List of works - Jesper Tegnér

A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity

scientific article published on 15 August 2018

A Review of Graph and Network Complexity from an Algorithmic Information Perspective

scientific article published on 25 July 2018

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

scientific article

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

scientific article published on 29 March 2017

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

scientific article

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

scientific article

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

scientific article published on April 2013

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

scientific article

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

scientific article

An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

scientific article published on 08 August 2019

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

scientific article published on 19 February 2013

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

scientific article

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

scientific article

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

scientific article

Biomedical research in a Digital Health Framework

scientific article (publication date: 28 November 2014)

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

scientific article published on 17 March 2011

Bridging the gap between systems biology and medicine

scientific article published on 29 September 2009

Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using Linked Self-Organizing Maps

article

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

scientific article (publication date: 7 April 2011)

Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization

scientific article published on 06 November 2019

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

scientific article

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

scientific article

Comment on "Epigenetics in the pathogenesis of RA".

scientific article

Comparative Analysis of Protocols to Induce Human CD4+Foxp3+ Regulatory T Cells by Combinations of IL-2, TGF-beta, Retinoic Acid, Rapamycin and Butyrate

scientific article published on 17 February 2016

Computational Modeling Under Uncertainty: Challenges and Opportunities

Corrigendum to "Methods of information theory and algorithmic complexity for network biology" [Semin. Cell Dev. Biol. 51 (2016) 32-43].

scientific article published in December 2016

Data Integration: Towards Understanding Biological Complexity

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

scientific article

Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder

scientific article published on 12 February 2020

Detecting multivariate differentially expressed genes

scientific article

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

scientific article

Editorial overview

Electrotonic signals along intracellular membranes may interconnect dendritic spines and nucleus

scientific article

Epigenetic alterations in autoimmune disease

scientific article published on 23 November 2011

Evaluating network inference methods in terms of their ability to preserve the topology and complexity of genetic networks

scientific article published on 3 February 2016

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

scientific article published on 14 July 2008

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

article

From Systems Understanding to Personalized Medicine: Lessons and Recommendations Based on a Multidisciplinary and Translational Analysis of COPD.

scientific article published on January 2016

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

scientific article

Fronto-parietal connection asymmetry regulates working memory distractibility

scientific article published in December 2007

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

scientific article published on 14 February 2017

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells

scientific article published on 03 July 2021

Harmonization of quality metrics and power calculation in multi-omic studies

scientific article published on 18 June 2020

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

scientific article

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

scholarly article

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

scientific article published on 8 January 2013

Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma

scientific article published on 03 February 2020

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

scientific article published on 8 January 2018

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

scientific article published on 2 April 2013

Importance of mitochondrial P(O2) in maximal O2 transport and utilization: a theoretical analysis

scientific article published on 5 September 2013

In Vitro Differentiation of Human CD4+FOXP3+ Induced Regulatory T Cells (iTregs) from Naïve CD4+ T Cells Using a TGF-β-containing Protocol

scientific article

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

scientific article

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

scientific article published on 08 January 2008

Introduction to Data Types in Epigenomics

List of Contributors

Low-algorithmic-complexity entropy-deceiving graphs

scientific article published on 7 July 2017

Mechanism for top-down control of working memory capacity

scholarly article

Methods of information theory and algorithmic complexity for network biology

scientific article

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

scholarly article by Sabrina Ruhrmann et al published October 2014 in Journal of Neuroimmunology

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

scientific article

Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study

scientific article

Network Biology Empowering Detection and Understanding of Interactions Between Genetic Factors in Development of Complex Phenotypes

article

Neuroswarm: A Methodology to Explore the Constraints that Function Imposes on Simulation Parameters in Large-Scale Networks of Biological Neurons

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

scientific article published on 20 August 2014

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

scientific article

On reliable discovery of molecular signatures

scientific article

Optimization in Biology Parameter Estimation and the Associated Optimization Problem

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

scientific article

ParkDB: a Parkinson's disease gene expression database

scientific article

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

scientific article published on 31 January 2013

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

scientific article published on 15 November 2011

Predicting Causal Relationships from Biological Data: Applying Automated Causal Discovery on Mass Cytometry Data of Human Immune Cells

scientific article published on 5 October 2017

Prediction of novel virus–host interactions by integrating clinical symptoms and protein sequences

scientific article published on 25 April 2020

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

scientific article

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

scientific article published on 15 April 2016

Reverse engineering of gene networks with LASSO and nonlinear basis functions

scientific article published in March 2009

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

scientific article

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

scientific article

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

scientific article published on 31 October 2019

STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline

scientific article published on 04 March 2021

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

scientific article

Symmetry and Correspondence of Algorithmic Complexity over Geometric, Spatial and Topological Representations

scientific article published on 18 July 2018

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

scientific article published on 28 November 2014

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

scientific article published on 28 November 2014

Systems Toxicology: Systematic Approach to Predict Toxicity

scientific article

Systems biology of innate immunity

scientific article

Systems medicine and integrated care to combat chronic noncommunicable diseases

scientific article

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

scientific article

The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy

scientific article published on 03 June 2019

The dynamical stability of reverberatory neural circuits

scientific article

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

scientific article

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

scientific article

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

Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits

scientific article published on December 2006

Transcription Regulatory Networks Analysis Using CAGE

Transcriptional network dynamics in macrophage activation

scientific article published on 12 May 2006

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

scientific article

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

scientific article published on 19 May 2015

Workflow for generating competing hypothesis from models with parameter uncertainty

scientific article published on 30 March 2011

List of works by Jesper Tegnér

A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity

A Review of Graph and Network Complexity from an Algorithmic Information Perspective

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

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

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

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

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

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

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

An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

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

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

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

Biomedical research in a Digital Health Framework

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

Bridging the gap between systems biology and medicine

Building gene regulatory networks from single-cell ATAC-seq and RNA-seq using Linked Self-Organizing Maps

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

Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization

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

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

Comment on "Epigenetics in the pathogenesis of RA".

Comparative Analysis of Protocols to Induce Human CD4+Foxp3+ Regulatory T Cells by Combinations of IL-2, TGF-beta, Retinoic Acid, Rapamycin and Butyrate

Computational Modeling Under Uncertainty: Challenges and Opportunities

Corrigendum to "Methods of information theory and algorithmic complexity for network biology" [Semin. Cell Dev. Biol. 51 (2016) 32-43].

Data Integration: Towards Understanding Biological Complexity

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

Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder

Detecting multivariate differentially expressed genes

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

Editorial overview

Electrotonic signals along intracellular membranes may interconnect dendritic spines and nucleus

Epigenetic alterations in autoimmune disease

Evaluating network inference methods in terms of their ability to preserve the topology and complexity of genetic networks

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

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

From Systems Understanding to Personalized Medicine: Lessons and Recommendations Based on a Multidisciplinary and Translational Analysis of COPD.

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

Fronto-parietal connection asymmetry regulates working memory distractibility

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

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells

Harmonization of quality metrics and power calculation in multi-omic studies

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

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

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

Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma

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

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

Importance of mitochondrial P(O2) in maximal O2 transport and utilization: a theoretical analysis

In Vitro Differentiation of Human CD4+FOXP3+ Induced Regulatory T Cells (iTregs) from Naïve CD4+ T Cells Using a TGF-β-containing Protocol

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

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Introduction to Data Types in Epigenomics

List of Contributors

Low-algorithmic-complexity entropy-deceiving graphs

Mechanism for top-down control of working memory capacity

Methods of information theory and algorithmic complexity for network biology

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

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

Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study

Network Biology Empowering Detection and Understanding of Interactions Between Genetic Factors in Development of Complex Phenotypes

Neuroswarm: A Methodology to Explore the Constraints that Function Imposes on Simulation Parameters in Large-Scale Networks of Biological Neurons

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

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

On reliable discovery of molecular signatures

Optimization in Biology Parameter Estimation and the Associated Optimization Problem

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

ParkDB: a Parkinson's disease gene expression database

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

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

Predicting Causal Relationships from Biological Data: Applying Automated Causal Discovery on Mass Cytometry Data of Human Immune Cells

Prediction of novel virus–host interactions by integrating clinical symptoms and protein sequences

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

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

Reverse engineering of gene networks with LASSO and nonlinear basis functions

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