Publications

ZORA Publication List

Publications

• 2016

  • Journal Article

    • Weber, L. M., & Robinson, M. D. (2016). Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data Cytometry. Part A, 89, 1084–1096. https://doi.org/10.1002/cyto.a.23030
    • Burri, A., Marinova, Z., Robinson, M. D., Kühnel, B., Waldenberger, M., Wahl, S., Kunze, S., Gieger, C., Livshits, G., & Williams, F. (2016). Are epigenetic factors implicated in chronic widespread pain? PLoS ONE, 11, e0165548. https://doi.org/10.1371/journal.pone.0165548
    • Nowicka, M., & Robinson, M. D. (2016). DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics F1000Research, 5, 1356. https://doi.org/10.12688/f1000research.8900.2

• 2015

  • Journal Article

    • Kulic, I., et al, & Robinson, M. D. (2015). Loss of the Notch effector RBPJ promotes tumorigenesis Journal of Experimental Medicine, 212, 37–52. https://doi.org/10.1084/jem.20121192
    • Zhou, X., & Robinson, M. D. (2015). Do count-based differential expression methods perform poorly when genes are expressed in only one condition? Genome Biology, 16, online. https://doi.org/10.1186/s13059-015-0781-3
    • Schmid, C. A., Robinson, M. D., Scheifinger, N. A., Müller, S., Cogliatti, S., Tzankov, A., & Müller, A. (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. https://doi.org/10.1084/jem.20141957
    • Bilgin Sonay, T., Carvalho, T., Robinson, M. D., Greminger, M. P., Krützen, M., Comas, D., Highnam, G., Mittelman, D., Sharp, A., Marques-Bonet, T., & Wagner, A. (2015). Tandem repeat variation in human and great ape populations and its impact on gene expression divergence Genome Research, 25, 1591–1599. https://doi.org/10.1101/gr.190868.115
    • Baker, E. K., Taylor, S., Gupte, A., Chalk, A. M., Bhattacharya, S., Green, A. C., Martin, T. J., Strbenac, D., Robinson, M. D., Purton, L. E., & Walkley, C. 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. https://doi.org/10.1016/j.bone.2014.12.063
    • Gu, L., Frommel, S. C., Oakes, C. C., Simon, R., Grupp, K., Gerig, C. Y., Bär, D., Robinson, M. D., Baer, C., Weiss, M., Gu, Z., Schapira, M., Kuner, R., Sültmann, H., Provenzano, M., Yaspo, M.-L., Brors, B., Korbel, J., Schlomm, T., … Santoro, R. (2015). BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence Nature Genetics, 47, 22–30. https://doi.org/10.1038/ng.3165
    • Stirzaker, C., Zotenko, E., Song, J. Z., Qu, W., Nair, S. S., Locke, W. J., Stone, A., Armstong, N. J., Robinson, M. D., Dobrovic, A., Avery-Kiejda, K. A., Peters, K. M., French, J. D., Stein, S., Korbie, D. J., Trau, M., Forbes, J. F., Scott, R. J., Brown, M. A., … Clark, S. J. (2015). Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value Nature Communications, 6, 5899. https://doi.org/10.1038/ncomms6899
    • Petrella, V., Aceto, S., Musacchia, F., Colonna, V., Robinson, M. 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. https://doi.org/10.1186/s12864-015-2088-x
    • Locke, W. J., Zotenko, E., Stirzaker, C., Robinson, M. D., Hinshelwood, R. A., Stone, A., Reddel, R. R., Huschtscha, L. I., & Clark, S. J. (2015). Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis Clinical Epigenetics, 7, 52. https://doi.org/10.1186/s13148-015-0086-0
    • Soneson, C., Love, M. I., & Robinson, M. D. (2015). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences F1000Research, 4, 1521. https://doi.org/10.12688/f1000research.7563.2
    • Robinson, M. D., & Pelizzola, M. (2015). Computational epigenomics: challenges and opportunities Frontiers in Genetics, 6, 88. https://doi.org/10.3389/fgene.2015.00088

• 2014

  • Journal Article

    • Zhou, X., Lindsay, H., & Robinson, M. D. (2014). Robustly detecting differential expression in RNA sequencing data using observation weights Nucleic Acids Research, 42, e91. https://doi.org/10.1093/nar/gku310
    • Hickey, P. F., & Robinson, M. D. (2014). Genomics by the beach Genome Biology, 15, 304. https://doi.org/10.1186/gb4171
    • Riebler, A., Menigatti, M., Song, J. Z., Statham, A. L., Stirzaker, C., Mahmud, N., Mein, C. A., Clark, S. J., & Robinson, M. D. (2014). BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach Genome Biology, 15, R35. https://doi.org/10.1186/gb-2014-15-2-r35
    • Robinson, M. D., Kahraman, A., Law, C. W., Lindsay, H., Nowicka, M., Weber, L. M., & Zhou, X. (2014). Statistical methods for detecting differentially methylated loci and regions Frontiers in Genetics, 5:324. https://doi.org/10.3389/fgene.2014.00324
    • Cai, H., Kumar, N., Bagheri, H. C., von Mering, C., Robinson, M. D., & Baudis, M. (2014). Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens BMC Genomics, 15, 82. https://doi.org/10.1186/1471-2164-15-82
    • Nikolayeva, O., & Robinson, M. D. (2014). edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology Methods in Molecular Biology, 1150, 45–79. https://doi.org/10.1007/978-1-4939-0512-6_3

• 2013

  • Journal Article

    • Anders, S., McCarthy, D. J., Chen, Y., Okoniewski, M., Smyth, G. K., Huber, W., & Robinson, M. D. (2013). Count-based differential expression analysis of RNA sequencing data using R and Bioconductor Nature Protocols, 8, 1765–1786. https://doi.org/10.1038/nprot.2013.099
    • Maier, L., Vyas, R., Cordova, C. D., Lindsay, H., Schmidt, T. S. B., Brugiroux, S., Periaswamy, B., Bauer, R., Sturm, A., Schreiber, F., von Mering, C., Robinson, M. D., Stecher, B., & Hardt, W.-D. (2013). Microbiota-derived hydrogen fuels salmonella typhimurium invasion of the gut ecosystem Cell Host & Microbe, 14, 641–651. https://doi.org/10.1016/j.chom.2013.11.002
    • Zhou, X., Oshlack, A., & Robinson, M. D. (2013). miRNA-Seq normalization comparisons need improvement RNA, 19, 733–734. https://doi.org/10.1261/rna.037895.112
    • Bert, S. A., Robinson, M. D., Strbenac, D., Statham, A. L., Song, J. Z., Hulf, T., Sutherland, R. L., Coolen, M. W., Stirzaker, C., & Clark, S. J. (2013). Regional activation of the cancer genome by long-range epigenetic remodeling Cancer Cell, 23, 9–22. https://doi.org/10.1016/j.ccr.2012.11.006
    • Omasits, U., Quebatte, M., Stekhoven, D. J., Fortes, C., Roschitzki, B., Robinson, M. D., Dehio, C., & Ahrens, C. H. (2013). Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome Genome Research, 23, 1916–1927. https://doi.org/10.1101/gr.151035.112
    • Menigatti, M., Staiano, T., Manser, C. N., Bauerfeind, P., Komljenovic, A., Robinson, M. D., Jiricny, J., Buffoli, F., & Marra, G. (2013). Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions Oncogenesis, 2, e56. https://doi.org/10.1038/oncsis.2013.21

• 2012

  • Journal Article

    • Valdés-Mora, F., Song, J. Z., Statham, A. L., Strbenac, D., Robinson, M. D., Nair, S. S., Patterson, K. I., Tremethick, D. J., Stirzaker, C., & Clark, S. J. (2012). Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer Genome Research, 22, 307–321. https://doi.org/10.1101/gr.118919.110
    • Robinson, M. D., Strbenac, D., Stirzaker, C., Statham, A. L., Song, J., Speed, T. P., & Clark, S. J. (2012). Copy-number-aware differential analysis of quantitative DNA sequencing data Genome Research, 22, 2489–2496. https://doi.org/10.1101/gr.139055.112
    • Statham, A. L., Robinson, M. D., Song, J. Z., Coolen, M. W., Stirzaker, C., & Clark, S. J. (2012). Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA Genome Research, 22, 1120–1127. https://doi.org/10.1101/gr.132076.111
    • Fiume, M., Smith, E. J. M., Brook, A., Strbenac, D., Turner, B., Mezlini, A. M., Robinson, M. D., Wodak, S. J., & Brudno, M. (2012). Savant Genome Browser 2: visualization and analysis for population-scale genomics Nucleic Acids Research, 40, W615–W621. https://doi.org/10.1093/nar/gks427

• 2007

  • Journal Article

    • Robinson, M. D., & Speed, T. P. (2007). A comparison of Affymetrix gene expression arrays BMC Bioinformatics, 8, 449. https://doi.org/10.1186/1471-2105-8-449

• 2003

  • Journal Article

    • Peng, W.-T., Robinson, M. D., Mnaimneh, S., Krogan, N. J., Cagney, G., Morris, Q., Davierwala, A. P., Grigull, J., Yang, X., Zhang, W., Mitsakakis, N., Ryan, O. W., Datta, N., Jojic, V., Pal, C., Canadien, V., Richards, D., Beattie, B., Wu, L. F., … Hughes, T. R. (2003). A panoramic view of yeast noncoding RNA processing Cell, 113, 919–933. https://doi.org/10.1016/S0092-8674(03)00466-5

• 2002

  • Journal Article

    • Wu, L. F., Hughes, T. R., Davierwala, A. P., Robinson, M. D., Stoughton, R., & Altschuler, S. J. (2002). Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters Nature Genetics, 31, 255–265. https://doi.org/10.1038/ng906

Pagination