TY - JOUR AU - Griffith, F. PY - 1928 DA - 1928// TI - The significance of pneumococcal types JO - J Hyg VL - 27 UR - https://doi.org/10.1017/S0022172400031879 DO - 10.1017/S0022172400031879 ID - Griffith1928 ER - TY - JOUR AU - Riley, D. R. AU - Sieber, K. B. AU - Robinson, K. M. AU - White, J. R. AU - Ganesan, A. AU - Nourbakhsh, S. AU - Dunning Hotopp, J. C. PY - 2013 DA - 2013// TI - Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003107 DO - 10.1371/journal.pcbi.1003107 ID - Riley2013 ER - TY - JOUR AU - Robinson, K. AU - Hotopp, J. D. PY - 2014 DA - 2014// TI - Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen JO - Cancer Lett VL - 352 UR - https://doi.org/10.1016/j.canlet.2014.05.021 DO - 10.1016/j.canlet.2014.05.021 ID - Robinson2014 ER - TY - JOUR AU - Parkin, D. PY - 2006 DA - 2006// TI - The global health burden of infection-associated cancers in the year 2002 JO - Int J Cancer VL - 118 UR - https://doi.org/10.1002/ijc.21731 DO - 10.1002/ijc.21731 ID - Parkin2006 ER - TY - JOUR AU - Morissette, G. AU - Flamand, L. PY - 2010 DA - 2010// TI - Herpesviruses and chromosomal integration JO - J Virol VL - 84 UR - https://doi.org/10.1128/JVI.01169-10 DO - 10.1128/JVI.01169-10 ID - Morissette2010 ER - TY - JOUR AU - Read, S. AU - Douglas, M. PY - 2014 DA - 2014// TI - Virus induced inflammation and cancer development JO - Cancer Lett VL - 345 UR - https://doi.org/10.1016/j.canlet.2013.07.030 DO - 10.1016/j.canlet.2013.07.030 ID - Read2014 ER - TY - JOUR AU - Shibata, D. AU - Weiss, L. M. PY - 1992 DA - 1992// TI - Epstein-Barr virus-associated gastric adenocarcinoma JO - Am J Pathol VL - 140 ID - Shibata1992 ER - TY - JOUR AU - Fahraeus, R. AU - Fu, H. L. AU - Ernberg, I. AU - Finke, J. AU - Rowe, M. AU - Klein, G. AU - Falk, K. AU - Nilsson, E. AU - Yadav, M. AU - Busson, P. PY - 1988 DA - 1988// TI - Expression of Epstein-Barr virus-encoded proteins in nasopharyngeal carcinoma JO - Int J Cancer VL - 42 UR - https://doi.org/10.1002/ijc.2910420305 DO - 10.1002/ijc.2910420305 ID - Fahraeus1988 ER - TY - JOUR AU - McLaughlin-Drubin, M. E. AU - Munger, K. PY - 2008 DA - 2008// TI - Viruses associated with human cancer JO - Biochim Biophys Acta VL - 1782 UR - https://doi.org/10.1016/j.bbadis.2007.12.005 DO - 10.1016/j.bbadis.2007.12.005 ID - McLaughlin-Drubin2008 ER - TY - JOUR AU - Sung, W. AU - Zheng, H. AU - Li, S. AU - Chen, R. AU - Liu, X. AU - Li, Y. AU - Lee, N. AU - Lee, W. AU - Ariyaratne, P. AU - Tennakoon, C. PY - 2012 DA - 2012// TI - Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma JO - Nat Genet VL - 44 UR - https://doi.org/10.1038/ng.2295 DO - 10.1038/ng.2295 ID - Sung2012 ER - TY - JOUR AU - Das, P. AU - Thomas, A. AU - Mahantshetty, U. AU - Shrivastava, S. AU - Deodhar, K. AU - Mulherkar, R. PY - 2012 DA - 2012// TI - HPV genotyping and site of viral integration in cervical cancers in Indian women JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0041012 DO - 10.1371/journal.pone.0041012 ID - Das2012 ER - TY - JOUR AU - Corden, S. AU - Sant-Cassia, L. AU - Easton, A. AU - Morris, A. PY - 1999 DA - 1999// TI - The integration of HPV-18 DNA in cervical carcinoma JO - J Clin Pathol VL - 52 ID - Corden1999 ER - TY - JOUR AU - Melsheimer, P. AU - Vinokurova, S. AU - Wentzensen, N. AU - Bastert, G. AU - Doeberitz, M. K. PY - 2004 DA - 2004// TI - DNA aneuploidy and integration of human papillomavirus type 16 E6/E7 oncogenes in intraepithelial neoplasia and invasive squamous cell carcinoma of the cervix uteri JO - Clin Canc Res VL - 10 UR - https://doi.org/10.1158/1078-0432.CCR-03-0565 DO - 10.1158/1078-0432.CCR-03-0565 ID - Melsheimer2004 ER - TY - JOUR AU - Tsakogiannis, D. AU - Gortsilas, P. AU - Kyriakopoulou, Z. AU - Ruether, I. AU - Dimitriou, T. AU - Orfanoudakis, G. AU - Markoulatos, P. PY - 2015 DA - 2015// TI - Sites of disruption within E1 and E2 genes of HPV15 and association with cervical dysplasia JO - J Med Virol VL - 87 UR - https://doi.org/10.1002/jmv.24256 DO - 10.1002/jmv.24256 ID - Tsakogiannis2015 ER - TY - JOUR AU - Sastre-Garau, X. AU - Peter, M. AU - Avril, M. AU - Laude, H. AU - Couturier, J. AU - Rozenberg, F. AU - Almeida, A. AU - Boitier, F. AU - Carlotti, A. AU - Couturaud, B. PY - 2009 DA - 2009// TI - Merkel cell carcinoma of the skin: pathological and molecular evidence for a causative role of MCV in oncogenesis JO - J Pathol VL - 218 UR - https://doi.org/10.1002/path.2532 DO - 10.1002/path.2532 ID - Sastre-Garau2009 ER - TY - JOUR AU - Feng, H. AU - Shuda, M. AU - Chang, Y. AU - Moore, P. PY - 2008 DA - 2008// TI - Clonal integration of a polyomavirus in human Merkel cell carcinoma JO - Science VL - 319 UR - https://doi.org/10.1126/science.1152586 DO - 10.1126/science.1152586 ID - Feng2008 ER - TY - JOUR AU - Li, J. AU - Wang, X. AU - Diaz, J. AU - Tsang, S. AU - Buck, C. AU - You, J. PY - 2013 DA - 2013// TI - Merkel cell polyomavirus large T antigen disrupts host genomic integrity and inhibits cellular proliferation JO - J Virol VL - 87 UR - https://doi.org/10.1128/JVI.01216-13 DO - 10.1128/JVI.01216-13 ID - Li2013 ER - TY - JOUR AU - Bornkamm, G. PY - 2009 DA - 2009// TI - Epstein-Barr virus and the pathogenesis of Burkitt's lymphoma: more questions than answers JO - Int J Cancer VL - 124 UR - https://doi.org/10.1002/ijc.24223 DO - 10.1002/ijc.24223 ID - Bornkamm2009 ER - TY - STD TI - Hau PM, Tsao SW. Epstein-Barr virus hijacks DNA damage response transducers to orchestrate its life cycle. Viruses. 2017;9(11):341. ID - ref19 ER - TY - JOUR AU - Khoury, J. AU - Tannir, N. AU - Williams, M. AU - Xhen, Y. AU - Yao, H. AU - Zhang, J. AU - Thompson, E. AU - Network, T. AU - Meric-Bernstam, F. AU - Medeiros, L. PY - 2013 DA - 2013// TI - Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq JO - J Virol VL - 87 UR - https://doi.org/10.1128/JVI.00340-13 DO - 10.1128/JVI.00340-13 ID - Khoury2013 ER - TY - JOUR AU - Tang, K. AU - Alaei-Mahabadi, B. AU - Samuelsson, T. AU - Lindh, M. AU - Larsson, E. PY - 2013 DA - 2013// TI - The landscape of viral expression and host gene fusion and adaptation in human cancer JO - Nature Comm VL - 4 UR - https://doi.org/10.1038/ncomms3513 DO - 10.1038/ncomms3513 ID - Tang2013 ER - TY - JOUR AU - Fimereli, D. AU - Gacquer, D. AU - Fumgalli, D. AU - Salgado, R. AU - Rothé, F. AU - Larsimont, D. AU - Sotiriou, C. AU - Detours, V. PY - 2015 DA - 2015// TI - No significant viral transcription detected in whole breast cancer transcriptomes JO - BMC Cancer VL - 15 UR - https://doi.org/10.1186/s12885-015-1176-2 DO - 10.1186/s12885-015-1176-2 ID - Fimereli2015 ER - TY - JOUR AU - Chen, Y. AU - Yao, H. AU - Thompson, E. J. AU - Tannir, N. M. AU - Weinstein, J. N. AU - Su, X. PY - 2013 DA - 2013// TI - VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts665 DO - 10.1093/bioinformatics/bts665 ID - Chen2013 ER - TY - JOUR AU - Li, J. W. AU - Wan, R. AU - Yu, C. S. AU - Co, N. N. AU - Wong, N. AU - Chan, T. F. PY - 2013 DA - 2013// TI - ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt011 DO - 10.1093/bioinformatics/btt011 ID - Li2013 ER - TY - JOUR AU - Wang, Q. AU - Jia, P. AU - Zhao, Z. PY - 2013 DA - 2013// TI - VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0064465 DO - 10.1371/journal.pone.0064465 ID - Wang2013 ER - TY - JOUR AU - Wang, Q. AU - Jia, P. AU - Zhao, Z. PY - 2015 DA - 2015// TI - VERSE: a novel approach to detect virus integration in host genomes through reference genome customization JO - Genome Med VL - 7 UR - https://doi.org/10.1186/s13073-015-0126-6 DO - 10.1186/s13073-015-0126-6 ID - Wang2015 ER - TY - JOUR AU - Tennakoon, C. AU - Sung, W. K. PY - 2017 DA - 2017// TI - BATVI: fast, sensitive and accurate detection of virus integrations JO - BMC Bioinformatics VL - 18 UR - https://doi.org/10.1186/s12859-017-1470-x DO - 10.1186/s12859-017-1470-x ID - Tennakoon2017 ER - TY - JOUR AU - Hu, Z. AU - Zhu, D. AU - Wang, W. AU - Li, W. AU - Jia, W. AU - Zeng, X. AU - Ding, W. AU - Yu, L. AU - Wang, X. AU - Wang, L. PY - 2015 DA - 2015// TI - Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism JO - Nat Genet VL - 47 UR - https://doi.org/10.1038/ng.3178 DO - 10.1038/ng.3178 ID - Hu2015 ER - TY - JOUR PY - 2012 DA - 2012// TI - Comprehensive molecular portraits of human breast tumours JO - Nature VL - 490 UR - https://doi.org/10.1038/nature11412 DO - 10.1038/nature11412 ID - ref29 ER - TY - STD TI - The Cancer Genome Atlas Network: Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell 2017, 169(7):1327-1341.e1323. ID - ref30 ER - TY - STD TI - Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv e-prints 2013. ID - ref31 ER - TY - STD TI - Pruitt K BG, Tatusova T, et al. The Reference Sequence (RefSeq) Database. In: The NCBI handbook [Internet] Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information 2002. ID - ref32 ER - TY - JOUR AU - Gabrielian, A. AU - Bolshoy, A. PY - 1999 DA - 1999// TI - Sequence complexity and DNA curvature JO - Comput Chem VL - 23 UR - https://doi.org/10.1016/S0097-8485(99)00007-8 DO - 10.1016/S0097-8485(99)00007-8 ID - Gabrielian1999 ER - TY - STD TI - Smit AFA, Hubley,R, Green P. RepeatMasker Open-3.0; 1996-2010. [http://www.repeatmasker.org/]. UR - http://www.repeatmasker.org/ ID - ref34 ER - TY - JOUR AU - Quail, M. A. AU - Kozarewa, I. AU - Smith, F. AU - Scally, A. AU - Stephens, P. J. AU - Durbin, R. AU - Swerdlow, H. AU - Turner, D. J. PY - 2008 DA - 2008// TI - A large genome center's improvements to the Illumina sequencing system JO - Nat Methods VL - 5 UR - https://doi.org/10.1038/nmeth.1270 DO - 10.1038/nmeth.1270 ID - Quail2008 ER - TY - JOUR AU - Untergasser, A. AU - Cutcutache, I. AU - Koressaar, T. AU - Ye, J. AU - Faircloth, B. AU - Reem, M. AU - Rozen, S. PY - 2012 DA - 2012// TI - Primer3--new capabilities and interfaces JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks596 DO - 10.1093/nar/gks596 ID - Untergasser2012 ER - TY - STD TI - Li H, Wgsim. 2011. [https://github.com/lh3/wgsim]. UR - https://github.com/lh3/wgsim ID - ref37 ER - TY - JOUR AU - Zhang, J. AU - Gao, Y. PY - 2017 DA - 2017// TI - CCAT-1 promotes proliferation and inhibits apoptosis of cervical cancer cells via the Wnt signaling pathway JO - Oncotarget VL - 8 ID - Zhang2017 ER - TY - JOUR AU - Nakamura, Y. AU - Migita, T. AU - Hosoda, F. AU - Okada, N. AU - Gotoh, M. AU - Arai, Y. AU - Fukushima, M. AU - Ohki, M. AU - Miyata, S. AU - Takeuchi, K. PY - 2009 DA - 2009// TI - Kruppel-like factor 12 plays a significant role in poorly differentiated gastric cancer progression JO - Int J Cancer VL - 125 UR - https://doi.org/10.1002/ijc.24538 DO - 10.1002/ijc.24538 ID - Nakamura2009 ER - TY - JOUR AU - Godin-Heymann, N. AU - Brabetz, S. AU - Murillo, M. M. AU - Saponaro, M. AU - Santos, C. R. AU - Lobley, A. AU - East, P. AU - Chakravarty, P. AU - Matthews, N. AU - Kelly, G. PY - 2016 DA - 2016// TI - Tumour-suppression function of KLF12 through regulation of anoikis JO - Oncogene VL - 35 UR - https://doi.org/10.1038/onc.2015.394 DO - 10.1038/onc.2015.394 ID - Godin-Heymann2016 ER - TY - JOUR AU - Xuan, Y. H. AU - Jung, H. S. AU - Choi, Y. L. AU - Shin, Y. K. AU - Kim, H. J. AU - Kim, K. H. AU - Kim, W. J. AU - Lee, Y. J. AU - Kim, S. H. PY - 2006 DA - 2006// TI - Enhanced expression of hedgehog signaling molecules in squamous cell carcinoma of uterine cervix and its precursor lesions JO - Mod Pathol VL - 19 UR - https://doi.org/10.1038/modpathol.3800600 DO - 10.1038/modpathol.3800600 ID - Xuan2006 ER - TY - JOUR AU - Nault, J. C. AU - Zucman-Rossi, J. PY - 2016 DA - 2016// TI - TERT promoter mutations in primary liver tumors JO - Clin Res Hepatol Gastroenterol VL - 40 UR - https://doi.org/10.1016/j.clinre.2015.07.006 DO - 10.1016/j.clinre.2015.07.006 ID - Nault2016 ER - TY - JOUR AU - Quaas, A. AU - Oldopp, T. AU - Tharun, L. AU - Klingenfeld, C. AU - Krech, T. AU - Sauter, G. AU - Grob, T. J. PY - 2014 DA - 2014// TI - Frequency of TERT promoter mutations in primary tumors of the liver JO - Virchows Arch VL - 465 UR - https://doi.org/10.1007/s00428-014-1658-7 DO - 10.1007/s00428-014-1658-7 ID - Quaas2014 ER - TY - JOUR AU - Caldon, C. E. AU - Musgrove, E. A. PY - 2010 DA - 2010// TI - Distinct and redundant functions of cyclin E1 and cyclin E2 in development and cancer JO - Cell Div VL - 5 UR - https://doi.org/10.1186/1747-1028-5-2 DO - 10.1186/1747-1028-5-2 ID - Caldon2010 ER - TY - JOUR AU - Cashman, R. AU - Cohen, H. AU - Ben-Hamo, R. AU - Zilberberg, A. AU - Efroni, S. PY - 2014 DA - 2014// TI - SENP5 mediates breast cancer invasion via a TGFbetaRI SUMOylation cascade JO - Oncotarget VL - 5 UR - https://doi.org/10.18632/oncotarget.1783 DO - 10.18632/oncotarget.1783 ID - Cashman2014 ER - TY - JOUR AU - Soikkeli, J. AU - Podlasz, P. AU - Yin, M. AU - Nummela, P. AU - Jahkola, T. AU - Virolainen, S. AU - Krogerus, L. AU - Heikkila, P. AU - von Smitten, K. AU - Saksela, O. PY - 2010 DA - 2010// TI - Metastatic outgrowth encompasses COL-I, FN1, and POSTN up-regulation and assembly to fibrillar networks regulating cell adhesion, migration, and growth JO - Am J Pathol VL - 177 UR - https://doi.org/10.2353/ajpath.2010.090748 DO - 10.2353/ajpath.2010.090748 ID - Soikkeli2010 ER - TY - JOUR AU - Rao, R. C. AU - Dou, Y. PY - 2015 DA - 2015// TI - Hijacked in cancer: the KMT2 (MLL) family of methyltransferases JO - Nat Rev Cancer VL - 15 UR - https://doi.org/10.1038/nrc3929 DO - 10.1038/nrc3929 ID - Rao2015 ER - TY - JOUR AU - Young, J. M. AU - Whiddon, J. L. AU - Yao, Z. AU - Kasinathan, B. AU - Snider, L. AU - Geng, L. N. AU - Balog, J. AU - Tawil, R. AU - van der Maarel, S. M. AU - Tapscott, S. J. PY - 2013 DA - 2013// TI - DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003947 DO - 10.1371/journal.pgen.1003947 ID - Young2013 ER - TY - JOUR AU - Etemadmoghadam, D. AU - Weir, B. A. AU - Au-Yeung, G. AU - Alsop, K. AU - Mitchell, G. AU - George, J. AU - Davis, S. AU - D'Andrea, A. D. AU - Simpson, K. AU - Hahn, W. C. PY - 2013 DA - 2013// TI - Synthetic lethality between CCNE1 amplification and loss of BRCA1 JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1314302110 DO - 10.1073/pnas.1314302110 ID - Etemadmoghadam2013 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. AU - Marth, G. AU - Abecasis, G. AU - Durbin, R. PY - 2009 DA - 2009// TI - 1000 genome project data processing subgroup: the sequence alignment/map (SAM) format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - Quinlan, A. R. AU - Hall, I. M. PY - 2010 DA - 2010// TI - BEDTools: a flexible suite of utilities for comparing genomic features JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq033 DO - 10.1093/bioinformatics/btq033 ID - Quinlan2010 ER - TY - JOUR AU - Zhang, H. AU - Meltzer, P. AU - Davis, S. PY - 2013 DA - 2013// TI - RCircos: an R package for Circos 2D track plots JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-244 DO - 10.1186/1471-2105-14-244 ID - Zhang2013 ER -