Publications

ZORA Publication List

Publications

• 2026

  • Journal Article

    • Bauer, A., Zambounis, L., Kritikos, I., Lütge, A., SABINE, A., Heron, C., Petkova, M., Giampietro, C., Blatter, K., Bianco, S. D., Gschwend Rodes, D. A., Restivo, G., Proulx, S., Levesque, M. P., Lindenblatt, N., Mazza, E., Detmar, M., Gousopoulos, E., Robinson, M. D., … Halin, C. (2026). Transcriptomics- and 3D imaging-based characterization of the lymphatic vasculature in human skin Journal of Experimental Medicine, 223(1), e20242353. https://doi.org/10.1084/jem.20242353
    • Bauer, A., Zambounis, L., Kritikos, I., Lütge, A., Sabine, A., Heron, C., Petkova, M., Giampietro, C., Blatter, K., Bianco, S. D., Gschwend, D., Restivo, G., Proulx, S. T., Levesque, M. P., Lindenblatt, N., Mazza, E., Detmar, M., Gousopoulos, E., Robinson, M. D., … Halin, C. (2026). Transcriptomics- and 3D imaging-based characterization of the lymphatic vasculature in human skin Journal of Experimental Medicine, 223(1), e20242353. https://doi.org/10.1084/jem.20242353

• 2025

  • Journal Article

    • Papadopoulou, C., Cheng, H.-W., Lütge, A., Lütge, M., De Martin, A., Robinson, M. D., Ludewig, B., & Onder, L. (2025). Protocol to investigate fibroblastic reticular cell-immune cell interaction in human lung cancer STAR Protocols, 6(4), 104256. https://doi.org/10.1016/j.xpro.2025.104256
    • Germain, P.-L., Wang, J., & Robinson, M. D. (2025). Bulk-based hypothesis weighing increases power in single-cell differential expression analysis Peer Community Journal, 5, e136. https://doi.org/10.24072/pcjournal.663
    • Mallona, I., Soneson, C., Carrillo, B., Lütge, A., Incicau, D., Gerber, R., Sonrel, A., & Robinson, M. D. (2025). Building a continuous benchmarking ecosystem in bioinformatics PLoS Computational Biology, 21(11), e1013658. https://doi.org/10.1371/journal.pcbi.1013658
    • Wang, J., Crowell, H. L., & Robinson, M. D. (2025). On feature selection to disentangle cell type and state transcriptional programs BMC Genomics, 26(1), 1006. https://doi.org/10.1186/s12864-025-12085-9
    • Emons, M., Gunz, S., Crowell, H. L., Mallona, I., Kuehl, M., Furrer, R., & Robinson, M. (2025). Harnessing the potential of spatial statistics for spatial omics data with $pasta$ Nucleic Acids Research, 53(17), gkaf870. https://doi.org/10.1093/nar/gkaf870
    • Onder, L., Papadopoulou, C., Lütge, A., Cheng, H.-W., Lütge, M., Perez-Shibayama, C., Gil-Cruz, C., et al. (2025). Fibroblastic reticular cells generate protective intratumoral T cell environments in lung cancer Cell, 188(2), 430-446.e20. doi:10.1016/j.cell.2024.10.042

• 2024

  • Journal Article

    • Signal, Brandon; Phipps, Andrew J; Giles, Katherine A; Huskins, Shannon N; Mercer, Timothy R; Robinson, Mark D; Woodhouse, Adele; Taberlay, Phillippa C (2024). Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons Cells, 13(16):1393.
    • Li, Xuan; Visser, Sander; Son, Jae Hak; Geuverink, Elzemiek; Kıvanç, Ece Naz; Wu, Yanli; Schmeing, Stephan; Pippel, Martin; Anvar, Seyed Yahya; Schenkel, Martijn A; Marec, František; Robinson, Mark D; Meisel, Richard P; Wimmer, Ernst A; van de Zande, Louis; Bopp, Daniel; Beukeboom, Leo W (2024). Divergent evolution of male-determining loci on proto-Y chromosomes of the housefly Nature Communications, 15(1):5984.
    • Edalat, Sam G; Gerber, Reto; Houtman, Miranda; Lückgen, Janine; Teixeira, Rui Lourenço; Palacios Cisneros, Maria Del Pilar; Pfanner, Tamara; Kuret, Tadeja; Ižanc, Nadja; Micheroli, Raphael; Polido-Pereira, Joaquim; Saraiva, Fernando; Lingam, Swathi; Burki, Kristina; Burja, Blaž; Pauli, Chantal; Rotar, Žiga; Tomšič, Matija; Čučnik, Saša; Fonseca, João Eurico; Distler, Oliver; Calado, Ângelo; Romão, Vasco C; Ospelt, Caroline; Sodin-Semrl, Snežna; Robinson, Mark D; Frank Bertoncelj, Mojca (2024). Molecular maps of synovial cells in inflammatory arthritis using an optimized synovial tissue dissociation protocol iScience, 27(6):109707.
    • Cai, Peiying; Robinson, Mark D; Tiberi, Simone (2024). DESpace: spatially variable gene detection via differential expression testing of spatial clusters Bioinformatics, 40(2):btae027.
    • Robinson, Mark D; Cai, Peiying; Emons, Martin; Gerber, Reto; Germain, Pierre-Luc; Gunz, Samuel; Luo, Siyuan; Moro, Giulia; Sonder, Emanuel; Sonrel, Anthony; Wang, Jiayi; Wissel, David; Mallona, Izaskun (2024). Ten simple rules for computational biologists collaborating with wet lab researchers PLoS Computational Biology, 20(6):e1012174.

  • Working Paper

    • Kocere, Agnese; Chiavacci, Elena; Méndez-Acevedo, Kevin Manuel; Soneson, Charlotte; Hiltabidle, Max S; Raghunath, Azhwar; MacGowan, Jacalyn S; Shavit, Jordan A; Panáková, Daniela; Williams, Margot L K; Robinson, Mark D; Mosimann, Christian; Burger, Alexa (2024). TAR Syndrome-associated Rbm8a deficiency causes hematopoietic defects and attenuates Wnt/PCP signaling bioRxiv 536513, University of Zurich.

• 2023

  • Journal Article

    • Moursy, Ahmed; Cléry, Antoine; Gerhardy, Stefan; Betz, Katharina M; Rao, Sanjana; Mazur, Jarosław; Campagne, Sébastien; Beusch, Irene; Duszczyk, Malgorzata M; Robinson, Mark D; Panse, Vikram Govind; Allain, Frédéric H-T (2023). RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing Nature Communications, 14(1):7166.
    • Sajibu, Sija; Sonder, Emanuel; Tiwari, Amit; Orjuela, Stephany; Parker, Hannah R; Frans, Olivier The; Gubler, Christoph; Marra, Giancarlo; Robinson, Mark D (2023). Validation of hypermethylated DNA regions found in colorectal cancers as potential aging-independent biomarkers of precancerous colorectal lesions BMC Cancer, 23(1):998.
    • Sonrel, Anthony; Luetge, Almut; Soneson, Charlotte; Mallona, Izaskun; Germain, Pierre-Luc; Knyazev, Sergey; Gilis, Jeroen; Gerber, Reto; Seurinck, Ruth; Paul, Dominique; Sonder, Emanuel; Crowell, Helena L; Fanaswala, Imran; Al-Ajami, Ahmad; Heidari, Elyas; Schmeing, Stephan; Milosavljevic, Stefan; Saeys, Yvan; Mangul, Serghei; Robinson, Mark D (2023). Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability Genome Biology, 24(1):119.
    • de Souza, Vladimir B C; Jordan, Ben T; Tseng, Elizabeth; Nelson, Elizabeth A; Hirschi, Karen K; Sheynkman, Gloria; Robinson, Mark D (2023). Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data Genome Biology, 24(1):91.
    • Crowell, Helena L; Morillo Leonardo, Sarah X; Soneson, Charlotte; Robinson, Mark D (2023). The shaky foundations of simulating single-cell RNA sequencing data Genome Biology, 24(1):62.
    • Macnair, Will; Robinson, Mark (2023). SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data. Genome Biology, 24(1):23.
    • Lütge, Mechthild; De Martin, Angelina; Gil-Cruz, Cristina; Perez-Shibayama, Christian; Stanossek, Yves; Onder, Lucas; Cheng, Hung-Wei; Kurz, Lisa; Cadosch, Nadine; Soneson, Charlotte; Robinson, Mark D; Stoeckli, Sandro J; Ludewig, Burkhard; Pikor, Natalia B (2023). Conserved stromal-immune cell circuits secure B cell homeostasis and function Nature Immunology, 24(7):1149-1160.
    • Schmeing, Stephan; Robinson, Mark D (2023). Gapless provides combined scaffolding, gap filling, and assembly correction with long reads Life Science Alliance, 6(7):e202201471.
    • Tiberi, Simone; Crowell, Helena L; Samartsidis, Pantelis; Weber, Lukas M; Robinson, Mark D (2023). distinct: A novel approach to differential distribution analyses Annals of Applied Statistics, 17(2):1681-1700.

  • Working Paper

    • Tiberi, Simone; Meili, Joël; Cai, Peiying; Soneson, Charlotte; He, Dongze; Sarkar, Hirak; Avalos-Pacheco, Alejandra; Patro, Rob; Robinson, Mark D (2023). DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes bioRxiv 553679, Cold Spring Harbor Laboratory.

• 2022

  • Journal Article

    • Prummel, Karin D; Crowell, Helena L; Nieuwenhuize, Susan; Brombacher, Eline C; Daetwyler, Stephan; Soneson, Charlotte; Kresoja-Rakic, Jelena; Kocere, Agnese; Ronner, Manuel; Ernst, Alexander; Labbaf, Zahra; Clouthier, David E; Firulli, Anthony B; Sánchez-Iranzo, Héctor; Naganathan, Sundar R; O’Rourke, Rebecca; Raz, Erez; Mercader, Nadia; Burger, Alexa; Felley-Bosco, Emanuela; Huisken, Jan; Robinson, Mark D; Mosimann, Christian (2022). Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Nature Communications, 13(1):1677.
    • 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.
    • Rubinstein, Mark P; Williams, Cameron; Mart, Caroline; Beall, Jonathan; MacPherson, Linda; Azar, Joseph; Swiderska-Syn, Marzena; Manca, Paolo; Gibney, Barry C; Robinson, Mark D; Krieg, Carsten; Hill, Elizabeth G; Taha, Sharif A; Rock, Amy D; Lee, John H; Soon-Shiong, Patrick; Wrangle, John (2022). Phase I Trial Characterizing the Pharmacokinetic Profile of N-803, a Chimeric IL-15 Superagonist, in Healthy Volunteers Journal of Immunology, 208(6):1362-1370.
    • 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.
    • Schmeing, Stephan; Robinson, Mark D (2021). ReSeq simulates realistic Illumina high-throughput sequencing data Genome Biology, 22:67.
    • 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.
    • 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.
    • Germain, Pierre-Luc; Lun, Aaron; Garcia Meixide, Carlos; Macnair, Will; Robinson, Mark D (2021). Doublet identification in single-cell sequencing data using scDblFinder F1000Research, 10:979.
    • Gerber, Reto; Robinson, Mark D (2021). pubassistant.ch: consolidating publication profiles of researchers F1000Research, 10:989.

• 2020

  • Journal Article

    • Tiberi, Simone; Robinson, Mark D (2020). BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty Genome Biology, 21:69.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.

• 2019

  • Journal Article

    • Robinson, Mark D; Vitek, Olga (2019). Benchmarking comes of age Genome Biology, 20(1):205.

Pagination