Welcome, Dear Reader!

This is the newsletter of the Pharma-IT Platform of the Leiden / Amsterdam Center for Drug Research (LACDR), the Leiden Institute for Advanced Computer Science (LIACS) and the Mathematical Institute (MI) of Leiden University.

For up-to-the-minute information please visit our website at
http://www.PHARMA-IT.net.

Our Next Event:

The 6th Pharma IT Interaction Meeting on "Networks and Graphs in Life Science and Pharma-IT" is coming!

Day and time: Thursday, 25 February 2010, 4.00pm
Location: Gorlaeus Laboratoria (Einsteinweg 55), Room L144, Leiden University. Interested to present and network or just to listen? Feel free to join us! (For details please see '4. Events' below)


What else happened in the Pharma-IT Platform?

1. Research / Collaborator News

LIACS, CML and MI received a NWO grant for the BetNet project (http://natcomp.liacs.nl/index.php?page=BETNET) working on "The evolution of stochastic heterogeneous networks as bet-hedging adaptations to fluctuating environments". In this context Dr. Sella has assumed a postdoctoral position within LIACS.

Anton den Hoed started his BSc thesis with Johannes Kruisselbrink and Michael Emmerich on "Parsing and Conversion of SMILES-strings to Molecular Graphs".

Olaf van den Hoven joined the Pharma-IT Platform to work at the LACDR on his MSc thesis, supervised by Gerard van Westen and Andreas Bender, on "Predicting the Activity Profile of Compounds on Adenosine Receptor Subtypes Using Proteochemometric Models".

Also Marysa van den Berg joined Gerard van Westen and Andreas Bender at the LACDR to work on her MSc thesis with the topic "Homology modeling of the nicotinic acid receptors GPR109A and B and the determination of ligand binding modes through docking".

Welcome to all new collaborators!


2. New publications

"Chemogenomics: Looking at biology through the lens of chemistry"
(A result of joint LIACS and LACDR work)
Statistical Analysis and Data Mining,
http://www3.interscience.wiley.com/journal/122564072/abstract

"Predicting the functions of proteins in PPI networks from global information"
(From a collaboration of LIACS, LACDR and KU Leuven)
Journal of Machine Learning Research (in press)

"Mining protein dynamics from Sets of crystal structures using Consensus Structures"
(A collaboration between the company Tibotec and the LACDR)
Protein Science,
http://www3.interscience.wiley.com/journal/123268578/abstract

"Adaptive Niche-Radii and Niche-Shapes Approaches for Niching with the CMA-ES"
(Originating from LIACS research)
Evolutionary Computation,
http://www.mitpressjournals.org/toc/evco/0/0

Please follow the links if you are interested in the above publications for further information.


3. Pharma-IT Internal News

Starting in summer 2010, Michael Emmerich will join the group of Prof. Carlos Fonseca at the Universidade do Algarve (http://www.ualg.pt/) for six months on a FCT Individual Postdoctoral Grant. Carlos Fonsenca is one of the eminent researchers in the field of multi-objective optimization and the aim of the stay is to work on the theoretical foundations of indicator-based multiobjective optimization algorithms and to foster new collaborations within this field. 

Starting in May 2010, Andreas Bender will join the Unilever Center for Molecular Sciences Informatics at the University of Cambridge (http://www-ucc.ch.cam.ac.uk/) in a group leader position. He will retain strong ties with Leiden University with regular visits and continue to develop his current research collaborations in the future.


4. Events: "Networks and Graphs in Life Science and Pharma-IT" Interaction Meeting 

The 6th 'Pharma IT Interaction Meeting' is coming!
Topic: "Networks and Graphs in Life Science and Pharma-IT"
Day and time: Thursday, 25 February 2010, 4-5pm in room L144 of the Gorlaeus Laboratoria (Einsteinweg 55, Leiden University)

The topic of this meeting will be the use of networks (graphs) in various areas of chem- and bioinformatics, and various research groups from the LACDR, LIACS, the Metabolomics Center, the Biology Department and other institutes will give short (10min) presentations on their current research for networking purposes. ** You are interested in presenting as well? Please drop us an e-mail (emmerich@liacs.nl or bendera@lacdr.leidenuniv.nl)!** After the meeting we will visit the recently opened Science Bar for further extension of the networking.


Best wishes and looking forward to seeing you at the Interaction Meeting!
Andreas Bender and Michael Emmerich

Academic Leadership Team of the Pharma-IT Platform
http://www.PHARMA-IT.net