​Quantifying loss of information in network-based dimensionality reduction techniques

Authors: H. Zenil, N. Kiani, J. Tegnér
Dimensionality reduction techniques Graph motifs Graph sparsification Graph spectra Kolmogorov complexity

Network based drug repositioning methodology for neurodegenerative diseases

Authors: M.-M. Shang, N. Kiani, J. Tegnér
Biological Network analisys Neurodegenerative disease Drug repositioning Flow cytometry Statin

Systems Toxicology: systematic approach to predict toxicity

Authors: N. Kiani, Ming-Mei Shang, J. Tegnér
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

Authors: S. Éliás, A. Schmidt, V. Kannan, J. Andersson, J. Tegnér
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

Authors: A. Schmidt, E. Szabolcs, R. Joshi, J. Tegnér
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

Authors: J. Tegnér, H. Zenil, N. Kiani, G. Ball, D. Gomez-Cabrero
Big data Computational Biology Living systems Model reduction Modelling Systems biology

Human cytomegalovirus may promote tumour progression by upregulating arginase-2

Authors: 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, K.-C. Yaiw
Arginase Cytomegalovirus Glioblastoma Treatment

Conditional disease development extracted from longitudinal health care cohort data using layered network construction

Authors: V. Kannan, F. Swartz, I. Abugessaisa, N.A. Kiani, G. Silberberg, G. Tsipras, D. Gomez-Cabrero, K. Alexanderson, J. Tegnér
Layered network construction Conditional disease Health care data

Adaptive input data transformation for improved network reconstruction with information theoretic algorithms

Authors: V. Kannan, J. Tegnér
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

Authors: 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, T.J. Ekström
ACPA Bioinformatics DNA methylation Epigenetics Rheumatoid arthritis

From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration

Authors: D. Gomez-Cabrero, J. Menche, C. Vargas, I. Cano, D. Maier, A.L. Barabási, J. Tegnér J. Roca
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

Authors: A. Schmidt, M. Eriksson, M.-M. Shang, H. Weyd, J. Tegnér
Animal experiment CD4+ Foxp3+ regulatory T cell Cell isolation Comparative study Controlled study

Methods of information theory and algorithmic complexity for network biology

Authors: H. Zenil, N. Kiani, J. Tegnér
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

Authors: N. Kiani, H. Zenil, J. Olczak, J. Tegnér
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

Authors: 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, L. Canard
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

Authors: M. Moharra, E. Vela, I. Dueñas-Espín, S. Pauws, C. Bescos, I. Cano, J. Tegnér, L. Kular Et Al.
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

Year:2016 ISSN:DOI: 10.1038/icb.2016.34
Authors: A. Schmidt, X.-M. Zhang, R.N. Joshi, S. Iqbal, C. Wahlund, S. Gabrielsson, R.A. Harris, J. Tegnér
Adoptive transfer CD4+ T lymphocyte Cell differentiation Controlled study Cytokine production

Inferring causal molecular networks: empirical assessment through a community-based effort

Authors: S. Hill, L. Kular Et Al.
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

Authors: F. Marabita, P. de Candia, A. Torri, J. Tegnér, S. Abrignani, R.L. Rossi
Normfinder Circulating miRNA GeNorm Normalization qPCR Reference genes

Optimization in biology parameter estimation and the associated optimization problem

Authors: G. Cedersund, O. Samuelsson, G. Ball, J. Tegnér, D. Gomez-Cabrero
Parameter estimation Optimization Heuristic Fitness function

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