1999
Dandekar,T., Schuster,S.,
Snel,B., Huynen,M. & Bork,P.
Pathway alignment: application
to the comparative analysis of glycolytic enzymes.
Biochem J 1999, 115-124
Huynen,M.A., Dandekar,T. &
Bork,P.
Variation and evolution of
the citric-acid cycle: a genomic perspective.
Trends Microbiol 1999, 7,
281-291
Huynen, M.A., Snel, B. and
Bork, P.
Lateral Gene Transfer, Genome
Surveys and the Phylogeny of Prokaryotes.
Science 19999, 286, 1443a
Rojas-Mujica, I.; Bornberg-Bauer,
E.
A Comprehensible Database
Model for the Computation of Biochemical Pathways
In: Proc. Workshop on Computation
of Biochemical and Genetic Networks, Heidelberg, 95-100 Eds. E. Bornberg-Bauer,
U. Kummer, U. Rost , Logos, Berlin 1999
2000
Bork P.
Powers and pitfalls in sequence
analysis: the 70% hurdle.
Genome Res. 2000 Apr;10(4):398-400
Dandekar T, Huynen M, Regula
JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sanchez-Pulido L, Snel
B, Suyama M, Yuan YP, Herrmann R, Bork P.
Re-annotating the Mycoplasma
pneumoniae genome sequence: adding value, function and reading frames.
Nucleic Acids Res. 2000 Sep
1;28(17):3278-3288.
Göhlmann, H.W.H., Weiner,
J. III, Schön, A. and Herrmann, R. (2000) Identification of a Small
RNA within the pdh Gene Cluster of Mycoplasma pneumoniae and Mycoplasma
genitalium. J. of Bacteriol. 182, Vol. 11, 3281-3284
Huynen M, Snel B, Lathe W,
Bork P.
Exploitation of gene context.
Curr Opin Struct Biol. 2000a
Jun;10(3):366-70.
Huynen, M., Snel,B., Lathe,W.
and Bork, P.
Predicting protein function
by genomic context: quantitative evaluation and qualitative inferences
Genome Research 2000b, Aug;10(8):1204-10
Lathe, W., Snel, B. and Bork,
P.
The Uberoperon: gene context
conservation at a higher order than operons
Trends Biochem.Sci. 2000
Oct;25(10):474-9
Snel B, Bork P, Huynen M.
Genome evolution. Gene fusion
versus gene fission.
Trends Genet. 2000 Jan;16(1):9-11.
Snel B, Lehmann G, Bork P,
Huynen MA.
STRING: a web-server to retrieve
and display the repeatedly occurring neighbourhood of a gene.
Nucleic Acids Res. 2000 28(18):3442-4.
2001
Becker, M.Y. and Rojas, I.
A graph layout algorithm
for drawing metabolic pathways
Bioinformatics 2001 May,
17(5): 461-7
Huynen MA, Snel B and Bork,
P.
Inversions and the dynamics
of eukaryotic gene order.
Trends Genet. 2001 Jun;17(6):304-6.
Suyama M and Bork P.
Evolution of prokaryotic
gene order: genome rearrangements in closely related species.
Trends Genet. 2001 Jan;17(1):10-3.
Wittig, U. and De Beuckelaer,
A.
Analysis and comparison of
metabolic pathway databases
Briefings in Bioinformatics
2001 May, 2(2): 126-42
2002
Bornberg-Bauer, E. and Weiner,
J. 3rd
A putative transcription
factor inducing mobility in Mycoplasma pneumoniae.
Microbiology, 148: 3764-3765
Pollack, J. D., Myers, M.
A., Dandekar, T. and Herrmann, R.
Suspected utility of enzymes
with multiple activities in the small genome Mycoplasma species: the replacement
of the missing “household” nucleoside diphosphate kinase gene and activity
by glycolytic kinases.
OMICS 6 (3), 247-259.
Reyle, U. and Saric, J.
Corpus Driven Information
Extraction
In Robert Baud and Patrick
Ruch, editors, Proceedings of the EFMI Workshop on Natural Language Processing
in Biomedical Applications, Nicosia, Cyprus.
Rojas-Mujica, I. and Bornberg-Bauer,
E.
Database Systems for the
Analysis of Biochemical Pathways
In Shmuel Razin and Richard
Herrmann, editors, Molecular biology and Pathogenicity of Mycoplasmas.
Kluwer Academic/ Plenum Publishers (2002); 201-220
Rojas I, Bernardi L, Ratsch
E, Kania R, Wittig U, Saric J
A database system for the
analysis of biochemical pathways
In Silico Biol. 2, 2 (2002)
75-86
Schell, M.A., Karmirantzou,
M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M.C., Desiere,
F., Bork, P., Delley, M., Pridmore, R.D. and Arigoni, F.
The genome sequence of Bifidobacterium
longum reflects its adaptation to the human gastrointestinal tract.
Proc Natl Acad Sci U S A.
2002 Oct 29;99(22):14422-7.
Snel, B., Bork, P. and Huynen,
M.A.
The identification of functional
modules from the genomic association of genes.
Proc Natl Acad Sci U S A.
2002 Apr 30;99(9):5890-5.
Snel, B., Bork, P. and Huynen,
M.
Conservation of gene co-regulation
in prokaryotes and eukaryotes.
Trends Biotechnol. 2002 Oct;20(10):410.
Snel, B., Bork, P. and Huynen,
M.A..
Genomes in flux: the evolution
of archaeal and proteobacterial gene content.
Genome Res. 2002 Jan;12(1):17-25.
von Mering, C., Krause, R.,
Snel, B., Cornell, M., Oliver, S.G., Fields, S., Bork, P.
Comparative assessment of
large-scale data sets of protein-protein interactions.
Nature. 2002 May 23;417(6887):399-403.
2003
Gabdoulline, R.R., Hoffmann,
R., Leitner, F. and Wade, R.C.
ProSAT: Functional annotation
of protein 3D structures
Bioinformatics 2003 in press
Gabdoulline, R., Wade, R.C.
and Walther, D.
MolSurfer: a macromolecular
interface navigator
Nucleic Acids Res. (2003),
in press.
Huynen MA, Snel B, Mering
C, Bork P.
Function prediction and protein
networks.
Curr Opin Cell Biol. 2003
Apr;15(2):191-8.
Ratsch, E., Schultz, J., Saric,
J., Cimiano Lavin, P., Wittig, U., Reyle, U. and Rojas, I.
Developing a protein -interactions
ontology
Comp Funct Genom; 4: 85-89;
February 2003.
von Mering C, Huynen M, Jaeggi
D, Schmidt S, Bork P, Snel B.
STRING: a database of predicted
functional associations between proteins.
Nucleic Acids Res. 2003 Jan
1;31(1):258-61.
Posters
Hella Knäble, Esther
Ratsch, Renate Kania, Ulrike Wittig, Isabel Rojas
„Integration and Visualisaton
of Experimental Data“,
European Conference on Computational
Biology, Saarbrücken, Germany, October 6-9, 2002
Uwe Reyle, Jasmin Saric, Philipp
Lavin, Heike Zinsmeister
Ontology-driven disambiguation
of syntactic and semantic ambiguities in GenIE
Workshop on Ontology for
Biology. European Media Laboratory, Heidelberg, Nov. 7-8, 2002.
Uwe Reyle, Jasmin Saric, Wolfgang
Lezius, Esther König
TIGERSearch attacks Proteins
Workshop on Ontology for
Biology. European Media Laboratory, Heidelberg, Nov. 7-8, 2002.