My research visit to another lab - in which ways did I benefit from it

EL did a six month exchange visit to the algorithms group of ICSI Berkeley from July 2006 till January 2007 under the supervision of EH. EL is a PhD student at the ISB graduate school. He is doing his research work at the Quantitative Biology and Bioinformatics Group in VTT (henceforth QBIX) under the supervision of MO. His research focuses on biological networks. The purpose of this visit was to establish a collaboration between QBIX and EH's algorithms group. QBIX has established an informative rich system for visualizing heterogeneous biological data [1], and EH has successfully applied effective algorithms to many bioinformatics problems. We developed a method for detecting phenotype specific molecular interaction pathways. Our initial study context was in Type 1 Diabetes. We constructed an integrated protein interaction, metabolic pathway and signal transduction network in mouse. We used a color coding algorithm [2] to detect pathways in context of NOD (=Non ObeseDiabetic) mouse phenotypes. As a result we obtained several statistically significant pathways, which may therefore be associated with Type 1 Diabetes incidence and insulitis development. We are about to submit a paper from this study soon. We are continuing to use this method in our research at QBIX, and will possibly extend it. We believe it can be used to associate almost any molecular network with almost any phenotype. We have huge amounts of data available for elucidation. Our immediate next plan is to elucidate human pancreas islets, mold and yeast data. This may open up new collaborations as well. [1] Gopalacharyulu et al., Bioinformatics 21, i177-i185 (2005). [2] Alon et al., Color Coding, J. ACM 42 (1995) 844-856.