Genome Biology

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MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype

Cherie Blenkiron, Leonard D Goldstein, Natalie P Thorne, Inmaculada Spiteri, Suet-Feung Chin, Mark J Dunning, Nuno L Barbosa-Morais, Andrew E Teschendorff, Andrew R Green, Ian O Ellis, Simon Tavaré, Carlos Caldas* and Eric A Miska*

Genome Biology 2007, 8:R214 doi:10.1186/gb-2007-8-10-r214

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Methodology article   Open Access Highly Accessed

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis

Jing Tu, Qinyu Ge, Shengqin Wang, Lei Wang, Beili Sun, Qi Yang, Yunfei Bai, Zuhong Lu BMC Genomics 2012, 13:43 (25 January 2012)

Research article   Open Access

Deciphering causal and statistical relations of molecular aberrations and gene expressions in NCI-60 cell lines

Shyh-Dar Li, Tatsuaki Tagami, Ying-Fu Ho, Chen-Hsiang Yeang BMC Systems Biology 2011, 5:186 (4 November 2011)

Methodology article   Open Access

DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference

Yan Jiao, Katherine Lawler, Gargi S Patel, Arnie Purushotham, Annette F Jones, Anita Grigoriadis, Andrew Tutt, Tony Ng, Andrew E Teschendorff BMC Bioinformatics 2011, 12:403 (19 October 2011)

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Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage

Min Zhu, Ming Yi, Chang Hee Kim, Chuxia Deng, Yi Li, Daniel Medina, Robert M Stephens, Jeffrey E Green Genome Biology 2011, 12:R77 (16 August 2011)

Expression profiling in mouse models of mammary tumors identifies miRNA signatures particular to lineages or driver oncogenes

Methodology article   Open Access Highly Accessed

New miRNA labeling method for bead-based quantification

Alberto Biscontin, Silvia Casara, Stefano Cagnin, Lucia Tombolan, Angelo Rosolen, Gerolamo Lanfranchi, Cristiano De Pittà BMC Molecular Biology 2010, 11:44 (16 June 2010)

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MicroRNAs and their target gene networks in breast cancer

Elizabeth O'Day, Ashish Lal Breast Cancer Research 2010, 12:201 (19 March 2010)

Research article   Open Access

Characterisation of microRNA expression in post-natal mouse mammary gland development

Stefanie Avril-Sassen, Leonard D Goldstein, John Stingl, Cherie Blenkiron, John Le Quesne, Inmaculada Spiteri, Konstantina Karagavriilidou, Christine J Watson, Simon Tavaré, Eric A Miska, Carlos Caldas BMC Genomics 2009, 10:548 (20 November 2009)

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mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer

Chao Cheng, Xuping Fu, Pedro Alves, Mark Gerstein Genome Biology 2009, 10:R90 (1 September 2009)

Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers

Research article   Open Access Highly Accessed

MicroRNA expression profiling of male breast cancer

Matteo Fassan, Raffaele Baffa, Juan P Palazzo, Joshua Lloyd, Marco Crosariol, Chang-Gong Liu, Stefano Volinia, Hannes Alder, Massimo Rugge, Carlo M Croce, Anne Rosenberg Breast Cancer Research 2009, 11:R58 (10 August 2009)

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Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing

Sanne Nygaard, Anders Jacobsen, Morten Lindow, Jens Eriksen, Eva Balslev, Henrik Flyger, Niels Tolstrup, Søren Møller, Anders Krogh, Thomas Litman BMC Medical Genomics 2009, 2:35 (9 June 2009)

Analysis of breast cancer and adjacent tissue using deep-sequencing technology and a novel computational pipeline identifies 5 new microRNAs, and indicates that sequence end variability may be used as a discriminatory feature to aid future microRNA discovery.

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MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer

Aoife J Lowery, Nicola Miller, Amanda Devaney, Roisin E McNeill, Pamela A Davoren, Christophe Lemetre, Vladimir Benes, Sabine Schmidt, Jonathon Blake, Graham Ball, Michael J Kerin Breast Cancer Research 2009, 11:R27 (11 May 2009)

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Identification and characterization of new miRNAs cloned from normal mouse mammary gland

Nezha Sdassi, Licia Silveri, Johann Laubier, Gaëlle Tilly, José Costa, Sarah Layani, Jean-Luc Vilotte, Fabienne Le Provost BMC Genomics 2009, 10:149 (7 April 2009)

Research   Open Access

Finding microRNA regulatory modules in human genome using rule induction

Dang Tran, Kenji Satou, Tu Ho BMC Bioinformatics 2008, 9(Suppl 12):S5 (12 December 2008)

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Unlocking the power of cross-species genomic analyses: identification of evolutionarily conserved breast cancer networks and validation of preclinical models

Christina N Bennett, Jeffrey E Green Breast Cancer Research 2008, 10:213 (11 September 2008)

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PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes

Anna Git, Inmaculada Spiteri, Cherie Blenkiron, Mark J Dunning, Jessica CM Pole, Suet-Feung Chin, Yanzhong Wang, James Smith, Frederick J Livesey, Carlos Caldas Breast Cancer Research 2008, 10:R54 (27 June 2008)

Breast cancer cell line PMC42 is a good model for normal breast epithelium, providing a unique biological tool to study breast differentiation and the function of key miRNAs typically lost in cancer.

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Meta-analysis confirms BCL2 is an independent prognostic marker in breast cancer

Grace M Callagy, Mark J Webber, Paul DP Pharoah, Carlos Caldas BMC Cancer 2008, 8:153 (29 May 2008)

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Effects of common germline genetic variation in cell cycle control genes on breast cancer survival: results from a population-based cohort

Elizabeth M Azzato, Kristy E Driver, Fabienne Lesueur, Mitul Shah, David Greenberg, Douglas F Easton, Andrew E Teschendorff, Carlos Caldas, Neil E Caporaso, Paul DP Pharoah Breast Cancer Research 2008, 10:R47 (28 May 2008)

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Reasons for breast cancer heterogeneity

François Bertucci, Daniel Birnbaum Journal of Biology 2008, 7:6 (22 February 2008)