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A sequence-based survey of the complex structural organization of tumor genomes
Benjamin J Raphael, Stanislav Volik, Peng Yu, Chunxiao Wu, Guiqing Huang, Elena V Linardopoulou, Barbara J Trask, Frederic Waldman, Joseph Costello, Kenneth J Pienta, Gordon B Mills, Krystyna Bajsarowicz, Yasuko Kobayashi, Shivaranjani Sridharan, Pamela L Paris, Quanzhou Tao, Sarah J Aerni, Raymond P Brown, Ali Bashir, Joe W Gray, Jan-Fang Cheng, Pieter de Jong, Mikhail Nefedov, Thomas Ried, Hesed M Padilla-Nash, Colin C Collins
Genome Biol. 2008; 9(3): R59. Published online 2008 March 25. doi: 10.1186/gb-2008-9-3-r59
PMCID:
PMC2397511
Abstract Full Text PDF–1.3M Supplementary Material

Is Cited by the Following 12 Articles in this Archive:

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
Axel M. Hillmer, Fei Yao, Koichiro Inaki, Wah Heng Lee, Pramila N. Ariyaratne, Audrey S.M. Teo, Xing Yi Woo, Zhenshui Zhang, Hao Zhao, Leena Ukil, Jieqi P. Chen, Feng Zhu, Jimmy B.Y. So, Manuel Salto-Tellez, Wan Ting Poh, Kelson F.B. Zawack, Niranjan Nagarajan, Song Gao, Guoliang Li, Vikrant Kumar, Hui Ping J. Lim, Yee Yen Sia, Chee Seng Chan, See Ting Leong, Say Chuan Neo, Poh Sum D. Choi, Hervé Thoreau, Patrick B.O. Tan, Atif Shahab, Xiaoan Ruan, Jonas Bergh, Per Hall, Valère Cacheux-Rataboul, Chia-Lin Wei, Khay Guan Yeoh, Wing-Kin Sung, Guillaume Bourque, Edison T. Liu, Yijun Ruan
Genome Res. 2011 May; 21(5): 665–675. doi: 10.1101/gr.113555.110
PMCID:
PMC3083083
Abstract Full Text PDF–2.2M
Transcriptional consequences of genomic structural aberrations in breast cancer
Koichiro Inaki, Axel M. Hillmer, Leena Ukil, Fei Yao, Xing Yi Woo, Leah A. Vardy, Kelson Folkvard Braaten Zawack, Charlie Wah Heng Lee, Pramila Nuwantha Ariyaratne, Yang Sun Chan, Kartiki Vasant Desai, Jonas Bergh, Per Hall, Thomas Choudary Putti, Wai Loon Ong, Atif Shahab, Valere Cacheux-Rataboul, Radha Krishna Murthy Karuturi, Wing-Kin Sung, Xiaoan Ruan, Guillaume Bourque, Yijun Ruan, Edison T. Liu
Genome Res. 2011 May; 21(5): 676–687. doi: 10.1101/gr.113225.110
PMCID:
PMC3083084
Abstract Full Text PDF–886K
Are there any differences between features of proteins expressed in malignant and benign breast cancers?
Mansour Ebrahimi, Esmaeil Ebrahimie, Narges Shamabadi, Mahdi Ebrahimi
J Res Med Sci. 2010 Nov-Dec; 15(6): 299–309.
PMCID:
PMC3082830
Abstract Full Text
Challenges of sequencing human genomes
Daniel C. Koboldt, Li Ding, Elaine R. Mardis, Richard K. Wilson
Brief Bioinform. 2010 September; 11(5): 484–498. Published online 2010 September 20. doi: 10.1093/bib/bbq016
PMCID:
PMC2980933
Abstract Full Text PDF–822K
Analysis of next-generation genomic data in cancer: accomplishments and challenges
Li Ding, Michael C. Wendl, Daniel C. Koboldt, Elaine R. Mardis
Hum Mol Genet. 2010 October 15; 19(R2): R188–R196. Published online 2010 September 15. doi: 10.1093/hmg/ddq391
PMCID:
PMC2953747
Abstract Full Text PDF–321K
Cancer gene discovery in mouse and man
Jenny Mattison, Louise van der Weyden, Tim Hubbard, David J. Adams
Biochim Biophys Acta. 2009 December; 1796(2-2): 140–161. doi: 10.1016/j.bbcan.2009.03.001
PMCID:
PMC2756404
Abstract Full Text
Statistical aspects of discerning indel-type structural variation via DNA sequence alignment
Michael C Wendl, Richard K Wilson
BMC Genomics. 2009; 10: 359. Published online 2009 August 5. doi: 10.1186/1471-2164-10-359
PMCID:
PMC2748092
Abstract Full Text PDF–401K
A geometric approach for classification and comparison of structural variants
Suzanne Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael
Bioinformatics. 2009 June 15; 25(12): i222–i230. Published online 2009 May 27. doi: 10.1093/bioinformatics/btp208
PMCID:
PMC2687962
Abstract Full Text PDF–598K
The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma
Cinzia Di Pietro, Marco Ragusa, Davide Barbagallo, Laura R Duro, Maria R Guglielmino, Alessandra Majorana, Rosario Angelica, Marina Scalia, Luisa Statello, Loredana Salito, Luisa Tomasello, Salvo Pernagallo, Salvo Valenti, Vito D'Agostino, Patrizio Triberio, Igor Tandurella, Giuseppe A Palumbo, Piera La Cava, Viviana Cafiso, Taschia Bertuccio, Maria Santagati, Giovanni Li Destri, Salvatore Lanzafame, Francesco Di Raimondo, Stefania Stefani, Bud Mishra, Michele Purrello
BMC Med Genomics. 2009; 2: 20. Published online 2009 April 30. doi: 10.1186/1755-8794-2-20
PMCID:
PMC2683874
Abstract Full Text PDF–8.2M Supplementary Material
Signatures of Selection in Fusion Transcripts Resulting From Chromosomal Translocations in Human Cancer
Iñigo Ortiz de Mendíbil, José L. Vizmanos, Francisco J. Novo
PLoS ONE. 2009; 4(3): e4805. Published online 2009 March 12. doi: 10.1371/journal.pone.0004805
PMCID:
PMC2653638
Abstract Full Text PDF–385K Supplementary Material
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
Jan O Korbel, Alexej Abyzov, Xinmeng Jasmine Mu, Nicholas Carriero, Philip Cayting, Zhengdong Zhang, Michael Snyder, Mark B Gerstein
Genome Biol. 2009; 10(2): R23. Published online 2009 February 23. doi: 10.1186/gb-2009-10-2-r23
PMCID:
PMC2688268
Abstract Full Text PDF–656K Supplementary Material
A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
Oliver A. Hampton, Petra Den Hollander, Christopher A. Miller, David A. Delgado, Jian Li, Cristian Coarfa, Ronald A. Harris, Stephen Richards, Steven E. Scherer, Donna M. Muzny, Richard A. Gibbs, Adrian V. Lee, Aleksandar Milosavljevic
Genome Res. 2009 February; 19(2): 167–177. doi: 10.1101/gr.080259.108
PMCID:
PMC2652200
Abstract Full Text PDF–2.2M
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