{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:06:07Z","timestamp":1787162767517,"version":"build-2736575974"},"reference-count":51,"publisher":"Elsevier BV","issue":"1","content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Gene"],"published-print":{"date-parts":[[2014,6]]},"DOI":"10.1016\/j.gene.2014.03.057","type":"journal-article","created":{"date-parts":[[2014,4,1]],"date-time":"2014-04-01T18:03:16Z","timestamp":1396375396000},"page":"108-117","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"title":["Systems biology approach for mutational and site-specific structural investigation of DNA repair genes for xeroderma pigmentosum"],"prefix":"10.1016","volume":"543","author":[{"given":"Manika","family":"Sehgal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiratha Raj","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.gene.2014.03.057_bb0005","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nature Methods"},{"key":"10.1016\/j.gene.2014.03.057_bb0010","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1006\/jmbi.1999.3310","article-title":"Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites","volume":"294","author":"Blom","year":"1999","journal-title":"Journal of Molecular Biology"},{"key":"10.1016\/j.gene.2014.03.057_bb0015","first-page":"677","article-title":"Nucleotide excision repair syndromes: xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy","volume":"vol. 1","author":"Bootsma","year":"2001"},{"key":"10.1016\/j.gene.2014.03.057_bb0020","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1136\/jmg.2010.083022","article-title":"Cancer and neurologic degeneration in xeroderma pigmentosum: long term follow-up characterizes the role of DNA repair","volume":"48","author":"Bradford","year":"2011","journal-title":"Journal of Medical Genetics"},{"key":"10.1016\/j.gene.2014.03.057_bb0025","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1007\/s11033-010-0258-0","article-title":"Effects of selected genetic polymorphisms in xeroderma pigmentosum complementary group D on gastric cancer","volume":"38","author":"Chen","year":"2011","journal-title":"Molecular Biology Reports"},{"key":"10.1016\/j.gene.2014.03.057_bb0030","doi-asserted-by":"crossref","first-page":"W621","DOI":"10.1093\/nar\/gkl071","article-title":"PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes","volume":"34","author":"Conde","year":"2006","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/j.gene.2014.03.057_bb0035","first-page":"87","article-title":"Xeroderma pigmentosum: a case report and review of the literature","volume":"51","author":"Feller","year":"2010","journal-title":"Journal of Preventive Medicine and Hygiene"},{"key":"10.1016\/j.gene.2014.03.057_bb0040","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/35094000","article-title":"How nucleotide excision repair protects against cancer","volume":"1","author":"Friedberg","year":"2001","journal-title":"Nature Reviews Cancer"},{"key":"10.1016\/j.gene.2014.03.057_bb9000","series-title":"DNA Repair and Mutagenesis","author":"Friedberg","year":"2006"},{"key":"10.1016\/j.gene.2014.03.057_bb0045","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S1478-5382(03)02370-9","article-title":"CellDesigner: a process diagram editor for gene-regulatory and biochemical networks","volume":"1","author":"Funahashi","year":"2003","journal-title":"BIOSILICO"},{"key":"10.1016\/j.gene.2014.03.057_bb0050","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/S0163-7258(98)00056-4","article-title":"Protein phosphorylation and signal transduction","volume":"82","author":"Graves","year":"1999","journal-title":"Pharmacology & Therapeutics"},{"key":"10.1016\/j.gene.2014.03.057_bb0055","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/elps.1150181505","article-title":"SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling","volume":"18","author":"Guex","year":"1997","journal-title":"Electrophoresis"},{"key":"10.1016\/j.gene.2014.03.057_bb0060","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.mrfmmm.2006.06.010","article-title":"Heterozygous individuals bearing a founder mutation in the XPA DNA repair gene comprise nearly 1% of the Japanese population","volume":"601","author":"Hirai","year":"2006","journal-title":"Mutation Research"},{"key":"10.1016\/j.gene.2014.03.057_bb0065","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/35077232","article-title":"Genome maintenance mechanisms for preventing cancer","volume":"411","author":"Hoeijmakers","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.gene.2014.03.057_bb0070","doi-asserted-by":"crossref","first-page":"15898","DOI":"10.1074\/jbc.271.27.15898","article-title":"A 3\u2032\u21925\u2032 XPB helicases defect in repair\/transcription factor TFIIH of xeroderma pigmentosum group B affects both DNA repair and transcription","volume":"271","author":"Hwang","year":"1996","journal-title":"The Journal of Biological Chemistry"},{"key":"10.1016\/j.gene.2014.03.057_bb0075","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"10.1016\/j.gene.2014.03.057_bb0080","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1016\/j.neuroscience.2006.12.020","article-title":"Xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome: a complex genotype\u2013phenotype relationship","volume":"145","author":"Kraemer","year":"2007","journal-title":"Neuroscience"},{"key":"10.1016\/j.gene.2014.03.057_bb0085","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/nar\/27.1.237","article-title":"PhosphoBase, a database of phosphorylation sites: release 2.0","volume":"27","author":"Kreegipuu","year":"1999","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/j.gene.2014.03.057_bb0090","doi-asserted-by":"crossref","first-page":"9784","DOI":"10.1128\/MCB.25.22.9784-9792.2005","article-title":"Xeroderma pigmentosum complementation group E protein (XPE\/DDB2): purification of various complexes of XPE and analyses of their damaged DNA binding and putative DNA repair properties","volume":"25","author":"Kulaksiz","year":"2005","journal-title":"Molecular and Cellular Biology"},{"key":"10.1016\/j.gene.2014.03.057_bb0095","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1007\/s11693-013-9105-7","article-title":"A quantitative study of gene regulatory pathways in Bacillus subtilis for virulence and competence phenotype by quorum sensing","volume":"7","author":"Kumar","year":"2013","journal-title":"Systems and Synthetic Biology"},{"key":"10.1016\/j.gene.2014.03.057_bb0100","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/nprot.2009.86","article-title":"Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm","volume":"4","author":"Kumar","year":"2009","journal-title":"Nature Protocols"},{"key":"10.1016\/j.gene.2014.03.057_bb0105","doi-asserted-by":"crossref","first-page":"W299","DOI":"10.1093\/nar\/gki370","article-title":"The projection of evolutionary conservation scores of residues on protein structures","volume":"33","author":"Landau","year":"2005","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/j.gene.2014.03.057_bb0110","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"Laskoswki","year":"1993","journal-title":"Journal of Applied Crystallography"},{"key":"10.1016\/j.gene.2014.03.057_bb0115","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1073\/pnas.72.1.219","article-title":"Xeroderma pigmentosum cells with normal levels of excision repair have a defect in DNA synthesis after UV irradiation","volume":"72","author":"Lehmann","year":"1975","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/j.gene.2014.03.057_bb0120","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/1750-1172-6-70","article-title":"Xeroderma pigmentosum","volume":"6","author":"Lehmann","year":"2011","journal-title":"Orphanet Journal of Rare Diseases"},{"key":"10.1016\/j.gene.2014.03.057_bb0125","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1128\/MCB.26.4.1398-1413.2006","article-title":"DNA polymerase \u03b7, the product of the xeroderma pigmentosum variant gene and a target of p53, modulates the DNA damage checkpoint and p53 activation","volume":"26","author":"Liu","year":"2006","journal-title":"Molecular and Cellular Biology"},{"key":"10.1016\/j.gene.2014.03.057_bb0130","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1016\/j.jaad.2008.06.030","article-title":"Skin cancers, blindness, and anterior tongue mass in African brothers","volume":"59","author":"Mahindra","year":"2008","journal-title":"Journal of the American Academy of Dermatology"},{"key":"10.1016\/j.gene.2014.03.057_bb0135","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/j.str.2011.03.010","article-title":"Relative solvent accessible surface area predicts protein conformational changes upon binding","volume":"19","author":"Marsh","year":"2011","journal-title":"Structure"},{"key":"10.1016\/j.gene.2014.03.057_bb0140","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1038\/21447","article-title":"The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta","volume":"399","author":"Masutani","year":"1999","journal-title":"Nature"},{"key":"10.1016\/j.gene.2014.03.057_bb0145","doi-asserted-by":"crossref","first-page":"20862","DOI":"10.1074\/jbc.270.35.20862","article-title":"Human DNA repair excision nuclease. Analysis of the roles of the subunits involved in dual incisions by using anti-XPG and anti-ERCC1 antibodies","volume":"270","author":"Matsunaga","year":"1995","journal-title":"The Journal of Biological Chemistry"},{"key":"10.1016\/j.gene.2014.03.057_bb0150","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1186\/1471-2164-14-496","article-title":"Gene bionetworks that regulate ovarian primordial follicle assembly","volume":"14","author":"Nilsson","year":"2013","journal-title":"BMC Genomics"},{"key":"10.1016\/j.gene.2014.03.057_bb0155","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1038\/371432a0","article-title":"XPG endonuclease makes the 3\u2032 incision in human DNA nucleotide excision repair","volume":"371","author":"O'Donovan","year":"1994","journal-title":"Nature"},{"key":"10.1016\/j.gene.2014.03.057_bb0160","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.jtbi.2013.06.013","article-title":"Computational studies on Alzheimer's disease associated pathways and regulatory patterns using microarray gene expression and network data: revealed association with aging and other diseases","volume":"334C","author":"Panigrahi","year":"2013","journal-title":"Journal of Theoretical Biology"},{"key":"10.1016\/j.gene.2014.03.057_bb0165","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/1472-6807-9-51","article-title":"A generic method for assignment of reliability scores applied to solvent accessibility predictions","volume":"9","author":"Petersen","year":"2009","journal-title":"BMC Structural Biology"},{"key":"10.1016\/j.gene.2014.03.057_bb0170","doi-asserted-by":"crossref","first-page":"1442","DOI":"10.1212\/WNL.55.10.1442","article-title":"Cockayne syndrome and xeroderma pigmentosum","volume":"55","author":"Rapin","year":"2000","journal-title":"Neurology"},{"key":"10.1016\/j.gene.2014.03.057_bb0175","doi-asserted-by":"crossref","first-page":"221","DOI":"10.7326\/0003-4819-80-2-221","article-title":"Xeroderma pigmentosum: an inherited disease with sun-sensitivity, multiple cutaneous neoplasms, and abnormal DNA repair","volume":"80","author":"Robbins","year":"1974","journal-title":"Annals of Internal Medicine"},{"key":"10.1016\/j.gene.2014.03.057_bb0180","doi-asserted-by":"crossref","first-page":"e67461","DOI":"10.1371\/journal.pone.0067461","article-title":"High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications","volume":"8","author":"Rohr","year":"2013","journal-title":"PloS One"},{"key":"10.1016\/j.gene.2014.03.057_bb0185","doi-asserted-by":"crossref","first-page":"2388","DOI":"10.1002\/j.1460-2075.1994.tb06522.x","article-title":"The ERCC2\/DNA repair protein is associated with the class II BTF2\/TFIIH transcription factor","volume":"13","author":"Schaeffer","year":"1994","journal-title":"The EMBO Journal"},{"key":"10.1016\/j.gene.2014.03.057_bb0190","first-page":"139","article-title":"Identification and analysis of biomarkers for repair proteins: a bioinformatic approach","volume":"3","author":"Sehgal","year":"2012","journal-title":"JNSBM"},{"key":"10.1016\/j.gene.2014.03.057_bb0195","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.dnarep.2014.01.004","article-title":"DRGAS: a database of functional genetic variants and their phosphorylation states in human DNA repair systems","volume":"16","author":"Sehgal","year":"2014","journal-title":"DNA Repair"},{"key":"10.1016\/j.gene.2014.03.057_bb0200","first-page":"e34","article-title":"Computational identification and analysis of single-nucleotide polymorphisms and insertions\/deletions in expressed sequence tag data of eucalyptus","volume":"90","author":"Singh","year":"2011","journal-title":"Journal of Genetics"},{"key":"10.1016\/j.gene.2014.03.057_bb0205","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1093\/carcin\/bgm282","article-title":"Xeroderma pigmentosum genes: functions inside and outside DNA repair","volume":"29","author":"Sugasawa","year":"2008","journal-title":"Carcinogenesis"},{"key":"10.1016\/j.gene.2014.03.057_bb0210","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.cell.2005.02.035","article-title":"UV-induced ubiquitylation of XPC protein mediated by UV-DDB\u2013ubiquitin ligase complex","volume":"121","author":"Sugasawa","year":"2005","journal-title":"Cell"},{"key":"10.1016\/j.gene.2014.03.057_bb0215","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1093\/protein\/12.5.387","article-title":"PSIC: profile extraction from sequence alignments with position specific counts of independent observations","volume":"12","author":"Sunyaev","year":"1999","journal-title":"Protein Engineering"},{"key":"10.1016\/j.gene.2014.03.057_bb0220","doi-asserted-by":"crossref","first-page":"1592","DOI":"10.1101\/gr.4413105","article-title":"The International HapMap Project website","volume":"15","author":"Thorisson","year":"2005","journal-title":"Genome Research"},{"key":"10.1016\/j.gene.2014.03.057_bb0225","doi-asserted-by":"crossref","first-page":"W65","DOI":"10.1093\/nar\/gks364","article-title":"SNPnexus: a web server for functional annotation of novel and publicly known genetic variants","volume":"40","author":"Ullah","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/j.gene.2014.03.057_bb0230","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/S1097-2765(01)00281-7","article-title":"Sequential assembly of the nucleotide excision repair factors in vivo","volume":"8","author":"Volker","year":"2001","journal-title":"Molecular Cell"},{"key":"10.1016\/j.gene.2014.03.057_bb0235","doi-asserted-by":"crossref","first-page":"4258","DOI":"10.1074\/jbc.275.6.4258","article-title":"TFIIH with inactive XPD helicases functions in transcription initiation but is defective in DNA repair","volume":"275","author":"Winkler","year":"2000","journal-title":"The Journal of Biological Chemistry"},{"key":"10.1016\/j.gene.2014.03.057_bb0240","doi-asserted-by":"crossref","first-page":"2997","DOI":"10.1158\/0008-5472.CAN-05-3403","article-title":"Phosphorylation of nucleotide excision repair factor xeroderma pigmentosum group A by ataxia telangiectasia mutated and Rad3-related-dependent checkpoint pathway promotes cell survival in response to UV irradiation","volume":"66","author":"Wu","year":"2006","journal-title":"Cancer Research"},{"key":"10.1016\/j.gene.2014.03.057_bb0245","doi-asserted-by":"crossref","first-page":"W635","DOI":"10.1093\/nar\/gkl236","article-title":"FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization","volume":"34","author":"Yuan","year":"2006","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/j.gene.2014.03.057_bb0250","first-page":"1163","article-title":"Correlation of XPD gene with susceptibility to gastric cancer","volume":"28","author":"Zhang","year":"2009","journal-title":"Ai Zheng"}],"container-title":["Gene"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0378111914003953?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0378111914003953?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2019,8,9]],"date-time":"2019-08-09T00:11:01Z","timestamp":1565309461000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0378111914003953"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,6]]},"references-count":51,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,6]]}},"alternative-id":["S0378111914003953"],"URL":"https:\/\/doi.org\/10.1016\/j.gene.2014.03.057","relation":{},"ISSN":["0378-1119"],"issn-type":[{"value":"0378-1119","type":"print"}],"subject":[],"published":{"date-parts":[[2014,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Systems biology approach for mutational and site-specific structural investigation of DNA repair genes for xeroderma pigmentosum","name":"articletitle","label":"Article Title"},{"value":"Gene","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.gene.2014.03.057","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2014 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}]}}