Publications

ZORA Publication List

Publications

• 2020

  • Journal Article

    • Shaul, M. E., Eyal, O., Guglietta, S., Aloni, P., Zlotnik, A., Forkosh, E., Levy, L., Weber, L. M., Levin, Y., Pomerantz, A., Nechushtan, H., Eruslanov, E., Singhal, S., Robinson, M. D., Krieg, C., & Fridlender, Z. G. (2020). Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis FASEB Journal, 34, 4204–4218. https://doi.org/10.1096/fj.201902467r

• 2019

  • Journal Article

    • Robinson, M. D., & Vitek, O. (2019). Benchmarking comes of age Genome Biology, 20, 205. https://doi.org/10.1186/s13059-019-1846-5
    • Meccariello, A., Salvemini, M., Primo, P., Hall, B., Koskinioti, P., Dalíková, M., Gravina, A., Gucciardino, M. A., Forlenza, F., Gregoriou, M.-E., Ippolito, D., Monti, S. M., Petrella, V., Perrotta, M. M., Schmeing, S., Ruggiero, A., Scolari, F., Giordano, E., Tsoumani, K. T., … Saccone, G. (2019). Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests Science, 365, 1457–1460. https://doi.org/10.1126/science.aax1318
    • Knop, J., Spilgies, L. M., Rufli, S., Reinhart, R., Vasilikos, L., Yabal, M., Owsley, E., Jost, P. J., Marsh, R. A., Wajant, H., Robinson, M. D., Kaufmann, T., & Wong, W. W.-L. (2019). TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP Cell Death and Disease, 10, 700. https://doi.org/10.1038/s41419-019-1938-x
    • Soneson, C., Yao, Y., Bratus-Neuenschwander, A., Patrignani, A., Robinson, M. D., & Hussain, S. (2019). A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes Nature Communications, 10, 3359. https://doi.org/10.1038/s41467-019-11272-z
    • Van den Berge, K., Hembach, K. M., Soneson, C., Tiberi, S., Clement, L., Love, M. I., Patro, R., & Robinson, M. D. (2019). RNA Sequencing Data: Hitchhiker’s Guide to Expression Analysis. Annual Review of Biomedical Data Science, 2, 139–173. https://doi.org/10.1146/annurev-biodatasci-072018-021255
    • Orjuela, S., Huang, R., Hembach, K. M., Robinson, M. D., & Soneson, C. (2019). ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data G3 : Genes, Genomes, Genetics, 9, 2089–2096. https://doi.org/10.1534/g3.119.400185
    • D’Agati, G., Cabello, E. M., Frontzek, K., Rushing, E. J., Klemm, R., Robinson, M. D., White, R. M., Mosimann, C., & Burger, A. (2019). Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish Disease Models & Mechanisms, 12, dmm039545. https://doi.org/10.1242/dmm.039545
    • Weber, L. M., Saelens, W., Cannoodt, R., Soneson, C., Hapfelmeier, A., Gardner, P. P., Boulesteix, A.-L., Saeys, Y., & Robinson, M. D. (2019). Essential guidelines for computational method benchmarking Genome Biology, 20, 125. https://doi.org/10.1186/s13059-019-1738-8
    • Mariani, S. A., Li, Z., Rice, S., Krieg, C., Fragkogianni, S., Robinson, M. D., Vink, C. S., Pollard, J. W., & Dzierzak, E. (2019). Pro-inflammatory Aorta-Associated Macrophages Are Involved in Embryonic Development of Hematopoietic Stem Cells Immunity, 50, 1439-1452.e5. https://doi.org/10.1016/j.immuni.2019.05.003
    • Kaiser, J., Maibach, M., Salpeter, I., Hagenbuch, N., de Souza, V. B. C., Robinson, M. D., & Schwab, M. E. (2019). The Spinal Transcriptome after Cortical Stroke: In Search of Molecular Factors Regulating Spontaneous Recovery in the Spinal Cord Journal of Neuroscience, 39, 4714–4726. https://doi.org/10.1523/JNEUROSCI.2571-18.2019
    • Cheng, H.-W., Onder, L., Novkovic, M., Soneson, C., Lütge, M., Pikor, N., Scandella, E., Robinson, M. D., Miyazaki, J.-I., Tersteegen, A., Sorg, U., Pfeffer, K., Rülicke, T., Hehlgans, T., & Ludewig, B. (2019). Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp Nature Communications, 10, 1739. https://doi.org/10.1038/s41467-019-09728-3
    • Doumpas, N., Lampart, F., Robinson, M. D., Lentini, A., Nestor, C. E., Cantù, C., & Basler, K. (2019). TCF/LEF dependent and independent transcriptional regulation of Wnt/β-catenin target genes The EMBO Journal, 38, e98873. https://doi.org/10.15252/embj.201798873
    • Bick, J. T., Zeng, S., Robinson, M. D., Ulbrich, S. E., & Bauersachs, S. (2019). Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. Database, 2019, 86. https://doi.org/10.1093/database/baz086
    • Krattinger, S. G., Kang, J., Bräunlich, S., Boni, R., Chauhan, H., Selter, L. L., Robinson, M. D., Schmid, M. W., Wiederhold, E., Hensel, G., Kumlehn, J., Sucher, J., Martinoia, E., & Keller, B. (2019). Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34 New Phytologist, 223, 853–866. https://doi.org/10.1111/nph.15815
    • Chatterjee, B., Deng, Y., Holler, A., Núñez, N. G., Azzi, T., Vanoaica, L. D., Müller, A., Zdimerova, H., Antsiferova, O., Zbinden, A., Capaul, R., Dreyer, J. H., Nadal, D., Becher, B., Robinson, M. D., Stauss, H., & Münz, C. (2019). CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo PLoS Pathogens, 15, e1007748. https://doi.org/10.1371/journal.ppat.1007748
    • Soneson, C., Love, M. I., Patro, R., Hussain, S., Malhotra, D., & Robinson, M. D. (2019). A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs Life Science Alliance, 2, e201800175. https://doi.org/10.26508/lsa.201800175
    • Weber, L. M., Nowicka, M., Soneson, C., & Robinson, M. D. (2019). diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering Communications Biology, 2, 183. https://doi.org/10.1038/s42003-019-0415-5
    • Nowicka, M., Krieg, C., Crowell, H. L., Weber, L. M., Hartmann, F. J., Guglietta, S., Becher, B., Levesque, M. P., & Robinson, M. D. (2019). CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets F1000Research, 6, 748. https://doi.org/10.12688/f1000research.11622.4

  • Newspaper Article

    • Robinson, M. D., Thommen, M., & Stöcklin, S. (2019, December). Die Wissenschaft öffnet sich UZH Journal, 8–9. https://www.ius.uzh.ch/dam/jcr:c06e40b8-1bfa-4337-9db8-6f12575a1eee/UZH-Journal_1904.pdf

• 2018

  • Journal Article

    • Parker, H. R., Orjuela, S., Martinho Oliveira, A., Cereatti, F., Sauter, M., Heinrich, H., Tanzi, G., Weber, A., Komminoth, P., Vavricka, S., Albanese, L., Buffoli, F., Robinson, M. D., & Marra, G. (2018). The proto CpG island methylator phenotype of sessile serrated adenomas/polyps Epigenetics, 13, 1088–1105. https://doi.org/10.1080/15592294.2018.1543504
    • Bick, J. T., Flöter, V. L., Robinson, M. D., Bauersachs, S., & Ulbrich, S. E. (2018). Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression BMC Genomics, 19, 590. https://doi.org/10.1186/s12864-018-4954-9
    • Savic, N., Ringnalda, F. C. A. S., Lindsay, H., Berk, C., Bargsten, K., Li, Y., Neri, D., Robinson, M. D., Ciaudo, C., Hall, J., Jinek, M., & Schwank, G. (2018). Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair ELife, 7, 33761. https://doi.org/10.7554/eLife.33761
    • Chevrier, S., Crowell, H. L., Zanotelli, V. R. T., Engler, S., Robinson, M. D., & Bodenmiller, B. (2018). Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry Cell Systems, 6, 612-620.e5. https://doi.org/10.1016/j.cels.2018.02.010
    • Praz, C. R., Menardo, F., Robinson, M. D., Müller, M. C., Wicker, T., Bourras, S., & Keller, B. (2018). Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen Frontiers in Plant Science, 9, 49. https://doi.org/10.3389/fpls.2018.00049
    • Krieg, C., Nowicka, M., Guglietta, S., Schindler, S., Hartmann, F. J., Weber, L. M., Dummer, R., Robinson, M. D., Levesque, M. P., & Becher, B. (2018). Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy Nature Medicine, 24, 1773–1775. https://doi.org/10.1038/s41591-018-0094-7
    • Villiger, L., Grisch-Chan, H. M., Lindsay, H., Ringnalda, F., Pogliano, C. B., Allegri, G., Fingerhut, R., Häberle, J., Matos, J., Robinson, M. D., Thöny, B., & Schwank, G. (2018). Treatment of a metabolic liver disease by in vivo genome base editing in adult mice Nature Medicine, 24, 1519–1525. https://doi.org/10.1038/s41591-018-0209-1
    • Perez-Shibayama, C., Gil-Cruz, C., Cheng, H.-W., Onder, L., Printz, A., Mörbe, U., Novkovic, M., Li, C., Lopez-Macias, C., Buechler, M. B., Turley, S. J., Mack, M., Soneson, C., Robinson, M. D., Scandella, E., Gommerman, J., & Ludewig, B. (2018). Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity Science Immunology, 3, eaar4539. https://doi.org/10.1126/sciimmunol.aar4539
    • Soneson, C., & Robinson, M. D. (2018). Towards unified quality verification of synthetic count data with countsimQC Bioinformatics, 34, 691–692. https://doi.org/10.1093/bioinformatics/btx631
    • Krieg, C., Nowicka, M., Guglietta, S., Schindler, S., Hartmann, F. J., Weber, L. M., Dummer, R., Robinson, M. D., Levesque, M. P., & Becher, B. (2018). High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy Nature Medicine, 24, 144–153. https://doi.org/10.1038/nm.4466
    • Wrangle, J. M., Velcheti, V., Patel, M. R., Garrett-Mayer, E., Hill, E. G., Ravenel, J. G., et al, Robinson, M. D., & Rubinstein, M. P. (2018). ALT-803, an IL-15 superagonist, in combination with nivolumab in patients with metastatic non-small cell lung cancer: a non-randomised, open-label, phase 1b trial Lancet Oncology, 19, 694–704. https://doi.org/10.1016/s1470-2045(18)30148-7
    • Duò, A., Robinson, M. D., & Soneson, C. (2018). A systematic performance evaluation of clustering methods for single-cell RNA-seq data F1000Research, 7, 1141. https://doi.org/10.12688/f1000research.15666.2
    • Van den Berge, K., Perraudeau, F., Soneson, C., Love, M. I., Risso, D., Vert, J.-P., Robinson, M. D., Dudoit, S., & Clement, L. (2018). Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications Genome Biology, 19, 24. https://doi.org/10.1186/s13059-018-1406-4
    • Soneson, C., & Robinson, M. D. (2018). Bias, robustness and scalability in single-cell differential expression analysis Nature Methods, 15, 255–261. https://doi.org/10.1038/nmeth.4612
    • Littringer, K., Moresi, C., Rakebrandt, N., Zhou, X., Schorer, M., Dolowschiak, T., Kirchner, F., Rost, F., Keller, C. W., McHugh, D., LeibundGut-Landmann, S., Robinson, M. D., & Joller, N. (2018). Common features of regulatory T cell specialization during Th1 responses Frontiers in Immunology, 9, 1344. https://doi.org/10.3389/fimmu.2018.01344

• 2017

  • Journal Article

    • Omasits, U., Varadarajan, A. R., Schmid, M., Goetze, S., Melidis, D., Bourqui, M., Nikolayeva, O., Québatte, M., Patrignani, A., Dehio, C., Frey, J. E., Robinson, M. D., Wollscheid, B., & Ahrens, C. H. (2017). An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics Genome Research, 27, 2083–2095. https://doi.org/10.1101/gr.218255.116
    • Van den Berge, K., Soneson, C., Robinson, M. D., & Clement, L. (2017). stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage Genome Biology, 18, 151. https://doi.org/10.1186/s13059-017-1277-0
    • Sharma, A., Heinze, S. D., Wu, Y., Kohlbrenner, T., Morilla, I., Brunner, C., Wimmer, E. A., van de Zande, L., Robinson, M. D., Beukeboom, L. W., & Bopp, D. (2017). Male sex in houseflies is determined byMdmd, a paralog of the generic splice factor geneCWC22 Science, 356, 642–645. https://doi.org/10.1126/science.aam5498
    • Marinova, Z., Maercker, A., Küffer, A., Robinson, M. D., Wojdacz, T. K., Walitza, S., Grünblatt, E., & Burri, A. (2017). DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma BMC Medical Genetics, 18, 21. https://doi.org/10.1186/s12881-017-0370-2
    • Sauerwald, J., Soneson, C., Robinson, M. D., & Luschnig, S. (2017). Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila Development, 144, 657–663. https://doi.org/10.1242/dev.144535
    • Herdman, C., Mars, J.-C., Stefanovsky, V. Y., Tremblay, M. G., Sabourin-Felix, M., Lindsay, H., Robinson, M. D., & Moss, T. (2017). A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription PLoS Genetics, 13, e1006899. https://doi.org/10.1371/journal.pgen.1006899
    • Nowicka, M., Krieg, C., Weber, L. M., Hartmann, F. J., Guglietta, S., Becher, B., Levesque, M. P., & Robinson, M. D. (2017). CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets F1000Research, 6, 748. https://doi.org/10.12688/f1000research.11622.1
    • Meccariello, A., Monti, S. M., Romanelli, A., Colonna, R., Primo, P., Inghilterra, M. G., Del Corsano, G., Ramaglia, A., Iazzetti, G., Chiarore, A., Patti, F., Heinze, S. D., Salvemini, M., Lindsay, H., Chiavacci, E., Burger, A., Robinson, M. D., Mosimann, C., Bopp, D., & Saccone, G. (2017). Highly efficient DNA-free gene disruption in the agricultural pest Ceratitis capitata by CRISPR-Cas9 ribonucleoprotein complexes Scientific Reports, 7, e1–e11. https://doi.org/10.1038/s41598-017-10347-5

• 2016

  • Journal Article

    • Hartmann, F. J., Bernard-Valnet, R., Quériault, C., Mrdjen, D., Weber, L. M., Galli, E., Krieg, C., Robinson, M. D., Nguyen, X.-H., Dauvilliers, Y., Liblau, R. S., & Becher, B. (2016). High-dimensional single-cell analysis reveals the immune signature of narcolepsy Journal of Experimental Medicine, 213, 2621–2633. https://doi.org/10.1084/jem.20160897
    • Hawkins, E. D., Duarte, D., Akinduro, O., Khorshed, R. A., Passaro, D., Nowicka, M., Straszkowski, L., Scott, M. K., Rothery, S., Ruivo, N., Foster, K., Waibel, M., Johnstone, R. W., Harrison, S. J., Westerman, D. A., Quach, H., Gribben, J., Robinson, M. D., Purton, L. E., … Lo Celso, C. (2016). T-cell acute leukaemia exhibits dynamic interactions with bone marrow microenvironments Nature, 538, 518–522. https://doi.org/10.1038/nature19801
    • Lindsay, H., Burger, A., Biyong, B., Felker, A., Hess, C., Zaugg, J., Chiavacci, E., Anders, C., Jinek, M., Mosimann, C., & Robinson, M. D. (2016). CrispRVariants charts the mutation spectrum of genome engineering experiments Nature Biotechnology, 34, 701–702. https://doi.org/10.1038/nbt.3628
    • Burger, A., Lindsay, H., Felker, A., Hess, C., Anders, C., Chiavacci, E., Zaugg, J., Weber, L. M., Catena, R., Jinek, M., Robinson, M. D., & Mosimann, C. (2016). Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes Development, 143, 2025–2037. https://doi.org/10.1242/dev.134809
    • Soneson, C., & Robinson, M. D. (2016). iCOBRA: open, reproducible, standardized and live method benchmarking Nature Methods, 13, 283. https://doi.org/10.1038/nmeth.3805
    • Soneson, C., Matthes, K. L., Nowicka, M., Law, C. W., & Robinson, M. D. (2016). Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage Genome Biology, 17, 12. https://doi.org/10.1186/s13059-015-0862-3
    • Flori, M., Schmid, C. A., Sumrall, E. T., Tzankov, A., Law, C. W., Robinson, M. D., & Müller, A. (2016). The hematopoietic oncoprotein FOXP1 promotes tumor cell survival in diffuse large B-cell lymphoma by repressing S1PR2 signaling Blood, 127, 1438–1448. https://doi.org/10.1182/blood-2015-08-662635

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