Genome Biology | Tags

1.

The mutational landscape of chromatin regulatory factors across 4623 tumor samples

Abel Gonzalez-Perez, Alba Jene-Sanz, Nuria Lopez-Bigas Genome Biology 2013, 14:r106 (24 September 2013)

Abstract | Provisional PDF | PubMed | Editor’s summary

Identification of mutations in chromatin regulatory factors and their potential role in tumorigenesis

2.

Virmid: accurate detection of somatic mutations with sample impurity inference

Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, Jeong Lee, Anand Patel, Eric Scott, Hojung Nam, Hayan Lee, Joseph G Gleeson, Vineet Bafna Genome Biology 2013, 14:R90 (29 August 2013)

Abstract | Provisional PDF | PubMed | Editor’s summary

Virmid is a method for estimating the proportion of healthy cells in a disease sample to facilitate variant calling

3.

BreakTrans: uncovering the genomic architecture of gene fusions

Ken Chen, Nicholas E Navin, Yong Wang, Heather K Schmidt, John W Wallis, Beifang Niu, Xian Fan, Hao Zhao, Michael D McLellan, Katherine A Hoadley, Elaine R Mardis, Timothy J Ley, Charles M Perou, Richard K Wilson, Li Ding Genome Biology 2013, 14:R87 (23 August 2013)

Abstract | Provisional PDF | PubMed | Editor’s summary

A new bioinformatic tool for the detection of cancer-related gene fusions and underlying genomic structural rearrangements

4.

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

Layla Oesper, Ahmad Mahmoody, Benjamin J Raphael Genome Biology 2013, 14:R80 (29 July 2013)

Abstract | Full text | PDF | PubMed | Editor’s summary

A method for determining tumor heterogeneity from high-throughput DNA sequencing data

5.

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

Adam D Ewing, Tracy J Ballinger, Dent Earl, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013)

An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues

6.

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer

Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G Huntsman, Carlos Caldas, Samuel A Aparicio, Sohrab P Shah Genome Biology 2012, 13:R124 (22 December 2012)

DriverNet is a method for identifying driver mutations in cancer samples based on their effects on the transcriptional network

7.

Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data

Matthew Parker, Xiang Chen, Armita Bahrami, James Dalton, Michael Rusch, Gang Wu, John Easton, Nai-Kong Cheung, Michael Dyer, Elaine R Mardis, Richard K Wilson, Charles Mullighan, Richard Gilbertson, Suzanne J Baker, Gerard Zambetti, David W Ellison, James R Downing, Jinghui Zhang, Genome Biology 2012, 13:R113 (11 December 2012)

Abstract | Full text | PDF | PubMed | Editor’s summary

A comprehensive analysis of telomere length changes in a large collection of pediatric tumors

8.

A network module-based method for identifying cancer prognostic signatures

Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012)

Abstract | Full text | PDF | PubMed | Editor’s summary

A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis

9.

InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor

Alain Coletta, Colin Molter, Robin Duqué, David Steenhoff, Jonatan Taminau, Virginie de Schaetzen, Stijn Meganck, Cosmin Lazar, David Venet, Vincent Detours, Ann Nowé, Hugues Bersini, David Y Weiss Solís Genome Biology 2012, 13:R104 (18 November 2012)

A web-based data storage hub that connects genomics datasets to GUI and command line data analysis tools

10.

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns

Duncan Sproul, Robert R Kitchen, Colm E Nestor, J Michael Dixon, Andrew H Sims, David J Harrison, Bernard H Ramsahoye, Richard R Meehan Genome Biology 2012, 13:R84 (3 October 2012)

Aberrant promoter hypermethylation in cancer does not promote tumorigenesis, but instead reinforces repression inherited from pre-cancerous tissue

11.

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman Genome Biology 2012, 13:R61 (11 July 2012)

A model-based SNP caller for bisulfite sequencing data improves methylation estimates and imprinting analysis

12.

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack Genome Biology 2012, 13:R44 (15 June 2012)

A method for normalizing the Illumina 450k methylation array data, allowing analysis of the genome-wide methylation status of the human genome

13.

Integrating diverse genomic data using gene sets

Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani Genome Biology 2011, 12:R105 (21 October 2011)

A method for integrating multiple genomic data types for the identification of enriched gene sets

14.

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz Genome Biology 2011, 12:R41 (28 April 2011)

Identification of genes affected by somatic copy number variations that drive human cancer growth.

15.

A human functional protein interaction network and its application to cancer data analysis

Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010)

A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.

	All
	1.	Research The mutational landscape of chromatin regulatory factors across 4623 tumor samples Abel Gonzalez-Perez, Alba Jene-Sanz, Nuria Lopez-Bigas Genome Biology 2013, 14:r106 (24 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Identification of mutations in chromatin regulatory factors and their potential role in tumorigenesis
	2.	Method Virmid: accurate detection of somatic mutations with sample impurity inference Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, Jeong Lee, Anand Patel, Eric Scott, Hojung Nam, Hayan Lee, Joseph G Gleeson, Vineet Bafna Genome Biology 2013, 14:R90 (29 August 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Virmid is a method for estimating the proportion of healthy cells in a disease sample to facilitate variant calling
	3.	Software BreakTrans: uncovering the genomic architecture of gene fusions Ken Chen, Nicholas E Navin, Yong Wang, Heather K Schmidt, John W Wallis, Beifang Niu, Xian Fan, Hao Zhao, Michael D McLellan, Katherine A Hoadley, Elaine R Mardis, Timothy J Ley, Charles M Perou, Richard K Wilson, Li Ding Genome Biology 2013, 14:R87 (23 August 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new bioinformatic tool for the detection of cancer-related gene fusions and underlying genomic structural rearrangements
	4.	Method THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data Layla Oesper, Ahmad Mahmoody, Benjamin J Raphael Genome Biology 2013, 14:R80 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for determining tumor heterogeneity from high-throughput DNA sequencing data
	5.	Research Retrotransposition of gene transcripts leads to structural variation in mammalian genomes Adam D Ewing, Tracy J Ballinger, Dent Earl, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
	6.	Method DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G Huntsman, Carlos Caldas, Samuel A Aparicio, Sohrab P Shah Genome Biology 2012, 13:R124 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary DriverNet is a method for identifying driver mutations in cancer samples based on their effects on the transcriptional network
	7.	Research Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data Matthew Parker, Xiang Chen, Armita Bahrami, James Dalton, Michael Rusch, Gang Wu, John Easton, Nai-Kong Cheung, Michael Dyer, Elaine R Mardis, Richard K Wilson, Charles Mullighan, Richard Gilbertson, Suzanne J Baker, Gerard Zambetti, David W Ellison, James R Downing, Jinghui Zhang, Genome Biology 2012, 13:R113 (11 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of telomere length changes in a large collection of pediatric tumors
	8.	Method A network module-based method for identifying cancer prognostic signatures Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis
	9.	Software InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor Alain Coletta, Colin Molter, Robin Duqué, David Steenhoff, Jonatan Taminau, Virginie de Schaetzen, Stijn Meganck, Cosmin Lazar, David Venet, Vincent Detours, Ann Nowé, Hugues Bersini, David Y Weiss Solís Genome Biology 2012, 13:R104 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A web-based data storage hub that connects genomics datasets to GUI and command line data analysis tools
	10.	Research Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns Duncan Sproul, Robert R Kitchen, Colm E Nestor, J Michael Dixon, Andrew H Sims, David J Harrison, Bernard H Ramsahoye, Richard R Meehan Genome Biology 2012, 13:R84 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Aberrant promoter hypermethylation in cancer does not promote tumorigenesis, but instead reinforces repression inherited from pre-cancerous tissue
	11.	Method Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman Genome Biology 2012, 13:R61 (11 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A model-based SNP caller for bisulfite sequencing data improves methylation estimates and imprinting analysis
	12.	Method SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack Genome Biology 2012, 13:R44 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for normalizing the Illumina 450k methylation array data, allowing analysis of the genome-wide methylation status of the human genome
	13.	Method Integrating diverse genomic data using gene sets Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani Genome Biology 2011, 12:R105 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for integrating multiple genomic data types for the identification of enriched gene sets
	14.	Method GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz Genome Biology 2011, 12:R41 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Identification of genes affected by somatic copy number variations that drive human cancer growth.
	15.	Research A human functional protein interaction network and its application to cancer data analysis Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.

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