Peer-reviewed Research Publications

Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments
Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, Thomas Skøt Jensen
Nucleic Acids Research, 36(Database Issue), D854-859, 2008 (Epub 2007 Oct 16)
[PDF] [PubMed]

Evolution of cell cycle control: Same molecular machines, different regulation
Ulrik de Lichtenberg, Thomas Skøt Jensen, Søren Brunak, Peer Bork and Lars Juhl Jensen
Cell Cycle, 6 (15), e1-e7, 2007
[PDF] [PubMed]

A high-quality catalog of the Drosophila melanogaster proteome
Erich Brunner, Christian H Ahrens, Sonali Mohanty, Hansruedi Baetschmann, Sandra Loevenich, Frank Potthast, Eric W Deutsch, Christian Panse, Ulrik de Lichtenberg, Oliver Rinner, Hookeun Lee, Patrick G A Pedrioli, Johan Malmstrom, Katja Koehler, Sabine Schrimpf, Jeroen Krijgsveld, Floyd Kregenow, Albert J R Heck, Ernst Hafen, Ralph Schlapbach & Ruedi Aebersold
Nature Biotechnology, 25(5), 576-83, 2007 (Epub 2007 Apr 22) [PDF] [PubMed]

Co-evolution of transcriptional and post-translational cell cycle regulation
Lars Juhl Jensen, Thomas Skøt Jensen, Ulrik de Lichtenberg, Søren Brunak and Peer Bork
Nature, 443 (7111), 594-597, 2006 (Epub 2006 Sep 27)
[PDF] [Commentary in Nature] [PubMed] [Danish Press release] [Supplementary Information]

The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast
Samuel Marguerat, Thomas Skøt Jensen, Ulrik de Lichtenberg, Lars Juhl Jensen & Jürg Bähler
Yeast, 23 (4), 261-277, 2006 [PubMed]

Bioinformatics and systems biology of the cell cycle
Ulrik de Lichtenberg
PhD Thesis, June 2005

New weakly expressed cell cycle-regulated genes in yeast
Ulrik de Lichtenberg, Rasmus Wernersson, Thomas Skøt Jensen, Henrik Bjørn Nielsen, Anders Fausbøll, Peer Schmidt, Flemming Bryde Hansen, Steen Knudsen, Søren Brunak
Yeast, 22 (15), 1191-2017, 2005 [PubMed]

Crystal Ball: Systems biology - in the broadest sense of the word
David W. Ussery, Ulrik de Lichtenberg & Lars Juhl Jensen
Environmental Microbiology, 7 (4), 482-483, 2005 [PubMed]

Dynamic complex formation during the yeast cell cycle
Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak & Peer Bork
Science, 307 (5710), 724-727, 2005 [PubMed] [Commentary in Nature Reviews] [Press release]

Comparison of computational methods for the identification of cell cycle regulated genes
Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork & Søren Brunak
Bioinformatics, 21 (7), 1164-1171, 2005 (Epub Oct 2004) [PubMed]

Predicting Protein Structure Classes from Function Predictions
Ingolf Sommer, Jorg Rahnenführer, Francisco S. Domingues, Ulrik de Lichtenberg & Thomas Lengauer
Bioinformatics, 20 (5), 770-776, 2004 [PubMed]

Protein Feature Based Identification of Cell Cycle Regulated Proteins in Yeast
Ulrik de Lichtenberg, Thomas Skøt Jensen, Lars Juhl Jensen & Søren Brunak
Journal of Molecular Biology, 239 (4), 663-674, 2003 [PubMed]


Supplementary information for these papers can be found at www.cbs.dtu.dk/cellcycle
If you are unable to access any of the papers, just drop me an email and I'll send the .pdf version.

 

Invited and Contributed Talks Given

Dynamic complex formation during the cell cycle
University of Rome - Tor Vergata, Rome, Italy, 18 July 2007

Dynamic complex formation during the cell cycle
2nd Danish Conference on Molecular Biology and Biotechnology
Munkebjerg hotel, Vejle, Denmark, 25 May 2007

Systems biology of the mitotic cell cycle
Annual Award Lecture of the Danish Biotechnological Society
Ingeniørhuset, Copenhagen, Denmark, 30 November 2006

Data Integration and Systems Biology
Institute for Informatics and Mathematical Modelling
Technical University of Denmark, 19 April 2006

Dynamics of the yeast cell cycle interactome - modeling through integration of high-throughput data
Bioinformatics Seminar
University of Copenhagen, Denmark, 17 February 2006

Modeling the dynamics of the yeast cell cycle interactome through integration of high-throughput data
Workshop at the 4th European Conference on Computational Biology (ECCB) [link]
Madrid, Spain, 28 September 2005

Dynamic Complex formation during the Yeast Cell Cycle
Intelligent Systems for Molecular Biology (ISMB) 2005 [link]
Detroit, USA, 29 June 2005

Dynamics of the yeast cell cycle interactome - modeling through integration of high-throughput data
BioPathways 2005 (ISMB affiliated meeting) [link]
Detroit, USA, 23 June 2005

Dynamics of the yeast cell cycle interaction network
EuroFung Consortium meeting
Wageningen, Holland, 19 November 2004

Dynamics of the yeast cell cycle interactome - an integrative systems biology approach
Yeast Systems Biology Network meeting
Villa Bosch, Heidelberg, Germany, 14 October 2004

Protein Feature Integration – Function Prediction & System Component Identification
Workshop on Cellular Networks
Norrköping Campus, Linköping University, Sweden, 15 - 16 December 2003

Protein Feature Integration – Function Prediction and System Dynamics
AstraZeneca internal seminar
AstraZeneca, Lund, Sweden, 10 December 2003

Protein Feature Integration - Function Prediction and System Dynamics
BioPathways SIG at ISMB 2003 - Regulation, Evolution and Data Integration
Brisbane Convention Center, Australia, 27 - 28 June 2003

An introduction to neural networks
Seminar: Methods in Medicine and Biotechnology
The State Serum Institute, Copenhagen, Denmark, 27 February 2003

Bioinformatics – the enabling factor for functional genomics
Øresund Food Network Seminar: Genomics in Food Science
The Royal Veterinary and Argricultural University, Copenhagen, Denmark, 24 October 2002

Characterization and identification of cell cycle regulated genes from sequence derived protein features
Novo Nordisk and Novozymes Minisymposium
Bagsværd, Denmark, 29 January 2002
Awarded first prize for best research presentation

 

Posters Presented

Dynamic Complex formation during the Yeast Cell Cycle
ISMB 2005, Detroit, USA, 25 - 29 June 2005

Comparison of computational methods for the identification of cell cycle regulated genes
ISMB 2005, Detroit, USA, 25 - 29 June 2005

Identification of GPI modification signal peptides and prediction of their cleavage sites
ISMB 2005, Detroit, USA, 25 - 29 June 2005
Winner of the SGI Best Poster Award

Interaction Networks in Time and Space - a model of the mitotic cell cycle
Danish Center for Scientific Computing Seminar, Odense, Denmark, 15 September 2004

Feature Plots: Visualizing System Dynamics in Cyclic Processes
ISMB/ECCB 2004, Glasgow, Scotland, 31 July - 4 August 2004
Winner of the SGI Best Poster Award

Interaction Networks in Time and Space - a model of the mitotic cell cycle
ISMB/ECCB 2004, Glasgow, Scotland, 31 July - 4 August 2004

Combining bioinformatics prediction and validation to identify new cell cycle regulated genes
Bioinformatics 2004, Linköping, Sweden, 3 - 6 June 2004

Feature Plots: A Technique for Visualizing System-wide Dynamics and Correlations in Temporal Processes
Bioinformatics 2004, Linköping, Sweden, 3 - 6 June 2004

Protein Feature Based Identification of Cell Cycle Regulated Proteins in Yeast
Spring meeting 2004 of the EuroFung Consortium, Holland, 25 April 2004
Winner of the Best Poster Award

Feature Plots: A Technique for Visualizing System-wide Dynamics and Correlations in Temporal Processes
First International Workshop on Systems Biology of yeast, St. Louis, Missouri, USA, 4 November 2003

In-Silico View of the Proteome Dynamics of the Eukaryote Cell Cycle
Intelligent Systems for Molecular Biology (ISMB) 2003, Brisbane, Australia, 29 June – 3 July 2003

Protein Feature Based Identification of Cell Cycle Regulated Proteins
Intelligent Systems for Molecular Biology (ISMB) 2003, Brisbane, Australia, 29 June – 3 July 2003

Protein Feature Based Identification of Cell Cycle Regulated Proteins in Yeast
Bioinformatics 2003, Helsinki, Finland, 22 - 24 May 2003

Protein Feature Based Identification of Cell Cycle Regulated Proteins in Yeast
Danish Society for Cancer Research, 16. annual meeting, Charlottenlund, Denmark, 2 May 2003