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 the corresponding filename you will retrieve a copy.



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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.

FILENAME: chemphyschem5_2004_367.pdf (173 kB)




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.

FILENAME: softwaretools.pdf (523 kB)




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.

FILENAME: DNASeqGenDNA7_FINAL.ps.gz (221 kB)




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.

FILENAME: PubKey.pdf (221 kB)




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.

FILENAME: DNASeqComp.pdf (72 kB)




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".

FILENAME: DigDNAMol.pdf (85 kB)




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.

FILENAME: DNA_Crypt_final.ps.gz (794 kB) or DNA_Crypt_final.pdf (225 kB)




Wolfgang Banzhaf
Last updated: Oct 1, 2006