Research Topics
Genomes and Genes | Tim BeissbarthSummaryAffiliation: The Walter and Eliza Hall Institute of Medical Research Country: Australia Publications
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Detail Information
Publications
GOstat: find statistically overrepresented Gene Ontologies within a group of genesTim Beissbarth
Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3050, Australia
Bioinformatics 20:1464-5. 2004..This results in a list of GO terms sorted by their specificity. AVAILABILITY: Our program GOstat is accessible via the Internet at http://gostat.wehi.edu.au..- Statistical modeling of sequencing errors in SAGE librariesTim Beissbarth
Walter and Eliza Hall Institute of Medical Research, Genetics and Bioinformatics, Parkville, Vic, Australia
Bioinformatics 20:i31-9. 2004..Current sequencing technology generates quite accurate estimates of sequencing error rates. Here we make use of the sequence neighborhood of SAGE tags and error estimates from the base-calling software to correct for such errors... - A systematic approach for comprehensive T-cell epitope discovery using peptide librariesTim Beissbarth
Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Australia
Bioinformatics 21:i29-37. 2005..We were interested in the study of celiac disease (CD) and used the ELISPOT technique to perform a large number of T-cell assays. We therefore needed to compensate for the lack of statistical data analysis methods for ELISPOT assays... - Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profilingKing Hwa Ling
Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
Genome Biol 10:R104. 2009..It is proposed that transcriptome profiling of the cerebral cortex at various developmental time points or regions will reveal candidate genes and associated molecular pathways involved in cerebral corticogenesis... - A serial analysis of gene expression profile of the Alzheimer's disease Tg2576 mouse modelAmee J George
Department of Pathology, The University of Melbourne and The Mental Health Research Institute of Victoria, Parkville, VIC 3052, Australia
Neurotox Res 17:360-79. 2010..The novel approach of profiling the Tg2576 mouse brain using SAGE has identified different genes that could subsequently be examined for their potential as peripheral diagnostic and prognostic markers for Alzheimer's disease... - Comprehensive, quantitative mapping of T cell epitopes in gluten in celiac diseaseJason A Tye-Din
Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
Sci Transl Med 2:41ra51. 2010..Our findings show that pathogenic T cells in celiac disease show limited diversity, and therefore suggest that peptide-based therapeutics for this disease and potentially other strongly HLA-restricted immune diseases should be possible... - Nedd4-WW domain-binding protein 5 (Ndfip1) is associated with neuronal survival after acute cortical brain injuryQian Sang
Howard Florey Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
J Neurosci 26:7234-44. 2006..These results identify N4WBP5 as a neuroprotective protein and, based on its known interaction with the ubiquitin ligase Nedd4, would suggest protein ubiquitination as a possible survival strategy in neuronal injury... - SAGE analysis of genes differentially expressed in presymptomatic TgSOD1G93A transgenic mice identified cellular processes involved in early stage of ALS pathologyMichel Guipponi
Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3050, Australia
J Mol Neurosci 41:172-82. 2010.... - GOSim--an R-package for computation of information theoretic GO similarities between terms and gene productsHolger Frohlich
German Cancer Research Center DKFZ, Div Molecular Genome Analysis, Im Neuenheimer Feld 580, Heidelberg, Germany
BMC Bioinformatics 8:166. 2007.... - Predicting pathway membership via domain signaturesHolger Frohlich
German Cancer Research Center DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
Bioinformatics 24:2137-42. 2008..However, only a small fraction of genes is annotated with pathway information up to now. In contrast, information on contained protein domains can be obtained for a significantly higher number of genes, e.g. from the InterPro database... - Integrative analysis of RUNX1 downstream pathways and target genesJoelle Michaud
Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3050, Victoria, Australia
BMC Genomics 9:363. 2008..We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia... - Extending pathways based on gene lists using InterPro domain signaturesFlorian Hahne
German Cancer Research Center, Molecular Genome Analysis, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
BMC Bioinformatics 9:3. 2008..This works by comparing InterPro domain signatures of the candidate gene lists with domain signatures of gene sets derived from known classifications, e.g. KEGG pathways... - Modeling breast cell cycle regulation--overcoming drug resistanceDorit Arlt
Div. of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
Conf Proc IEEE Eng Med Biol Soc 1:40-3. 2006 - A structural and immunological basis for the role of human leukocyte antigen DQ8 in celiac diseaseKate N Henderson
The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
Immunity 27:23-34. 2007..Accordingly, nondietary therapeutic interventions in celiac disease might need to be tailored to the genotype of the individual... - Interpreting experimental results using gene ontologiesTim Beissbarth
The Walter and Eliza Hall Institute of Medical Research, Bioinformatics Group, Victoria, Australia
Methods Enzymol 411:340-52. 2006..This chapter focuses primarily on the tool GOstat (http://gostat.wehi.edu.au). Other tools exist that enable similar analyses, but are not described in detail here... - Analysis of CREM-dependent gene expression during mouse spermatogenesisTim Beissbarth
Molecular Biology of the Cell 1, German Cancer Research Center, DKFZ, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
Mol Cell Endocrinol 212:29-39. 2003.... - Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arraysMarcel Scheideler
Functional Genome Analysis and Theoretical Bioinformatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
J Biol Chem 277:10555-61. 2002..Furthermore, our data showed potentially important changes in areas of metabolism, such as the glyoxylate metabolism, hitherto not suspected to be components of plant defense...