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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 -
MACA: Marker-based automatic cell-type annotation for single cell expression data2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Simon J. Baumgart, Christian M. Stegmann, Sikander Hayat
2citations -
SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Ping Zhu, Rafael Kramann, Sikander Hayat, +1 more
1citations -
Combinatorial multimer staining and spectral flow cytometry facilitate quantification and characterization of polysaccharide-specific B cell immunity2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology T-cell and B-cell Immunology Open access
Dennis Hoving, A.H.C. Marques, Wesley Huisman, Beckley A. Nosoh, Alicia C. de Kroon, Oscar R. J. van Hengel, +8 more
0citations -
Single cell micro-pillar-based characterization of endothelial and fibroblast cell mechanics2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cellular Mechanics and Interactions Open access
Julia Eckert, Yasmine Abouleila, Thomas Schmidt, Alireza Mashaghi
2citations -
Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tommaso Andreani, Linda M. Slot, Samuel Gabillard, Carsten Struebing, Claus Reimertz, Yaligara Veeranagouda, +6 more
4citations -
Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis2021 medRxiv preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Lennart P. L. Landsmeer, Kai Cui, Marie A.C. Depuydt, Maarten C. Verwer, Joost M. Mekke, +17 more
4citations -
Post-transcriptional regulatory mechanisms in human islets inferred from cell type-specific eQTLs detected by single-cell RNA-seq2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Twan J. J. de Winter, Miha Sovrovic, Han Sun, James D. Johnson, Patrick Edward MacDonald, Anna L. Gloyn, +3 more
0citations -
Human pluripotent stem cells-derived inner ear organoids recapitulate otic development in vitro2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Hearing, Cochlea, Tinnitus, Genetics Open access
Daniela Doda, Sara Alonso Jimenez, Hubert Rehrauer, Jose F. Carreño, Victoria Valsamides, Stefano Di Santo, +7 more
1citations -
Pulmonary ductal coarctation and left pulmonary artery interruption; pathology and role of neural crest and second heart field during development2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Adriana C. Gittenberger–de Groot, Joshua Craiger Peterson, Lambertus J. Wisse, Arno A.W. Roest, Robert E. Poelmann, Regina Bökenkamp, +5 more
5citations -
Sex-dependent gene regulation of human atherosclerotic plaques by DNA methylation and transcriptome integration points to smooth muscle cell involvement in women2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Epigenetics and DNA Methylation Open access
Robin J. G. Hartman, Marten A. Siemelink, Saskia Haitjema, Koen F. Dekkers, Lotte Slenders, Arjan Boltjes, +8 more
3citations -
nsGSLs on tumors impair anti-tumor immune responses by OT-I T cells in vitro and support tumor growth in vivo2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Glycosylation and Glycoproteins Research
Tamara Verkerk, Aimee Selten, Nordin D. Zandhuis, Tao Zhang, Manfred Wuhrer, Robbert M. Spaapen, +1 more
0citations -
Temporal Dynamics of Neocortical Development in Organotypic Mouse Cultures: A Comprehensive Analysis2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Neural dynamics and brain function Open access
Aniella Bak, Katharina Schmied, M. Jakob, Francesco Bedogni, Olivia A Squire, Birgit Gittel, +6 more
0citations -
Haploinsufficiency of eNOS mitigates beneficial effects of maternal exercise on fetal heart development during pregestational diabetes2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Ryleigh van Neck, Xiangru Lu, Lambertus J. Wisse, Marco C. DeRuiter, Qingping Feng
0citations -
The NSL complex promotes neural development by preventing R-loop induced replication stress2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genomics and Chromatin Dynamics Open access
Jolanthe Lingeman, Diana van den Heuvel, Jeroen van den Berg, Jenny Kaur Singh, Rosanne van Hooijdonk, Wouter W. Wiegant, +15 more
0citations -
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods2025 eLife preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Ziv Rafael Yaniv, Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando Arroyo-Mejías, Rebecca T. Beuschel, Katy Börner, +55 more
0citations -
Zebrafish eye development and function is affected by crude oil exposure – line of evidence from underlying molecular effects to behavioral consequences2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Environmental Science Environmental Toxicology and Ecotoxicology Open access
Leonie K. Mueller, Sarah Johann, Bernd Denecke, Ali Taleb Abdallah, Markus Hecker, Henner Hollert, +1 more
1citations -
Plasmodium falciparum SET10 is a histone H3 lysine K18 methyltransferase that participates in a chromatin modulation network crucial for intraerythrocytic development2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Malaria Research and Control Open access
Jean-Pierre Musabyimana, Sherihan Musa, Janice Manti, Ute Distler, Stefan Tenzer, Che Julius Ngwa, +1 more
0citations -
In Vitro Generation and Characterization of The Wu Syndrome Model That Causes Mental Retardation in Neural Cell Lines2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetics and Neurodevelopmental Disorders Open access
Sumeyye Seher Karaman, Tuba Sevik, Selin Akdemir, Esra Karadeli, Dilay Yalcin, Buse Baran, +5 more
0citations -
Generation and Culture of Cardiac Microtissues in a Microfluidic Chip with a Reversible Open Top Enables Electrical Pacing, Dynamic Drug Dosing and Endothelial Cell Co-Culture2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Engineering 3D Printing in Biomedical Research Open access
Aisen Vivas, Camilo IJspeert, Jesper Yue Pan, Kim Vermeul, Albert van den Berg, Robert C. J. J. Passier, +2 more
1citations -
Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Joshua Hislop, Amir Alavi, Qi Song, Rayna Schoenberger, Kamyar Keshavarz F., Ryan LeGraw, +11 more
18citations -
The IBEX knowledge-base a community resource enabling adoption and development of immunofluorescence imaging methods2025 eLife preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Ziv Rafael Yaniv, Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando Arroyo-Mejías, Rebecca T. Beuschel, Katy Börner, +56 more
2citations -
The IBEX Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluorescence Imaging Methods2026 eLife preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Ziv Rafael Yaniv, Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando Arroyo-Mejías, Rebecca T. Beuschel, Katy Börner, +56 more
0citations