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ComplexDis publications

  1. WANG, H., BARRENÄS, F., BRUHN, S., MOBINI, R. & BENSON, M. 2009. Increased IFN-gamma activity in seasonal allergic rhinitis is decreased by corticosteroid treatment. The Journal of Allergy and Clinical Immunology, 124, 1360-1362 %U www.ncbi.nlm.nih.gov/pubmed/19910031.
  2. BAKER, E. J., JAY, J. J., PHILIP, V. M., ZHANG, Y., LI, Z., KIROVA, R., LANGSTON, M. A. & CHESLER, E. J. 2009. Ontological Discovery Environment: a system for integrating gene-phenotype associations. Genomics, 94, 377-87.
  3. BARRENAS, F., ANDERSSON, B., CARDELL, L. O., LANGSTON, M., MOBINI, R., PERKINS, A., SOINI, J., STAHL, A. & BENSON, M. 2008. Gender differences in inflammatory proteins and pathways in seasonal allergic rhinitis. Cytokine, 42, 325-9.
  4. BARRENAS, F., CHAVALI, S., HOLME, P., MOBINI, R. & BENSON, M. 2009. Network Properties of Complex Human Disease Genes Identified through Genome-Wide Association Studies. PLoS ONE, 4, e8090 %U dx.doi.org/10.1371/journal.pone.0008090.
  5. BARRENAS F, B. S., WANG H, BENSON M. Interactomal susceptibility regions to prioritize complex disease genes (submitted).
  6. BENSON, M., CARDELL, L. O., HOHMANN, S., JIRSTRAND, M., LANGSTON, M., MOBINI, R. & NERMAN, O. 2007. [Systems biology can radically change health care. Basis for individualized prediction, prevention and treatment]. Läkartidningen, 104, 3037-3041 %U www.ncbi.nlm.nih.gov/pubmed/17985710.
  7. BENSON, M., FRANSSON, M., MARTINSSON, T., NALUAI, A. T., UDDMAN, R. & CARDELL, L. O. 2007. Inverse relation between nasal fluid Clara Cell Protein 16 levels and symptoms and signs of rhinitis in allergen-challenged patients with intermittent allergic rhinitis. Allergy, 62, 178-183 %U www.ncbi.nlm.nih.gov/pubmed/17298427.
  8. BENSON, M., MOBINI, R., BARRENÄS, F., HALLDÉN, C., NALUAI, A. T., SÄLL, T. & CARDELL, L. O. 2009. A haplotype in the inducible T-cell tyrosine kinase is a risk factor for seasonal allergic rhinitis. Allergy, 64, 1286-1291 %U www.ncbi.nlm.nih.gov/pubmed/19222422.
  9. BENSON, M., STEENHOFF HOV, D. A., CLANCY, T., HOVIG, E., RUDEMO, M. & CARDELL, L. O. 2007. Connectivity can be used to identify key genes in DNA microarray data: a study based on gene expression in nasal polyps before and after treatment with glucocorticoids. Acta Oto-Laryngologica, 127, 1074-1079 %U www.ncbi.nlm.nih.gov/pubmed/17851899.
  10. BEULE, J. D. 2007. Compositionality, Hierarchy and Recursion in Language: a Case Study in Fluid Construction Grammar. Doctoral Dissertation, Vrije Universiteit.
  11. BOGEFORS, J., RYDBERG, C., UDDMAN, R., FRANSSON, M., MÅNSSON, A., BENSON, M., ADNER, M. & CARDELL, L. O. 2010. Nod1, Nod2 and Nalp3 receptors, new potential targets in treatment of allergic rhinitis? %U www.ncbi.nlm.nih.gov/pubmed/20384614. Allergy.
  12. BORATE, B., CHESLER, E., LANGSTON, M., SAXTON, A. & VOY, B. 2009. Comparison of threshold selection methods for microarray gene co-expression matrices. BMC Research Notes, 2, 240 %U www.biomedcentral.com/1756-0500/2/240.
  13. BRYBORN M, F. M., BENSON M, UDDMAN R, VIRTALA R, BROBERG P, JANSSON L, ADNER M, RIESBECK K, CARDELL LO. 2010. S100A7, a novel protein in allergic rhinitis. Resp Res.
  14. CHAVALI S, B. A., BENSON M Complex disease genes mainly encode proteins that interact with the environment (in manuscript).
  15. CHAVALI S, B. F., KANDURI K, BENSON M 2010. Topology in Protein Interaction Network and Tissue Specificity of Shared and Specific Human Disease Genes. BMC Systems Biology, in press.
  16. CLERMONT, G., AUFFRAY, C., MOREAU, Y., ROCKE, D. M., DALEVI, D., DUBHASHI, D., MARSHALL, D. R., RAASCH, P., DEHNE, F., PROVERO, P., TEGNER, J., ARONOW, B. J., LANGSTON, M. A. & BENSON, M. 2009. Bridging the gap between systems biology and medicine. Genome Medicine, 1, 88 %U www.ncbi.nlm.nih.gov/pubmed/19754960.
  17. DE BEULE J, H. E., Hovig E, BENSON M 2010. Introducing dynamics into the field of Biosemiotics. Biosemiotics, cond accepted
  18. DELL'ACQUA, G. & CASTIGLIONE, F. 2009. Stability and phase transitions in a mathematical model of Duchenne muscular dystrophy. J Theor Biol, 260, 283-9.
  19. EBLEN JD, J. J., ZHANG Y, BENSON M, PERKINS AD, SAXTON AM, VOY BH, CHESLER EJ, LANGSTON M Systematic Comparisons of Biological Data Clustering Algorithms (in manuscript).
  20. F. CASTIGLIONE, D. S., N. RAPIN, M. BERNASCHI CTLs’ repertoire shaping in the thymus: a Montecarlo simulation (submitted to Autoimmunity).
  21. F. CASTIGLIONE, D. S. A. M. P. 2010. Implementing agent’s rules with gene regulatory networks in mesoscopic-level models of cellular interactions. A practical guide to bioinformatics analysis. iConcept Press
  22. FRANSSON, M., BENSON, M., ERJEFÄLT, J. S., JANSSON, L., UDDMAN, R., BJÖRNSSON, S., CARDELL, L.-O. & ADNER, M. 2007. Expression of Toll-like receptor 9 in nose, peripheral blood and bone marrow during symptomatic allergic rhinitis. Respiratory Research, 8, 17 %U www.ncbi.nlm.nih.gov/pubmed/17328813.
  23. GONI, J., ESTEBAN, F. J., DE MENDIZABAL, N. V., SEPULCRE, J., ARDANZA-TREVIJANO, S., AGIRREZABAL, I. & VILLOSLADA, P. 2008. A computational analysis of protein-protein interaction networks in neurodegenerative diseases. BMC Syst Biol, 2, 52.
  24. GOÑI J, A. G., SEPULCRE J, MARTINCORENA I, VELEZ DE MENDIZABAL N, BEJARANO B, ARDANZA-TREVIJANO S, PERAITA H, WALL DP, VILLOSLADA P Topology, semantic modularity and search in lexical networks: evidences from verbal fluency tasks (under review).
  25. GOÑI J, C.-M. B., SOLE R AND RODRIGUEZ-CASO C Exploring the randomness of directed acyclic networks. (Submitted in Physical Rev E).
  26. GOÑI J, C.-M. B., VELEZ N, ARRONDO G, SOLE RV, VILLOSLADA P Evolution of conceptual networks during the acquisition of semantic categories. (Under review).
  27. GOÑI J, R.-C. C., SOLÉ RV, VILLOSLADA P, MUNTEANU A. Year. Goals and pitfalls of the gene network inference methods: A comparative study from virtual microarrays and network dynamics. In: Modeling and Computation on Complex Networks and related topics, June 9-11 2008 Pamplona, Spain.
  28. GUILLOT, G., OLSSON, M., BENSON, M. & RUDEMO, M. 2007. Discrimination and scoring using small sets of genes for two-sample microarray data. Mathematical Biosciences, 205, 195-203 %U www.ncbi.nlm.nih.gov/pubmed/17087979.
  29. LAJOS A.RÉTHY, E. K., ZSOLT BELLA,MÁRIA KISS,EDINA GARACZI, MIKAEL BENSON, LAJOS KEMÉNY Old molecules as new markers for poor response to local steroid treatment in ragweed-induced allergic rhinitis? (in manuscript).
  30. M. PEDICINI, F. B., BARRENAS F, T. CLANCY, F. CASTIGLIONE, E. HOVIG, K. KANDURI, D. SANTONI, M. BENSON Combined network modeling and gene expression microarray analysis to model the dynamics of Th1 and Th2 cell regulation (Plos Comp Biol, under revision).
  31. MÅNSSON, A., FRANSSON, M., ADNER, M., BENSON, M., UDDMAN, R., BJÖRNSSON, S. & CARDELL, L.-O. 2010. TLR3 in human eosinophils: functional effects and decreased expression during allergic rhinitis. International Archives of Allergy and Immunology, 151, 118-128 %U www.ncbi.nlm.nih.gov/pubmed/19752565.
  32. MOBINI, R., ANDERSSON, B., ERJEFALT, J., HAHN-ZORIC, M., LANGSTON, M., PERKINS, A., CARDELL, L. & BENSON, M. 2009. A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation. BMC Systems Biology, 3, 19 %U www.biomedcentral.com/1752-0509/3/19.
  33. MOBINI R, B. F., CHAVALI S, ANDERSSON B, EGAN BS, HOVIG E, LANGSTON M, PERKINS A, BENSON M Combined ChIP-chip and gene expression analysis shows that ETS1 has a key role for Th2 cell differentiation and effector mechanisms. (in manuscript).
  34. WANG H, MOBINI R, M. A., BARRENAS F, BRUHN S, BENSON M. 2010 Combined proteomics and gene expression microarrays to identify nasal fluid protein markers for respose to treatment with corticosteroids in seasonal allergic rhinitis. Allergy (in press).
  35. MONTAÑEZ, R., MEDINA, M. A., SOLÉ, R. V. & RODRÍGUEZ-CASO, C. 2010. When metabolism meets topology: Reconciling metabolite and reaction networks. BioEssays, 32, 246-256 %U dx.doi.org/10.1002/bies.200900145.
  36. N, R.-C. C. A. C.-P. 2008. Topological analysis of cellular networks. In: V, K. (ed.) Data Mining in Medical and Biological Research. Austria: I-Tech Education and Publishing.
  37. P, I. J. V. Modeling the immune system as an asymmetric probabilistic adaptive system (Manuscript in Preparation).
  38. PALACIOS, R., GONI, J., MARTINEZ-FORERO, I., IRANZO, J., SEPULCRE, J., MELERO, I. & VILLOSLADA, P. A Network Analysis of the Human T-Cell Activation Gene Network Identifies Jagged1 as a Therapeutic Target for Autoimmune Diseases. PLoS ONE, 2.
  39. PAPPALARDO, F., PENNISI, M., CASTIGLIONE, F. & MOTTA, S. 2010. Vaccine protocols optimization: in silico experiences. Biotechnol Adv, 28, 82-93.
  40. PERKINS, A. 2008. Addressing Challenges in a Graph-Based Analysis of High-Throughput Biological Data %U trace.tennessee.edu/utk_graddiss/584. Doctoral Dissertations.
  41. PERKINS, A. & LANGSTON, M. 2009. Threshold selection in gene co-expression networks using spectral graph theory techniques. BMC Bioinformatics, 10, S4 %U www.biomedcentral.com/1471-2105/10/S11/S4.
  42. RODRIGUEZ-CASO, C., COROMINAS-MURTRA, B. & SOLE, R. V. 2009. On the basic computational structure of gene regulatory networks. Mol Biosyst, 5, 1617-29.
  43. RODRIGUEZ-CASO C, C.-M. B., SOLÉ RV Dynamical hierarchy and Modularity in Gene regulatory networks (Manuscript submitted).
  44. RODRIGUEZ-CASO C, V. S. A. C.-P. N. K-scaffold subgraph: a measure to uncover the backbone of biological networks (Manuscript in preparation).
  46. SANTONI, D., PEDICINI, M. & CASTIGLIONE, F. 2008. Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions. Bioinformatics, 24, 1374-80.
  47. TEGNER, J. N., COMPTE, A., AUFFRAY, C., AN, G., CEDERSUND, G., CLERMONT, G., GUTKIN, B., OLTVAI, Z. N., STEPHAN, K. E., THOMAS, R. & VILLOSLADA, P. 2009. Computational disease modeling - fact or fiction? BMC Syst Biol, 3, 56.
  48. UDDMAN R, T. J., ADNER M, BENSON M, MALM L, CARDELL LO. Peroxisome proliferator–activated receptor gamma (PPARg) expression in cranial ganglia during culture induced inflammation (in manuscript).
  49. VANDENBROECK, K., COMABELLA, M., TOLOSA, E., GOERTSCHES, R., BRASSAT, D., HINTZEN, R., INFANTE-DUARTE, C., FAVOROV, A., ESCORZA, S., PALACIOS, R., OKSENBERG, J. R. & VILLOSLADA, P. 2009. United Europeans for development of pharmacogenomics in multiple sclerosis network. Pharmacogenomics, 10, 885-894 %U www.ncbi.nlm.nih.gov/pubmed/19450134.
  50. VÉLEZ DE MENDIZÁBAL N, B. J., GOÑI J, MARTINEZ-FORERO I, MARTINEZ-PASAMAR S, SEPULCRE J, TORREALDEA J, VILLOSLADA P The relapsing dynamics of autoimmune diseases depends on control properties of peripheral immune tolerance. (Under review).
  51. VILLOSLADA, P., STEINMAN, L. & BARANZINI, S. E. 2009. Systems biology and its application to the understanding of neurological diseases. Ann Neurol, 65, 124-39.
  52. WANG H, B. F., MOBINI M, XIANG Z, BENSON M 2010. Increased IL-17RB activity in allergen-challenged PBMC from patients with seasonal allergic rhinitis regulates both Th2 cells and basophils. Clinical and Experimental Allergy, in press.


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