Fast detection of differential chromatin domains with SCIDDO
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[1] Michael Q. Zhang,et al. Integrative analysis of 111 reference human epigenomes , 2015, Nature.
[2] Dustin E. Schones,et al. High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.
[3] Marc D. Perry,et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia , 2012, Genome research.
[4] Madapura M. Pradeepa,et al. Causal role of histone acetylations in enhancer function , 2016, Transcription.
[5] A. Valencia,et al. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis , 2016, bioRxiv.
[6] D. Bartel,et al. Predicting effective microRNA target sites in mammalian mRNAs , 2015, eLife.
[7] Oliver Brüstle,et al. Leveling Waddington: the emergence of direct programming and the loss of cell fate hierarchies , 2013, Nature Reviews Molecular Cell Biology.
[8] Raymond K. Auerbach,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[9] Kevin C. Chen,et al. Spectacle: fast chromatin state annotation using spectral learning , 2015, Genome Biology.
[10] E. Lander,et al. The Mammalian Epigenome , 2007, Cell.
[11] ENCODEConsortium,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[12] Jianhua Lin,et al. Divergence measures based on the Shannon entropy , 1991, IEEE Trans. Inf. Theory.
[13] Doron Lancet,et al. GeneHancer: genome-wide integration of enhancers and target genes in GeneCards , 2017, Database J. Biol. Databases Curation.
[14] Selin Jessa,et al. chromswitch: a flexible method to detect chromatin state switches , 2018, Bioinform..
[15] Manolis Kellis,et al. Large-scale epigenome imputation improves data quality and disease variant enrichment , 2015, Nature Biotechnology.
[16] W. Reik,et al. Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal , 2009, Nature Reviews Molecular Cell Biology.
[17] Peter A. Jones,et al. The Epigenomics of Cancer , 2007, Cell.
[18] Maureen A. Sartor,et al. PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data , 2014, Bioinform..
[19] Danny Reinberg,et al. A double take on bivalent promoters. , 2013, Genes & development.
[20] P. Flicek,et al. The Ensembl Regulatory Build , 2015, Genome Biology.
[21] S. Karlin,et al. Applications and statistics for multiple high-scoring segments in molecular sequences. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[22] R. Lowdon,et al. Evolution of Epigenetic Regulation in Vertebrate Genomes. , 2016, Trends in genetics : TIG.
[23] William Stafford Noble,et al. Unsupervised pattern discovery in human chromatin structure through genomic segmentation , 2012, Nature Methods.
[24] Aaron R. Quinlan,et al. Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .
[25] Julia A. Lasserre,et al. Histone modification levels are predictive for gene expression , 2010, Proceedings of the National Academy of Sciences.
[26] M. Robinson,et al. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences , 2015, F1000Research.
[27] Steven J. M. Jones,et al. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery , 2016, Cell.
[28] Timothy J. Durham,et al. Systematic analysis of chromatin state dynamics in nine human cell types , 2011, Nature.
[29] A. Visel,et al. ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.
[30] Manolis Kellis,et al. ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.
[31] Walter L. Ruzzo,et al. A Linear Time Algorithm for Finding All Maximal Scoring Subsequences , 1999, ISMB.
[32] G. Orphanides,et al. A Unified Theory of Gene Expression , 2002, Cell.
[33] Nathaniel D. Heintzman,et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.
[34] Ho-Ryun Chung,et al. Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome , 2015, Genome Biology.
[35] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[36] T. Mikkelsen,et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.
[37] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[38] R. Young,et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.
[39] Manolis Kellis,et al. Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type , 2015, Nature Communications.
[40] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[41] Edwin Cuppen,et al. Sambamba: fast processing of NGS alignment formats , 2015, Bioinform..
[42] B. Tjaden,et al. De novo assembly of bacterial transcriptomes from RNA-seq data , 2015, Genome Biology.
[43] Rob Patro,et al. Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.
[44] F. van Nieuwerburgh,et al. Library construction for next-generation sequencing: overviews and challenges. , 2014, BioTechniques.
[45] William R Pearson,et al. Selecting the Right Similarity‐Scoring Matrix , 2013, Current protocols in bioinformatics.
[46] Jie Zhang,et al. Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data , 2013, PLoS Comput. Biol..
[47] Bronwen L. Aken,et al. GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.
[48] A. Dean,et al. Enhancer function: mechanistic and genome-wide insights come together. , 2014, Molecular cell.
[49] T. Kouzarides. Chromatin Modifications and Their Function , 2007, Cell.
[50] Stefan Wallner,et al. Epigenetic dynamics of monocyte-to-macrophage differentiation , 2016, Epigenetics & Chromatin.
[51] S. Karlin,et al. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[52] Amir Dembo,et al. Statistical Composition of High-Scoring Segments from Molecular Sequences , 1990 .
[53] James A. Cuff,et al. A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.
[54] Thomas Lengauer,et al. BLUEPRINT to decode the epigenetic signature written in blood , 2012, Nature Biotechnology.
[55] A. Coulon,et al. Eukaryotic transcriptional dynamics: from single molecules to cell populations , 2013, Nature Reviews Genetics.