Dysregulated expression of Fau and MELK is associated with poor prognosis in breast cancer (2009)
Pickard, Mark R, Green, Andrew R, Ellis, Ian O, Caldas, Carlos, Hedge, Vanessa L, Mourtada-Maarabouni, Mirna, ...
Abstract Introduction Programmed cell death through apoptosis plays an essential role in the hormone-regulated physiological turnover of mammary tissue. Failure of this active gene-dependent process...
The breast cancer somatic 'muta-ome': tackling the complexity (2009)
Teschendorff, Andrew E, Caldas, Carlos
Abstract Acquired somatic mutations are responsible for approximately 90% of breast tumours. However, only one somatic aberration, amplification of the HER2 locus, is currently used to define a...
Germline CDH1 deletions in hereditary diffuse gastric cancer families (2009)
Oliveira, Carla, Senz, Janine, Kaurah, Pardeep, Pinheiro, Hugo, Sanges, Remo, Haegert, Anne, ...
Germline CDH1 point or small frameshift mutations can be identified in 30–50% of hereditary diffuse gastric cancer (HDGC) families. We hypothesized that CDH1 genomic rearrangements would be found...
CancerGrid: developing open standards for clinical cancer informatics (2008)
James Brenton, Carlos Caldas, Jim Davies, Steve Harris, Peter Maccallum
CancerGrid is a consortium developing open standards for clinical cancer informatics based on data and metadata representation, distributed service-oriented architectures, and collaborative working...
Reyal, Fabien, Van Vliet, Martin H, Armstrong, Nicola J, Horlings, Hugo M, De Visser, Karin E, Kok, Marlen, ...
Abstract Introduction Several gene expression signatures have been proposed and demonstrated to be predictive of outcome in breast cancer. In the present article we address the following issues: Do...
High-resolution array CGH clarifies events occurring on 8p in carcinogenesis (2008)
Cooke, Susanna L, Pole, Jessica CM, Chin, Suet-Feung, Ellis, Ian O, Caldas, Carlos, Edwards, Paul AW
Abstract Background Rearrangement of the short arm of chromosome 8 (8p) is very common in epithelial cancers such as breast cancer. Usually there is an unbalanced translocation breakpoint in 8p12...
Models for locating RFID nodes (2008)
François Caron, Saiedeh Navabzadeh Razavi, Jongchul Song, Emmanuel Duflos, Carlos Caldas, Carl Haas
Localization of randomly distributed wireless sensor nodes is a significant and fundamental problem in a broad range of emerging civil engineering applications. Densely deployed in physical...
PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes (2008)
Git, Anna, Spiteri, Inmaculada, Blenkiron, Cherie, Dunning, Mark J, Pole, Jessica CM, Chin, Suet-Feung, ...
Abstract Introduction The use of cultured cell lines as model systems for normal tissue is limited by the molecular alterations accompanying the immortalisation process, including changes in the mRNA...
Meta-analysis confirms BCL2 is an independent prognostic marker in breast cancer (2008)
Callagy, Grace M, Webber, Mark J, Pharoah, Paul DP, Caldas, Carlos
Abstract Background A number of protein markers have been investigated as prognostic adjuncts in breast cancer but their translation into clinical practice has been impeded by a lack of appropriate...
Azzato, Elizabeth M, Driver, Kristy E, Lesueur, Fabienne, Shah, Mitul, Greenberg, David, Easton, Douglas F, ...
Abstract Introduction Somatic alterations have been shown to correlate with breast cancer prognosis and survival, but less is known about the effects of common inherited genetic variation. Of...
Allele-Specific Up-Regulation of FGFR2 Increases Susceptibility to Breast Cancer (2008)
Kerstin B. Meyer, Ana-Teresa Maia, Martin O'Reilly, Andrew E. Teschendorff, Suet-Feung Chin, Carlos Caldas, ...
The recent whole-genome scan for breast cancer has revealed the FGFR2 (fibroblast growth factor receptor 2) gene as a locus associated with a small, but highly significant, increase in the risk of...
Capellá, Gabriel, Pera, Guillem, Sala, Núria, Agudo, Antonio, Rico, Francisco, Del Giudicce, Giuseppe, ...
Background The contribution of genetic variation in DNA repair genes to gastric cancer (GC) risk remains essentially unknown. The aim of this study was to explore the relative contribution of DNA...
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype (2007)
Blenkiron, Cherie, Goldstein, Leonard D, Thorne, Natalie P, Spiteri, Inmaculada, Chin, Suet-Feung, Dunning, Mark J, ...
Abstract Background MicroRNAs (miRNAs), a class of short non-coding RNAs found in many plants and animals, often act post-transcriptionally to inhibit gene expression. Results Here we report the...
Chin, Suet F, Teschendorff, Andrew E, Marioni, John C, Wang, Yanzhong, Barbosa-Morais, Nuno L, Thorne, Natalie P, ...
Abstract Background The characterization of copy number alteration patterns in breast cancer requires high-resolution genome-wide profiling of a large panel of tumor specimens. To date, most...
Teschendorff, Andrew E, Miremadi, Ahmad, Pinder, Sarah E, Ellis, Ian O, Caldas, Carlos
Abstract Background Estrogen receptor (ER)-negative breast cancer specimens are predominantly of high grade, have frequent p53 mutations, and are broadly divided into HER2-positive and basal...
Andrew E. Teschendorff, Michel Journée, Pierre A. Absil, Rodolphe Sepulchre, Carlos Caldas
The quantity of mRNA transcripts in a cell is determined by a complex interplay of cooperative and counteracting biological processes. Independent Component Analysis (ICA) is one of a few number of...
Cancer genetics of epigenetic genes (2007)
Miremadi, Ahmad, Oestergaard, Mikkel Z., Pharoah, Paul D.P., Caldas, Carlos
The cancer epigenome is characterised by specific DNA methylation and chromatin modification patterns. The proteins that mediate these changes are encoded by the epigenetics genes here defined as:...
Andrew Erich Teschendorff, Michel Journee, Pierre A Absil, Rodolphe Sepulchre, Carlos Caldas
The quantity of mRNA transcripts in a cell is determined by a complex interplay of cooperative and counteracting biological processes. Independent Component Analysis (ICA) is one of a few number of...
A quantum leap in our knowledge of breast cancer mutations (2006)
Caldas, Carlos, Edwards, Paul AW
No abstract available.
A consensus prognostic gene expression classifier for ER positive breast cancer (2006)
Teschendorff, Andrew E, Naderi, Ali, Barbosa-Morais, Nuno L, Pinder, Sarah E, Ellis, Ian O, Aparicio, Sam, ...
Abstract Background A consensus prognostic gene expression classifier is still elusive in heterogeneous diseases such as breast cancer. Results Here we perform a combined analysis of three major...
Differential expression of selected histone modifier genes in human solid cancers (2006)
Özdağ, Hilal, Teschendorff, Andrew E, Ahmed, Ahmed, Hyland, Sarah J, Blenkiron, Cherie, Bobrow, Linda, ...
Abstract Background Post-translational modification of histones resulting in chromatin remodelling plays a key role in the regulation of gene expression. Here we report characteristic patterns of...
The Brazilian tradition of religious studies is characterized by an intensive use of auxiliary tools in the field of the Social Sciences, especially Sociology. Nevertheless, it is possible to use...
PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer (2006)
Teschendorff, Andrew E., Naderi, Ali, Barbosa-Morais, Nuno L., Caldas, Carlos
Motivation: Elucidating the molecular taxonomy of cancers and finding biological and clinical markers from microarray experiments is problematic due to the large number of variables being measured....
Gorringe, Kylie L., Chin, Suet-Feung, Pharoah, Paul, Staines, Joanne M., Oliveira, Carla, Edwards, Paul A. W., ...
Cancer cells contain many genetic alterations, and genetic instability may be important in tumourigenesis. We evaluated 58 breast and ovarian cancer cell lines for microsatellite instability (MSI)...
Human and mouse oligonucleotide-based array CGH (2005)
Van Den IJssel, Paul, Tijssen, Marianne, Chin, Suet-Feung, Eijk, Paul, Carvalho, Beatriz, Hopmans, Erik, ...
Array-based comparative genomic hybridization is a high resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide...
Teschendorff, Andrew E., Wang, Yanzhong, Barbosa-Morais, Nuno L., Brenton, James D., Caldas, Carlos
Motivation: Accurate subcategorisation of tumour types through gene expression profiling requires analytical techniques that estimate the number of categories or clusters rigorously and reliably....
Gorringe, Kylie L., Chin, Suet-Feung, Pharoah, Paul, Staines, Joanne M., Oliveira, Carla, Edwards, Paul A.W., ...
Cancer cells contain many genetic alterations, and genetic instability may be important in tumourigenesis. We evaluated 58 breast and ovarian cancer cell lines for microsatellite instability (MSI)...
Naderi, Ali, Ahmed, Ahmed A, Barbosa-Morais, Nuno L, Aparicio, Samuel, Brenton, James D, Caldas, Carlos
Abstract Background Expression microarrays have evolved into a powerful tool with great potential for clinical application and therefore reliability of data is essential. RNA amplification is used...
Microarray segmentation methods significantly influence data precision (2004)
Ahmed, Ahmed Ashour, Vias, Maria, Iyer, N. Gopalakrishna, Caldas, Carlos, Brenton, James D.
Little consideration has been given to the effect of different segmentation methods on the variability of data derived from microarray images. Previous work has suggested that the significant source...
BMC Genomics BioMed Central Methodology article (2004)
Ali Naderi, Ahmed A Ahmed, Samuel Aparicio, James D Brenton, Carlos Caldas
Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling
Daigo, Yataro, Takayama, Ichiro, Ponder, Bruce AJ, Caldas, Carlos, Ward, Sean M, Sanders, Kenton M, ...
Abstract Background We previously identified eight known and novel genes differentially expressed in the small intestines of wild type and W/W V mice, which have greatly reduced populations of the...
Differential gene expression in the murine gastric fundus lacking interstitial cells of Cajal (2003)
Daigo, Yataro, Takayama, Ichiro, Ponder, Bruce AJ, Caldas, Carlos, Ward, Sean M, Sanders, Kenton M, ...
Abstract Background The muscle layers of murine gastric fundus have no interstitial cells of Cajal at the level of the myenteric plexus and only possess intramuscular interstitial cells and this...
Suriano, Gianpaolo, Oliveira, Carla, Ferreira, Paulo, Machado, José C., Bordin, Maria C., De Wever, Olivier, ...
E-cadherin is involved in the formation of cell-junctions and the maintenance of epithelial integrity. Direct evidence of E-cadherin mutations triggering tumorigenesis has come from the finding of...
Figueiredo, Céu, Machado, José Carlos, Pharoah, Paul, Seruca, Raquel, Sousa, Sónia, Carvalho, Ralph, ...
Background: Both Helicobacter pylori genotype and host genetic polymorphisms play a role in determining the clinical consequences of H. pylori infection. We investigated whether there are any...
Molecular profiling of breast cancer: portraits but not physiognomy (2000)
Brenton, James D, Aparicio, Samuel AJR, Caldas, Carlos
Abstract Breast cancers differ in response to treatment and may have a divergent clinical course despite having a similar histopathological appearance. New technology using DNA microarrays provides a...
Aparicio, Samuel AJR, Caldas, Carlos, Ponder, Bruce
Abstract Transcriptional analysis of all the genes expressed by breast tumors has provided the first steps towards defining a molecular signature for the disease, and might ultimately make...
So, Chi Wai, Caldas, Carlos, Liu, Meng-Min, Chen, Sai-Juan, Huang, Qiu-Hua, Gu, Long-Jun, ...
The MLL gene, the closest human homologue to the Drosophila trithorax gene, undergoes chromosomal translocation with a large number of different partner genes in both acute lymphoid and acute myeloid...
Molecular profiling of breast cancer: portraits but not physiognomy
Brenton, James D, Aparicio, Samuel AJR, Caldas, Carlos
Breast cancers differ in response to treatment and may have a divergent clinical course despite having a similar histopathological appearance. New technology using DNA microarrays provides a...
Aparicio, Samuel AJR, Caldas, Carlos, Ponder, Bruce
Transcriptional analysis of all the genes expressed by breast tumors has provided the first steps towards defining a molecular signature for the disease, and might ultimately make conventional...
Differential gene expression in the murine gastric fundus lacking interstitial cells of Cajal
Daigo, Yataro, Takayama, Ichiro, Ponder, Bruce AJ, Caldas, Carlos, Ward, Sean M, Sanders, Kenton M, ...
Daigo, Yataro, Takayama, Ichiro, Ponder, Bruce AJ, Caldas, Carlos, Ward, Sean M, Sanders, Kenton M, ...
Naderi, Ali, Ahmed, Ahmed A, Barbosa-Morais, Nuno L, Aparicio, Samuel, Brenton, James D, Caldas, Carlos
Microarray segmentation methods significantly influence data precision
Ahmed, Ahmed Ashour, Vias, Maria, Iyer, N. Gopalakrishna, Caldas, Carlos, Brenton, James D.
Little consideration has been given to the effect of different segmentation methods on the variability of data derived from microarray images. Previous work has suggested that the significant source...
Iyer, N. Gopalakrishna, Chin, Suet-Feung, Ozdag, Hilal, Daigo, Yataro, Hu, De-En, Cariati, Massimiliano, ...
Activation of the tumor suppressor p53 by DNA damage induces either cell cycle arrest or apoptosis, but what determines the choice between cytostasis and death is not clear. In this report, we show...
Human and mouse oligonucleotide-based array CGH
Van Den IJssel, Paul, Tijssen, Marianne, Chin, Suet-Feung, Eijk, Paul, Carvalho, Beatriz, Hopmans, Erik, ...
Array-based comparative genomic hybridization is a high resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide...
Differential expression of selected histone modifier genes in human solid cancers
Özdağ, Hilal, Teschendorff, Andrew E, Ahmed, Ahmed Ashour, Hyland, Sarah J, Blenkiron, Cherie, Bobrow, Linda, ...
So, Chi Wai, Caldas, Carlos, Liu, Meng-Min, Chen, Sai-Juan, Huang, Qiu-Hua, Gu, Long-Jun, ...
The MLL gene, the closest human homologue to the Drosophila trithorax gene, undergoes chromosomal translocation with a large number of different partner genes in both acute lymphoid and acute myeloid...
Molecular profiling of breast cancer: portraits but not physiognomy
Brenton, James D, Aparicio, Samuel AJR, Caldas, Carlos
Breast cancers differ in response to treatment and may have a divergent clinical course despite having a similar histopathological appearance. New technology using DNA microarrays provides a...
Aparicio, Samuel AJR, Caldas, Carlos, Ponder, Bruce
Transcriptional analysis of all the genes expressed by breast tumors has provided the first steps towards defining a molecular signature for the disease, and might ultimately make conventional...
Differential gene expression in the murine gastric fundus lacking interstitial cells of Cajal
Daigo, Yataro, Takayama, Ichiro, Ponder, Bruce AJ, Caldas, Carlos, Ward, Sean M, Sanders, Kenton M, ...
Daigo, Yataro, Takayama, Ichiro, Ponder, Bruce AJ, Caldas, Carlos, Ward, Sean M, Sanders, Kenton M, ...
Naderi, Ali, Ahmed, Ahmed A, Barbosa-Morais, Nuno L, Aparicio, Samuel, Brenton, James D, Caldas, Carlos
Microarray segmentation methods significantly influence data precision
Ahmed, Ahmed Ashour, Vias, Maria, Iyer, N. Gopalakrishna, Caldas, Carlos, Brenton, James D.
Little consideration has been given to the effect of different segmentation methods on the variability of data derived from microarray images. Previous work has suggested that the significant source...
Iyer, N. Gopalakrishna, Chin, Suet-Feung, Ozdag, Hilal, Daigo, Yataro, Hu, De-En, Cariati, Massimiliano, ...
Activation of the tumor suppressor p53 by DNA damage induces either cell cycle arrest or apoptosis, but what determines the choice between cytostasis and death is not clear. In this report, we show...
Human and mouse oligonucleotide-based array CGH
Van Den IJssel, Paul, Tijssen, Marianne, Chin, Suet-Feung, Eijk, Paul, Carvalho, Beatriz, Hopmans, Erik, ...
Array-based comparative genomic hybridization is a high resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide...
Differential expression of selected histone modifier genes in human solid cancers
Özdağ, Hilal, Teschendorff, Andrew E, Ahmed, Ahmed Ashour, Hyland, Sarah J, Blenkiron, Cherie, Bobrow, Linda, ...
A consensus prognostic gene expression classifier for ER positive breast cancer
Teschendorff, Andrew E, Naderi, Ali, Barbosa-Morais, Nuno L, Pinder, Sarah E, Ellis, Ian O, Aparicio, Sam, ...
A consensus prognostic classifier for estrogen receptor positive breast tumors has been developed and shown to be valid in nearly 900 samples across different microarray platforms.
Daigo, Yataro, Chin, Suet-Feung, Gorringe, Kylie L., Bobrow, Lynda G., Ponder, Bruce A. J., Pharoah, Paul D. P., ...
We have developed a protocol for degenerate oligonucleotide-primed-polymerase chain reaction-based array comparative genomic hybridization (array CGH) that, when combined with a laser microdissection...
Teschendorff, Andrew E, Journée, Michel, Absil, Pierre A, Sepulchre, Rodolphe, Caldas, Carlos
The quantity of mRNA transcripts in a cell is determined by a complex interplay of cooperative and counteracting biological processes. Independent Component Analysis (ICA) is one of a few number of...
Ahmed, Ahmed Ashour, Mills, Anthony D., Ibrahim, Ashraf E.K., Temple, Jillian, Blenkiron, Cherie, Vias, Maria, ...
The extracellular matrix (ECM) can induce chemotherapy resistance via AKT-mediated inhibition of apoptosis. Here, we show that loss of the ECM protein TGFBI (transforming growth factor beta induced)...
MicroRNA—implications for cancer
Sassen, Stefanie, Miska, Eric A., Caldas, Carlos
MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression post-transcriptionally. After the discovery of the first miRNA in the roundworm Caenorhabditis elegans, these short regulatory...
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype
Blenkiron, Cherie, Goldstein, Leonard D, Thorne, Natalie P, Spiteri, Inmaculada, Chin, Suet-Feung, Dunning, Mark J, ...
Integrated analysis of miRNA expression and genomic changes in human breast tumors allows the classification of tumor subtypes.
Chin, Suet F, Teschendorff, Andrew E, Marioni, John C, Wang, Yanzhong, Barbosa-Morais, Nuno L, Thorne, Natalie P, ...
High resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer, and provides a genome-wide list of common copy number alterations associated with...
Development of a benchmarking framework for pharmaceutical capital projects
Bon-Gang Hwang, Stephen Thomas, Deborah Degezelle, Carlos Caldas
Benchmarking is a proven technique for improving project performance and, as such, is a critical component of any mature project delivery system. Competitive benchmarking requires industry-specific...
Teschendorff, Andrew E, Miremadi, Ahmad, Pinder, Sarah E, Ellis, Ian O, Caldas, Carlos
A feature selection method was used in an analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in estrogen receptor-negative breast cancer,...
Allele-Specific Up-Regulation of FGFR2 Increases Susceptibility to Breast Cancer
Meyer, Kerstin B, Maia, Ana-Teresa, O'Reilly, Martin, Teschendorff, Andrew E, Chin, Suet-Feung, Caldas, Carlos, ...
The recent whole-genome scan for breast cancer has revealed the FGFR2 (fibroblast growth factor receptor 2) gene as a locus associated with a small, but highly significant, increase in the risk of...
Regulation of p53 tetramerization and nuclear export by ARC
Foo, Roger S.-Y., Nam, Young-Jae, Ostreicher, Marc Jason, Metzl, Mark D., Whelan, Russell S., Peng, Chang-Fu, ...
Inactivation of the transcription factor p53 is central to carcinogenesis. Yet only approximately one-half of cancers have p53 loss-of-function mutations. Here, we demonstrate a mechanism for p53...
Meta-analysis confirms BCL2 is an independent prognostic marker in breast cancer
Callagy, Grace M, Webber, Mark J, Pharoah, Paul DP, Caldas, Carlos
Azzato, Elizabeth M, Driver, Kristy E, Lesueur, Fabienne, Shah, Mitul, Greenberg, David, Easton, Douglas F, ...
PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes
Git, Anna, Spiteri, Inmaculada, Blenkiron, Cherie, Dunning, Mark J, Pole, Jessica CM, Chin, Suet-Feung, ...
High-resolution array CGH clarifies events occurring on 8p in carcinogenesis
Cooke, Susanna L, Pole, Jessica CM, Chin, Suet-Feung, Ellis, Ian O, Caldas, Carlos, Edwards, Paul AW
Carlos Caldas, Chien-Cheng Chou, Jim O'connor
Highway projects in metropolitan areas often require that adjacent utilities be relocated to accommodate new or expanded highway facilities. Traditionally, utility owners have been responsible for...
Reyal, Fabien, Van Vliet, Martin H, Armstrong, Nicola J, Horlings, Hugo M, De Visser, Karin E, Kok, Marlen, ...
The development of infrastructure contributes to the social and economic improvement of a country, and generally requires huge and immediate investments. To decide on appropriate infrastructure...
The breast cancer somatic 'muta-ome': tackling the complexity
Teschendorff, Andrew E, Caldas, Carlos
Acquired somatic mutations are responsible for approximately 90% of breast tumours. However, only one somatic aberration, amplification of the HER2 locus, is currently used to define a clinical...
Germline CDH1 deletions in hereditary diffuse gastric cancer families
Oliveira, Carla, Senz, Janine, Kaurah, Pardeep, Pinheiro, Hugo, Sanges, Remo, Haegert, Anne, ...
Germline CDH1 point or small frameshift mutations can be identified in 30–50% of hereditary diffuse gastric cancer (HDGC) families. We hypothesized that CDH1 genomic rearrangements would be found...