BREW 2005

Program

Sunday, April 24

Arrival, optionally meeting for Dinner.

Monday, April 25

8:30 – 9:00         Registration/Coffee

9:00 – 10:00        invited talk: Knut Reinert, Free University, Berlin, "Algorithms for differential quantification using HPLC/MS" (abstract).

10:05 – 10:45      Sérgio A. de Carvalho Jr., Bielefeld, "Improving the layout of oligonucleotide microarrays" (pdf).

10:45 – 11:10      Coffeebreak

11:10 – 11:35      Laura Elo, Helsinki, "The effect of replication on gene rankings: a practical comparison of methods for detecting differential expression in microarray experiments" (pdf).

11:35 – 12:00      Rashi Gupta, Helsinki, "Improving microarray image acquisition and quantification" (pdf).

12:00 – 12:25      Ivan G. Costa Filho, Berlin, "On external indices for mixtures: validating mixtures of genes" (pdf).

12:25 – 13:30      Lunch

13:30 – 13:55      Leo Lahti, Helsinki, "Validity studies on alternative interpretation of microarray data" (ps).

13:55 – 14:35      Niina Haiminen, Helsinki, "Probabilistic modelling of binary segmentations" .

14:35 – 15:00      Evimaria Terzi, Helsinki, "Models and algorithms for network immunization" (ps).

15:00 – 16:00      invited talk: Frank Cordes, Zuse Institute Berlin, "Structural-based virtual screening and the role of metastability"

16:00 – 16:30      Coffeebreak

16:30 – 17:10      Julia Mixtacki, Bielefeld, "On sorting by translocations" (ps).

17:10 – 17:50      Lauri Eronen, Helsinki, "Haplotype reconstruction with Markov models" (ps).

17:50 – 18:15      Merja Oja, Helsinki, "Expression of human endogeneous retroviruses" (ps).

Tuesday, April 26

9:00 – 10:00        invited talk: Reinhart Heinrich, Humboldt University, Berlin, "Dynamics and design of metabolic pathways and signal transduction networks".

10:05 – 10:45      Philipp W. Messer, Berlin, "Sequence evolution and long-range correlations in genomic base composition" (ps).

10:45 – 11:10      Coffeebreak

11:10 – 11:35      Abhishek Kumar, Bielefeld, "Delving into vertebrate serpins for understanding their evolution".

11:35 – 12:00      Utz J. Pape, Berlin, "Prediction of genes involved in lignification" (pdf).

12:00 – 12:25      Wasinee Rungsarityotin, Berlin, "Graph cut for identification of bacterial clonal complexes from multi-locus sequence types" (pdf).

12:25 – 13:30      Lunch

13:30 – 14:10      Jens Reeder, Bielefeld, "Consensus shapes: An alternative to the Sankoff algorithm for RNA consensus structure prediction" (pdf).

14:10 – 14:35      Janina Reeder, Bielefeld, "A visual RNA motif editor for generating thermodynamic matchers" (pdf).

14:35 – 14:50      Coffeebreak

14:50 – 15:30      Markus Bauer, Berlin, "Structural alignment of RNA sequences with Langrangian relaxation" (pdf).

15:45                  Going together to city center by subway

16:45                  Meeting at Reichstag (Westeingang Paul-Löbe-Haus, Konrad-Adenauer-Str.)

17:00 – 18:30      Tour through Reichstag

19:30                  Conference Dinner at "Max und Moritz", Oranienstr. 162, Kreuzberg.

Wednesday, April 27

9:00 – 10:00        invited talk: Hanah Margalit, Hebrew University, Jerusalem, "Lessons from cellular networks" (abstract).

10:05 – 10:45      Sylvain Gaudan, Hinxton, "Resolving abbreviations to their senses in Medline".

10:45 – 11:10      Coffeebreak

11:10 – 11:35      Perttu Haimi, Helsinki, "Analysis of complex lipid samples by mass spectrometry" (pdf).

11:35 – 12:00      Gisle Sælensminde, Bergen, "A pipeline for finding characteristic amino acid subsitutions for cold-adapted proteins" (pdf).

12:00 – 12:40      James W. Torrance, Hinxton, "Using structural templates to recognise metal binding sites" (pdftext, pdffigure).

12:40 – 13:45      Lunch

13:45 – 14:10      Margus Lukk, Helsinki, "Searching regulatory factors for genes in higher eukaryotes" (pdf).

14:10 – 14:50      Abha Singh Bais, Berlin, "Simultaneous alignment and annotation of cis-regulatory regions" (pdf).

14:50 – 15:15      Holger Klein, Berlin, "Detection of preferentially co-occuring transcription factor binding sites" (pdf).

15:15 – 16:00      Coffee/Closing remarks