Publications

ZORA Publication List

Publications

• 2016

  • Journal Article

    • Burri, Andrea; Marinova, Zoya; Robinson, Mark D; Kühnel, Brigitte; Waldenberger, Melanie; Wahl, Simone; Kunze, Sonja; Gieger, Christian; Livshits, Gregory; Williams, Frances (2016). Are epigenetic factors implicated in chronic widespread pain? PLoS ONE, 11(11):e0165548.
    • Nowicka, Malgorzata; Robinson, Mark D (2016). DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics F1000Research, 5:1356.

• 2015

  • Journal Article

    • Kulic, Iva; et al; Robinson, Mark D (2015). Loss of the Notch effector RBPJ promotes tumorigenesis Journal of Experimental Medicine, 212(1):37-52.
    • Zhou, Xiaobei; Robinson, Mark D (2015). Do count-based differential expression methods perform poorly when genes are expressed in only one condition? Genome Biology, 16(222):online.
    • Schmid, Corina A; Robinson, Mark D; Scheifinger, Nicole A; Müller, Sebastian; Cogliatti, Sergio; Tzankov, Alexandar; Müller, Anne (2015). DUSP4 deficiency caused by promoter hypermethylation drives JNK signaling and tumor cell survival in diffuse large B cell lymphoma Journal of Experimental Medicine:1-18.
    • Bilgin Sonay, Tugce; Carvalho, Tiago; Robinson, Mark D; Greminger, Maja P; Krützen, Michael; Comas, David; Highnam, Gareth; Mittelman, David; Sharp, Andrew; Marques-Bonet, Tomàs; Wagner, Andreas (2015). Tandem repeat variation in human and great ape populations and its impact on gene expression divergence Genome Research, 25(11):1591-1599.
    • Baker, Emma K; Taylor, Scott; Gupte, Ankita; Chalk, Alistair M; Bhattacharya, Shreya; Green, Alanna C; Martin, T John; Strbenac, Dario; Robinson, Mark D; Purton, Louise E; Walkley, Carl R (2015). Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma Bone, 73:223-232.
    • Gu, Lei; Frommel, Sandra C; Oakes, Christopher C; Simon, Ronald; Grupp, Katharina; Gerig, Cristina Y; Bär, Dominik; Robinson, Mark D; Baer, Constance; Weiss, Melanie; Gu, Zuguang; Schapira, Matthieu; Kuner, Ruprecht; Sültmann, Holger; Provenzano, Maurizio; Yaspo, Marie-Laure; Brors, Benedikt; Korbel, Jan; Schlomm, Thorsten; Sauter, Guido; Eils, Roland; Plass, Christoph; Santoro, Raffaella (2015). BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence Nature Genetics, 47(1):22-30.
    • Soneson, Charlotte; Love, Michael I; Robinson, Mark D (2015). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences F1000Research, 4:1521.
    • 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.
    • Locke, Warwick J; Zotenko, Elena; Stirzaker, Clare; Robinson, Mark D; Hinshelwood, Rebecca A; Stone, Andrew; Reddel, Roger R; Huschtscha, Lily I; Clark, Susan J (2015). Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis Clinical Epigenetics, 7(1):52.
    • Robinson, Mark D; Pelizzola, Mattia (2015). Computational epigenomics: challenges and opportunities Frontiers in Genetics, 6:88.
    • Petrella, V; Aceto, S; Musacchia, F; Colonna, V; Robinson, Mark D; Benes, V; Cicotti, G; Bongiorno, G; Gradoni, L; Volf, P; Salvemini, M (2015). De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum BMC Genomics, 16:847.

• 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.
    • Hickey, Peter F; Robinson, Mark D (2014). Genomics by the beach Genome Biology, 15:304.
    • 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.
    • 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.
    • 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.
    • 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.

• 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.
    • 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.
    • Zhou, X., Oshlack, A., & Robinson, M. D. (2013). miRNA-Seq normalization comparisons need improvement RNA, 19(6), 733–734. doi:10.1261/rna.037895.112
    • 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