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\huge \bf 
Universit\"at Bonn \\
Institut f\"ur Informatik IV

Seminar SS1997 \\
Diskrete Algorithmen f\"ur biologische Anwendungen
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\section*{Shotgun Sequencing}

\begin{itemize}
\item J. D. Kececioglou, E. W. Myers: Combinatorial Algorithms for DNA Sequence Assembly, Algorithmica, Vol. 13, 1995, 7--51
\item J. D. Kececioglou: Exact and Approximation Algorithms for DNA Sequence Reconstruction, Ph.D. thesis, TR 91-26, University of Arizona, 1991 
\item H. Peltola, H. S\"oderlund, J. Tarhio, E. Ukkonen: Algorithms for some string matching problems arising in molecular genetics, IFIP 1983, 59--64
\end{itemize}

\section*{Shortest Superstring Problem}

\begin{itemize}
\item D. Breslauer, T. Jiang, Z. Jiang: Rotation of Periodic Strings and Short Superstrings, BRICS Report Series, RS-96-21, June 1996
\item M. S. Waterman: Introduction to Computational Biology, chap. 7.1, Chapman \& Hall, 1995
\end{itemize}


\section*{Sequencing by Hybridization}

\begin{itemize}
\item D. Gusfield et al.: Graph Traversals, Genes, and Matroids: An Efficient Case of the Travelling Salesman Problem, 7th Symp. on Combinatorial Pattern Matching (CPM'96), Lecture Notes in Computer Science, Vol. 1075, Springer-Verlag, 1996, 304--319
\item M. S. Waterman: Introduction to Computational Biology, chap. 7.2, Chapman \& Hall, 1995
\item P. A. Pevzner, R. J. Lipshutz: Towards DNA Sequencing Chips, 19th Symp. on Mathematical Foundations in Computer Science, Lecture Notes in Computer Science, Vol. 841, Springer-Verlag, 1994, 143--158
\end{itemize}

\section*{Multiple Sequence Alignment}

\begin{itemize}
\item J. Kececioglou: The Maximum Weight Trace Problem in Multiple Sequence Alignment, CPM'93, LNCS, Vol. 684, 1993, 106--118
\item K. Reinert, H. P. Lenhof, P. Mutzel, K. Mehlhorn, J. Kececioglou: A Branch and Cut Algorithm for Multiple Sequence Alignment, RECOMB'97, ACM Press, 1997, 241--251 
\end{itemize}

\begin{itemize}
\item Z. Zhang, B. Raghavachari, R. Hardison, W. Miller: Chaining Multiple-Alignment Blocks, Journal of Computational Biology, Vol. 1, No. 3, 1994, 217--226
\item Henikoff, Henikoff: Automated Assembly of Protein Blocks for Database Searching, Nucleic Acids Research, Vol. 19, No. 23, 6565--6572
\end{itemize}

\section*{Motif Recognition}

\begin{itemize}
\item A. Neuwald, P. Green: Detecting Patterns in Protein Sequences, Journal of Molecular Biology, Vol. 239, 1994, 698--712
\item I. Jonassen, J. Collins, D. Higgins: Finding Flexible Patterns in Unaligned Protein Sequences, Protein Science, Vol. 4, 1995, 1587--1595
\end{itemize}

\begin{itemize}
\item L. Hui: Color Set Size Problem with Applications to String Matching, CPM'92, LNCS, Vol. 644, 1992, 230--243
\end{itemize}

\section*{Repeats}

\begin{itemize}
\item G. Landau, J. Schmidt: An Algorithm for Approximate Tandem Repeats, CPM'93, LNCS, Vol. 684, 1993, 120--133
\end{itemize}

\section*{Genome Rearrangements}

\begin{itemize}
\item H. Kaplan, R. Shamir, R. Tarjan: Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals, Symp. on Discrete Algorithms 1997, 344--351
\end{itemize}

\section*{DNA-Computer}

\begin{itemize}
\item L. M. Adleman: Molecular Computation of Solutions to Combinatorial Problems, Science, Vol. 266, 1994, 1021--1024
\item D. Beaver: Computing with DNA, Journal of Computational Biology, Vol. 2, No. 1, 1995, 1--7
\item J. Hartmanis: On the Weight of Computations, Bulletin of the EATCS, No. 55, 1995, 136--138
\end{itemize}

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\section*{Allgemeine Literatur zum Thema des Seminars}

\begin{itemize}
\item Jens Reich: Die Informationslawine im Gefolge des Human Genom Projektes, GMD-Spiegel 4/1996, 56--60
\item Martin Vingron, Hans Peter Lenhof, Petra Mutzel: Computational Molecular Biology, Report MPI-I-96-1-015, Max-Planck-Institut f\"ur Informatik, Saarbr\"ucken, 1996, (eine kommentierte Bibliographie)
\item Michael S. Waterman: Introduction to Computational Biology, Chapman \& Hall, 1995
\end{itemize}

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