Hidden Markov models approach to the analysis of array CGH data

By Jane Fridlyand, Antoine Snijders, Dan Pinkel, Donna Albertson, Ajay N. Jain. 2004

383 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/88ff7c158c4fa072cbf0093ece0ac8a66069f9db

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. P. Park
2. Nancy Ruonan Zhang
3. David O. Siegmund
4. John W. Emerson
5. Chandra Erdman
6. Dan Pinkel
7. Donna Albertson
8. Jean-Jacques Daudin

In Molecular Biology

1. P. Park
2. David O. Siegmund
3. Nancy Ruonan Zhang
4. John W. Emerson
5. Chandra Erdman
6. Dan Pinkel
7. Donna Albertson
8. David S. Matteson

In Plant Science

1. P. Park
2. Nancy Ruonan Zhang
3. David O. Siegmund
4. John W. Emerson
5. Chandra Erdman
6. Dan Pinkel
7. Donna Albertson
8. Idris Arthur Eckley

Citations in the corpus

• A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data (2007, methodology): “After the merging of states, the complete procedure from Fridlyand et al. (2004) reports 69 change-points for this data series.”
• Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data (2005, methodology): “1 (R) E HMM Fridlyand et al. (2004) Hidden Markov Model aCGH, v1.1.4 (R) E Wavelet Hsu et al. (2005) Maximal Overlap Discrete Wavelet Transform waveslim, v1.4 (R)∗ S Lowess Locally Weighted Regression stats, v2.0.1 (R)∗ S ChARM Myers et al. (2004) Chromosomal Aberration Region Miner ChARM, v1.6 (JAV”
• A statistical approach for array CGH data analysis (2005, background): “A second approach is based on Hidden Markov Models (aCGH R-package [12]), where the purpose is to cluster individual data points into a finite number of hidden groups.”
• Development of query strategies to identify a histologic lymphoma subtype in a large linked database system. (2006, positive): “Moreover, this method has been used to extrapolate levels of copy number when accounting for such factors as tissue heterogeneity as the expected ratio change for a single copy gain and loss would be dampened (Fridlyand et al. 2004).”
• bcp: An R Package for Performing a Bayesian Analysis of Change Point Problems (2007, methodology): “The CGH studies of the Coriell cell lines were used by Venkatraman and Olshen (2006) to demonstrate CBS in DNAcopy , and by Fridlyand et al. (2004) to demonstrate their hidden markov model approach.”
• Array comparative genomic hybridization and its applications in cancer (2005, methodology): “Among the approaches that have been used are hidden Markov model”