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Cellular Factors Involved in Transcriptome Dynamics in Early Zebrafish Embryogenesis2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Developmental Biology and Gene Regulation Open access
Han Rauwerda, Johanna F.B. Pagano, Wim C. de Leeuw, Wim A. Ensink, Marina F van Olst, Ulrike Nehrdich, +3 more
0citations -
Metabolic predictors of phenotypic traits can replace and complement measured clinical variables in transcriptome-wide association studies2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Anna Niehues, Daniele Bizzarri, Marcel J. T. Reinders, P. Eline Slagboom, Alain J. van Gool, Erik B. van den Akker, +1 more
0citations -
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 -
Probing the transcriptome response to shivering in skeletal muscle using a multilayered bioinformatics approach2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Adipose Tissue and Metabolism Open access
Rosalie Baak, Guido J. E. J. Hooiveld, Patrick Schrauwen, Joris Hoeks, Reinier Raymakers, Anja van de Stolpe, +2 more
0citations -
GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
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 -
Combi-Seq: Multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Lukas Mathur, Bence Szalai, Ramesh Utharala, Martine Ballinger, Jonathan J. M. Landry, Michaël Ryckelynck, +3 more
4citations -
A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Tooba Abbassi‐Daloii, Salma el Abdellaoui, Lenard M. Voortman, Thom T. J. Veeger, Davy Cats, Hailiang Mei, +5 more
2citations -
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 -
Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications2025 Research Square preprint Biochemistry, Genetics and Molecular Biology RNA modifications and cancer Open access
Susanne Gerber, Charlotte Hewel, Anna Wierczeiko, Johannes Miedema, Stephan Weißbach, Johannes H. Friedrich, +14 more
1citations -
Mapping the glial transcriptome in Huntington’s disease using snRNAseq: Selective disruption of glial signatures across brain regions2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Genetic Neurodegenerative Diseases Open access
Sunniva M. K. Bøstrand, Luise A. Seeker, Nina-Lydia Kazakou, Nadine Bestard-Cuche, Sarah Jäkel, Boyd Kenkhuis, +5 more
1citations -
Temporal transcriptome analysis of the endothelial response to tumour necrosis factor2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology interferon and immune responses Open access
EC Struck, Tatiana Belova, Ping‐Han Hsieh, Jacob Odeberg, Marieke L. Kuijjer, Philip Dusart, +1 more
0citations -
A combined lifestyle intervention induces a sensitization of the blood transcriptomic response to a nutrient challenge2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Nutrition, Genetics, and Disease Open access
Thies Gehrmann, Marian Beekman, Joris Deelen, Linda Partridge, Ondine van de Rest, Leon Mei, +6 more
5citations -
Mycobacterium leprae and host immune transcriptomic signatures for reactional states in leprosy2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Leprosy Research and Treatment Open access
Madhusmita Das, Diana David, Ilse Horo, Anouk van Hooij, Maria Tió Coma, Annemieke Geluk, +1 more
0citations -
Multiomics Analyses Reveal Dynamic Bioenergetic Pathways and Functional Remodeling of the Heart During Intermittent Fasting2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Dietary Effects on Health Open access
Thiruma Valavan Arumugam, Asfa Alli Shaik, Elisa Anamaria Liehn, Sharmelee Selvaraji, Luting Poh, Vismitha Rajeev, +19 more
2citations -
Integrating Gene Expression Analysis and Ecophysiological Responses to Water Deficit in Leaves of Tomato Plants2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Agricultural and Biological Sciences Plant Stress Responses and Tolerance Open access
Giovanni Bortolami, Tobias de Werk, Maximilian Larter, Ajaree Thonglim, Bernd Mueller‐Roeber, Salma Balazadeh, +1 more
1citations -
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Martin Guilliams, Johnny Bonnardel, Birthe Haest, Bart Vanderborght, Anna Bujko, Liesbet Martens, +30 more
97citations -
Multi-omics phenotyping of the gut-liver axis allows health risk predictability from in vivo subchronic toxicity tests of a low-dose pesticide mixture2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Agricultural and Biological Sciences Pesticide Exposure and Toxicity Open access
Robin Mesnage, Maxime Teixeira, Daniele Mandrioli, Laura Falcioni, Quinten R. Ducarmon, Romy Daniëlle Zwittink, +7 more
5citations -
Myofibre-specific knockout of TGF-β type I receptors triggers muscle hypertrophy and promotes contraction and oxidative metabolism2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders
Andi Shi, Michèle MG Hillege, Carla Offringa, Gang Wu, Tymour Forouzanfar, Willem M.H. Hoogaars, +2 more
1citations