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RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

P. S. Novichkov, D. A. Rodionov, E. D. Stavrovskaya, E. S. Novichkova, A. E. Kazakov, M. S. Gelfand, A. P. Arkin, A. A. Mironov, I. Dubchak
2010 Nucleic Acids Research  
RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach.  ...  An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources.  ...  , Anna Gerasimova, Olga Tsoy for thorough testing of the server and useful suggestions, Alex Poliakov for technical assistance, and to Tatiana Paley for assistance in web interface development, and to  ... 
doi:10.1093/nar/gkq531 pmid:20542910 pmcid:PMC2896116 fatcat:hifo7rl75vf7db2x5ngckp5gmu

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

Michael J Cipriano, Pavel N Novichkov, Alexey E Kazakov, Dmitry A Rodionov, Adam P Arkin, Mikhail S Gelfand, Inna Dubchak
2013 BMC Genomics  
, and a large set of curated by experts transcription factor binding sites used in regulon inference by a variety of tools.  ...  It uses a collection of validated regulatory sequences that can be easily extracted and used to infer regulatory interactions by comparative genomics techniques thus assisting researchers in the interpretation  ...  Acknowledgements The authors are grateful to Igor Lukashin for obtaining the genome alignment data, MicrobesOnline team for useful discussions and encouragement, and to Tatiana Smirnova for the artistic  ... 
doi:10.1186/1471-2164-14-213 pmid:23547897 pmcid:PMC3639892 fatcat:jxw5uguocbfezmuuuatz7yqlf4

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

P. S. Novichkov, T. S. Brettin, E. S. Novichkova, P. S. Dehal, A. P. Arkin, I. Dubchak, D. A. Rodionov
2012 Nucleic Acids Research  
The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes.  ...  RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics.  ...  ACKNOWLEDGEMENTS The authors are grateful to Andrei Osterman, Alexey Kazakov and KBase team for testing and useful discussions.  ... 
doi:10.1093/nar/gks562 pmid:22700702 pmcid:PMC3394319 fatcat:goxml4edjbbfhlgzoupuk7v2za

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

Pavel S Novichkov, Alexey E Kazakov, Dmitry A Ravcheev, Semen A Leyn, Galina Y Kovaleva, Roman A Sutormin, Marat D Kazanov, William Riehl, Adam P Arkin, Inna Dubchak, Dmitry A Rodionov
2013 BMC Genomics  
The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches).  ...  Description: RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics.  ...  Figure 2 Comparative genomics-driven strategy for regulon inference in RegPrecise. We utilized a similar workflow for reconstruction of regulogs operated by RNA motifs.  ... 
doi:10.1186/1471-2164-14-745 pmid:24175918 pmcid:PMC3840689 fatcat:iplkoe5e4jbhppl7tq7hy5ypgm

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

J. P. Faria, R. Overbeek, F. Xia, M. Rocha, I. Rocha, C. S. Henry
2013 Briefings in Bioinformatics  
He is an expert in the reconstruction, optimization and analysis of genome-scale metabolic models.  ...  She conducts her research in the fields of metabolic engineering and systems biology. Christopher S.  ...  The webserver comprises a large set of comparative genomics tools available in two reconstruction frameworks; the first reconstructs regulons for known PWMs and the second performs de novo regulon inference  ... 
doi:10.1093/bib/bbs071 pmid:23422247 fatcat:w2hl2w5hrbcixcya6hdbr7tbta

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis

S. A. Leyn, M. D. Kazanov, N. V. Sernova, E. O. Ermakova, P. S. Novichkov, D. A. Rodionov
2013 Journal of Bacteriology  
We used the knowledge-driven comparative-genomics approach implemented in the RegPredict Web server to infer TRN in the model Gram-positive bacterium Bacillus subtilis and 10 related Bacillales species  ...  The inferred TRN in B. subtilis comprises regulons for 129 TFs and 24 regulatory RNA families.  ...  For regulon inference in the Bacillales group of genomes, we utilized a comparative-genomic approach implemented in the RegPredict Web server (35) .  ... 
doi:10.1128/jb.00140-13 pmid:23504016 pmcid:PMC3676070 fatcat:cq5dxdlr7nfxrkntrgmludrhjq

Inference of Self-Regulated Transcriptional Networks by Comparative Genomics

Joseph P. Cornish, Fialelei Matthews, Julien R. Thomas, Ivan Erill
2012 Evolutionary Bioinformatics  
Furthermore, the inferred motif provides a more robust search pattern for comparative genomics than the experimental motifs defined in reference organisms.  ...  These motifs can in principle be used to elucidate the nature and scope of transcriptional networks through comparative genomics.  ...  Acknowledgements Writing of this paper was supported by a UMBC SFF award. FM was supported by the UMBC Meyerhoff Scholars Program.  ... 
doi:10.4137/ebo.s9205 pmid:23032607 pmcid:PMC3422134 fatcat:sfeawknmhrcmnpaigtjps6igny

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

Dmitry A Rodionov, Pavel S Novichkov, Elena D Stavrovskaya, Irina A Rodionova, Xiaoqing Li, Marat D Kazanov, Dmitry A Ravcheev, Anna V Gerasimova, Alexey E Kazakov, Galina Kovaleva, Elizabeth A Permina, Olga N Laikova (+7 others)
2011 BMC Genomics  
Comparative analysis of transcriptional regulation in the Shewanella spp To infer TRNs in the Shewanella spp., we used the integrative comparative genomics approach that combines identification of TFs  ...  At the same time, a growing number of complete prokaryotic genomes allows us to extensively use comparative genomics approaches to infer conserved cis-acting regulatory elements (e.g.  ...  DARo, IAR, DARa, AEK, EAP, AVG, ONL, GYK performed comparative genomic analysis to infer novel transcription factor regulons. MDK identified riboswitches.  ... 
doi:10.1186/1471-2164-12-s1-s3 pmid:21810205 pmcid:PMC3223726 fatcat:eg4kpwh3dzhchbaq7fvtu45k2u

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough

Alexey E. Kazakov, Lara Rajeev, Amy Chen, Eric G. Luning, Inna Dubchak, Aindrila Mukhopadhyay, Pavel S. Novichkov
2015 BMC Genomics  
These predictions were supported by our reconstruction of σ 54 -dependent promoters by comparative genomics.  ...  Our study provides a representative collection of σ 54 -dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.  ...  This material by ENIGMA-Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory is based  ... 
doi:10.1186/s12864-015-2176-y pmid:26555820 pmcid:PMC4641369 fatcat:ymsugevel5h43knwetqdcbiine

Genomic reconstruction of σ54 regulons in Clostridiales

Xiaoqun Nie, Wenyue Dong, Chen Yang
2019 BMC Genomics  
Results: For systematic analysis of the regulatory functions of σ 54 , we performed comparative genomic reconstruction of transcriptional regulons of σ 54 in 57 species from the Clostridiales order.  ...  The predicted σ 54 binding sites in the genomes of Clostridiales spp. were verified by in vitro binding assays.  ...  comparative genomics approach that combines identification of candidate DNA binding sites of EBPs and σ 54 with cross-genomic comparison of regulons (see Methods for details).  ... 
doi:10.1186/s12864-019-5918-4 fatcat:nmtxqlj56rgwboetkexowce3me

New Family of Tungstate-Responsive Transcriptional Regulators in Sulfate-Reducing Bacteria

A. E. Kazakov, L. Rajeev, E. G. Luning, G. M. Zane, K. Siddartha, D. A. Rodionov, I. Dubchak, A. P. Arkin, J. D. Wall, A. Mukhopadhyay, P. S. Novichkov
2013 Journal of Bacteriology  
Using a comparative genomics approach, we identified DNA motifs and reconstructed regulons for 40 TunR family members.  ...  A predicted 30-bp TunRbinding motif was confirmed by in vitro binding assays.  ...  For regulon reconstruction, we used a comparative genomics approach implemented in the RegPredict Web server (21) and the Genome Explorer software package (22) .  ... 
doi:10.1128/jb.00679-13 pmid:23913324 pmcid:PMC3807478 fatcat:a65vxepo7vh5vk2ozdewxcbnku

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

David J. Reiss, Christopher L. Plaisier, Wei-Ju Wu, Nitin S. Baliga
2015 Nucleic Acids Research  
The cMonkey integrated biclustering algorithm identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of  ...  gene co-regulation, and optimizes biclusters to be supported simultaneously by one or more of these prior constraints.  ...  We would like to acknowledge Eliza Peterson for filtering and providing the Mtb ChIP-seq and TFOE data in machine-readable format.  ... 
doi:10.1093/nar/gkv300 pmid:25873626 pmcid:PMC4513845 fatcat:3nkbr7wbojcg5mzuwoh3wtrqd4

Two novel regulators ofN-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections

Huimin Zhang, Dmitry A. Ravcheev, Dan Hu, Fengyu Zhang, Xiufang Gong, Lina Hao, Min Cao, Dmitry A. Rodionov, Changjun Wang, Youjun Feng
2015 MicrobiologyOpen  
Here, we report the genomic reconstruction of GalN/GalNAc utilization pathway in Streptococci and the diversified aga regulons.  ...  As anticipated, the dysfunction in AgaR2mediated regulation of S. suis impairs its pathogenicity in experimental models of both mice and piglets.  ...  Acknowledgments This work was supported by the start-up package of Zhejiang University (Youjun Feng), the Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars (grant no.  ... 
doi:10.1002/mbo3.307 pmid:26540018 pmcid:PMC4694137 fatcat:zxx3ad5t4rflvhr45x4wbhp5m4

The Nitrogen-regulated Response Regulator NrrA Controls Cyanophycin Synthesis and Glycogen Catabolism in the CyanobacteriumSynechocystissp. PCC 6803

Deng Liu, Chen Yang
2013 Journal of Biological Chemistry  
In this study, we combined a comparative genomic reconstruction of NrrA regulons in 15 diverse cyanobacterial species with detailed experimental characterization of NrrAmediated regulation in Synechocystis  ...  A predicted NrrA-binding motif consisting of two direct repeats of TG(T/ A)CA separated by an 8-bp A/T-rich spacer was verified by in vitro binding assays with purified NrrA protein.  ...  Acknowledgment-We thank Dmitry Rodionov for useful discussions and providing support with RegPredict software.  ... 
doi:10.1074/jbc.m113.515270 pmid:24337581 pmcid:PMC3900954 fatcat:l44p5m2q6ffdhiu6cw4rhrhw6i

Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network inThermotoga maritima

Irina A. Rodionova, David A. Scott, Nick V. Grishin, Andrei L. Osterman, Dmitry A. Rodionov
2012 Environmental Microbiology  
Its function was also confirmed by genetic complementation of the growth of the Escherichia coli uxaB knockout mutant strain on * For correspondence. rodionov@burnham.org; Tel.  ...  Galacturonate and glucuronate, two abundant hexuronic acids in pectin and xylan, respectively, are catabolized via committed metabolic pathways to supply carbon and energy for a variety of microorganisms  ...  In addition, the project was supported by COMBREX as a part of GO grant from National Institute of General Medical Sciences (1RC2GM092602-01) and by Russian Foundation for Basic Research (10-04-01768).  ... 
doi:10.1111/j.1462-2920.2012.02856.x pmid:22925190 pmcid:PMC4505799 fatcat:luduzrqelbezdppqyubuhygnpu
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