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
