References
- Ressom HW, Varghese RS, Zhang Z, Xuan J, Clarke R. Classification algorithms for phenotype prediction in genomics and proteomics. Front Biosci. 2008;13:691–708.
- Sernova NV, Gelfand MS. Identification of replication origins in prokaryotic genomes. Brief Bioinform. 2008;9(5):376–391.
- Aguilar-Ruiz JS, Moore JH, Ritchie MD. Filling the gap between biology and computer science. BioData Min. 2008;1(1):1.
- Cao Y, Liu D, Tavanapong W, Wong J, Oh J, de Groen PC. Computer-aided detection of diagnostic and therapeutic operations in colonoscopy videos. IEEE Trans BiomedEng. 2007;54(7):1268–1279.
- Kim SH, Lee JM, Lee JG, et al. Computer-aided detection of colonic polyps at CT colonography using a Hessian matrix-based algorithm: preliminary study. AJR Am J Roentgenol. 2007;189(1):41–51.
- Sivashankari S, Shanmughavel P. Functional annotation of hypothetical proteins - A review. Bioinformation. 2006;1(8):335–338.
- Lovering RC, Camon EB, Blake JA, Diehl AD. Access to immunology through the Gene Ontology. Immunology. 2008;125(2):154–160.
- Overbeek R, Bartels D, Vonstein V, Meyer F. Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev 2007;107(8):3431–3447.
- Thomas PD, Mi H, Lewis S. Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol. 2007;11(1):4–11.
- Yan Q. Bioinformatics databases and tools in virology research: an overview. In Silico Biol. 2008;8(2):71–85.
- Harrill AH, Rusyn I. Systems biology and functional genomics approaches for the identification of cellular responses to drug toxicity. Expert Opin DrugMetab Toxicol. 2008;4(11):1379–1389.
- Sorokin V Severinov K, Gelfand MS. Systematic prediction of control proteins and their DNA binding sites. Nucleic Acids Res. 2009;37(2):441–451.
- Sadovskaya NS, Sutormin RA, Gelfand MS. Recognition of transmembrane segments in proteins: review and consistency-based benchmarking of internet servers. JBioinform ComputBiol. 2006;4(5):1033–1056.
- Hauck CR. Cell adhesion receptors - signaling capacity and exploitation by bacterial pathogens. Med Microbiol Immunol. 2002;191(2):55–62.
- Stoolman LM, Kaldjian E. Adhesion molecules involved in the trafficking of normal and malignant leukocytes. Invasion Metastasis. 1992;12(2):101–111.
- Klemm P, Schembri MA. Bacterial adhesins: function and structure. Int J Med Microbiol. 2000;290(1):27–35.
- Wizemann TM, Adamou JE, Langermann S. Adhesins as targets for vaccine development. Emerg Infect Dis. 1999;5(3):395–403.
- Buckley CD, Rainger GE, Bradfield PF, Nasg GB, Simmons DL. Cell adhesion: more than just glue. Mol Membr Biol. 1998;15(4):167–176.
- Magie CR, Martindale MQ. Cell-cell adhesion in the cnidaria: insights into the evolution of tissue morphogenesis. Biol Bull. 2008;214(3):218–232.
- Buckley CD, Simmons DL. Cell adhesion: a new target for therapy. Mol Med Today. 1997;3(10):449–456.
- Klaile E, Muller MM, Kannicht C, et al. The cell adhesion receptor carcinoembryonic antigen-related cell adhesion molecule 1 regulates nucleocytoplasmic trafficking of DNA polymerase delta-interacting protein 38. J Biol Chem. 2007;282(36):26629–26640.
- Martin M, Simon-Assmann P, Kedinger M. et al. DCC regulates cell adhesion in human colon cancer derived HT-29 cells and associates with ezrin. Eur J Cell Biol. 2006;85(8):769–783.
- Sivalenka RR, Jessberger R. SWAP-70 regulates c-kit-induced mast cell activation, cell-cell adhesion, and migration. Mol Cell Biol. 2004;24(23):10277–10288.
- Smith SF. Homology search with binary and trinary scoring matrices. Int J Bioinform Res Appl. 2006;2(2):119–131.
- Deller MC, Yvonne Jones E. Cell surface receptors. Curr Opin Struct Biol. 2000;10(2):213–219.
- Keller JM, Gray MR, Givens JA. Fuzzy k-nearest neighbor algorithm. IEEE Trans Syst Man Cybern. 1985;15(4):580–585.
- Tung TQ, Lee D. A method to improve protein subcellular localization prediction by integrating various biological data sources. BMC Bioinformatics. 2009;10(Suppl 1):S43.
- Nasibov E, Kandemir-Cavas C. Protein subcellular location prediction using optimally weighted fuzzy k-NN algorithm. Comput Biol Chem. 2008;32(6):448–451.
- Sengur A. An expert system based on principal component analysis, artificial immune system and fuzzy k-NN for diagnosis of valvular heart diseases. Comput Biol Med. 2008;38(3):329–338.
- Hynes RO. Cell adhesion: old and new questions. Trends Cell Biol. 1999;9(12):M33-M37.
- Wheelock MJ, Shintani Y, Maeda M. Fukumoto Y, Johnson KR. Cadherin switching. JCell Sci. 2008;121(Pt 6):727–735.
- Boggon TJ, Murray J, Chappuis-Flament S, Wong E, Gumbiner BM, Shapiro L. C-cadherin ectodomain structure and implications for cell adhesion mechanisms. Science. 2002;296(5571):1308–1313.
- Zhang Y, Yeh J, Richardson PM, Bo X. Cell adhesion molecules of the immunoglobulin superfamily in axonal regeneration and neural repair. Restor Neurol Neurosci. 2008;26(2–3):81–96.
- Aricescu AR, Jones EY. Immunoglobulin superfamily cell adhesion molecules: zippers and signals. Curr Opin Cell Biol. 2007;19(5):543–550.
- Doebis C, Siegmund K, Loddenkemper C, et al. Cellular players and role of selectin ligands in leukocyte recruitment in a T-cell-initiated delayed-type hypersensitivity reaction. Am J Pathol. 2008;173(4):1067–1076.
- Schreiber T, Ehlers S, Aly S, et al. Selectin ligand-independent priming and maintenance of T cell immunity during airborne tuberculosis. J Immunol. 2006;176(2):1131–1140.
- Smalley DM, Ley K. L-selectin: mechanisms and physiological significance of ectodomain cleavage. J Cell Mol Med. 2005;9(2):255–266.
- Akiyama SK. Integrins in cell adhesion and signaling. Hum Cell. 1996;9(3):181–186.
- Dedhar S. Integrins and signal transduction. Curr Opin Hematol. 1999;6(1):37–43.
- Tuckwell DS. Weston SA, Humphries MJ. Integrins: a review of their structure and mechanisms of ligand binding. Symp Soc Exp Biol. 1993;47:107–136.
- Haquin S, Oeuillet E, Pajon A, et al. Data management in structural genomics: an overview. Methods Mol Biol. 2008;426:49–79.
- Kazakov AE, Vassieva O, Gelfand MS, Osterman A, Overbeek R. Bioinformatics classification and functional analysis of PhoH homologs. In Silico Biol. 2003;3(1–2):3–15.
- Kurmangaliyev YZ, Gelfand MS. Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics. 2008;9:13.
- Liu H, Wong L. Data mining tools for biological sequences. JBioinform Comput Biol. 2003;1(1):139–167.
- Serini G, Napione L, Bussolino F. Integrins team up with tyrosine kinase receptors and plexins to control angiogenesis. Curr Opin Hematol. 2008;15(3):235–242.
- Kingsford C, Salzberg SL. What are decision trees? Nat Biotechnol. 2008;26(9):1011–1013.
- Han L, Wang Y, Bryant SH. Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem. BMC Bioinformatics. 2008;9:401.
- Ge G, Wong GW. Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles. BMC Bioinformatics. 2008;9:275.
- Levitsky VG, Ignatieva EV, Ananko EA, et al. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC Bioinformatics 2007;8:481.
- Zhang MQ. Discriminant analysis and its application in DNA sequence motif recognition. Brief Bioinform. 2000;1(4):331–342.
- Dai W, Teodoridis JM, Graham J, et al. Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands. BMC Bioinformatics. 2008;9:337.
- Mereghetti P, Ganadu ML, Papaleo E, Fantucci P, De Gioia L. Validation of protein models by a neural network approach. BMC Bioinformatics. 2008;9:66.
- Yang ZR, Hamer R. Bio-basis function neural networks in protein data mining. Curr Pharm Des. 2007;13(14):1403–1413.
- Jung E, Kim J, Kim M, et al. Artificial neural network models for prediction of intestinal permeability of oligopeptides. BMC Bioinformatics. 2007;8:245.
- Brummendorf T, Lemmon V Immunoglobulin superfamily receptors: cis-interactions, intracellular adapters and alternative splicing regulate adhesion. Curr Opin Cell Biol. 2001;13(5):611–618.
- Halloran MC, Wolman MA. Repulsion or adhesion: receptors make the call. Curr Opin Cell Biol. 2006;18(5):533–540.
- Hauck CR, Agerer F, Muenzner P, Schmitter T. Cellular adhesion molecules as targets for bacterial infection. Eur J Cell Biol. 2006;85(3–4):235–242.
- Van Roy F, Berx G. The cell-cell adhesion molecule E-cadherin. Cell Mol Life Sci. 2008;65(23):3756–3788.