{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T01:26:17Z","timestamp":1768267577095,"version":"3.49.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,11,21]],"date-time":"2014-11-21T00:00:00Z","timestamp":1416528000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/s12859-014-0380-4","type":"journal-article","created":{"date-parts":[[2014,11,21]],"date-time":"2014-11-21T02:02:40Z","timestamp":1416535360000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":53,"title":["Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning"],"prefix":"10.1186","volume":"15","author":[{"given":"Audrey M","family":"Michel","sequence":"first","affiliation":[]},{"given":"Dmitry E","family":"Andreev","sequence":"additional","affiliation":[]},{"given":"Pavel V","family":"Baranov","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,11,21]]},"reference":[{"issue":"80","key":"380_CR1","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1126\/science.1168978","volume":"324","author":"NT Ingolia","year":"2009","unstructured":"Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS: Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009, 324 (80): 218-223. 10.1126\/science.1168978.","journal-title":"Science"},{"key":"380_CR2","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1002\/wrna.1172","volume":"4","author":"AM Michel","year":"2013","unstructured":"Michel AM, Baranov PV: Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale. Wiley Interdiscip Rev RNA. 2013, 4: 473-490. 10.1002\/wrna.1172.","journal-title":"Wiley Interdiscip Rev RNA"},{"issue":"4","key":"380_CR3","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2011.10.002","volume":"147","author":"NT Ingolia","year":"2011","unstructured":"Ingolia NT, Lareau LF, Weissman JS: Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell. 2011, 147 (4): 789-802. 10.1016\/j.cell.2011.10.002.","journal-title":"Cell"},{"key":"380_CR4","doi-asserted-by":"publisher","first-page":"E2424","DOI":"10.1073\/pnas.1207846109","volume":"109","author":"S Lee","year":"2012","unstructured":"Lee S, Liu B, Lee S, Huang S-X, Shen B, Qian S-B: Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. ProcNatlAcad Sci U S A. 2012, 109: E2424-E2432. 10.1073\/pnas.1207846109.","journal-title":"ProcNatlAcad Sci U S A"},{"key":"380_CR5","doi-asserted-by":"publisher","first-page":"2208","DOI":"10.1101\/gr.139568.112","volume":"22","author":"C Fritsch","year":"2012","unstructured":"Fritsch C, Herrmann A, Nothnagel M, Szafranski K, Huse K, Schumann F, Schreiber S, Platzer M, Krawczak M, Hampe J, Brosch M: Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res. 2012, 22: 2208-2218. 10.1101\/gr.139568.112.","journal-title":"Genome Res"},{"key":"380_CR6","doi-asserted-by":"publisher","first-page":"3621","DOI":"10.1128\/MCB.5.12.3621","volume":"5","author":"CW Anderson","year":"1985","unstructured":"Anderson CW, Buzash-Pollert E: Can ACG serve as an initiation codon for protein synthesis in eucaryoticcells?. Mol Cell Biol. 1985, 5: 3621-3624.","journal-title":"Mol Cell Biol"},{"key":"380_CR7","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/0092-8674(88)90507-7","volume":"52","author":"SR Hann","year":"1988","unstructured":"Hann SR, King MW, Bentley DL, Anderson CW, Eisenman RN: A non-AUG translational initiation in c-myc exon 1 generates an N-terminally distinct protein whose synthesis is disrupted in Burkitt\u2019slymphomas. Cell. 1988, 52: 185-195. 10.1016\/0092-8674(88)90507-7.","journal-title":"Cell"},{"key":"380_CR8","doi-asserted-by":"crossref","first-page":"5031","DOI":"10.1016\/S0021-9258(18)83694-8","volume":"264","author":"DS Peabody","year":"1989","unstructured":"Peabody DS: Translation initiation at non-AUG triplets in mammalian cells. J Biol Chem. 1989, 264: 5031-5035.","journal-title":"J Biol Chem"},{"key":"380_CR9","doi-asserted-by":"publisher","first-page":"4220","DOI":"10.1093\/nar\/gkr007","volume":"39","author":"IP Ivanov","year":"2011","unstructured":"Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV: Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res. 2011, 39: 4220-4234. 10.1093\/nar\/gkr007.","journal-title":"Nucleic Acids Res"},{"key":"380_CR10","doi-asserted-by":"publisher","first-page":"5073","DOI":"10.1128\/MCB.9.11.5073","volume":"9","author":"M Kozak","year":"1989","unstructured":"Kozak M: Context effects and inefficient initiation at non-AUG codons in eucaryotic cell-free translation systems. Mol Cell Biol. 1989, 9: 5073-5080.","journal-title":"Mol Cell Biol"},{"key":"380_CR11","doi-asserted-by":"publisher","first-page":"4533","DOI":"10.1128\/MCB.8.10.4533","volume":"8","author":"JM Clements","year":"1988","unstructured":"Clements JM, Laz TM, Sherman F: Efficiency of translation initiation by non-AUG codons in saccharomyces cerevisiae. Mol Cell Biol. 1988, 8: 4533-4536.","journal-title":"Mol Cell Biol"},{"key":"380_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0378-1119(02)01056-9","volume":"299","author":"M Kozak","year":"2002","unstructured":"Kozak M: Pushing the limits of the scanning mechanism for initiation of translation. Gene. 2002, 299: 1-34. 10.1016\/S0378-1119(02)01056-9.","journal-title":"Gene"},{"key":"380_CR13","first-page":"51","volume":"280","author":"SE Dmitriev","year":"2013","unstructured":"Dmitriev SE, Akulich KA, Andreev DE, Terenin IM, Shastky IN: The peculiar mode of translation elongation inhibition by antitumor drug harringtonin. FEBS J. 2013, 280: 51-","journal-title":"FEBS J"},{"key":"380_CR14","doi-asserted-by":"publisher","first-page":"3438","DOI":"10.1128\/MCB.7.10.3438","volume":"7","author":"M Kozak","year":"1987","unstructured":"Kozak M: Effects of intercistronic length on the efficiency of reinitiation by eucaryoticribosomes. Mol Cell Biol. 1987, 7: 3438-3445.","journal-title":"Mol Cell Biol"},{"key":"380_CR15","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1101\/gad.276504","volume":"18","author":"TAA P\u00f6yry","year":"2004","unstructured":"P\u00f6yry TAA, Kaminski A, Jackson RJ: What determines whether mammalian ribosomes resume scanning after translation of a short upstream open reading frame?. Genes Dev. 2004, 18: 62-75. 10.1101\/gad.276504.","journal-title":"Genes Dev"},{"key":"380_CR16","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1146\/annurev.micro.59.031805.133833","volume":"59","author":"A Hinnebusch","year":"2005","unstructured":"Hinnebusch A: Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol. 2005, 59: 407-450. 10.1146\/annurev.micro.59.031805.133833.","journal-title":"Annu Rev Microbiol"},{"key":"380_CR17","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/0092-8674(86)90762-2","volume":"44","author":"M Kozak","year":"1986","unstructured":"Kozak M: Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell. 1986, 44: 283-292. 10.1016\/0092-8674(86)90762-2.","journal-title":"Cell"},{"key":"380_CR18","doi-asserted-by":"publisher","first-page":"8125","DOI":"10.1093\/nar\/15.20.8125","volume":"15","author":"M Kozak","year":"1987","unstructured":"Kozak M: An analysis of 5\u2032-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 1987, 15: 8125-8148. 10.1093\/nar\/15.20.8125.","journal-title":"Nucleic Acids Res"},{"key":"380_CR19","doi-asserted-by":"publisher","first-page":"2482","DOI":"10.1093\/emboj\/16.9.2482","volume":"16","author":"M Kozak","year":"1997","unstructured":"Kozak M: Recognition of AUG and alternative initiator codons is augmented by G in position +4 but is not generally affected by the nucleotides in positions +5 and +6. EMBO J. 1997, 16: 2482-2492. 10.1093\/emboj\/16.9.2482.","journal-title":"EMBO J"},{"key":"380_CR20","doi-asserted-by":"publisher","first-page":"890","DOI":"10.1093\/bioinformatics\/17.10.890","volume":"17","author":"IB Rogozin","year":"2001","unstructured":"Rogozin IB, Kochetov AV, Kondrashov A, Koonin EV, Milanesi L: Presence of ATG triplets in 5\u2032 untranslated regions of eukaryotic cDNAs correlates with a \u201cweak\u201d context of the start codon. Bioinformatics. 2001, 17: 890-900. 10.1093\/bioinformatics\/17.10.890.","journal-title":"Bioinformatics"},{"key":"380_CR21","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1093\/nar\/gkm1102","volume":"36","author":"S Nakagawa","year":"2008","unstructured":"Nakagawa S, Niimura Y, Gojobori T, Tanaka H, Miura K: Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nucleic Acids Res. 2008, 36: 861-871. 10.1093\/nar\/gkm1102.","journal-title":"Nucleic Acids Res"},{"key":"380_CR22","doi-asserted-by":"publisher","first-page":"7134","DOI":"10.1073\/pnas.92.15.7134","volume":"92","author":"M Kozak","year":"1995","unstructured":"Kozak M: Adherence to the first-AUG rule when a second AUG codon follows closely upon the first. Proc Natl Acad Sci U S A. 1995, 92: 7134-10.1073\/pnas.92.15.7134.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"380_CR23","doi-asserted-by":"publisher","first-page":"5226","DOI":"10.1093\/nar\/29.24.5226","volume":"29","author":"M Kozak","year":"2001","unstructured":"Kozak M: Constraints on reinitiation of translation in mammals. Nucleic Acids Res. 2001, 29: 5226-5232. 10.1093\/nar\/29.24.5226.","journal-title":"Nucleic Acids Res"},{"key":"380_CR24","doi-asserted-by":"publisher","first-page":"5555","DOI":"10.1093\/nar\/gkr147","volume":"39","author":"KS Vassilenko","year":"2011","unstructured":"Vassilenko KS, Alekhina OM, Dmitriev SE, Shatsky IN, Spirin AS: Unidirectional constant rate motion of the ribosomal scanning particle during eukaryotic translation initiation. Nucleic Acids Res. 2011, 39: 5555-5567. 10.1093\/nar\/gkr147.","journal-title":"Nucleic Acids Res"},{"key":"380_CR25","doi-asserted-by":"publisher","first-page":"e1003136","DOI":"10.1371\/journal.pcbi.1003136","volume":"9","author":"H Zur","year":"2013","unstructured":"Zur H, Tuller T: New universal rules of eukaryotic translation initiation fidelity. PLoS Comput Biol. 2013, 9: e1003136-10.1371\/journal.pcbi.1003136.","journal-title":"PLoS Comput Biol"},{"key":"380_CR26","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1002\/wrna.1212","volume":"5","author":"B Liu","year":"2013","unstructured":"Liu B, Qian S-B: Translational reprogramming in cellular stress response. Wiley Interdiscip Rev RNA. 2013, 5: 301-315. 10.1002\/wrna.1212.","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"380_CR27","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1126\/science.1234907","volume":"341","author":"BD Hopkins","year":"2013","unstructured":"Hopkins BD, Fine B, Steinbach N, Dendy M, Rapp Z, Shaw J, Pappas K, Yu JS, Hodakoski C, Mense S, Klein J, Pegno S, Sulis M-L, Goldstein H, Amendolara B, Lei L, Maurer M, Bruce J, Canoll P, Hibshoosh H, Parsons R: A secreted PTEN phosphatase that enters cells to alter signaling and survival. Science. 2013, 341: 399-402. 10.1126\/science.1234907.","journal-title":"Science"},{"key":"380_CR28","doi-asserted-by":"publisher","first-page":"D845","DOI":"10.1093\/nar\/gkt1085","volume":"42","author":"J Wan","year":"2014","unstructured":"Wan J, Qian S-B: TISdb: a database for alternative translation initiation in mammalian cells. Nucleic Acids Res. 2014, 42: D845-D850. 10.1093\/nar\/gkt1085.","journal-title":"Nucleic Acids Res"},{"key":"380_CR29","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nchembio.1120","volume":"9","author":"SA Slavoff","year":"2013","unstructured":"Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A: Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol. 2013, 9: 59-64. 10.1038\/nchembio.1120.","journal-title":"Nat Chem Biol"},{"key":"380_CR30","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.1021\/pr401280w","volume":"13","author":"J Ma","year":"2014","unstructured":"Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A: Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. J Proteome Res. 2014, 13: 1757-1765. 10.1021\/pr401280w.","journal-title":"J Proteome Res"},{"key":"380_CR31","doi-asserted-by":"publisher","first-page":"1780","DOI":"10.1074\/mcp.M113.027540","volume":"12","author":"G Menschaert","year":"2013","unstructured":"Menschaert G, Van Criekinge W, Notelaers T, Koch A, Crapp\u00e9 J, Gevaert K, Van Damme P: Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events. Mol Cell Proteomics. 2013, 12: 1780-1790. 10.1074\/mcp.M113.027540.","journal-title":"Mol Cell Proteomics"},{"issue":"3","key":"380_CR32","first-page":"301","volume":"5","author":"P Van Damme","year":"2014","unstructured":"Van Damme P, Gawron D, Van Criekinge W, Menschaert G: N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol Cell Proteomics. 2014, 5 (3): 301-315.","journal-title":"Mol Cell Proteomics"},{"key":"380_CR33","doi-asserted-by":"publisher","first-page":"D859","DOI":"10.1093\/nar\/gkt1035","volume":"42","author":"AM Michel","year":"2014","unstructured":"Michel AM, Fox G, M Kiran A, De Bo C, O\u2019Connor PBF, Heaphy SM, Mullan JPA, Donohue CA, Higgins DG, Baranov PV: GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res. 2014, 42: D859-D864. 10.1093\/nar\/gkt1035.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-014-0380-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0380-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0380-4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0380-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T06:30:00Z","timestamp":1630564200000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0380-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,21]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["380"],"URL":"https:\/\/doi.org\/10.1186\/s12859-014-0380-4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,21]]},"assertion":[{"value":"3 July 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 November 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 November 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"380"}}