Research Topics
| Mark D RobinsonSummaryAffiliation: The Walter and Eliza Hall Institute of Medical Research Country: Australia Publications
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Detail Information
Publications
Moderated statistical tests for assessing differences in tag abundanceMark D Robinson
Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
Bioinformatics 23:2881-7. 2007....- edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataMark D Robinson
Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
Bioinformatics 26:139-40. 2010..The software may have other applications beyond sequencing data, such as proteome peptide count data. AVAILABILITY: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org)... - A comparison of Affymetrix gene expression arraysMark D Robinson
Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3050, Australia
BMC Bioinformatics 8:449. 2007..In this study, we use publicly available data from Affymetrix to gauge the performance of three human gene expression arrays: Human Genome U133 Plus 2.0 (U133), Human Exon 1.0 ST (HuEx) and Human Gene 1.0 ST (HuGene)... - A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experimentsMark D Robinson
The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3050, Australia
BMC Bioinformatics 8:419. 2007..Automated retention time correction is particularly important in non-targeted profiling studies... - Small-sample estimation of negative binomial dispersion, with applications to SAGE dataMark D Robinson
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, and Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
Biostatistics 9:321-32. 2008..The impact of dispersion estimation on hypothesis testing is studied. We derive an "exact" test that outperforms the standard approximate asymptotic tests... - A scaling normalization method for differential expression analysis of RNA-seq dataMark D Robinson
Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Australia
Genome Biol 11:R25. 2010..We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets... - Protocol matters: which methylome are you actually studying?Mark D Robinson
Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
Epigenomics 2:587-98. 2010..There is promise for this to change, as the third generation of sequencing technologies is expected to again 'revolutionize' the way that we study genomes and epigenomes... - Differential splicing using whole-transcript microarraysMark D Robinson
Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
BMC Bioinformatics 10:156. 2009..We explore the possibility of using the Gene 1.0 ST platform to identify differential splicing events... - Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage biasShalima S Nair
Epigenetics Laboratory, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
Epigenetics 6:34-44. 2011..Our study highlights the importance of understanding the nuances of the methods used for DNA genome-wide methylation analyses so that accurate interpretation of the biology is not overlooked... - Repitools: an R package for the analysis of enrichment-based epigenomic dataAaron L Statham
Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
Bioinformatics 26:1662-3. 2010..We have created a toolbox of procedures to interrogate and visualize epigenomic data (both array- and sequencing-based) and make available a software package for the cross-platform R language... - Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variationMark D Robinson
Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
Genome Res 20:1719-29. 2010.... - Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticityMarcel W Coolen
Epigenetics Laboratory, Cancer Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
Nat Cell Biol 12:235-46. 2010..We propose that consolidation or effective reduction of the cancer genome commonly occurs in domains through a combination of LRES and LOH or genomic deletion, resulting in reduced transcriptional plasticity within these regions... - From RNA-seq reads to differential expression resultsAlicia Oshlack
Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
Genome Biol 11:220. 2010..Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression... - Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancerFatima Valdes-Mora
Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
Genome Res 22:307-21. 2012..Z anti-correlates with promoter H3K27me3 and DNA methylation. We show for the first time, that acetylation of H2A.Z is a key modification associated with gene activity in normal cells and epigenetic gene deregulation in tumorigenesis... - Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcriptionToby Hulf
Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
BMC Genomics 12:54. 2011..Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression. In this study, we established a robust discovery pipeline to identify epigenetically deregulated miRNAs in cancer... - High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutantsPaul Jorgensen
Department of Medical Genetics and Microbiology, University of Toronto, Ontario M5S 1A8, Canada
Genetics 162:1091-9. 2002..In principle, SGAM should be applicable to the analysis of multigenic traits. Large-scale construction of ordered mutations in other model organisms would broaden the application of this approach... - A panoramic view of yeast noncoding RNA processingWen Tao Peng
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
Cell 113:919-33. 2003..These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA... - High-definition macromolecular composition of yeast RNA-processing complexesNevan J Krogan
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
Mol Cell 13:225-39. 2004..This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery... - Transcriptional networks: reverse-engineering gene regulation on a global scaleGordon Chua
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Room 307, Toronto, Ontario M5G 1L6, Canada
Curr Opin Microbiol 7:638-46. 2004..The results indicate that a complete and comprehensive yeast transcriptional network will ultimately be achieved... - The functional landscape of mouse gene expressionWen Zhang
Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
J Biol 3:21. 2004.... - Genome-wide analysis of mouse transcripts using exon microarrays and factor graphsBrendan J Frey
Electrical and Computer Engineering, University of Toronto, 10 King s College Rd, Toronto, Ontario M5S 3G4, Canada
Nat Genet 37:991-6. 2005..GenRate also detected tens of thousands of potential new exons and reconciled discrepancies in current cDNA databases by 'stitching' new transcribed regions into previously annotated genes... - Identifying transcription factor functions and targets by phenotypic activationGordon Chua
Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 1A8
Proc Natl Acad Sci U S A 103:12045-50. 2006..The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology... - Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clustersLani F Wu
Rosetta Inpharmatics, Kirkland, Washington, USA
Nat Genet 31:255-65. 2002..We present experimental validation confirming the involvement of several of these proteins in ribosomal RNA processing. Our methodology can be applied to a variety of genomics data types and organisms...