-
1
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
The 1000 Genomes Project Consortium
-
The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
-
2
-
-
84881401766
-
The haplotype-resolved genome and epigenome of the aneuploid hela cancer cell line
-
Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP,Martin BK, Qiu R, Lee C, Shendure J. 2013. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature 500: 207-211.
-
(2013)
Nature
, vol.500
, pp. 207-211
-
-
Adey, A.1
Burton, J.N.2
Kitzman, J.O.3
Hiatt, J.B.4
Lewis, A.P.5
Martin, B.K.6
Qiu, R.7
Lee, C.8
Shendure, J.9
-
3
-
-
80052177544
-
Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in notch1
-
Agrawal N, FrederickMJ, Pickering CR, Bettegowda C,Chang K, Li RJ, Fakhry C, Xie TX, Zhang J,Wang J, et al. 2011. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 333: 1154-1157.
-
(2011)
Science
, vol.333
, pp. 1154-1157
-
-
Agrawal, N.1
Frederick, M.J.2
Pickering, C.R.3
Bettegowda, C.4
Chang, K.5
Li, R.J.6
Fakhry, C.7
Xie, T.X.8
Zhang, J.9
Wang, J.10
-
4
-
-
0032763848
-
Establishment and characterization of four cell lines derived from human head and neck squamous cell carcinomas for an autologous tumor-fibroblast in vitro model
-
Ballo H, Koldovsky P, Hoffmann T, Balz V, Hildebrandt B, Gerharz CD, Bier H. 1999. Establishment and characterization of four cell lines derived from human head and neck squamous cell carcinomas for an autologous tumor-fibroblast in vitro model. Anticancer Res 19: 3827-3836.
-
(1999)
Anticancer Res
, vol.19
, pp. 3827-3836
-
-
Ballo, H.1
Koldovsky, P.2
Hoffmann, T.3
Balz, V.4
Hildebrandt, B.5
Gerharz, C.D.6
Bier, H.7
-
5
-
-
84864192630
-
Role of p63 in development, tumorigenesis and cancer progression
-
Bergholz J, Xiao ZX. 2012. Role of p63 in development, tumorigenesis and cancer progression. Cancer Microenviron 5: 311-322.
-
(2012)
Cancer Microenviron
, vol.5
, pp. 311-322
-
-
Bergholz, J.1
Xiao, Z.X.2
-
6
-
-
80052565730
-
Human papillomavirus and rising oropharyngeal cancer incidence in the united states
-
Chaturvedi A, Engels E, Pfeiffer R, Hernandez B, Xiao W, Kim E, Jiang B, Goodman M, Sibug-Saber M, Cozen W, et al. 2011. Human papillomavirus and rising oropharyngeal cancer incidence in the United States. J Clin Oncol 29: 4294-4301.
-
(2011)
J Clin Oncol
, vol.29
, pp. 4294-4301
-
-
Chaturvedi, A.1
Engels, E.2
Pfeiffer, R.3
Hernandez, B.4
Xiao, W.5
Kim, E.6
Jiang, B.7
Goodman, M.8
Sibug-Saber, M.9
Cozen, W.10
-
7
-
-
79952523494
-
Aurora b regulates formin mdia3 in achieving metaphase chromosome alignment
-
Cheng L, Zhang J, Ahmad S, Rozier L, Yu H, Deng H, Mao Y. 2011. Aurora B regulates formin mDia3 in achieving metaphase chromosome alignment. Dev Cell 20: 342-352.
-
(2011)
Dev Cell
, vol.20
, pp. 342-352
-
-
Cheng, L.1
Zhang, J.2
Ahmad, S.3
Rozier, L.4
Yu, H.5
Deng, H.6
Mao, Y.7
-
8
-
-
84862777955
-
Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration
-
Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR et al. 2012. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet 44: 390-397.
-
(2012)
Nat Genet
, vol.44
, pp. 390-397
-
-
Chiang, C.1
Jacobsen, J.C.2
Ernst, C.3
Hanscom, C.4
Heilbut, A.5
Blumenthal, I.6
Mills, R.E.7
Kirby, A.8
Lindgren, A.M.9
Rudiger, S.R.10
-
9
-
-
0023629535
-
Integration of human papillomavirus type 16 into cellular dna of cervical carcinoma: Preferential deletion of the e2 gene and invariable retention of the long control region and the e6/e7 open reading frames
-
Choo KB, Pan CC, Han SH. 1987. Integration of human papillomavirus type 16 into cellular DNA of cervical carcinoma: Preferential deletion of the E2 gene and invariable retention of the long control region and the E6/E7 open reading frames. Virology 161: 259-261.
-
(1987)
Virology
, vol.161
, pp. 259-261
-
-
Choo, K.B.1
Pan, C.C.2
Han, S.H.3
-
10
-
-
84864012296
-
Human papillomavirus type 16 genetic variants: Phylogeny and classification based on e6 and lcr
-
Cornet I, Gheit T, Franceschi S, Vignat J, Burk RD, Sylla BS, Tommasino M, Clifford GM. 2012. Human papillomavirus type 16 genetic variants: Phylogeny and classification based on E6 and LCR. J Virol 86: 6855-6861.
-
(2012)
J Virol
, vol.86
, pp. 6855-6861
-
-
Cornet, I.1
Gheit, T.2
Franceschi, S.3
Vignat, J.4
Burk, R.D.5
Sylla, B.S.6
Tommasino, M.7
Clifford, G.M.8
-
11
-
-
84856424908
-
Dna breaks and chromosome pulverization from errors in mitosis
-
Crasta K, Ganem NJ, Dagher R, Lantermann AB, Ivanova EV, Pan Y, Nezi L, Protopopov A, Chowdhury D, Pellman D. 2012. DNA breaks and chromosome pulverization from errors in mitosis. Nature 482: 53-58.
-
(2012)
Nature
, vol.482
, pp. 53-58
-
-
Crasta, K.1
Ganem, N.J.2
Dagher, R.3
Lantermann, A.B.4
Ivanova, E.V.5
Pan, Y.6
Nezi, L.7
Protopopov, A.8
Chowdhury, D.9
Pellman, D.10
-
13
-
-
79955550445
-
A user's guide to the encyclopedia of dna elements (encode)
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.
-
(2011)
PLoS Biol
, vol.9
-
-
-
14
-
-
84880473591
-
Back to the origin: Reconsidering replication, transcription, epigenetics, and cell cycle control
-
Evertts AG, Coller HA. 2012. Back to the origin: Reconsidering replication, transcription, epigenetics, and cell cycle control. Genes Cancer 3: 678-696.
-
(2012)
Genes Cancer
, vol.3
, pp. 678-696
-
-
Evertts, A.G.1
Coller, H.A.2
-
15
-
-
0030751044
-
Evidence for a switch in the mode of human papillomavirus type 16 dna replication during the viral life cycle
-
Flores ER, Lambert PF. 1997. Evidence for a switch in the mode of human papillomavirus type 16 DNA replication during the viral life cycle. J Virol 71: 7167-7179.
-
(1997)
J Virol
, vol.71
, pp. 7167-7179
-
-
Flores, E.R.1
Lambert, P.F.2
-
16
-
-
84875321843
-
Global burden of human papillomavirus and related diseases
-
Forman D, de Martel C, Lacey CJ, Soerjomataram I, Lortet-Tieulent J, Bruni L, Vignat J, Ferlay J, Bray F, Plummer M, et al. 2012. Global burden of human papillomavirus and related diseases. Vaccine (Suppl 5) 30: F12-F23.
-
(2012)
Vaccine
, vol.30
, Issue.SUPPL. 5
-
-
Forman, D.1
De Martel, C.2
Lacey, C.J.3
Soerjomataram, I.4
Lortet-Tieulent, J.5
Bruni, L.6
Vignat, J.7
Ferlay, J.8
Bray, F.9
Plummer, M.10
-
17
-
-
84866728909
-
Chromothripsis and cancer: Causes and consequences of chromosome shattering
-
Forment JV, Kaidi A, Jackson SP. 2012. Chromothripsis and cancer: Causes and consequences of chromosome shattering. Nat Rev Cancer 12: 663-670.
-
(2012)
Nat Rev Cancer
, vol.12
, pp. 663-670
-
-
Forment, J.V.1
Kaidi, A.2
Jackson, S.P.3
-
18
-
-
0014878448
-
Studies on a new human cell line (siha) derived from carcinoma of uterus. I. Its establishment and morphology
-
Friedl F, Kimura I, Osato T, Ito Y. 1970. Studies on a new human cell line (SiHa) derived from carcinoma of uterus. I. Its establishment and morphology. Proc Soc Exp Biol Med 135: 543-545.
-
(1970)
Proc Soc Exp Biol Med
, vol.135
, pp. 543-545
-
-
Friedl, F.1
Kimura, I.2
Osato, T.3
Ito, Y.4
-
19
-
-
84866178768
-
Human papillomaviruses recruit cellular dna repair and homologous recombination factors to viral replication centers
-
Gillespie KA, Mehta KP, Laimins LA, Moody CA. 2012. Human papillomaviruses recruit cellular DNA repair and homologous recombination factors to viral replication centers. J Virol 86: 9520-9526.
-
(2012)
J Virol
, vol.86
, pp. 9520-9526
-
-
Gillespie, K.A.1
Mehta, K.P.2
Laimins, L.A.3
Moody, C.A.4
-
20
-
-
0142125389
-
Chapter 9: Role of mucosal human papillomavirus in nongenital cancers
-
Gillison ML, Shah KV. 2003. Chapter 9: Role of mucosal human papillomavirus in nongenital cancers. J Natl Cancer Inst Monogr 2003: 57-65.
-
(2003)
J Natl Cancer Inst Monogr
, vol.2003
, pp. 57-65
-
-
Gillison, M.L.1
Shah, K.V.2
-
21
-
-
0034600339
-
Evidence for a causal association between human papillomavirus and a subset of head and neck cancers
-
Gillison ML, Koch WM, Capone RB, Spafford M, Westra WH, Wu L, Zahurak ML, Daniel RW, Viglione M, Symer DE, et al. 2000. Evidence for a causal association between human papillomavirus and a subset of head and neck cancers. J Natl Cancer Inst 92: 709-720.
-
(2000)
J Natl Cancer Inst
, vol.92
, pp. 709-720
-
-
Gillison, M.L.1
Koch, W.M.2
Capone, R.B.3
Spafford, M.4
Westra, W.H.5
Wu, L.6
Zahurak, M.L.7
Daniel, R.W.8
Viglione, M.9
Symer, D.E.10
-
22
-
-
0023764848
-
Two new human tumor cell lines derived from squamous cell carcinomas of the tongue: Establishment, characterization and response to cytotoxic treatment
-
Gioanni J, Fischel JL, Lambert JC, Demard F, Mazeau C, Zanghellini E, Ettore F, Formento P, Chauvel P, Lalanne CM, et al. 1988. Two new human tumor cell lines derived from squamous cell carcinomas of the tongue: Establishment, characterization and response to cytotoxic treatment. Eur J Cancer Clin Oncol 24: 1445-1455.
-
(1988)
Eur J Cancer Clin Oncol
, vol.24
, pp. 1445-1455
-
-
Gioanni, J.1
Fischel, J.L.2
Lambert, J.C.3
Demard, F.4
Mazeau, C.5
Zanghellini, E.6
Ettore, F.7
Formento, P.8
Chauvel, P.9
Lalanne, C.M.10
-
23
-
-
84855185866
-
Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data
-
Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S. 2012. Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics 28: 40-47.
-
(2012)
Bioinformatics
, vol.28
, pp. 40-47
-
-
Gusnanto, A.1
Wood, H.M.2
Pawitan, Y.3
Rabbitts, P.4
Berri, S.5
-
24
-
-
0034614637
-
The hallmarks of cancer
-
Hanahan D, Weinberg RA. 2000. The hallmarks of cancer. Cell 100: 57-70.
-
(2000)
Cell
, vol.100
, pp. 57-70
-
-
Hanahan, D.1
Weinberg, R.A.2
-
25
-
-
0024804363
-
Hpv16 e6 and e7 proteins cooperate to immortalize human foreskin keratinocytes
-
Hawley-Nelson P, Vousden KH, Hubbert NL, Lowy DR, Schiller JT. 1989. HPV16 E6 and E7 proteins cooperate to immortalize human foreskin keratinocytes. EMBO J 8: 3905-3910.
-
(1989)
EMBO J
, vol.8
, pp. 3905-3910
-
-
Hawley-Nelson, P.1
Vousden, K.H.2
Hubbert, N.L.3
Lowy, D.R.4
Schiller, J.T.5
-
26
-
-
0030841013
-
Advanced-stage cervical carcinomas are defined by a recurrent pattern of chromosomal aberrations revealing high genetic instability and a consistent gain of chromosome arm 3q
-
Heselmeyer K, Macville M, Schrock E, Blegen H, Hellstrom AC, Shah K, Auer G, Ried T. 1997. Advanced-stage cervical carcinomas are defined by a recurrent pattern of chromosomal aberrations revealing high genetic instability and a consistent gain of chromosome arm 3q. Genes Chromosomes Cancer 19: 233-240.
-
(1997)
Genes Chromosomes Cancer
, vol.19
, pp. 233-240
-
-
Heselmeyer, K.1
Macville, M.2
Schrock, E.3
Blegen, H.4
Hellstrom, A.C.5
Shah, K.6
Auer, G.7
Ried, T.8
-
27
-
-
79955555195
-
Comprehensive long-span pairedend-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
-
Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, et al. 2011. Comprehensive long-span pairedend-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res 21: 665-675.
-
(2011)
Genome Res
, vol.21
, pp. 665-675
-
-
Hillmer, A.M.1
Yao, F.2
Inaki, K.3
Lee, W.H.4
Ariyaratne, P.N.5
Teo, A.S.6
Woo, X.Y.7
Zhang, Z.8
Zhao, H.9
Ukil, L.10
-
28
-
-
4444291843
-
Detection of large-scale variation in the human genome
-
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
-
(2004)
Nat Genet
, vol.36
, pp. 949-951
-
-
Iafrate, A.J.1
Feuk, L.2
Rivera, M.N.3
Listewnik, M.L.4
Donahoe, P.K.5
Qi, Y.6
Scherer, S.W.7
Lee, C.8
-
29
-
-
40949118920
-
Human papillomaviruses
-
IARC Working Group on the Evaluation of Carcinogenic Risks to Humans
-
IARC Working Group on the Evaluation of Carcinogenic Risks to Humans. 2007. Human papillomaviruses. IARC Monogr Eval Carcinog Risks Hum 90: 1-636.
-
(2007)
IARC Monogr Eval Carcinog Risks Hum
, vol.90
, pp. 1-636
-
-
-
30
-
-
0003676646
-
-
International Standing Committee on Human Cytogenetic Nomenclature. Karger Medical Scientific, Basel, Switzerland
-
International Standing Committee on Human Cytogenetic Nomenclature. 2009. ICSN 2009: An international system for human cytogenetic nomenclature. Karger Medical Scientific, Basel, Switzerland.
-
(2009)
ICSN 2009: An International System for Human Cytogenetic Nomenclature
-
-
-
31
-
-
0028900490
-
Integration of human papillomavirus type 16 dna into the human genome leads to increased stability of e6 and e7 mrnas: Implications for cervical carcinogenesis
-
Jeon S, Lambert PF. 1995. Integration of human papillomavirus type 16 DNA into the human genome leads to increased stability of E6 and E7 mRNAs: Implications for cervical carcinogenesis. Proc Natl Acad Sci 92: 1654-1658.
-
(1995)
Proc Natl Acad Sci
, vol.92
, pp. 1654-1658
-
-
Jeon, S.1
Lambert, P.F.2
-
32
-
-
84859553856
-
The effects of hepatitis b virus integration into the genomes of hepatocellular carcinoma patients
-
Jiang Z, Jhunjhunwala S, Liu J, Haverty PM, Kennemer MI, Guan Y, Lee W, Carnevali P, Stinson J, Johnson S, et al. 2012. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res 22: 593-601.
-
(2012)
Genome Res
, vol.22
, pp. 593-601
-
-
Jiang, Z.1
Jhunjhunwala, S.2
Liu, J.3
Haverty, P.M.4
Kennemer, M.I.5
Guan, Y.6
Lee, W.7
Carnevali, P.8
Stinson, J.9
Johnson, S.10
-
33
-
-
34247198246
-
Genomic instability of the host cell induced by the human papillomavirus replication machinery
-
Kadaja M, Sumerina A, Verst T, Ojarand M, Ustav E, Ustav M. 2007. Genomic instability of the host cell induced by the human papillomavirus replication machinery. EMBO J 26: 2180-2191.
-
(2007)
EMBO J
, vol.26
, pp. 2180-2191
-
-
Kadaja, M.1
Sumerina, A.2
Verst, T.3
Ojarand, M.4
Ustav, E.5
Ustav, M.6
-
35
-
-
0036226603
-
Blat -The blast-like alignment tool
-
Kent WJ. 2002. BLAT -The BLAST-like alignment tool. Genome Res 12: 656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
36
-
-
84881229283
-
Landscape of dna virus associations across human malignant cancers: Analysis of 3,775 cases using rna-seq
-
Khoury JD, Tannir NM,Williams MD, Chen Y, Yao H, Zhang J, Thompson EJ, TCGA Network, Meric-Bernstam F, Medeiros LJ, et al. 2013. Landscape of DNA virus associations across human malignant cancers: Analysis of 3,775 cases using RNA-Seq. J Virol 87: 8916-8926.
-
(2013)
J Virol
, vol.87
, pp. 8916-8926
-
-
Khoury, J.D.1
Tannir, N.M.2
Williams, M.D.3
Chen, Y.4
Yao, H.5
Zhang, J.6
Thompson, E.J.7
Tcga, N.8
Meric-Bernstam, F.9
Medeiros, L.J.10
-
37
-
-
0033572319
-
Detection of high-risk cervical intraepithelial neoplasia and cervical cancer by amplification of transcripts derived from integrated papillomavirus oncogenes
-
Klaes R,Woerner SM, Ridder R,Wentzensen N, Duerst M, Schneider A, Lotz B, Melsheimer P, von Knebel Doeberitz M. 1999. Detection of high-risk cervical intraepithelial neoplasia and cervical cancer by amplification of transcripts derived from integrated papillomavirus oncogenes. Cancer Res 59: 6132-6136.
-
(1999)
Cancer Res
, vol.59
, pp. 6132-6136
-
-
Klaes, R.1
Woerner, S.M.2
Ridder, R.3
Wentzensen, N.4
Duerst, M.5
Schneider, A.6
Lotz, B.7
Melsheimer, P.8
Von Knebel Doeberitz, M.9
-
38
-
-
84875135862
-
Criteria for inference of chromothripsis in cancer genomes
-
Korbel JO, Campbell PJ. 2013. Criteria for inference of chromothripsis in cancer genomes. Cell 152: 1226-1236.
-
(2013)
Cell
, vol.152
, pp. 1226-1236
-
-
Korbel, J.O.1
Campbell, P.J.2
-
39
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: An information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
-
(2009)
Genome Res
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
Horsman, D.6
Jones, S.J.7
Marra, M.A.8
-
40
-
-
78951491211
-
Human papillomavirus type 16 (hpv-16) genomes integrated in head and neck cancers and in hpv-16-immortalized human keratinocyte clones express chimeric virus-cell mrnas similar to those found in cervical cancers
-
LaceMJ, Anson JR, Klussmann JP,Wang DH, Smith EM, Haugen TH, Turek LP. 2011. Human papillomavirus type 16 (HPV-16) genomes integrated in head and neck cancers and in HPV-16-immortalized human keratinocyte clones express chimeric virus-cell mRNAs similar to those found in cervical cancers. J Virol 85: 1645-1654.
-
(2011)
J Virol
, vol.85
, pp. 1645-1654
-
-
Lace, M.J.1
Anson, J.R.2
Klussmann, J.P.3
Wang, D.H.4
Smith, E.M.5
Haugen, T.H.6
Turek, L.P.7
-
41
-
-
84877612139
-
The genomic and transcriptomic landscape of ahela cell line
-
Landry JJ, Pyl PT, Rausch T, Zichner T, TekkedilMM, Stutz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, et al. 2013. The genomic and transcriptomic landscape of aHeLa cell line. G3 (Bethesda) 3: 1213-1224.
-
(2013)
G3 (Bethesda)
, vol.3
, pp. 1213-1224
-
-
Landry, J.J.1
Pyl, P.T.2
Rausch, T.3
Zichner, T.4
Tekkedil, M.M.5
Stutz, A.M.6
Jauch, A.7
Aiyar, R.S.8
Pau, G.9
Delhomme, N.10
-
42
-
-
0000311975
-
-
Kluwer Academic Publishers, London
-
Lansford C, Grenman R, Bier H, Somers K, Kim S, Whiteside T, Clayman G, Welkoborsky H, Carey T. 1999. Head and neck cancers. Kluwer Academic Publishers, London.
-
(1999)
Head and Neck Cancers.
-
-
Lansford, C.1
Grenman, R.2
Bier, H.3
Somers, K.4
Kim, S.5
Whiteside, T.6
Clayman, G.7
Welkoborsky, H.8
Carey, T.9
-
43
-
-
77949587649
-
Fast and accurate long-read alignment with burrows-wheeler transform
-
Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
44
-
-
68549104404
-
The sequence alignment/map format and samtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
45
-
-
84876062367
-
Genomic and functional characterizations of phosphodiesterase subtype 4d in human cancers
-
Lin DC, Xu L, Ding LW, Sharma A, Liu LZ, Yang H, Tan P, Vadgama J, Karlan BY, Lester J, et al. 2013. Genomic and functional characterizations of phosphodiesterase subtype 4D in human cancers. Proc Natl Acad Sci 110: 6109-6114.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 6109-6114
-
-
Lin, D.C.1
Xu, L.2
Ding, L.W.3
Sharma, A.4
Liu, L.Z.5
Yang, H.6
Tan, P.7
Vadgama, J.8
Karlan, B.Y.9
Lester, J.10
-
46
-
-
80052916562
-
Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements
-
Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, et al. 2011. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146: 889-903.
-
(2011)
Cell
, vol.146
, pp. 889-903
-
-
Liu, P.1
Erez, A.2
Nagamani, S.C.3
Dhar, S.U.4
Kolodziejska, K.E.5
Dharmadhikari, A.V.6
Cooper, M.L.7
Wiszniewska, J.8
Zhang, F.9
Withers, M.A.10
-
47
-
-
84877113990
-
Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homologyindependent mechanisms
-
Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. 2013. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homologyindependent mechanisms. Genome Res 23: 762-776.
-
(2013)
Genome Res
, vol.23
, pp. 762-776
-
-
Malhotra, A.1
Lindberg, M.2
Faust, G.G.3
Leibowitz, M.L.4
Clark, R.A.5
Layer, R.M.6
Quinlan, A.R.7
Hall, I.M.8
-
48
-
-
57149092794
-
Replication and partitioning of papillomavirus genomes
-
McBride AA. 2008. Replication and partitioning of papillomavirus genomes. Adv Virus Res 72: 155-205.
-
(2008)
Adv Virus Res
, vol.72
, pp. 155-205
-
-
McBride, A.A.1
-
49
-
-
77955405475
-
Deriving the consequences of genomic variants with the ensembl api and snp effect predictor
-
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. 2010. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26: 2069-2070.
-
(2010)
Bioinformatics
, vol.26
, pp. 2069-2070
-
-
McLaren, W.1
Pritchard, B.2
Rios, D.3
Chen, Y.4
Flicek, P.5
Cunningham, F.6
-
50
-
-
84859216598
-
Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes
-
Molenaar JJ, Koster J, Zwijnenburg DA, van Sluis P, Valentijn LJ, van der Ploeg I, Hamdi M, van Nes J, Westerman BA, van Arkel J, et al. 2012. Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature 483: 589-593.
-
(2012)
Nature
, vol.483
, pp. 589-593
-
-
Molenaar, J.J.1
Koster, J.2
Zwijnenburg, D.A.3
Van Sluis, P.4
Valentijn, L.J.5
Van Der Ploeg, I.6
Hamdi, M.7
Van Nes, J.8
Westerman, B.A.9
Van Arkel, J.10
-
51
-
-
77954955259
-
Human papillomavirus oncoproteins: Pathways to transformation
-
Moody CA, Laimins LA. 2010. Human papillomavirus oncoproteins: Pathways to transformation. Nat Rev Cancer 10: 550-560.
-
(2010)
Nat Rev Cancer
, vol.10
, pp. 550-560
-
-
Moody, C.A.1
Laimins, L.A.2
-
52
-
-
0024428508
-
The e6 and e7 genes of the human papillomavirus type 16 together are necessary and sufficient for transformation of primary human keratinocytes
-
Munger K, Phelps WC, Bubb V, Howley PM, Schlegel R. 1989. The E6 and E7 genes of the human papillomavirus type 16 together are necessary and sufficient for transformation of primary human keratinocytes. J Virol 63: 4417-4421.
-
(1989)
J Virol
, vol.63
, pp. 4417-4421
-
-
Munger, K.1
Phelps, W.C.2
Bubb, V.3
Howley, P.M.4
Schlegel, R.5
-
54
-
-
0017641967
-
Tumor antigen and human chorionic gonadotropin in caski cells: A new epidermoid cervical cancer cell line
-
Pattillo RA, Hussa RO, Story MT, Ruckert AC, Shalaby MR, Mattingly RF. 1977. Tumor antigen and human chorionic gonadotropin in CaSki cells: A new epidermoid cervical cancer cell line. Science 196: 1456-1458.
-
(1977)
Science
, vol.196
, pp. 1456-1458
-
-
Pattillo, R.A.1
Hussa, R.O.2
Story, M.T.3
Ruckert, A.C.4
Shalaby, M.R.5
Mattingly, R.F.6
-
55
-
-
33749187258
-
Myc activation associated with the integration of hpv dna at the myc locus in genital tumors
-
Peter M, Rosty C, Couturier J, Radvanyi F, Teshima H, Sastre-Garau X. 2006. MYC activation associated with the integration of HPV DNA at the MYC locus in genital tumors. Oncogene 25: 5985-5993.
-
(2006)
Oncogene
, vol.25
, pp. 5985-5993
-
-
Peter, M.1
Rosty, C.2
Couturier, J.3
Radvanyi, F.4
Teshima, H.5
Sastre-Garau, X.6
-
56
-
-
77953501153
-
Frequent genomic structural alterations at hpv insertion sites in cervical carcinoma
-
Peter M, Stransky N, Couturier J, Hupe P, Barillot E, de Cremoux P, Cottu P, Radvanyi F, Sastre-Garau X. 2010. Frequent genomic structural alterations at HPV insertion sites in cervical carcinoma. J Pathol 221: 320-330.
-
(2010)
J Pathol
, vol.221
, pp. 320-330
-
-
Peter, M.1
Stransky, N.2
Couturier, J.3
Hupe, P.4
Barillot, E.5
De Cremoux, P.6
Cottu, P.7
Radvanyi, F.8
Sastre-Garau, X.9
-
57
-
-
0015040732
-
A permanent heteroploid human cell line with type b glucose-6-phosphate dehydrogenase
-
Peterson WD Jr, Stulberg CS, Simpson WF. 1971. A permanent heteroploid human cell line with type B glucose-6-phosphate dehydrogenase. Proc Soc Exp Biol Med 136: 1187-1191.
-
(1971)
Proc Soc Exp Biol Med
, vol.136
, pp. 1187-1191
-
-
Peterson Jr., W.D.1
Stulberg, C.S.2
Simpson, W.F.3
-
58
-
-
1242316161
-
Acquisition of high-level chromosomal instability is associated with integration of human papillomavirus type 16 in cervical keratinocytes
-
Pett MR, Alazawi WO, Roberts I, Dowen S, Smith DI, Stanley MA, Coleman N. 2004. Acquisition of high-level chromosomal instability is associated with integration of human papillomavirus type 16 in cervical keratinocytes. Cancer Res 64: 1359-1368.
-
(2004)
Cancer Res
, vol.64
, pp. 1359-1368
-
-
Pett, M.R.1
Alazawi, W.O.2
Roberts, I.3
Dowen, S.4
Smith, D.I.5
Stanley, M.A.6
Coleman, N.7
-
59
-
-
77951770756
-
Bedtools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. 2010. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
60
-
-
84862907577
-
Genome sequencing of pediatric medulloblastoma links catastrophic dna rearrangements with tp53 mutations
-
Rausch T, Jones DT, Zapatka M, Stutz AM, Zichner T, Weischenfeldt J, Jager N, Remke M, Shih D, Northcott PA, et al. 2012. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell 148: 59-71.
-
(2012)
Cell
, vol.148
, pp. 59-71
-
-
Rausch, T.1
Jones, D.T.2
Zapatka, M.3
Stutz, A.M.4
Zichner, T.5
Weischenfeldt, J.6
Jager, N.7
Remke, M.8
Shih, D.9
Northcott, P.A.10
-
61
-
-
84871981670
-
Engagement of the atr-dependentdna damage response at the human papillomavirus 18 replication centers during the initial amplification
-
Reinson T, Toots M, Kadaja M, Pipitch R, Allik M, Ustav E, Ustav M. 2013. Engagement of the ATR-dependentDNA damage response at the human papillomavirus 18 replication centers during the initial amplification. J Virol 87: 951-964.
-
(2013)
J Virol
, vol.87
, pp. 951-964
-
-
Reinson, T.1
Toots, M.2
Kadaja, M.3
Pipitch, R.4
Allik, M.5
Ustav, E.6
Ustav, M.7
-
62
-
-
0032472376
-
Apm-1, a novel human gene, identified by aberrant co-transcription with papillomavirus oncogenes in a cervical carcinoma cell line, encodes a btb/poz-zinc finger protein with growth inhibitory activity
-
Reuter S, Bartelmann M, Vogt M, Geisen C, Napierski I, Kahn T, Delius H, Lichter P, Weitz S, Korn B, et al. 1998. APM-1, a novel human gene, identified by aberrant co-transcription with papillomavirus oncogenes in a cervical carcinoma cell line, encodes a BTB/POZ-zinc finger protein with growth inhibitory activity. EMBO J 17: 215-222.
-
(1998)
EMBO J
, vol.17
, pp. 215-222
-
-
Reuter, S.1
Bartelmann, M.2
Vogt, M.3
Geisen, C.4
Napierski, I.5
Kahn, T.6
Delius, H.7
Lichter, P.8
Weitz, S.9
Korn, B.10
-
63
-
-
0019471387
-
Tumorigenic keratinocyte lines requiring anchorage and fibroblast support cultured from human squamous cell carcinomas
-
Rheinwald JG, Beckett MA. 1981. Tumorigenic keratinocyte lines requiring anchorage and fibroblast support cultured from human squamous cell carcinomas. Cancer Res 41: 1657-1663.
-
(1981)
Cancer Res
, vol.41
, pp. 1657-1663
-
-
Rheinwald, J.G.1
Beckett, M.A.2
-
64
-
-
84863215000
-
Loss of gene function as a consequence of human papillomavirus dna integration
-
Schmitz M, Driesch C, Beer-Grondke K, Jansen L, Runnebaum IB, Durst M. 2012. Loss of gene function as a consequence of human papillomavirus DNA integration. Int J Cancer 131: E593-E602.
-
(2012)
Int J Cancer
, vol.131
-
-
Schmitz, M.1
Driesch, C.2
Beer-Grondke, K.3
Jansen, L.4
Runnebaum, I.B.5
Durst, M.6
-
65
-
-
0038214755
-
Multicolor spectral karyotyping of human chromosomes
-
Schrock E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MA, Ning Y, Ledbetter DH, Bar-Am I, Soenksen D, et al. 1996. Multicolor spectral karyotyping of human chromosomes. Science 273: 494-497.
-
(1996)
Science
, vol.273
, pp. 494-497
-
-
Schrock, E.1
Du Manoir, S.2
Veldman, T.3
Schoell, B.4
Wienberg, J.5
Ferguson-Smith, M.A.6
Ning, Y.7
Ledbetter, D.H.8
Bar-Am, I.9
Soenksen, D.10
-
66
-
-
18744406283
-
A c-terminal inhibitory domain controls the activity of p63 by an intramolecular mechanism
-
Serber Z, Lai HC, Yang A,Ou HD, SigalMS, Kelly AE, Darimont BD, Duijf PH, Van Bokhoven H, McKeon F, et al. 2002. A C-terminal inhibitory domain controls the activity of p63 by an intramolecular mechanism. Mol Cell Biol 22: 8601-8611.
-
(2002)
Mol Cell Biol
, vol.22
, pp. 8601-8611
-
-
Serber, Z.1
Lai, H.C.2
Yang, A.3
Ou, H.D.4
Sigal, M.S.5
Kelly, A.E.6
Darimont, B.D.7
Duijf, P.H.8
Van Bokhoven, H.9
McKeon, F.10
-
67
-
-
0035173378
-
Dbsnp: The ncbi database of genetic variation
-
Sherry ST,Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
Ward, M.H.2
Kholodov, M.3
Baker, J.4
Phan, L.5
Smigielski, E.M.6
Sirotkin, K.7
-
68
-
-
80052158097
-
The mutational landscape of head and neck squamous cell carcinoma
-
Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence MS, Sougnez C, McKenna A, et al. 2011. The mutational landscape of head and neck squamous cell carcinoma. Science 333: 1157-1160.
-
(2011)
Science
, vol.333
, pp. 1157-1160
-
-
Stransky, N.1
Egloff, A.M.2
Tward, A.D.3
Kostic, A.D.4
Cibulskis, K.5
Sivachenko, A.6
Kryukov, G.V.7
Lawrence, M.S.8
Sougnez, C.9
McKenna, A.10
-
69
-
-
84862999344
-
Genome-wide survey of recurrent hbv integration in hepatocellular carcinoma
-
Sung WK, Zheng H, Li S, Chen R, Liu X, Li Y, Lee NP, Lee WH, Ariyaratne PN, Tennakoon C, et al. 2012. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet 44: 765-769.
-
(2012)
Nat Genet
, vol.44
, pp. 765-769
-
-
Sung, W.K.1
Zheng, H.2
Li, S.3
Chen, R.4
Liu, X.5
Li, Y.6
Lee, N.P.7
Lee, W.H.8
Ariyaratne, P.N.9
Tennakoon, C.10
-
70
-
-
0037047396
-
Human l1 retrotransposition is associated with genetic instability in vivo
-
Symer DE, Connelly C, Szak ST, Caputo EM, Cost GJ, Parmigiani G, Boeke JD. 2002. Human L1 retrotransposition is associated with genetic instability in vivo. Cell 110: 327-338.
-
(2002)
Cell
, vol.110
, pp. 327-338
-
-
Symer, D.E.1
Connelly, C.2
Szak, S.T.3
Caputo, E.M.4
Cost, G.J.5
Parmigiani, G.6
Boeke, J.D.7
-
71
-
-
60749110613
-
Palindromic gene amplification -An evolutionarily conserved role for dna inverted repeats in the genome
-
Tanaka H, Yao MC. 2009. Palindromic gene amplification -an evolutionarily conserved role for DNA inverted repeats in the genome. Nat Rev Cancer 9: 216-224.
-
(2009)
Nat Rev Cancer
, vol.9
, pp. 216-224
-
-
Tanaka, H.1
Yao, M.C.2
-
72
-
-
84866364082
-
Um-scc-104: A new human papillomavirus-16-positive cancer stem cell-containing head and neck squamous cell carcinoma cell line
-
Tang AL, Hauff SJ, Owen JH, Graham MP, CzerwinskiMJ, Park JJ,Walline H, Papagerakis S, Stoerker J, McHugh JB, et al. 2012. UM-SCC-104: A new human papillomavirus-16-positive cancer stem cell-containing head and neck squamous cell carcinoma cell line. Head Neck 34: 1480-1491.
-
(2012)
Head Neck
, vol.34
, pp. 1480-1491
-
-
Tang, A.L.1
Hauff, S.J.2
Owen, J.H.3
Graham, M.P.4
Czerwinski, M.J.5
Park, J.J.6
Walline, H.7
Papagerakis, S.8
Stoerker, J.9
McHugh, J.B.10
-
73
-
-
0023441712
-
The bpv1-e2 trans-acting protein can be either an activator or a repressor of the hpv18 regulatory region
-
Thierry F, Yaniv M. 1987. The BPV1-E2 trans-acting protein can be either an activator or a repressor of the HPV18 regulatory region. EMBO J 6: 3391-3397.
-
(1987)
EMBO J
, vol.6
, pp. 3391-3397
-
-
Thierry, F.1
Yaniv, M.2
-
74
-
-
84875634162
-
Integrative genomics viewer (igv): High-performance genomics data visualization and exploration
-
Thorvaldsdottir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform 14: 178-192.
-
(2013)
Brief Bioinform
, vol.14
, pp. 178-192
-
-
Thorvaldsdottir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
75
-
-
84875932668
-
Deep sequencing of the hepatitis b virus in hepatocellular carcinoma patients reveals enriched integration events, structural alterations and sequence variations
-
Toh ST, Jin Y, Liu L,Wang J, Babrzadeh F, Gharizadeh B, Ronaghi M, Toh HC, Chow PK, Chung AY, et al. 2013. Deep sequencing of the hepatitis B virus in hepatocellular carcinoma patients reveals enriched integration events, structural alterations and sequence variations. Carcinogenesis 34: 787-798.
-
(2013)
Carcinogenesis
, vol.34
, pp. 787-798
-
-
Toh, S.T.1
Jin, Y.2
Liu, L.3
Wang, J.4
Babrzadeh, F.5
Gharizadeh, B.6
Ronaghi, M.7
Toh, H.C.8
Chow, P.K.9
Chung, A.Y.10
-
76
-
-
65449136284
-
Tophat: Discovering splice junctions with rna-seq
-
Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: Discovering splice junctions with RNA-seq. Bioinformatics 25: 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
77
-
-
84859885816
-
Differential gene and transcript expression analysis of rna-seq experiments with tophat and cufflinks
-
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7: 562-578.
-
(2012)
Nat Protoc
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
78
-
-
0032840918
-
Human papillomavirus is a necessary cause of invasive cervical cancer worldwide
-
Walboomers JM, Jacobs MV, Manos MM, Bosch FX, Kummer JA, Shah KV, Snijders PJ, Peto J, Meijer CJ, Munoz N. 1999. Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol 189: 12-19.
-
(1999)
J Pathol
, vol.189
, pp. 12-19
-
-
Walboomers, J.M.1
Jacobs, M.V.2
Manos, M.M.3
Bosch, F.X.4
Kummer, J.A.5
Shah, K.V.6
Snijders, P.J.7
Peto, J.8
Meijer, C.J.9
Munoz, N.10
-
79
-
-
2542550364
-
Systematic review of genomic integration sites of human papillomavirus genomes in epithelial dysplasia and invasive cancer of the female lower genital tract
-
Wentzensen N, Vinokurova S, von Knebel Doeberitz M. 2004. Systematic review of genomic integration sites of human papillomavirus genomes in epithelial dysplasia and invasive cancer of the female lower genital tract. Cancer Res 64: 3878-3884.
-
(2004)
Cancer Res
, vol.64
, pp. 3878-3884
-
-
Wentzensen, N.1
Vinokurova, S.2
Von Knebel Doeberitz, M.3
-
80
-
-
38949118675
-
Inverse relationship between human papillomavirus-16 infection and disruptive p53 gene mutations in squamous cell carcinoma of the head and neck
-
Westra WH, Taube JM, Poeta ML, Begum S, Sidransky D, Koch WM. 2008. Inverse relationship between human papillomavirus-16 infection and disruptive p53 gene mutations in squamous cell carcinoma of the head and neck. Clin Cancer Res 14: 366-369.
-
(2008)
Clin Cancer Res
, vol.14
, pp. 366-369
-
-
Westra, W.H.1
Taube, J.M.2
Poeta, M.L.3
Begum, S.4
Sidransky, D.5
Koch, W.M.6
-
81
-
-
23744454779
-
Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution
-
Wheelan SJ, Aizawa Y, Han JS, Boeke JD. 2005. Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution. Genome Res 15: 1073-1078.
-
(2005)
Genome Res
, vol.15
, pp. 1073-1078
-
-
Wheelan, S.J.1
Aizawa, Y.2
Han, J.S.3
Boeke, J.D.4
-
82
-
-
34447302548
-
The influence of clinical and demographic risk factors on the establishment of head and neck squamous cell carcinoma cell lines
-
White JS, Weissfeld JL, Ragin CC, Rossie KM, Martin CL, Shuster M, Ishwad CS, Law JC, Myers EN, Johnson JT, et al. 2007. The influence of clinical and demographic risk factors on the establishment of head and neck squamous cell carcinoma cell lines. Oral Oncol 43: 701-712.
-
(2007)
Oral Oncol
, vol.43
, pp. 701-712
-
-
White, J.S.1
Weissfeld, J.L.2
Ragin, C.C.3
Rossie, K.M.4
Martin, C.L.5
Shuster, M.6
Ishwad, C.S.7
Law, J.C.8
Myers, E.N.9
Johnson, J.T.10
-
83
-
-
77951820899
-
Fast and snp-tolerant detection of complex variants and splicing in short reads
-
Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
-
(2010)
Bioinformatics
, vol.26
, pp. 873-881
-
-
Wu, T.D.1
Nacu, S.2
-
84
-
-
84879135702
-
Multiplex identification of human papillomavirus 16 dna integration sites in cervical carcinomas
-
Xu B, Chotewutmontri S, Wolf S, Klos U, Schmitz M, Durst M, Schwarz E. 2013. Multiplex identification of human papillomavirus 16 DNA integration sites in cervical carcinomas. PLoS ONE 8: e66693.
-
(2013)
PLoS ONE
, vol.8
-
-
Xu, B.1
Chotewutmontri, S.2
Wolf, S.3
Klos, U.4
Schmitz, M.5
Durst, M.6
Schwarz, E.7
-
85
-
-
77949511368
-
Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet shortread de novo assembler
-
Zerbino DR, McEwen GK, Margulies EH, Birney E. 2009. Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet shortread de novo assembler. PLoS ONE 4: e8407.
-
(2009)
PLoS ONE
, vol.4
-
-
Zerbino, D.R.1
McEwen, G.K.2
Margulies, E.H.3
Birney, E.4
|