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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Computational Biology

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Disease relevance of Computational Biology


High impact information on Computational Biology


Chemical compound and disease context of Computational Biology

  • Using the rat femoral fracture model, bioinformatics, cloning, expression assays, fusion proteins, and transfection, we report on the identification and characterization of one such differentially expressed gene, termed Mustang (musculoskeletal temporally activated novel gene) [10].

Biological context of Computational Biology

  • A bioinformatics approach combining comparative genomic analysis and gene expression studies of a BBS-knockout mouse model was used to prioritize BBS candidate genes within the newly identified loci for mutation screening [11].
  • By a combined use of bioinformatics, published expression data, and knock-out phenotypes, we identified the cytochrome P450 CYP83B1 as the oxime-metabolizing enzyme in the glucosinolate pathway as evidenced by characterization of the recombinant protein expressed in Escherichia coli [12].
  • Bioinformatics analyses identified a novel domain in HIP-1 with homology to death effector domains (DEDs) present in proteins involved in apoptosis [13].
  • Genome data mining of lactic acid bacteria: the impact of bioinformatics [14].
  • The sequence data are grouped and identified using the tools of bioinformatics and the results are displayed through a web site where they can be interrogated by keyword search, chromosome location, by Blast (sequence comparison) or by alignment on completed genomes [15].

Anatomical context of Computational Biology


Associations of Computational Biology with chemical compounds

  • By combining the use of a phosphospecific antibody recognizing a substrate motif of serine/threonine kinases with bioinformatics, we found that the translational regulators ribosomal protein S6 and 4E-BP1 are constitutively phosphorylated in CML cells [18].
  • Here, we identify by bioinformatics and mutational analyses three functional domains of the hSlu7 protein that have distinct roles in its subcellular localization: a nuclear localization signal, a zinc-knuckle motif, and a lysine-rich region [19].
  • We then describe the subsequent identification of HM74A in follow-up bioinformatics searches and demonstrate that it acts as a high affinity receptor for nicotinic acid and other compounds with related pharmacology [20].
  • Using bioinformatics strategies, cDNAs were identified that encode a novel protein of 110 kDa containing a PAAD domain followed by a putative nucleotide-binding (NACHT) domain and several leucine-rich repeat domains [21].
  • The database is available on the internet (, from EMBL-European Bioinformatics Institute (, or as a Macintosh FilemakerPro or Word file ( [22].

Gene context of Computational Biology


Analytical, diagnostic and therapeutic context of Computational Biology


  1. Interleukin 20: discovery, receptor identification, and role in epidermal function. Blumberg, H., Conklin, D., Xu, W.F., Grossmann, A., Brender, T., Carollo, S., Eagan, M., Foster, D., Haldeman, B.A., Hammond, A., Haugen, H., Jelinek, L., Kelly, J.D., Madden, K., Maurer, M.F., Parrish-Novak, J., Prunkard, D., Sexson, S., Sprecher, C., Waggie, K., West, J., Whitmore, T.E., Yao, L., Kuechle, M.K., Dale, B.A., Chandrasekher, Y.A. Cell (2001) [Pubmed]
  2. Serum proteomic patterns for detection of prostate cancer. Petricoin, E.F., Ornstein, D.K., Paweletz, C.P., Ardekani, A., Hackett, P.S., Hitt, B.A., Velassco, A., Trucco, C., Wiegand, L., Wood, K., Simone, C.B., Levine, P.J., Linehan, W.M., Emmert-Buck, M.R., Steinberg, S.M., Kohn, E.C., Liotta, L.A. J. Natl. Cancer Inst. (2002) [Pubmed]
  3. Identification of Down's syndrome critical locus gene SIM2-s as a drug therapy target for solid tumors. DeYoung, M.P., Tress, M., Narayanan, R. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  4. Ubiquitin-mediated sequestration of normal cellular proteins into polyglutamine aggregates. Donaldson, K.M., Li, W., Ching, K.A., Batalov, S., Tsai, C.C., Joazeiro, C.A. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  5. Somatically mutated regions of immunoglobulin on human B-cell lymphomas code for peptides that bind to autologous major histocompatibility complex class I, providing a potential target for cytotoxic T cells. Gricks, C.S., Rawlings, E., Foroni, L., Madrigal, J.A., Amlot, P.L. Cancer Res. (2001) [Pubmed]
  6. The biology of chemokines and their receptors. Rossi, D., Zlotnik, A. Annu. Rev. Immunol. (2000) [Pubmed]
  7. PTEN and myotubularin phosphoinositide phosphatases: bringing bioinformatics to the lab bench. Wishart, M.J., Taylor, G.S., Slama, J.T., Dixon, J.E. Curr. Opin. Cell Biol. (2001) [Pubmed]
  8. Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Udekwu, K.I., Darfeuille, F., Vogel, J., Reimegård, J., Holmqvist, E., Wagner, E.G. Genes Dev. (2005) [Pubmed]
  9. TinyGRAP database: a bioinformatics tool to mine G-protein-coupled receptor mutant data. Beukers, M.W., Kristiansen, I., IJzerman, A.P., Edvardsen, I. Trends Pharmacol. Sci. (1999) [Pubmed]
  10. Molecular cloning and characterization of Mustang, a novel nuclear protein expressed during skeletal development and regeneration. Lombardo, F., Komatsu, D., Hadjiargyrou, M. FASEB J. (2004) [Pubmed]
  11. Comparative genomics and gene expression analysis identifies BBS9, a new Bardet-Biedl syndrome gene. Nishimura, D.Y., Swiderski, R.E., Searby, C.C., Berg, E.M., Ferguson, A.L., Hennekam, R., Merin, S., Weleber, R.G., Biesecker, L.G., Stone, E.M., Sheffield, V.C. Am. J. Hum. Genet. (2005) [Pubmed]
  12. CYP83b1 is the oxime-metabolizing enzyme in the glucosinolate pathway in Arabidopsis. Hansen, C.H., Du, L., Naur, P., Olsen, C.E., Axelsen, K.B., Hick, A.J., Pickett, J.A., Halkier, B.A. J. Biol. Chem. (2001) [Pubmed]
  13. Huntingtin interacting protein 1 induces apoptosis via a novel caspase-dependent death effector domain. Hackam, A.S., Yassa, A.S., Singaraja, R., Metzler, M., Gutekunst, C.A., Gan, L., Warby, S., Wellington, C.L., Vaillancourt, J., Chen, N., Gervais, F.G., Raymond, L., Nicholson, D.W., Hayden, M.R. J. Biol. Chem. (2000) [Pubmed]
  14. Genome data mining of lactic acid bacteria: the impact of bioinformatics. Siezen, R.J., van Enckevort, F.H., Kleerebezem, M., Teusink, B. Curr. Opin. Biotechnol. (2004) [Pubmed]
  15. The NEIBank project for ocular genomics: data-mining gene expression in human and rodent eye tissues. Wistow, G. Progress in retinal and eye research. (2006) [Pubmed]
  16. T-cell epitopes within the complementarity-determining and framework regions of the tumor-derived immunoglobulin heavy chain in multiple myeloma. Hansson, L., Rabbani, H., Fagerberg, J., Osterborg, A., Mellstedt, H. Blood (2003) [Pubmed]
  17. MAPPP: MHC class I antigenic peptide processing prediction. Hakenberg, J., Nussbaum, A.K., Schild, H., Rammensee, H.G., Kuttler, C., Holzhütter, H.G., Kloetzel, P.M., Kaufmann, S.H., Mollenkopf, H.J. Appl. Bioinformatics (2003) [Pubmed]
  18. Bcr-Abl kinase modulates the translation regulators ribosomal protein S6 and 4E-BP1 in chronic myelogenous leukemia cells via the mammalian target of rapamycin. Ly, C., Arechiga, A.F., Melo, J.V., Walsh, C.M., Ong, S.T. Cancer Res. (2003) [Pubmed]
  19. Splicing factor hSlu7 contains a unique functional domain required to retain the protein within the nucleus. Shomron, N., Reznik, M., Ast, G. Mol. Biol. Cell (2004) [Pubmed]
  20. Molecular identification of high and low affinity receptors for nicotinic acid. Wise, A., Foord, S.M., Fraser, N.J., Barnes, A.A., Elshourbagy, N., Eilert, M., Ignar, D.M., Murdock, P.R., Steplewski, K., Green, A., Brown, A.J., Dowell, S.J., Szekeres, P.G., Hassall, D.G., Marshall, F.H., Wilson, S., Pike, N.B. J. Biol. Chem. (2003) [Pubmed]
  21. A novel PAAD-containing protein that modulates NF-kappa B induction by cytokines tumor necrosis factor-alpha and interleukin-1beta. Fiorentino, L., Stehlik, C., Oliveira, V., Ariza, M.E., Godzik, A., Reed, J.C. J. Biol. Chem. (2002) [Pubmed]
  22. Update of the androgen receptor gene mutations database. Gottlieb, B., Beitel, L.K., Lumbroso, R., Pinsky, L., Trifiro, M. Hum. Mutat. (1999) [Pubmed]
  23. Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics. Scheel, H., Tomiuk, S., Hofmann, K. Hum. Mol. Genet. (2003) [Pubmed]
  24. A bioinformatics-based strategy identifies c-Myc and Cdc25A as candidates for the Apmt mammary tumor latency modifiers. Cozma, D., Lukes, L., Rouse, J., Qiu, T.H., Liu, E.T., Hunter, K.W. Genome Res. (2002) [Pubmed]
  25. The Trypanosoma brucei signal recognition particle lacks the Alu-domain-binding proteins: purification and functional analysis of its binding proteins by RNAi. Lustig, Y., Goldshmidt, H., Uliel, S., Michaeli, S. J. Cell. Sci. (2005) [Pubmed]
  26. NopA is associated with cell surface appendages produced by the type III secretion system of Rhizobium sp. strain NGR234. Deakin, W.J., Marie, C., Saad, M.M., Krishnan, H.B., Broughton, W.J. Mol. Plant Microbe Interact. (2005) [Pubmed]
  27. A family of 12 human genes containing oxysterol-binding domains. Jaworski, C.J., Moreira, E., Li, A., Lee, R., Rodriguez, I.R. Genomics (2001) [Pubmed]
  28. Shear-induced cyclooxygenase-2 via a JNK2/c-Jun-dependent pathway regulates prostaglandin receptor expression in chondrocytic cells. Abulencia, J.P., Gaspard, R., Healy, Z.R., Gaarde, W.A., Quackenbush, J., Konstantopoulos, K. J. Biol. Chem. (2003) [Pubmed]
  29. Identification of two hERR2-related novel nuclear receptors utilizing bioinformatics and inverse PCR. Chen, F., Zhang, Q., McDonald, T., Davidoff, M.J., Bailey, W., Bai, C., Liu, Q., Caskey, C.T. Gene (1999) [Pubmed]
  30. PCP: a program for supervised classification of gene expression profiles. Buturović, L.J. Bioinformatics (2006) [Pubmed]
  31. Gene expression in sheep skin and wool (hair). Adelson, D.L., Cam, G.R., DeSilva, U., Franklin, I.R. Genomics (2004) [Pubmed]
  32. Identification and characterization of a lymphocytic Rho-GTPase effector: rhotekin-2. Collier, F.M., Gregorio-King, C.C., Gough, T.J., Talbot, C.D., Walder, K., Kirkland, M.A. Biochem. Biophys. Res. Commun. (2004) [Pubmed]
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