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Publications

2026
- Journal Article
  - Guo, Y., Mallona, I., Robinson, M. D., & Li, L. (2026). BiCLUM: Bilateral contrastive learning for unpaired single-cell multi-omics integration PLoS Computational Biology, 22(2), e1013932. https://doi.org/10.1371/journal.pcbi.1013932
  - 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, 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, e20242353. https://doi.org/10.1084/jem.20242353
- Master's Thesis
  - Quintas, M. (2026). Parent-of-Origin Rare Variant Gene-Based Burden Tests (Master’s thesis, University of Zurich) https://doi.org/10.5167/uzh-433678
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, 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, 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, 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., De Martin, A., Kurz, L., Cadosch, N., Pikor, N. B., Rodriguez, R., Born, D., Jochum, W., Leskow, P., Dutly, A., Robinson, M. D., & Ludewig, B. (2025). Fibroblastic reticular cells generate protective intratumoral T cell environments in lung cancer Cell, 188, 430-446.e20. https://doi.org/10.1016/j.cell.2024.10.042
2024
- Journal Article
  - Signal, B., Phipps, A. J., Giles, K. A., Huskins, S. N., Mercer, T. R., Robinson, M. D., Woodhouse, A., & Taberlay, P. C. (2024). Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons Cells, 13, 1393. https://doi.org/10.3390/cells13161393
  - Li, X., Visser, S., Son, J. H., Geuverink, E., Kıvanç, E. N., Wu, Y., Schmeing, S., Pippel, M., Anvar, S. Y., Schenkel, M. A., Marec, F., Robinson, M. D., Meisel, R. P., Wimmer, E. A., van de Zande, L., Bopp, D., & Beukeboom, L. W. (2024). Divergent evolution of male-determining loci on proto-Y chromosomes of the housefly Nature Communications, 15, 5984. https://doi.org/10.1038/s41467-024-50390-1
  - Edalat, S. G., Gerber, R., Houtman, M., Lückgen, J., Teixeira, R. L., Palacios Cisneros, M. D. P., Pfanner, T., Kuret, T., Ižanc, N., Micheroli, R., Polido-Pereira, J., Saraiva, F., Lingam, S., Burki, K., Burja, B., Pauli, C., Rotar, Ž., Tomšič, M., Čučnik, S., … Frank Bertoncelj, M. (2024). Molecular maps of synovial cells in inflammatory arthritis using an optimized synovial tissue dissociation protocol IScience, 27, 109707. https://doi.org/10.1016/j.isci.2024.109707
  - Cai, P., Robinson, M. D., & Tiberi, S. (2024). DESpace: spatially variable gene detection via differential expression testing of spatial clusters Bioinformatics, 40, btae027. https://doi.org/10.1093/bioinformatics/btae027
  - Robinson, M. D., Cai, P., Emons, M., Gerber, R., Germain, P.-L., Gunz, S., Luo, S., Moro, G., Sonder, E., Sonrel, A., Wang, J., Wissel, D., & Mallona, I. (2024). Ten simple rules for computational biologists collaborating with wet lab researchers PLoS Computational Biology, 20, e1012174. https://doi.org/10.1371/journal.pcbi.1012174
- Working Paper
  - Kocere, A., Chiavacci, E., Méndez-Acevedo, K. M., Soneson, C., Hiltabidle, M. S., Raghunath, A., MacGowan, J. S., Shavit, J. A., Panáková, D., Williams, M. L. K., Robinson, M. D., Mosimann, C., & Burger, A. (2024). TAR Syndrome-associated Rbm8a deficiency causes hematopoietic defects and attenuates Wnt/PCP signaling (No. 536513; BioRxiv). https://doi.org/10.1101/2023.04.12.536513
2023
- Journal Article
  - Moursy, A., Cléry, A., Gerhardy, S., Betz, K. M., Rao, S., Mazur, J., Campagne, S., Beusch, I., Duszczyk, M. M., Robinson, M. D., Panse, V. G., & Allain, F. H.-T. (2023). RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing Nature Communications, 14, 7166. https://doi.org/10.1038/s41467-023-42962-4
  - Sajibu, S., Sonder, E., Tiwari, A., Orjuela, S., Parker, H. R., Frans, O. T., Gubler, C., Marra, G., & Robinson, M. D. (2023). Validation of hypermethylated DNA regions found in colorectal cancers as potential aging-independent biomarkers of precancerous colorectal lesions BMC Cancer, 23, 998. https://doi.org/10.1186/s12885-023-11487-w
  - Sonrel, A., Luetge, A., Soneson, C., Mallona, I., Germain, P.-L., Knyazev, S., Gilis, J., Gerber, R., Seurinck, R., Paul, D., Sonder, E., Crowell, H. L., Fanaswala, I., Al-Ajami, A., Heidari, E., Schmeing, S., Milosavljevic, S., Saeys, Y., Mangul, S., & Robinson, M. D. (2023). Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability Genome Biology, 24, 119. https://doi.org/10.1186/s13059-023-02962-5
  - de Souza, V. B. C., Jordan, B. T., Tseng, E., Nelson, E. A., Hirschi, K. K., Sheynkman, G., & Robinson, M. D. (2023). Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data Genome Biology, 24, 91. https://doi.org/10.1186/s13059-023-02923-y
  - Crowell, H. L., Morillo Leonardo, S. X., Soneson, C., & Robinson, M. D. (2023). The shaky foundations of simulating single-cell RNA sequencing data Genome Biology, 24, 62. https://doi.org/10.1186/s13059-023-02904-1
  - Macnair, W., & Robinson, M. (2023). SampleQC: robust multivariate, multi-cell type, multi-sample quality control for single-cell data Genome Biology, 24, 23. https://doi.org/10.1186/s13059-023-02859-3
  - Schmeing, S., & Robinson, M. D. (2023). Gapless provides combined scaffolding, gap filling, and assembly correction with long reads Life Science Alliance, 6, e202201471. https://doi.org/10.26508/lsa.202201471
  - Lütge, M., De Martin, A., Gil-Cruz, C., Perez-Shibayama, C., Stanossek, Y., Onder, L., Cheng, H.-W., Kurz, L., Cadosch, N., Soneson, C., Robinson, M. D., Stoeckli, S. J., Ludewig, B., & Pikor, N. B. (2023). Conserved stromal-immune cell circuits secure B cell homeostasis and function Nature Immunology, 24, 1149–1160. https://doi.org/10.1038/s41590-023-01503-3
  - Tiberi, S., Crowell, H. L., Samartsidis, P., Weber, L. M., & Robinson, M. D. (2023). distinct: A novel approach to differential distribution analyses Annals of Applied Statistics, 17, 1681–1700. https://doi.org/10.1214/22-AOAS1689
- Working Paper
  - Tiberi, S., Meili, J., Cai, P., Soneson, C., He, D., Sarkar, H., Avalos-Pacheco, A., Patro, R., & Robinson, M. D. (2023). DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes (No. 553679; BioRxiv). https://doi.org/10.1101/2023.08.17.553679
2022
- Journal Article
  - Prummel, K. D., Crowell, H. L., Nieuwenhuize, S., Brombacher, E. C., Daetwyler, S., Soneson, C., Kresoja-Rakic, J., Kocere, A., Ronner, M., Ernst, A., Labbaf, Z., Clouthier, D. E., Firulli, A. B., Sánchez-Iranzo, H., Naganathan, S. R., O’Rourke, R., Raz, E., Mercader, N., Burger, A., … Mosimann, C. (2022). Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Nature Communications, 13, 1677. https://doi.org/10.1038/s41467-022-29311-7
  - Orjuela, S., Parker, H. R., Sajibu, S., Cereatti, F., Sauter, M., Buffoli, F., Robinson, M. D., & Marra, G. (2022). Disentangling tumorigenesis-associated DNA methylation changes in colorectal tissues from those associated with ageing Epigenetics, 17, 677–694. https://doi.org/10.1080/15592294.2021.1952375
  - Rubinstein, M. P., Williams, C., Mart, C., Beall, J., MacPherson, L., Azar, J., Swiderska-Syn, M., Manca, P., Gibney, B. C., Robinson, M. D., Krieg, C., Hill, E. G., Taha, S. A., Rock, A. D., Lee, J. H., Soon-Shiong, P., & Wrangle, J. (2022). Phase I Trial Characterizing the Pharmacokinetic Profile of N-803, a Chimeric IL-15 Superagonist, in Healthy Volunteers Journal of Immunology, 208, 1362–1370. https://doi.org/10.4049/jimmunol.2100066
  - Wagner, J., Masek, M., Jacobs, A., Soneson, C., Sivapatham, S., Damond, N., de Souza, N., Robinson, M. D., & Bodenmiller, B. (2022). Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines Scientific Data, 9, 44–60. https://doi.org/10.1038/s41597-022-01137-4
  - Burja, B., Paul, D., Tastanova, A., Edalat, S. G., Gerber, R., Houtman, M., Elhai, M., Bürki, K., Staeger, R., Restivo, G., Lang, R., Sodin-Šemrl, S., Lakota, K., Tomšič, M., Levesque, M. P., Distler, O., Rotar, Ž., Robinson, M. D., & Frank-Bertoncelj, M. (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. https://doi.org/10.3389/fcell.2022.872688
2021
- Journal Article
  - Bai, Y., Caussinus, E., Leo, S., Bosshardt, F., Myachina, F., Rot, G., Robinson, M. D., & Lehner, C. F. (2021). A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells BMC Genomics, 22, 771. https://doi.org/10.1186/s12864-021-08057-4
  - Schmeing, S., & Robinson, M. D. (2021). ReSeq simulates realistic Illumina high-throughput sequencing data Genome Biology, 22, 67. https://doi.org/10.1186/s13059-021-02265-7
  - Sahadevan, S., Hembach, K. M., Tantardini, E., Pérez-Berlanga, M., Hruska-Plochan, M., Megat, S., Weber, J., Schwarz, P., Dupuis, L., Robinson, M. D., De Rossi, P., & Polymenidou, M. (2021). Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS Nature Communications, 12, 3027. https://doi.org/10.1038/s41467-021-23188-8
  - Gerber, R., & Robinson, M. D. (2021). Censcyt: censored covariates in differential abundance analysis in cytometry BMC Bioinformatics, 22, 235. https://doi.org/10.1186/s12859-021-04125-4
  - Milosavljevic, S., Kuo, T., Decarli, S., Mohn, L., Sese, J., Shimizu, K. K., Shimizu-Inatsugi, R., & Robinson, M. D. (2021). ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw BMC Genomics, 22, 547. https://doi.org/10.1186/s12864-021-07845-2
  - Lütge, A., Zyprych-Walczak, J., Brykczynska Kunzmann, U., Crowell, H. L., Calini, D., Malhotra, D., Soneson, C., & Robinson, M. D. (2021). CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data Life Science Alliance, 4, e202001004. https://doi.org/10.26508/lsa.202001004
  - Huang, R., Soneson, C., Germain, P.-L., Schmidt, T. S. B., von Mering, C., & Robinson, M. D. (2021). treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses Genome Biology, 22, 157. https://doi.org/10.1186/s13059-021-02368-1
  - Wang, Y., Soneson, C., Malinowska, A. L., Laski, A., Ghosh, S., Kanitz, A., Gebert, L. F. R., Robinson, M. D., & Hall, J. (2021). MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome Nucleic Acids Research, 49, 25–37. https://doi.org/10.1093/nar/gkaa1117
  - Germain, P.-L., Lun, A., Garcia Meixide, C., Macnair, W., & Robinson, M. D. (2021). Doublet identification in single-cell sequencing data using scDblFinder F1000Research, 10, 979. https://doi.org/10.12688/f1000research.73600.2
  - Gerber, R., & Robinson, M. D. (2021). pubassistant.ch: consolidating publication profiles of researchers F1000Research, 10, 989. https://doi.org/10.12688/f1000research.73493.3
2020
- Journal Article
  - Germain, P.-L., Sonrel, A., & Robinson, M. D. (2020). pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools Genome Biology, 21, 227. https://doi.org/10.1186/s13059-020-02136-7
  - Tiberi, S., & Robinson, M. D. (2020). BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty Genome Biology, 21, 69. https://doi.org/10.1186/s13059-020-01967-8
  - Crowell, H. L., Soneson, C., Germain, P.-L., Calini, D., Collin, L., Raposo, C., Malhotra, D., & Robinson, M. D. (2020). muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data Nature Communications, 11, 6077. https://doi.org/10.1038/s41467-020-19894-4
  - Huang, R., Soneson, C., Ernst, F. G. M., Rue-Albrecht, K. C., Yu, G., Hicks, S. C., & Robinson, M. D. (2020). TreeSummarizedExperiment: a S4 class for data with hierarchical structure F1000Research, 9, 1246. https://doi.org/10.12688/f1000research.26669.1
  - Malan-Müller, S., de Souza, V. B. C., Daniels, W. M. U., Seedat, S., Robinson, M. D., & Hemmings, S. 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, 352–369. https://doi.org/10.1089/omi.2020.0031
  - Orjuela, S., Machlab, D., Menigatti, M., Marra, G., & Robinson, M. D. (2020). DAMEfinder: a method to detect differential allele-specific methylation Epigenetics & Chromatin, 13, 25. https://doi.org/10.1186/s13072-020-00346-8
  - Orjuela, S., Menigatti, M., Schraml, P., Kambakamba, P., Robinson, M. D., & Marra, G. (2020). The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers BMC Cancer, 20, 290. https://doi.org/10.1186/s12885-020-06777-6
  - 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. (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, 56. https://doi.org/10.1038/s41419-020-2261-2
  - Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., & et al. (2020). Eleven grand challenges in single-cell data science Genome Biology, 21, 31. https://doi.org/10.1186/s13059-020-1926-6

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