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Analysis tools for the interplay between genome layout and regulation

Costas Bouyioukos, Mohamed Elati, François Képès
2016 BMC Bioinformatics  
Conclusions: We demonstrate the capabilities of these tools by studying on one hand the regular patterns of genome layout in the major regulons of the bacterium Escherichia coli.  ...  ) and gene regulatory network predictions based on gene positional information.  ...  Acknowledgements We thank François Bucchini for his help with the web application, Ivan Junier for sharing his preliminary observations on the coincidence of macrodomain and periodic region boundaries,  ... 
doi:10.1186/s12859-016-1047-0 pmid:27294345 pmcid:PMC4905612 fatcat:d7kk4ccnizhwzbi66b5q4v3ijm

Network integration and graph analysis in mammalian molecular systems biology

A. Ma'ayan
2008 IET Systems Biology  
This review highlights the currently available varieties of mammalian biomolecular networks, and surveys methods and tools to construct, compare, integrate, visualise and analyse such networks. 2 Different  ...  The fields of structure biology and network biology are coming closer as more attention is given to structural elements of protein-protein interaction networks [43] .  ...  There is a rapid emergence of desktop and web-based applications for pathway and network visualisation [110, 111] .  ... 
doi:10.1049/iet-syb:20070075 pmid:19045817 pmcid:PMC2745214 fatcat:t55zchkczrfflpdeolrf7wxn2y

ourSpaces – Design and Deployment of a Semantic Virtual Research Environment [chapter]

Peter Edwards, Edoardo Pignotti, Alan Eckhardt, Kapila Ponnamperuma, Chris Mellish, Thomas Bouttaz
2012 Lecture Notes in Computer Science  
This paper introduces the main semantic components of the system: a framework to capture the provenance of the research process, a collection of services to create and visualise metadata and a policy reasoning  ...  In this paper we discuss our experience with the design, development and deployment of the ourSpaces Virtual Research Environment. ourSpaces makes use of Semantic Web technologies to create a platform  ...  In the example shown in Figure 6 , the Transcript artefact has a producedInProject property with a value of E. coli O157 risk.  ... 
doi:10.1007/978-3-642-35173-0_4 fatcat:av5dhxpl5jgffeicxs7gnyj7eu

Community-based Linking of Biological Network Resources: Databases, Formats and Tools

Michael Telgkamp, Dirk Koschützki, Henning Schwöbbermeyer, Falk Schreiber
2007 Journal of Integrative Bioinformatics  
Computer-based analysis tools are exploited for the investigation of these networks.  ...  The collaborative character of a wiki system supports easy sharing of information and allows the community-based extension of the information already stored in BiNCo-wiki.  ...  This work was partly supported by the German Ministry of Education and Research (BMBF) under grant 0312706A.  ... 
doi:10.1515/jib-2007-71 fatcat:qz62jbgq2nh6jgih6w4kbt7rky

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species

Goksel Misirli, Jennifer Hallinan, Richard Röttger, Jan Baumbach, Anil Wipat
2014 Journal of Integrative Bioinformatics  
In this paper, we describe a system, BacillusRegNet, for the use of a model organism, Bacillus subtilis, to infer genome-wide regulatory networks in less well-studied close relatives.  ...  The putative transcription factors, their binding sequences and predicted promoter sequences along with annotations are available from the associated BacillusRegNet website (  ...  There is a large amount of information already available for model organisms such as Bacillus subtilis and Escherichia coli.  ... 
doi:10.2390/biecoll-jib-2014-244 pmid:25001169 fatcat:auaf276rlbgunh2s3v3va4bxo4

Human gene correlation analysis (HGCA): A tool for the identification of transcriptionally co-expressed genes

Ioannis Michalopoulos, Georgios A Pavlopoulos, Apostolos Malatras, Alexandros Karelas, Myrto-Areti Kostadima, Reinhard Schneider, Sophia Kossida
2012 BMC Research Notes  
The aim of the tool is the identification of closely correlated genes for a given gene of interest and/or the prediction of its biological function, which is based on the annotations of the respective  ...  Bioinformatics and high-throughput technologies such as microarray studies allow the measure of the expression levels of large numbers of genes simultaneously, thus helping us to understand the molecular  ...  CSB.DB [7] currently focuses on Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana model organisms.  ... 
doi:10.1186/1756-0500-5-265 pmid:22672625 pmcid:PMC3441226 fatcat:d5r5w27yffhujehf6j5ydfle5m

BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species

Goksel Misirli, Jennifer Hallinan, Richard Röttger, Jan Baumbach, Anil Wipat
2014 Journal of Integrative Bioinformatics  
In this paper, we describe a system, BacillusRegNet, for the use of a model organism, Bacillus subtilis, to infer genome-wide regulatory networks in less well-studied close relatives.  ...  The putative transcription factors, their binding sequences and predicted promoter sequences along with annotations are available from the associated BacillusRegNet website (  ...  JB and RR were both supported by the Cluster of Excellence for Multimodal Computing and Interaction (MMCI) from the German Research Foundation.  ... 
doi:10.1515/jib-2014-244 fatcat:mxuc6fm7inhqbnl6wxa3kyrhla

Pathway annotation and analysis with Reactome: The solute carrier class of membrane transporters

Bijay Jassal
2011 Human Genomics  
The pathway browser, search and data-mining tools facilitate searching and visualising pathway data and the analysis of user-supplied high-throughput datasets.  ...  Reactome is an expert-authored, peer-reviewed knowledge base of human reactions and pathways that functions as a data-mining resource and electronic textbook.  ...  Acknowledgments Development of the Reactome data model and database is a collaborative project and this work benefited greatly from interactions with fellow Reactome team members (http://  ... 
doi:10.1186/1479-7364-5-4-310 pmid:21712192 pmcid:PMC3525243 fatcat:quudcehbjfdm7ldockexuog5si

Global gene expression in Escherichia coli, isolated from the diseased ocular surface of the human eye with a potential to form biofilm

Konduri Ranjith, Kotakonda Arunasri, Gundlapally Sathyanarayana Reddy, HariKrishna Adicherla, Savitri Sharma, Sisinthy Shivaji
2017 Gut Pathogens  
Escherichia coli, the gastrointestinal commensal, is also known to cause ocular infections such as conjunctivitis, keratitis and endophthalmitis.  ...  Results: Out of 12 ocular E. coli isolated from patients ten isolates were resistant to one or more of the nine antibiotics tested and majority of the isolates were positive for biofilm formation.  ...  Acknowledgements Our thanks to the Director Centre for Cellular and Molecular Biology and Director of Research Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad for funds and facilities  ... 
doi:10.1186/s13099-017-0164-2 pmid:28392838 pmcid:PMC5379667 fatcat:6lshsi74hrhlplp7zifsriuklm

On-Chip Living-Cell Microarrays for Network Biology [chapter]

Ronnie Willaert, Hichem Sahli
2011 Bioinformatics - Trends and Methodologies  
VisANT is a web-based software framework for visualising and analysing many types of networks of biological interactions and associations (Hu et al., 2005) .  ...  The utility of single-cell measurements with high temporal resolution has been demonstrated by bacterial studies, which used optical microscopy to observe Escherichia coli over long time periods and reveal  ...  Because of the rapid development of new technologies in molecular biology, new bioinformatic techniques emerge accordingly to keep the pace of in silico development of life science.  ... 
doi:10.5772/20499 fatcat:vscqipttvbhotg2i2jyrbc6oni

Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines

Mireia Valles-Colomer, Youssef Darzi, Sara Vieira-Silva, Gwen Falony, Jeroen Raes, Marie Joossens
2016 Journal of Crohn's & Colitis  
Meta-omics [metagenomics, metatranscriptomics, and metaproteomics] are rapidly expanding our knowledge of the gut microbiota in health and disease.  ...  We give guidelines on proper sample collection and preparation methods, and on performing the analyses and interpreting the results, reporting available user-friendly tools and pipelines.  ...  Acknowledgments We thank all members of the Raes Laboratory for lively discussions. MVC and YD performed the literature review and drafted the manuscript.  ... 
doi:10.1093/ecco-jcc/jjw024 pmid:26802086 fatcat:dccwiqhofzgvvalmldalbdupym

Protein interaction networks as metric spaces: a novel perspective on distribution of hubs

Emad Fadhal, Junaid Gamieldien, Eric C Mwambene
2014 BMC Systems Biology  
Results: By analysing how the human functional protein interaction network, the human signalling network, Saccharomyces cerevisiae, Arabidopsis thaliana and Escherichia coli protein-protein interaction  ...  One of the key features that have implicitly been presumed is the existence of hubs, highly connected proteins considered to play a crucial role in biological networks.  ...  network [17] , to visualise large scale complex networks in two dimensions [18] , to identify drug targets [19, 20] , to identify essential genes in Escherichia coli [21] and to determination of dynamics  ... 
doi:10.1186/1752-0509-8-6 pmid:24438364 pmcid:PMC3902029 fatcat:32eqlircwnbzdiehaehk5i4sya

Assessing and characterising the repertoire of constitutive promoter elements in soil metagenomic libraries in Escherichia coli [article]

Caua Antunes Westmann, Luana de Fatima Alves, Rafael Silva-Rocha, Maria-Eugenia Guazzaroni
2017 bioRxiv   pre-print
Through the construction and screening of plasmid-based metagenomic libraries followed by in silico analyses, we were able to provide both (i) a consensus exogenous promoter elements recognizable by Escherichia  ...  coli and (ii) an estimation of the accessible promoter sequences in a metagenomic library, which was close to 1% of the whole set of available promoters.  ...  Elucidation of the transcription unit architecture of the Escherichia coli K-12 MG1655 41 genome. Nat. Biotechnol. 27, 1043-1049 (2009).  ... 
doi:10.1101/211367 fatcat:omhlfyj2fbaozcwcy5uouhse34

Evolution of computational models in BioModels Database and the Physiome Model Repository

Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath
2018 BMC Systems Biology  
To support the analysis of changes in model repositories we developed MoSt, an online tool for visualisations of changes in models.  ...  To demonstrate the impact of changes, we explored the history of a Repressilator model in BioModels Database. Results: We observed continuous updates in the majority of models.  ...  Funding This work was supported by the German Federal Ministry of Education and Research (BMBF) as part of the e:Bio programs SEMS (FKZ 031 6194) and SBGN-ED+ (FKZ 031 6181) .  ... 
doi:10.1186/s12918-018-0553-2 pmid:29650016 pmcid:PMC5898004 fatcat:r636hi3sjnh23b5sgt44jiir54

Modelling microbial communities: harnessing consortia for biotechnological applications

Maziya Ibrahim, Lavanya Raajaraam, Karthik Raman
2021 Computational and Structural Biotechnology Journal  
In this review, we discuss key principles of microbial interactions, followed by a deep dive into genome-scale metabolic models, focussing on a vast repertoire of constraint-based modelling methods that  ...  With impending advancements in high-throughput omics of microbial communities, the stage is set for the rapid expansion of microbial community engineering, with a significant impact on biotechnological  ...  A colour-coded interaction network based on the community interactions can also be visualised.  ... 
doi:10.1016/j.csbj.2021.06.048 pmid:34584635 pmcid:PMC8441623 fatcat:23mbuti53nbz7aonpukurnw3ri
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