Zobrazeno 1 - 10
of 27
pro vyhledávání: '"Jiří Vohradský"'
Autor:
Jiri Vohradsky, Marek Schwarz, Olga Ramaniuk, Olatz Ruiz-Larrabeiti, Viola Vaňková Hausnerová, Hana Šanderová, Libor Krásný
Publikováno v:
Microorganisms, Vol 9, Iss 1, p 112 (2021)
The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using
Externí odkaz:
https://doaj.org/article/bf8edd3fd5df420293a327a8773ac290
Autor:
Jiří Pospíšil, Marek Schwarz, Alice Ziková, Dragana Vítovská, Miluše Hradilová, Michal Kolář, Alena Křenková, Martin Hubálek, Libor Krásný, Jiří Vohradský
Publikováno v:
Communications Biology, Vol 7, Iss 1, Pp 1-16 (2024)
Abstract σ factors are considered as positive regulators of gene expression. Here we reveal the opposite, inhibitory role of these proteins. We used a combination of molecular biology methods and computational modeling to analyze the regulatory acti
Externí odkaz:
https://doaj.org/article/f78d9ae48e1f449baab58082cc7107ca
Publikováno v:
Frontiers in Genetics, Vol 11 (2020)
Searching for similar sequences in a database via BLAST or a similar tool is one of the most common bioinformatics tasks applied in general, and to non-coding RNAs in particular. However, the results of the search might be difficult to interpret due
Externí odkaz:
https://doaj.org/article/2afc38781dd3496abe724d79cf30a84e
Autor:
Martin Modrák, Jiří Vohradský
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-9 (2018)
Abstract Background Identifying regulons of sigma factors is a vital subtask of gene network inference. Integrating multiple sources of data is essential for correct identification of regulons and complete gene regulatory networks. Time series of exp
Externí odkaz:
https://doaj.org/article/23165c574da749dea20d60c69967fbcc
Publikováno v:
Bioinformatics (Oxford, England).
Summary We present a web service for improving characterization of non-coding RNAs (ncRNAs) from NCBI BLAST outputs, based on a command-line application rboAnalyzer. Briefly, the application extends subject sequences of selected high scoring pairs (H
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4ccedfcc8a339c19f12d13b03c0cb295
https://pubmed.ncbi.nlm.nih.gov/33523120
https://pubmed.ncbi.nlm.nih.gov/33523120
Publikováno v:
Frontiers in Genetics
Frontiers in Genetics, Vol 11 (2020)
Frontiers in Genetics, Vol 11 (2020)
Searching for similar sequences in a database via BLAST or a similar tool is one of the most common bioinformatics tasks applied in general, and to non-coding RNAs in particular. However, the results of the search might be difficult to interpret due
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::af4291524a5bf18192cb13a4413b341d
http://europepmc.org/articles/PMC7401326
http://europepmc.org/articles/PMC7401326
Publikováno v:
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1860:894-904
This study describes the meta-analysis and kinetic modelling of gene expression control by sigma factor SigA of Bacillus subtilis during germination and outgrowth based on microarray data from 14 time points. The analysis computationally models the d
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2625a3c3b61385e55bc329ac4bc8d5de
https://doi.org/10.1016/j.bbagrm.2017.06.003
https://doi.org/10.1016/j.bbagrm.2017.06.003
Autor:
Jan Drozen, Tomáš Hladík, Jiří Vohradský, Jan Jelínek, Josef Pánek, Jan Hajič, Michal Klimpera, David Hoksza, Jan Pešek
Publikováno v:
Database: The Journal of Biological Databases and Curation
Secondary data structure of RNA molecules provides insights into the identity and function of RNAs. With RNAs readily sequenced, the question of their structural characterization is increasingly important. However, RNA structure is difficult to acqui
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d1534cb4463e947cb2d696a8fa9c4368
https://doi.org/10.1093/database/baz047
https://doi.org/10.1093/database/baz047
Autor:
Jiri Vohradsky
Publikováno v:
Biology, Vol 13, Iss 8, p 614 (2024)
Bacillus subtilis is a model organism used to study molecular processes in Gram-positive bacteria. Sigma factor B, which associates with RNA polymerase, is one of the transcriptional regulators involved in the cell’s response to environmental stres
Externí odkaz:
https://doaj.org/article/495eca071d0644e5a689a60aeba99080
Publikováno v:
PROTEOMICS. 20:2070135
In this paper, correlation analysis of protein and mRNA levels in the soil dwelling bacteria Streptomyces coelicolor (S. coelicolor M145) is presented during development of the population as it grew in liquid medium using three biological and two tec
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9831fb78b4af38dfe8e7a5e4a7037717
https://doi.org/10.1002/pmic.202070135
https://doi.org/10.1002/pmic.202070135