2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

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

Year:2016

Authors: G. Cedersund, O. Samuelsson, G. Ball, J. Tegnér, D. Gomez-Cabrero

Parameter estimation Optimization Heuristic Fitness function

Quantifying loss of information in network-based dimensionality reduction techniques

Network based drug repositioning methodology for neurodegenerative diseases

Systems Toxicology: systematic approach to predict toxicity

TGF-β affects the differentiation of human GM-CSF+ CD4+ T cells in an activation- and sodium-dependent manner

In viotro differentiation of human CD4+FOXP3+ induced regulatory T cells (iTregs) from Naïve CD4+ T cells using a TGF-β-containing protocol

A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

Human cytomegalovirus may promote tumour progression by upregulating arginase-2

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

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

High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared novel markers for ACPA and ACPA-positive rheumatoid arthritis

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

Comparative analysis of protocols to induce human CD4+Foxp3+regulatory T cells by combinations of IL-2, TGF-beta, retinoic acid, rapamycin and butyrate

Methods of information theory and algorithmic complexity for network biology

Evaluating network inference methods in preserving the topology and complexity of reconstructed genetic networks

Bioinformatics mining and modeling methods for the identification of disease mechanisms in neurodegenerative disorders

Health risk assessment and stratification in an integrated care scenario

Human macrophages induce CD4 + Foxp3 + regulatory T cells via binding and re-release of TGF-β

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

Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR

Optimization in biology parameter estimation and the associated optimization problem

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