{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T23:05:46Z","timestamp":1765667146077},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Med Genomics"],"published-print":{"date-parts":[[2016,8]]},"DOI":"10.1186\/s12920-016-0189-2","type":"journal-article","created":{"date-parts":[[2016,8,12]],"date-time":"2016-08-12T05:16:28Z","timestamp":1470978988000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Inferring Crohn\u2019s disease association from exome sequences by integrating biological knowledge"],"prefix":"10.1186","volume":"9","author":[{"given":"Chan-Seok","family":"Jeong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongsup","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,8,12]]},"reference":[{"issue":"R1","key":"189_CR1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/hmg\/dds387","volume":"21","author":"R Do","year":"2012","unstructured":"Do R, Kathiresan S, Abecasis GR. Exome sequencing and complex disease: practical aspects of rare variant association studies. Hum Mol Genet. 2012; 21(R1):1\u20139.","journal-title":"Hum Mol Genet"},{"issue":"40","key":"189_CR2","doi-asserted-by":"crossref","first-page":"6721","DOI":"10.3748\/wjg.v19.i40.6721","volume":"19","author":"CJ Cardinale","year":"2013","unstructured":"Cardinale CJ, Kelsen JR, Baldassano RN, Hakonarson H. Impact of exome sequencing in inflammatory bowel disease. World J Gastroenterol. 2013; 19(40):6721\u2013729.","journal-title":"World J Gastroenterol"},{"issue":"2","key":"189_CR3","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1053\/j.gastro.2013.04.040","volume":"145","author":"D Ellinghaus","year":"2013","unstructured":"Ellinghaus D, Zhang H, Zeissig S, Lipinski S, Till A, Jiang T, Stade B, Bromberg Y, Ellinghaus E, Keller A, Rivas MA, Skieceviciene J, Doncheva NT, Liu X, Liu Q, Jiang F, Forster M, Mayr G, Albrecht M, Hasler R, Boehm BO, Goodall J, Berzuini CR, Lee J, Andersen V, Vogel U, Kupcinskas L, Kayser M, Krawczak M, Nikolaus S, Weersma RK, Ponsioen CY, Sans M, Wijmenga C, Strachan DP, McArdle WL, Vermeire S, Rutgeerts P, Sanderson JD, Mathew CG, Vatn MH, Wang J, Nothen MM, Duerr RH, Buning C, Brand S, Glas J, Winkelmann J, Illig T, Latiano A, Annese V, Halfvarson J, DAmato M, Daly MJ, Nothnagel M, Karlsen TH, Subramani S, Rosenstiel P, Schreiber S, Parkes M, Franke A. Association Between Variants of PRDM1 and NDP52 and Crohn\u2019s Disease, Based on Exome Sequencing and Functional Studies. Gastroenterology. 2013; 145(2):339\u201347.","journal-title":"Gastroenterology"},{"issue":"5\u20136","key":"189_CR4","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.ygeno.2013.08.008","volume":"102","author":"DL Dinwiddie","year":"2013","unstructured":"Dinwiddie DL, Bracken JM, Bass JA, Christenson K, Soden SE, Saunders CJ, Miller NA, Singh V, Zwick DL, Roberts CC, Dalal J, Kingsmore SF. Molecular diagnosis of infantile onset inflammatory bowel disease by exome sequencing. Genomics. 2013; 102(5\u20136):442\u20137.","journal-title":"Genomics"},{"issue":"7","key":"189_CR5","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1136\/gutjnl-2011-301833","volume":"62","author":"K Christodoulou","year":"2013","unstructured":"Christodoulou K, Wiskin AE, Gibson J, Tapper W, Willis C, Afzal NA, Upstill- Goddard R, Holloway JW, Simpson MA, Beattie RM, Collins A, Ennis S. Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes. Gut. 2013; 62(7):977\u201384.","journal-title":"Gut"},{"issue":"6090","key":"189_CR6","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1126\/science.1219240","volume":"337","author":"JA Tennessen","year":"2012","unstructured":"Tennessen JA, Bigham AW, O\u2019Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM, Broad GO, Seattle GO, NHLBI Exome Sequencing Project. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012; 337(6090):64\u20139.","journal-title":"Science"},{"issue":"6","key":"189_CR7","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/ng.2303","volume":"44","author":"A Kiezun","year":"2012","unstructured":"Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Lehner T, Shugart YY, Price AL, de Bakker PIW, Purcell SM, Sunyaev SR. Exome sequencing and the genetic basis of complex traits. Nature Genetics. 2012; 44(6):623\u201330.","journal-title":"Nature Genetics"},{"issue":"7497","key":"189_CR8","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/nature13127","volume":"508","author":"DG MacArthur","year":"2014","unstructured":"MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C. Guidelines for investigating causality of sequence variants in human disease. Nature. 2014; 508(7497):469\u201376.","journal-title":"Nature"},{"issue":"Suppl 2","key":"189_CR9","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1755-8794-8-S2-S4","volume":"8","author":"YJ Na","year":"2015","unstructured":"Na YJ, Sohn KA, Kim JH. Interpretation of personal genome sequencing data in terms of disease ranks based on mutual information. BMC Medical Genomics. 2015; 8(Suppl 2):4.","journal-title":"BMC Medical Genomics"},{"key":"189_CR10","volume-title":"Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. KDD \u201906","author":"C Ding","year":"2006","unstructured":"Ding C, Li T, Peng W, Park H. Orthogonal nonnegative matrix t-factorizations for clustering. In: Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. KDD \u201906. New York, NY: ACM: 2006. p. 126\u201335."},{"issue":"19","key":"189_CR11","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1093\/nar\/gks615","volume":"40","author":"T Hwang","year":"2012","unstructured":"Hwang T, Atluri G, Xie M, Dey S, Hong C, Kumar V, Kuang R. Co-clustering phenome-genome for phenotype classification and disease gene discovery. Nucleic Acids Res. 2012; 40(19):146\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"189_CR12","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","volume":"7","author":"IA Adzhubei","year":"2010","unstructured":"Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010; 7(4):248\u20139.","journal-title":"Nat Methods"},{"issue":"Database issue","key":"189_CR13","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1093\/nar\/gks1244","volume":"41","author":"K Peng","year":"2013","unstructured":"Peng K, Xu W, Zheng J, Huang K, Wang H, Tong J, Lin Z, Liu J, Cheng W, Fu D, Du P, Kibbe WA, Lin SM, Xia T. The Disease and Gene Annotations (DGA): an annotation resource for human disease. Nucleic Acids Res. 2013; 41(Database issue):553\u201360.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"189_CR14","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1101\/gr.118992.110","volume":"21","author":"I Lee","year":"2011","unstructured":"Lee I, Blom UM, Wang PI, Shim JE, Marcotte EM. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res. 2011; 21(7):1109\u2013121.","journal-title":"Genome Res"},{"key":"189_CR15","volume-title":"Advances in Neural Information Processing Systems 13. NIPS 2000","author":"DD Lee","year":"2000","unstructured":"Lee DD, Seung SH. Algorithms for Non-negative Matrix Factorization. In: Advances in Neural Information Processing Systems 13. NIPS 2000. Cambridge, MA: MIT Press: 2000. p. 556\u201362."},{"issue":"5","key":"189_CR16","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1101\/gr.176601","volume":"11","author":"PC Ng","year":"2001","unstructured":"Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001; 11(5):863\u201374.","journal-title":"Genome Res"},{"issue":"8","key":"189_CR17","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1093\/hmg\/ddu733","volume":"24","author":"C Dong","year":"2015","unstructured":"Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, Liu X. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015; 24(8):2125\u201337.","journal-title":"Hum Mol Genet"},{"issue":"8","key":"189_CR18","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nmeth0810-575","volume":"7","author":"JM Schwarz","year":"2010","unstructured":"Schwarz JM, R\u00f6delsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010; 7(8):575\u20136.","journal-title":"Nat Methods"},{"issue":"12","key":"189_CR19","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1093\/bioinformatics\/btt182","volume":"29","author":"HA Shihab","year":"2013","unstructured":"Shihab HA, Gough J, Cooper DN, Day INM, Gaunt TR. Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinforma. 2013; 29(12):1504\u201310.","journal-title":"Bioinforma"},{"issue":"9","key":"189_CR20","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1101\/gr.772403","volume":"13","author":"PD Thomas","year":"2003","unstructured":"Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003; 13(9):2129\u201341.","journal-title":"Genome Res"},{"issue":"12","key":"189_CR21","doi-asserted-by":"crossref","first-page":"1001025","DOI":"10.1371\/journal.pcbi.1001025","volume":"6","author":"EV Davydov","year":"2010","unstructured":"Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol. 2010; 6(12):1001025.","journal-title":"PLoS Comput Biol"},{"issue":"7","key":"189_CR22","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1101\/gr.3577405","volume":"15","author":"GM Cooper","year":"2005","unstructured":"Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005; 15(7):901\u201313.","journal-title":"Genome Res"},{"issue":"Database issue","key":"189_CR23","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1093\/nar\/gkt1196","volume":"42","author":"P Flicek","year":"2014","unstructured":"Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho- Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Gir\u00f3n CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, K\u00e4h\u00e4ri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJP, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR, Searle SMJ. Ensembl 2014,. Nucleic Acids Res. 2014; 42(Database issue):749\u201355.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"189_CR24","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1093\/bioinformatics\/btn593","volume":"25","author":"X Wu","year":"2009","unstructured":"Wu X, Liu Q, Jiang R. Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinforma. 2009; 25(1):98\u2013104.","journal-title":"Bioinforma"}],"container-title":["BMC Medical Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12920-016-0189-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T16:34:56Z","timestamp":1498322096000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcmedgenomics.biomedcentral.com\/articles\/10.1186\/s12920-016-0189-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8]]},"references-count":24,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2016,8]]}},"alternative-id":["189"],"URL":"https:\/\/doi.org\/10.1186\/s12920-016-0189-2","relation":{},"ISSN":["1755-8794"],"issn-type":[{"value":"1755-8794","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8]]},"article-number":"35"}}