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SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

Mikhail Pachkov, Piotr J. Balwierz, Phil Arnold, Evgeniy Ozonov, Erik van Nimwegen
2012 Nucleic Acids Research  
SwissRegulon (http:// swissregulon.unibas.ch) is a database containing genome-wide annotations of regulatory motifs, promoters and TF binding sites (TFBSs) in promoter regions across model organisms.  ...  However, rigorous computational methods are necessary to derive accurate genome-wide annotations of regulatory sites from such data.  ...  regulatory sites in cis-regulatory regions genome wide.  ... 
doi:10.1093/nar/gks1145 pmid:23180783 pmcid:PMC3531101 fatcat:ziikp5jqffcx3gpmxj3xof6zwi

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin
2009 Nucleic Acids Research  
As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions.  ...  JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a  ...  We thank the laboratories of Yair Benita, Martha Bulyk, Richard Gronostajski, Steven Jones, and Zhiping Weng for suggestions and/or contributions of  ... 
doi:10.1093/nar/gkp950 pmid:19906716 pmcid:PMC2808906 fatcat:tt5yy255ufbxlj6v7xxsbiylwa

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Heinz Stockinger, Adrian M. Altenhoff, Konstantin Arnold, Amos Bairoch, Frederic Bastian, Sven Bergmann, Lydie Bougueleret, Philipp Bucher, Mauro Delorenzi, Lydie Lane, Philippe Le Mercier, Frédérique Lisacek (+12 others)
2014 Nucleic Acids Research  
The SIB Swiss Institute of Bioinformatics (www.isbsib.ch) was created in 1998 as an institution to foster excellence in bioinformatics.  ...  It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal  ...  SwissRegulon (http://swissregulon.unibas.ch) (21) is a database of genome-wide annotations of promoters, curated regulatory motifs, and predicted regulatory sites for these motifs across a wide range of  ... 
doi:10.1093/nar/gku380 pmid:24792157 pmcid:PMC4086091 fatcat:ps6txa3xijhpxbpl2radc6dvdi

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Anastasiia V. Soboleva, Artem S. Kasianov, Haitham Ashoor, Wail Ba-alawi, Vladimir B. Bajic, Yulia A. Medvedeva, Fedor A. Kolpakov, Vsevolod J. Makeev
2015 Nucleic Acids Research  
Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts  ...  The update is based on the analysis of massive ChIP-Seq and HT-SELEX datasets, with the validation of the resulting models on in vivo data.  ...  This limits the practical application of sequence analysis in regulatory genomics.  ... 
doi:10.1093/nar/gkv1249 pmid:26586801 pmcid:PMC4702883 fatcat:ghirymw7vjf7zgixzc5bmzvtka

The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

Xosé M. Fernández-Suárez, Michael Y. Galperin
2012 Nucleic Acids Research  
The NAR online Molecular Biology Database Collection, available at http://www. oxfordjournals.org/nar/database/a/, has been updated and currently lists 1512 online databases.  ...  This year's highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure  ...  , a database of transcriptional regulation in E. coli; and SwissRegulon, a database of regulatory sites in human, mouse and yeast genomes and in model bacteria (16) (17) (18) (19) (20) .  ... 
doi:10.1093/nar/gks1297 pmid:23203983 pmcid:PMC3531151 fatcat:rmfh245otzh3hp3l446rfsqivy

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

Peter L. Freddolino, Haley M. Amemiya, Thomas J. Goss, Saeed Tavazoie, Matthew K. Waldor
2021 PLoS Biology  
a bacterial genome.  ...  We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium.  ...  Christine Ziegler for optimization of the Miller assay as used in Fig 4 .  ... 
doi:10.1371/journal.pbio.3001306 pmid:34170902 pmcid:PMC8282354 fatcat:zft56u6r5jgpjeg4snejdejome

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Cory C. Funk, Alex M. Casella, Segun Jung, Matthew A. Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner (+9 others)
2020 Cell Reports  
DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously.  ...  Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation.  ...  The genomic background for this analysis is the set of all genome-wide instances of the sequence motifs recognized by a given TF.  ... 
doi:10.1016/j.celrep.2020.108029 pmid:32814038 pmcid:PMC7462736 fatcat:lnjt2ouxv5ag3ehjzvygmbwsqe

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data Across 27 Tissue Types [article]

Cory C Funk, Segun Jung, Matthew A Richards, Alex Rodriguez, Paul Shannon, Rory Donovan, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Erteskin-Taner, Todd Golde (+8 others)
2018 bioRxiv   pre-print
DNase-seq footprinting provides a means to predict the genome-wide binding sites for hundreds of transcription factors (TFs) simultaneously.  ...  There is intense interest in mapping the tissue-specific binding sites of transcription factors in the human genome to reconstruct gene regulatory networks and predict functions for non-coding genetic  ...  Several major efforts have aimed at expanding functional annotation of the genome for a variety of reasons.  ... 
doi:10.1101/252023 fatcat:w3nhtnqyknajta3clsc2623imu

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

2015 Nucleic Acids Research  
Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources.  ...  The SIB Swiss Institute of Bioinformatics (www. isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia  ...  SwissRegulon (37) is a database of genome-wide annotations of regulatory motifs, promoters and transcription factor binding sites in promoter regions across a collection of model organisms (17 prokaryotes  ... 
doi:10.1093/nar/gkv1310 pmid:26615188 pmcid:PMC4702916 fatcat:oxgje3pvj5hv5mqgjcvm4w2xiy

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

Yi-Fei Huang, Brad Gulko, Adam Siepel
2017 Nature Genetics  
LINSIGHT combines a simple neural network for functional genomic data with a probabilistic model of molecular evolution.  ...  Here, we introduce a new computational method, called LINSIGHT, that substantially improves the prediction of noncoding nucleotide sites at which mutations are likely to have deleterious fitness consequences  ...  We thank other members of the Siepel Laboratory for helpful discussions. Author Contributions. YFH and AS conceived and designed the study. YFH designed and im-  ... 
doi:10.1038/ng.3810 pmid:28288115 pmcid:PMC5395419 fatcat:taxvf6jg3nat7k5t2w3spkmv6m

ePIANNO: ePIgenomics ANNOtation tool

Chia-Hsin Liu, Bing-Ching Ho, Chun-Ling Chen, Ya-Hsuan Chang, Yi-Chiung Hsu, Yu-Cheng Li, Shin-Sheng Yuan, Yi-Huan Huang, Chi-Sheng Chang, Ker-Chau Li, Hsuan-Yu Chen, Hodaka Fujii
2016 PLoS ONE  
genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions.  ...  Recently, with the development of next generation sequencing (NGS), the combination of chromatin immunoprecipitation (ChIP) and NGS, namely ChIP-seq, has become a powerful technique to capture potential  ...  Acknowledgments We especially thank that Integrated Core Facility for Functional Genomics (C5), Pharmacogenomics Lab (TR6), and Mathematics in Biology Group of Institute of Statistical Science AS helped  ... 
doi:10.1371/journal.pone.0148321 pmid:26859295 pmcid:PMC4747527 fatcat:ry5k4stohzdshkkwlpebctdjey

Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data

Michal Dabrowski, Norbert Dojer, Izabella Krystkowiak, Bozena Kaminska, Bartek Wilczynski
2015 BMC Bioinformatics  
sites in a genome of interest and there is little published information regarding the optimality of different choices.  ...  Results: We focus on the task of identifying potential transcription factor binding sites in the human genome.  ...  These include: HOCOMOCO [14] , SwissRegulon [15] and HT-SELEX [13] . The Jaspar database has recently been expanded and updated [16] .  ... 
doi:10.1186/s12859-015-0573-5 pmid:25927199 pmcid:PMC4436866 fatcat:n2hy6c5smrf3ldmzvjmam6zqbu

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data [article]

Yi-Fei Huang, Brad Gulko, Adam Siepel
2016 bioRxiv   pre-print
LINSIGHT combines a simple neural network for functional genomic data with a probabilistic model of molecular evolution.  ...  Here, we introduce a new computational method, called LINSIGHT, that substantially improves the prediction of noncoding nucleotide sites at which mutations are likely to have deleterious fitness consequences  ...  We thank other members of the Siepel Laboratory for helpful discussions.  ... 
doi:10.1101/069682 fatcat:nyqfz6nbqfejldrc6ebk2bhuzi

Databases for Microbiologists: TABLE 1

Igor B. Zhulin, W. W. Margolin
2015 Journal of Bacteriology  
The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.  ...  Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development.  ...  Work in my laboratory is supported by grants GM072285 and DE024463 from the National Institutes of Health.  ... 
doi:10.1128/jb.00330-15 pmid:26013493 pmcid:PMC4505447 fatcat:6eyuvuplzjc7ravlhhmk6isg6i

Multiomics dissection of molecular regulatory mechanisms underlying autoimmune-associated noncoding SNPs

Xiao-Feng Chen, Ming-Rui Guo, Yuan-Yuan Duan, Feng Jiang, Hao Wu, Shan-Shan Dong, Xiao-Rong Zhou, Hlaing Nwe Thynn, Cong-Cong Liu, Lin Zhang, Yan Guo, Tie-Lin Yang
2020 JCI Insight  
Here, we prioritized functional noncoding SNPs with regulatory gene targets associated with 19 autoimmune diseases by incorporating hundreds of immune cell-specific multiomics data.  ...  Therefore, to reduce the gap between traditional genetic findings and mechanistic understanding of disease etiologies and clinical drug development, it is important to translate systematically the regulatory  ...  Acknowledgments This work was supported by the National Natural Science Foundation of China (31871264, 31970569); the Innovative Talent Promotion Plan of Shaanxi Province for Young Sci-Tech New Star (2018KJXX  ... 
doi:10.1172/jci.insight.136477 pmid:32879140 fatcat:pzbbepk4zfcjnef7yposjmrb2m
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