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PathCase in Literature

    Computational Approaches for Translational Clinical Research in Disease Progression

    2011

    McGuire, M. F., Iyengar, M.S., Mercer, DD. W., Computational Approaches for Translational Clinical Research in Disease Progression. Journal of Investigative Medicine, 2011

    Wong L., Using Biological Networks in Protein Function Prediction and Gene Expression Analysis. Internet Maathematics , 2011

    2010

    Sophia Ananiadou, Sampo Pyysalo, Jun’ichi Tsujii, Douglas B. Kell, Event extraction for systems biology by text mining the literature. Trends in Biotechnology, 2010

    A. Dilek, M.E. Belviranli, U. Dogrusoz. VISIBIOweb: visualization and layout services for BioPAX pathway models. Nucleic Acids Research, 2010

    Z. Ezziane. Attempt to design a bio-medical knowledge discovery system. International Journal of Bio-Inspired Computation, 2010

    O. Babur, U. Dogrusoz, E. Demir, C. Sander. ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics 2010 26(3):429-431; doi:10.1093/bioinformatics/btp665


    2009

    Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, et al. Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google. Maps API. PLoS ONE 4(11): e7710. doi:10.1371/journal.pone.0007710. 2009


    2008

    EG Giannopoulou, G Lepouras, ES Manolakos. VIP: Visualization of Integrated Proteomics Data. 8th IEEE International Conference on BioInformatics and …, 2008.

    P. Jia-yang, Y. Lu-ming, W. Jian-xin, L. Zheng, L. Ming. An Efficient Algorithm for Detecting Closed Frequent Subgraphs in Biological Networks. BioMedical Engineering and Informatics, 2008.

    Y Li, D de Ridder, MJL de Groot, MJT Reinders. Metabolic pathway alignment between species using a com-prehensive and flexible similarity measure. BMC Systems Biology, 2008.

    YP Phoebe Chen, F. Chen. Identifying targets for drug discovery using bioinformatics. Expert Opin. Ther. Targets, 2008 - Informa Pharma Science


    2007

    Mingyu Liang. Integrative pathway knowledge bases as a tool for systems molecular medicine. Physiol. Genomics 30: 209-212, 2007

    Oliver Ruebenacker, Ion. I. Moraru, James C. Schaff, and Michael L. Blinov. Kinetic Modeling Using BioPAX Ontology. IEEE International Conference on Bioinformatics and Biomedicine, 2007. (BIBM 2007)

    S Kneitz, T Dandekar. Bioinformatics: Data Mining Among Genome Sequences. Pathogenomics: Genome Analysis of Pathogenic Microbes, 2007. books.google.com

    W Huber, V Carey, L Long, S Falcon, R Gentleman. Graphs in molecular biology< BMC bioinformatics, 2007 - biomedcentral.com


    2006

    CK Tuggle, JCM Dekkers, JM Reecy. Integration of structural and functional genomics. Animal Genetics, 2006 - pt.wkhealth.com

    Ernesto Estrada, Juan A. Rodríguez-Velázquez. Subgraph centrality and clustering in complex hyper-networks. Physica A: Statistical Mechanics and its Applications, Volume 364, 15 May 2006, Pages 581-594

    Jennifer Crebs. Systems Cartography. Genome Technology, September 2006 Issue.

    JE Stenger, SG Gregory. Genomics and Bioinformatics, Genetic Analysis of Complex Diseases, 2006 – books.google.com

    Jiang, K., Nash, C. Application of XML Database Technology to Biological Pathway Datasets. IEEE International Conference on Engineering in Medicine and Biology, 2006. (EMBS'06)

    Lena Strömbäck, Vaida Jakoniene, He Tan, Patrick Lambrix. Representing, storing and accessing molecular interaction data: a review of models and tools. Briefings in Bioinformatics 2006 7(4):331-338.

    M Baitaluk, M Sedova, A Ray, A Gupta. BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W466-W471.

    Mehmet Koyutürk , Yohan Kim , Shankar Subramaniam , Wojciech Szpankowski , Ananth Grama. Detecting conserved interaction patterns in biological networks. Journal of Computational Biology, 2006

    Michael Baitaluk, Xufei Qian, Shubhada Godbole, Alpan Raval, Animesh Ray, Amarnath Gupta. PathSys: integrating molecular interaction graphs for systems biology. BMC bioinformatics, 2006 - biomedcentral.com

    T Jung, K Kim, S Jung, T Kim, M Ahn, J Lee, W Cho. SPDBS: An SBML-Based Biochemical Pathway Database System. Computational Intelligence and Bioinformatics, 2006

    Z Wang, XG Zhu, Y Chen, Y Li, J Hou, Y Li, L Liu. Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria. BMC genomics, 2006 - biomedcentral.com


    2005

    ALP Guedes, L Markenzon. Directed hypergraph planarity. Pesquisa Operacional, 2005 - SciELO Brasil

    A Scharlott. Biological Pathways Databases. 2005 CiteSeerX

    Dittrich M, Birschmann I, Stuhlfelder C, Sickmann A, Herterich S, Nieswandt B, Walter U, Dandekar T. Understanding platelets. Lessons from proteomics, genomics and promises from network analysis. Thromb Haemost. 2005 Nov;94(5):916-25.

    E Estrada, JA Rodriguez-Velazquez. Complex Networks as Hypergraphs. Arxiv preprint physics/0505137, 2005 - arxiv.org

    M Holford, N Li, P Nadkarni, H Zhao. VitaPad: visualization tools for the analysis of pathway data. Bioinformatics, 2005 - Oxford Univ Press

    PBT Neerincx, JAM Leunisse. Evolution of web services in bioinformatics. Briefings in bioinformatics, 2005 - Oxford Univ Press

    P Saraiya, C North, K Duca. Visualizing biological pathways: requirements analysis, systems evaluation and research agenda. Information Visualization, 2005 - staging-www.palgrave-journals.com

    Victor M. Markowitz , Frank Korzeniewski , Ernest Szeto , Natalia Ivanova , Nikos C. Kyrpides. The integrated microbial genomes (IMG) system: a case study in biological data management. VLDB 2005.

    Wilma Ziebuhr, Ke Xiao, Boubacar Coulibaly, Roland Schwarz, Thomas Dandekar. Pharmacogenomic strategies against resistance development in microbial infections. Pharmacogenomics - June 2004, Vol. 5, No. 4, Pages 361-379 , DOI 10.1517/14622416.5.4.361

    Y Zhang, XC Bo, J Yang, SQ Wang. HBVPathDB: A database of HBV infection-related molecular interaction network. World J Gastroenterol, 2005 - wjg.wjgnet.com


    2004

    C. F. Schaefer. Pathway Databases. Annals of New York Academy of Sciences, May 1, 2004; 1020(1): 77-91

    CM Keet. Aspects of ontology integration – 2004 www.meteck.org/AspectsOntologyIntegration.pdf

    M Dünßer, R Lampidis, S Schmidt, D Seipel, T. Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework. Journal of Integrative Bioinformatics. 2004.


    2003

    CM Keet. Biological data and conceptual modelling methods. Journal of Conceptual Modeling, 2003 /p>

    CM Keet. Conceptual modelling for applied bioscience: The bacteriocin database - CSPS: Computational intelligence, 2003 - meteck.org

    T Kaminuma. The pathways and networks of nuclear receptors and modeling of syndrome X. Chem-Bio Informatics Journal, 2003 - cbi.or.jp

    Y Deville, D Gilbert, J Van Helden, SJ Wodak. An overview of data models for the analysis of biochemical pathways. Briefings in Bioinformatics, 2003 - Oxford Univ Press


    Others

    A Koukoutsaki, T Dalamagas, T Sellis, P Bouros. P at M an: A Visual Database System to Manipulate Path Patterns and Data in Hierarchical Catalogs - Sigma - dblab.ntua.gr

    EG Giannopoulou, S Kossida. Data Mining Applications in the Post-Genomic Era journals.i-techonline.com

    H Zantema, S Wagemans, D Bosnacki. Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets - Springer

    M Koyuturk, A Grama, W Szpankowski. Mining Biological Networks for Frequent Interaction Patterns. cs.purdue.edu

    WJ Zheng. Engineering Approaches Toward Biological Information Integration at the Systems Level. ingentaconnect.com




Last update: May, 2010