DOI 10.1007/s00251-004-0647-4 ORIGINAL PAPER (2008)
Ole Lund, Morten Nielsen, Can Kesmir, Anders Gorm, Petersen Claus Lundegaard, Peder Worning, ...
Definition of supertypes for HLA molecules using clustering of specificity matrices
A wiring of the human nucleolus (2006)
Hinsby, A. M., Kiemer, L., Karlberg, E. O., Lage, K., Fausboll, A., Juncker, A. S., ...
Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA (2004)
Prediction of splice sites in non‐coding regions of genes is one of the most challenging aspects of gene structure recognition. We perform a rigorous analysis of such splice sites embedded in...
Prediction of human protein function according to Gene Ontology categories (2003)
Jensen, L. J., Gupta, R., Stærfeldt, H.-H., Brunak, S.
Motivation: The human genome project has led to the discovery of many human protein coding genes which were previously unknown. As a large fraction of these are functionally uncharacterized, it is of...
of backbone fragments in homologous and non-homologous proteins. (2002)
N. N. Alex, R. Nussinov, N. N. Alex, K. Takahashi, N. Go. Common Spatial Arrangements, J Mol Biol, ...
secondary structure captures protein flexibility. Structure, 10(2):175–184,
L. J. Jensen, R. Gupta, N. Blom, D. Devos, J. Tamames, C. Kesmir, ...
Out of the 35,000 to 50,000 genes believed to be present in the human genome, no more than 40–60 % can be assigned a functional role based on homology to proteins with known function. 1,2
O. Lund, K. Frim, J. Gorodkin, H. Bohr, J. Bohr, J. Hansen, ...
3To whom correspondence should be addressed We predict interatomic Cα distances by two independent data driven methods. The first method uses statistically derived probability distributions of the...
Displaying the in formation contents of structural RNA alignments: the structure logos (1997)
Gorodkin, J., Heyer, L.J., Brunak, S., Storomo, G.D.
Motivation: We extend the standard ‘Sequence Logo’method of Schneider and Stevens (Nucleic Acids Res., 18, 6097–6100, 1990) to incorporate prior frequencies on the bases, allow ft,r gaps in the...
Protein distance constraints predicted by neural networks and probability density functions (1997)
Lund, O, Frimand, K, Gorodkin, J, Bohr, H, Bohr, J, Hansen, J, ...
N. Blom, J. Hansen, D. Blaas, S. Brunak, Email Alerting, Nikolaj Blom, ...
Article cited in:
Distance distributions in proteins: A six parameter representation (1996)
M. G. Reese, O. Lund, H. Bohr, H. Bohr, J. E. Hansen, S. Brunak
We present a statistical analysis of protein structures based on inter atomic C ff -distances. The overall distance distributions reflect in detail the contents of sequence specific substructures...
Distance distributions in proteins: a six-parameter representation (1996)
Reese, M.G., Lund, O., Bohr, J., Bohr, H., Hansen, J.E., Brunak, S.
We present a statistical analysis of protein structures based on interatomic Ca distances. The overall distance distributions reflect in detail the contents of sequence-specific substructures...
Cavitation of Matter in the Universe into a Degenerated Voronoi Foam (1993)
Norretranders, T., Bohr, J., Brunak, S.
Fluids suspended in expanding laboratory systems cavitate into Voronoi foams that degenerate through secondary cavitation of the foam walls. This robust morphological mechanism results from a virtual...
O-GLYCBASE: a revised database of O-glycosylated proteins.
Hansen, J E, Lund, O, Nielsen, J O, Hansen, J E, Brunak, S
O-GLYCBASE is a comprehensive database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the SWISS-PROT and PIR databases as well as...
Cleaning the GenBank Arabidopsis thaliana data set.
Korning, P G, Hebsgaard, S M, Rouze, P, Brunak, S
Data driven computational biology relies on the large quantities of genomic data stored in international sequence data banks. However, the possibilities are drastically impaired if the stored data is...
Hebsgaard, S M, Korning, P G, Tolstrup, N, Engelbrecht, J, Rouzé, P, Brunak, S
Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction...
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins.
Hansen, J E, Lund, O, Rapacki, K, Brunak, S
O-GLYCBASE is an updated database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the SWISS-PROT database....
Tolstrup, N, Rouzé, P, Brunak, S
Little knowledge exists about branch points in plants; it has even been claimed that plant introns lack conserved branch point sequences similar to those found in vertebrate introns. A putative...
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins.
Hansen, J E, Lund, O, Nilsson, J, Rapacki, K, Brunak, S
O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries...
PhosphoBase: a database of phosphorylation sites.
Blom, N, Kreegipuu, A, Brunak, S
PhosphoBase is a database of experimentally verified phosphorylation sites. Version 1.0 contains 156 entries and 398 experimentally determined phosphorylation sites. Entries are compiled and revised...
PhosphoBase, a database of phosphorylation sites: release 2.0.
Kreegipuu, A, Blom, N, Brunak, S
PhosphoBase contains information about phosphorylated residues in proteins and data about peptide phosphorylation by a variety of protein kinases. The data are collected from literature and compiled...
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
Gupta, R, Birch, H, Rapacki, K, Brunak, S, Hansen, J E
O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries with at least one experimentally verified O-glycosylation site have been compiled from protein sequence databases...
Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal.
Larsen, N I, Engelbrecht, J, Brunak, S
A general data study of eukaryotic promoter sequences from widely different species is presented. Mammalian promoters with known transcription initiation sites represented the largest subclass of the...
Neural network detects errors in the assignment of mRNA splice sites.
Brunak, S, Engelbrecht, J, Knudsen, S
The use of databanks in genetic research assumes reliability of the information they contain. Currently, error-detection in the manually or electronically entered data contained in the nucleotide...
Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA
Prediction of splice sites in non-coding regions of genes is one of the most challenging aspects of gene structure recognition. We perform a rigorous analysis of such splice sites embedded in human...
Multiple alignment using simulated annealing: branch point definition in human mRNA splicing.
Lukashin, A V, Engelbrecht, J, Brunak, S
A method for the simultaneous alignment of a very large number of sequences using simulated annealing is presented. The total running time of the algorithm does not depend explicitly on the number of...
O-GLYCBASE: a revised database of O-glycosylated proteins.
Hansen, J E, Lund, O, Nielsen, J O, Hansen, J E, Brunak, S
O-GLYCBASE is a comprehensive database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the SWISS-PROT and PIR databases as well as...
Cleaning the GenBank Arabidopsis thaliana data set.
Korning, P G, Hebsgaard, S M, Rouze, P, Brunak, S
Data driven computational biology relies on the large quantities of genomic data stored in international sequence data banks. However, the possibilities are drastically impaired if the stored data is...
Hebsgaard, S M, Korning, P G, Tolstrup, N, Engelbrecht, J, Rouzé, P, Brunak, S
Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction...
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins.
Hansen, J E, Lund, O, Rapacki, K, Brunak, S
O-GLYCBASE is an updated database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the SWISS-PROT database....
Tolstrup, N, Rouzé, P, Brunak, S
Little knowledge exists about branch points in plants; it has even been claimed that plant introns lack conserved branch point sequences similar to those found in vertebrate introns. A putative...
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins.
Hansen, J E, Lund, O, Nilsson, J, Rapacki, K, Brunak, S
O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries...
PhosphoBase: a database of phosphorylation sites.
Blom, N, Kreegipuu, A, Brunak, S
PhosphoBase is a database of experimentally verified phosphorylation sites. Version 1.0 contains 156 entries and 398 experimentally determined phosphorylation sites. Entries are compiled and revised...
PhosphoBase, a database of phosphorylation sites: release 2.0.
Kreegipuu, A, Blom, N, Brunak, S
PhosphoBase contains information about phosphorylated residues in proteins and data about peptide phosphorylation by a variety of protein kinases. The data are collected from literature and compiled...
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
Gupta, R, Birch, H, Rapacki, K, Brunak, S, Hansen, J E
O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries with at least one experimentally verified O-glycosylation site have been compiled from protein sequence databases...
Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal.
Larsen, N I, Engelbrecht, J, Brunak, S
A general data study of eukaryotic promoter sequences from widely different species is presented. Mammalian promoters with known transcription initiation sites represented the largest subclass of the...
Multiple alignment using simulated annealing: branch point definition in human mRNA splicing.
Lukashin, A V, Engelbrecht, J, Brunak, S
A method for the simultaneous alignment of a very large number of sequences using simulated annealing is presented. The total running time of the algorithm does not depend explicitly on the number of...
Neural network detects errors in the assignment of mRNA splice sites.
Brunak, S, Engelbrecht, J, Knudsen, S
The use of databanks in genetic research assumes reliability of the information they contain. Currently, error-detection in the manually or electronically entered data contained in the nucleotide...
Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA
Prediction of splice sites in non-coding regions of genes is one of the most challenging aspects of gene structure recognition. We perform a rigorous analysis of such splice sites embedded in human...
Relationship between protein structure and geometrical constraints.
Lund, O., Hansen, J., Brunak, S., Bohr, J.
We evaluate to what extent the structure of proteins can be deduced from incomplete knowledge of disulfide bridges, surface assignments, secondary structure assignments, and additional distance...
Blom, N., Hansen, J., Blaas, D., Brunak, S.
Picornaviral proteinases are responsible for maturation cleavages of the viral polyprotein, but also catalyze the degradation of cellular targets. Using graphical visualization techniques and neural...