Can modular analysis identify disease-associated candidate genes for therapeutics? (2009)
Abstract Complex diseases such as allergy change gene expression in several cell types and tissues. Benson and colleagues have now shown, in a paper in BMC Systems Biology , that this complexity can...
On reliable discovery of molecular signatures (2009)
Nilsson, Roland, Björkegren, Johan, Tegnér, Jesper
Abstract Background Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods...
On reliable discovery of molecular signatures (2009)
Nilsson, Roland, Bjorkegren, Johan, Tegnér , Jesper
Background: Plasmid encoded (CTX)-C-bla-M enzymes represent an important sub-group of class A beta-lactamases causing the ESBL phenotype which is increasingly found in Enterobacteriaceae including...
Genome-wide system analysis reveals stable yet flexible network dynamics in yeast (2009)
Gustafsson, Mika, Hörnquist, Michael, Bjorkegren, J, Tegnér, Jesper
Recently, important insights into static network topology for biological systems have been obtained, but still global dynamical network properties determining stability and system responsiveness have...
Consistent Feature Selection for Pattern Recognition in Polynomial Time (2008)
Roland Nilsson, José M. Peña, Johan Björkegren, Jesper Tegnér, Leon Bottou
We analyze two different feature selection problems: finding a minimal feature set optimal for classification (MINIMAL-OPTIMAL) vs. finding all features relevant to the target variable...
Jesper Tegnér, Josefin Skogsberg, Johan Björkegren
Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits
Evaluating Feature Selection for SVMs in High Dimensions (2008)
José M. Peña, Johan Björkegren, Jesper Tegnér
Abstract. We perform a systematic evaluation of feature selection (FS) methods for support vector machines (SVMs) using simulated high-dimensional data (up to 5000 dimensions). Several findings...
Learning Dynamic Bayesian Network Models Via Cross-Validation (2008)
Jose M. Peña, Johan Björkegren, Jesper Tegnér
We study cross-validation as a scoring criterion for learning dynamic Bayesian network models that generalize well. We argue that cross-validation is more suitable than the Bayesian scoring criterion...
Abstract Towards scalable and data efficient learning of Markov boundaries (2008)
Nilsson A, Johan Björkegren B, Jesper Tegnér
We propose algorithms for learning Markov boundaries from data without having to learn a Bayesian network first. We study their correctness, scalability and data efficiency. The last two properties...
Towards Scalable and Data Efficient Learning of Markov Boundaries Abstract (2008)
Nilsson A, Johan Björkegren B, Jesper Tegnér
We propose algorithms for learning Markov boundaries from data without having to learn a Bayesian network first. We study their correctness, scalability and data efficiency. The last two properties...
Jose M. Peña, Roland Nilsson, Johan Björkegren, Jesper Tegnér
We present a sound and complete graphical criterion for reading dependencies from the minimal undirected independence map of a graphoid that satisfies weak transitivity. We argue that assuming weak...
Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae (2008)
Jesper Lundström, Johan Björkegren, Jesper Tegnér
Uncovering interactions between genes, gene networks, is important to increase our understanding of intrinsic cellular processes and responses to external stimuli such as drugs. Gene networks can be...
Skogsberg, Josefin, Dicker, Andrea, Rydén, Mikael, Aström, Gaby, Nilsson, Roland, Bhuiyan, Hasanuzzaman, ...
BACKGROUND: Free fatty acids released from adipose tissue affect the synthesis of apolipoprotein B-containing lipoproteins and glucose metabolism in the liver. Whether there also exists a reciprocal...
Skogsberg, Josefin, Dicker, Andrea, Rydén, Mikael, Aström, Gaby, Nilsson, Roland, Bhuiyan, Hasanuzzaman, ...
BACKGROUND: Free fatty acids released from adipose tissue affect the synthesis of apolipoprotein B-containing lipoproteins and glucose metabolism in the liver. Whether there also exists a reciprocal...
Skogsberg, Josefin, Dicker, Andrea, Rydén, Mikael, Aström, Gaby, Nilsson, Roland, Bhuiyan, Hasanuzzaman, ...
BACKGROUND: Free fatty acids released from adipose tissue affect the synthesis of apolipoprotein B-containing lipoproteins and glucose metabolism in the liver. Whether there also exists a reciprocal...
Detecting multivariate differentially expressed genes (2007)
Nilsson, Roland, Peña, José M, Björkegren, Johan, Tegnér, Jesper
Abstract Background Gene expression is governed by complex networks, and differences in expression patterns between distinct biological conditions may therefore be complex and multivariate in nature....
Brain Activity Related to Working Memory and Distraction in Children and Adults (2007)
Olesen, Pernille J., Macoveanu, Julian, Tegnér, Jesper, Klingberg, Torkel
In order to retain information in working memory (WM) during a delay, distracting stimuli must be ignored. This important ability improves during childhood, but the neural basis for this development...
BMC Bioinformatics Methodology article Detecting multivariate differentially expressed genes (2007)
José M Peña, Johan Björkegren, Jesper Tegnér, Jesper Tegnér
Background: Gene expression is governed by complex networks, and differences in expression patterns between distinct biological conditions may therefore be complex and multivariate in nature. Yet,...
Hallén, Kristofer, Björkegren, Johan, Tegnér, Jesper
Abstract Background A key problem of drug development is to decide which compounds to evaluate further in expensive clinical trials (Phase I- III). This decision is primarily based on the primary...
Brain Activity Related to Working Memory and Distraction in Children and Adults (2006)
Olesen, Pernille J., Macoveanu, Julian, Tegnér, Jesper, Klingberg, Torkel
In order to retain information in working memory (WM) during a delay, distracting stimuli must be ignored. This important ability improves during childhood, but the neural basis for this development...
Brain Activity Related to Working Memory and Distraction in Children and Adults (2006)
Olesen, Pernille J., Macoveanu, Julian, Tegnér, Jesper, Klingberg, Torkel
In order to retain information in working memory (WM) during a delay, distracting stimuli must be ignored. This important ability improves during childhood, but the neural basis for this development...
Systems Biology Is Taking Off (2003)
Ehrenberg, Måns, Elf, Johan, Aurell, Erik, Sandberg, Rickard, Tegnér, Jesper
Reverse engineering gene networks using singular value decomposition and robust regression
Yeung, M. K. Stephen, Tegnér, Jesper, Collins, James J.
We propose a scheme to reverse-engineer gene networks on a genome-wide scale using a relatively small amount of gene expression data from microarray experiments. Our method is based on the empirical...
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
Tegnér, Jesper, Yeung, M. K. Stephen, Hasty, Jeff, Collins, James J.
While the fundamental building blocks of biology are being tabulated by the various genome projects, microarray technology is setting the stage for the task of deducing the connectivity of...
Reverse engineering gene networks using singular value decomposition and robust regression
Yeung, M. K. Stephen, Tegnér, Jesper, Collins, James J.
We propose a scheme to reverse-engineer gene networks on a genome-wide scale using a relatively small amount of gene expression data from microarray experiments. Our method is based on the empirical...
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
Tegnér, Jesper, Yeung, M. K. Stephen, Hasty, Jeff, Collins, James J.
While the fundamental building blocks of biology are being tabulated by the various genome projects, microarray technology is setting the stage for the task of deducing the connectivity of...
Detecting multivariate differentially expressed genes
Nilsson, Roland, Peña, José M, Björkegren, Johan, Tegnér, Jesper
Kovacs, Alexander, Tornvall, Per, Nilsson, Roland, Tegnér, Jesper, Hamsten, Anders, Björkegren, Johan
Increased baseline values of the acute-phase reactant C-reactive protein (CRP) are significantly associated with future cardiovascular disease, and some in vitro studies have claimed that human CRP...
Transcriptional Profiling Uncovers a Network of Cholesterol-Responsive Atherosclerosis Target Genes
Skogsberg, Josefin, Lundström, Jesper, Kovacs, Alexander, Nilsson, Roland, Noori, Peri, Maleki, Shohreh, ...
Despite the well-documented effects of plasma lipid lowering regimes halting atherosclerosis lesion development and reducing morbidity and mortality of coronary artery disease and stroke, the...
Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus
Shemer, Isaac, Brinne, Björn, Tegnér, Jesper, Grillner, Sten
Synapses on dendritic spines of pyramidal neurons show a remarkable ability to induce phosphorylation of transcription factors at the nuclear level with a short latency, incompatible with a diffusion...
Skogsberg, Josefin, Dicker, Andrea, Rydén, Mikael, Åström, Gaby, Nilsson, Roland, Bhuiyan, Hasanuzzaman, ...
Can modular analysis identify disease-associated candidate genes for therapeutics?
Complex diseases such as allergy change gene expression in several cell types and tissues. Benson and colleagues have now shown, in a paper in BMC Systems Biology, that this complexity can be studied...
Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae
Lundström, Jesper, Björkegren, Johan, Tegnér, Jesper
Uncovering interactions between genes, gene networks, is important to increase our understanding of intrinsic cellular processes and responses to external stimuli such as drugs. Gene networks can be...
Mechanism for top-down control of working memory capacity
Edin, Fredrik, Klingberg, Torkel, Johansson, Pär, McNab, Fiona, Tegnér, Jesper, Compte, Albert
Working memory capacity, the maximum number of items that we can transiently store in working memory, is a good predictor of our general cognitive abilities. Neural activity in both dorsolateral...