{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T01:36:15Z","timestamp":1722821775143},"reference-count":34,"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\/s12864-015-2305-7","type":"journal-article","created":{"date-parts":[[2016,1,11]],"date-time":"2016-01-11T10:02:21Z","timestamp":1452506541000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Identifying micro-inversions using high-throughput sequencing reads"],"prefix":"10.1186","volume":"17","author":[{"given":"Feifei","family":"He","sequence":"first","affiliation":[]},{"given":"Yang","family":"Li","sequence":"additional","affiliation":[]},{"given":"Yu-Hang","family":"Tang","sequence":"additional","affiliation":[]},{"given":"Jian","family":"Ma","sequence":"additional","affiliation":[]},{"given":"Huaiqiu","family":"Zhu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,1,11]]},"reference":[{"issue":"2","key":"2305_CR1","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/nmeth.1858","volume":"9","author":"M Baker","year":"2012","unstructured":"Baker M. Structural variation: the genome\u2019s hidden architecture. Nat Methods. 2012;9(2):133\u20137.","journal-title":"Nat Methods"},{"key":"2305_CR2","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1038\/ng1090","volume":"33","author":"D Botstein","year":"2003","unstructured":"Botstein D, Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet. 2003;33:228\u201337.","journal-title":"Nat Genet"},{"key":"2305_CR3","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1186\/1471-2148-11-141","volume":"11","author":"EL Braun","year":"2011","unstructured":"Braun EL, Kimball RT, Han K, Iuhaszvelez NR, Bonilla AJ, Chojnowski JL, et al. Homoplastic microinversions and the avian tree of life. BMC Evol Biol. 2011;11:141.","journal-title":"BMC Evol Biol"},{"issue":"11 Suppl","key":"2305_CR4","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1038\/nmeth.1374","volume":"6","author":"P Medvedev","year":"2009","unstructured":"Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods. 2009;6(11 Suppl):S13\u201320.","journal-title":"Nat Methods"},{"issue":"9","key":"2305_CR5","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1363","volume":"6","author":"K Chen","year":"2009","unstructured":"Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohi CS, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009;6(9):677\u201381.","journal-title":"Nat Methods"},{"issue":"21","key":"2305_CR6","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","volume":"25","author":"K Ye","year":"2009","unstructured":"Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25(21):2865\u201371.","journal-title":"Bioinformatics"},{"issue":"20","key":"2305_CR7","doi-asserted-by":"crossref","first-page":"2576","DOI":"10.1093\/bioinformatics\/bts484","volume":"28","author":"Y Jiang","year":"2012","unstructured":"Jiang Y, Wang Y, Brudno M. PRISM: pair-read informed splitread mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics. 2012;28(20):2576\u201383.","journal-title":"Bioinformatics"},{"issue":"18","key":"2305_CR8","doi-asserted-by":"crossref","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","volume":"28","author":"T Rausch","year":"2012","unstructured":"Rausch T, Zichner T, Schlattl A, St\u00fctz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28(18):i333\u20139.","journal-title":"Bioinformatics"},{"key":"2305_CR9","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","volume":"21","author":"A Abyzov","year":"2011","unstructured":"Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011;21:974\u201384.","journal-title":"Genome Res"},{"issue":"24","key":"2305_CR10","doi-asserted-by":"crossref","first-page":"3484","DOI":"10.1093\/bioinformatics\/btu431","volume":"30","author":"K Trappe","year":"2014","unstructured":"Trappe K, Emde AK, Ehrlich HC, Reinert K. Gustaf: detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics. 2014;30(24):3484\u201390.","journal-title":"Bioinformatics"},{"key":"2305_CR11","doi-asserted-by":"crossref","unstructured":"Lin K, Smit S, Bonnema G, Sanchez-Perez G, de Ridder D. Making the difference: integrating structural variation detection tools. Brief Bioinform. 2015;16(5):852\u201364.","DOI":"10.1093\/bib\/bbu047"},{"issue":"52","key":"2305_CR12","doi-asserted-by":"crossref","first-page":"19824","DOI":"10.1073\/pnas.0603984103","volume":"103","author":"MJ Chaisson","year":"2006","unstructured":"Chaisson MJ, Raphael BJ, Pevzner PA. Microinversions in mammalian evolution. PNAS. 2006;103(52):19824\u20139.","journal-title":"PNAS"},{"issue":"12","key":"2305_CR13","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1101\/gr.5383506","volume":"16","author":"J Ma","year":"2006","unstructured":"Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, et al. Reconstructing contiguous regions of an ancestral genome. Genome Res. 2006;16(12):1557\u201365.","journal-title":"Genome Res"},{"key":"2305_CR14","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/gm132","volume":"2","author":"L Feuk","year":"2010","unstructured":"Feuk L. Inversion variants in the human genome: role in disease and genome architecture. Genome Medicine. 2010;2:11.","journal-title":"Genome Medicine"},{"key":"2305_CR15","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1016\/j.cancergen.2013.11.002","volume":"206","author":"HJ Abel","year":"2013","unstructured":"Abel HJ, Duncavage EJ. Detection of structural DNA variation from next generation sequencing data: a review of informatics approaches. Cancer Genet. 2013;206:432\u201340.","journal-title":"Cancer Genet"},{"issue":"7422","key":"2305_CR16","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","volume":"491","author":"GR Abecasis","year":"2012","unstructured":"The 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56\u201365.","journal-title":"Nature"},{"issue":"8","key":"2305_CR17","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/nmeth.1628","volume":"8","author":"J Wang","year":"2011","unstructured":"Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, et al. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods. 2011;8(8):652\u20134.","journal-title":"Nat Methods"},{"issue":"Suppl 14","key":"2305_CR18","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2105-12-S14-S7","volume":"12","author":"S Suzuki","year":"2001","unstructured":"Suzuki S, Yasuda T, Shiraishi Y, Miyano S, Nagasaki M. ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics. 2001;12 Suppl 14:S7.","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"2305_CR19","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H Li","year":"2008","unstructured":"Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008;18(11):1851\u20138.","journal-title":"Genome Res"},{"issue":"14","key":"2305_CR20","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754\u201360.","journal-title":"Bioinformatics"},{"issue":"9","key":"2305_CR21","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1101\/gr.135350.111","volume":"22","author":"J Harrow","year":"2012","unstructured":"Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res. 2012;22(9):1760\u201374.","journal-title":"Genome Res"},{"key":"2305_CR22","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"ENCODE Project Consortium","year":"2012","unstructured":"ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57\u201374.","journal-title":"Nature"},{"issue":"3","key":"2305_CR23","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1111\/joim.12231","volume":"276","author":"L Siggens","year":"2014","unstructured":"Siggens L, Ekwall K. Epigenetics, chromatin and genome organization: recent advances from the ENCODE project. J Intern Med. 2014;276(3):201\u201314.","journal-title":"J Intern Med"},{"key":"2305_CR24","doi-asserted-by":"crossref","unstructured":"Puig M, Casillas S, Villatoro S, Caceres M. Human inversions and their functional consequences. Brief Funct Genomics. 2015;14(5):369\u201379.","DOI":"10.1093\/bfgp\/elv020"},{"issue":"1","key":"2305_CR25","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1086\/498852","volume":"78","author":"J Jaeken","year":"2006","unstructured":"Jaeken J, Martens K, Francois I, Eyskens F, Lecointre C, Derua R, et al. Deletion of PREPL, a Gene Encoding a Putative Serine Oligopeptidase, in Patients with Hypotonia-Cystinuria Syndrome. Am J Hum Genet. 2006;78(1):38\u201351.","journal-title":"Am J Hum Genet"},{"issue":"5","key":"2305_CR26","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1136\/jmg.2007.055475","volume":"45","author":"B Chabrol","year":"2008","unstructured":"Chabrol B, Martens K, Meulemans S, Cano A, Jaeken J, Creemers GMWM. Deletion of c2orf34, prepl and slc3a1 causes atypical hypotonia\u2013cystinuria syndrome. J Med Genet. 2008;45(5):314\u20138.","journal-title":"J Med Genet"},{"issue":"10","key":"2305_CR27","volume":"5","author":"S Lew","year":"2007","unstructured":"Lew S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, et al. The diploid genome sequence of an individual human. PLoS Biol. 2007;5(10), e254.","journal-title":"PLoS Biol"},{"issue":"R2","key":"2305_CR28","doi-asserted-by":"crossref","first-page":"R163","DOI":"10.1093\/hmg\/ddp396","volume":"18","author":"ER Mardis","year":"2009","unstructured":"Mardis ER, Wilson RK. Cancer genome sequencing: a review. Hum Mol Genet. 2009;18(R2):R163\u20138.","journal-title":"Hum Mol Genet"},{"key":"2305_CR29","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","volume":"483","author":"J Barretina","year":"2012","unstructured":"Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, et al. The CancerCell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483:603\u20137.","journal-title":"Nature"},{"issue":"3","key":"2305_CR30","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/S0169-5002(02)00300-8","volume":"38","author":"C Shen","year":"2012","unstructured":"Shen C, Hui-Zhao, Wang D, Jiang G, Wang J, Zhang G. Molecular cloning, identification and analysis of lung squamous cell carcinoma-related genes. Lung Cancer. 2012;38(3):235\u201341.","journal-title":"Lung Cancer"},{"issue":"9","key":"2305_CR31","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1038\/nrg1945","volume":"7","author":"RJ Klose","year":"2006","unstructured":"Klose RJ, Kallin EM, Zhang Y. JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet. 2006;7(9):715\u201327.","journal-title":"Nat Rev Genet"},{"key":"2305_CR32","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.","journal-title":"Genome Biol"},{"key":"2305_CR33","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":"2305_CR34","unstructured":"Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. The Pennsylvania State University, College of Engineering; 2007."}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-015-2305-7","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T03:26:06Z","timestamp":1498274766000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.biomedcentral.com\/1471-2164\/17\/S1\/4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1]]},"references-count":34,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2016,1]]}},"alternative-id":["2305"],"URL":"https:\/\/doi.org\/10.1186\/s12864-015-2305-7","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,1]]},"article-number":"4"}}