[1] Nekrutenko A, Makova K D, Li W H. The Ka/Ks ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study [J]. Genome Research, 2002, 12(1): 198-202.
[2] Camby I, le Mercier M, Lefranc F, et al. Galectin-1: A small protein with major functions [J]. Glycobiology,2006, 16(11): 137R-157R.
[3] Ikeuchi M, Yamaguchi T, Kazama T, et al. ROTUNDIFOLIA4 regulates cell proliferation along the body axis in arabidopsis shoot [J]. Plant and Cell Physiology,2011, 52(1): 59-69.
[4] Galindo M I, Pueyo J I, Fouix S, et al. Peptides encoded by short ORFs control development and define a new eukaryotic gene family [J]. PLoS Biology,2007, 5(5): e106.
[5] Kondo T, Hashimoto Y, Kato K, et al. Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA [J]. Nature Cell Biology,2007, 9(6): 660-665.
[6] Savard J, Marques-Souza H, Aranda M, et al.A segmentation gene in tribolium produces a polycistronic mRNA that codes for multiple conserved peptides[J]. Cell, 2006, 126(3): 559-569.
[7] Basrai M A, Hieter P, Boeke J D. Small open reading frames: Beautiful needles in the haystack [J].Genome Research, 1997, 7(8): 768-771.
[8] N¨asel D R, Winther °A M E. Drosophila neuropeptides in regulation of physiology and behavior [J].Progress in Neurobiology, 2010, 92(1): 42-104.
[9] Kastenmayer J P, Ni L, Chu A, et al. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae [J]. Genome Research, 2006,16(3): 365-373.
[10] Hanada K, Akiyama K, Sakurai T, et al. sORF finder: A program package to identify small open reading frames with high coding potential [J]. Bioinformatics,2010, 26(3): 399-400.
[11] Ladoukakis E, Pereira V, Magny E G, et al.Hundreds of putatively functional small open reading frames in drosophila [J]. Genome Biol, 2011, 12(11):R118.
[12] The Uniprot Consortium. Update on activities at the universal protein resource (UniProt) in 2013 [J]. Nucleic Acids Research, 2013, 41(D1): D43-D47.
[13] Werner M, Feller A, Messenguy F, et al. The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression [J]. Cell, 1987,49(6): 805-813.
[14] Akimoto C, Sakashita E, Kasashima K, et al.Translational repression of the McKusick-Kaufman syndrome transcript by unique upstream open reading frames encoding mitochondrial proteins with alternative polyadenylation sites [J]. Biochimica et Biophysica Acta, 2013, 1830(3): 2728-2738.
[15] Casson S A, Chilley P M, Topping J F, et al. The POLARIS gene of arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning [J]. The Plant Cell, 2002, 14(8): 1705-1721.
[16] Magny E G, Pueyo J I, Pearl F M, et al.Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames [J]. Science, 2013,341(6150): 1116-1120.
[17] Vanderperre B, Staskevicius A B, Tremblay G,et al. An overlapping reading frame in the PRNP gene encodes a novel polypeptide distinct from the prion protein [J]. The FASEB Journal, 2011, 25(7): 2373-2386.
[18] Slavoff S A, Mitchell A J, Schwaid A G, et al. Peptidomic discovery of short open reading frameencoded peptides in human cells [J]. Nature Chemical Biology, 2013, 9(1): 59-64.
[19] Ghaemmaghami S, Huh W K, Bower K, et al.Global analysis of protein expression in yeast [J]. Nature,2003, 425(6959): 737-741.
[20] Ingolia N T, Brar G A, Rouskin S, et al. The ribosome profiling strategy for monitoring translationin vivo by deep sequencing of ribosome-protected mRNA fragments [J]. Nature Protocols, 2012, 7(8): 1534-1550.
[21] Brar G A, Yassour M, Friedman N, et al. Highresolution view of the yeast meiotic program revealed by ribosome profiling [J]. Science, 2012, 335(6068):552-557.
[22] Dunn J G, Foo C K, Belletier N G, et al. Ribosome profiling reveals pervasive and regulated stop codon readthrough in drosophila melanogaster [J].eLife, 2013, 2: e01179.
[23] Li G W, Oh E, Weissman J S. The anti-shinedalgarno sequence drives translational pausing and codon choice in bacteria [J]. Nature, 2012, 484(7395):538-541.
[24] Stern-Ginossar N, Weisburd B, Michalski A,et al. Decoding human cytomegalovirus [J]. Science,2012, 338(6110): 1088-1093.
[25] Ingolia N T, Lareau L F, Weissman J S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes [J]. Cell, 2011, 147(4): 789-802.
[26] Lee S, Liu B, Lee S, et al. Global mapping of translation initiation sites in mammalian cells at singlenucleotide resolution [J]. Proceedings of the National Academy of Sciences, 2012, 109(37): 2424-2432.
[27] Guttman M, Russell P, Ingolia N T, et al. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins [J]. Cell, 2013, 154(1):240-251.
[28] Chew G L, Pauli A, Rinn J L, et al. Ribosome profiling reveals resemblance between long non-coding RNAs and 5’ leaders of coding RNAs [J]. Development,2013, 140(13): 2828-2834.
[29] Brannan C I, Dees E C, Ingram R S, et al. The product of the H19 gene may function as an RNA [J].Molecular and Cellular Biology, 1990, 10(1): 28-36.
[30] Sotomaru Y, Katsuzawa Y, Hatada I, et al.Unregulated expression of the imprinted genes H19 and Igf2r in mouse uniparental fetuses [J]. Journal of Biological Chemistry, 2002, 277(14): 12474-12478.
[31] Lin M F, Jungreis I, Kellis M. PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions [J]. Bioinformatics, 2011,27(13): 275-282.
[32] Washietl S, Findei S, M¨uler S A, et al. RNAcode:Robust discrimination of coding and noncoding regions in comparative sequence data [J]. RNA, 2011, 17(4):578-594.
[33] Kong L, Zhang Y, Ye Z Q, et al. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine [J]. Nucleic Acids Research, 2007, 35(Sup 2): W345-W349.
[34] Wang L, Park H J, Dasari S, et al. CPAT: Codingpotential assessment tool using an alignment-free logistic regression model [J]. Nucleic Acids Research, 2013,41(6): e74.
[35] Sun K, Chen X, Jiang P, et al. iSeeRNA: Identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data [J]. BMC Genomics,2013, 14(Sup 2): S1-S7.
[36] Crapp′e J, Van Criekinge W, Trooskens G, et al.Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs [J]. BMC Genomics, 2013, 14(1): 648-660.
[37] Yang X, Tschaplinski T J, Hurst G B, et al.Discovery and annotation of small proteins using genomics,proteomics, and computational approaches [J].Genome Research, 2011, 21(4): 634-641.
[38] Gascoigne D K, Cheetham S W, Cattenoz P B,et al. Pinstripe: A suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of proteincoding and non-coding genes [J]. Bioinformatics, 2012,28(23): 3042-3050.
[39] Menschaert G, Van Criekinge W, Notelaers T,et al. 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 [J]. Molecular & Cellular Proteomics,2013, 12(7): 1780-1790.
