Mark D Robinson

Summary

Affiliation: The Walter and Eliza Hall Institute of Medical Research
Country: Australia

Publications

  1. ncbi Moderated statistical tests for assessing differences in tag abundance
    Mark D Robinson
    Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
    Bioinformatics 23:2881-7. 2007
  2. pmc edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    Mark D Robinson
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
    Bioinformatics 26:139-40. 2010
  3. pmc Differential splicing using whole-transcript microarrays
    Mark D Robinson
    Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
    BMC Bioinformatics 10:156. 2009
  4. pmc 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
  5. pmc A scaling normalization method for differential expression analysis of RNA-seq data
    Mark D Robinson
    Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Australia
    Genome Biol 11:R25. 2010
  6. pmc A comparison of Affymetrix gene expression arrays
    Mark D Robinson
    Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3050, Australia
    BMC Bioinformatics 8:449. 2007
  7. pmc A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments
    Mark D Robinson
    The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3050, Australia
    BMC Bioinformatics 8:419. 2007
  8. ncbi Small-sample estimation of negative binomial dispersion, with applications to SAGE data
    Mark 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
  9. doi Regional activation of the cancer genome by long-range epigenetic remodeling
    Saul A Bert
    Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
    Cancer Cell 23:9-22. 2013
  10. pmc Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer
    Fatima Valdes-Mora
    Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Genome Res 22:307-21. 2012

Collaborators

Detail Information

Publications26

  1. ncbi Moderated statistical tests for assessing differences in tag abundance
    Mark D Robinson
    Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
    Bioinformatics 23:2881-7. 2007
    ....
  2. pmc edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    Mark 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...
  3. pmc Differential splicing using whole-transcript microarrays
    Mark 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...
  4. pmc 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...
  5. pmc A scaling normalization method for differential expression analysis of RNA-seq data
    Mark 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...
  6. pmc A comparison of Affymetrix gene expression arrays
    Mark 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)...
  7. pmc A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments
    Mark 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...
  8. ncbi Small-sample estimation of negative binomial dispersion, with applications to SAGE data
    Mark 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...
  9. doi Regional activation of the cancer genome by long-range epigenetic remodeling
    Saul A Bert
    Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
    Cancer Cell 23:9-22. 2013
    ..These findings have wide ramifications for cancer diagnosis, progression, and epigenetic-based gene therapies...
  10. pmc Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer
    Fatima 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...
  11. doi Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias
    Shalima 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...
  12. pmc Repitools: an R package for the analysis of enrichment-based epigenomic data
    Aaron 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...
  13. pmc Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
    Aaron L Statham
    Cancer Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
    Genome Res 22:1120-7. 2012
    ..BisChIP-seq is a novel approach that can be widely applied to directly interrogate the genomic relationship between allele-specific DNA methylation, histone modification, or other important epigenetic regulators...
  14. pmc Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation
    Mark D Robinson
    Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
    Genome Res 20:1719-29. 2010
    ....
  15. pmc Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
    Marcel 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...
  16. pmc From RNA-seq reads to differential expression results
    Alicia 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...
  17. pmc Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
    Toby 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...
  18. pmc High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants
    Paul 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...
  19. pmc Identifying transcription factor functions and targets by phenotypic activation
    Gordon 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...
  20. ncbi A panoramic view of yeast noncoding RNA processing
    Wen 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...
  21. ncbi High-definition macromolecular composition of yeast RNA-processing complexes
    Nevan 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...
  22. pmc Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors
    Jorg Grigull
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    Mol Cell Biol 24:5534-47. 2004
    ..Our results indicate that the abundance of ribosome biogenesis factors is controlled at the level of mRNA stability...
  23. ncbi Transcriptional networks: reverse-engineering gene regulation on a global scale
    Gordon 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...
  24. pmc The functional landscape of mouse gene expression
    Wen 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
    ....
  25. ncbi Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
    Brendan 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...
  26. ncbi Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
    Lani 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...