Unsupervised pattern discovery in human chromatin structure through genomic segmentation

doi:10.1038/nmeth.1937

PMID: 22426492DOI: 10.1038/nmeth.1937Mar 20, 2012

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Nature Methods

Michael M HoffmanWilliam Stafford Noble

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Abstract

We trained Segway, a dynamic Bayesian network method, simultaneously on chromatin data from multiple experiments, including positions of histone modifications, transcription-factor binding and open chromatin, all derived from a human chronic myeloid leukemia cell line. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, transcriptional regulator CTCF-binding regions and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/proj/segway/.

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iSeg: an efficient algorithm for segmentation of genomic and epigenomic data

Apr 13, 2018·BMC Bioinformatics·Senthil B GirimuruganJinfeng Zhang

Data integration and predictive modeling methods for multi-omics datasets

May 5, 2018·Molecular Omics·Minseung Kim, Ilias Tagkopoulos

Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response

Jun 7, 2018·Genetics·Charles-Henri LecellierAnthony Mathelier

ChromTime: modeling spatio-temporal dynamics of chromatin marks

Aug 12, 2018·Genome Biology·Petko Fiziev, Jason Ernst

Automatic detection of genomic regions with informative epigenetic patterns

Nov 30, 2018·BMC Genomics·Florencio PazosJuan C Oliveros

AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification

Mar 15, 2019·Nucleic Acids Research·Naozumi HiranumaSu-In Lee

Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development

Aug 17, 2019·Frontiers in Cellular Neuroscience·Elena PerenthalerTahsin Stefan Barakat

Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

Apr 2, 2020·Genome Biology·Jacob SchreiberWilliam Stafford Noble

Evolutionary conserved role of neural cell adhesion molecule-1 in memory

Jul 8, 2020·Translational Psychiatry·Vanja VukojevicAttila Stetak

Progress and challenges in bioinformatics approaches for enhancer identification

Dec 5, 2015·Briefings in Bioinformatics·Dimitrios KleftogiannisVladimir B Bajic

Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci

Dec 20, 2013·The Journal of Immunology : Official Journal of the American Association of Immunologists·Alexander V PredeusMaxim N Artyomov

Choosing panels of genomics assays using submodular optimization

Nov 17, 2016·Genome Biology·Kai WeiWilliam Stafford Noble

Computational methodology for ChIP-seq analysis

Mar 1, 2013·Quantitative Biology·Hyunjin ShinX Shirley Liu

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

Feb 15, 2017·Proceedings of the National Academy of Sciences of the United States of America·Yupeng HeJoseph R Ecker

Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses

Jul 13, 2017·PLoS Genetics·Jumpei ItoIturo Inoue

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods

Jun 2, 2018·BMC Bioinformatics·Yifeng LiWyeth W Wasserman

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition

Apr 13, 2018·Nature Communications·Timothy DurhamWilliam Stafford Noble

Chromosome Conformation Capture Reveals Two Elements That Interact with the PTBP3 (ROD1 ) Transcription Start Site

Jan 13, 2019·International Journal of Molecular Sciences·Marta KubiakMarzena Anna Lewandowska

CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features

Feb 8, 2019·BMC Bioinformatics·Yao YaoStephen A Ramsey

A Pretraining-Retraining Strategy of Deep Learning Improves Cell-Specific Enhancer Predictions

Jan 24, 2020·Frontiers in Genetics·Xiaohui NiuXuehai Hu

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling

Feb 8, 2020·Nature Communications·Mariano I GabittoRichard Bonneau

Splicing of enhancer-associated lincRNAs contributes to enhancer activity

Feb 23, 2020·Life Science Alliance·Jennifer Y TanAna C Marques

Q-Nuc: a bioinformatics pipeline for the quantitative analysis of nucleosomal profiles

Dec 18, 2019·Interdisciplinary Sciences, Computational Life Sciences·Yuan WangZhifeng Shao

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Aug 2, 2020·Nature Methods·Anurag SethiMark Gerstein

In Silico Functional Annotation of Genomic Variation

Jan 3, 2016·Current Protocols in Human Genetics·Mariusz Butkiewicz, William S Bush

Zinc transporter genes and urological cancers: integrated analysis suggests a role for ZIP11 in bladder cancer

Apr 23, 2015·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Lang WuGloria M Petersen

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

Nov 1, 2016·Nature Biotechnology·Jason ErnstManolis Kellis

A new method for enhancer prediction based on deep belief network

Oct 27, 2017·BMC Bioinformatics·Hongda BuJihong Guan

A computational approach for the functional classification of the epigenome

May 19, 2017·Epigenetics & Chromatin·Francesco Gandolfi, Anna Tramontano

Denoising genome-wide histone ChIP-seq with convolutional neural networks

Sep 9, 2017·Bioinformatics·Pang Wei KohAnshul Kundaje

Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation

Oct 4, 2017·Nucleic Acids Research·Yu Zhang, Ross C Hardison

Similarity-Based Segmentation of Multi-Dimensional Signals

Sep 29, 2017·Scientific Reports·Rainer MachnéPeter F Stadler

Xenbase: a genomic, epigenomic and transcriptomic model organism database

Oct 24, 2017·Nucleic Acids Research·Kamran KarimiPeter D Vize

An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences

Dec 19, 2018·Nature Genetics·Brad Gulko, Adam Siepel

Chromatin-state discovery and genome annotation with ChromHMM

Nov 10, 2017·Nature Protocols·Jason Ernst, Manolis Kellis

Recent advances in functional genome analysis

Jan 8, 2019·F1000Research·Roderic Guigo, Michiel de Hoon

Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells

Jan 31, 2019·Frontiers in Genetics·Sharmi BanerjeeHehuang Xie

EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences

May 3, 2019·Nucleic Acids Research·Xinzhou GeJingyi Jessica Li

Obesity remodels activity and transcriptional state of a lateral hypothalamic brake on feeding

Jun 30, 2019·Science·Mark A RossiGarret D Stuber

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq

Jun 15, 2019·Nucleic Acids Research·Evan D Tarbell, Tao Liu

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

Jan 24, 2020·Genome Biology·Jill E MooreZhiping Weng

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

Nov 27, 2019·IUBMB Life·Ross C HardisonBerthold Göttgens

Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

Apr 2, 2020·Genome Biology·Jacob SchreiberWilliam Stafford Noble

Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

Sep 22, 2020·ELife·Hajnalka L PálinkásBeáta G Vértessy

Evaluating the informativeness of deep learning annotations for human complex diseases

Sep 19, 2020·Nature Communications·Kushal K DeyAlkes L Price

A supervised learning framework for chromatin loop detection in genome-wide contact maps

Jul 11, 2020·Nature Communications·Tarik J SalamehFeng Yue

Transcription factor-associated combinatorial epigenetic pattern reveals higher transcriptional activity of TCF7L2-regulated intragenic enhancers

May 14, 2017·BMC Genomics·Qi LiuVictor X Jin

Unboxing cluster heatmaps

Mar 3, 2017·BMC Bioinformatics·Sophie EngleKatherine S Pollard

Integrating ChIP-seq with other functional genomics data

Mar 27, 2018·Briefings in Functional Genomics·Shan Jiang, Ali Mortazavi

BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone

Mar 24, 2017·Bioinformatics·Bite YangWenjie Shu

Prediction of enhancer-promoter interactions via natural language processing

May 17, 2018·BMC Genomics·Wanwen ZengRui Jiang

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

Nov 28, 2018·Nature Genetics·Natsuhiko KumasakaDaniel J Gaffney

Semi-nonparametric modeling of topological domain formation from epigenetic data

Mar 15, 2019·Algorithms for Molecular Biology : AMB·Emre Sefer, Carl Kingsford

HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures

Sep 5, 2018·BMC Bioinformatics·Hani Z GirgisZachary E Reyes

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Sep 24, 2020·Biology·Girum Fitihamlak Ejigu, Jaehee Jung

Index and biological spectrum of human DNase I hypersensitive sites

Jul 31, 2020·Nature·Wouter MeulemanJohn Stamatoyannopoulos

Identification of introns harboring functional sequence elements through positional conservation

Jun 25, 2017·Scientific Reports·Michal ChorevLiran Carmel

Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells

Dec 21, 2019·Epigenetics & Chromatin·Ryuichiro NakatoKatsuhiko Shirahige

Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks

Oct 21, 2020·BMC Bioinformatics·Arnaud CeolMarco Masseroli

Fast detection of differential chromatin domains with SCIDDO

Nov 25, 2020·Bioinformatics·Peter Ebert, Marcel H Schulz

Linkage analysis identifies an isolated strabismus locus at 14q12 overlapping with FOXG1 syndrome region

Dec 2, 2020·Journal of Medical Genetics·Xin Cynthia YeWyeth W Wasserman

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

Dec 10, 2020·Genome Biology·Donghoon LeeMark Gerstein

Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale

Sep 23, 2020·Genome Génome / Conseil National De Recherches Canada·Ian C TobiasJennifer A Mitchell

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

Apr 1, 2020·Computational and Structural Biotechnology Journal·Hang XuMulin Jun Li

IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity

Jul 3, 2020·Computational and Structural Biotechnology Journal·Alireza Sahaf NaeiniJunbai Wang

Zero-shot imputations across species are enabled through joint modeling of human and mouse epigenomics

Nov 10, 2020·Jacob SchreiberWilliam Noble

Related Concepts

Bayesian Prediction

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