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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 and Colin C Collins*

Genome Biology 2008, 9:R59 doi:10.1186/gb-2008-9-3-r59

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Research article   Open Access

Statistical aspects of discerning indel-type structural variation via DNA sequence alignment

Michael C Wendl, Richard K Wilson BMC Genomics 2009, 10:359 (5 August 2009)

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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 Medical Genomics 2009, 2:20 (30 April 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Software   Open Access

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 Mu, Nicholas Carriero, Philip Cayting, Zhengdong Zhang, Michael Snyder, Mark B Gerstein Genome Biology 2009, 10:R23 (23 February 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

Paired-End Mapper (PEMer) enables mapping of genomic structural variants at considerably enhanced sensitivity, specificity and resolution over previous approaches.

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