{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T04:58:29Z","timestamp":1725512309743},"publisher-location":"Berlin, Heidelberg","reference-count":32,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540720300"},{"type":"electronic","value":"9783540720317"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-72031-7_34","type":"book-chapter","created":{"date-parts":[[2007,8,5]],"date-time":"2007-08-05T14:16:24Z","timestamp":1186323384000},"page":"372-381","source":"Crossref","is-referenced-by-count":0,"title":["The Identification of Antisense Gene Pairs Through Available Software"],"prefix":"10.1007","author":[{"given":"Mark J.","family":"Lawson","sequence":"first","affiliation":[]},{"given":"Liqing","family":"Zhang","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"issue":"18","key":"34_CR1","doi-asserted-by":"publisher","first-page":"2102","DOI":"10.1007\/s00018-006-6070-2","volume":"63","author":"S.H. Munroe","year":"2006","unstructured":"Munroe, S.H., Zhu, J.: Overlapping transcripts, double-stranded RNA and antisense regulation: A genomic perspective. Cellular and Molecular Life Sciences\u00a063(18), 2102\u20132118 (2006)","journal-title":"Cellular and Molecular Life Sciences"},{"issue":"4","key":"34_CR2","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nbt808","volume":"21","author":"R. Yelin","year":"2003","unstructured":"Yelin, R., et al.: Widespread occurrence of antisense transcription in the human genome. Nature Biotechnology\u00a021(4), 379\u2013386 (2003)","journal-title":"Nature Biotechnology"},{"issue":"6B","key":"34_CR3","doi-asserted-by":"crossref","first-page":"1324","DOI":"10.1101\/gr.982903","volume":"13","author":"H. Kiyosawa","year":"2003","unstructured":"Kiyosawa, H., et al.: Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Research 13(6B), 1324\u20131334 (2003)","journal-title":"Genome Research"},{"issue":"5740","key":"34_CR4","doi-asserted-by":"publisher","first-page":"1564","DOI":"10.1126\/science.1112009","volume":"309","author":"S. Katayama","year":"2005","unstructured":"Katayama, S., et al.: Antisense transcription in the mammalian transcriptome. Science\u00a0309(5740), 1564\u20131566 (2005)","journal-title":"Science"},{"issue":"16","key":"34_CR5","doi-asserted-by":"publisher","first-page":"4812","DOI":"10.1093\/nar\/gkh818","volume":"32","author":"J.J. Chen","year":"2004","unstructured":"Chen, J.J., et al.: Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Research\u00a032(16), 4812\u20134820 (2004)","journal-title":"Nucleic Acids Research"},{"key":"34_CR6","doi-asserted-by":"crossref","unstructured":"Wang, X.J., Gaasterland, T., Chua, N.H.: Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biology 6(4) (2005)","DOI":"10.1186\/gb-2005-6-4-r30"},{"key":"34_CR7","doi-asserted-by":"crossref","unstructured":"Wang, H., Chua, N.-H., Wang, X.-J.: Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biology, 7(10), R92 (2006)","DOI":"10.1186\/gb-2006-7-10-r92"},{"issue":"1","key":"34_CR8","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1038\/nbt925","volume":"22","author":"O. Rosok","year":"2004","unstructured":"Rosok, O., Sioud, M.: Systematic identification of sense-antisense transcripts in mammalian cells. Nature Biotechnology\u00a022(1), 104\u2013108 (2004)","journal-title":"Nature Biotechnology"},{"issue":"3","key":"34_CR9","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1101\/gr.3308405","volume":"15","author":"D. Dahary","year":"2005","unstructured":"Dahary, D., Elroy-Stein, O., Sorek, R.: Naturally occurring antisense: Transcriptional leakage or real overlap? Genome Research\u00a015(3), 364\u2013368 (2005)","journal-title":"Genome Research"},{"issue":"2","key":"34_CR10","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.tibs.2003.12.002","volume":"29","author":"G. Lavorgna","year":"2004","unstructured":"Lavorgna, G., et al.: In search of antisense. Trends in Biochemical Sciences\u00a029(2), 88\u201394 (2004)","journal-title":"Trends in Biochemical Sciences"},{"issue":"1","key":"34_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.compbiolchem.2004.12.006","volume":"29","author":"I. Makalowska","year":"2005","unstructured":"Makalowska, I., Lin, C.F., Makalowski, W.: Overlapping genes in vertebrate genomes. Computational Biology and Chemistry\u00a029(1), 1\u201312 (2005)","journal-title":"Computational Biology and Chemistry"},{"issue":"3","key":"34_CR12","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/S0197-0186(96)00108-8","volume":"31","author":"R. Knee","year":"1997","unstructured":"Knee, R., Murphy, P.R.: Regulation of gene expression by natural antisense RNA transcripts. Neurochemistry International\u00a031(3), 379\u2013392 (1997)","journal-title":"Neurochemistry International"},{"issue":"7","key":"34_CR13","doi-asserted-by":"publisher","first-page":"3400","DOI":"10.1074\/jbc.270.7.3400","volume":"270","author":"C.M. Farrell","year":"1995","unstructured":"Farrell, C.M., Lukens, L.N.: Naturally-Occurring Antisense Transcripts Are Present in Chick-Embryo Chondrocytes Simultaneously with the down-Regulation of the Alpha-1(I) Collagen Gene. Journal of Biological Chemistry\u00a0270(7), 3400\u20133408 (1995)","journal-title":"Journal of Biological Chemistry"},{"issue":"13","key":"34_CR14","doi-asserted-by":"publisher","first-page":"8796","DOI":"10.1073\/pnas.132270899","volume":"99","author":"E.M. Prescott","year":"2002","unstructured":"Prescott, E.M., Proudfoot, N.J.: Transcriptional collision between convergent genes in budding yeast. Proceedings of the National Academy of Sciences of the United States of America\u00a099(13), 8796\u20138801 (2002)","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"33","key":"34_CR15","doi-asserted-by":"crossref","first-page":"22083","DOI":"10.1016\/S0021-9258(18)54535-X","volume":"266","author":"S.H. Munroe","year":"1991","unstructured":"Munroe, S.H., Lazar, M.A.: Inhibition of C-Erba Messenger-Rna Splicing by a Naturally-Occurring Antisense Rna. Journal of Biological Chemistry\u00a0266(33), 22083\u201322086 (1991)","journal-title":"Journal of Biological Chemistry"},{"issue":"15","key":"34_CR16","doi-asserted-by":"publisher","first-page":"11507","DOI":"10.1074\/jbc.275.15.11507","volume":"275","author":"M.L. Hastings","year":"2000","unstructured":"Hastings, M.L., et al.: Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. Journal of Biological Chemistry\u00a0275(15), 11507\u201311513 (2000)","journal-title":"Journal of Biological Chemistry"},{"issue":"4","key":"34_CR17","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1038\/7734","volume":"21","author":"J.T. Lee","year":"1999","unstructured":"Lee, J.T., Davidow, L.S., Warshawsky, D.: Tsix, a gene antisense to Xist at the X-inactivation centre. Nature Genetics\u00a021(4), 400\u2013404 (1999)","journal-title":"Nature Genetics"},{"key":"34_CR18","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1146\/annurev.biochem.71.110601.135501","volume":"71","author":"B.L. Bass","year":"2002","unstructured":"Bass, B.L.: RNA editing by adenosine deaminases that act on RNA. Annual Review of Biochemistry\u00a071, 817\u2013846 (2002)","journal-title":"Annual Review of Biochemistry"},{"issue":"6","key":"34_CR19","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1261\/rna.2120703","volume":"9","author":"N.T. Peters","year":"2003","unstructured":"Peters, N.T., et al.: RNA editing and regulation of Drosophila 4f-rnp expression by sas-10 antisense readthrough mRNA transcripts. Rna-a Publication of the Rna Society\u00a09(6), 698\u2013710 (2003)","journal-title":"Rna-a Publication of the Rna Society"},{"issue":"6894","key":"34_CR20","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1038\/418244a","volume":"418","author":"G.J. Hannon","year":"2002","unstructured":"Hannon, G.J.: RNA interference. Nature\u00a0418(6894), 244\u2013251 (2002)","journal-title":"Nature"},{"issue":"13","key":"34_CR21","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1016\/S0960-9822(01)00299-8","volume":"11","author":"A.A. Aravin","year":"2001","unstructured":"Aravin, A.A., et al.: Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D-melanogaster germline. Current Biology\u00a011(13), 1017\u20131027 (2001)","journal-title":"Current Biology"},{"issue":"23","key":"34_CR22","doi-asserted-by":"publisher","first-page":"2687","DOI":"10.1093\/hmg\/10.23.2687","volume":"10","author":"M. Runte","year":"2001","unstructured":"Runte, M., et al.: The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Human Molecular Genetics\u00a010(23), 2687\u20132700 (2001)","journal-title":"Human Molecular Genetics"},{"issue":"2","key":"34_CR23","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1038\/ng1157","volume":"34","author":"C. Tufarelli","year":"2003","unstructured":"Tufarelli, C., et al.: Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nature Genetics\u00a034(2), 157\u2013165 (2003)","journal-title":"Nature Genetics"},{"key":"34_CR24","doi-asserted-by":"crossref","unstructured":"Zhang, Y., et al.: NATsDB: Natural Antisense Transcripts DataBase. Nucl. Acids Res. 35(suppl. 1), D156\u2013161 (2007)","DOI":"10.1093\/nar\/gkl782"},{"issue":"12","key":"34_CR25","doi-asserted-by":"publisher","first-page":"3465","DOI":"10.1093\/nar\/gkl473","volume":"34","author":"Y. Zhang","year":"2006","unstructured":"Zhang, Y., et al.: Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Research\u00a034(12), 3465\u20133475 (2006)","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"34_CR26","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1093\/bioinformatics\/btg460","volume":"20","author":"G. Lavorgna","year":"2004","unstructured":"Lavorgna, G., et al.: AntiHunter: searching BLAST output for EST antisense transcripts. Bioinformatics\u00a020(4), 583\u2013585 (2004)","journal-title":"Bioinformatics"},{"key":"34_CR27","doi-asserted-by":"crossref","first-page":"W665","DOI":"10.1093\/nar\/gki448","volume":"33","author":"G. Lavorgna","year":"2005","unstructured":"Lavorgna, G., et al.: AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts. Nucleic Acids Research 33, W665\u2013W668 (2005)","journal-title":"Nucleic Acids Research"},{"key":"34_CR28","doi-asserted-by":"crossref","first-page":"W577","DOI":"10.1093\/nar\/gki591","volume":"33","author":"N.R. Markham","year":"2005","unstructured":"Markham, N.R., Zuker, M.: DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Research 33, W577\u2013W581 (2005)","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"34_CR29","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1529\/biophysj.103.020743","volume":"87","author":"R.A. Dimitrov","year":"2004","unstructured":"Dimitrov, R.A., Zuker, M.: Prediction of hybridization and melting for double-stranded nucleic acids. Biophysical Journal\u00a087(1), 215\u2013226 (2004)","journal-title":"Biophysical Journal"},{"key":"34_CR30","doi-asserted-by":"crossref","unstructured":"Kurtz, S., et al.: Versatile and open software for comparing large genomes. Genome Biology 5(2) (2004)","DOI":"10.1186\/gb-2004-5-2-r12"},{"key":"34_CR31","unstructured":"Ensembl Genome Browser [cited 2006 12\/20], Available from: http:\/\/www.ensembl.org"},{"issue":"2","key":"34_CR32","first-page":"197","volume":"15","author":"O. Rosok","year":"2005","unstructured":"Rosok, O., Sioud, M.: Systematic search for natural antisense transcripts in eukaryotes - (Review). International Journal of Molecular Medicine\u00a015(2), 197\u2013203 (2005)","journal-title":"International Journal of Molecular Medicine"}],"container-title":["Lecture Notes in Computer Science","Bioinformatics Research and Applications"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-72031-7_34.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,21]],"date-time":"2021-08-21T07:12:15Z","timestamp":1629529935000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-72031-7_34"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540720300","9783540720317"],"references-count":32,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-72031-7_34","relation":{},"subject":[]}}