Correspondence Circular reasoning rather than cyclic expression (2008)
Lars Juhl Jensen, Ulrik De Lichtenberg, Thomas Skøt Jensen, Søren Brunak, Peer Bork, A Combined, ...
The electronic version of this article is the complete one and can be
Cyclebase.org a comprehensive multi-organism online database of cell-cycle experiments (2008)
Gauthier, Nicholas Paul, Larsen, Malene Erup, Wernersson, Rasmus, De Lichtenberg, Ulrik, Jensen, Lars Juhl, Brunak, Søren, ...
The past decade has seen the publication of a large number of cell-cycle microarray studies and many more are in the pipeline. However, data from these experiments are not easy to access, combine and...
SuperTarget and Matador: resources for exploring drug-target relationships (2008)
Günther, Stefan, Kuhn, Michael, Dunkel, Mathias, Campillos, Monica, Senger, Christian, Petsalaki, Evangelia, ...
The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of...
eggNOG: automated construction and annotation of orthologous groups of genes (2008)
Jensen, Lars Juhl, Julien, Philippe, Kuhn, Michael, Von Mering, Christian, Muller, Jean, Doerks, Tobias, ...
The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering...
NetworKIN: a resource for exploring cellular phosphorylation networks (2008)
Linding, Rune, Jensen, Lars Juhl, Pasculescu, Adrian, Olhovsky, Marina, Colwill, Karen, Bork, Peer, ...
Protein kinases control cellular responses by phosphorylating specific substrates. Recent proteome-wide mapping of protein phosphorylation sites by mass spectrometry has discovered thousands of in...
STITCH: interaction networks of chemicals and proteins (2008)
Kuhn, Michael, Von Mering, Christian, Campillos, Monica, Jensen, Lars Juhl, Bork, Peer
The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely...
Christopher Workman, Lars Juhl Jensen, Hanne Jarmer, Y Berka, Laurent Gautier, Henrik Bjørn Nielsen, ...
new non-linear normalization method for reducing variability in
Lars Juhl Jensen, David W. Ussery, Søren Brunak, Hans-henrik Stærfeldt
We have performed a computational analysis of DNA structural features in 18 fully sequenced prokaryotic genomes using models for DNA curvature, DNA flexibility, and DNA stability. The structural...
Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik De Lichtenberg, Lars Juhl Jensen, Søren Brunak, ...
Cyclebase.org—a comprehensive multi-organism
Identification and analysis of evolutionarily cohesive functional modules in protein networks (2006)
Campillos, Mónica, Von Mering, Christian, Jensen, Lars Juhl, Bork, Peer
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in...
Identification and analysis of evolutionarily cohesive functional modules in protein networks (2006)
Campillos, Mónica, Von Mering, Christian, Jensen, Lars Juhl, Bork, Peer
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in...
Extraction of regulatory gene/protein networks from Medline (2006)
Saric, Jasmin, Jensen, Lars Juhl, Ouzounova, Rossitza, Rojas, Isabel, Bork, Peer
Motivation: We have previously developed a rule-based approach for extracting information on the regulation of gene expression in yeast. The biomedical literature, however, contains information on...
Extraction of regulatory gene/protein networks from Medline (2005)
Ari, Jasmin, Jensen, Lars Juhl, Ouzounova, Rossitza, Rojas, Isabel, Bork, Peer
Motivation: We have previously developed a rule based approach for extracting information on the regulation of gene expression in yeast. The biomedical literature, however, contains information on...
Comparison of computational methods for the identification of cell cycle regulated genes (2004)
De Lichtenberg, Ulrik, Jensen, Lars Juhl, Fausbøll, Anders, Jensen, Thomas Skøt, Bork, Peer, Brunak, Søren
Motivation: DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been...
Jensen, Lars Juhl, Lagarde, Julien, Von Mering, Christian, Bork, Peer
DNA microarray experiments have provided vast amounts of data which can be used for inferring gene function. However, most methods for predicting functional associations between genes from expression...
Feature based prediction of non-classical and leaderless protein secretion (2004)
Bendtsen, Jannick Dyrløv, Jensen, Lars Juhl, Blom, Nikolaj, Von Heijne, Gunnar, Brunak, Søren
We present a sequence based method-SecretomeP-for prediction of mammalian secretory proteins targeted to the non-classical secretory pathway, i.e. proteins without an N-terminal signal peptide. So...
Feature-based prediction of non-classical and leaderless protein secretion (2004)
Bendtsen, Jannick Dyrløv, Jensen, Lars Juhl, Blom, Nikolaj, Von Heijne, Gunnar, Brunak, Søren
We present a sequence-based method, SecretomeP, for the prediction of mammalian secretory proteins targeted to the non-classical secretory pathway, i.e. proteins without an N-terminal signal peptide....
Comparison of computational methods for the identification of cell cycle regulated genes (2004)
De Lichtenberg, Ulrik, Jensen, Lars Juhl, Fausbøll, Anders, Jensen, Thomas Skøt, Bork, Peer, Brunak, Søren
Motivation: DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been...
Feature based prediction of non-classical and leaderless protein secretion (2004)
Bendtsen, Jannick Dyrløv, Jensen, Lars Juhl, Blom, Nikolaj, Von Heijne, Gunnar, Brunak, Søren
We present a sequence based method-SecretomeP-for prediction of mammalian secretory proteins targeted to the non-classical secretory pathway, i.e. proteins without an N-terminal signal peptide. So...
Functionality of System Components: Conservation of Protein Function in Protein Feature Space (2003)
Jensen, Lars Juhl, Ussery, David W., Brunak, Søren
Many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties....
Functionality of System Components: Conservation of Protein Function in Protein Feature Space (2003)
Jensen, Lars Juhl, Ussery, David W., Brunak, Søren
Many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties....
from sequence-derived features (2002)
Lars Juhl Jensen, Marie Skovgaard, Søren Brunak, Email Alerting, Lars Juhl Jensen, Marie Skovgaard, ...
Prediction of novel archaeal enzymes from sequence-derived features
Prediction of novel archaeal enzymes from sequence-derived features (2002)
Jensen, Lars Juhl, Skovgaard, Marie, Brunak, Søren
The completely sequenced archaeal genomes potentially encode, among their many functionally uncharacterized genes, novel enzymes of biotechnological interest. We have developed a prediction method...
A DNA structural atlas for escherichia coli (2000)
Anders Gorm Pedersen, Lars Juhl Jensen, Sùren Brunak, Hans-henrik Stñrfeldt, David W. Ussery
Although B-form DNA is typically depicted as a uniformly straight and rigid double helix, it has in fact been found to possess inherent structural {These authors contributed equally to this work.
A new non-linear normalization method for reducing variability in DNA microarray experiments
Workman, Christopher, Jensen, Lars Juhl, Jarmer, Hanne, Berka, Randy, Gautier, Laurent, Nielser, Henrik Bjørn, ...
A simple and robust non-linear method is presented for normalization using array signal distribution analysis and cubic splines. Both the regression and spline-based methods described performed...
Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
Jensen, Lars Juhl, Skovgaard, Marie, Sicheritz-Pontén, Thomas, Jørgensen, Merete Kjær, Lundegaard, Christiane, Pedersen, Corinna Cavan, ...
Functionality of System Components: Conservation of Protein Function in Protein Feature Space
Jensen, Lars Juhl, Ussery, David W., Brunak, Søren
Many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties....
ArrayProspector: a web resource of functional associations inferred from microarray expression data
Jensen, Lars Juhl, Lagarde, Julien, Von Mering, Christian, Bork, Peer
DNA microarray experiments have provided vast amounts of data which can be used for inferring gene function. However, most methods for predicting functional associations between genes from expression...
Identification and analysis of evolutionarily cohesive functional modules in protein networks
Campillos, Mónica, Von Mering, Christian, Jensen, Lars Juhl, Bork, Peer
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in...
A new non-linear normalization method for reducing variability in DNA microarray experiments
Workman, Christopher, Jensen, Lars Juhl, Jarmer, Hanne, Berka, Randy, Gautier, Laurent, Nielser, Henrik Bjørn, ...
A simple and robust non-linear method is presented for normalization using array signal distribution analysis and cubic splines. Both the regression and spline-based methods described performed...
Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
Jensen, Lars Juhl, Skovgaard, Marie, Sicheritz-Pontén, Thomas, Jørgensen, Merete Kjær, Lundegaard, Christiane, Pedersen, Corinna Cavan, ...
Functionality of System Components: Conservation of Protein Function in Protein Feature Space
Jensen, Lars Juhl, Ussery, David W., Brunak, Søren
Many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties....
ArrayProspector: a web resource of functional associations inferred from microarray expression data
Jensen, Lars Juhl, Lagarde, Julien, Von Mering, Christian, Bork, Peer
DNA microarray experiments have provided vast amounts of data which can be used for inferring gene function. However, most methods for predicting functional associations between genes from expression...
Identification and analysis of evolutionarily cohesive functional modules in protein networks
Campillos, Mónica, Von Mering, Christian, Jensen, Lars Juhl, Bork, Peer
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in...
STITCH: interaction networks of chemicals and proteins
Kuhn, Michael, Von Mering, Christian, Campillos, Monica, Jensen, Lars Juhl, Bork, Peer
The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely...
SuperTarget and Matador: resources for exploring drug-target relationships
Günther, Stefan, Kuhn, Michael, Dunkel, Mathias, Campillos, Monica, Senger, Christian, Petsalaki, Evangelia, ...
The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of...
NetworKIN: a resource for exploring cellular phosphorylation networks
Linding, Rune, Jensen, Lars Juhl, Pasculescu, Adrian, Olhovsky, Marina, Colwill, Karen, Bork, Peer, ...
Protein kinases control cellular responses by phosphorylating specific substrates. Recent proteome-wide mapping of protein phosphorylation sites by mass spectrometry has discovered thousands of in...
Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments
Gauthier, Nicholas Paul, Larsen, Malene Erup, Wernersson, Rasmus, De Lichtenberg, Ulrik, Jensen, Lars Juhl, Brunak, Søren, ...
The past decade has seen the publication of a large number of cell-cycle microarray studies and many more are in the pipeline. However, data from these experiments are not easy to access, combine and...
eggNOG: automated construction and annotation of orthologous groups of genes
Jensen, Lars Juhl, Julien, Philippe, Kuhn, Michael, Von Mering, Christian, Muller, Jean, Doerks, Tobias, ...
The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering...
Taxis, Christof, Keller, Philipp, Kavagiou, Zaharoula, Jensen, Lars Juhl, Colombelli, Julien, Bork, Peer, ...
Spindle pole bodies (SPBs) provide a structural basis for genome inheritance and spore formation during meiosis in yeast. Upon carbon source limitation during sporulation, the number of haploid...
Prediction of novel archaeal enzymes from sequence-derived features
Jensen, Lars Juhl, Skovgaard, Marie, Brunak, Søren
The completely sequenced archaeal genomes potentially encode, among their many functionally uncharacterized genes, novel enzymes of biotechnological interest. We have developed a prediction method...
Circular reasoning rather than cyclic expression
Jensen, Lars Juhl, De Lichtenberg, Ulrik, Jensen, Thomas Skøt, Brunak, Søren, Bork, Peer
A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146.
Text mining for biology - the way forward: opinions from leading scientists
Altman, Russ B, Bergman, Casey M, Blake, Judith, Blaschke, Christian, Cohen, Aaron, Gannon, Frank, ...
This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process, what the...
Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation
Csikász-Nagy, Attila, Kapuy, Orsolya, Tóth, Attila, Pál, Csaba, Jensen, Lars Juhl, Uhlmann, Frank, ...
The eukaryotic cell cycle requires precise temporal coordination of the activities of hundreds of ‘executor' proteins (EPs) involved in cell growth and division. Cyclin-dependent protein kinases...