List of Publications in Molecular Computing and Bioinformatics
Wolfgang Banzhaf
We give titles and links. If you click the underlined words in a title
you will see an abstract and source information of the paper. If you click
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List of Abstracts and Sources
TITLE: Network motifs in natural and artificial transcriptional regulatory
networks
AUTHORS:
Wolfgang Banzhaf and Paul Dwight Kuo
SOURCE:
Journal of Biological Physics and Chemistry, 4 (2004) pp. 85 - 92
ABSTRACT:
We show that network motifs found in natural regulatory networks may also be found
in an artificial regulatory network model created through a duplication/divergence
process. It is shown that these network motifs exist more frequently in a genome
created through the aforementioned process than in randomly generated genomes.
These results are then compared with a network motif analysis of the gene
expression networks of Escherichia coli and Saccharomyces cerevisiae.
In addition, it is shown that certain individual network motifs may arise
directly from the duplication/divergence mechanism.
FILENAME: JBPC.pdf
(351 kB)
TITLE: Microarray-Based in vitro Evaluation of DNA Oligomer Libraries Designed
in silico
AUTHORS:
Udo Feldkamp, Ron Wacker, Hendrik Schroeder, Wolfgang Banzhaf and Christoph Niemeyer
SOURCE:
ChemPhysChem, 5 (2004) pp. 367 - 372
ABSTRACT:
We report on the microarray-based in vitro evaluation of two libraries of DNA
oligonucleotide sequences,designed in silico for applications in supramolecular
self-assembly,such as DNA com- puting and DNA-based nanosciences.
In this first study which is devoted to the comparison of sequence motif properties
theoretically predicted with their performance in real-life, the DNA-directed
immobilization (DDI)of proteins was used as an example of DNA-based self-assembly.
Since DDI technologies, DNA computing, and DNA nanoconstruction essentially
depend on similar prerequisites, in particular, large and uniform hybridization
efficiencies combined with low nonspecific cross-reactivity between individual
sequences, we anticipate that the microarray approach demonstrated here will
enable rapid evaluation of other DNA sequence libraries.
TITLE: Software Tools for DNA Sequence Design
AUTHORS: Udo Feldkamp, Hilmar Rauhe und Wolfgang Banzhaf
SOURCE:
Special Issue on Biomolecular Computation (M.Garzon, guest editor)
Genetic Programming and Evolvable Machines, 4 (2003) pp. 153 - 171
ABSTRACT:
The design of DNA sequences is a key problem for implementing molecular self-assembly
with nucleic acid molecules. These molecules must meet several physical, chemical
and logical requirements, mainly to avoid mishybridization. Since manual selection
of proper sequences is too time-consuming for more than a handful of molecules,
the aid of computer programs is advisable. In this paper two software tools for
designing DNA sequences are presented, the DNASequenceGenerator and the
DNASequenceCompiler. Both employ an approach of sequence dissimilarity
based on the uniqueness of overlapping subsequences and a graph based algorithm
for sequence generation. Other sequence properties like melting temperature or
forbidden subsequences are also regarded, but not secondary structure errors or
equilibrium chemistry. Fields of application are DNA computing and DNA-based nanotechnology.
In the second part of this paper, sequences generated with the DNASequenceGenerator are
compared to those from several publications of other groups, an example application for
the DNASequenceCompiler is presented, and the advantages and disadvantages of the
presented approach are discussed.
TITLE: DNASequenceGenerator: A Program for the
construction of DNA sequences
AUTHORS: Udo Feldkamp, Sam Sagafi, Wolfgang Banzhaf and Hilmar Rauhe
SOURCE: 7th DIMACS Workshop on DNA Computing, South Florida, 2001
ABSTRACT: In DNA Computing and DNA nanotechnology the design of proper DNA sequences
turned out to be an elementary problem [1-9]. We here present a software program
for the construction of sets ("pools") of DNA sequences. The program can create
DNA sequences to meet logical and physical parameters such as uniqueness, melting
temperature and GC ratio as required by the user. It can create sequences de novo,
complete sequences with gaps and allows import and recycling of sequences that are
still in use. The program always creates sequences that are - in terms of uniqueness,
GC ratio and melting temperature - "compatible" to those already in the pool, no
matter whether those were added manually or created or completed by the program
itself. The software comes with a GUI and a Sequence Wizard. In vitro tests of
the program's output were done by generating a set of oligomers designed for
self-assembly. The software is available for download
here.
TITLE: Private and public key DNA steganography
AUTHORS: Andre Leier, Christoph Richter, Wolfgang Banzhaf and Hilmar Rauhe
SOURCE: Extended Manuscript from 6th DIMACS Workshop on DNA Computing, Leiden, 2000
ABSTRACT: In this paper steganographic approaches to DNA cryptography are presented.
The first approach shows how digital DNA strands can be used for steganography
to provide rapid encryption and decryption. The second approach is based on a method
of graphical subtraction of gel-images. It can be used to constitute a molecular
checksum and can be combined with the rst approach to support encryption. The second
part of this paper explains a public key steganographic system. It is based on the usage
of a certain double stranded DNA ring molecule which can be constructed by means of
grammar rule molecules.
TITLE: A DNA Sequence Compiler
AUTHORS: Udo Feldkamp, Wolfgang Banzhaf and Hilmar Rauhe
SOURCE: Extended Manuscript from 6th DIMACS Workshop on DNA Computing, Leiden, 2000
ABSTRACT:
Various approaches to the self-assembly of molecules have been introduced already.
A step further toward flexible design and construction of precisely defined molecules
are approaches to programmable self-assembly . In order to allow arbitrary
programming, a sufficient solution of the negative design problem is needed.
We present a computer program which translates formal grammars directly into DNA molecules.
It allows the construction of DNA molecules with defined logical structure and physical properties.
Applications of the compiler are DNA-computing algorithms, nano-frameworks and the
construction of biochips.
TITLE: Digital DNA molecules
AUTHORS: Hilmar Rauhe, Gaby Vopper, Udo Feldkamp, Wolfgang Banzhaf and Jonathan Howard
SOURCE: Extended Manuscript from 6th DIMACS Workshop on DNA Computing, Leiden, 2000
ABSTRACT:
An approach based on programmable self-assembly of DNA oligonucleotides was used
to create digital DNA molecules representing binary datastructures which are equivalent
to those used in computers. Utilizing plasmids as a kind of computer memory, the digital
molecules could be isolated, amplified and read out using common genetic techniques.
Programmability allowed several applications to be realized in vitro such as a fast
physical random number generator and digital DNA-"barcodes".
TITLE: Cryptography with DNA binary strands
AUTHORS: Andre Leier, Christoph Richter, Wolfgang Banzhaf and Hilmar Rauhe
SOURCE: BioSystems, 57 (2000) 13 - 22
ABSTRACT:
Biotechnological methods can be used for cryptography. Here two di erent cryptographic
approaches based on DNA binary strands are shown. The rst approach shows how DNA binary
strands can be used for steganography to provide rapid encryption and decryption.
It is shown that DNA steganogra- phy based on DNA binary strands is secure under
the assumption that an interceptor has the same technological capabilities as sender
and receiver of encrypted messages. The second approach shown here is based on steganography
and a method of graphical subtraction of binary gel-images. It can be used to constitute
a molecular checksum and can be combined with the rst approach to support encryption.
Wolfgang Banzhaf
Last updated: Sep 10, 2021