Publications

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2022
- Journal Article
  - Orjuela, Stephany; Parker, Hannah R; Sajibu, Sija; Cereatti, Fabrizio; Sauter, Matthias; Buffoli, Federico; Robinson, Mark D; Marra, Giancarlo (2022). Disentangling tumorigenesis-associated DNA methylation changes in colorectal tissues from those associated with ageing. Epigenetics, 17(6):677-694.
  - Wagner, Johanna; Masek, Markus; Jacobs, Andrea; Soneson, Charlotte; Sivapatham, Sujana; Damond, Nicolas; de Souza, Natalie; Robinson, Mark D; Bodenmiller, Bernd (2022). Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines. Scientific Data, 9:44-60.
  - Burja, Blaž; Paul, Dominique; Tastanova, Aizhan; Edalat, Sam Galen; Gerber, Reto; Houtman, Miranda; Elhai, Muriel; Bürki, Kristina; Staeger, Ramon; Restivo, Gaetana; Lang, Ramon; Sodin-Šemrl, Snežna; Lakota, Katja; Tomšič, Matija; Levesque, Mitchell P; Distler, Oliver; Rotar, Žiga; Robinson, Mark D; Frank-Bertoncelj, Mojca (2022). An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies. Frontiers in Cell and Developmental Biology, 10:872688.
2021
- Journal Article
  - Bai, Yu; Caussinus, Emmanuel; Leo, Stefano; Bosshardt, Fritz; Myachina, Faina; Rot, Gregor; Robinson, Mark D; Lehner, Christian F (2021). A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. BMC Genomics, 22:771.
  - Milosavljevic, Stefan; Kuo, Tony; Decarli, Samuele; Mohn, Lucas; Sese, Jun; Shimizu, Kentaro K; Shimizu-Inatsugi, Rie; Robinson, Mark D (2021). ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. BMC Genomics, 22:547.
  - Sahadevan, Sonu; Hembach, Katharina M; Tantardini, Elena; Pérez-Berlanga, Manuela; Hruska-Plochan, Marian; Megat, Salim; Weber, Julien; Schwarz, Petra; Dupuis, Luc; Robinson, Mark D; De Rossi, Pierre; Polymenidou, Magdalini (2021). Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS. Nature Communications, 12(1):3027.
  - Gerber, Reto; Robinson, Mark D (2021). Censcyt: censored covariates in differential abundance analysis in cytometry. BMC Bioinformatics, 22(1):235.
  - Schmeing, Stephan; Robinson, Mark D (2021). ReSeq simulates realistic Illumina high-throughput sequencing data. Genome Biology, 22:67.
  - Lütge, Almut; Zyprych-Walczak, Joanna; Brykczynska Kunzmann, Urszula; Crowell, Helena L; Calini, Daniela; Malhotra, Dheeraj; Soneson, Charlotte; Robinson, Mark D (2021). CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data. Life science alliance, 4(6):e202001004.
  - Huang, Ruizhu; Soneson, Charlotte; Germain, Pierre-Luc; Schmidt, Thomas S B; von Mering, Christian; Robinson, Mark D (2021). treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses. Genome Biology, 22:157.
  - Wang, Yuluan; Soneson, Charlotte; Malinowska, Anna L; Laski, Artur; Ghosh, Souvik; Kanitz, Alexander; Gebert, Luca F R; Robinson, Mark D; Hall, Jonathan (2021). MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome. Nucleic Acids Research, 49(1):25-37.
2020
- Journal Article
  - Crowell, Helena L; Soneson, Charlotte; Germain, Pierre-Luc; Calini, Daniela; Collin, Ludovic; Raposo, Catarina; Malhotra, Dheeraj; Robinson, Mark D (2020). muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Nature Communications, 11:6077.
  - Germain, Pierre-Luc; Sonrel, Anthony; Robinson, Mark D (2020). pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools. Genome Biology, 21(1):227.
  - Tiberi, Simone; Robinson, Mark D (2020). BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty. Genome Biology, 21:69.
  - Huang, Ruizhu; Soneson, Charlotte; Ernst, Felix G M; Rue-Albrecht, Kevin C; Yu, Guangchuang; Hicks, Stephanie C; Robinson, Mark D (2020). TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Research, 9:1246.
  - Malan-Müller, Stefanie; de Souza, Vladimir B C; Daniels, Willie M U; Seedat, Soraya; Robinson, Mark D; Hemmings, Sîan M J (2020). Shedding Light on the Transcriptomic Dark Matter in Biological Psychiatry: Role of Long Noncoding RNAs in D-cycloserine-Induced Fear Extinction in Posttraumatic Stress Disorder. Omics : a journal of integrative biology, 24(6):352-369.
  - Orjuela, Stephany; Machlab, Dania; Menigatti, Mirco; Marra, Giancarlo; Robinson, Mark D (2020). DAMEfinder: a method to detect differential allele-specific methylation. Epigenetics & Chromatin, 13:25.
  - Orjuela, Stephany; Menigatti, Mirco; Schraml, Peter; Kambakamba, Patryk; Robinson, Mark D; Marra, Giancarlo (2020). The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers. BMC Cancer, 20:290.
  - Knop, Janin; Spilgies, Lisanne M; Rufli, Stefanie; Reinhart, Ramona; Vasilikos, Lazaros; Yabal, Monica; Owsley, Erika; Jost, Philipp J; Marsh, Rebecca A; Wajant, Harald; Robinson, Mark D; Kaufmann, Thomas; Wong, W Wei-Lynn (2020). Correction: TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP. Cell Death and Disease, 11(1):56.
  - Lähnemann, David; Köster, Johannes; Szczurek, Ewa; McCarthy, Davis J; Hicks, Stephanie C; Robinson, Mark D; et al (2020). Eleven grand challenges in single-cell data science. Genome Biology, 21:31.
  - Shaul, Merav E; Eyal, Ophir; Guglietta, Silvia; Aloni, Pazzit; Zlotnik, Asaf; Forkosh, Ester; Levy, Liran; Weber, Lukas M; Levin, Yonathan; Pomerantz, Alon; Nechushtan, Hovav; Eruslanov, Evgeniy; Singhal, Sunil; Robinson, Mark D; Krieg, Carsten; Fridlender, Zvi G (2020). Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis. FASEB Journal, 34(3):4204-4218.
2019
- Journal Article
  - Robinson, Mark D; Vitek, Olga (2019). Benchmarking comes of age. Genome Biology, 20(1):205.
  - Meccariello, Angela; Salvemini, Marco; Primo, Pasquale; Hall, Brantley; Koskinioti, Panagiota; Dalíková, Martina; Gravina, Andrea; Gucciardino, Michela Anna; Forlenza, Federica; Gregoriou, Maria-Eleni; Ippolito, Domenica; Monti, Simona Maria; Petrella, Valeria; Perrotta, Maryanna Martina; Schmeing, Stephan; Ruggiero, Alessia; Scolari, Francesca; Giordano, Ennio; Tsoumani, Konstantina T; Marec, František; Windbichler, Nikolai; Arunkumar, Kallare P; Bourtzis, Kostas; Mathiopoulos, Kostas D; Ragoussis, Jiannis; Vitagliano, Luigi; Tu, Zhijian; Papathanos, Philippos Aris; Robinson, Mark D; Saccone, Giuseppe (2019). Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests. Science, 365(6460):1457-1460.
  - Knop, Janin; Spilgies, Lisanne M; Rufli, Stefanie; Reinhart, Ramona; Vasilikos, Lazaros; Yabal, Monica; Owsley, Erika; Jost, Philipp J; Marsh, Rebecca A; Wajant, Harald; Robinson, Mark D; Kaufmann, Thomas; Wong, W Wei-Lynn (2019). TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP. Cell Death and Disease, 10(10):700.
  - Soneson, Charlotte; Yao, Yao; Bratus-Neuenschwander, Anna; Patrignani, Andrea; Robinson, Mark D; Hussain, Shobbir (2019). A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes. Nature Communications, 10(1):3359.
  - Van den Berge, Koen; Hembach, Katharina M; Soneson, Charlotte; Tiberi, Simone; Clement, Lieven; Love, Michael I; Patro, Rob; Robinson, Mark D (2019). RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis. Annual Review of Biomedical Data Science, 2(1):139-173.
  - Orjuela, Stephany; Huang, Ruizhu; Hembach, Katharina M; Robinson, Mark D; Soneson, Charlotte (2019). ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data. G3 : Genes, Genomes, Genetics, 9(7):2089-2096.
  - D'Agati, Gianluca; Cabello, Elena María; Frontzek, Karl; Rushing, Elisabeth J; Klemm, Robin; Robinson, Mark D; White, Richard M; Mosimann, Christian; Burger, Alexa (2019). Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish. Disease Models & Mechanisms, 12(7):dmm039545.
  - Krattinger, Simon G; Kang, Joohyun; Bräunlich, Stephanie; Boni, Rainer; Chauhan, Harsh; Selter, Liselotte L; Robinson, Mark D; Schmid, Marc W; Wiederhold, Elena; Hensel, Goetz; Kumlehn, Jochen; Sucher, Justine; Martinoia, Enrico; Keller, Beat (2019). Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34. New Phytologist, 223(2):853-866.
  - Weber, Lukas M; Saelens, Wouter; Cannoodt, Robrecht; Soneson, Charlotte; Hapfelmeier, Alexander; Gardner, Paul P; Boulesteix, Anne-Laure; Saeys, Yvan; Robinson, Mark D (2019). Essential guidelines for computational method benchmarking. Genome Biology, 20:125.
  - Mariani, Samanta Antonella; Li, Zhuan; Rice, Siobhan; Krieg, Carsten; Fragkogianni, Stamatina; Robinson, Mark D; Vink, Chris Sebastiaan; Pollard, Jeffrey William; Dzierzak, Elaine (2019). Pro-inflammatory Aorta-Associated Macrophages Are Involved in Embryonic Development of Hematopoietic Stem Cells. Immunity, 50(6):1439-1452.e5.
  - Kaiser, Julia; Maibach, Martina; Salpeter, Iris; Hagenbuch, Niels; de Souza, Vladimir B C; Robinson, Mark D; Schwab, Martin E (2019). The Spinal Transcriptome after Cortical Stroke: In Search of Molecular Factors Regulating Spontaneous Recovery in the Spinal Cord. Journal of Neuroscience, 39(24):4714-4726.
  - Chatterjee, Bithi; Deng, Yun; Holler, Angelika; Núñez, Nicolás Gonzalo; Azzi, Tarik; Vanoaica, Liliana Danusia; Müller, Anne; Zdimerova, Hana; Antsiferova, Olga; Zbinden, Andrea; Capaul, Riccarda; Dreyer, Johannes H; Nadal, David; Becher, Burkhard; Robinson, Mark D; Stauss, Hans; Münz, Christian (2019). CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo. PLoS Pathogens, 15(5):e1007748.
  - Cheng, Hung-Wei; Onder, Lucas; Novkovic, Mario; Soneson, Charlotte; Lütge, Mechthild; Pikor, Natalia; Scandella, Elke; Robinson, Mark D; Miyazaki, Jun-Ichi; Tersteegen, Anne; Sorg, Ursula; Pfeffer, Klaus; Rülicke, Thomas; Hehlgans, Thomas; Ludewig, Burkhard (2019). Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp. Nature Communications, 10(1):1739.
  - Soneson, Charlotte; Love, Michael I; Patro, Rob; Hussain, Shobbir; Malhotra, Dheeraj; Robinson, Mark D (2019). A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. Life Science Alliance, 2(1):e201800175.
  - Doumpas, Nikolaos; Lampart, Franziska; Robinson, Mark D; Lentini, Antonio; Nestor, Colm E; Cantù, Claudio; Basler, Konrad (2019). TCF/LEF dependent and independent transcriptional regulation of Wnt/β-catenin target genes. EMBO Journal Online, 38(2):e98873.
  - Bick, Jochen T; Zeng, Shuqin; Robinson, Mark D; Ulbrich, Susanne E; Bauersachs, Stefan (2019). Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms.. Database, 2019:86.
  - Nowicka, Malgorzata; Krieg, Carsten; Crowell, Helena L; Weber, Lukas M; Hartmann, Felix J; Guglietta, Silvia; Becher, Burkhard; Levesque, Mitchell P; Robinson, Mark D (2019). CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research, 6:748.
  - Weber, Lukas M; Nowicka, Malgorzata; Soneson, Charlotte; Robinson, Mark D (2019). diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering. Communications Biology, 2:183.
2018
- Journal Article
  - Parker, Hannah R; Orjuela, Stephany; Martinho Oliveira, Andreia; Cereatti, Fabrizio; Sauter, Matthias; Heinrich, Henriette; Tanzi, Giulia; Weber, Achim; Komminoth, Paul; Vavricka, Stephan; Albanese, Luca; Buffoli, Federico; Robinson, Mark D; Marra, Giancarlo (2018). The proto CpG island methylator phenotype of sessile serrated adenomas/polyps. Epigenetics, 13(10/11):1088-1105.
  - Krieg, Carsten; Nowicka, Malgorzata; Guglietta, Silvia; Schindler, Sabrina; Hartmann, Felix J; Weber, Lukas M; Dummer, Reinhard; Robinson, Mark D; Levesque, Mitchell P; Becher, Burkhard (2018). Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy. Nature Medicine, 24(11):1773-1775.
  - Villiger, Lukas; Grisch-Chan, Hiu Man; Lindsay, Helen; Ringnalda, Femke; Pogliano, Chiara B; Allegri, Gabriella; Fingerhut, Ralph; Häberle, Johannes; Matos, Joao; Robinson, Mark D; Thöny, Beat; Schwank, Gerald (2018). Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nature Medicine, 24(10):1519-1525.
  - Bick, Jochen T; Flöter, Veronika L; Robinson, Mark D; Bauersachs, Stefan; Ulbrich, Susanne 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(1):590.
  - Savic, Natasa; Ringnalda, Femke Cas; Lindsay, Helen; Berk, Christian; Bargsten, Katja; Li, Yizhou; Neri, Dario; Robinson, Mark D; Ciaudo, Constance; Hall, Jonathan; Jinek, Martin; Schwank, Gerald (2018). Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. eLife, 7:33761.
  - Chevrier, Stéphane; Crowell, Helena L; Zanotelli, Vito R T; Engler, Stefanie; Robinson, Mark D; Bodenmiller, Bernd (2018). Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry. Cell Systems, 6(5):612-620.e5.
  - Praz, Coraline R; Menardo, Fabrizio; Robinson, Mark D; Müller, Marion C; Wicker, Thomas; Bourras, Salim; Keller, Beat (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.
  - Van den Berge, Koen; Perraudeau, Fanny; Soneson, Charlotte; Love, Michael I; Risso, Davide; Vert, Jean-Philippe; Robinson, Mark D; Dudoit, Sandrine; Clement, Lieven (2018). Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. Genome Biology, 19:24.
  - Soneson, Charlotte; Robinson, Mark D (2018). Bias, robustness and scalability in single-cell differential expression analysis. Nature Methods, 15(4):255-261.
  - Wrangle, John M; Velcheti, Vamsidhar; Patel, Manish R; Garrett-Mayer, Elizabeth; Hill, Elizabeth G; Ravenel, James G; et al; Robinson, Mark D; Rubinstein, Mark 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(5):694-704.
  - Perez-Shibayama, Christian; Gil-Cruz, Cristina; Cheng, Hung-Wei; Onder, Lucas; Printz, Andrea; Mörbe, Urs; Novkovic, Mario; Li, Conglei; Lopez-Macias, Constantino; Buechler, Matthew B; Turley, Shannon J; Mack, Matthias; Soneson, Charlotte; Robinson, Mark D; Scandella, Elke; Gommerman, Jennifer; Ludewig, Burkhard (2018). Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity. Science Immunology, 3(26):eaar4539.

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