Carlos Caldas publications

PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes
Git A;Spiteri I;Blenkiron C;Dunning MJ;Pole JCM;Chin SF;Wang YZ;Smith J;Livesey FJ;Caldas C
Breast Cancer Res 2008; 10 (3):R54.
UKPubMed (open access);  PubMed;  DOI: 10.1186/bcr2109.

Effects of common germline genetic variation in cell cycle control genes on breast cancer survival: results from a population-based cohort
Azzato EM;Driver KE;Lesueur F;Shah M;Greenberg D;Easton DF;Teschendorff AE;Caldas C;Caporaso NE;Pharoah PDP
Breast Cancer Res 2008; 10 (3):R47.
UKPubMed (open access);  PubMed;  DOI: 10.1186/bcr2100.

ESR1 gene amplification in breast cancer: a common phenomenon?
Brown LA;Hoog J;Chin SF;Tao Y;Zayed AA;Chin K;Teschendorff AE;Quackenbush JF;Marioni JC;Leung S;Perou CM;Neilsen TO;Ellis M;Gray JW;Bernard PS;Huntsman DG;Caldas C
Nat Genet 2008; 40 (7):806-807.

Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer
Meyer KB;Maia AT;O'Reilly M;Teschendorff AE;Chin SF;Caldas C;Ponder BAJ
PLoS Biol 2008; 6 (5):e108.
UKPubMed (open access);  PubMed;  DOI: 10.1371/journal.pbio.0060108.

Meta-analysis confirms BCL2 is an independent prognostic marker in breast cancer
Callagy GM;Webber MJ;Pharoah PDP;Caldas C
BMC Cancer 2008; 8 ():153.

High-resolution array-based comparative genomic hybridization of bladder cancers identifies mouse double minute 4 (MDM4) as an amplification target exclusive of MDM2 and TP53
Veerakumarasivam A;Scott HE;Chin SF;Warren A;Wallard MJ;Grimmer D;Ichimura K;Caldas C;Collins VP;Neal DE;Kelly JD
Clin Cancer Res 2008; 14 (9):2527-2534.

Array comparative genomic hybridization copy number profiling: A new tool for translational research in solid malignancies
Costa JL;Meijer G;Ylstra B;Caldas C
Semin Radiat Oncol 2008; 18 (2):98-104.

Alpha-6 integrin is necessary for the tumourigenicity of a stem cell-like subpopulation within the MCF7 breast cancer cell line
Cariati M;Naderi A;Brown JP;Smalley MJ;Pinder SE;Caldas C;Purushotham AD
Int J Cancer 2008; 122 (2):298-304.

MicroRNA - implications for cancer
Sassen S;Miska EA;Caldas C
Virchows Arch 2008; 452 (1):1-10.

An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer
Teschendorff AE;Miremadi A;Pinder SE;Ellis IO;Caldas C
Genome Biol 2007; 8 (8):R157.

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
Chin SF;Teschendorff AE;Marioni JC;Wang Y;Barbosa-Morais NL;Thorne NP;Costa JL;Pinder SE;De Wiel MAV;Green AR;Ellis IO;Porter PL;Tavare S;Brenton JD;Ylstra B;Caldas C
Genome Biol 2007; 8 (10):R215.

MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype
Blenkiron C;Goldstein LD;Thorne NP;Spiteri I;Chin SF;Dunning MJ;Barbosa-Morais NL;Teschendorff AE;Green AR;Ellis IO;Tavare S;Caldas C;Miska EA
Genome Biol 2007; 8 (10):R214.

Regulation of p53 tetramerization and nuclear export by ARC
Foo RSY;Nam YJ;Ostreicher MJ;Metzl MD;Whelan RS;Peng CF;Ashton AW;Fu W;Mani K;Chin SF;Provenzano E;Ellis I;Figg N;Pinder S;Bennett MR;Caldas C;Kitsis RN
Proc Natl Acad Sci U S A 2007; 104 (52):20826-20831.

The extracellular matrix protein TGFBI induces microtubule stabilization and sensitizes ovarian cancers to paclitaxel
Ahmed AA;Mills AD;Ibrahim AEK;Temple J;Blenkiron C;Vias M;Massie CE;Iyer NG;McGeoch A;Crawford R;Nicke B;Downward J;Swanton C;Bell SD;Earl HM;Laskey RA;Caldas C;Brenton JD
Cancer Cell 2007; 12 (6):514-527.

p400 function is required for the adenovirus E1A-mediated suppression of EGFR and tumour cell killing
Flinterman MB;Mymryk JS;Klanrit P;Yousef AF;Lowe SW;Caldas C;Gaken J;Farzaneh F;Tavassoli M
Oncogene 2007; 26 (48):6863-6874.

Elucidating the altered transcriptional programs in breast cancer using independent component analysis
Teschendorff AE;Journee M;Absil PA;Sepulchre R;Caldas C
PLoS Comput Biol 2007; 3 (8):1539-1554.

Opinion - Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis
Stingl J;Caldas C
Nat Rev Cancer 2007; 7 (10):791-799.

Cancer genetics of epigenetic genes
Miremadi A;Oestergaard MZ;Pharoah PDP;Caldas C
Hum Mol Genet 2007; 16 (Spec Iss 1):R28-R49.

Common germline genetic variation in antioxidant defense genes and survival after diagnosis of breast cancer
Udler M;Maia AT;Cebrian A;Brown C;Greenberg D;Shah M;Caldas C;Dunning A;Easton D;Ponder B;Pharoah P
J Clin Oncol 2007; 25 (21):3015-3023.

BEX2 is overexpressed in a subset of primary breast cancers and mediates nerve growth factor/nuclear factor-kappa B inhibition of apoptosis in breast cancer cell lines
Naderi A;Teschendorff AE;Beigel J;Cariati M;Ellis IO;Brenton JD;Caldas C
Cancer Res 2007; 67 (14):6725-6736.

Pathology findings and validation of gastric and esophageal cancer cases in a European cohort (EPIC/EUR-GAST)
Carneiro F;Moutinho C;Pera G;Caldas C;Fenger C;Offerhaus J;Save V;Stenling R;Nesi G;Mahlke U;Blaker H;Torrado J;Roukos DH;Sabourin JC;Boeing H;Palli D;Bueno-De-Mesquita HB;Overvad K;Bingham S;Clavel-Chapelon F;Lund E;Trichopoulou A;Manjer J;Riboli E;Gonzalez CA
Scand J Gastroenterol 2007; 42 (5):618-627.

Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers
Chin SF;Wang Y;Thorne NP;Teschendorff AE;Pinder SE;Vias M;Naderi A;Roberts I;Barbosa-Morais NL;Garcia MJ;Iyer NG;Kranjac T;Robertson JFR;Aparicio S;Tavare S;Ellis I;Brenton JD;Caldas C
Oncogene 2007; 26 (13):1959-1970.

Co-amplification of 8p 12 and 1 1q 13 in breast cancers is not the result of a single genomic event
Paterson AL;Pole JCM;Blood KA;Garcia MJ;Cooke SL;Teschendorff AE;Wang YZ;Chin SF;Ylstra B;Caldas C;Edwards PAW
Genes Chromosomes Cancer 2007; 46 (5):427-439.

A gene-expression signature to predict survival in breast cancer across independent data sets
Naderi A;Teschendorff AE;Barbosa-Morais NI;Pinder SE;Green AR;Powe DG;Robertson JFR;Aparicio S;Ellis IO;Brenton JD;Caldas C
Oncogene 2007; 26 (10):1507-1516.

Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors
Jong K;Marchiori E;van der Vaart A;Chin SF;Carvalho B;Tijssen M;Eijk PP;van den IJssel P;Grabsch H;Quirke P;Oudejans JJ;Meijer GA;Caldas C;Ylstra B
Oncogene 2007; 26 (10):1499-1506.

Genetic unmasking of an epigenetically silenced microRNA in human cancer cells
Lujambio A;Ropero S;Ballestar E;Fraga MF;Cerrato C;Setien F;Casado S;Suarez-Gauthier A;Sanchez-Cespedes M;Gitt A;Spiteri I;Das PP;Caldas C;Miska E;Esteller M
Cancer Res 2007; 67 (4):1424-1429.

p300 is required for orderly G1/S transition in human cancer cells
Iyer NG;Xian J;Chin SF;Bannister AJ;Daigo Y;Aparicio S;Kouzarides T;Caldas C
Oncogene 2007; 26 (1):21-29.

Genomic analysis of the 8p11-12 amplicon in familial breast cancer
Melchor L;Garcia MJ;Honrado E;Pole JCM;Alvarez S;Edwards PAW;CaldaS C;Brenton JD;Benitez J
Int J Cancer 2007; 120 (3):714-717.

A quantum leap in our knowledge of breast cancer mutations
Caldas C;Edwards PAW
Breast Cancer Res 2006; 8 (6):304.

A novel mutation in the E-cadherin gene in the first family with hereditary diffuse gastric cancer reported in Spain
Rodriguez-Sanjuan JC;Fontalba A;Mayorga M;Bordin MC;Hyland SJ;Trugeda S;Garcia RA;Gomez-Fleitas M;Fernandez F;Caldas C;Fernandez-Luna JL
Eur J Surg Oncol 2006; 32 (10):1110-1113.

Pharmacogenetics of cancer chemotherapy
Abraham J;Earl HM;Pharoah PD;Caldas C
Biochim Biophys Acta [Rev Cancer] 2006; 1766 (2):168-183.

A consensus prognostic gene expression classifier for ER positive breast cancer
Teschendorff AE;Naderi A;Barbosa-Morais NL;Pinder SE;Ellis IO;Aparicio S;Brenton JD;Caldas C
Genome Biol 2006; 7 (10):R101.

ZNF198, a zinc finger protein rearranged in myeloproliferative disease, localizes to the PML nuclear bodies and interacts with SUMO-1 and PML
Kunapuli P;Kasyapaa CS;Chin SF;Caldas C;Cowell JK
Exp Cell Res 2006; 312 (19):3739-3751.

Familial gastric cancer - clinical management
Fitzgerald RC;Caldas C
Best Pract Res Clin Gastroenterol 2006; 20 (4):735-743.

Familial gastric cancer - aetiology and pathogenesis
Barber M;Fitzgerald RC;Caldas C
Best Pract Res Clin Gastroenterol 2006; 20 (4):721-734.

High-resolution analysis of chromosome rearrangements on 8p in breast, colon and pancreatic cancer reveals a complex pattern of loss, gain and translocation
Pole JCM;Courtay-Cahen C;Garcia MJ;Blood KA;Cooke SL;Alsop AE;Tse DML;Caldas C;Edwards PAW
Oncogene 2006; 25 (41):5693-5706.

PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
Teschendorff AE;Naderi A;Barbosa-Morais NL;Caldas C
Bioinformatics 2006; 22 (18):2269-2275.

Metabolic consequences of p300 gene deletion in human colon cancer cells
Bundy JG;Iyer NG;Gentile MS;Hu DE;Kettunen M;Maia AT;Thorne NP;Brenton JD;Caldas C;Brindle KM
Cancer Res 2006; 66 (15):7606-7614.

Genomic imbalances and patterns of karyotypic variability in mantle-cell lymphoma cell lines
Camps J;Salaverria I;Garcia MJ;Prat E;Bea S;Pole JC;Hernandez L;Del Rey J;Cigudosa JC;Bernues M;Caldas C;Colomer D;Miro R;Campo E
Leuk Res 2006; 30 (8):923-934.

Differential expression of selected histone modifier genes in human solid cancers
Ozdag H;Teschendorff AE;Ahmed AA;Hyland SJ;Blenkiron C;Bobrow L;Veerakumarasivam A;Burtt G;Subkhankulova T;Arends MJ;Collins VP;Bowtell D;Kouzarides T;Brenton JD;Caldas C
BMC Genomics 2006; 7 ():90.

Absence of p300 induces cellular phenotypic changes characteristic of epithelial to mesenchyme transition
Krubasik D;Iyer NG;English WR;Ahmed AA;Vias M;Roskelley C;Brenton JD;Caldas C;Murphy G
Br J Cancer 2006; 94 (9):1326-1332.

Bcl-2 is a prognostic marker in breast cancer independently of the Nottingham Prognostic Index
Callagy GM;Pharoah PD;Pinder SE;Hsu FD;Nielsen TO;Ragaz J;Ellis IO;Huntsman D;Caldas C
Clin Cancer Res 2006; 12 (8):2468-2475.

Telomerase- and alternative telomere lengthening-independent telomere stabilization in a metastasis-derived human non-small cell lung cancer cell line: Effect of ectopic hTERT
Brachner A;Sasgary S;Pirker C;Rodgarkia C;Mikula M;Mikulits W;Bergmeister H;Setinek U;Wieser M;Chin SF;Caldas C;Micksche M;Cerni C;Berger W
Cancer Res 2006; 66 (7):3584-3592.

Molecular forecasting of breast cancer: Time to move forward with clinical testing - In reply
Brenton JD;Ahmed AA;Caldas C
J Clin Oncol 2006; 24 (4):722-723.

Human and mouse oligonucleotide-based array CGH
van den IJssel P;Tijssen M;Chin SF;Eijk P;Carvalho B;Hopmans E;Holstege H;Bangarusamy DK;Jonkers J;Meijer GA;Caldas C;Ylstra B
Nucleic Acids Res 2005; 33 (22):e192.

Chromatin modifier enzymes, the histone code and cancer
Santos-Rosa H;Caldas C
Eur J Cancer 2005; 41 (16):2381-2402.

Chromosome abnormalities in 10 lung cancer cell lines of the NCI-H series analyzed with spectral karyotyping
Grigorova M;Lyman RC;Caldas C;Edwards PAW
Cancer Genet Cytogenet 2005; 162 (1):1-9.

Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling
Naderi A;Ahmed AA;Barbosa-Morais NL;Aparicio S;Brenton JD;Caldas C
BMC Genomics 2004; 5 ():9.

Model of the early development of diffuse gastric cancer in E-cadherin mutation carriers and its implications for patient screening
Carneiro F;Huntsman DG;Smyrk TC;Owen DA;Seruca R;Pharoah P;Caldas C;Sobrinho-Simoes M
J Pathol 2004; 203 (2):681-687.

A recurrent chromosome breakpoint in breast cancer at the NRG1/Neuregulin 1/Heregulin gene
Huang HE;Chin SF;Ginestier C;Bardou VJ;Adelaide J;Iyer NG;Garcia MJ;Pole JC;Callagy GM;Hewitt SM;Gullick WJ;Jacquemier J;Caldas C;Chaffanet M;Birnbaum D;Edwards PAW
Cancer Res 2004; 64 (19):6840-6844.

Possible causes of chromosome instability: comparison of chromosomal abnormalities in cancer cell lines with mutations in BRCA1, BRCA2, CHK2 and BUB1
Grigorova M;Staines JM;Ozdag H;Caldas C;Edwards PAW
Cytogenet Genome Res 2004; 104 (1-4):333-340.

Germline E-cadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria
Brooks-Wilson AR;Kaurah P;Suriano G;Leach S;Senz J;Grehan N;Butterfield YSN;Jeyes J;Schinas J;Bacani J;Kelsey M;Ferreira P;MacGillivray B;Macleod P;Micek M;Ford J;Foulkes W;Australie K;Greenberg C;LaPointe M;Gilpin C;Nikkel S;Gilchrist D;Hughes R;Jackson CE;Monaghan KG;Oliveira MJ;Seruca R;Gallinger S;Caldas C;Huntsman D
J Med Genet 2004; 41 (7):508-517.

P300 regulates p53-dependent apoptosis after DNA damage in colorectal cancer cells by modulation of PUMA/p21 levels
Iyer NG;Chin SF;Ozdag H;Daigo Y;Hu DE;Cariati M;Brindle K;Aparicio S;Caldas C
Proc Natl Acad Sci U S A 2004; 101 (19):7386-7391.

p300/CBP and cancer
Iyer NG;Ozdag H;Caldas C
Oncogene 2004; 23 (24):4225-4231.

Clinical implications of E-cadherin associated hereditary diffuse gastric cancer
Fitzgerald RC;Caldas C
Gut 2004; 53 (6):775-778.

Microarray segmentation methods significantly influence data precision
Ahmed AA;Vias M;Iyer NG;Caldas C;Brenton JD
Nucleic Acids Res 2004; 32 (5):e5.

A proinflammatory genetic profile increases the risk for chronic atrophic gastritis and gastric carcinoma
Machado JC;Figueiredo C;Canedo P;Pharoah P;Carvalho R;Nabais S;Alves CC;Campos ML;Van Doorn LJ;Caldas C;Seruca R;Carneiro F;Sobrinho-Simoes M
Gastroenterology 2003; 125 (2):364-371.

Genetic screening for hereditary diffuse gastric cancer
Oliveira C;Seruca R;Caldas C
Expert Rev Mol Diagn 2003; 3 (2):201-215.

A simple and reliable pretreatment protocol facilitates fluorescent in situ hybridisation on tissue microarrays of paraffin wax embedded tumour samples
Chin SF;Daigo Y;Huang HE;Iyer NG;Callagy G;Kranjac T;Gonzalez M;Sangan T;Earl H;Caldas C
J Clin Pathol Mol Pathol 2003; 56 (5):275-279.

Predictive cancer genomics - what do we need?
Brenton JD;Caldas C
Lancet 2003; 362 (9381):340-341.

Identification of CDH1 germline missense mutations associated with functional inactivation of the E-cadherin protein in young gastric cancer probands
Suriano G;Oliveira C;Ferreira P;Machado JC;Bordin MC;De Wever O;Bruyneel EA;Moguilevsky N;Grehan N;Porter TR;Richards FM;Hruban RH;Roviello F;Huntsman D;Mareel M;Carneiro F;Caldas C;Seruca R
Hum Mol Genet 2003; 12 (5):575-582.

Molecular classification of breast carcinomas using tissue microarrays
Callagy G;Cattaneo E;Daigo Y;Happerfield L;Bobrow LG;Pharoah PDP;Caldas C
Diagn Mol Pathol 2003; 12 (1):27-34.

EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer
Hughes-Davies L;Huntsman D;Ruas M;Fuks F;Bye J;Chin SF;Milner J;Brown LA;Hsu F;Gilks B;Nielsen T;Schulzer M;Chia S;Ragaz J;Cahn A;Linger L;Ozdag H;Cattaneo E;Jordanova ES;Schuuring E;Yu DS;Venkitaraman A;Ponder B;Doherty A;Aparicio S;Bentley D;Theillet C;Ponting CP;Caldas C;Kouzarides T
Cell 2003; 115 (5):523-535.

Helicobacter pylori and interleukin 1 genotyping: An opportunity to identify high-risk individuals for gastric carcinoma
Figueiredo C;Machodo JC;Pharoah P;Seruca R;Sousa S;Carvalho R;Capelinha AF;Quint W;Caldas C;van Doorn LJ;Carneiro F;Sobrinho-Simoes M
J Natl Cancer Inst 2002; 94 (22):1680-1687.

CDH1 c-160a promotor polymorphism is not associated with risk of stomach cancer
Pharoah PDP;Oliveira C;Machado JC;Keller G;Vogelsang H;Laux H;Becker KF;Hahn H;Paproski SM;Brown LA;Caldas C;Huntsman D
Int J Cancer 2002; 101 (2):196-197.

Mutation analysis of CBP and PCAF reveals rare inactivating mutations in cancer cell lines but not In primary tumours
Ozdag H;Batley SJ;Forsti A;Iyer NG;Daigo Y;Boutell J;Arends MJ;Ponder BAJ;Kouzarides T;Caldas C
Br J Cancer 2002; 87 (10):1162-1165.

E-cadherin mutations and hereditary gastric cancer: Prevention by resection?
Fitzgerald RC;Caldas C
Dig Dis 2002; 20 (1):23-31.

Screening E-cadherin in gastric cancer families reveals germline mutations only in hereditary diffuse gastric cancer kindred
Oliveira C;Bordin MC;Grehan N;Huntsman D;Suriano G;Machado JC;Kiviluoto T;Aaltonen L;Jackson CE;Seruca R;Caldas C
Hum Mutat 2002; 19 (5):510-517.

Cancer - The molecular outlook
Caldas C;Aparicio SAJ
Nature 2002; 415 (6871):484-485.