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Total result(s) found: 30
  • ​Quantifying loss of information in network-based dimensionality reduction techniques
    H. Zenil, N. Kiani, J.Tegnér
    Journal of Complex Networks, Volume 4, Issue 3, Pages 342-362, 2016
Keywords:
Dimensionality reduction techniques; Graph motifs; Graph sparsification; Graph spectra; kolmogorov complexity
  • ​Network based drug repositioning methodology for neurodegenerative diseases
    M.-M. Shang, N. Kiani, J. Tegnér
    International Work Conference on Bioinformatics and Bioengineering, IWBBIO 2016
Keywords:
Biological Network analisys; Neurodegenerative disease; Drug repositioning; Flow cytometry; Statin
  • ​Systems Toxicology: systematic approach to predict toxicity
    N. Kiani, Ming-Mei Shang, J. Tegnér
    Curr Pharm Des., 22(46):6911-6917, 2016
Keywords:
Drug adverse effects; Network analysis; Predictive modeling; System pharmacology
  • ​TGF-β affects the differentiation of human GM-CSF+ CD4+ T cells in an activation- and sodium-dependent manner
    S. Éliás, A. Schmidt, V. Kannan, J. Andersson, J. Tegnér
    Frontiers in Immunology, 7:603, 2016
Keywords:
Autoimmune diseases; Differentiation; GM-CSF; Human CD4+ T cells; Multiple sclerosis; Multivariate analysis; Sodium; TGF-β
  • ​In viotro differentiation of human CD4+FOXP3+ induced regulatory T cells (iTregs) from Naïve CD4+ T cells using a TGF-β-containing protocol
    A. Schmidt, E. Szabolcs, R. Joshi, and J. Tegnér
    J Vis Exp (118). 2016
Keywords:
Immunology; Regulatory T cells; Treg, CD4+ T cells; Magnetic cell isolation; In vitro differentiation; Cytokines; FOXP3; TGF-β; IL-2; Intracellular Flow cytometry; qRT-PCR
  • ​A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference
    J. Tegnér, H. Zenil, N. Kiani, G. Ball, D. Gomez-Cabrero
    Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences: Volume 374, Issue 2080, Article number 20160144, 2016
Keywords:
Big data; Computational biology; Living systems; Model reduction; Modelling; Systems biology
  • ​Human cytomegalovirus may promote tumour progression by upregulating arginase-2
    X. Xu, H. Costa, G. Overbeek, S. Vasaikar, C. Pawan K. Patro, G. Shafi, S. Ananthaseshan, G. Tsipras, B. Davoudi, A.-A. Mohammad, H. Lam, K. Straat, J. Tegnér, J.C. Tong, K.T. Wong, C. Söderberg-Naucler, and K.-C. Yaiw
    Oncotarget, 7(30):47221-47231, 2016
Keywords:
Arginase; Cytomegalovirus; Glioblastoma; Treatment
  • ​Conditional disease development extracted from longitudinal health care cohort data using layered network construction
    V. Kannan, F. Swartz, I. Abugessaisa, N.A. Kiani, G. Silberberg, G. Tsipras, D. Gomez-Cabrero, K. Alexanderson, and J. Tegnér
    Scientific Reports 6, Article number: 26170, 2016
Keywords:
Layered network construction; Conditional disease; Health care data
  • ​Adaptive input data transformation for improved network reconstruction with information theoretic algorithms
    V. Kannan, and J. Tegnér
    Stat. Appl. Genet. Mol. Biol., 1;15(6):507-520, 2016
Keywords:
Algoithms; Mutual information; Numerical estimation
  • ​High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared novel markers for ACPA and ACPA-positive rheumatoid arthritis
    D. Gomez-Cabrero, M. Almgren, L.K. Sjöholm, A. Hensvold, R. Tryggvadottir, J. Kere, A. Scheynius, N. Acevedo, L. Reinius, M.A. Taub, C. Montano, M.J. Aryee, J.I. Feinberg, A.P. Feinberg, J. Tegnér, L. Klareskog, A.I. Catrina, and T.J. Ekström
    Genome Medicine, Volume 8, Issue 1, Article number 124, 2016
Keywords:
ACPA; Bioinformatics; DNA methylation; Epigenetics; Rheumatoid arthritis
  • ​From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration
    D. Gomez-Cabrero, J. Menche, C. Vargas, I. Cano, D. Maier, A.L. Barabási, J. Tegnér J. Roca
    BMC Bioinformatics 17 (15), 441, 2016
Keywords:
Associated mechanism; Chronic obstructive pulmonary disease; Disease initiations; Generative mechanism; Molecular mechanism
  • ​Comparative analysis of protocols to induce human CD4+Foxp3+regulatory T cells by combinations of IL-2, TGF-beta, retinoic acid, rapamycin and butyrate
    A. Schmidt, M. Eriksson, M.-M. Shang, H. Weyd, and J. Tegnér
    PLoS One, Volume 11, Issue 2, Article number e0148474, 2016
Keywords:
Animal experiment; CD4+ Foxp3+ regulatory T cell; Cell isolation; Comparative study; Controlled study
  • ​Methods of information theory and algorithmic complexity for network biology
    H. Zenil, N. Kiani, J. Tegnér
    Seminars of Developmental and Cell Biology March 51: 32-43, 2016
Keywords:
Algorithmic probability; Algorithmic randomness; Biological networks; Complex networks; Information theory; Kolmogorov complexity
  • Evaluating network inference methods in preserving the topology and complexity of reconstructed genetic networks
    N. Kiani, H. Zenil, J. Olczak, J. Tegnér
    Seminars of Developmental and Cell Biology March 51 :44-52, 2016
Keywords:
Network reverse engineering; Network reconstruction; Evaluation of networks; Information content; Shannon entropy; Algorithmic complexity
  • Bioinformatics mining and modeling methods for the identification of disease mechanisms in neurodegenerative disorders
    M. Hofmann-Apitius, G. Ball, S. Gebel, S. Bagewadi, B. de Bono, R. Schneider, M. Page, A. Tom Kodamullil, E. Younesi, C. Ebeling, J. Tegnér and L. Canard
    International journal of molecular science, 16(12) 29179-29206, 2016 
Keywords:
Bioinformatics; Data integration; Disease models; Genetics; Graphical models; Knowledge-based modeling; Mechanism-identification; Multiscale; Neurodegeneration
  • ​Health risk assessment and stratification in an integrated care scenario
    M. Moharra, E. Vela, I. Dueñas-Espín, S. Pauws, C. Bescos, I. Cano, J. Tegnér, at all.
    International Journal of Integrated Care, 16(6): A322, pp. 1-8, 2016
Keywords:
Case finding, Clinical decision making, Chronic care, Health risk assessment, Patient stratification
  • ​Human macrophages induce CD4 + Foxp3 + regulatory T cells via binding and re-release of TGF-β
    A. Schmidt, X.-M. Zhang, R.N. Joshi, S. Iqbal, C. Wahlund, S. Gabrielsson, R.A. Harris and J. Tegnér
    Immunology and Cell Biology 94, 747-762, 2016
Keywords:
Adoptive transfer; CD4+ T lymphocyte; Cell differentiation; Controlled study; Cytokine production
  • Inferring causal molecular networks: empirical assessment through a community-based effort
    S. Hill, et al.
    Nature Methods 13, 310–318, 2016
Keywords:
Algorithms; Causality; Computational Biology; Computer Simulation; Gene Expression Profiling; Gene Regulatory Networks; Humans
  • Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR
    F. Marabita, P. de Candia, A. Torri, J. Tegnér, S. Abrignani, R.L. Rossi
    Briefings Bioinformatics, 204-212, 2016
Keywords:
Normfinder; Circulating miRNA; GeNorm; Normalization; qPCR; Reference genes
  • ​Optimization in biology parameter estimation and the associated optimization problem
    G. Cedersund, O. Samuelsson, G. Ball, J. Tegnér, D. Gomez-Cabrero
    Book chapter in Uncertainty in Biology, Volume 17 of the series Studies in Mechanobiology, Tissue Engineering and Biomaterials pp 177-197, 2016
Keywords:
Parameter estimation; Optimization; Heuristic; Fitness function
  • Computational modeling under uncertainty: challenges and opportunities
    D. Gomez-Cabrero, J. Tegnér, L. Geris
    Book chapter in Uncertainty in Biology, Volume 17 of the series Studies in Mechanobiology, Tissue Engineering and Biomaterials pp 467-476, 2016
Keywords:
Computational modeling; Uncertainty; Challenges; HPC; Hypothesis generation
  • Neuroswarm: a methodology to explore the constraints that function imposes on simulation parameters in large-scale networks of biological neurons
    D. Gomez-Cabrero, S. Ardid, M. Cano-Colino, J. Tegnér, A. Compte
    Book chapter in Uncertainty in Biology, Volume 17 of the series Studies in Mechanobiology, Tissue Engineering and Biomaterials pp 427-447, 2016
Keywords:
Prefrontal cortex; Workflow; Ensemble analysis; Working memory model; Neuroscience; Computational biology
  • Modeling and model simplification to facilitate biological insights and predictions
    O. Eriksson, J. Tegnér
    Book chapter in Uncertainty in Biology, Volume 17 of the series Studies in Mechanobiology, Tissue Engineering and Biomaterials pp 301-325, 2016
Keywords:
Model simplificaton; Model reduction; Data integration; Dynamical models; Ordinary differential equations; Piecewise linear; Dynamical modules
  • ​Probabilistic computational causal discovery for systems biology
    V. Lagani, S. Triantafillou, G. Ball, J. Tegnér, I. Tsamardinos
    Book chapter in Uncertainty in Biology, Volume 17 of the series Studies in Mechanobiology, Tissue Engineering and Biomaterials pp 33-73, 2016
Keywords:
Causality; Causal graphical models; Bayesian networks; Systems biology; Biological networks
  • Systems understanding to personalized medicine - lessons and recommendations based on a multi-disciplinary and translational analysis of COPD
    J. Roca, D. Gomez-Cabrero, J. Tegnér
    Systems Biology for Medicine, Springer series "Methods in Molecular Biology"- 283-303, 2016
Keywords:
Clinical decision support; Integrated care; Comorbidity; Disease modeling; Knowledge management
  • ​Proposals for enhanced health risk assessment and stratification in an integrated care scenario
    I. Dueñas-Espín, E. Vela, S. Pauws, C. Bescos, I. Cano, M. Cleries, J.C. Contel, E. de Manuel Keenoy, J. Garcia-Aymerich, D. Gomez-Cabrero, R. Kaye, M.M.H. Lahr, M. Lluch-Ariet, M. Moharra, D. Monterde, J. Mora, M. Nalin, A. Pavlickova, J. Piera, S. Ponce, S. Santaeugenia, H. Schonenberg, S. Störk, J. Tegnér, F. Velickovski, C. Westerteicher, J. Roca
    BMJ Open, Volume 6, Issue 4, 2016
Keywords:
Human experiment; Information processing; Morbidity; Population model; Prediction; Risk assessment; Scotland; Stratification; Telehealth
  • ​Human regulatory T cells rapidly rewire the phosphoproteome of suppressed conventional T cells
    R.N. Joshi, N. Binai, F. Marabita, J. Tegnér, A. Schmidt
    Scandinavian Journal of Immunology 83 (5), 376-377, 2016
Keywords:
Regulatory T cells; Phosphoproteome; Conventional T cells
  • Integrative molecular profiling during human induced regulatory T cell (itreg) generation reveals novel regulators of Foxp3
    A. Schmidt, F. Marabita, H. Johansson, J. Lehtiö, M. Eriksson, S. Éliás, D. Gomez-Cabrero, A. Rao, J. Tegnér
    Scandinavian Journal of Immunology 83 (5), 353, 2016
Keywords:
Molecular profiling, human induced regulatory T cell (itreg)
  • Characterization and mechanistic dissection of the differentiation of Gm-csf+ Cd4+ T cells
    S. Éliás, A. Schmidt, V. Kannan, J. Andersson, J. Tegnér
    Scandinavian Journal of Immunology 83 (5), 354-355, 2016
Keywords:
Gm-csf+ Cd4+ T cells
  • Topological evaluation of methods for reconstruction of genetic regulatory networks
    J. Olczak, N. Kiani, H. Zenil, J. Tegnér
    Proceedings - 11th International Conference on Signal-Image Technology and Internet-Based Systems, SITIS 2015, Article number 7400604, Pages 468-473, 2016
Keywords:
Evaluating measure; Inference methods evaluation; Network reconstruction; Topological properties