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Capture of Post-Pluripotency Human Neuromesodermal and Neural Tube Axial Stem Cell States2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Dolunay Kelle, Enes Ugur, Ejona Rusha, Dmitry Shaposhnikov, Alessandra Livigni, Sandra Horschitz, +16 more
4citations -
Continuous Capture of recombinant AAV Particles Using Twin-Column CaptureSMB2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Virus-based gene therapy research Open access
Julia M Mueller, Daniela Tobler, Jules Buehler, Damian Hauri, Ralf Plieninger, Sven Göbel, +5 more
0citations -
GraphComm: A Graph-based Deep Learning Method to Predict Cell-Cell Communication in single-cell RNAseq data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Emily So, Sikander Hayat, Sisira Kadambat Nair, Bo Wang, Benjamin Haibe‐Kains
13citations -
Comparison of the performance of two targeted metagenomic virus capture probe-based methods using synthetic viral sequences and clinical samples2023 medRxiv preprint Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Kees Mourik, Igor A. Sidorov, Ellen C. Carbo, David van der Meer, Arnoud Boot, Aloys C.M. Kroes, +3 more
4citations -
Identifying commonalities between cell lines and tumors at the single cell level using Sobolev Alignment of deep generative models2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Soufiane M. C. Mourragui, Joseph C. Siefert, Marcel J. T. Reinders, Marco Loog, Lodewyk F.A. Wessels
2citations -
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing2021 Genome Research preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Brian D. Aevermann, Yun Zhang, Mark A. Novotny, Mohamed Keshk, Trygve E. Bakken, Jeremy A. Miller, +4 more
96citations -
NS-Forest: A machine learning method for the objective identification of minimum marker gene combinations for cell type determination from single cell RNA sequencing2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Brian D. Aevermann, Yun Zhang, Mark A. Novotny, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, +3 more
12citations -
Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Leonie van Steijn, Clément Sire, Loı̈c Dupré, Guy Théraulaz, Roeland M. H. Merks
4citations -
Immunophenotyping of T cells Combined with Vβ antibodies identifies long lasting CMV related T cell Expansions with a consistent TIGIT and PD-1 phenotype2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology T-cell and B-cell Immunology
Monique M. van Ostaijen-ten Dam, Marco W. Schilham, Arjan C. Lankester, Janine E. Melsen
0citations -
The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Shrey Parikh, Daniel C. Strobl, Sara Jiménez, Julia Beckmann, Lucas Arnoldt, Eljas Roellin, +18 more
0citations -
Interindividual HLA Evolutionary Divergence in Single HLA-Mismatched Unrelated Donor Hematopoietic Cell Transplantation for Malignant Hematological Disorders: A Report on Behalf of the Cellular Therapy and Immunobiology Working Party of the EBMT
Simona Pagliuca, Jarl Mooyaart, Francis Ayuketang Ayuk, Robert Zeiser, Victoria T. Potter, Peter Dreger, +23 more
0citations -
scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments0citations
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PHLOWER - Single cell trajectory analysis using Hodge Decomposition2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mingbo Cheng, Jitske Jansen, Katharina C. Reimer, James Shiniti Nagai, Zhijian Li, Paul Kießling, +5 more
0citations -
SIRV: Spatial inference of RNA velocity at the single-cell resolution2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Laurens M. Grossouw, R. Jeroen Pasterkamp, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Essam Mahfouz
12citations -
SIngle cell level Genotyping Using scRna Data (SIGURD)2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Martin Graßhoff, Milena Kalmer, Nicolas Chatain, Kim Kricheldorf, Angela Maurer, Ralf Weiskirchen, +2 more
0citations -
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data2024 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ping‐Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien‐Yu Chen, +3 more
0citations -
Cell Painting PLUS reveals phenotypic signatures for nephrotoxicity profiling in human RPTEC/TERT12026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Marlene Wedler, José M. Muiño, Christopher Wolff, Palle Steen Helmke, Gerhard Franz Ecker, Joshua Harrill, +6 more
0citations -
Single-Cell Resolution of Cellular Damage Illuminates Disease Progression2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tsimafei Padvitski, Paula Unger Avila, He Chen, Fabian Braun, David Unnersjö‐Jess
1citations -
Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM202021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology RNA Research and Splicing Open access
Carlos H. Vieira-Vieira, Vita Dauksaite, Michael Gotthardt, Matthias Selbach
0citations -
Spatial transcriptomics defines the mechanisms of hiPSC-derived stem cell-mediated repair in human articular cartilage2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Osteoarthritis Treatment and Mechanisms Open access
Y.F. Ramos, Sayedeh Sana Sayedipour, Georgina Shaw, Margo Tuerlings, Timo Schomann, H. Eka D. Suchiman, +7 more
0citations -
Comparative human embryo-mapping reveals neural bias of neuromesodermal progenitors in stem cell axial elongation models2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Developmental Biology and Gene Regulation Open access
Yuting Wang, Rafaella Buzatu, Cecile Herbermann, Micha Drukker, Christian J. Schröter
0citations -
Development of covalent probes to capture Legionella pneumophila effector enzymes2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Legionella and Acanthamoeba research Open access
Max S. Kloet, Rishov Mukhopadhyay, Rukmini Mukherjee, Mohit Misra, Minwoo Jeong, Cami M. P. Talavera Ormeño, +7 more
1citations -
Spatio-temporal transcriptomic analysis reveals distinct nephrotoxicity, DNA damage and regeneration response after cisplatin2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Chemotherapy-induced organ toxicity mitigation Open access
Lukas S. Wijaya, Steven J. Kunnen, Panuwat Trairatphisan, Ciaran P. Fisher, Meredith E. Crosby, Kai Schaefer, +11 more
0citations