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Model-based deconvolution of genome-wide DNA binding
2007
Computer applications in the biosciences : CABIOS
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"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
2018
Bioinformatics
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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]
2018
bioRxiv
pre-print
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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
2021
Nature Computational Science
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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
2014
Microbiology spectrum
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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
2013
BMC Genomics
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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]
2020
bioRxiv
pre-print
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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
2015
Critical reviews in biochemistry and molecular biology
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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
2016
Drug Discovery Today
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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
2017
Genes
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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
2006
Nature Biotechnology
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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
2003
Chemistry and Biology
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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
2013
PLoS Computational Biology
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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
2020
Briefings in Bioinformatics
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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
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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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