Gene regulatory network of human GM-CSF secreting T helper cells

Authors: S. Elias, A. Schmidt, D. Gomez-Cabrero, J. Tegner
T helper cells Gene regulatory network

STATegra: a comprehensive multi-omics dataset of B-cell differentiation in mouse

Authors: D. Gomez-Cabreroc, S. Tarazona, I. Ferreirós-Vidal, R. Ramirez, A. Schmidt, T. Reijmers, (...), J. Tegner, A. Conesa
Mouse Chromatin structure

On the prediction of protein abundance from RNA

Authors: R. Magnusson, O. Rundquist, M. Kim, S. Hellberg, C. Na, M. Benson, D. Gomez-Cabrero, I. Kochum, J. Tegner, at al.
Protein abundance RNA Complex diseases

Deriving Disease Modules from the Compressed Transcriptional Space Embedded in a Deep Auto-encoder

Authors: S. Dwivedi, A. Tjarnberg, J. Tegner, M. Gustafsson
Disease modules Deep Auto-encoder Disease-related genes

TcellSubC: an atlas of the subcellular proteome of human T cells

Authors: R. Joshi, C. Stadler, R. Lehmann, J. Lehtiö, J. Tegner, A. Schmidt, M. Vesterlund
TcellSubC Subcellular Proteome Human T cells

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Authors: M. Menden, D. Wang, M. Mason, B. Sjalai, AstraZeneca-Sanger Drug Combination DREAM Consortium, at al.
Cancer research Drug antagonism Pharmacogenomic screen

Associations of Plasma 3-Methylhistidine with Frailty Status in French Cohorts of the FRAILOMIC Initiative

Authors: B. Kochlik, W. Stuetz, K. Peres, C. Feart, J. Tegner, L. Rodriguez-Manãs, T. Grune, D. Weber
Frailty Aging Methylhistidine Biomarkers Muscle protein turnover

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients

Authors: S. Fernandes, H. Morikawa, E. Ewing, S. Ruhrmann, R. Joshi, V. Lagani, N. Karathanasis, M. Khademi, N. Planell, A. Schmidt, I. Tsamardinos, T. Olsson, F. Piehl, I. Kochum, M. Jagodic, J. Tegner, D. Gomez-Cabrero
T cells Multiple sclerosis RNA-seq

Exhaustion of CD4+ T-cells mediated by the Kynurenine Pathway in Melanoma

Authors: S.R. Pour, H. Morikawa, N. Kiani, M. Yang, A. Azimi, G. Shafi, M. Shang, R. Baumgartner, D. Ketelhuth, M. Kamleh, C.E. Weelock, A. Lundqvist, J. Hansson, J. Tegner
CD4+ T cells Melanoma Kynurenine Pathway

DNA methylation changes in brains from multiple sclerosis patients

Authors: L. Kular, M. Needhamsen, M. Zeitelhofer-Adzemovich, T. Kramarova, D. Gomez-Cabrero, E. Ewing, E. Picket, J. Tegner, S. Beck, F. Piehl, L. Brundin, M. Jagodic
DNA methylation Multiple sclerosis

Paired ATAC Seq and RNA Seq in blood derived CD4, CD8, CD14 and CD19 cells of MS patients and healthy controls

Authors: S.J. Fernandes, M. Eriksson, M.Khademi, T. Olsson, D. Gomez-Cabrero, I. Kockum, J. Tegner
Multiple sclerosis Immune cells ATAC Seq RNA sequencing (RNA-Seq) DNA methylation Omics integration

Algorithmic probability-guided supervised Machine Learning on non-differentiable spaces

Authors: S. Hernández-Orozco, H. Zenil, J. Riendel, A. Uccello, N. Kiani, J. Tegner

Challenges in the multivariate analysis of mass cytometry data: the effect of randomization

Authors: G. Papoutsoglou, V. Lagani, A. Schmidt, K. Tsirlis, D. Gomez-Cabrero, J. Tegner, I. Tsamardinos
Mass cytometry Pre‐processing High dimensional Data analysis Randomization Clustering algorithms

Neuronal methylation reveals CREB-asociated neuro-axonal impairment in Multiple Sclerosis

Authors: L. Kular Et Al.
Multiple sclerosis Neurons DNA methylation DNA hydroxymethylation Axonal guidance Synaptic plasticity CREB Neurodegeneration

The thermodynamics of network coding, and an algorithmic refinement of the principle of maximum entropy

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Second law of thermodynamics Reprogrammability Algorithmic complexity Generative mechanisms Deterministic systems Algorithmic randomness

Algorithmic information dynamics of emergent, persistent, and colliding particles in the game of life

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Kolmogorov-Chaitin complexity Cellular automata Algo-rithmic probability Algorithmic Coding Theorem Turing machines

Causal deconvolution by algorithmic generative models

Authors: H. Zenil, N. Kiani, A.A. Zea, J. Tegnér
Algorithmic generative models Algorithmic probability Algorithmic framework

Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression

Authors: E. Ewing, L. Kular, S.J. Fernandes, N. Karathanasis, V. Lagani, S. Ruhrmann, I. Tsamardinos, J. Tegner, F. Piehl, D. Gomez-Cabrero, M. Jagodic
450 K DNA methylation EPIC Epigenetics Immune cells Multiple sclerosis

Feedforward regulation of Myc coordinates lineage-speciifc with housekeeping gene expression during B cell progenitor cell differentiation

Authors: I. Ferreirós-Vidal, T. Carroll, (...) J. Tegner*, M. Merkenschlager*, D. Gomez-Cabrero
Cell differentiation B cells Gene expression Gene regulation Transcription factors Cell metabolism

Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg‐mediated suppression of cytokine expression

Authors: R.N. Joshi, S.J. Fernandes, M.-M. Shang, N.A. Kiani, D. Gomez‐Cabrero, J. Tegnér, A. Schmidt
CD4 T cell T cell resistance Immune suppression Immunotherapy Phosphatase Regulatory T cell

MAPK pathways and B cells overactivation in multiple sclerosis revealed by phospoproteomics and genomic analysis

Authors: E. Kotelnikova, N.A. Kiani, (...), J. Tegner, P. Villoslada
Multiple sclerosis Phosphoproteomics Signaling pathways B cells Autoimmunity

Estimations of integrated information based on algorithmic complexity and dynamic querying

Authors: A. Hernández-Espinosa, H. Zenil, N.A. Kiani, J. Tegnér
Integrated information Algorithmic complexity Algorithmicinformation theory Algorithmic randomness

An algorithmic information calculus for causal discovery and reprogramming systems

Authors: H. Zenil, N.A. Kiani, F. Marabita, Y. Deng, S. Elias, A. Schmidt, G. Ball, J. Tegnér
Reprogramming systems

Controllability, multiplexing, and transfer learning in networks using evolutionary learning

Authors: R. Ooi, C.-H. Huck Yang, P.-Y. Chen, V. Eguiluz, N. Kiani, H. Zenil, D. Gomez-Cabrero, J. Tegner
Controllability Multiplexing Evolutionary learning

Synthesizing new retinal symptom images by multiple generative models

Authors: Y.-C. Liu, H.-H. Yang, C.-H. Huck Yang, J.-H. Huang, M. Tian, H. Morikawa, J. Tegner
Age-Related Macular Degeneration (AMD) Machine learning Generative Adversarial Networks (GANs)

Auto-classification of retinal diseases in the limit of sparse data using a two-streams machine learning model

Authors: C.-H. Huck Yang, F. Liu, J.-H. Huang, M. Tian, H. Morikawa, I-H. Lin M.D., Y.C. Liu, H.-H. Yang, J. Tegner
Machine learning Retinal deseases Vascular disorders Auto classification Support vector machine Deep neural networks

A novel hybrid machine learning model for auto-classification of retinal diseases

Authors: C.-H. H. Yang, J.-H. Huang, F. Liu, F.-Y. Chiu, M. Gao, W. Lyu, J. Tegner, L. Kular Et Al.
Machine learning Retinal deseases Auto classification Support vector machine Deep neural networks

Learning functions in large networks requires modularity and produces multi-agent dynamics

Authors: C.H.H. Yang, R. Ooi, T. Hiscock, V. Eguiluz, J. Tegner
Large networks Multi-agent dynamics biological systems Machine learning

DNA methylation as a mediator of HLA-DRB1* 15: 01 and a protective variant in multiple sclerosis

Authors: L. Kular, Y. Liu, S. Ruhrmann, G. Zheleznyakova, F. Marabita, D. Gomez-Cabrero, T. James, E. Ewing, (...), Jesper Tegnér, L. Kular Et Al.
HLA DRB1 antigen DNA Methylation In vitro study Multiple sclerosis

An algorithmic refinement of maxent induces a thermodynamic-like behaviour in the reprogrammability of generative mechanisms

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Second law of thermodynamics Reprogrammability Algorith- mic complexity Generative mechanisms

Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using linked self-organizing maps

Authors: C. Jansen, R. Ramirez, N. El-Ali, D. Gomez-Cabrero, J. Tegner, M. Merkenschlager, A. Conesa, A. Mortazavi
Single-cell Gene Regulatory Networks Self-organizing maps RNA-seq

A decomposition method for global evaluation of shannon entropy and local estimations of algorithmic complexity

Authors: Zenil, Hernández-Orozco, Kiani, Soler-Toscano, Rueda-Toicen, Tegner
Algorithmic probability Algorithmic randomness Information content Information theory Kolmogorov-Chaitin complexity Shannon Entropy Thue-Morse sequence

Symmetry and correspondence of algorithmic complexity over geometric, spatial and topological representations

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Algorithmic Coding Theorem Algorithmic probability Information content Kolmogorov-Chaitin complexity Molecular complexity Polyhedral networks Polyominoes Polytopes Recursive transformation Shannon Entropy Symmetry breaking Turing machines

A review of graph and network complexity from an algorithmic information perspective

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Algorithmic information theory Algorithmic probability Algorithmic randomness Biological networks Complex networks Kolmogorov-Chaitin complexity

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

Authors: A. Schmidt, F. Marabita, N.A. Kiani, C.C. Gross, (...), H. Wiendl, R. Lahesmaa, J. Tegnér
Regulatory T cells Treg iTreg FOXP3 T cell differentiation RNA sequencing (RNA-Seq) Data integration TGF-β

Overexpression of endothelin B receptor in glioblastoma: a prognostic marker and therapeutic target?

Authors: S. Vasaikar, G. Tsipras, N. Landázuri, H. Costa, (...), J. Tegner, K.-C. Yaiw, C. Söderberg-Naucler
Glioblastoma Endothelin B receptor Endothelin receptor antagonists

Algorithmic complexity and reprogrammability of chemical structure networks

Authors: H. Zenil, N.A. Kiani, M.M. Shang, J. Tegnér
Algorithmic information theory Algorithmic probability Causal path Causality Chemical compound complexity Information signature Kolmogorov-Chaitin complexity Molecular complexity Shannon Entropy

Symmetry and algorithmic complexity of polyominoes and polyhedral graphs

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Algorithmic symmetry Geometric symmetry Kolmogorov-Chaitin complexity

Ab initio algorithmic causal deconvolution of intertwined programs and networks by generative mechanism

Authors: H. Zenil, N.A. Kiani, J. Tegner
Complex data Algorithmic probability

Unsupervised and universal data reduction and network sparsification methods by minimal algorithmic information loss

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Data reduction Network sparsification Algorithmic information theory

Predictive systems toxicology

Authors: N.A. Kiani, M.M. Shang, H. Zenil, J. Tegnér
Toxicity Machine learning techniques Molecular mechanisms

Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients

Authors: T. James, M. Lindén, H. Morikawa, S.J. Fernandes, S. Ruhrmann, M. Huss, M. Brandi, F. Piehl, M. Jagodic, J. Tegnér, M. Khademi, T. Olsson, D. Gomez-Cabrero, I. Kockum
Kappa-B activation RNA-SEQ data Functional variation Disease Variants Annotation Genome Association Autoimmune Leukocytes

The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells

Authors: N. Sumida, E. Sifakis, B.A. Scholz, A.F. Woodbridge, N. Kiani, D. Gomez-Cabrero, J.P. Svensson, J. Tegner, A. Gondor, R. Ohlsson
Stochastic transcriptional bursts Dynamic 3D chromatin states Ultra-sensitive Nodewalk technique Cancer cells

Phosphoproteomics reveals regulatory T cell-Mediated DeF6 dephosphorylation that affects cytokine expression in human conventional T cells

Authors: R.N. Joshi, N.A. Binai, F. Marabita, Z. Sui, A. Altman, A.J.R. Heck, J. Tegnér, A. Schmidt
Regulatory T cell Treg CD4 T cell Phosphoproteomics DEF6 SLAT NFAT TCR signaling

Dynamics and heterogeneity of brain damage in multiple sclerosis

Authors: E. Kotelnikova, N.A. Kiani, E. Abad, E.H. Martinez-Lapiscina, M. Andorra, I. Zubizarreta, I. Pulido-Valdeolivas, I. Pertsovskaya, L.G. Alexopoulos, T. Olsson, R. Martin, F. Paul, J. Tegnér, J. Garcia-Ojalvo, P. Villoslada
Central-nervous-system Demyelinating diseases Pathology Multiple sclerosis Neurodegeneration Remyelination Pathogenesis Inflammation

Guidelines for developing successful short advanced courses in systems medicine and systems biology

Authors: D. Gomez-Cabrero, F. Marabita, S. Tarazona, I. Cano, J. Roca, A. Conesa, P. Sabatier, J. Tegnér
Systems medicine Systems biology

Hypermethylation of MIR21 in CD4+ T cells from patients with relapsing-remitting multiple sclerosis associates with lower miRNA-21 levels and concomitant up-regulation of its target genes

Authors: S. Ruhrmann, E. Ewing, E. Piket, L. Kular, J.C.C. Lorenzi, S.J. Fernandes, H. Morikawa, S. Aeinehband, S. Sayols-Baixeras, S. Aslibekyan, D.M. Absher, D.K. Arnett, J. Tégner, D. Gomez-Cabrero, F. Piehl, M. Jagodic
CD4+ T cells DNA methylation Autoimmunity Epigenetics MicroRNAs Multiple sclerosis Relapsing-remitting

Low-algorithmic-complexity entropy-deceiving graphs

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Computational complexity Algorithmic complexity Entropy rates Information theoretic measure

Omic signatures in frailty and frailty diagnosis

Authors: D. Gomez-Cabrero, S. Walter, I. Abugessaisa, L. Rodríguez-Mañas, J. Tégner
Omic signatures

HiDi: An efficient reverse engineering schema for large scale dynamic regulatory network reconstruction using adaptive differentiation

Authors: Y. Deng, H. Zenil, J. Tégner, N.A. Kiani
Adaptive differentiation Reverse engineering

Viva Europa, a land of excellence in research and innovation for health and wellbeing

Authors: C. Auffray, M. Sagner, S. Abdelhak, I. Adcock, A. Agusti, M. Amaral, J. Tegnér, L. Kular Et Al.
Europe Research

Editorial overview for the thematic issue on Clinical and translational systems biology

Authors: J. Tegnér, D. Gomez-Cabrero
Living systems

SCENERY: a web application for (causal) network reconstruction from cytometry data

Authors: G. Papoutsoglou, G. Athineou, V. Lagani, I. Xanthopoulos, A. Schmidt, S. Éliás, J. Tegnér, I. Tsamardinos
Biological markers Cells Multimedia Reconstructive surgical procedures Machine learning

Comment on" Epigenetics in the pathogenesis of RA".

Authors: D. Gomez-Cabrero, J. Tegnér, T.J. Ekström, C. Ospelt
Rheumatoid arthritis Autoimmune disorders Immunopathology

Iterative systems biology for medicine – time for advancing from network signature to mechanistic equations

Authors: D. Gomez-Cabrero, J. Tegnér
Systems medicine Kitano Mathematical modeling Causality

Predicting causal relationships from biological data: applying automated casual discovery on mass cytometry data of human immune cells

Authors: S. Triantafillou, V. Lagani, C. Heinze-Deml, A. Schmidt, J. Tegner, I. Tsamardinos
Biological data Human immune cells Molecular system Immune system Systems biology

The information theoretic and algorithmic approach to human, animal, and artificial cognition

Authors: N. Gauvit, H. Zenil, J. Tegnér
Theoretic approach Algorithmic approach Human Animal Artificial cognition

Causality, Information and Biological computation: an algorithmic software approach to life, disease and the immune system

Authors: H. Zenil, A. Schmidt, J. Tegnér
Causality Information Biological Computation Disease Immune system

A minimal unified model of disease trajectories captures hallmarks of multiple sclerosis

Authors: V. Kannan, N.A. Kiani, F. Piehl, J. Tegnér
Multiple sclerosis Disease trajectories Disease progression Central nervous system

Functional genomics analysis of vitamin D effects on CD4+ T-cells in vivo in experimental autoimmune encephalomyelitis

Authors: M. Zeitelhofera, M.Z. Adzemovica, D. Gomez-Cabreroc, P. Bergmana, S. Hochmeisterf, M. N’diayea, A. Paulsona, S. Ruhrmanna, M. Almgrena, J. Tegnér, T.J. Ekströma, A.O. Guerreiro-Cacaisa, M. Jagodica
DNA methylation Epigenetics Experimental autoimmune encephalomyelitis Multiple sclerosis Vitamin D

​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

Computational modeling under uncertainty: challenges and opportunities

Authors: D. Gomez-Cabrero, J. Tegnér, L. Geris
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

Authors: D. Gomez-Cabrero, S. Ardid, M. Cano-Colino, J. Tegnér, A. Compte
Prefrontal cortex Workflow Ensemble analysis Working memory model Neuroscience Computational Biology

Modeling and model simplification to facilitate biological insights and predictions

Authors: O. Eriksson, J. Tegnér
Model simplificaton Model reduction Data integration Dynamical models Ordinary differential equations Piecewise linear Dynamical modules

Probabilistic computational causal discovery for systems biology

Authors: V. Lagani, S. Triantafillou, G. Ball, J. Tegnér, I. Tsamardinos
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

Authors: J. Roca, D. Gomez-Cabrero, J. Tegnér
Clinical decision support Integrated care Comorbidity Disease modeling Knowledge management

Proposals for enhanced health risk assessment and stratification in an integrated care scenario

Authors: I. Dueñas-Espín, E. Vela, S. Pauws, C. Bescos, I. Cano, M. Cleries (...) J. Tegnér, F. Velickovski, C. Westerteicher, J. Roca
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

Authors: R.N. Joshi, N. Binai, F. Marabita, J. Tegnér, A. Schmidt
Regulatory T cells Phosphoproteome Conventional T cells

Integrative molecular profiling during human induced regulatory T cell (itreg) generation reveals novel regulators of Foxp3

Authors: A. Schmidt, F. Marabita, H. Johansson, J. Lehtiö, M. Eriksson, S. Éliás, D. Gomez-Cabrero, A. Rao, J. Tegnér
Molecular profiling human induced regulatory T cell (itreg)

Characterization and mechanistic dissection of the differentiation of Gm-csf+ Cd4+ T cells

Authors: S. Éliás, A. Schmidt, V. Kannan, J. Andersson, J. Tegnér
Gm-csf+ Cd4+ T cells

Topological evaluation of methods for reconstruction of genetic regulatory networks

Authors: J. Olczak, N. Kiani, H. Zenil, J. Tegnér
Evaluating measure Inference methods evaluation Network reconstruction Topological properties

Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition

Authors: V. Rodríguez-Cortez, L. Pino-Molina, J. Rodríguez-Ubreva, L. Ciudad, D. Gómez-Cabrero, C. Company, J. Urquiza, J. Tegnér, C. Rodríguez-Gallego, E. López-Granados, E. Ballestar
DNA Gene expression Germ cell Memory Methylation

VEGF-B promotes cancer metastasis through a VEGF-A–independent mechanism and serves as a marker of poor prognosis for cancer patients

Authors: X. Yang, Y. Zhang, K. Hosaka, P. Andersson, J. Wang, F. Tholander, Z. Cao, H. Morikawa, J. Tegnér, Y. Yang, H. Iwamoto, S. Lim, Y. Cao
Angiogenesis Metastasis VEGF-A VEGF-B VEGFR1

IL-1β promotes Th17 differentiation by inducing alternative splicing of FOXP3

Authors: R.K.W. Mailer, A.-L. Joly, S. Liu, S. Elias, J. Tegnér, J. Andersson
Crohn's disease Interleukins Peripheral tolerance Transcription

The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation

Authors: Reiner K.W. Mailer, A.-L. Joly, S. Liu, Sz. Elias, J. Tegnér, J. Andersson
Cell proliferation Cancer metabolism Computational models

Laboratory biomarkers and frailty: presentation of the frailomic initiative

Authors: G. Lippi, P. Jansen-Duerr, J. Viña, A. Durrance-Bagale, I. Abugessaisa, D. Gomez-Cabrero, J. Tegnér, J. Grillari, J. Erusalimsky, A. Sinclair, L. Rodriguez-Manãs, FRAILOMIC consortium
Ageing Biomarkers Frailty Sarcopenia

Signaling networks in MS: A systems-based approach to developing new pharmacological therapies

Authors: E. Kotelnikova, M. Bernardo-Faura, G. Silberberg, N.A. Kiani, D. Messinis, I.N. Melas, L. Artigas, E. Schwartz, I. Mazo, M. Masso, L.G. Alexopoulos, J. Manuel Mas, T. Olsson, J. Tegnér, R. Martin, A. Zamora, F. Paul, J. Saez-Rodriguez, P. Villoslada
Drug discovery Multiple sclerosis Pathways Signaling Systems biology

DNA methylation: an epigenetic marker of breast cancer influenced by nutrients acting as an environmental factor

Authors: T.N. Hasan, G. Shafi, B. Leena Grace, J. Tegnér, A. Munshi
DNA DNA methylation Epigenetics Breast canser

Introduction to data types in epigenomics

Authors: F. Marabita, J. Tegnér, D. Gomez-Cabrero
Epigenomics DNA Methylation Histone modifications ChIP-seq Bioinformatics

Numerical investigation of graph spectra and information interpretability of eigenvalues

Year:2015 ISSN:03029743
Authors: H. Zenil, N.A. Kiani, J. Tegnér
Algorithmic complexity Algorithmic probability Eigenvalues meaning Graph spectra behavior Information content Network science

Approximations of algorithmic and structural complexity validate cognitive-behavioural experimental results

Authors: H. Zenil, J.A.R. Marshall, J. Tegnér
Behavioural biases Ant behaviour Mouse behaviour Drosophila behaviour Communication complexity Tradeoffs of complexity measures Shannon Entropy Kolmogorov-Chaitin complexity Logical Depth

An integrative analysis reveals coordinated reprogramming of the epigenome in human skeletal muscle after training

Authors: M.E. Lindholm, F. Marabita, D. Gomez-Cabrero, H. Rundqvist, T.J. Ekström, J. Tegnér, C.J. Sundberg
450k arrays DNA methylation Environment Epigenomics Exercise Integrative analysis Lifestyle Transcriptional network

Accelerating translational research by clinically driven development of an informatics platform – a case study

Authors: A. Imad, S. Saevarsdottir, G. Tsipras, S. Lindblad, C. Sandin, P. Nikamo, M. Ståhle, V. Malmström, L. Klareskog, J. Tegnér
Arthritis Rheumatoid Autoantibodies Biological markers Decision Support Systems Gene Frequency Polymorphism Single Nucleotide

Data integration in the era of omics: current and future challenges

Authors: D. Gomez-Cabrero, I. Abugessaisa, D. Maier, A. Teschendorff, M. Merkenschlager, A. Gisel, E. Ballestar, E. Bongcam-Rudloff, A. Conesa, J. Tegnér
Biological Science Computational Biology Data Collection Data integration

Biomedical research in a Digital Health Framework

Authors: I. Cano, M. Lluch-Ariet, D. Gomez-Cabrero, D. Maier, S. Kalko, M. Cascante, J. Tegnér, F. Miralles, D. Herrera, J. Roca
Decision Support Systems Program Development Pulmonary Disease Chronic Obstructive

Chronic Obstructive Pulmonary Disease heterogeneity: challenges for health risk assessment, stratification and management

Authors: J. Roca, C. Vargas, I. Cano, V. Selivanov, E. Barreiro, D. Maier, F. Falciani, P. Wagner, M. Cascante, J. Garcia-Aymerich, S. Kalko, I. Marin De Mas, J. Tegnér, J. Escarrabill, A. Agustí, D. Gomez-Cabrero
Cluster analysis Gene Expression Profiling Lung diseases Lung Injury Oxygen Consumption Pulmonary Disease

Systems Medicine: from molecular features and models to the clinic in COPD

Authors: D. Gomez-Cabrero, I. Cano, I. Abugessaisa, M. Huertas-Migueláñez, A. Tenyi, I. Marin De Mas, N. Kiani, F. Marabita, F. Falciani, K. Burrowes, D. Maier, P. Wagner, V. Selivanov, M. Cascante, J. Roca, A. Barabási, J. Tegnér
Biomarkers Comorbidity Computer simulation Decision Support Systems Energy metabolism Reactive Oxygen Species Translational medical research

Predictive medicine: outcomes, challenges and opportunities in the Synergy-COPD project

Authors: F. Miralles, D. Gomez-Cabrero, M. Lluch-Ariet, J. Tegnér, M. Cascante, J. Roca
Chronic disease Cluster analysis Lung diseases Pulmonary medicine Risk assessment Translational medical research

Synergy-COPD: a systems approach for understanding and managing chronic diseases

Authors: D. Gomez-Cabrero, Magi Lluch-Ariet, J. Tegnér, M. Cascante, F. Miralles, J. Roca
Computer simulation Decision Support Systems Delivery of Health Care Electronic Health Records Program Development

Oxygen pathway modeling estimates high reactive oxygen species production above the highest permanent human habitation

Authors: I. Cano, V. Selivanov, D. Gomez-Cabrero, J. Tegnér, J. Roca, P.D. Wagner, M. Cascante
Altitude Computer simulation Mitochondria Models Oxidative Stress Oxygen

Methylome characterization of CD4+ T cells in multiple sclerosis — Establishing a role for miR-21 in autoimmune disease

Authors: S. Ruhrmann, E. Piket, P. Bergman, L. Kular, J. Cesar, C. Lorenzi, S. Aeinehband, R. Parsa, D. Gomez-Cabrero, J. Tegnér, F. Piehl, M. Jagodic
T cells Multiple sclerosis Autoimmune disease

Non-HLA genes PTPN22, CDK6 and PADI4 are associated with specific autoantibodies in HLA-defined subgroups of rheumatoid arthritis

Authors: O. Snir, D. Gomez-Cabrero, A. Montes, E. Perez-Pampin, J. Gómez-Reino, M. Seddighzadeh, K.U. Klich, L. Israelsson, B. Ding, A.I. Catrina, R. Holmdahl, L. Alfredsson, L. Klareskog, J. Tegnér, A. Gonzalez, V. Malmström, L. Padyukov
Autoantigens Cyclin-Dependent Kinase 6 Enzyme-Linked Immunosorbent Assay Genetic Predisposition to Disease Genotype HLA-DRB1 Chains

On the Theory and Algorithm for rigorous discretization in applications of Information Theory

Authors: V. Kannan, J. Tegnér
Information theory Algorithmic probability

Molecular foundations of computational biomedicine

Year:2014 ISSN:ISBN: 9780199658183
Authors: J. Tegnér, I. Abugessaisa, D. Gomez-Cabrero
Computational bioscience Nucleic acid Protein Computational modeling

Breast cancer MicroRNAs: clinical biomarkers for the diagnosis and treatment strategies

Authors: G. Shafi, T.N. Hasan, N.A. Syed, A. Paine, J. Tegnér, A. Munshi
Breast cancer Breast cancer staging Diagnosis MicroRNA Prognosis Treatment strategies

Network biology empowering detection and understanding of interactions between genetic factors in development of complex phenotypes

Authors: J. Tegnér, F. Marabita, D. Gomez-Cabrero
Big data Computing Genetic interactions Network biology Prediction Systems biology

STATegra EMS: an Experiment Management System for complex next-generation omics experiments

Authors: R. Hernández-de-Diego, N. Boix-Chova, D. Gómez-Cabrero, J. Tegnér, I. Abugessaisa, A. Conesa
Metabolomics Proteomics High throughput sequencing Human

Integrative approaches to computational biomedicine

Authors: P.V. Coveney, V. Diaz-Zuccarini, N. Graf, P. Hunter, P. Kohl, J. Tegner, M. Viceconti
Computational biomedicine To human health Virtual physiological human

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation 450 BeadChip platform

Authors: F. Marabita, M. Almgren, M.E. Lindholm, S. Ruhrmann, F. Fagerström-Billai, M. Jagodic, C.J. Sundberg, T.J. Ekström, A.E. Teschendorff, J. Tegnér, D. Gomez-Cabrero
DNA methylation Illumina 450K Microarray Normalization Technical variability

Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register

Authors: I. Abugessaisa, D. Gomez-Cabrero, O. Snir, S. Lindblad, L. Klareskog, V. Malmström, J. Tegnér
Patient de-identification Secondary use of clinical data Swedish Rheumatology Quality Register (SRQ)

Pediatric systems medicine: evaluating needs and opportunities using congenital heart block as a case study

Authors: J. Tegnér, I. Abugessaisa
Computational Biology Genomics Heart Block Newborn Pediatrics Risk Factors

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinum 450k DNA methylation data

Authors: A.E. Teschendorff, F. Marabita, M. Lechner, T. Bartlett, J. Tegnér, D. Gomez-Cabrero, S. Beck
Algorithms DNA methylation Neoplasms Normal distribution Nucleic acid probes Oligonucleotide array sequence analysis

Identification of novel markers in rheumatiod arthritis through integrated analysis of DNA methylation and microRNA expression

Authors: L. de la Rica, J.M. Urquiza, D. Gómez-Cabrero, A.B. Islam, N. López-Bigas, J. Tegnér, R.E. Toes, E. Ballestar
Rheumatoid arthritis Rheumatoid arthritis synovial fibroblasts DNA methylation Epigenetic MicroRNAs

Algorithmic complexity of motifs clusters superfamilies of networks

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Algorithmic probability Complex networks Information content Information theory Kolmogorov complexity Network motifs Network typology

Importance of mitochondrial PO2 in maximal O2 transport and utilization: A theoretical analysis

Authors: I. Cano, M. Mickael, D. Gomez-Cabrero, J. Tegnér, J. Roca, P.D. Wagner
Bioenergetics Mitochondrial PO2 Mitochondrial respiration Oxygen transport V̇O2max

Testing biological models for non-linear sensitivity with a programmability test

Authors: H. Zenil, G. Ball, J. Tegnér
Biological models Non-linear sensitivity Programmability test

A vision and strategy for the virtual physiological human: 2012 update

Authors: P. Hunter, T. Chapman, P.V. Coveney, B. De Bono, V. Diaz, J. Fenner, A.F. Frangi, P. Harris, R. Hose, P. Kohl, P. Lawford, K. McCormack, M. Mendes, S. Omholt, A. Quarteroni, N. Shublaq, J. Skår, K. Stroetmann, J. Tegnér, M. Viceconti
Computational physiology Multiscale modelling Physiome Systems biology Virtual physiological human

Identifying the relevant nodes without learning the model

Authors: J.M. Pena, R. Nilsson, J. Björkegren, J. Tegnér
Relevant nodes Bayesian network Databases

Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes

Authors: J. Rodríguez-Ubreva, L. Ciudad, D. Gómez-Cabrero, M. Parra, L.H. Bussmann, A. di Tullio, J. Tegnér, T. Graf, E. Ballestar
Cell transdifferentiation Cells DNA methylation Epigenesis B-Lymphoid Promoter regions

Data integration: towards understanding biological complexity

Authors: D. Gomez-Cabrero, J. Tegner
Data integration Biological entities Knowledge Databases and Ontologies Open Biomedical Ontologies (OBOs) KDs and Ontologies Clustering algorithms Gene-set analysis

Workflow for generating competing hypothesis from models with parameter uncertainty

Authors: D. Gomez-Cabrero, A. Compte, J. Tegnér
Bioinformatics Computational Biology Systems biology

Decoding complex biological networks – tracing essential and modulatory parameter combinations in complex and simplified models of the cell cycle

Authors: O. Eriksson, T. Andersson, Y. Zhou, J. Tegnér
Complex biological networks Cell cycle Cell division Mathematical models

ParkDB: a Parkinson´s disease gene expression database

Authors: C. Taccioli, J. Tegnér, V. Maselli, D. Gomez-Cabrero, G. Altobelli, W. Emmett, F. Lescai, S. Gustincich, E. Stupka
Databases Gene expression regulation Molecular sequence annotation Parkinson disease

Epigenetic alterations in autoimmune disease

Authors: E. Ballestar, B.M. Javierre, L. de la Rica, D. Gómez-Cabrero, J. Tegnér, C. Gomez-Vaquero, J. Narvaez, H. Hernando, V.C. Rodriguez, R. Vento, J. Rodriguez Ubreva
Autoimmune disease Epigenetics DNA Epstein Barr-virus

Blood levels of dual-specificity phosphatase-1independently predict risk for post-operative morbidities causing prolonged hospitilization after coronary artery bypass grafting

Authors: S. Hägg, M. Salehpour, P. Noori, J. Lundström, G. Possnert, R. Takolander, P. Konrad, S. Rosfors, A. Ruusalepp, J. Skogsberg, J. Tegnér, J. Björkegren
Biological marker Coronary artery disease Dual-specificity phosphatase-1 Gene Expression Profiling

Carotid plaque age is a feature of plaque stability inversely related to levels of plasma insulin

Authors: S. Hägg, T. Alserius, P. Noori, J. Skogsberg, A. Ruusalepp, T. Ivert, J. Tegnér, J. Björkegren
Carotid artery diseases Carotid stenosis Immunohistochemistry Insulin Mass spectrometry

Systems medicine and integrated care to combat chronic noncommunicable diseases

Authors: J. Bousquet, J.M. Anto, P.J. Sterk, I.M. Adcock, (…) J. Tegnér, S. Verjovski-Almeida, P. Wellstead, O. Wolkenhauer, E. Wouters, R. Balling, A.J. Brookes, D. Charron, C. Pison, Z. Chen, L. Hood, C. Auffray
Systems medicine Cardiovascular disease Chronic disease Systems biology

An atlas of combinatorial transcriptional regulation in mouse and man

Authors: T. Ravasi et al, J. Tegnér was part of the core author team
DNA Gene expression Immune system

DGAT1 participates in the effect of HNF4A on hepatic secretion of triglyceride-rich lipoproteins

Authors: S. Krapivner, M.J. Iglesias, A. Silveira, J. Tegnér, J. Björkegren, A. Hamsten, F.M. van't Hooft
Gene expression Lipoproteins Liver Metabolism Transcription

A vision and strategy for the virtual physiological human in 2010 and beyond

Authors: P. Hunter, P. V. Coveney, B. de Bono, V. Diaz, J. Tegnér, S. Randall Thomas, I. Tollis, I. Tsamardinos, J.H.G.M. van Beek, M. Viceconti
Computational physiology Multi-scale modelling Physiome Virtual physiological huma

Multi-Organ Expression Profiling Uncovers a Gene Modulein Coronary Artery Disease Involving TransendothelialMigration of Leukocytes and LIM Domain Binding 2: TheStockholm Atherosclerosis Gene Expression (STAGE) Study

Authors: S. Hägg, J. Skogsberg, J. Lundström, P. Noori, R. Nilsson, H. Zhong, S. Maleki, M.-M. Shang, B. Brinne, M. Bradshaw, V.B. Bajic, (...) J. Tegner*
Lim domain binding 2 Messenger RNA Transcription factor Unclassified drug Gene Expression Profiling Genetic transcription

The transcriptional network controls growth arrest and differentiation in a human myeloid leukemia cell line

Authors: The FANTOM consortium, RIKEN Genome Exploration Research Group: H. Suzuki et al.
Base sequence Cell differentiation Cell proliferation Gene Expression Profiling Gene Regulatory Networks Leukemia Molecular sequence data

Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit IET

Authors: O. Eriksson, B. Brinne, Y., Zhou, J. Björkegren, J. Tegnér
Cell cycles Complex models Computational Biology Model complexity Molecular networks Nonlinear computational models Protein networks System analysis

Bridging the gap between systems biology and medicine

Authors: G. Clermont, C. Auffray, Y. Moreau, D.M. Rocke, D. Dalevi, D. Dubhashi, D.R. Marshall, P. Raasch, F. Dehne, P. Provero, J. Tegnér, B.J. Aronow, M.A. Langston, M. Benson
Experimental design Gene regulatory network Integrative medicine Microarray analysis Priority journal Protein interaction Systems biology

Can modular analysis identify disease-associated candidate genes for therapeutics?

Authors: J. Tegnér
Anti-allergic agents Automatic data processing Gene Expression Profiling Gene expression regulation Hypersensitivity

Computational disease modeling – fact or fiction?

Authors: J. Tegnér, A. Compte, C. Auffray, G. An, G. Cedersund, G. Clermont, B. Gutkin, Z.N. Oltvai, K. Enno Stephan, R. Thomas, P. Villoslada
Biology Computational Biology Computer simulation Disease Uncertainty

Reverse engineering of gene networks with LASSO and non-linear basis functions

Authors: M. Gustafsson, M. Hörnqvist, J. Lundström, J. Björkegren, J. Tegnér
DREAM conference LARS LASSO Network inference Nonlinear Reverse engineering

An algorithm for reading dependencies from the minimal undirected independence map of a graphoid that satisfies weak transitivity

Year:2009 ISSN:15324435
Authors: J. Pena, R. Nilsson, J. Björkegren, J. Tegnér
Bioinformaties Graphical models Graphoids Vertex separation Weak transitivity

Mechanism for Top-down control of working memory capacity

Authors: F. Edin, T. Klingberg, P. Johansson, F. McNab, J. Tegnér, A. Compte
Computer model fMRI Lateral inhibition Parietal Prefrontal Short-term memory

On reliable discovery of molecular signatures

Authors: R. Nilsson, J. Björkegren, J. Tegnér
Accurate prediction Cancer gene expression False discovery rate Molecular signatures Predictive accuracy Signature discovery Statistical framework Statistical hypothesis testing

Genome-wide system analysis reveals stable yet flexible network dynamics in yeast

Authors: M. Gustafsson, M. Hörnkvist, J. Björkegren, J. Tegnér
Cell cycle Cellular network Design Principles Dynamical networks Expression data Flexible networks Gene Regulatory Networks Higher-order dynamics Literature mining Modular coupling

Transcription regulatory network analysis using CAGE

Authors: J. Tegnér, J. Björkegren, T. Ravasi, V. Bajic
Network analysis CAGE Gene expression

On stability of limit cycles of a prototype problem of piecewise linear systems

Authors: O. Eriksson, J. Tegnér, Y. Zhou
Cell membranes Delta sigma modulation Linear systems Machinery Nonlinear systems Piecewise linear techniques

Networks in Biology – from identification, analysis to interpretation

Authors: J. Tegnér
Biological networks Medical applications

Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes

Authors: J. Skogsberg, J. Lundström, A. Kovacs, R. Nilsson, P. Noori, S. Maleki, M. Köhler, A. Hamsten, J. Tegnér, J. Björkegren
Apolipoprotein B-100 Atherosclerosis Carrier proteins Cholesterol Foam cells Gene Expression Profiling Macrophages Mutant strains

Evidence of highly regulated genes (in-hubs) in gene networks of Saccharomyces cerevisiae

Authors: J. Lundström, J. Björkegren J. Tegnér
Gene expression Network Algorithm Transcription regulation Protein-protein interactions In-hubs

ApoB100-LDL Acts as a metabolic signal from liver to peripheral fat causing inhibition of lipolysis in adipocytes

Authors: J. Skogsberg, A. Dicker, M. Rydén, G. Åström, R. Nilsson, A. Mairal, D. Langin, P. Alberts, E. Walum, J. Tegnér, A. Hamsten, P. Arner, J. Björkegren
ApoB100-LDL Cholesterol blood level Energy metabolism lipolysis Metabolic syndrome X

Electrotonic signals along intracellular membranes may interconnect dendritic spines and nucleus

Authors: I. Sheemer, B. Brinne, J. Tegnér, S. Grillner
Action potentials Cell nucleus Computer simulation Endoplasmic reticulum Intracellular membranes Synaptic transmission

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Authors: K. Tan, J. Tegnér, T. Ravasi
Bioinformatics Cellular networks ChIp-chip Dynamics Gene expression Gene networks Genomics Networks Personalized medicine Protein interaction maps Protein-protein interaction networks Systems biology

Detecting multivariate differentially expressed genes

Authors: R. Nilsson, J. M. Peña, J. Björkegren, J. Tegnér
Breast neoplasms Diabetes Mellitus Gene expression regulation Multivariate analysis Protein array analysis

Human C-reactive protein slows atherosclerosis development in a mouse model with human-like hypercholesterolemia

Authors: A. Kovacs, P. Tornvall, R. Nilsson, J. Tegnér, A. Hamsten, J. Björkegren
Acute-phase protein Apolipoprotein B100 Coronary artery disease Low-density lipoprotein Plaques

Fronto-parietal connection asymmetry regulates working memory distractibility

Authors: F. Edin, T. Klingberg, J. Stödberg, J. Tegnér
Computational neuroscience Connectivity Cortico-cortical interactions Directed transfer function Distractibility EEG Frontal cortex Neuronal circuits Parietal cortex Working memory

Perturbations to uncover gene networks

Authors: J. Tegnér, J. Björkegren
Algorithms Computational Biology Gene Regulatory Networks Genomics Research design Systems theory

Consistent feature selection for pattern recognition in polynomial time

Year:2007 ISSN:15324435
Authors: R. Nilsson, J.M., Peña, J. Björkegren, J. Tegnér
Bioinformatics Classification Learning theory Markov blanket Relevance

Neuronal firing rates account for distractor effects on mnemonic accuracy in a visuo-spatial working memory task

Authors: J. Macoveanu, T. Klingberg, J. Tegnér
Action potentials Memory Nerve net Space perception Visual perception

Stronger synaptic connectivity as a mechanism behind development of working memory-related brain activity during childhood

Authors: F. Edin, J. Macoveanu, P. Olesen, J. Tegnér, T. Klingberg
Adolescent Brain mapping Child development Computer simulation Magnetic resonance imaging

​Towards scalable and data efficient learning of Markov Boundaries

Authors: J. M. Peña, R. Nilsson, J. Björkegren, J. Tegnér
Bayesian networks Classification Feature subset selection

Brain activity related to working memory and distraction in children and adults

Authors: P. Olsen, J. Macoveanu, J. Tegnér, T. Klingberg
Development Dorsolateral Event related fMRI Prefrontal Visuospatial

Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits

Authors: J. Tegnér, J. Skogsberg, J. Björkegren
Computational modeling Coronary atherosclerosis Global gene expression Individualized medicine Multicellular disease

Systembiologin ger möjlighet att förstå komplex sjukdom i detalj

Year:2007 ISSN:00237205
Authors: J. Björkegren, J. Tegnér
Atherosclerosis Gene expression Gene Regulatory Networks Genetic screening Genome Systems biology

Learning and validating Bayesian network models of genetic regulatory networks

Authors: J. M. Peña, J. Björkegren, J. Tegnér
Bayesian network Genetic regulatory networks

Systems biology of innate immunity

Authors: J. Tegnér, R. Nilsson, V.B. Bajic, J. Björkegren, T. Ravasi
Dynamics Genome Innate immunity Macrophages Networks Protein-protein interactions Regulatory circuits Systems biology Transcriptional regulation

A biophysical model of multiple-item working memory: a computational and neuromaging

Authors: J. Macoveanu, T. Klingberg, J. Tegnér
Developmental mechanisms Neural network models Parietal lobe

Transcriptional network dynamics in macrophage activation

Authors: R. Nilsson, V.B. Bajic, S. Katayama, H. Suzuki, D. di Bernardo, J. Björkegren, M.J. Sweet, P. Carninci, Y. Hayashizaki, D.A. Hume, J. Tegnér, T. Ravasi
Complex systems Genome Inflammation Innate immunity Macrophages Network dynamics Regulatory networks System biology Transcriptional regulation

Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations

Authors: K. Hallen, J. Björkegren, J. Tegnér
Drug development Expression measurements Expression profile Prior information Regulatory network Search strategies Short interfering RNA (siRNA) Target identification

A flexible implementation for Support Vector Machines

Authors: R. Nilsson, J. Björkegren, J. Tegnér
Support vector machines (SVM) Pattern recognition Nonlinear regression

Evaluating feature selection for SVMs in high dimensions

Year:2006 ISSN:03029743
Authors: R. Nilsson, J. Pena, J. Björkegren, J. Tegnér
Computer simulation Data reduction Regularization Support vector machines (SVM)

Identifying relevant nodes without learning the model

Authors: J. Pena, R. Nilsson, J. Björkegren, J. Tegnér
Conditional probability distributions Artificial intelligence Bayesian networks Gene expression

Reading dependencies from the minimal undirected independence map of a graphoid that satisfies weak transitivity

Authors: J. Pena, R. Nilsson, J. Björkegren, J. Tegnér
Graphical criteria Sound and complete Weak transitivity

The transcriptional landscape of the mammalian genome

Authors: The FANTOM Consortium: P. Carninci, et al.
Base sequence Conserved sequence Genome Regulatory sequences RNA Splicing Terminator regions (Genetics)

Growing Bayesian Network models of gene networks from seed genes

Authors: J. M. Peña, J. Björkegren, J. Tegnér
Artificial intelligence Bayes theorem Computer simulation Gene Expression Profiling Neural network

Learning dynamic Bayesian Network models via cross-validation

Authors: J. M. Peña, J. Björkegren, J. Tegner
Cross-validation Dynamic Bayesian network models Learning

Scalable, efficient and correct learning of Markov Boundaries under the faithfulness assumption

Year:2005 ISSN:03029743
Authors: J. M. Peña, J. Björkegrenand, J. Tegnér
Database systems Markov processes Random processes Statistical methods

Division of labor among distinct subtypes of inhibitory neurons in a cortical microcircuit of working memory

Authors: X.J. Wang, J. Tegnér, C. Constantinidis, P. Goldman-Rakic
Synaptic inhibition Working memory Brain cortex Spatial memory Calcium-Binding Protein Vitamin D-Dependent

A powerful differential expression test for probe-level oligonucleotide microarray data

Authors: R. Nilsson, J. Björkegren, J. Tegnér
Gene expression Bayesian statistical test

Modeling complex cellular networks - robust switching in the cell cycle ensures a piecewise linear reduction of the regulatory network

Authors: O. Eriksson, Y. Zhou, J. Tegnér
Biological complexity Cellular networks Modular structures Regulatory network

A working memory model based on fast Hebbian learning

Authors: A.J. Sandberg, J. Tegnér, A. Lansner
Long-term potentiation Prefrontal cortex Associative memory Attractor network Recurrent network Spiking neurons Visual-cortex Dynamics Mechanisms Synapses

Reverse engineering gene networks - integrating genetic perturbations with dynamical modeling

Authors: J. Tegnér, S. Yeung J. Hasty, J.J. Collins
Gene networks Genetic perturbations Dynamical modeling

Temporally irregular mnemonic persistent activity in prefrontal neurons of monkeys during a delayed response task

Authors: A. Compte, C. Constantinidis, J. Tegnér, S. Raghavachari, M.V. Chafee, P.S. Goldman-Rakic, X.-J. Wang
Macaca mulatta Memory Neurons Prefrontal cortex Psychomotor performance Reaction time Time factors

Systems biology is taking off

Authors: M. Ehrenberg, J. Elf, E. Aurell, R. Sandberg, J. Tegnér
Computational Biology Genetic engineering Molecular biology Systems theory

The logic of life

Authors: E. Aurell, M. Ehrenberg, J. Elf, R. Sandberg, J. Tegnér
Complementary DNA Gene identification Gene replication Quantitative analysis Signal transduction

An adaptive spike dependent plasticity rule

Authors: J. Tegnér, A. Kepecs
Hebbian Homeostatic mechanisms Learning Spike correlations

The dynamical stability of reverberatory neural circuits

Authors: J. Tegnér, A. Compte, X.J. Wang
Animals Cerebral cortex Neurological N-Methylaspartate Neurons AMPA Receptors N-Methyl-D-Aspartate Synapses Time factors

Reverse engineering gene networks using singular value decomposition and robust regression

Authors: S. Yeung, J. Tegnér, J.J. Collins
Algorithms Oligonucleotide array sequence analysis Regression analysis Reproducibility of results Statistics

Spike-timing-dependent plasticity: common themes and divergent vistas

Authors: A. Kepecs, M.C. van Rossum, S., Song, J. Tegnér
Long-term potentiation Dominance column development Synaptic plasticity Hippocampal-neurons Hebbian plasticity Visual-cortex Monocular deprivation Pyramidal cells Barrel cortex

Why neuronal dynamics should control synaptic learning rules

Authors: J. Tegnér, A. Kepecs, T. G. Dietterich, S. Becker, Z. Ghahramani (eds.)
Control scheme STDP LTP Hebbian learning rule Potentia

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