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Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Michael M Hoffman, Orion J Buske, Jie Wang, Zhiping Weng, Jeff A Bilmes, William Stafford Noble
2012 Nature Methods  
Kundaje for helpful Gene structure in Segway labels. (a) Segmentation of the human BRD2 locus, as shown in the University of California, Santa Cruz (UCSC) Genome Browser.  ...  The patterns of chromatin structure in proteincoding genes fit well with existing knowledge (Supplementary Results and Supplementary Figs. 3 and 7) .  ...  We used the genome structure correction mar ginal region overlap test in block_bootstrap 32 , as implemented in Statmap (http://www.statmapbio.org/), to test each segment label for enrichment in matches  ... 
doi:10.1038/nmeth.1937 pmid:22426492 pmcid:PMC3340533 fatcat:2e4tzmczdbhy7fi7j2mt7vkepm

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Michael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble
2007 Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13  
Kundaje for helpful Gene structure in Segway labels. (a) Segmentation of the human BRD2 locus, as shown in the University of California, Santa Cruz (UCSC) Genome Browser.  ...  The patterns of chromatin structure in proteincoding genes fit well with existing knowledge (Supplementary Results and Supplementary Figs. 3 and 7) .  ...  We used the genome structure correction mar ginal region overlap test in block_bootstrap 32 , as implemented in Statmap (http://www.statmapbio.org/), to test each segment label for enrichment in matches  ... 
doi:10.1145/2506583.2506701 dblp:conf/bcb/HoffmanBWWBN13 fatcat:damfgb2pdbdptdagsaqblkq7c4

Big Data Bioinformatics

Casey S. Greene, Jie Tan, Matthew Ung, Jason H. Moore, Chao Cheng
2014 Journal of Cellular Physiology  
In between sequence and structure, measurements are performed through, and even beyond, the components of the central dogma.  ...  New high throughput technologies allow biologists to generate enormous amounts of data ranging from measurements of genomic sequence to images of physiological structures.  ...  Genome segmentation based on histone modification patterns Unsupervised machine learning techniques have been used to separate human genome into different functional segmentations based on genome wide  ... 
doi:10.1002/jcp.24662 pmid:24799088 pmcid:PMC5604462 fatcat:4hsmk23sizepbnm77pgehltsky

Big Data Bioinformatics

Xue-wen Chen, Jean X. Gao
2016 Methods  
In between sequence and structure, measurements are performed through, and even beyond, the components of the central dogma.  ...  New high throughput technologies allow biologists to generate enormous amounts of data ranging from measurements of genomic sequence to images of physiological structures.  ...  Genome segmentation based on histone modification patterns Unsupervised machine learning techniques have been used to separate human genome into different functional segmentations based on genome wide  ... 
doi:10.1016/j.ymeth.2016.11.017 pmid:27908398 pmcid:PMC5219000 fatcat:ggx5efv5ebcgddtkhvaztzmsra

Chromatin signature discovery via histone modification profile alignments

Jianrong Wang, Victoria V. Lunyak, I. King Jordan
2012 Nucleic Acids Research  
We report on the development of an unsupervised algorithm for the genome-wide discovery and analysis of chromatin signatures.  ...  We applied ChAT to genomic maps of 39 histone modifications in human CD4 + T cells to identify both known and novel chromatin signatures.  ...  Here, we are more interested in the unsupervised approach to the analysis of chromatin given the potential this approach holds for novel discoveries.  ... 
doi:10.1093/nar/gks848 pmid:22989711 pmcid:PMC3505981 fatcat:w73nl2yfdjbqxjloewcw6cn57y

Integrative annotation of chromatin elements from ENCODE data

Michael M. Hoffman, Jason Ernst, Steven P. Wilder, Anshul Kundaje, Robert S. Harris, Max Libbrecht, Belinda Giardine, Paul M. Ellenbogen, Jeffrey A. Bilmes, Ewan Birney, Ross C. Hardison, Ian Dunham (+2 others)
2012 Nucleic Acids Research  
into discrete annotation maps of regulatory regions and other chromatin elements across the human genome.  ...  The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines.  ...  In this work, we apply unsupervised chromatin state annotation methods that simultaneously discover the locations of functional elements in the human genome and assign to each element one of a small number  ... 
doi:10.1093/nar/gks1284 pmid:23221638 pmcid:PMC3553955 fatcat:rb2ozaqkb5ftfbq4rfcjkdawu4

The Ensembl Regulatory Build

Daniel R Zerbino, Steven P Wilder, Nathan Johnson, Thomas Juettemann, Paul R Flicek
2015 Genome Biology  
We collected public data on epigenetic marks and transcription factor binding in human cell types and used it to construct an intuitive summary of regulatory regions in the human genome.  ...  Most genomic variants associated with phenotypic traits or disease do not fall within gene coding regions, but in regulatory regions, rendering their interpretation difficult.  ...  Ensembl receives majority funding from the Wellcome Trust (grant number WT095908) with additional funding for specific project components from the National Human Genome Research Institute (1U01 HG004695  ... 
doi:10.1186/s13059-015-0621-5 pmid:25887522 pmcid:PMC4407537 fatcat:xa25ozonobb3nhpoxfv3ekqbza

Genome-wide mapping of global-to-local genetic effects on human facial shape

Peter Claes, Jasmien Roosenboom, Julie D. White, Tomek Swigut, Dzemila Sero, Jiarui Li, Myoung Keun Lee, Arslan Zaidi, Brooke C. Mattern, Corey Liebowitz, Laurel Pearson, Tomás González (+11 others)
2018 Nature Genetics  
All 15 replicated loci highlighted distinctive patterns of global-to-local genetic effects on facial shape and showed enrichment for active chromatin elements in human cranial neural crest cells, suggesting  ...  Genome-wide association scans of complex multipartite traits like the human face typically use preselected phenotypic measures.  ...  Chromatin modification visualization in the genome browser.  ... 
doi:10.1038/s41588-018-0057-4 pmid:29459680 fatcat:ijbdri4c7vb7ngm3krbjni2ima

Fish-Ing for Enhancers in the Heart

Costantino Parisi, Shikha Vashisht, Cecilia Lanny Winata
2021 International Journal of Molecular Sciences  
Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery.  ...  Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/ijms22083914 pmid:33920121 pmcid:PMC8069060 fatcat:2wvue5flenhchksp2b2itrgjca

Novel genotype-phenotype associations in human cancers enabled by advanced molecular platforms and computational analysis of whole slide images

Lee AD Cooper, Jun Kong, David A Gutman, William D Dunn, Michael Nalisnik, Daniel J Brat
2015 Laboratory Investigation  
We show how these approaches can be used to explore the relation of the tumor microenvironment to genomic alterations and gene expression patterns and to define nuclear morphometric features that are predictive  ...  Commensurate advances in computing and image analysis algorithms enable mining of archives to extract descriptions of histology, ranging from basic human annotations to automatic and precisely quantitative  ...  MAIN BODY The Cancer Genome Atlas TCGA was established in 2005 to improve understanding of the molecular basis of human cancers through large-scale genomic analysis.  ... 
doi:10.1038/labinvest.2014.153 pmid:25599536 pmcid:PMC4465352 fatcat:zdkjhyj3rvegfcxbw656wm2vca

Computational epigenetics

C. Bock, T. Lengauer
2007 Bioinformatics  
In addition, incomplete erasure of epigenetic information can lead to complex patterns of non-Mendelian inheritance.  ...  Patterns of epigenetic information are faithfully propagated over multiple cell divisions, which makes epigenetic regulation a key mechanism for cellular differentiation and cell fate decisions.  ...  Transcription factors can also affect chromatin structure, e.g. through recruitment of histone acetylases.  ... 
doi:10.1093/bioinformatics/btm546 pmid:18024971 fatcat:woekovxr7rdptkz3on6ulu7qli

A computational approach for the functional classification of the epigenome

Francesco Gandolfi, Anna Tramontano
2017 Epigenetics & Chromatin  
Our method is based on non-negative matrix factorization (NMF), an unsupervised learning technique originally employed to decompose high-dimensional data in a reduced number of meaningful patterns.  ...  between chromatin organization and genome function.  ...  Epigenetic signals are then processed through an unsupervised learning algorithm to infer the most probable chromatin state in each interval (i.e., a recurrent pattern of a given combination of marks).  ... 
doi:10.1186/s13072-017-0131-7 pmid:28515787 pmcid:PMC5433140 fatcat:66ispyojwfdtpex4uafp4adb5y

De novoidentification of replication-timing domains in the human genome by deep learning

Feng Liu, Chao Ren, Hao Li, Pingkun Zhou, Xiaochen Bo, Wenjie Shu
2015 Bioinformatics  
A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure.  ...  Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing.  ...  Furthermore, the molecular mechanisms through which the chromatin patterns are established and maintained within the ERD and LRD in the human genome remain poorly understood.  ... 
doi:10.1093/bioinformatics/btv643 pmid:26545821 pmcid:PMC4795613 fatcat:wc6eaqmjcfdk5ohossjzo5jhci

Semi-supervised segmentation and genome annotation [article]

Rachel C.W. Chan, Matthew McNeil, Eric G. Roberts, Mickaël Mendez, Maxwell W. Libbrecht, Michael M. Hoffman
2020 bioRxiv   pre-print
Segmentation and genome annotation methods automatically discover joint signal patterns in whole genome datasets.  ...  Previously, researchers trained these algorithms in a fully unsupervised way, with no prior knowledge of the functions of particular regions.  ...  Most SAGA methods, including ChromHMM, only learn in an unsupervised mode, meaning they discover genomic signal patterns without any prior information about known categories of genomic elements.  ... 
doi:10.1101/2020.01.30.926923 fatcat:h6iymyr2tzeafdyqivzi6hgvfe

Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

Hang Xu, Shijie Zhang, Xianfu Yi, Dariusz Plewczynski, Mulin Jun Li
2020 Computational and Structural Biotechnology Journal  
In this review, we summarized the current methods for detecting EPIs and described how developing techniques facilitate the identification of EPI through assessing the merits and drawbacks of these methods  ...  We also reviewed recent state-of-art EPI prediction methods in terms of their rationale, data usage and characterization.  ...  These cis-regulatory elements (CREs) are often located in the non-coding genomic regions, which make up of over 98% of the human genome [2] .  ... 
doi:10.1016/j.csbj.2020.02.013 pmid:32226593 pmcid:PMC7090358 fatcat:lmblms64vvcp7b6lkcrkrh7fyy
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