2016 (updated in July 2016), publications from CompMed Unit

New Paper
Published in Journal
New Paper
Published in Journal
 
 
 
 
 
Systems toxicology: Systematic Approach to Predicting Toxicity
Published in Current Pharmaceutical Design
Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic beta-Cells.
Published in Pancreas
A Perspective on Bridging Scales and Design of Models using Low-Dimensional Manifolds & Data-driven Model Inference
Published in Philosophical Transactions A (PDF)
In vitro differentiation of human CD4+FOXP3+ induced regulatory T cells (iTregs) from naïve CD4+ T cells using a TGF-beta containing protocol
Published in Journal of Visualized Experiments
Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus
Published in Journal of Virological Methods (PDF)
Characterization and reduction of variability in selection based on effect-size using association measures in cohort study of heterogeneous diseases
Published in arXiv (PDF)
Fractal Dimension Versus Computational Complexity
Published in Advances in Mathematical Physics (PDF)
The Limits of Decidable States on Open-Ended Evolution and Emergence
Published in 15th International Conference on the Synthesis and Simulation of Living Systems, Artificial Life Conference (ALIFE), 2016 (PDF)
A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions
Published in BMC Bioinformatics (PDF)
Human cytomegalovirus may promote tumour progression by upregulating arginase-2
Published in Oncotarget (PDF)
Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction
Published in Scientific reports, Nature Publishing Group (PDF)
Network based Drug Repositioning Methodology for Neurodegenerative Diseases
Published in Proceedings from IWBBIO (PDF)
Human macrophages induce CD4+Foxp3+ regulatory T cells via binding and re-release of TGF-beta
Published in Immunology&Cell Biology
Proposals for enhanced health risk assessment and stratification in an integrated care scenario
Published in BMJ Open (PDF)
Methods of information theory and algorithmic complexity for network biology
Published in Seminars in Cell and Developmental Biology (PDF)
A Survey of Best Practices for RNA-seq Data Analysis
Published in Genome Biology (PDF)
Asymptotic Intrinsic Universality and Reprogrammability by Behavioural Emulation
Published in arXiv (PDF)
Flow of Information in Biological Systems
Published in Seminars in Cell and Developmental Biology (PDF)
Inferring causal molecular networks: empirical assessment through a community-based effort
Published in Nature Methods (PDF)
Metabolite Profiling and Stable Isotope Tracing in Sorted 2 Subpopulations of Mammalian Cells Analytical Chemistry
Published in Analytical Chemistry (PDF)
Serum micrornas as novel biomarkers for primary sclerosing cholangitis and cholangiocarcinoma
Published in Clin Exp Immunol. (PDF)
Comparative Analysis of Protocols to Induce Human CD4+Foxp3+ Regulatory T Cells by Combinations of IL-2, TGF-beta, Retinoic Acid, Rapamycin and Butyrate
Published in Plos One (PDF)
A Minimal Unified Model of Disease Trajectories Captures Hallmarks of Multiple Sclerosis
Published in submitted
Adaptive input data transformation for improved network reconstruction with information theoretic algorithms
Published in in revision
High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared novel markers for ACPA and ACPA-positive rheumatoid arthritis
Published in in revision
Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system
Published in Information and Causality: From Matter to Life, Cambridge University Press (PDF)
From Systems Understanding to Personalized Medicine: Lessons and Recommendations Based on a Multidisciplinary and Translational Analysis of COPD.
Published in Methods Mol Biol. (PDF)
ChainRank, a chain prioritisation method for contextualisation of biological networks
Published in BMC bioinformatics (PDF)
Evaluating Network Inference Methods in Preserving the Topology and Complexity of Reconstructed Genetic Networks
Published in Seminars in Cell and Developmental Biology (PDF)
Neuroswarm: A Methodology to Explore the Constraints that Function Imposes on Simulation Parameters in Large-Scale Networks of Biological Neurons
Published in Studies in Mechanobiology, Tissue Engineering and Biomaterials, In Press, Springer International Publishing
Uncertainty in biology: a computational modelling approach-Introductory Chapter
Published in Studies in Mechanobiology, Tissue Engineering and Biomaterials, In Press, Springer International Publishing
Uncertainty in biology: a computational modelling approach-Causal Inference and Modeling
Published in Studies in Mechanobiology, Tissue Engineering and Biomaterials, In Press, Springer International Publishing
Uncertainty in biology: a computational modelling approach-Parameter Fitting and the Optimization Problem
Published in Studies in Mechanobiology, Tissue Engineering and Biomaterials, In Press, Springer International Publishing
Uncertainty in biology: a computational modelling approach-Simplification and reduction of large dynamical cellular models using biological constraints facilitate insights and derivation of model predictions
Published in Studies in Mechanobiology, Tissue Engineering and Biomaterials, In Press, Springer International Publishing
Uncertainty in biology: a computational modelling approach-Generation of Hypothesis under Uncertainty
Published in Studies in Mechanobiology, Tissue Engineering and Biomaterials, In Press, Springer International Publishing
Uncertainty in biology: a computational modelling approach- The Future of Modeling in Life Sciences
Published in Studies in Mechanobiology, Tissue Engineering and Biomaterials, In Press, Springer International Publishing

2015

Forskningen måste inriktas på individanpassad medicin
Published in Dagens Nyheter (PDF)
Information conservation in graph spectral and network motif analysis,
Published in Complex Networks and their Applications, SITIS, IEEE
IL-1beta promotes Th17 differentiation by inducing alternative splicing of FOXP3
Published in Scientific reports, Nature Publishing Group (PDF)
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders
Published in International Journal of Molecular Sciences (PDF)
The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.
Published in Scientific reports, Nature Publishing Group (PDF)
Open-Ended Evolution and Innovation in a Deterministic Cellular Automata Universe
Published in Bulletin of the American Physical Society (PDF)
Two-dimensional Kolmogorov complexity and an empirical validation of the Coding theorem method by compressibility
Published in PeerJ Computer Science (PDF)
The Information-theoretic and Algorithmic Approach to Human, Animal and Artificial Cognition
Published in Representation and reality: Humans, animals and machines. Springer (PDF)
Public data and open source tools for multi-assay genomic investigation of disease
Published in Briefings in bioinformatics (PDF)
Approximations of Algorithmic and Structural Complexity Validate Cognitive-behavioural Experimental Results
Published in arXiv (PDF)
Numerical Estimations of Algorithmic Complexity and of Logical Depth Applied to Behavioural Sequences
Published in "Submitted"
Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR
Published in Briefings in Bioinformatics (PDF)
Monozygotic Twins Discordant for Common Variable Immunodeficiency Reveal Impaired DNA Demethylation during Naïve-to-Memory B-Cell Transition
Published in Nature Communications (PDF)
In search of "Omics"-based biomarkers to predict risk of frailty and its consequences in older individuals—The FRAILOMIC Initiative Gerontology
Published in In Press
Introduction to Data Types in Epigenomics
Published in Computational and Statistical Epigenomics Translational Bioinformatics (PDF)
Assessing the consistency of public human tissue RNA-seq data sets
Published in Briefings in Bioinformatics (PDF)
Assessment of health status and program performance in patients on long-term oxygen therapy
Published in Respiratory Medicine (PDF)
Laboratory biomarkers and frailty: presentation of the FRAILOMIC initiative
Published in Clin Chem Lab Med (PDF)
Algorithmic complexity for psychology: A user-friendly implementation of the coding theorem method
Published in Behavioral Research Methods (PDF)
Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues.
Published in LNCS, Springer (PDF)
Quantifying Loss of Information in Network-based Dimensionality Reduction Techniques
Published in Journal of Complex Networks, Oxford (PDF)
DNA Methylation: An Epigenetic Marker of Breast Cancer Influenced by Nutrients Acting as an Environmental Factor
Published in Noninvasive Molecular Markers in Gynecologic Cancers
Algorithmicity and Programmability in Natural Computing with the Game of Life as an In Silico Case Study
Published in Journal of Experimental & Theoretical Artificial Intelligence (PDF)
Complexity Measurement Based on Information Theory and Kolmogorov Complexity
Published in Artificial Life
Two-Dimensional Kolmogorov Complexity and Validation of the Coding Theorem Method by Compressibility
Published in PeerJ Computer Science (PDF)
Quantifying Natural and Artificial Intelligence in Robots and Natural Systems with an Algorithmic Behavioural Test
Published in Springer Cosmos Series, Cognitive Systems Monographs, Springer (PDF)
VEGF-B promotes cancer metastasis through a VEGF-A–independent mechanism and serves as a marker of poor prognosis for cancer patients
Published in PNAS (PDF)

2014

Classes and methods for multi-omics data integration
Published in Bioconductor (PDF)
Oxygen Pathway Modeling Estimates High Reactive Oxygen Species Production above the Highest Permanent Human Habitation
Published in PLoS One (PDF)
Levels of Abstraction and the Apparent Contradictory Philosophical Legacy of Turing and Shannon
Published in AISB Quarterly (PDF)
Systems Medicine: from molecular features and models to the clinic in COPD
Published in Journal of Translational Medicine (PDF)
STATegra EMS: an Experiment Management System for complex next-generation omics experiments
Published in BMC Systems Biology (PDF)
Testing Biological Models for Non-linear Sensitivity with a Programmability Test
Published in ECAL (PDF)
An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training
Published in Epigenetics (PDF)
Signaling networks in MS: A systems-based approach to developing new pharmacological therapies
Published in Multiple Sclerosis Journal (PDF)
The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research
Published in Journal of Translational Medicine (PDF)
Accelerating Translational Research by Clinically Driven Development of an Informatics Platform–A Case Study
Published in PLoS One (PDF)
Calculating Kolmogorov Complexity from the Output Frequency Distributions of Small Turing Machines
Published in PLoS One (PDF)
Methods of Information Theory and Algorithmic Complexity for Network Biology
Published in Seminars of Cell Development Biology (PDF)
Breast Cancer MicroRNAs: Clinical Biomarkers for the Diagnosis and Treatment Strategies
Published in Springer (PDF)
Biomedical research in a Digital Health Framework
Published in Journal of Translational Medicine (PDF)
Synergy-COPD: a systems approach for understanding and managing chronic diseases
Published in Journal of Translational Medicine (PDF)
Simulation environment and graphical visualization environment: a COPD use-case
Published in Journal of Translational Medicine (PDF)
Workforce preparation: the Biohealth computing model for Master and PhD students
Published in Journal of Translational Medicine (PDF)
Natural scene statistics mediate the perception of image complexity
Published in Visual Cognition (PDF)
Correlation of automorphism group size and topological properties with program-size complexity evaluations of graphs and complex networks
Published in Physica A : Statistical Mechanics and Its Applications (PDF)
Cesarean delivery and hematopoietic stem cell epigenetics in the newborn infant: implications for future health?
Published in American Journal of Obstetrics & Gynecology (PDF)
Data integration in the era of omics: current and future challenges
Published in BMC Systems Biology (PDF)
Predictive medicine: outcomes, challenges and opportunities in the Synergy-COPD project
Published in Journal of Translational Medicine (PDF)
Methylome characterization of CD4 + T cells in multiple sclerosis — Establishing a role for miR-21 in autoimmune disease
Published in Journal of Neuroimmunity (PDF)
Chronic Obstructive Pulmonary Disease heterogeneity: challenges for health risk assessment, stratification and management
Published in Journal of Translational Medicine (PDF)
Algorithmicity and programmability in natural computing with the Game of Life as in silico case study
Published in Journal of Experimental & Theoretical Artificial Intelligence (PDF)
On the Theory and Algorithm for rigorous discretization in applications of Information Theory
Published in arXiv (PDF)
Molecular foundations of computational biomedicine
Published in computational biomedicine, oxford university press
 
 
 

2013

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
Published in Bioinformatics (PDF)
Network Biology Empowering Detection and Understanding of Interactions Between Genetic Factors in Development of Complex Phenotypes
Published in L. Padyukov (Ed): Between the Lines of Genetic Code (PDF)
Algorithmic complexity of motifs clusters superfamilies of networks
Published in Published in IEEE Bioinformatics and Biomedicine (BIBM) (PDF)
Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression
Published in Journal of Autoimmunity (PDF)
Implementation of the CDC translational informatics platform – from genetic variants to the national Swedish Rheumatology Quality Register
Published in Journal of Translational Medicine (PDF)
Identification of a novel flow-mediated gene expression signature in patients with bicuspid aortic valve
Published in J Mol Med (PDF)
An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform
Published in Epigenetics (PDF)
Identification of serum and tissue micro-RNA expression profiles in different stages of inflammatory bowel disease
Published in The Journal of Translational Immunology (PDF)
Serotonin Regulates Performance Nonmonotonically in a Spatial Working Memory Network
Published in Cerebral Cortex (PDF)
Pediatric systems medicine: evaluating needs and opportunities using congenital heart block as a case study
Published in Pediatric Research (PDF)
A vision and strategy for the virtual physiological human: 2012 update
Published in Interface Focus (PDF)
Integrative approaches to computational biomedicine
Published in Interface Focus (PDF)
Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register
Published in Journal of Translational Medicine (PDF)
Importance of mitochondrial PO2in maximal O2transport andutilization: A theoretical analysisI
Published in Respiratory Physiology & Neurobiology (PDF)

2012

Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation.
Published in Science (PDF)
Supplementary Material for Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation.
Published in Science (PDF)
Comparison of the prevalence and distribution of human papillomavirus infection and cervical lesions between urban and native habitants of an Amazonian region of Peru
Published in Genetics and Molecular Research (PDF)
Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes
Published in Nucleic Acids Research (PDF)

2011

Systems medicine and integrated care to combat chronic noncommunicable diseases
Published in Genome Medicine (PDF)
Workflow for generating competing hypothesis from models with parameter uncertainty
Published in Interface Focus (PDF)
Decoding complex biological networks - tracing essential and modulatory parameters in complex and simplified models of the cell cycle
Published in BMC Systems Biology (PDF)
Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes
Published in Nucleic Acids Research (PDF)
Blood levels of dual-Specificity Phosphatase-1 independently predict risk for post-operative morbidities causing Prolonged hospitilization after Coronary Artery Bypass Grafting
Published in International Journal of Molecular Medicine (PDF)
ParkDB: a Parkinson´s disease gene expression database
Published in Database (PDF)
Decoding complex biological networks – tracing essential and modulatory parameter combinations in complex and simplified models of the cell cycle
Published in BMC Systems Biology (PDF)
Carotid Plaque Age Is a Feature of Plaque Stability Inversely Related to Levels of Plasma Insulin
Published in PLoS One (PDF)
Epigenetic alterations in autoimmune disease
Published in Journal of Translational Medicine (PDF)
Data Integration: Towards Understanding Biological Complexity
Published in Handbook of Statistical System Biology (PDF)

2010

DGAT1 Participates in the Effect of HNF4A on Hepatic Secretion of Triglyceride-Rich Lipoproteins
Published in Arterioscler Thromb Vasc Biol (PDF)
Reconciling Coherent Oscillation with Modulation of Irregular Spiking Activity in Selective Attention: Gamma-Range Synchronization between Sensory and Executive Cortical Areas
Published in J Neurosci (PDF)
An atlas of combinatorial transcriptional regulation in mouse and man
Published in Cell (PDF)
Prevalence and distribution of human papillomavirus fi ndings in swab specimens from gynaecology clinics of the east coast of Spain
Published in Scandinavian Journal of Infectious Diseases (PDF)
A vision and strategy for the virtual physiological human in 2010 and beyond
Published in Phil. Trans. R. Soc. A (PDF)

2009

Mechanism for top-down control of working memory capacity
Published in PNAS (PDF)
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Published in Nature Genetics (PDF)
Bridging the gap between systems biology and medicine
Published in Genome Medicine (PDF)
Networks in Biology – From Identification, Analysis to Interpretation
Published in Springer (PDF)
On reliable discovery of molecular signatures
Published in BMC Bioinformatics (PDF)
Can modular analysis identify disease-associated candidate genes for therapeutics?
Published in Journal of Biology (PDF)
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
Published in PLoS Genetics (PDF)
Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions
Published in The Challenges of Systems Biology (PDF)
Computational disease modeling – fact or fiction?
Published in BMC Systems Biology (PDF)
A Computational Screen for Regulators of Oxidative Phosphorylation Implicates SLIRP in Mitochondrial RNA Homeostasis
Published in PLoS Genetics (PDF)
On Stability of Limit Cycles of a Prototype Problem of Piecewise Linear Systems
Published in Lecture Notes in Control and Information Sciences (PDF)
An Algorithm for Reading Dependencies from the Minimal Undirected Independence Map of a Graphoid that Satisfies Weak Transitivity
Published in Journal of Machine Learning Research (PDF)
Genome-wide system analysis reveals stable yet flexible network dynamics in yeast
Published in IET Systems Biology (PDF)

2008

Transcriptional Profiling Uncovers a Network of Cholesterol-Responsive Atherosclerosis Target Genes
Published in PLoS Genetics (PDF)
ApoB100-LDL Acts as a Metabolic Signal from Liver to Peripheral Fat Causing Inhibition of Lipolysis in Adipocytes
Published in PLoS One (PDF)
Integrated approaches to uncovering transcription regulatory networks in mammalian cells
Published in Genomics (PDF)
Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit
Published in IET Systems Biology (PDF)
Supplementary Material to the paper Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit
Published in IET Systems Biology (PDF)
Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae
Published in Bioinformatics and Biology Insights (PDF)
Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus
Published in PLoS Computational Biology (PDF)

2007

Human C-reactive protein slows atherosclerosis development in a mouse model with human-like hypercholesterolemia
Published in PNAS (PDF)
Stronger Synaptic Connectivity as a Mechanism behind Development of Working Memory–related Brain Activity during Childhood
Published in Journal of Cognitive Neuroscience (PDF)
Detecting multivariate differentially expressed genes
Published in BMC Bioinformatics (PDF)
Neuronal firing rates account for distractor effects on mnemonic accuracy in a visuo-spatial working memory task
Published in Biol Cybern (PDF)
Systembiologin ger möjlighet att förstå komplex sjukdom i detalj
Published in Läkartidningen (PDF)
Brain Activity Related to Working Memory and Distraction in Children and Adults
Published in Cerebral Cortex (PDF)
Consistent Feature Selection for Pattern Recognition in Polynomial Time
Published in Journal of Machine Learning Research (PDF)
Learning and Validating Bayesian Network Models of Gene Networks
Published in Advances in Probabilistic Graphical Models (PDF)
Fronto-parietal connection asymmetry regulates working memory distractibility
Published in Journal of Integrative Neuroscience (PDF)

2006

Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits
Published in Journal of Lipid Research (PDF)
Reading Dependencies from the Minimal Undirected Independence Map of a Graphoid that Satisfies Weak Transitivity
Published in EWGP (PDF)
Transcriptional network dynamics in macrophage activation
Published in Genomics (PDF)
Perturbations to uncover gene networks
Published in Trends in Genetics (PDF)
A biophysical model of multiple-item working memory: a computational and neuroimaging study
Published in Neuroscience (PDF)
Towards scalable and data efficient learning of Markov boundaries
Published in International Journal of Approximate Reasoning (PDF)
Evaluating Feature Selection for SVMs in High Dimensions
Published in Springer-Verlag (PDF)
A Flexible Implementation for Support Vector Machines
Published in The Mathematica Journal (PDF)
Systems biology of innate immunity
Published in Cellular Immunology (PDF)
Identifying the Relevant Nodes Without Learning the Model
Published in arXiv (PDF)
Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations
Published in BMC Bioinformatics (PDF)

2005

Scalable, Effcient and Correct Learning of Markov Boundaries under the Faithfulness Assumption
Published in Lecture Notes in Artificial Intellingence (PDF)
Learning dynamic Bayesian network models via cross-validation
Published in Pattern Recognition Letters (PDF)
Growing Bayesian network models of gene networks from seed genes
Published in Bioinformatics (PDF)
The Transcriptional Landscape of the Mammalian Genome
Published in Science (PDF)

2004

Systems Biology Is Taking Off
Published in Genome Research (PDF)
Division of labor among distinct subtypes of inhibitory neurons in a cortical microcircuit of working memory
Published in PNAS (PDF)
A powerful differential expression test for probe-level oligonucleotide microarray data
Published in IEEE international Workshop on Genomic Signal Processing and Statistics (PDF)

2003

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
Published in PNAS (PDF)
Temporally Irregular Mnemonic Persistent Activity in Prefrontal Neurons of Monkeys During a Delayed Response Task
Published in J Neurophysiol (PDF)
A working memory model based on fast Hebbian learning
Published in Network: Comput. Neural Syst (PDF)
The Logic of Life
Published in Genome Research (PDF)

2002

Reverse engineering gene networks using singular value decomposition and robust regression
Published in PNAS (PDF)
The dynamical stability of reverberatory neural circuits
Published in Biol. Cybern (PDF)
An adaptive spike-timing-dependent plasticity rule
Published in Neurocomputing (PDF)
Spike-timing-dependent plasticity: common themes and divergent vistas
Published in Biol. Cybern (PDF)
Why neuronal dynamics should control synaptic learning rules
Published in Advances in Neural Information Processing Systems (PDF)
 
 
 

Unit of Computational Medicine

Karolinska University Hospital, L8:05
SE-171 76 Stockholm


Phone: +46 8 517 708 69
Cell phone: + 46 72 530 75 53