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CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, +5 more
4citations -
Evolution of Bone Lesions in Adults with Chronic Nonbacterial Osteitis (Cno): A Long-Term Follow-Up Study2024 SSRN Electronic Journal preprint Medicine Osteomyelitis and Bone Disorders Research Open access
Anne T Leerling, Christophe J. Weizenbach, Ana Navas-Cañete, Olaf M. Dekkers, Liesbeth Winter
1citations -
Resolving the immune response across clonal cancer evolution in situ with Atera whole transcriptome profiling2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Maarten van der Linde, Chunfang Zhu, Robert B. West, David G.P. van IJzendoorn, Magdalena Matusiak
1citations -
Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access
Noah F. Greenwald, Iris Nederlof, Daisy Yi Ding, Seongyeol Park, Alex Kong, Kathleen E. Houlahan, +29 more
7citations -
Lack of detectable neoantigen depletion in treatment-naïve cancers2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access
Maarten Slagter, Lorenzo F. Fanchi, Marit M. van Buuren, Arno Velds, Gergana Bounova, Lodewyk F.A. Wessels, +1 more
0citations -
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Darvish Shafighi, Szymon M. Kiełbasa, Hugo W van Kessel, Ruben A. L. de Groen, +6 more
1citations -
Overcoming Observation Bias for Cancer Progression Modeling2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access
Rudolf Schill, Maren Klever, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, +2 more
1citations -
Distinct colorectal cancer genotypes shape microbial ecosystems and reveal stage-specific microbiota dependencies2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gut microbiota and health Open access
Valentina Brunner, Nicholas Bodenstein, Antonio Enrico Zaurito, M Silva, Frederic Saab, Fabian Springer, +18 more
0citations -
Improving Mathematical Models of Cancer through Game-Theoretic Modelling: A Study in Non-Small Cell Lung Cancer2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Mathematics Mathematical Biology Tumor Growth Open access
Virginia Ardévol Martínez, Narmin Ghaffari Laleh, Frank Thuijsman, Joel S. Brown, Rachel Cavill, Jakob Nikolas Kather, +1 more
7citations
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