{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T18:56:02Z","timestamp":1773341762239,"version":"3.50.1"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1624-x","type":"journal-article","created":{"date-parts":[[2017,4,18]],"date-time":"2017-04-18T09:33:59Z","timestamp":1492508039000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization"],"prefix":"10.1186","volume":"18","author":[{"given":"Sarvesh","family":"Nikumbh","sequence":"first","affiliation":[]},{"given":"Nico","family":"Pfeifer","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,4,18]]},"reference":[{"issue":"3","key":"1624_CR1","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1186\/gb-2010-11-3-204","volume":"11","author":"N Cope","year":"2010","unstructured":"Cope N, Fraser P, Eskiw C. The yin and yang of chromatin spatial organization. Genome Biol. 2010; 11(3):204. doi:\n                        10.1186\/gb-2010-11-3-204\n                        \n                    .","journal-title":"Genome Biol"},{"issue":"1","key":"1624_CR2","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1146\/annurev-genom-091212-153515","volume":"14","author":"WA Bickmore","year":"2013","unstructured":"Bickmore WA. The spatial organization of the human genome. Annu Rev Genomics Hum Genet. 2013; 14(1):67\u201384. doi:\n                        10.1146\/annurev-genom-091212-153515\n                        \n                    . PMID: 23875797. \n                        http:\/\/dx.doi.org\/10.1146\/annurev-genom-091212-153515","journal-title":"Annu Rev Genomics Hum Genet"},{"issue":"1","key":"1624_CR3","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1101\/gad.179804.111","volume":"26","author":"E de Wit","year":"2012","unstructured":"de Wit E, de Laat W. A decade of 3C technologies: insights into nuclear organization. Gene Dev. 2012; 26(1):11\u201324. doi:\n                        10.1101\/gad.179804.111\n                        \n                    .","journal-title":"Gene Dev"},{"issue":"5558","key":"1624_CR4","doi-asserted-by":"publisher","first-page":"1306","DOI":"10.1126\/science.1067799","volume":"295","author":"J Dekker","year":"2002","unstructured":"Dekker J, et al. Capturing chromosome conformation. Science. 2002; 295(5558):1306\u201311. doi:\n                        10.1126\/science.1067799\n                        \n                    . \n                        http:\/\/www.sciencemag.org\/content\/295\/5558\/1306.full.pdf\n                        \n                    .","journal-title":"Science"},{"issue":"11","key":"1624_CR5","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1038\/ng1896","volume":"38","author":"M Simonis","year":"2006","unstructured":"Simonis M, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 2006; 38(11):1348\u201354. doi:\n                        10.1038\/ng1896\n                        \n                    .","journal-title":"Nat Genet"},{"issue":"11","key":"1624_CR6","doi-asserted-by":"publisher","first-page":"1341","DOI":"10.1038\/ng1891","volume":"38","author":"Z Zhao","year":"2006","unstructured":"Zhao Z, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet. 2006; 38(11):1341\u20137. doi:\n                        10.1038\/ng1891\n                        \n                    .","journal-title":"Nat Genet"},{"issue":"10","key":"1624_CR7","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1101\/gr.5571506","volume":"16","author":"J Dostie","year":"2006","unstructured":"Dostie J, et al. Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006; 16(10):1299\u2013309. doi:\n                        10.1101\/gr.5571506\n                        \n                    . \n                        http:\/\/genome.cshlp.org\/content\/16\/10\/1299.full.pdf+html\n                        \n                    .","journal-title":"Genome Res"},{"issue":"7269","key":"1624_CR8","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/nature08497","volume":"462","author":"MJ Fullwood","year":"2009","unstructured":"Fullwood MJ, et al. An oestrogen-receptor-[agr]-bound human chromatin interactome. Nature. 2009; 462(7269):58\u201364. doi:\n                        10.1038\/nature08497\n                        \n                    .","journal-title":"Nature"},{"issue":"5950","key":"1624_CR9","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1126\/science.1181369","volume":"326","author":"E Lieberman-Aiden","year":"2009","unstructured":"Lieberman-Aiden E, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289\u201393. doi:\n                        10.1126\/science.1181369\n                        \n                    . \n                        http:\/\/www.sciencemag.org\/content\/326\/5950\/289.full.pdf\n                        \n                    .","journal-title":"Science"},{"issue":"7","key":"1624_CR10","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","volume":"159","author":"SSP Rao","year":"2014","unstructured":"Rao SSP, et al. A 3d map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159(7):1665\u201380. doi:\n                        10.1016\/j.cell.2014.11.021\n                        \n                    .","journal-title":"Cell"},{"issue":"12","key":"1624_CR11","doi-asserted-by":"publisher","first-page":"1905","DOI":"10.1101\/gr.176586.114","volume":"24","author":"N Heidari","year":"2014","unstructured":"Heidari N, et al. Genome-wide map of regulatory interactions in the human genome. Genome Res. 2014; 24(12):1905\u20131917. doi:\n                        10.1101\/gr.176586.114\n                        \n                    . \n                        http:\/\/genome.cshlp.org\/content\/24\/12\/1905.full.pdf+html\n                        \n                    .","journal-title":"Genome Res"},{"issue":"9","key":"1624_CR12","doi-asserted-by":"publisher","first-page":"73974","DOI":"10.1371\/journal.pone.0073974","volume":"8","author":"MJ Zeitz","year":"2013","unstructured":"Zeitz MJ, et al. Genomic interaction profiles in breast cancer reveal altered chromatin architecture. PLoS ONE. 2013; 8(9):73974. doi:\n                        10.1371\/journal.pone.0073974\n                        \n                    .","journal-title":"PLoS ONE"},{"issue":"6","key":"1624_CR13","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1038\/nrg3454","volume":"14","author":"J Dekker","year":"2013","unstructured":"Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013; 14(6):390\u2013403. Review.","journal-title":"Nat Rev Genet"},{"key":"1624_CR14","unstructured":"Roy S, et al. A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res. 2015. doi:\n                        10.1093\/nar\/gkv865\n                        \n                    . \n                        http:\/\/nar.oxfordjournals.org\/content\/early\/2015\/09\/03\/nar.gkv865.full.pdf+html\n                        \n                    ."},{"issue":"7398","key":"1624_CR15","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature11082","volume":"485","author":"JR Dixon","year":"2012","unstructured":"Dixon JR, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485(7398):376\u201380. doi:\n                        10.1038\/nature11082\n                        \n                    .","journal-title":"Nature"},{"issue":"12","key":"1624_CR16","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1093\/bioinformatics\/btu268","volume":"30","author":"N Varoquaux","year":"2014","unstructured":"Varoquaux N, et al. A statistical approach for inferring the 3D structure of the genome. Bioinformatics (Oxford). 2014; 30(12):26\u201333. doi:\n                        10.1093\/bioinformatics\/btu268\n                        \n                    .","journal-title":"Bioinformatics (Oxford)"},{"key":"1624_CR17","volume-title":"Proceedings of the Fifth Annual Workshop on Computational Learning Theory. COLT \u201992","author":"BE Boser","year":"1992","unstructured":"Boser BE, Guyon IM, Vapnik VN. A training algorithm for optimal margin classifiers. In: Proceedings of the Fifth Annual Workshop on Computational Learning Theory. COLT \u201992. New York: ACM: 1992. p. 144\u201352. doi:\n                        10.1145\/130385.130401\n                        \n                    . \n                        http:\/\/doi.acm.org\/10.1145\/130385.130401\n                        \n                    ."},{"issue":"7414","key":"1624_CR18","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1038\/nature11279","volume":"489","author":"A Sanyal","year":"2012","unstructured":"Sanyal A, et al. The long-range interaction landscape of gene promoters. Nature. 2012; 489(7414):109\u201313. doi:\n                        10.1038\/nature11279\n                        \n                    .","journal-title":"Nature"},{"issue":"18","key":"1624_CR19","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.1093\/bioinformatics\/btl376","volume":"22","author":"T Lingner","year":"2006","unstructured":"Lingner T, Meinicke P. Remote homology detection based on oligomer distances. Bioinformatics (Oxford). 2006; 22(18):2224\u201331. doi:\n                        10.1093\/bioinformatics\/btl376\n                        \n                    . Accessed 24 May 2011","journal-title":"Bioinformatics (Oxford)"},{"issue":"4","key":"1624_CR20","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1007\/BF00196228","volume":"84","author":"P Vogt","year":"1990","unstructured":"Vogt P. Potential genetic functions of tandem repeated dna sequence blocks in the human genome are based on a highly conserved \"chromatin folding code\". Hum Genet. 1990; 84(4):301\u201336. doi:\n                        10.1007\/bf00196228\n                        \n                    .","journal-title":"Hum Genet"},{"issue":"12","key":"1624_CR21","doi-asserted-by":"publisher","first-page":"2610","DOI":"10.1128\/MCB.4.12.2610","volume":"4","author":"H Hamada","year":"1984","unstructured":"Hamada H, et al. Characterization of genomic poly(dt-dg).poly(dc-da) sequences: structure, organization, and conformation. Mol Cell Biol. 1984; 4(12):2610\u201321. 6098814.","journal-title":"Mol Cell Biol"},{"issue":"7","key":"1624_CR22","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1101\/gr.169243.113","volume":"24","author":"JO Y\u00e1\u00f1ez-Cuna","year":"2014","unstructured":"Y\u00e1\u00f1ez-Cuna JO, et al. Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Res. 2014; 24(7):1147\u201356. doi:\n                        10.1101\/gr.169243.113\n                        \n                    . \n                        http:\/\/genome.cshlp.org\/content\/24\/7\/1147.full.pdf+html\n                        \n                    .","journal-title":"Genome Res"},{"issue":"2","key":"1624_CR23","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.gene.2014.08.052","volume":"551","author":"S Ramamoorthy","year":"2014","unstructured":"Ramamoorthy S, et al. Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation. Gene. 2014; 551(2):167\u201375. doi:\n                        10.1016\/j.gene.2014.08.052\n                        \n                    .","journal-title":"Gene"},{"issue":"3-4","key":"1624_CR24","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1016\/S0361-9230(01)00597-4","volume":"56","author":"A Malaspina","year":"2001","unstructured":"Malaspina A, et al. A survey of trinucleotide\/tandem repeat-containing transcripts (tnrts) isolated from human spinal cord to identify genes containing unstable {DNA} regions as candidates for disorders of motor function. Brain Res Bull. 2001; 56(3-4):299\u2013306. doi:\n                        10.1016\/S0361-9230(01)00597-4\n                        \n                    . Triplet Repeat Diseases","journal-title":"Brain Res Bull"},{"issue":"5","key":"1624_CR25","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/j.ygeno.2013.03.003","volume":"101","author":"KJ Brookes","year":"2013","unstructured":"Brookes KJ. The {VNTR} in complex disorders: The forgotten polymorphisms? a functional way forward?. Genomics. 2013; 101(5):273\u201381. doi:\n                        10.1016\/j.ygeno.2013.03.003\n                        \n                    .","journal-title":"Genomics"},{"key":"1624_CR26","unstructured":"Knight PA, Ruiz D. A fast algorithm for matrix balancing. IMA J Numer Anal. 2012. doi:\n                        10.1093\/imanum\/drs019\n                        \n                    . \n                        http:\/\/imajna.oxfordjournals.org\/content\/early\/2012\/10\/26\/imanum.drs019.full.pdf+html\n                        \n                    ."},{"issue":"2","key":"1624_CR27","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1038\/ng.2871","volume":"46","author":"JR Hughes","year":"2014","unstructured":"Hughes JR, et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet. 2014; 46(2):205\u201312. Technical Report.","journal-title":"Nat Genet"},{"issue":"8","key":"1624_CR28","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1101\/gr.5113606","volume":"16","author":"A Tanay","year":"2006","unstructured":"Tanay A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res. 2006; 16(8):962\u201372. doi:\n                        10.1101\/gr.5113606\n                        \n                    . \n                        http:\/\/genome.cshlp.org\/content\/16\/8\/962.full.pdf+html\n                        \n                    .","journal-title":"Genome Res"},{"issue":"9","key":"1624_CR29","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1101\/gr.135350.111","volume":"22","author":"J Harrow","year":"2012","unstructured":"Harrow J, et al. Gencode: The reference human genome annotation for the encode project. Genome Res. 2012; 22(9):1760\u201374. doi:\n                        10.1101\/gr.135350.111\n                        \n                    . \n                        http:\/\/genome.cshlp.org\/content\/22\/9\/1760.full.pdf+html\n                        \n                    .","journal-title":"Genome Res"},{"issue":"1","key":"1624_CR30","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1093\/nar\/30.1.207","volume":"30","author":"R Edgar","year":"2002","unstructured":"Edgar R, Domrachev M, Lash AE. Gene expression omnibus: Ncbi gene expression and hybridization array data repository. Nucleic Acids Res. 2002; 30(1):207\u201310. doi:\n                        10.1093\/nar\/30.1.207\n                        \n                    . \n                        http:\/\/nar.oxfordjournals.org\/content\/30\/1\/207.full.pdf+html\n                        \n                    .","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1624_CR31","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1186\/1471-2105-5-169","volume":"5","author":"P Meinicke","year":"2004","unstructured":"Meinicke P, et al. Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites. BMC Bioinforma. 2004; 5(1):169. doi:\n                        10.1186\/1471-2105-5-169\n                        \n                    .","journal-title":"BMC Bioinforma"},{"key":"1624_CR32","volume-title":"Kernel Methods in Computational Biology. MIT Press series on Computational Molecular Biology","author":"G R\u00e4tsch","year":"2004","unstructured":"R\u00e4tsch G, Sonnenburg S. Accurate splice site prediction for caenorhabditis elegans. In: Kernel Methods in Computational Biology. MIT Press series on Computational Molecular Biology. Cambridge: MIT Press: 2004. p. 277\u201398."},{"issue":"suppl 1","key":"1624_CR33","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1093\/bioinformatics\/bti1053","volume":"21","author":"G R\u00e4tsch","year":"2005","unstructured":"R\u00e4tsch G, et al. Rase: recognition of alternatively spliced exons in c.elegans. Bioinformatics. 2005; 21(suppl 1):369\u201377. doi:\n                        10.1093\/bioinformatics\/bti1053\n                        \n                    . \n                        http:\/\/bioinformatics.oxfordjournals.org\/content\/21\/suppl_1\/i369.full.pdf+html\n                        \n                    .","journal-title":"Bioinformatics"},{"key":"1624_CR34","volume-title":"Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. KDD \u201904","author":"T Evgeniou","year":"2004","unstructured":"Evgeniou T, Pontil M. Regularized multi\u2013task learning. In: Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. KDD \u201904. New York: ACM: 2004. p. 109\u201317. doi:\n                        10.1145\/1014052.1014067\n                        \n                    . \n                        http:\/\/doi.acm.org\/10.1145\/1014052.1014067\n                        \n                    ."},{"key":"1624_CR35","first-page":"615","volume":"6","author":"T Evgeniou","year":"2005","unstructured":"Evgeniou T, et al. Learning multiple tasks with kernel methods. J Mach Learn Res. 2005; 6:615\u201337.","journal-title":"J Mach Learn Res"},{"issue":"3","key":"1624_CR36","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1093\/bioinformatics\/btm611","volume":"24","author":"L Jacob","year":"2008","unstructured":"Jacob L, Vert JP. Efficient peptide\u2014mhc-i binding prediction for alleles with few known binders. Bioinformatics. 2008; 24(3):358\u201366. doi:\n                        10.1093\/bioinformatics\/btm611\n                        \n                    . \n                        http:\/\/bioinformatics.oxfordjournals.org\/content\/24\/3\/358.full.pdf+html\n                        \n                    .","journal-title":"Bioinformatics"},{"key":"1624_CR37","first-page":"207","volume":"27","author":"C Widmer","year":"2012","unstructured":"Widmer C, R\u00e4tsch G. Multitask learning in computational biology. JMLR W&CP. ICML 2011 Unsupervised and Transfer Learning Workshop. 2012; 27:207\u201316.","journal-title":"JMLR W&CP. ICML 2011 Unsupervised and Transfer Learning Workshop"},{"issue":"1","key":"1624_CR38","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1186\/s13059-015-0745-7","volume":"16","author":"F Ay","year":"2015","unstructured":"Ay F, Noble W. Analysis methods for studying the 3d architecture of the genome. Genome Biol. 2015; 16(1):183. doi:\n                        10.1186\/s13059-015-0745-7\n                        \n                    .","journal-title":"Genome Biol"},{"key":"1624_CR39","volume-title":"Proceedings of the 17th International Joint Conference on Artificial Intelligence - Volume 2. IJCAI\u201901","author":"C Elkan","year":"2001","unstructured":"Elkan C. The foundations of cost-sensitive learning. In: Proceedings of the 17th International Joint Conference on Artificial Intelligence - Volume 2. IJCAI\u201901. San Francisco: Morgan Kaufmann Publishers Inc.: 2001. p. 973\u20138. \n                        http:\/\/dl.acm.org\/citation.cfm?id=1642194.1642224\n                        \n                    ."},{"key":"1624_CR40","doi-asserted-by":"publisher","first-page":"6097","DOI":"10.1093\/nar\/18.20.6097","volume":"18","author":"TD Schneider","year":"1990","unstructured":"Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990; 18:6097\u2013100.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1624-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,4,18]],"date-time":"2017-04-18T09:34:15Z","timestamp":1492508055000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1624-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,4,18]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1624"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1624-x","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,4,18]]},"article-number":"218"}}