Publications by authors named "Mark D Robinson"

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The shaky foundations of simulating single-cell RNA sequencing data.
Helena L Crowell, Sarah X Morillo Leonardo, Charlotte Soneson, Mark D Robinson

Genome Biol· March 2023

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Transcriptomics- and 3D imaging-based characterization of the lymphatic vasculature in human skin.
Aline Bauer, Lito Zambounis, Ioannis Kritikos, Almut Lütge, Amélie Sabine, Mark D Robinson

J Exp Med· January 2026

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Rbm8a deficiency causes hematopoietic defects by modulating Wnt/PCP signaling.
Agnese Kocere, Elena Chiavacci, Charlotte Soneson, Seth T Jacobson, Emma N Harrison, Mark D Robinson

Dev Biol· December 2025

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Protocol to investigate fibroblastic reticular cell-immune cell interaction in human lung cancer.
Chrysa Papadopoulou, Hung-Wei Cheng, Almut Lütge, Mechthild Lütge, Angelina De Martin, Mark D Robinson

STAR Protoc· December 2025

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RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.
Giulia Moro, Izaskun Mallona, Malwine J Barz, Joël Maillard, Michael David Brügger, Mark D Robinson

Nat Commun· December 2025

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Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering.
Jieran Sun, Kirti Biharie, Peiying Cai, Niklas Mueller-Boetticher, Paul Kiessling, Mark D Robinson

bioRxiv· November 2025

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On feature selection to disentangle cell type and state transcriptional programs.
Jiayi Wang, Helena L Crowell, Mark D Robinson

BMC Genomics· November 2025

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Building a continuous benchmarking ecosystem in bioinformatics.
Izaskun Mallona, Charlotte Soneson, Ben Carrillo, Almut Lütge, Daniel Incicau, Mark D Robinson

PLoS Comput Biol· November 2025

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Orchestrating Spatial Transcriptomics Analysis with Bioconductor.
Helena L Crowell, Yixing Dong, Ilaria Billato, Peiying Cai, Martin Emons, Mark D Robinson

bioRxiv· November 2025

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Harnessing the potential of spatial statistics for spatial omics data with pasta.
Martin Emons, Samuel Gunz, Helena L Crowell, Izaskun Mallona, Malte Kuehl, Mark D Robinson

Nucleic Acids Res· September 2025

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and derived macrophages occupy distinct phenotypic states.
Stéphane Chevrier, Vito R T Zanotelli, Daniel Schulz, Mark D Robinson, Laurie Ailles

bioRxiv· September 2025

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On metrics for subpopulation detection in single-cell and spatial omics data.
Siyuan Luo, Pierre-Luc Germain, Ferdinand von Meyenn, Mark D Robinson

Nucleic Acids Res· September 2025

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A Th17 signature correlates with response to dual CTLA-4 and PD-1 blockade in metastatic renal cell carcinoma.
Silvia Guglietta, Anne Bärenwaldt, Anthony Sonrel, Stephany Orjuela, Gianni Monaco, Mark D Robinson

medRxiv· September 2025

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MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments.
Reto Gerber, Jake Griner, Silvia Guglietta, Carsten Krieg, Mark D Robinson

bioRxiv· July 2025

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A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification.
David Wissel, Madison M Mehlferber, Khue M Nguyen, Vasilii Pavelko, Elizabeth Tseng, Mark D Robinson

bioRxiv· June 2025

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Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.
Yu-Ning Huang, Viorel Munteanu, Michael I Love, Cynthia Flaire Ronkowski, Dhrithi Deshpande, Mark D Robinson

Cell Genom· May 2025

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Fibroblastic reticular cells form reactive myeloid cell niches in human lymph nodes.
Mechthild Lütge, Lisa Kurz, Yves Stanossek, Samuel Meili, Hung-Wei Cheng, Mark D Robinson

Sci Immunol· May 2025

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T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis.
Ivan Jelcic, Reza Naghavian, Imran Fanaswala, Will Macnair, Cinzia Esposito, Mark D Robinson

Cell Rep Med· March 2025

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snRNA-seq stratifies multiple sclerosis patients into distinct white matter glial responses.
Will Macnair, Daniela Calini, Eneritz Agirre, Julien Bryois, Sarah Jäkel, Mark D Robinson

Neuron· February 2025

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Fibroblastic reticular cells generate protective intratumoral T cell environments in lung cancer.
Lucas Onder, Chrysa Papadopoulou, Almut Lütge, Hung-Wei Cheng, Mechthild Lütge, Mark D Robinson

Cell· January 2025

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On the identification of differentially-active transcription factors from ATAC-seq data.
Felix Ezequiel Gerbaldo, Emanuel Sonder, Vincent Fischer, Selina Frei, Jiayi Wang, Mark D Robinson

PLoS Comput Biol· October 2024

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Benchmarking computational methods for single-cell chromatin data analysis.
Siyuan Luo, Pierre-Luc Germain, Mark D Robinson, Ferdinand von Meyenn

Genome Biol· August 2024

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Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons.
Brandon Signal, Andrew J Phipps, Katherine A Giles, Shannon N Huskins, Timothy R Mercer, Mark D Robinson

Cells· August 2024

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Author Correction: The shaky foundations of simulating single-cell RNA sequencing data.
Helena L Crowell, Sarah X Morillo Leonardo, Charlotte Soneson, Mark D Robinson

Genome Biol· July 2024

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Divergent evolution of male-determining loci on proto-Y chromosomes of the housefly.
Xuan Li, Sander Visser, Jae Hak Son, Elzemiek Geuverink, Ece Naz Kıvanç, Mark D Robinson

Nat Commun· July 2024

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Ten simple rules for computational biologists collaborating with wet lab researchers.
Mark D Robinson, Peiying Cai, Martin Emons, Reto Gerber, Pierre-Luc Germain

PLoS Comput Biol· June 2024

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