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GeneNet: a database on structure and functional organisation of gene networks

E. A. Ananko
2002 Nucleic Acids Research  
Original technology applied in GeneNet enables description of not only a gene network structure and functional relationships between components, but also metabolic and signal transduction pathways.  ...  The GeneNet database is designed for accumulation of information on gene networks.  ...  A. Kolpakov  ... 
doi:10.1093/nar/30.1.398 pmid:11752348 pmcid:PMC99151 fatcat:itv5ka4nlrb43a3f77cemou4dy

Modeling and simulation of gene regulation and metabolic pathways

Julio Collado-Vides, Ralf Hofestädt, Michael Mavrovouniotis, Gerhard Michal
1999 Biosystems (Amsterdam. Print)  
Acknowledgements The organisers thank the Volkswagen Stiftung and the European Community (TMR Grant) for  ...  In order to exploit molecular data, one must investigate the link between genes and proteins; the link between protein structure and protein function; and the concerted effects of many proteins acting  ...  A first information system based on the integration of molecular databases and a grammatical simulation environment was introduced by Uwe Scholz and Ralf Hofestädt.  ... 
doi:10.1016/s0303-2647(98)00081-1 pmid:10091975 fatcat:iindqwxvenacroh6ywpmfpnrji

Revealing nuclear receptor hub modules from Basal-like breast cancer expression networks

Sharon Nienyun Hsu, Erika Wong En Hui, Mengzhen Liu, Di Wu, Thomas A. Hughes, James Smith, Francisco X. Real
2021 PLoS ONE  
Identification of gene correlation networks (GCNs) from Basal-like patients in both the TCGA and METABRIC databases revealed three critical transcriptional regulatory constellations that are enriched in  ...  Nuclear receptors are a class of transcriptional factors. Together with their co-regulators, they regulate development, homeostasis, and metabolism in a ligand-dependent manner.  ...  Acknowledgments The authors are very grateful to Richard Bayliss, Michele Vacca, Andrew Holding, Michaela Lorger and Chi-Ying Huang for their critical and helpful comments on this manuscript.  ... 
doi:10.1371/journal.pone.0252901 pmid:34161324 pmcid:PMC8221501 fatcat:vgwru536o5hrdccfjaifytll64

Iterative Reconstruction of High-Dimensional Gaussian Graphical Models Based on a New Method to Estimate Partial Correlations under Constraints

Vincent Guillemot, Andreas Bender, Anne-Laure Boulesteix, Francesco Pappalardo
2013 PLoS ONE  
Plus, we show on simulated and real data that iPACOSE shows very interesting properties with regards to sensitivity, positive predictive value and stability.  ...  If the goal is to estimate a GGM, our new procedure can be applied to re-estimate the partial correlations after a first graph has been estimated in the hope to improve the estimation of non-zero coefficients  ...  Acknowledgments We thank the reviewers for their comments and suggestions. Author Contributions Analyzed the data: VG AB. Wrote the paper: VG ALB.  ... 
doi:10.1371/journal.pone.0060536 pmid:23593235 pmcid:PMC3623825 fatcat:xkuljnolzbcbrfasbz3eyy72p4

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
National Research Council of Italy (CNR) and the Polish Academy of Sciences (PAN Acknowledgements This work is partial fulfillment of the research objective of "DM19410 -Laboratorio di Bioinformatica  ...  Acknowledgements The authors are partially supported by the FLAGSHIP "InterOmics" project (PB.P05) funded by the Italian MIUR and CNR institutions, and by the cooperative programme 2010-2012 between the  ...  The algorithm was applied on a network composed of three different types of nodes: genes/proteins, phenotypes and protein domains.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Dharmesh D. Bhuva, Joseph Cursons, Gordon K. Smyth, Melissa J. Davis
2019 Genome Biology  
Elucidation of regulatory networks, including identification of regulatory mechanisms specific to a given biological context, is a key aim in systems biology.  ...  of the resulting networks has been hindered by the lack of known context-specific regulatory interactions.  ...  Simulations and regulatory networks are encoded in S4 classes to ensure code stability and information organisation.  ... 
doi:10.1186/s13059-019-1851-8 pmid:31727119 pmcid:PMC6857226 fatcat:b7r56eln7fct5cg3vv5qckkixu

Integrative genomics study of microglial transcriptome reveals effect of DLG4 (PSD95) on white matter in preterm infants [article]

Michelle L Krishnan, Juliette Van Steenwinckel, Anne-Laure Schang, Jun Yan, Johanna Arnadottir, Tifenn Le Charpentier, Zsolt Csaba, Pascal Dournaud, Sara Cipriani, Constance Auvynet, Luigi Titomanlio, Julien Pansiot (+9 others)
2017 bioRxiv   pre-print
We examined preterm neuroinflammation in a mouse model of encephalopathy of prematurity induced by IL1B exposure, carrying out a gene network analysis of the cell-specific transcriptomic response to injury  ...  To characterise this pathology, we present a translational bioinformatics investigation, with integration of human and mouse molecular and neuroimaging datasets to provide a deeper understanding of the  ...  To investigate the genes, representing a set of general microglia function markers and a subset of genes from SPN1 349 and SPN2.  ... 
doi:10.1101/105288 fatcat:dib44lawr5hd7ehzyx7dmaj3nu

Incorporating prior information and borrowing information in high-dimensional sparse regression using the horseshoe and variational Bayes [article]

Gino B. Kpogbezan, Mark A. van de Wiel, Wessel N. van Wieringen and Aad W. van der Vaart
2019 arXiv   pre-print
Prior information may for instance come from previous studies or genomic databases, and information borrowed across a set of genes or genomic networks.  ...  We illustrate this by applications to the reconstruction of gene regulatory networks and to eQTL mapping.  ...  Network reconstruction The identification of gene regulatory networks is crucial for understanding gene function, and hence important for both treatment and prediction of diseases.  ... 
arXiv:1901.10217v1 fatcat:3v77zn7dqvawtokktnssyepn7q

Metabolic network failures in Alzheimer's disease: A biochemical road map

Jon B. Toledo, Matthias Arnold, Gabi Kastenmüller, Rui Chang, Rebecca A. Baillie, Xianlin Han, Madhav Thambisetty, Jessica D. Tenenbaum, Karsten Suhre, J. Will Thompson, Lisa St. John-Williams, Siamak MahmoudianDehkordi (+32 others)
2017 Alzheimer's & Dementia  
Partial correlation networks constructed for Aβ 1-42 , tau, imaging, and cognitive changes provided initial biochemical insights for disease-related processes.  ...  of Alzheimer's disease (AD) and propel the development of critically needed therapies.  ...  He is a coinventor on a use patent for metabolomics in Alzheimer's (through Duke University) that is unlicensed and he receives no royalties on this.  ... 
doi:10.1016/j.jalz.2017.01.020 pmid:28341160 pmcid:PMC5866045 fatcat:obfgvmioiva75pwi7arhxay7oa

Preface Modeling and Simulation of Gene Regulation and Metabolic Pathways

Julio Collado-Vides, Ralf Hofestädt, Michael Mavrovouniotis, Gerhard Michal, Julio Collado-Vides
1998 unpublished
In order to exploit molecular data, one must investigate the link between genes and proteins; the link between protein structure and protein function; and the concerted effects of many proteins acting  ...  A first information system based on the integration of molecular databases and a grammatical simulation environment was introduced by Uwe Scholz and Ralf Hofestädt.  ...  Acknowledgement The organisers thank the Volkswagen Stiftung and the European Community (TMR Grant) for its generous financial support.  ... 
fatcat:tw324dirsrhi7dcisfx5occ3iy

Modelling and Simulation of Gene and Cell Regulation and Metabolic Pathways (Dagstuhl Seminar 98251)

Julio Collado-Vides, Ralf Hofestädt, Michael Mavrovouniotis, Gerhard Michal
1998
Kinetic models of biochemical pathways and gene expression systems are becoming very important (Mendes 1998, these proceedings) now that full genome  ...  Acknowledgement The organisers thank the Volkswagen Stiftung and the European Community (TMR Grant) for its generous financial support.  ...  GeneNet: a Database for Gene Networks and its Automated Visualization through the Internet The gene network concept.  ... 
doi:10.4230/dagsemrep.215 fatcat:uc2tgmzmenanveonrv6p5wpopm

Index [chapter]

Essentials of Genomics and Bioinformatics  
access to the data by 405 fruit dehiscence 136 functional activity, of a protein 106 functional assignment 117ff, 336 functional genomics 133f function from structure 403 fungal pathogens 136 fuzzy  ...  systematicmapping 47 -number of genes 53 -patenting of 391 -physicalmap 121 -sequence variation 55 -working draft DNA sequence 48f Human Genome Organisation, Statement on Human Genome Project 41ff  ... 
doi:10.1002/9783527612642.index fatcat:u5eldwcccjfm5og25lj4moi7ai

Information and Simulation Systems for the Analysis of Gene Regulation and Metabolic Pathways (Dagstuhl Seminar 01261)

Ralf Hofestädt, John Reinitz, Nikolay Kolchanov
2002
The 2001 meeting is a sequel to the 1995 and 1998 meeting on the similar topic.  ...  The third Dagstuhl Seminar for Information and Simulation Systems for the Analysis of Gene Regulation and Metabolic Pathways was held from June, 24 to 29, 2001.  ...  Moreover, some genes code for proteins whose function is to turn other genes on and off. Groups of these genes form networks with complex behaviors.  ... 
doi:10.4230/dagsemrep.313 fatcat:imloyisgenaaxmkqav42bd77xy

Gemeinsame Jahrestagung der Deutschen, Österreichischen und Schweizerischen Gesellschaften für Hämatologie und Onkologie, pp 1–80

2009 Onkologie (Basel)  
The impact of impaired liver and kidney function as well as of diminished transportation facilities on their safety is now better known and cannot be disregarded.  ...  A significant deterioration of cardiac function was observed in three patients.  ...  HDACs are a family of alltogether 18 genes playing fundamental roles in normal development and cellular function.  ... 
doi:10.1159/000242462 fatcat:qkyirxzmxjh4llqnjcmma6a2vi

in Venice, Italy, covered BIOTECHNO 2011 Chairs Olivier Bodenreider, National Institutes of Health-Bethesda, USA Andreas Dress, Shanghai Institutes for Biological Sciences (SIBS) / Chinese Academy of Sciences (CAS) , China Victor Felea

Pei-Yuan Qian, Kaust, Cristina Seceleanu, Ravi Radhakrishnan, Olivier Bodenreider, Ravi Radhakrishnan, Luis Alexandre, Basim Alhadidi, Albalqa, Christine Amaldas, Nizamettin Aydin, Olivier Bodenreider (+45 others)
2011 Romania Attila Kertesz-Farkas   unpublished
Understanding and modeling biosystems requires simulation of biological behaviors and functions.  ...  Bioinformatics itself constitutes a vast area of research and specialization, as many classical domains such as databases, modeling, and regular expressions are used to represent, store, retrieve and process  ...  The creation of such a broad and high quality conference program would not have been possible without their involvement.  ... 
fatcat:26cfmxqebbcovmvktfkc4gqeyu
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