Summer School in Computational Biology

Gregory Kucherov Gregory.Kucherov at loria.fr
Wed Jan 27 12:42:00 EST 1999



               SUMMER SCHOOL IN COMPUTATIONAL BIOLOGY





Enclosed please you will find a Call for Partecipation to a Summer
School in Computational Biology that will take place in Italy in June
99. Apologies if you receive this announcement more than once.  The
first part of the message contains a text file and the second part a
standard Latex file. 


DEADLINE FOR APPLICATION IS APRIL 20, 1999. FOR INFORMATION AND APPLICATION
IN ELECTRONIC FORM, VISIT http://alpha.dipmat.unict.it/~lipari/lipari.html 

Raffaele Giancarlo
             
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                 11-th Lipari International Summer School
                        Computational Biology
                   June 20-July 3, 1999-Lipari- ITALY



                        SCIENTIFIC  COMMITTEE

Alfredo Ferro (Univ. of Catania, Co-Chair), Zvi Galil (Columbia
Univ.), Raffaele Giancarlo (Univ. of Palermo, Co-Chair), Thomas
Lengauer ( GMD and Univ. of Bonn), Fabrizio Luccio (Univ. of Pisa).


                             LECTURERS

Alberto Apostolico (Univ. of Padova and Purdue Univ.), Sorin Istrail
(Sandia National Labs), Arthur Lesk (Univ. of Cambridge Medical
School), Bud Mishra (New York Univ.), Pavel Pevzner ( Univ. Southern
California), Cecilia Saccone (Univ. of Bari), Marie-France Sagot
(Institut Pasteur, Paris), David Sankoff (Univ. of Montreal), Martin
Vingron (German National Cancer Research Center), Mike Waterman
(Univ. of Southern California), Shoshana Wodak (EMBL-EBI and
Univ. Libre de Bruxelles).

                           


                                 SPONSORS
Italian National Research Council, Dipartimento di  Matematica-Universita' 
di Catania, Dipartimento di Matematica-Universita' di Messina, 
Dipartimento di Matematica-Universita' di Palermo, Dipartimento
d'Informatica-Universita' di Pisa, Regional Government of Sicily,
AAPIT Messina, AAPIT Aeloian Islands, City of Lipari, L'Informatica
SNC, Eures Informat.







                           LIST OF TOPICS


MOLECULAR BIOLOGY and ITS MATHEMATICS - Mike Waterman. Acronym:
MBM. Content: Basic Background material in Biology.  The mathematical
and statistical tools that are used in Computational Biology, e.g.,
probabilistic models for physical maps, statistical significance of
sequence alignments etc.


PROTEIN STRUCTURE- Shoshana Wodak. Acronym: PS.  Content: Principles
of protein structures; fold and motif classification; structure
comparisons.


STRING ALGORITHMICS- Alberto Apostolico. Acronym:SA. Content:
Algorithmic techniques for string processing, i.e., string matching,
suffix trees etc..



PAIRWISE and MULTIPLE SEQUENCE ALIGNMENT- Raffaele Giancarlo. Acronym:
TMSA. Content: Global and Local alignment algorithms. Data base
searches. Algorithms for Multiple Sequence Alignment.


ALGORITHMS for PROTEIN STRUCTURE PREDICTION- Sorin
Istrail. Acronym:APS. Content: Contact maps and energy potential
inference.  Structure Alignment. Inverse folding. Statistical
mechanics of lattice models.



GENOMIC DISTANCE- David Sankoff. Acronym: GD. Content:
Biological motivations and mathematical models for comparing genomic
sequences.  Methods to identify Conserved Segments.



ALGORITHMS for GENOMIC SEQUENCES- Pavel Pevzner.  Acronym:
AGD. Content: Similarity based algorithms for gene hunting. Genomic
comparison and sorting by reversals.

ORGANIZATION of LARGE  BIOLOGICAL  DATA  BASES- Fabrizio 
Luccio. Acronym:OLDB. Content: Information overload: algorithmic and
data structural issues; Secondary memory devices and new computational
paradigms; Textual data and genomic databases; Indexing large textual
databases; Existing biological databases: open problems and
discussion.

MOLECULAR PHILOGENY: PROBLEM and PROSPECTIVES-Cecilia Saccone.
Acronym:MP. Problems from Molecular Philogeny will be
presented. In particular, the presentation will focus on the 
mathematical models that are perceived to be best suited for the area
as well as a comparison with non-molecular approaches. 


PHYLOGENY and ALGORITHMS- Martin Vingron. Acronym:PH.  Algorithms for
inferring the evolutionary tree of a set of species, given their DNA
or RNA Sequences. Relation of those algorithms to Multiple Sequence
Alignment.

DYNAMIC PROGRAMMING in COMPUTATIONAL BIOLOGY- Zvi Galil.Acronym:
DP. Content: Dynamic Programming techniques as they apply to problems
in Computational Biology, e.g., sequence alignment, prediction of RNA
Secondary Structure, comparison of philogenetic trees, etc.


MOTIFS in SEQUENCES- Marie France Sagot. Acronym: MS.  Content:
Algorithms to identify motifs in Biological Sequences. Matching and
Concerns. Motif Inference. Constrained Motifs.


PROTEIN-LIGAND DOCKING with DISCRETE MODELS and METHODS-Thomas
Lengauer. Acronym: DOC. Content: Significance of docking problems,
problem variants, models, and algorithms for docking.

THREE-DIMENSIONAL  PATTERN  MATCHING  PROBLEMS in PROTEIN  STRUCTURE
ANALYSIS- Arthur Lesk. Acronym:3DPM.  Content: Algorithms to identify
and match common substructures of Proteins via Data Base Search.



GENOMICS via OPTICAL MAPPING- Bud Mishra. Acronym:GOM.
 Content: Biochemical basis for Optical Mapping and Error
Models. Computational Problems: Map Construction, Genomic DNA Based
Reference Maps, Map-assisted Sequence Assembly, Sequence Verification,
Optical Sequencing. Comparison with traditional approaches.


                      REGISTRATION AND INFORMATION

Lipari International Summer School limits attendance to a
maximum of 40 selected graduate students and young researchers.
Moreover, a limited number of additional partecipants (not falling in the 
mentioned categories)  will also be
admitted. For applications, registration fees and further information,
please contact Professor Alfredo Ferro, Dipartimento di Matematica,
Universita' di Catania, Italy. Email ferro at dipmat.unict.it.
DEADLINE FOR APPLICATION IS APRIL 20, 1999. 
WE DO ENCOURAGE ELECTRONIC APPLICATIONS. 
ALL INFORMATION and APPLICATION forms are available at the following URL
address: http://alpha.dipmat.unict.it/~lipari/lipari.html It should
also be noted that June 20 and July 3 are arrival and departure dates.





                               LOCATION


 Lipari is one of the Aeloian islands, a group of islands off the
coast of Eastern Sicily.  The natural setting of those islands is
simply breathtaking. In fact they are a very popular vacation spot
from early Spring to Autumn and all the major nautical activities one
can enjoy are offered (including swimming and resting on the beach-no
charge). For a ``virtual view'' of those magnificent islands, please
visit http://www.netnet.it ; http://www.itwg.com/en_eol01.htm. Lipari
is easily reachable via hydrofoil boat or ferry from Naples, Messina
and Milazzo. However, for people attending the School, there will be
round-trip transportation service from Catania Airport to Lipari.
Weather at the end of June is warm and pleasant and it is definitely
possible to swim and sunbath.  The islands, Lipari in particular, are
very rich in archeological sites from various Ancient
Civilizations. Moreover, the Greeks made sure that grapes for
excellent wines would be grown here.  The Residents were delighted to
develop a cousine that would accompany those wines. The Arabs and the
Normans added a few touches of their own for a quite unique style of
Mediterranian cousine.




*******************************************************************************


\documentstyle[11pt]{article}

\begin{document}




\centerline{\bf 11-th Lipari International Summer School}
\centerline{\bf Computational Biology}
\centerline{\bf June 20-July 3, 1999-Lipari- ITALY}

\medskip

\noindent {\bf Scientific Committee}: Alfredo Ferro 
(Univ. of Catania, Co-Chair),
Zvi Galil (Columbia Univ.), Raffaele Giancarlo (Univ. of Palermo, Co-Chair),
Thomas Lengauer ( GMD and Univ. of Bonn), Fabrizio Luccio (Univ. of
Pisa).


\medskip

\noindent {\bf Lecturers}: Alberto Apostolico (Univ. of Padova and
Purdue Univ.), Sorin Istrail (Sandia National Labs), Arthur Lesk
(Univ. of Cambridge Medical School), Bud Mishra (New York Univ.),
Pavel Pevzner ( Univ. Southern California), Cecilia Saccone(Univ. of
Bari), Marie-France Sagot (Institut Pasteur, Paris), David Sankoff
(Univ. of Montreal), Martin Vingron (German National Cancer Research
Center), Mike Waterman (Univ. of Southern California), Shoshana Wodak
(EMBL-EBI and Univ. Libre de Bruxelles).

\medskip

\noindent {\bf Sponsors}: Italian National Research Council, Dipartimento di
 Matematica-Universit\'a di Catania, Dipartimento di
Matematica-Universit\'a di Messina, Dipartimento di
Matematica-Universit\'a di Palermo, Dipartimento
d'Informatica-Universit\'a di Pisa, Regional Government of Sicily,
AAPIT Messina, AAPIT Aeloian Islands, City of Lipari, L'Informatica
SNC, Eures Informat. 

\medskip


\noindent \centerline{\bf List of Topics}


\begin{itemize}


\item[$\bullet$] {\bf  Molecular  Biology and its Mathematics}- Mike 
Waterman. Acronym: MBM. Content: Basic Background material in Biology.
The mathematical and statistical tools 
that are used in Computational Biology, e.g., probabilistic models
for physical maps, statistical significance of sequence alignments
etc.


\item[$\bullet$] {\bf Protein Structure}- Shoshana Wodak. Acronym: PS.
Content: Principles of protein structures; fold and motif
         classification; structure comparisons.


\item[$\bullet$] {\bf  String Algorithmics}- Alberto Apostolico. Acronym:
SA. Content: Algorithmic techniques for string 
processing, i.e., string matching, suffix trees etc..



\item[$\bullet$] {\bf  Pairwise  and Multiple Sequence Alignment}- 
Raffaele Giancarlo. Acronym: TMSA. Content: Global and Local alignment
algorithms. Data base searches. Algorithms for Multiple Sequence
Alignment.



\item[$\bullet$] {\bf Algorithms for Protein Structure Prediction}- 
Sorin Istrail. Acronym:APS. Content: Contact maps and energy potential
inference.  Structure Alignment. Inverse folding. Statistical
mechanics of lattice models.


\item[$\bullet$] {\bf Genomic Distance}- David Sankoff. Acronym: GD. Content:
Biological motivations and mathematical models for comparing genomic
sequences.  Methods to identify Conserved Segments.



\item[$\bullet$] {\bf  Algorithms for Genomic Sequences}- Pavel Pevzner. 
Acronym: AGD. Content: Similarity based algorithms for gene hunting. Genomic
comparison and sorting by reversals.

\item[$\bullet$] {\bf Organization of Large Biological Data Bases}- Fabrizio 
Luccio. Acronym:OLDB. Content: Information overload: algorithmic and
data structural issues; Secondary memory devices and new computational
paradigms; Textual data and genomic databases; Indexing large textual
databases; Existing biological databases: open problems and
discussion.

\item[$\bullet$] {\bf Molecular Philogeny: Problems and
Prospectives}-Cecilia Saccone. Acronym:MP. Problems from Molecular
Philogeny will be presented. In particular, the presentation will
focus on the mathematical models that are perceived to be best suited
for the area as well as a comparison with non-molecular approaches.


\item[$\bullet$] {\bf  Phylogeny and Algorithms}- Martin Vingron. Acronym:PH. 
Algorithms for inferring the evolutionary 
tree of a set of species, given their DNA or RNA Sequences. Relation of
those algorithms to Multiple Sequence Alignment. 

\item[$\bullet$]{\bf Dynamic Programming in Computational Biology}-
Zvi Galil.Acronym: DP. Content: Dynamic Programming techniques as they
apply to problems in Computational Biology, e.g., sequence alignment,
prediction of RNA Secondary Structure, comparison of philogenetic
trees, etc.


\item{\bf Motifs in Sequences}- Marie France
Sagot. Acronym: MS.  Content: Algorithms to identify motifs in
Biological Sequences.  Matching and Concerns. Motif
Inference. Constrained Motifs.



\item[$\bullet$] {\bf  Protein-ligand docking with discrete models and 
methods}-Thomas Lengauer. Acronym: DOC. Content: Significance of docking 
problems, problem variants, models, and algorithms for docking.

\item[$\bullet$] {\bf Three-Dimensional Pattern Matching Problems in 
Protein Structure Analysis}- Arthur Lesk. Acronym:3DPM.  Content:
Algorithms to identify and match common substructures of Proteins via
Data Base Search.



\item[$\bullet$]{\bf  Genomics via Optical Mapping}- Bud Mishra. Acronym:GOM.
 Content: Biochemical basis for Optical Mapping and Error
Models. Computational Problems: Map Construction, Genomic DNA Based
Reference Maps, Map-assisted Sequence Assembly, Sequence Verification,
Optical Sequencing. Comparison with traditional approaches.


\end{itemize} 


\noindent {\bf Registration and Information}: Lipari International
Summer School limits attendance to a maximum of 40 selected graduate
students and young researchers.  Moreover, a limited number of
additional partecipants (not falling in the mentioned categories) will
also be admitted. For applications, registration fees and further
information, please contact Professor Alfredo Ferro, Dipartimento di
Matematica, Universita' di Catania, Italy. Email
ferro at dipmat.unict.it.  DEADLINE FOR APPLICATION IS APRIL 20, 1999. WE
DO ENCOURAGE ELECTRONIC APPLICATIONS.  ALL INFORMATION and APPLICATION
forms are available at the following URL address:
http://alpha.dipmat.unict.it/~lipari/lipari.html It should also be
noted that June 20 and July 3 are arrival and departure dates.

\medskip

\noindent {\bf Location}. Lipari is one  of the Aeloian islands, a group
of islands off the coast of Eastern Sicily.  The natural setting of
those islands is simply breathtaking. In fact they are a very popular
vacation spot from early Spring to Autumn and all the major nautical
activities one can enjoy are offered (including swimming and resting
on the beach-no charge). For a ``virtual view'' of those magnificent
islands, please visit http://www.netnet.it ;
http://www.itwg.com/en\_eol01.htm. Lipari is easily reachable via
hydrofoil boat or ferry from Naples, Messina and Milazzo. However, for
people attending the School, there will be round-trip transportation  
service from Catania Airport to Lipari. 
Weather at the end of
June is warm and pleasant and it is definitely possible to swim and
sunbath.  The islands, Lipari in particular, are very rich in
archeological sites from various Ancient Civilizations. Moreover, the
Greeks made sure that grapes for excellent wines would be grown here.
The Residents were delighted to develop a cousine that would
accompany those wines. The Arabs and the Normans added a few touches
of their own for a quite unique  style of Mediterranian cousine. 





\end{document}




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