Publications in bioinformatics - Ingvar Eidhammer:
- Using hydropathy features for function prediction of membrane proteins.
J. Panek, I. Eidhammer, and R. Aasland.
Molecular membrane biology 2007;24:304-312.
- Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering.
K. Flikka, L. Martens, J. Vandelkerchkofe, K. Gevaert, and I. Eidhammer.
Proteomics 2006; 6:2086-2094.
- MassSorter: a tool for administration and analyzing data from mass spectrometry experiments on proteins with
known amino acid sequence.
H. Barsnes, S-O. Mikalsen and I. Eidhammer.
BMC Bioinformatics 2006; 7:42.
- Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel
biocomputing tools.
F. Berven, O.A. Karlsen, A.H. Straume, K. Flikka, J.C. Murrell, A. Fjellbirkeland, J. Lillehaug, I. Eidhammer
and H.B. Jensen.
Archives of Microbiology 2006;184(6):362-377.
- Phylogenetic reconstruction of ancestral character states for gene
expression and mRNA splicing data.
R. Rossnes, I. Eidhammer, and D.A. Liberles.
BMC Bioinformatics 2005; 6:127.
- A New Method for Identification of Protein (Sub)Families in a Set of Proteins Based
on Hydropathy Distribution in Proteins.
J. Panek, I. Eidhammer, and R. Aasland
Proteins: Structure, Function, and Bioinformatics. 2005; 58:923-934.
- Genomic Insights into Methanotrophy:
The Complete Genome Sequence of Methylococcus capsulatus (Bath)
Naomi Ward et. al
Public library of science (PLOS) 2004; 2(10) e303.
- BOMP: a program to predict integral $\beta$-barrel outer membrane proteins
encoded within genomes of Gram-negative bacteria
F.S. Berven, K. Flikka, H.B. Jensen, and I. Eidhammer
Nu. Ac. Res., 32, Web Server issue W1-W6, 2004
- A fast top-down method for constructing reliable radiation hybrid
frameworks
T.H. Bø, I. Jonassen, I. Eidhammer, and C. Helgesen
Bioinformatics, 18(1):1-8,2002
- Structure motif discovery and mining the pdb.
Inge Jonassen, Ingvar Eidhammer, D.C. Conklin,and William R. Taylor
Bioinformatics, 18(2):362--367, 2002.
- A constraint based structure description language for biosequences.
I. Eidhammer, I. Jonassen, S.H. Grindhaug, D. Gilbert, and M. Ratnayake.
Constraints, 6:173--200, 2001.
- Multiple protein sequence alignment using double-dynamic programming
W.R. Taylor, G. Sælensminde, and I. Eidhammer
Computers & Chemistry, 24:3-12, 2000
- Structure Motif Discovery and Mining the PDB
Inge Jonassen, Ingvar Eidhammer, Darrell Conklin, William R. Taylor
German Conference on Bioinformatics 2000
pdf file
- Searching the Protein Structure Databank with Weak Sequence Patterns and Structural Constraints
Inge Jonassen, Ingvar Eidhammer, Svenn Grindhaug, William R. Taylor
Journal of Molecular Biology, 304 (4), 597-617 (2000).
Supportive web site
- Structure Comparison and Structure Patterns
Ingvar Eidhammer, Inge Jonassen, William R. Taylor
Journal of Computational Biology 7, 685-716 (2000).
- Discovery of Local Packing Motifs in Protein Structures
Inge Jonassen, Ingvar Eidhammer, William R. Taylor
Proteins: Structure, Function, and Genetics 34, 206-219 (1999).
-
Structure Prediction of the Zinc-finger protein family by the use of
a parallel genetic algorithm
Kjell Petersen, Ingvar Eidhammer, Rein Aasland, Inge Jonassen
Proceedings of NIK97
(Norwegian Informatics Conference), p 57-68, Tapir 1997.
-
Relation patterns and their automatic discovery in biosequences
Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, Esko Ukkonen
Dept.
of Informatics, Univ. of Bergen, Reports in Informatics no 135, June 1997.
More information,
Postscript paper.
-
CBSDL: a constraint based structure description language for biosequences
David Gilbert, Ingvar Eidhammer, Inge Jonassen
Presented at the Constraints and Bioinformatics/Biocomputing workshop at CP'97
More information.
-
StructWeb: Biosequence structure searching on the Web using clp(FD)
David Gilbert, Ingvar Eidhammer, Inge Jonassen
Presented at the CP'97 workshop on Constraint Reasoning on the Internet.
Also report 1997/05 from Dept. of Computer Science, City University,
London, UK.
More
information, postscript
paper, Web
server
-
A Constraint Based Structure Description Language for Biosequence
Ingvar Eidhammer, David Gilbert, Inge Jonassen, Madu Ratnayake
Dept. of Informatics, Univ. of Bergen, Reports in Informatics no 133,
May 1997, also Report 1997/04 from Dept. of Computer Science, City University,
London, UK.
More information,
Postscript paper.
-
Approaches to the automatic discovery of patterns in
biosequences.
Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David Gilbert.
Journal of Computational Biology 5, 279-305 (1998)
Earlier (and longer) version:
Dept. of Informatics, Univ. of Bergen, Reports in Informatics no 113,
Dec. 1995.
Postscript paper.
Ingvar Eidhammer's Home page.