Publications

ZORA Publication List

Publications

• 2015

  • Journal Article

    • Robinson, Mark D; Pelizzola, Mattia (2015). Computational epigenomics: challenges and opportunities. Frontiers in Genetics, 6:88.
    • Stirzaker, Clare; Zotenko, Elena; Song, Jenny Z; Qu, Wenjia; Nair, Shalima S; Locke, Warwick J; Stone, Andrew; Armstong, Nicola J; Robinson, Mark D; Dobrovic, Alexander; Avery-Kiejda, Kelly A; Peters, Kate M; French, Juliet D; Stein, Sandra; Korbie, Darren J; Trau, Matt; Forbes, John F; Scott, Rodney J; Brown, Melissa A; Francis, Glenn D; Clark, Susan J (2015). Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nature Communications, 6:5899.

• 2014

  • Journal Article

    • Zhou, Xiaobei; Lindsay, Helen; Robinson, Mark D (2014). Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Research, 42(11):e91.
    • Robinson, Mark D; Kahraman, Abdullah; Law, Charity W; Lindsay, Helen; Nowicka, Malgorzata; Weber, Lukas M; Zhou, Xiaobei (2014). Statistical methods for detecting differentially methylated loci and regions. Frontiers in Genetics:5:324.
    • Hickey, Peter F; Robinson, Mark D (2014). Genomics by the beach. Genome Biology, 15:304.
    • Nikolayeva, Olga; Robinson, Mark D (2014). edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods in Molecular Biology, 1150:45-79.
    • Cai, Haoyang; Kumar, Nitin; Bagheri, Homayoun C; von Mering, Christian; Robinson, Mark D; Baudis, Michael (2014). Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics, 15:82.
    • Riebler, Andrea; Menigatti, Mirco; Song, Jenny Z; Statham, Aaron L; Stirzaker, Clare; Mahmud, Nadiya; Mein, Charles A; Clark, Susan J; Robinson, Mark D (2014). BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach. Genome Biology, 15(2):R35.

• 2013

  • Journal Article

    • Anders, Simon; McCarthy, Davis J; Chen, Yunshun; Okoniewski, Michal; Smyth, Gordon K; Huber, Wolfgang; Robinson, Mark D (2013). Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols, 8(9):1765-1786.
    • Maier, Lisa; Vyas, Rounak; Cordova, Carmen Dolores; Lindsay, Helen; Schmidt, Thomas Sebastian Benedikt; Brugiroux, Sandrine; Periaswamy, Balamurugan; Bauer, Rebekka; Sturm, Alexander; Schreiber, Frank; von Mering, Christian; Robinson, Mark D; Stecher, Bärbel; Hardt, Wolf-Dietrich (2013). Microbiota-derived hydrogen fuels salmonella typhimurium invasion of the gut ecosystem. Cell Host & Microbe, 14(6):641-651.
    • Zhou, Xiaobei; Oshlack, Alicia; Robinson, Mark D (2013). miRNA-Seq normalization comparisons need improvement. RNA, 19(6):733-734.
    • Omasits, Ulrich; Quebatte, Maxime; Stekhoven, Daniel J; Fortes, Claudia; Roschitzki, Bernd; Robinson, Mark D; Dehio, Christoph; Ahrens, Christian H (2013). Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Research, 23(11):1916-1927.
    • Menigatti, M; Staiano, T; Manser, C N; Bauerfeind, P; Komljenovic, A; Robinson, Mark D; Jiricny, J; Buffoli, F; Marra, Giancarlo (2013). Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions. Oncogenesis, 2:e56.
    • Bert, Saul A; Robinson, Mark D; Strbenac, Dario; Statham, Aaron L; Song, Jenny Z; Hulf, Toby; Sutherland, Robert L; Coolen, Marcel W; Stirzaker, Clare; Clark, Susan J (2013). Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell, 23(1):9-22.

• 2012

  • Journal Article

    • Valdés-Mora, Fátima; Song, Jenny Z; Statham, Aaron L; Strbenac, Dario; Robinson, Mark D; Nair, Shalima S; Patterson, Kate I; Tremethick, David J; Stirzaker, Clare; Clark, Susan J (2012). Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer. Genome Research, 22(2):307-321.
    • Robinson, Mark D; Strbenac, Dario; Stirzaker, Clare; Statham, Aaron L; Song, Jenny; Speed, Terence P; Clark, Susan J (2012). Copy-number-aware differential analysis of quantitative DNA sequencing data. Genome Research, 22(12):2489-2496.
    • Statham, Aaron L; Robinson, Mark D; Song, Jenny Z; Coolen, Marcel W; Stirzaker, Clare; Clark, Susan J (2012). Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Research, 22(6):1120-1127.
    • Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael (2012). Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Research, 40(W1):W615-W621.

• 2007

  • Journal Article

    • Robinson, Mark D; Speed, Terence P (2007). A comparison of Affymetrix gene expression arrays. BMC Bioinformatics, 8:449.

• 2003

  • Journal Article

    • Peng, Wen-Tao; Robinson, Mark D; Mnaimneh, Sanie; Krogan, Nevan J; Cagney, Gerard; Morris, Quaid; Davierwala, Armaity P; Grigull, Jörg; Yang, Xueqi; Zhang, Wen; Mitsakakis, Nicholas; Ryan, Owen W; Datta, Nira; Jojic, Vladimir; Pal, Chris; Canadien, Veronica; Richards, Dawn; Beattie, Bryan; Wu, Lani F; Altschuler, Steven J; Roweis, Sam; Frey, Brendan J; Emili, Andrew; Greenblatt, Jack F; Hughes, Timothy R (2003). A panoramic view of yeast noncoding RNA processing. Cell, 113(7):919-933.

• 2002

  • Journal Article

    • Wu, Lani F; Hughes, Timothy R; Davierwala, Armaity P; Robinson, Mark D; Stoughton, Roland; Altschuler, Steven J (2002). Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genetics, 31(3):255-265.

Pagination