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The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal (+54 others)
2013 Journal of Biomedical Semantics  
Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting  ...  The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool  ...  Dataset against a possible interpretation of that dataset, defined by the ontology.  ... 
doi:10.1186/2041-1480-4-6 pmid:23398680 pmcid:PMC3598643 fatcat:fm5xaotu3nbafibe3pm3js4d7u

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
The Gene Ontology project is a combined effort for dealing with consistent descriptions of the gene products in different databases.  ...  The Gene Ontology project is a combined effort for dealing with consistent descriptions of the gene products in different databases.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164.1 fatcat:bo3ri2crajb5xk7kukxhe6affa

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
The Gene Ontology project is a combined effort for dealing with consistent descriptions of the gene products in different databases.  ...  The Gene Ontology project is a combined effort for dealing with consistent descriptions of the gene products in different databases.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164 fatcat:72ufu6ycfba55gi6bvhatcld3e

Finding gene regulatory network candidates using the gene expression knowledge base

Aravind Venkatesan, Sushil Tripathi, Alejandro Sanz de Galdeano, Ward Blondé, Astrid Lægreid, Vladimir Mironov, Martin Kuiper
2014 BMC Bioinformatics  
Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of ?  ...  We show how a combination of specific query definitions and additional selection criteria derived from gene expression data and prior knowledge concerning candidate proteins can be used to retrieve a set  ...  Acknowledgements Technical support was provided by the High-Performance Computing team at the Norwegian University of Science and Technology. The work was supported by The Norwegian Cancer Society.  ... 
doi:10.1186/s12859-014-0386-y pmid:25490885 pmcid:PMC4279962 fatcat:s2he2zgr3bbflg36gq2yl2qi5i

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, Georgios A. Pavlopoulos
2021 Biomolecules  
We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths  ...  Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between  ...  The complexity of biological processes and their innumerable underlying interactions is most effectively and efficiently conceptualized with the representation and visualization of biological pathways  ... 
doi:10.3390/biom11081245 pmid:34439912 pmcid:PMC8391349 fatcat:32aums2jtbc5vdcdknzfczajsy

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  ...  ., 2012) and IntAct databases were automatically parsed.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

pRB [chapter]

2016 Encyclopedia of Cancer  
P p21 3351 P 3352 p21 3354 p21 separation-of-function mutants of p21 in order to reduce its multifunctional character, which should enable us to gain greater insight into selected functions of this protein  ...  Acknowledgments We would like to thank the members of our research group for their critical inputs in shaping this article.  ...  The Future of Personalized Medicine in Cancer The Human Genome Project, and its successor the Cancer Genome Project, and related activities are expected to identify the majority of genes in most of the  ... 
doi:10.1007/978-3-662-46875-3_102471 fatcat:hpbwkhzjm5dzxf6cczo7hknhh4

Genome Scale Modeling in Systems Biology: Algorithms and Resources

Ali Najafi, Gholamreza Bidkhori, Joseph Bozorgmehr, Ina Koch, Ali Masoudi-Nejad
2014 Current Genomics  
to augment and assist in the development of a fully quantitative understanding of cellular dynamics.  ...  Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches  ...  ACKNOWLEDGEMENTS We would like to thank all members of the laboratory of systems biology and bioinformatics (LBB) for their help during course of this study.  ... 
doi:10.2174/1389202915666140319002221 pmid:24822031 pmcid:PMC4009841 fatcat:xh7tgip2yfdq3fe2typ74jlfkq

Spatial reconstruction of single-cell gene expression data

Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev
2015 Nature Biotechnology  
. † Second, for each landmark gene, Seurat must relate its continuous imputed RNA-seq expression levels to its binary state in the landmark map. Since the in situ color deposition Satija et al.  ...  Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species.  ...  Acknowledgements We thank members of the Regev and Schier labs for helpful discussion, Omri Wurtzel for assistance with the R markdown scripts, Andrea Pauli for sharing the aplnrb plasmid, Katherine Rogers  ... 
doi:10.1038/nbt.3192 pmid:25867923 pmcid:PMC4430369 fatcat:ramvkauauzatbj2nhsckcysbwy

Factors associated with survival in a large series of patients with malignant pleural mesothelioma in New South Wales

A Linton, N Pavlakis, R O'Connell, M Soeberg, S Kao, S Clarke, J Vardy, N van Zandwijk
2014 British Journal of Cancer  
Electron microscopic studies suggested that plasma membranes of the cells were directly injured by MWCNT resulting in necrotic cell death rather than apoptosis.  ...  Studies, Japan Health effects of carbon nanotubes (CNT) have been gaining attentions of toxicologists, because the shape of CNT is similar to that of asbestos and the potency of CNT to cause mesothelioma  ...  In spite of this, there was a highconcordance on identical genes, pathways and gene ontology.  ... 
doi:10.1038/bjc.2014.478 pmid:25188323 pmcid:PMC4453733 fatcat:cvajfefqozcuxcvzv2z54d664e

A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis

Ajay Mishra, Bénédicte Oulès, Angela Oliveira Pisco, Tony Ly, Kifayathullah Liakath-Ali, Gernot Walko, Priyalakshmi Viswanathan, Matthieu Tihy, Jagdeesh Nijjher, Sara-Jane Dunn, Angus I Lamond, Fiona M Watt
2017 eLife  
We conclude that an auto-regulatory phosphatase network maintains epidermal homeostasis by controlling the onset and duration of commitment.  ...  The phosphatases form a dynamic network of transient positive and negative interactions that change over time, with DUSP6 predominating at commitment.  ...  The authors also gratefully acknowledge the use of Core Facilities provided by the financial support from the Department of Health via the National Institute for Health Research (NIHR) comprehensive Biomedical  ... 
doi:10.7554/elife.27356 pmid:29043977 pmcid:PMC5667932 fatcat:c3iop4nj65ajfa7zsuof54mlve

Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk

Derek V. Seidel, M. Andrea Azcárate-Peril, Robert S. Chapkin, Nancy D. Turner
2017 Seminars in Cancer Biology  
DP increased Bacteroidetes and decreased Firmicutes in the distal colon, and increased Actinobacteria and decreased Lactobacillus throughout the colon.  ...  Evidence of an interaction between DP and radiation exposure in 40% of animals warrants further investigation. iii Sumac sorghum (SS) increased the anti-inflammatory genus Faecalibacterium, but had no  ...  The number of pairs equals the number of variables in each dataset (or in the smaller dataset if unequal).  ... 
doi:10.1016/j.semcancer.2017.06.009 pmid:28676459 fatcat:doxf7nrhwbdptinafy32bvv4pa

The effect of Alzheimer's disease-associated genetic variants on longevity [article]

Niccolo Tesi, Marc Hulsman, Sven van der Lee, Iris Jansen, Najada Stringa, Natasja van Schoor, Philip Scheltens, Wiesje van der Flier, Martijn Huisman, Marcel Reinders, Henne Holstege
2021 medRxiv   pre-print
The effect of the SNPs in AD- and Longevity-groups replicated in the largest GWAS on parental-longevity, while the effects on longevity of the SNPs in the Unexpected-group could not be replicated, suggesting  ...  As Alzheimer's disease (AD) represents one of the most common conditions at old age, an interplay between genetic factors for AD and longevity is expected.  ...  Figure S2 : S2 Schematic representation of the variant-pathway and variant-cell-type mapping.  ... 
doi:10.1101/2021.02.02.21250991 fatcat:pvelh2f6fvf73ct6uuiegagfme

A Glimpse to Background and Characteristics of Major Molecular Biological Networks

Md. Altaf-Ul-Amin, Tetsuo Katsuragi, Tetsuo Sato, Shigehiko Kanaya
2015 BioMed Research International  
These huge datasets have paved the way for system-level analysis of the processes and subprocesses of the cell.  ...  In this review, we briefly discuss both the biological background and topological properties of major types of omics networks to facilitate a comprehensive understanding and to conceptualize the foundation  ...  Acknowledgments This work is partly supported by the National Bioscience Database Center in Japan and NAIST Big Data Project.  ... 
doi:10.1155/2015/540297 pmid:26491677 pmcid:PMC4605226 fatcat:lwzn2z7nzrh7np6at6twisrvem

Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V

2013 Naunyn-Schmiedeberg's Archives of Pharmacology  
Acknowledgement: This work has been financially supported by DFG and Tubitak with a travel stipend to Aylin Üstündag. [1] Yu, P., Constien, R., Dear, N., Katan, M., Hanke, P., Bunney, T.D., Kunder, S.,  ...  Grosse, J., Wabnitz, P., Meyer, T.P.H., Yasuda, K., Schiemann, M., Schneider-Fresenius, C., Jagla, W., Russ, A., Popp, A., Josephs, M., Marquardt, A., Laufs, J., Schmittwolf, C., Wagner, H., Pfeffer, K., and  ...  The identification of the GO category "biological process" in which pain genes are involved was done by means of over-representation analysis (ORA) using the web-based Gene¬Trail system.  ... 
doi:10.1007/s00210-013-0832-9 pmid:23334796 fatcat:vp56yyyimzfgdgrczauhpodxou
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