|A Web Interface for Automatic Microarray Analysis|
Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
DNA-Microarray technology provides a diagnostic tool for studying cancer and genetic diseases, allowing the experimenter to identify disease related genes and predict the tumour type for new cell samples. However, the statistical analysis of microarray data is a time-consuming and error-prone process. To address this problem we have developed a web interface for automatic DNA-microarray analysis, ArrayMining.net, which guides the user through the analysis process and performs automatic parameter
|A modular and stochastic approach to the study of gene circuits using P systems|
Romero-Campero FJ, Blakes J, Cao H, Camara M, Krasnogor N.
presented at Genomes to Systems Manchester, UK March 17-19 2008
|Formal informatics and machine learning for more principled systems and synthetic biology|
Romero-Campero FJ, Blakes J, Camara M, Willams P, Perez-Jimenez MJ, Krasnogor N
presented at European Conference on Synthetic Biology (ESF-UB Conference in Biomedicine), Sant Feliu de Guixols, Spain, 24-29 November 2007.
|A systems analysis of the AHL Quorum Sensing system in Pseudomonas aeruginosa|
Romero-Campero FJ, Blakes J, Camara M, Krasnogor N.
presented at Systems Biology (ESF-UB Conference in Biomedicine), Sant Feliu de Guixols, Spain, 12-17 April 2008
|An Integrated Development Environment for Synthetic Biology Models|
Blakes J, Romero-Campero FJ, Twycross J, Cao H, Krasnogor N
presented at European Conference on Synthetic Biology (ECSB) II: Design, Programming and Optimisation of Biological Systems (ESF-UB Conference in Biomedicine), Sant Feliu de Guixols, Spain, 29 March - 03 April 2009
|T cell response to cholera infection|
Weil AA, Arifuzzaman M, Bhuiyan TR, Harris JB, Kendall EA, Hossain A, LaRocque RC, Harris AM, Tarique AA, Chowdhury F, Khan AI, Banerjee KK, Ryan ET, Qadri F, Calderwood SB
Natural Vibrio cholerae infection generates a robust B-cell response that wanes for T-cell independent antigens, suggesting that B-cell responses may be mediated in a T-cell dependent manner. Patients with cholera develop a memory-effector T-cell response to cholera antigens, and B-cell activation occurs after T-cell population expansion, suggesting that T-cells may play an important role in the development and maintenance of memory B-cell responses to T-cell dependent antigens.
|Data Management System for Distributed Virtual Screening|
Ting Zhou , Amedeo Caflisch
To manage HTD data effectively and efficiently, we have developed a distributed virtual screening data manage- ment system (DVSDMS) by integrating the open source database MySQL into high throughput docking.
|Resorufin - a lead for a new protein kinase CK2 inhibitor |
Iben Skjøth Sandholt1, Birgitte Brinkmann Olsen1, Barbara Guerra1, Olaf-Georg Issinger1, Brigitte Boldyreff2
Screening of a natural compound library led to the identification of resorufin, as a highly selective and potent inhibitor for protein kinase CK2. Out of 52 kinases tested only CK2 was inhibited. The IC50 values determined for the CK2 holoenzymes were 1.5 µM and for the free catalytic subunits ca. 4 µM. In different cancer cell lines treatment with resorufin led to cell death and endogenous CK2 was inhibited.
|Automation of cell proliferation assay sulforhodamine B fot the screening of stilbene derivatives|
Anne Soikkeli, Cristina Sempio, Erkki Mannila, Arto Urtti, Jouni Hirvonen, Marjo Yliperttula
The SRB assay was implemented on a TECAN Genesis workstation by optimizing cell numbers and liquid handling parameters. Anticancer drugs vinblastine, doxorubicin and 5-fluorouracil were used for standardizing the assay with a DU-145 cell line. To screen the antiproliferative activities of a series of stilbene derivatives, altogether 121 different stilbene structures, a plate layout was designed on 96-well format.