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Model-based deconvolution of genome-wide DNA binding

David J. Reiss, Marc T. Facciotti, Nitin S. Baliga
2007 Computer applications in the biosciences : CABIOS  
"Model-based deconvolution of genome-wide DNA binding", Bioinformatics; doi: 10.1093/bioinformatics/btm592.http://baliga.systemsbiology.net/medichi See Also deconv.entire.genome, fit.peak.profile, generate.fake.data  ...  fit.res Desired deconvolution resolution (base-pairs). kernel Required deconvolution kernel. See Details. max.steps Limit the number of LARS steps taken.  ... 
doi:10.1093/bioinformatics/btm592 pmid:18056063 fatcat:rx5vlmhnefacfpjd44yicdiica

Base-pair resolution detection of transcription factor binding site by deep deconvolutional network

Sirajul Salekin, Jianqiu Michelle Zhang, Yufei Huang, John Hancock
2018 Bioinformatics  
DeepSNR adopts a novel deconvolutional network (deconvNet) model and is inspired by the similarity to image segmentation by deconvNet.  ...  The proposed deconvNet architecture is constructed on top of 'Deep-Bind' and we trained the entire model using TF specific data from ChIP-exonuclease (ChIP-exo) experiments.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bty383 pmid:29757349 fatcat:57llsjy4yng4jbm7q4jymrq4hu

Base-pair resolution detection of transcription factor binding site by deep deconvolutional network [article]

Sirajul Salekin, Jianqiu (Michelle) Zhang, Yufei Huang
2018 bioRxiv   pre-print
DeepSNR adopts a novel deconvolutional network (deconvNet) model and is inspired by the similarity to image segmentation by deconvNet.  ...  However, there is a shortage of computational approach that can deliver single base pair (bp) resolution prediction of TFBS.  ...  Conflict of Interest: none declared.  ... 
doi:10.1101/254508 fatcat:aobq7kz7hbdklnc3avpfo3y5xy

Machine learning for deciphering cell heterogeneity and gene regulation

Michael Scherer, Florian Schmidt, Olga Lazareva, Jörn Walter, Jan Baumbach, Marcel H. Schulz, Markus List
2021 Nature Computational Science  
Furthermore, such models allow researchers to interpret genetic variants in non-coding parts of the genome identified, for instance, with genome-wide association studies.  ...  Here, the term epigenomics refers to genome-wide interrogation of diverse aspects of gene regulation.  ...  Fernando Chirigati was the primary editor on this Review and managed its editorial process and peer review in collaboration with the rest of the editorial team.  ... 
doi:10.1038/s43588-021-00038-7 fatcat:tw77ti33bvhdboy7wafma5auey

Transcription Factor Binding Site Mapping Using ChIP-Seq

Suma Jaini, Anna Lyubetskaya, Antonio Gomes, Matthew Peterson, Sang Tae Park, Sahadevan Raman, Gary Schoolnik, James Galagan
2014 Microbiology spectrum  
Yet until recently, studies of TF binding were limited to a small number of factors at a few genomic locations.  ...  for every DNA binding protein in a prokaryotic organism.  ...  When this method is combined with genome-wide expression data from the same experiment, ChIP-Seq and expression data for multiple TFs can be used to derive a system-wide regulatory network model.  ... 
doi:10.1128/microbiolspec.mgm2-0035-2013 pmid:26105820 fatcat:evqx47gj6rg47o4vetjvzuhqpa

Characterising ChIP-seq binding patterns by model-based peak shape deconvolution

Marco-Antonio Mendoza-Parra, Malgorzata Nowicka, Wouter Van Gool, Hinrich Gronemeyer
2013 BMC Genomics  
Using this model MeDiChISeq identifies significant genome-wide patterns of chromatin-bound factors or chromatin modification.  ...  Sequence reads that accumulate locally at the genome (peaks) reveal loci of selectively modified chromatin or specific sites of chromatin-binding factors.  ...  Acknowledgements We would like to thank members of our laboratory for discussions related to the applications of MeDiChISeq.  ... 
doi:10.1186/1471-2164-14-834 pmid:24279297 pmcid:PMC4046686 fatcat:m7daz4ildnctjem6eucmlwjuem

Deconvolving nuclesome binding energy from experimental errors [article]

Mark Heron, Johannes Soeding
2020 bioRxiv   pre-print
However, little is known for certain about the sequence preference of nucleosomes. Here we develop an integrated model of nucleosome binding and genome-wide measurements thereof.  ...  Eukaryotic genomes are compacted into nucleosomes, 147-bp of DNA wrapped around histone proteins.  ...  Other experimental techniques measure nucleosome binding genome-wide, e.g.  ... 
doi:10.1101/2020.02.20.957878 fatcat:b7mzrcc6xzgjvg7m3utkk4l74q

Protein–DNA binding in high-resolution

Shaun Mahony, B. Franklin Pugh
2015 Critical reviews in biochemistry and molecular biology  
Recent advances in experimental and computational methodologies are enabling ultra-high resolution genome-wide profiles of protein-DNA binding events.  ...  In this review, we survey current experimental and computational methods that yield genome-wide protein-DNA occupancy profiles at single base-pair resolution.  ...  Precision nuclear run-on sequencing (PRO-seq) enables single base resolution of transcriptionally competent Pol II genome-wide (Kwak et al., 2013) (Figure 1 ).  ... 
doi:10.3109/10409238.2015.1051505 pmid:26038153 pmcid:PMC4580520 fatcat:qygnojyg55ekfnej2nxsfvnkni

Identifying compound efficacy targets in phenotypic drug discovery

Markus Schirle, Jeremy L. Jenkins
2016 Drug Discovery Today  
In addition to efficacy targets, the characterization of epistatic proteins influencing compound activity often facilitates the elucidation of the underlying mechanism of action; and, further, early determination  ...  of off-targets that cause potentially unwanted secondary phenotypes helps in assessing potential liabilities.  ...  Acknowledgment We thank John Tallarico and Bill Forrester for critical reading of the manuscript and valuable discussions.  ... 
doi:10.1016/j.drudis.2015.08.001 pmid:26272035 fatcat:7ltkujfgjjcsvow62eanuxvwsy

Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction

Binhua Tang, Xiaolong Cheng, Yunlong Xi, Zixin Chen, Yufan Zhou, Victor Jin
2017 Genes  
However, the full understanding of genome regulation requires thorough knowledge in both genomic technologies and their related data analyses.  ...  It is now recognized that human genome functions as folded 3D chromatin units and looping paradigm is the basic principle of gene regulation.  ...  The Strings and Binders Switch (SBS) model was introduced based on the hypothesis that the chromatin conformation occurs during the interaction of specific binding sites with diffusing binding factors.  ... 
doi:10.3390/genes8090223 pmid:28885554 pmcid:PMC5615356 fatcat:bcjx2k6am5g5ljno56i25bsljm

High-resolution computational models of genome binding events

Yuan Qi, Alex Rolfe, Kenzie D MacIsaac, Georg K Gerber, Dmitry Pokholok, Julia Zeitlinger, Timothy Danford, Robin D Dowell, Ernest Fraenkel, Tommi S Jaakkola, Richard A Young, David K Gifford
2006 Nature Biotechnology  
Based on this probabilistic model of binding data, we further pursue improved spatial 1 resolution by using sequence information.  ...  We present a new method, Joint Binding Deconvolution (JBD), that uses additional easily obtainable experimental data about Chromatin Immunoprecipitation (ChIP) to improve the spatial resolution of the  ...  Acknowledgements We would like to thank Duncan Odom and Laurie Boyer for providing DNA fragment length data for human transcription factors.  ... 
doi:10.1038/nbt1233 pmid:16900145 fatcat:uirwumpht5fjjgtio5etavyiji

Accessibility of Nuclear Chromatin by DNA Binding Polyamides

Brigitte Dudouet, Ryan Burnett, Liliane A. Dickinson, Malcolm R. Wood, Christian Melander, Jason M. Belitsky, Benjamin Edelson, Nicholas Wurtz, Christoph Briehn, Peter B. Dervan, Joel M. Gottesfeld
2003 Chemistry and Biology  
Based on the to be useful for the regulation of gene expression in pairing rules for DNA recognition, polyamide 1 binds cell culture experiments, one pivotal issue is accessisequences of the type 5Ј-WGCWGCW  ...  In addition, the effects of polyamides on genomic tran-California Institute of Technology Pasadena, California 91125 scription are examined in lymphoid cells by DNA microarray analysis.  ...  Based on the number of base pairs present in these amounts of residues with piperidine, and subjected to ligation-mediated PCR (as described in Experimental Procedures). competing genomic DNA and the  ... 
doi:10.1016/j.chembiol.2003.09.001 pmid:14522056 fatcat:iygint34jfdjnfzs3yhzot5a44

dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data

Dongjun Chung, Dan Park, Kevin Myers, Jeffrey Grass, Patricia Kiley, Robert Landick, Sündüz Keleş, Roderic Guigo
2013 PLoS Computational Biology  
Because the compact genomes of prokaryotes harbor many binding sites separated by only few base pairs, applications of ChIP-Seq in this domain have not reached their full potential.  ...  Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) has been successfully used for genome-wide profiling of transcription factor binding sites, histone modifications, and nucleosome  ...  used for studying in vivo protein-DNA interactions genome-wide.  ... 
doi:10.1371/journal.pcbi.1003246 pmid:24146601 pmcid:PMC3798280 fatcat:4t37o4ef5jh2zprizwkr3mx3x4

Interpretation of deep learning in genomics and epigenomics

Amlan Talukder, Clayton Barham, Xiaoman Li, Haiyan Hu
2020 Briefings in Bioinformatics  
Machine learning methods have been widely applied to big data analysis in genomics and epigenomics research.  ...  In this review, we present current development in the model interpretation of DNNs, focusing on their applications in genomics and epigenomics.  ...  DeepBind was among the first studies to perform a large-scale genome-wide identification of sequence binding specificity of proteins using DNN models [14] .  ... 
doi:10.1093/bib/bbaa177 pmid:34020542 pmcid:PMC8138893 fatcat:4xlkzvvalrcipc2fcawu4kzigi

TFregulomeR reveals transcription factors' context-specific features and functions

2019 Nucleic Acids Research  
To date, thousands of ChIP-seq datasets have portrayed the genomic binding landscapes of numerous TFs in different cell types.  ...  Since genomic occupancy of a TF is highly dynamic, it is crucial to study TF binding sites (TFBSs) in a cell-specific context.  ...  Tenen for useful discussions and comments during the preparation of this manuscript, as well as Mathanapriya Naidu for her proof-reading.  ... 
doi:10.1093/nar/gkz1088 pmid:31754708 pmcid:PMC6954419 fatcat:joehczq4srhv7gy2hvvqdw4uma
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