A tiered hidden Markov model characterizes multi-scale chromatin states.
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John Quackenbush | Guo-Cheng Yuan | Curtis Huttenhower | Jessica L. Larson | C. Huttenhower | John Quackenbush | Guocheng Yuan | Jessica L Larson | Guo-cheng Yuan
[1] Timothy J. Durham,et al. Systematic analysis of chromatin state dynamics in nine human cell types , 2011, Nature.
[2] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[3] Jie Wang,et al. Unsupervised pattern discovery in human chromatin structure through genomic segmentation , 2013, BCB.
[4] Guo-Cheng Yuan,et al. Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model , 2010, BMC Bioinformatics.
[5] A. Feinberg,et al. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells , 2009, Nature Genetics.
[6] James A. Cuff,et al. A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.
[7] Guillaume J. Filion,et al. Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells , 2010, Cell.
[8] William Stafford Noble,et al. Unsupervised segmentation of continuous genomic data , 2007, Bioinform..
[9] J. Fleiss. Measuring nominal scale agreement among many raters. , 1971 .
[10] M. Gerstein,et al. The GENCODE pseudogene resource , 2012, Genome Biology.
[11] T. Mikkelsen,et al. The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.
[12] Amos Tanay,et al. Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos , 2009, PLoS biology.
[13] T. Mikkelsen,et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.
[14] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[15] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[16] R. Young,et al. Repressive Transcription , 2010, Science.
[17] R. Kornberg,et al. Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome , 1999, Cell.
[18] Lee E. Edsall,et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. , 2010, Cell stem cell.
[19] Robert Tibshirani,et al. Estimating the number of clusters in a data set via the gap statistic , 2000 .
[20] William Stafford Noble,et al. Automated mapping of large-scale chromatin structure in ENCODE , 2008, Bioinform..
[21] Dustin E. Schones,et al. High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.
[22] T. Kouzarides. Chromatin Modifications and Their Function , 2007, Cell.
[23] Antoine M. van Oijen,et al. Real-time single-molecule observation of rolling-circle DNA replication , 2009, Nucleic acids research.
[24] C. Allis,et al. Translating the Histone Code , 2001, Science.
[25] Guo-Cheng Yuan,et al. Chromatin States Accurately Classify Cell Differentiation Stages , 2012, PloS one.
[26] Nathaniel D. Heintzman,et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.
[27] J. Rinn,et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells , 2010, Nature Genetics.
[28] Michael F. Lin,et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.
[29] Raymond K. Auerbach,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[30] Durbin,et al. Biological Sequence Analysis , 1998 .
[31] Alvaro Rada-Iglesias,et al. Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. , 2012, Cell stem cell.
[32] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[33] Tatiana Tatusova,et al. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..
[34] L. Wessels,et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions , 2008, Nature.
[35] Jacob Cohen. A Coefficient of Agreement for Nominal Scales , 1960 .
[36] Manolis Kellis,et al. Discovery and characterization of chromatin states for systematic annotation of the human genome , 2010, Nature Biotechnology.
[37] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[38] Lovelace J. Luquette,et al. Comprehensive analysis of the chromatin landscape in Drosophila , 2010, Nature.
[39] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[40] Howard Y. Chang,et al. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.
[41] F. Ayala,et al. Pseudogenes: are they "junk" or functional DNA? , 2003, Annual review of genetics.
[42] J. Rinn,et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.
[43] Luca Pinello,et al. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. , 2012, Developmental cell.
[44] Bing Ren,et al. ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome , 2008, PLoS Comput. Biol..
[45] Brad T. Sherman,et al. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.
[46] A. Feinberg,et al. Increased methylation variation in epigenetic domains across cancer types , 2011, Nature Genetics.