Sparsely correlated hidden Markov models with application to genome-wide location studies

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

(2010) Zhaohui S Qin et al.   BMC BIOINFORMATICS

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data

(2009) Hyungwon Choi et al.   BIOINFORMATICS

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS