Learning smoothing models of copy number profiles using breakpoint annotations

[1]  Read OnlineThe,et al.  The Biology of Cancer , 2022, Nature.

[2]  Francis R. Bach,et al.  Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression , 2013, ICML.

[3]  Toby Dylan Hocking,et al.  SegAnnot: an R package for fast segmentation of annotated piecewise constant signals , 2012 .

[4]  Jeffrey Heer,et al.  D³ Data-Driven Documents , 2011, IEEE Transactions on Visualization and Computer Graphics.

[5]  M. Hoebeke,et al.  Joint segmentation, calling, and normalization of multiple CGH profiles. , 2011, Biostatistics.

[6]  Benjamin J. Raphael,et al.  Detection of recurrent rearrangement breakpoints from copy number data , 2011, BMC Bioinformatics.

[7]  P. Fearnhead,et al.  Optimal detection of changepoints with a linear computational cost , 2011, 1101.1438.

[8]  Jean-Philippe Vert,et al.  Fast detection of multiple change-points shared by many signals using group LARS , 2010, NIPS.

[9]  Gudrun Schleiermacher,et al.  Accumulation of segmental alterations determines progression in neuroblastoma. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[10]  G. Rigaill.  Pruned dynamic programming for optimal multiple change-point detection , 2010, 1004.0887.

[11]  Holger Hoefling.  A Path Algorithm for the Fused Lasso Signal Approximator , 2009, 0910.0526.

[12]  K. Lange,et al.  RECONSTRUCTING DNA COPY NUMBER BY PENALIZED ESTIMATION AND IMPUTATION. , 2009, The annals of applied statistics.

[13]  Achim Zeileis,et al.  Collaborative Software Development Using R-Forge , 2009, R J..

[14]  Gudrun Schleiermacher,et al.  Overall genomic pattern is a predictor of outcome in neuroblastoma. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[15]  Polina Golland,et al.  Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning , 2009, Proceedings of the National Academy of Sciences.

[16]  Antonio Torralba,et al.  LabelMe: A Database and Web-Based Tool for Image Annotation , 2008, International Journal of Computer Vision.

[17]  Yonina C. Eldar,et al.  A fast and flexible method for the segmentation of aCGH data , 2008, ECCB.

[18]  Antonio Ortega,et al.  Sparse representation and Bayesian detection of genome copy number alterations from microarray data , 2008, Bioinform..

[19]  David O Siegmund,et al.  A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data , 2007, Biometrics.

[20]  E. S. Venkatraman,et al.  A faster circular binary segmentation algorithm for the analysis of array CGH data , 2007, Bioinform..

[21]  Nigel P. Carter,et al.  Accurate and reliable high-throughput detection of copy number variation in the human genome. , 2006, Genome research.

[22]  Nicolas Stransky,et al.  VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles , 2006, Bioinform..

[23]  Kevin P. Murphy,et al.  Integrating copy number polymorphisms into array CGH analysis using a robust HMM , 2006, ISMB.

[24]  H. Willenbrock,et al.  A comparison study: applying segmentation to array CGH data for downstream analyses , 2005, Bioinform..

[25]  Marc Lavielle,et al.  Using penalized contrasts for the change-point problem , 2005, Signal Process..

[26]  Franck Picard,et al.  A statistical approach for array CGH data analysis , 2005, BMC Bioinformatics.

[27]  Emmanuel Barillot,et al.  Analysis of array CGH data: from signal ratio to gain and loss of DNA regions , 2004, Bioinform..

[28]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[29]  W. Kuo,et al.  High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays , 1998, Nature Genetics.

[30]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[31]  Toshiyuki Yamamoto,et al.  CONFLICT OF INTEREST: None declared. , 2013 .

[32]  R. Tibshirani,et al.  Spatial smoothing and hot spot detection for CGH data using the fused lasso. , 2008, Biostatistics.