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{\large \bf DIMACS Computational Molecular Biology Year}
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{\Large SEQUENCE ALIGNMENT WORKSHOP-PROGRAM}
 

DIMACS -  Princeton University

November 10 -- 12, 1994

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&{\bf Program Committee:}\\
& $\bullet$ S. Altschul (NIH) 
& $\bullet$ A. Apostolico (Padova and Purdue, Co-Chair) 
\\

&$\bullet$ D. Brutlag (Stanford) 
& $\bullet$  R. Doolittle (UCSD, Co-Chair) \\

&$\bullet$ M. Farach (Rutgers and DIMACS) 
& $\bullet$ R. Giancarlo (Bell and DIMACS, Scientific Secretary)\\ 

&$\bullet$ P. Green (Washington U.)&$\bullet$ D. Gusfield (UCD)\\

&$\bullet$ S. Henikoff (HHMI-FHCRC)&$\bullet$ J. Kececioglu (U. of Georgia)\\

&$\bullet$ D. Lipman (NIH)&$\bullet$ W. Miller (PennState)\\

&$\bullet$ W. Pearson (Virginia)&$\bullet$ P. Pevzner (PennState)\\

&$\bullet$ D. Sankoff (Montreal)&$\bullet$ J. Schmidt (Polytechnic U.)\\

&$\bullet$ G. Stormo (Colorado)&$\bullet$ M. Vingron (GMD)\\

&$\bullet$ M. Waterman (USC)\\

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For logistic information and registration, please contact Sandy Barbu
(barbu@cs.princeton.edu).
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\begin{description}
\item[{\bf Thursday, November 10}]  - E-Quad Building (Olden Street)


\begin{itemize}
\item[8:00 a.m.]   Registration-Continental Breakfast (Faculty Lounge, Room 225 E-Quad)

\item[9:00 a.m.]   Opening Session (Convocation Room)
            Fred Roberts, Rutgers Department of Mathematics and DIMACS, 
            Chair of Special Year;
            Andrew Yao, Department of Computer Science and Co-Director of DIMACS;
            James Wei, Dean of \hfil\break Engineering School, Princeton University.
\item[9:30 a.m.]    Foreword: Structure and Goals of the Scientific Program,
            Alberto Apostolico, Purdue CS Dept. and Padova Univ. D.E.I, 
            Workshop Co-Chair
\end{itemize}
\end{description}

\begin{description}
\item[{\bf Session 1}] (Chair: D. Gusfield)

\begin{itemize}
\item[10:00 a.m.]  M. Waterman: "Sequence Alignment: The First 15 Years"

\item[11:00 a.m.]   Coffee Break (Faculty Lounge)

\item[11:30 a.m.]  D. Sankoff: "Phylogenetic Motivation for Multiple Alignment"

\item[12:30]      Lunch (Faculty Lounge)
\end{itemize}
\end{description}

\begin{description}
\item[{\bf Session 2}] (Chair: R. Giancarlo)

\begin{itemize}
\item[2:00 p.m.]   G. Stormo:  "Using Thermodynamic Considerations as a
            Guide in Multiple Alignments"

\item[3:00 p.m.]   W. Pearson: "Comparing Sequence Comparison Algorithms - 
            is Optimal Best?" 

\item[4:00 p.m.]   Coffee Break (Faculty Lounge)

\item[4:30 p.m.]   Contributed Talks 

\item[]            M. Vingron and Arndt von Haesler, German National Research Center 
            for Computer Science and Dept. of Zoology, University of Munich:
            "Towards Integration of Multiple Alignment and Phylogenetic Tree
            Construction" 

 \item[]    P. Agarwal and D. J. States, Institute for Biomedical Computing,
            Washington University:
            "Computational Techniques for Repeat Analysis of DNA Sequences" 

\item[]     V. Fischetti, T.C. Ip and J. Schmidt, The Rockefeller University
            and  Polytechnic University: 
            "Matching Coiled-coil Proteins as Two Dimensional Structures"   

 \item[]    Z. Zhang and W. Miller, Dept. of Computer Science, Penn State: 
            "Enumerating Aligned Sequence Blocks"

\item[7:00 p.m.]   Reception (Eisenhart Lounge, top of Fine Tower, Fine Hall,

            Washington Road \& Ivy Lane)

\end{itemize}
\end{description}
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\begin{description}
\item[{\bf Friday,  November 11}] (Liberation Hall, Third World Center, 
corner of Olden \& Prospect)

\begin{itemize}
\item[8:30 a.m.]   Continental Breakfast (Liberation Hall)
\end{itemize}

\item[{\bf Session 3}] (Chair: M. Farach)

\begin{itemize}

\item[9:00 a.m.]   S. Altschul: "The Statistics of Pairwise Sequence Comparison
            and the Choice of Scoring Systems" 

\item[10:00 a.m.]  S. Henikoff: "Empirical Evaluation of Scoring in Sequence 
            Alignment"

\item[11:00 a.m.]  Coffee Break (Liberation Hall)

\item[11:30 a.m.] J. Schmidt  "Mathematical Models for Sequence Comparison"


\item[12:30]       Lunch (Liberation Hall)


\item[{\bf Session 4}] (Chair: M. Waterman)

\item[2:00 p.m.]   J. Kececioglu:  "Exact Algorithms for Multiple Sequence Alignment"

\item[3:00 p.m.]   P. Pevzner:  "Genomic Sequence Comparison"

\item[4:00 p.m.]   Coffee Break (Liberation Hall)

\item[4:30 p.m.]   Contributed Talks 

\item[]            T. Jiang, E.L. Lawler and L. Wang, Depts. of Computer Science and 
            Engineering, McMaster University and UC Berkeley:
            "Aligning Sequences via an Evolutionary Tree: Complexity and
            Approximation"

\item[5:30 p.m.]   Poster Session and Software Demonstration (CS Auditorium)
\end{itemize}
\end{description}
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\begin{description}
\item[{\bf Saturday, November 12}] (Liberation Hall, Third World Center, 
corner of Olden \& Prospect)
\begin{itemize}
\item[8:30 a.m.]   Continental Breakfast (Liberation Hall)
\end{itemize}

\item[{\bf Session 5}] (Chair: A. Apostolico)

\begin{itemize}
\item[9:00 a.m.]  W. Miller:  "Some Pathways for Applying Computer Science to
            Molecular Biology".



\item[10:00 a.m.]     Contributed Talks 

\item[]            J. Thompson, T. Gibson and D. Higgins, European Molecular 
            Biology Lab. and European Bioinformatics Lab.:   
            "Parameter Choice in Progressive Multiple Sequence Alignment" 

\item[]        G. Benson and M.S. Waterman, Dept. of Mathematics and Dept. of 
            Molecular Biology, University of Southern California:
            "On Finding Homologous Regions in a Set of Protein Sequences"







\item[11:00]       Coffee Break (Liberation Hall)

\item[11:30 a.m.]  M. Vingron: "Multiple Sequence Comparison and Consistency on 
            Multipartite Graphs". 

\item[12:30]       Farewell 

\end{itemize}
\end{description}
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