|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
|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.
|A Novel Multiplexed Digital Gene Expression Technology|
Gary K. Geiss1,#, Roger Bumgarner2, Brian Birditt1, Timothy Dahl1, Naeem Dowidar1, Dwayne L. Dunaway1, H. Perry Fell1, Sean Ferree1, Renee D. George1, Tammy Grogan1, Jeffrey J. James1, Malini Maysuria1, Jeffrey D. Mitton1, Paola Oliveri4, Jennifer L. Osborn3, Tao Peng2, Amber L. Ratcliffe1, Philippa J. Webster1, Eric H. Davidson4, and Leroy Hood5
We describe a novel platform, the nCounter Analysis System, for sensitive, highly multiplexed, digital gene expression analysis based on NanoString’s novel molecular barcoding technology. Detection of individual mRNA molecules using an assigned sequence of six different fluorescent spots per probe are detected, and then the number of times that code sequence appears in a sample are counted.
|Oligonucleotides with LNA and targeting of biologically important RNAs|
Peter Guterstam and Ülo Langel
Activity of RNA-targeting antisense oligonucleotides increases when introducing LNA monomers, implying that an 18 nucleotides long LNA/2OMe mixmer splice-switching oligonucleotide can be shortened to 12mer and have similar activity and specificity as an 18mer 2OMe oligonucleoyide. Positioning of LNA monomers has to be carefully considered when utilizing the potent LNA monomers in RNA-targeting antisense oligonucleotides.
|A comparison of siRNA activity predictors using advanced regression techniques|
Simone Sciabola, Qing Cao, Theresa Johnson, Lingling Shen, Robert Stanton, Xiaoyu Jiang, Simon Xi, Jason Hughes, Daniel Caffrey, Shobha Potluri, Steven Haney, Johnathan Cyr, Jeremy Little
Although considerable progress has been made recently in understanding how gene silencing is mediated by the RNAi pathway, the design of effective sequences is still a challenging task. To tackle the efficacy challenge and further improve accuracy for prediction of siRNA potency, we performed a comparison of advanced regression techniques and new in-house generated descriptors in the generation of siRNA efficiency models.