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1.	Lorenzini, T, et al. (author) Characterization of the Clinical and Immunological Phenotype and Management of 157 Individuals with 56 Distinct Heterozygous NFKB1 Mutations 2020 In: JOURNAL OF CLINICAL IMMUNOLOGY. - : Elsevier BV. - 0271-9142. ; 146:4, s. 901-911 Conference paper (other academic/artistic)
2.	Klammer, Martin, et al. (author) MetaTM - a consensus method for transmembrane protein topology prediction 2009 In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 10, s. 314- Journal article (peer-reviewed)abstract Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of the amino acid sequence are buried in the membrane and which are located on either side of the membrane), but only a few topologies are known. Consequently, various computational TM topology predictors have been developed, but their accuracies are far from perfect. The prediction quality can be improved by applying a consensus approach, which combines results of several predictors to yield a more reliable result. RESULTS: A novel TM consensus method, named MetaTM, is proposed in this work. MetaTM is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide predictors. On a large data set comprising 1460 sequences of TM proteins with known topologies and 2362 globular protein sequences it correctly predicts 86.7% of all topologies. CONCLUSION: Combining several TM predictors in a consensus prediction framework improves overall accuracy compared to any of the individual methods. Our proposed SVM-based system also has higher accuracy than a previous consensus predictor. MetaTM is made available both as downloadable source code and as DAS server at http://MetaTM.sbc.su.se.

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Type of publication: conference paper (1); journal article (1)

Type of content: other academic/artistic (1); peer-reviewed (1)

Author/Editor: Christiansen, M (1); Abolhassani, H (1); Hammarstrom, L (1); Fischer, U (1); Sonnhammer, Erik L L (1); Aghamohammadi, A (1); show more...; Shcherbina, A (1); Lougaris, V (1); Plebani, A (1); Chou, J (1); Cunningham-Rundles, ... (1); Burns, SO (1); Schroder, C. (1); Klein, C. (1); de Vries, E (1); Roifman, CM (1); Allende, LM (1); Schmitt, Thomas (1); Boztug, K (1); Niehues, T (1); Ameratunga, R (1); Cook, M. (1); Rae, W (1); Bakhtiar, S (1); Stepensky, P (1); Shadur, B (1); Varjosalo, M (1); Baris, S (1); Messina, David N. (1); Ip, W. (1); Gonzalez-Granado, LI (1); Proietti, M (1); Warnatz, K (1); Grimbacher, B (1); Frede, N (1); Kobbe, R (1); Seidl, M (1); Van der Meer, JWM (1); Fliegauf, M (1); Kinnunen, M (1); Camacho-Ordonez, N (1); Alsina, L (1); Atschekzei, F (1); Freeman, AF (1); Kuismin, O (1); Deya-Martinez, A (1); Kuijpers, TW (1); Schmidt, RE (1); Holzinger, D (1); Seppanen, MRJ (1); show less...

University: Stockholm University (1); Karolinska Institutet (1)

Language: English (2)

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