioinformatics 29, 2046\u20132048 (2013)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR61","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576\u2013589 (2010)","journal-title":"Mol. Cell"},{"key":"BFnature25784_CR62","doi-asserted-by":"publisher","first-page":"1565","DOI":"10.1093\/bioinformatics\/btt171","volume":"29","author":"J Meng","year":"2013","unstructured":"Meng, J., Cui, X., Rao, M. K., Chen, Y. & Huang, Y. Exome-based analysis for RNA epigenome sequencing data. Bioinformatics 29, 1565\u20131567 (2013)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR63","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C Trapnell","year":"2010","unstructured":"Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511\u2013515 (2010)","journal-title":"Nat. Biotechnol."},{"key":"BFnature25784_CR64","unstructured":"Joshi, N. & Fass, J. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files v.1.33 https:\/\/github.com\/najoshi\/sickle (2011)"},{"key":"BFnature25784_CR65","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012)","journal-title":"Nat. Methods"},{"key":"BFnature25784_CR66","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009)","journal-title":"Bioinformatics"},{"key":"BFnature25784_CR67","unstructured":"Andrews, S. SeqMonk: A tool to visualise and analyse high throughput mapped sequence data https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/seqmonk\/ (2014)"},{"key":"BFnature25784_CR68","doi-asserted-by":"publisher","first-page":"e3","DOI":"10.2202\/1544-6115.1027","volume":"3","author":"GK Smyth","year":"2004","unstructured":"Smyth, G. K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, e3 (2004)","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"BFnature25784_CR69","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","volume":"25","author":"KJ Livak","year":"2001","unstructured":"Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2\u2212\u0394\u0394Ct method. Methods 25, 402\u2013408 (2001)","journal-title":"Methods"},{"key":"BFnature25784_CR70","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/0003-2697(91)90500-S","volume":"198","author":"S Harrold","year":"1991","unstructured":"Harrold, S., Genovese, C., Kobrin, B., Morrison, S. L. & Milcarek, C. A comparison of apparent mRNA half-life using kinetic labeling techniques vs decay following administration of transcriptional inhibitors. Anal. Biochem. 198, 19\u201329 (1991)","journal-title":"Anal. Biochem."}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nature25784.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nature25784","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/doifinder\/10.1038\/nature25784","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/www.nature.com\/articles\/nature25784.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T10:15:14Z","timestamp":1693563314000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nature25784"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,2,28]]},"references-count":70,"journal-issue":{"issue":"7695","published-print":{"date-parts":[[2018,3]]}},"alternative-id":["BFnature25784"],"URL":"https:\/\/doi.org\/10.1038\/nature25784","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,2,28]]},"assertion":[{"value":"29 November 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 January 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 February 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}