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snRNA-seq analysis in multinucleated myogenic FSHD cells identifies heterogeneous FSHD transcriptome signatures associated with embryonic-like program activation and oxidative stress-induced apoptosis2023 Human Molecular Genetics article Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Dongxu Zheng, Annelot Wondergem, Susan L. Kloet, Iris M. Willemsen, Judit Balog, Stephen J. Tapscott, +3 more
15citations -
De novo transcriptome assembly and annotation of the common freshwater amphipod (Gammarus pulex) a valuable resource for ecotoxicogenomics2025 Scientific Data data-paper Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Camilo Escobar-Sierra, Sameer Hassan, Fabian G. Weichert, Henrik Aronsson, Kathrin P. Lampert, Henner Hollert, +2 more
1citations -
GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data2025 iScience article 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 -
Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake2021 Genome Biology and Evolution article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
David J. Gower, James F. Fleming, Davide Pisani, Freek J. Vonk, Harald M. I. Kerkkamp, Leo Peichl, +6 more
27citations -
Substantiate a read-across hypothesis by using transcriptome data—A case study on volatile diketones2023 Frontiers in Toxicology article Biochemistry, Genetics and Molecular Biology Carcinogens and Genotoxicity Assessment Open access
Matthias M. Wehr, Walter Zobl, Jeannette Koschmann, Britta Anna Kühne, Tanja Hansen, Jan Knebel, +5 more
7citations -
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 -
Facioscapulohumeral dystrophy transcriptome signatures correlate with different stages of disease and are marked by different MRI biomarkers2022 Scientific Reports article Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access cited by 2 patents
Anita van den Heuvel, Saskia Lassche, Karlien Mul, David San León, Arend Heerschap, Benno Küsters, +4 more
32citations -
A global survey of the transcriptome of the opium poppy (Papaver somniferum) based on single‐molecule long‐read isoform sequencing2022 The Plant Journal article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies
Tun Xu, Xiaofei Yang, Yanyan Jia, Zihang Li, Guangbo Tang, Xiujuan Li, +5 more
13citations -
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 -
Transcriptome‐wide association study of breast cancer risk by estrogen‐receptor status2020 Genetic Epidemiology article Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Helian Feng, Alexander Gusev, Bogdan Paşaniuc, Lang Wu, Jirong Long, Zomoroda Abu-Full, +90 more
45citations -
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 -
Transcriptome, metabolome and suppressor analysis reveal an essential role for the ubiquitin-proteasome system in seedling chloroplast development2022 BMC Plant Biology article Biochemistry, Genetics and Molecular Biology Photosynthetic Processes and Mechanisms Open access
Prabhavathi Talloji, Lilian Nehlin, Bruno Hüttel, Nikola Winter, Martin Černý, Hana Dufková, +9 more
3citations -
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 -
Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients2021 EMBO Molecular Medicine article Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access
Mirko Signorelli, Mitra Ebrahimpoor, Olga Veth, Kristina Maria Hettne, Nisha E. Verwey, Raquel García‐Rodríguez, +9 more
23citations -
Utility of Extrapolating Human S1500+ Genes to the Whole Transcriptome: Tunicamycin Case Study2020 Bioinformatics and Biology Insights article Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Deepak Mav, Dhiral P. Phadke, Michele R. Balik-Meisner, Bruce Alex Merrick, Scott S. Auerbach, Marije Niemeijer, +7 more
10citations -
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 for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets2022 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 4 patents
Lukas Mathur, Bence Szalai, N. H. Du, Ramesh Utharala, Martine Ballinger, Jonathan J. M. Landry, +4 more
27citations -
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 -
ADAR1-dependent editing regulates human β cell transcriptome diversity during inflammation2022 Frontiers in Endocrinology article Biochemistry, Genetics and Molecular Biology RNA regulation and disease Open access
Florian Szymczak, Roni Cohen‐Fultheim, Sofia Thomaidou, Alexandra Coomans de Brachène, Ângela Castela, Máikel L. Colli, +4 more
19citations -
Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Cornelis A.M. van Bergen, Ewa Szczurek
1citations -
Input data of manuscript "CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells"2021 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shadi Darvish Shafighi, Szymon M. Kiełbasa, Cornelis A.M. van Bergen, Ewa Szczurek
0citations -
Transcriptome analysis of conditionally immortalized atrial myocytes: identification of a novel atrium-enriched protein involved in sarcomere assembly and maintenance2021 European Heart Journal article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access
Pim R.R. van Gorp, Juan Zhang, J Liu, Roula Tsonaka, Hailiang Mei, S O Dekker, +6 more
0citations -
Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications2025 Nucleic Acids Research article Biochemistry, Genetics and Molecular Biology RNA modifications and cancer Open access
Charlotte Hewel, Anna Wierczeiko, Johannes Miedema, Johannes H. Friedrich, Stephan Weißbach, Laura Holthöfer, +15 more
39citations -
The role of melanocytes in the human choroidal microenvironment and inflammation: Insights from the transcriptome2021 Pigment Cell & Melanoma Research article Biochemistry, Genetics and Molecular Biology melanin and skin pigmentation
Adrian V. Cioanca, Chieh‐Lin Wu, Riccardo Natoli, Robert Max Conway, Peter McCluskey, Martine Johanna Jager, +3 more
27citations -
A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location2023 eLife article 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
19citations