The world's first wiki where authorship really matters (Nature Genetics, 2008). Due credit and reputation for authors. Imagine a global collaborative knowledge base for original thoughts. Search thousands of articles and collaborate with scientists around the globe.

wikigene or wiki gene protein drug chemical gene disease author authorship tracking collaborative publishing evolutionary knowledge reputation system wiki2.0 global collaboration genes proteins drugs chemicals diseases compound
Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review


Welcome! If you are familiar with the subject of this article, you can contribute to this open access knowledge base by deleting incorrect information, restructuring or completely rewriting any text. Read more.

Disease relevance of Software


Psychiatry related information on Software

  • METHODS: The prediction engine is a computer program that accesses a central database in which daily records of self-monitored blood glucose data and life-style parameters are stored [6].
  • With a computerized data base, a data retrieval system, and a computer program using the actuarial method of life-table analysis, we compared survival rates in different subgroups of patients with dementia of the Alzheimer type (DAT; n = 199) [7].
  • The Present State Examination (PSE)-Index of Definition (ID) computer program (CATEGO) was used to define total psychopathology (total PSE score), current clinical severity (ID), and clusters of psychiatric symptoms [8].
  • A computer program developed at the University of Pennsylvania School of Medicine and the Children's Hospital of Philadelphia presents simulated patient cases and then scores participants' clinical problem-solving in the cases by comparing their performances with those of five faculty members [9].

High impact information on Software

  • An ad hoc boolean computer program allowed for the separation of hemolytic from nonhemolytic disorders with a haptoglobin limit of 25 mg/dL or less [10].
  • First, the relative saturation ratio (RSR), the ratio of the dissolved calcium oxalate complex to the thermodynamic calcium oxalate solubility product, was estimated for 11 uremic (before and after dialysis) and 4 normal serum samples using a computer program [11].
  • From each spectrum, metabolite levels were estimated for glutamate and glutamine, as well as 10 other metabolites and 3 macromolecules, by means of a noninteractive computer program that combined modeled in vitro spectra of every metabolite to reconstruct each in vivo spectrum [12].
  • The computer program reliably estimated amikacin serum levels after either intravenous or intramuscular doses [13].
  • Automated feedback control methods were applied to a medical problem, in a computer program that used measured serum digoxin concentrations (as feedback) to predict future concentrations and to achieve desired concentrations [14].

Chemical compound and disease context of Software


Biological context of Software


Anatomical context of Software

  • By using computer programs designed to detect evolutionary relationships between proteins, we find that this part of protein S is similar to rat androgen-binding protein, a protein produced and secreted by testicular Sertoli cells [23].
  • KA caused significant reductions in the proportion of SN neurons with intact dendrites and in the total length of the dendrites, measured using a computer program [24].
  • New methods and software tools for high throughput CDR3 spectratyping. Application to T lymphocyte repertoire modifications during experimental malaria [25].
  • This approach was obtained from the freeware computer program 'Image Arithmetic'. In a test, three different consumer-type digital cameras (Sony, Nikon, Olympus) on different microscopes were used to obtain images of different types of histological specimens (cervical smear, bone marrow biopsy, and colonic biopsy) [26].
  • Furthermore, a computer program designed to isolate terminal structures in the spinal cord identified a differential depletion of 5-HT terminals in the dorsal horn versus the ventral horn [27].

Associations of Software with chemical compounds

  • Pulsatility of insulin was assessed by sampling every 2 min for 90 min after an overnight fast and identifying insulin pulses using the computer program Pulsar [28].
  • Analysis of the binding data by the LIGAND computer program indicated that HUVECs, in the presence of 2 mM CaCl2 and 100 microM ZnCl2 at 37 degrees C, bound 1.14 x 10(7) H-kininogen molecules per cell with an apparent dissociation constant of 55 nM [29].
  • Using a computer program (Ligand), we calculated the dissociation constants, binding capacities, and numbers of receptors per cell for each of the different cell types [30].
  • Using the PEST-FIND computer program, the computed PEST score for human and rat Sp1 is 10.4 and 13.7, respectively, indicating that Sp1 has a domain with a high concentration of proline, glutamic acid, serine, and threonine residues as reported for a number of proteins with inducible rates of degradation [31].
  • Proteins being synthesized were pulse-labelled with [35S]-methionine, separated by two-dimensional polyacrylamide gel electrophoresis, and quantified using the BioImage computer software [32].

Gene context of Software

  • By using computer programs predicting secondary structure, the dnaG RNase E cleavage site appears to be in a single stranded RNA loop [33].
  • According to analysis by the RAOARGOS computer program, this hydrophobic region in UGT1A1 is located between residues 159-177 and defines a buried helix centered over position 169-172 with a positive factor of 1.22 [34].
  • The genomic organization of the C8orf1/hT41 and NBS1 genes has been analyzed using the computer programs GRAIL 2 and GENSCAN [35].
  • The Kd (from a computer program LIGAND analysis) and Ki (from Dixon plot analysis) values of TAK-044 were 95 and 120 pM for the membranous ETA receptor and 41 and 60 nM for the ETB receptor, respectively [36].
  • Using a computer program designed to detect evolutionary relationships between proteins, I find that the PDC-109 protein is similar to the gelatin-binding domain of bovine fibronectin and part of a kringle domain of human tissue-type plasminogen activator (t-PA) [37].

Analytical, diagnostic and therapeutic context of Software


  1. Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. Bray, D., Bourret, R.B., Simon, M.I. Mol. Biol. Cell (1993) [Pubmed]
  2. Population pharmacokinetics of zidovudine. The Veterans Administration Cooperative Studies Group. Gitterman, S.R., Drusano, G.L., Egorin, M.J., Standiford, H.C. Clin. Pharmacol. Ther. (1990) [Pubmed]
  3. Motility and chemotaxis of Spirochaeta aurantia: computer-assisted motion analysis. Fosnaugh, K., Greenberg, E.P. J. Bacteriol. (1988) [Pubmed]
  4. Computerized detection of the lactate threshold in coronary artery disease. Eldridge, J.E., Giansiracusa, R.F., Jones, R.H., Hossack, K.F. Am. J. Cardiol. (1986) [Pubmed]
  5. A population pharmacokinetic model of trimethoprim in patients with pneumocystis pneumonia, made with parametric and nonparametric methods. Jelliffe, R.W., Gomis, P., Tahani, B., Ruskin, J., Sattler, F.R. Therapeutic drug monitoring. (1997) [Pubmed]
  6. Home blood glucose prediction: clinical feasibility and validation in islet cell transplantation candidates. Albisser, A.M., Baidal, D., Alejandro, R., Ricordi, C. Diabetologia (2005) [Pubmed]
  7. Factors associated with duration of survival in Alzheimer's disease. Barclay, L.L., Zemcov, A., Blass, J.P., McDowell, F.H. Biol. Psychiatry (1985) [Pubmed]
  8. Core mental state in irritable bowel syndrome. Trikas, P., Vlachonikolis, I., Fragkiadakis, N., Vasilakis, S., Manousos, O., Paritsis, N. Psychosomatic medicine. (1999) [Pubmed]
  9. Measuring the problem-solving ability of students and residents by microcomputer. Diserens, D., Schwartz, M.W., Guenin, M., Taylor, L.A. Journal of medical education. (1986) [Pubmed]
  10. The predictive value of serum haptoglobin in hemolytic disease. Marchand, A., Galen, R.S., Van Lente, F. JAMA (1980) [Pubmed]
  11. Evidence that serum calcium oxalate supersaturation is a consequence of oxalate retention in patients with chronic renal failure. Worcester, E.M., Nakagawa, Y., Bushinsky, D.A., Coe, F.L. J. Clin. Invest. (1986) [Pubmed]
  12. Measurement of glutamate and glutamine in the medial prefrontal cortex of never-treated schizophrenic patients and healthy controls by proton magnetic resonance spectroscopy. Bartha, R., Williamson, P.C., Drost, D.J., Malla, A., Carr, T.J., Cortese, L., Canaran, G., Rylett, R.J., Neufeld, R.W. Arch. Gen. Psychiatry (1997) [Pubmed]
  13. Amikacin serum concentrations: prediction of levels and dosage guidelines. Sarubbi, F.A., Hull, J.H. Ann. Intern. Med. (1978) [Pubmed]
  14. Improved computer-assisted digoxin therapy. A method using feedback of measured serum digoxin concentrations. Sheiner, L.B., Halkin, H., Peck, C., Rosenberg, B., Melmon, K.L. Ann. Intern. Med. (1975) [Pubmed]
  15. A computer model of fractal myocardial perfusion heterogeneity to elucidate mechanisms of changes in critical coronary stenosis and hypotension. Meier, J., Kleen, M., Messmer, K. Bull. Math. Biol. (2004) [Pubmed]
  16. Individualizing vancomycin dosing regimens: an evaluation of two pharmacokinetic dosing programs in critically ill patients. Fernández de Gatta, M.M., Fruns, I., Domínguez-Gil, A. Pharmacotherapy (1994) [Pubmed]
  17. Second-trimester maternal serum alpha-fetoprotein and human chorionic gonadotrophin screening for Down's syndrome in Hong Kong. Lam, Y.H., Ghosh, A., Tang, M.H., Tang, L.C., Lee, C.P., Sin, S.Y., Ho, P.K. Prenat. Diagn. (1998) [Pubmed]
  18. Kinetics and mechanism of the bactericidal action of human neutrophils against Escherichia coli. Hamers, M.N., Bot, A.A., Weening, R.S., Sips, H.J., Roos, D. Blood (1984) [Pubmed]
  19. Isolation and sequence of a cDNA clone which contains the complete coding region of rat phenylalanine hydroxylase. Structural homology with tyrosine hydroxylase, glucocorticoid regulation, and use of alternate polyadenylation sites. Dahl, H.H., Mercer, J.F. J. Biol. Chem. (1986) [Pubmed]
  20. Kinetics of inhibition by tyrphostins of the tyrosine kinase activity of the epidermal growth factor receptor and analysis by a new computer program. Posner, I., Engel, M., Gazit, A., Levitzki, A. Mol. Pharmacol. (1994) [Pubmed]
  21. Serine-23 is a major protein kinase A phosphorylation site on the amino-terminal head domain of the middle molecular mass subunit of neurofilament proteins. Sihag, R.K., Jaffe, H., Nixon, R.A., Rong, X. J. Neurochem. (1999) [Pubmed]
  22. Clinical coagulation laboratory and oral anticoagulant therapy treatment. Instrumentation and methodology. Barbui, T., Finazzi, G., Remuzzi, A. Thromb. Haemost. (1995) [Pubmed]
  23. Vitamin K-dependent protein S is similar to rat androgen-binding protein. Baker, M.E., French, F.S., Joseph, D.R. Biochem. J. (1987) [Pubmed]
  24. Degeneration of the dendritic arbor as an index of neurotoxicity in identified catecholamine neurons in rat brain slices. Johnson, S.M., Bywood, P.T. Exp. Neurol. (1998) [Pubmed]
  25. New methods and software tools for high throughput CDR3 spectratyping. Application to T lymphocyte repertoire modifications during experimental malaria. Collette, A., Cazenave, P.A., Pied, S., Six, A. J. Immunol. Methods (2003) [Pubmed]
  26. How to improve microscopic images obtained with consumer-type digital cameras. Regitnig, P., van Paasen, R., Tsybrovskyy, O. Histopathology (2003) [Pubmed]
  27. Differential effects of p-chlorophenylalanine on indoleamines in brainstem nuclei and spinal cord of rats. II. Identification of immunohistochemically stained structures using computer-assisted image enhancement techniques. Carlton, S.M., Steinman, J.L., Hillman, G.R., Willis, W.D. Brain Res. (1987) [Pubmed]
  28. Association between insulin secretory pulse frequency and peripheral insulin action in NIDDM and normal subjects. Hunter, S.J., Atkinson, A.B., Ennis, C.N., Sheridan, B., Bell, P.M. Diabetes (1996) [Pubmed]
  29. Assembly and expression of an intrinsic factor IX activator complex on the surface of cultured human endothelial cells. Berrettini, M., Schleef, R.R., Heeb, M.J., Hopmeier, P., Griffin, J.H. J. Biol. Chem. (1992) [Pubmed]
  30. Histamine type I (H1) receptor radioligand binding studies on normal T cell subsets, B cells, and monocytes. Cameron, W., Doyle, K., Rocklin, R.E. J. Immunol. (1986) [Pubmed]
  31. Epidermal growth factor and okadaic acid stimulate Sp1 proteolysis. Mortensen, E.R., Marks, P.A., Shiotani, A., Merchant, J.L. J. Biol. Chem. (1997) [Pubmed]
  32. Synthesis of ribosomal proteins during growth of Streptomyces coelicolor. Blanco, G., Rodicio, M.R., Puglia, A.M., Méndez, C., Thompson, C.J., Salas, J.A. Mol. Microbiol. (1994) [Pubmed]
  33. Selective decay of Escherichia coli dnaG messenger RNA is initiated by RNase E. Yajnik, V., Godson, G.N. J. Biol. Chem. (1993) [Pubmed]
  34. Required buried alpha-helical structure in the bilirubin UDP-glucuronosyltransferase, UGT1A1, contains a nonreplaceable phenylalanine. Ciotti, M., Cho, J.W., George, J., Owens, I.S. Biochemistry (1998) [Pubmed]
  35. Sequence analysis of an 800-kb genomic DNA region on chromosome 8q21 that contains the Nijmegen breakage syndrome gene, NBS1. Tauchi, H., Matsuura, S., Isomura, M., Kinjo, T., Nakamura, A., Sakamoto, S., Kondo, N., Endo, S., Komatsu, K., Nakamura, Y. Genomics (1999) [Pubmed]
  36. Receptor binding and antagonist properties of a novel endothelin receptor antagonist, TAK-044 [cyclo[D-alpha-aspartyl-3-[(4-phenylpiperazin-1-yl) carbonyl]-L-alanyl-L-alpha-aspartyl-D-2-(2-thienyl) glycyl-L-leucyl-D-tryptophyl]disodium salt], in human endothelinA and endothelinB receptors. Masuda, Y., Sugo, T., Kikuchi, T., Kawata, A., Satoh, M., Fujisawa, Y., Itoh, Y., Wakimasu, M., Ohtaki, T. J. Pharmacol. Exp. Ther. (1996) [Pubmed]
  37. The PDC-109 protein from bovine seminal plasma is similar to the gelatin-binding domain of bovine fibronectin and a kringle domain of human tissue-type plasminogen activator. Baker, M.E. Biochem. Biophys. Res. Commun. (1985) [Pubmed]
  38. Evidence of genetic heterogeneity in Romano-Ward long QT syndrome. Analysis of 23 families. Towbin, J.A., Li, H., Taggart, R.T., Lehmann, M.H., Schwartz, P.J., Satler, C.A., Ayyagari, R., Robinson, J.L., Moss, A., Hejtmancik, J.F. Circulation (1994) [Pubmed]
  39. Computer simulation of plasma insulin and glucose dynamics after subcutaneous insulin injection. Berger, M., Rodbard, D. Diabetes Care (1989) [Pubmed]
  40. Structure and location of gene product 8 in the bacteriophage T4 baseplate. Leiman, P.G., Shneider, M.M., Kostyuchenko, V.A., Chipman, P.R., Mesyanzhinov, V.V., Rossmann, M.G. J. Mol. Biol. (2003) [Pubmed]
  41. The renal vascular response to ANG II injection is reduced in the nonclipped kidney of two-kidney, one-clip hypertension. Bivol, L.M., Vågnes, O.B., Iversen, B.M. Am. J. Physiol. Renal Physiol. (2005) [Pubmed]
  42. An automated interpretation of MALDI/TOF postsource decay spectra of oligosaccharides. 1. Automated peak assignment. Mizuno, Y., Sasagawa, T., Dohmae, N., Takio, K. Anal. Chem. (1999) [Pubmed]
WikiGenes - Universities