Oscar M. Rueda
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
Research Subjects
Oscar M. Rueda has a total of 12 co-authors. Here are the top co-authors by number of shared publications:
- Ramon Diaz-Uriarte
Department of Biochemistry, School of Medicine, Universidad Autonoma de Madrid
3 shared publications - Carlos Caldas
Department of Clinical Biochemistry and Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, UK
2 shared publications Chin-Ann Johnny Ong
2 shared publicationsNicholas Shannon
2 shared publicationsRebecca Fitzgerald
2 shared publicationsRichard H. Hardwick
2 shared publications
Latest Publications
- 15 January 2013
- Published by Springer Nature
- Vol. 973, 339-353
Finding Common Regions of Alteration in Copy Number Data
In this chapter, we review some recent methods designed for detecting recurrent copy number regions, that is, genomic regions that show evidence of being altered in a set of samples. We analyze Affymetrix SNP6 data from 87 Her2-type breast tumors from a recent study using three different methods, showing different definitions and features of common regions: studying heterogeneity in copy number profiles, refining candidates for driver oncogenes, and consolidating broad amplifications.
- 15 January 2013
- Published by Springer Nature
- Vol. 973, 339-353
Finding Common Regions of Alteration in Copy Number Data
In this chapter, we review some recent methods designed for detecting recurrent copy number regions, that is, genomic regions that show evidence of being altered in a set of samples. We analyze Affymetrix SNP6 data from 87 Her2-type breast tumors from a recent study using three different methods, showing different definitions and features of common regions: studying heterogeneity in copy number profiles, refining candidates for driver oncogenes, and consolidating broad amplifications.
- 1 May 2012
- Published by Elsevier in Gastroenterology
- Vol. 142 (5)
254 TRIM44: From Prognosis to Therapy in Esophageal Adenocarcinoma and Breast Cancer
- 1 May 2012
- Published by Elsevier in Gastroenterology
- Vol. 142 (5)
254 TRIM44: From Prognosis to Therapy in Esophageal Adenocarcinoma and Breast Cancer
- 1 May 2012
- Published by Elsevier in Gastroenterology
- Vol. 142 (5)
Sa1795 Using Expression Array Data to Elucidate the Molecular Phenotype of a Novel Oncogene and Identify a Therapeutic Strategy
- 1 May 2012
- Published by Elsevier in Gastroenterology
- Vol. 142 (5)
Sa1795 Using Expression Array Data to Elucidate the Molecular Phenotype of a Novel Oncogene and Identify a Therapeutic Strategy
- Open Access
- 23 September 2009
- Published by Springer Nature in BMC Bioinformatics
- Vol. 10 (1) , 308
Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously
Alterations in the number of copies of genomic DNA that are common or recurrent among diseased individuals are likely to contain disease-critical genes. Unfortunately, defining common or recurrent copy number alteration (CNA) regions remains a challenge. Moreover, the heterogeneous nature of many diseases requires that we search for common or recurrent CNA regions that affect only some subsets of the samples (without knowledge of the regions and subsets affected), but this is neglected by most methods.
- 23 September 2009
- Published by Springer Nature in BMC Bioinformatics
- Vol. 10 (1) , 308
Open AccessDetection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously
Alterations in the number of copies of genomic DNA that are common or recurrent among diseased individuals are likely to contain disease-critical genes. Unfortunately, defining common or recurrent copy number alteration (CNA) regions remains a challenge. Moreover, the heterogeneous nature of many diseases requires that we search for common or recurrent CNA regions that affect only some subsets of the samples (without knowledge of the regions and subsets affected), but this is neglected by most methods.
- Open Access
- 6 May 2009
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 25 (15) , 1959-1960
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions
Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question ‘is this probe/region altered?’ RJaCGH fits a Non-Homogeneous Hidden Markov model to the aCGH data using Markov Chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found. Availability: RJaCGH is available as an R package from CRAN repositories (e.g. http://cran.r-project.org/web/packages). Contact: rueda.om@gmail.com; rueda.om@gmail.com
- 6 May 2009
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 25 (15) , 1959-1960
Open AccessRJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions
Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question ‘is this probe/region altered?’ RJaCGH fits a Non-Homogeneous Hidden Markov model to the aCGH data using Markov Chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found. Availability: RJaCGH is available as an R package from CRAN repositories (e.g. http://cran.r-project.org/web/packages). Contact: rueda.om@gmail.com; rueda.om@gmail.com