Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana

Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models

(2011) Michael Seifert et al.   BIOINFORMATICS

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data

(2011) Yufeng Shen et al.   BMC BIOINFORMATICS

Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids

(2011) Ali M. Banaei Moghaddam et al.   PLANT JOURNAL

CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals

(2010) Sebastian Zöllner   BIOINFORMATICS

VEGA: variational segmentation for copy number detection

(2010) Sandro Morganella et al.   BIOINFORMATICS

CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data

(2010) Sergii Ivakhno et al.   BIOINFORMATICS

Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana

(2010) Liam H Childs et al.   BMC GENOMICS

Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales

(2010) Seth DeBolt   Genome Biology and Evolution

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution

(2009) Björn Nilsson et al.   BIOINFORMATICS

Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data

(2009) M. Seifert et al.   BIOINFORMATICS

Copy number variant detection in inbred strains from short read sequence data

(2009) J. T. Simpson et al.   BIOINFORMATICS

RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions

(2009) O. M. Rueda et al.   BIOINFORMATICS

A New Data Mining Approach for the Detection of Bacterial Promoters Combining Stochastic and Combinatorial Methods

(2009) Catherine Eng et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Segmental copy number variation shapes tissue transcriptomes

(2009) Charlotte N Henrichsen et al.   NATURE GENETICS

Efficient backward decoding of high-order hidden Markov models

(2009) H.A. Engelbrecht et al.   PATTERN RECOGNITION

CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms

(2008) W. Lai et al.   BIOINFORMATICS

A segmental maximum a posteriori approach to genome-wide copy number profiling

(2008) Robin Andersson et al.   BIOINFORMATICS

A fast and flexible method for the segmentation of aCGH data

(2008) E. Ben-Yaacov et al.   BIOINFORMATICS

Sparse representation and Bayesian detection of genome copy number alterations from microarray data

(2008) Roger Pique-Regi et al.   BIOINFORMATICS

Parameter estimation for robust HMM analysis of ChIP-chip data

(2008) Peter Humburg et al.   BMC BIOINFORMATICS

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

(2008) G. Zeller et al.   GENOME RESEARCH

Bayesian Hidden Markov Modeling of Array CGH Data

(2008) Subharup Guha et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

(2008) Patrick Cahan et al.   NUCLEIC ACIDS RESEARCH

Extension of higher-order HMC modeling with application to image segmentation

(2007) Lamia Benyoussef et al.   DIGITAL SIGNAL PROCESSING