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Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
Chengyu Zhang, Feiran Li, Cheng Wei Quan Eiden, William Taussig Scott, Ulf W. Liebal, Lars M. Blank, +8 more
8citations -
Plant PhysioSpace: a robust tool to compare stress response across plant species2021 PLANT PHYSIOLOGY article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Ali Hadizadeh Esfahani, Janina Maß, Asis Hallab, David Nevarez, Björn Usadel, Mark‐Christoph Ott, +2 more
7citations -
SpaGE: Spatial Gene Enhancement using scRNA-seq2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 4 patents
Tamim Abdelaal, Soufiane M. C. Mourragui, Ahmed Essam Mahfouz, Marcel J. T. Reinders
7citations -
Biomarker identification for endometriosis as a target for real-time intraoperative fluorescent imaging: A new approach using transcriptomic analysis to broaden the search for potential biomarkers2023 European Journal of Obstetrics & Gynecology and Reproductive Biology article Medicine Endometriosis Research and Treatment Open access
Fokkedien H.M.P. Tummers, Maria K. Bazelmans, Frank Willem Jansen, Mathijs D. Blikkendaal, Alexander L. Vahrmeijer, Peter J.K. Kuppen
7citations -
Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Tendon Structure and Treatment Open access
Jolet Y. Mimpen, Mathew J. Baldwin, Claudia Paul, Lorenzo Ramos‐Mucci, Alina Kurjan, C. Cohen, +9 more
5citations -
SpaceWalker enables interactive gradient exploration for spatial transcriptomics data2023 Cell Reports Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Mitchell M. de Boer, Tamim Abdelaal, Thomas Höllt, +1 more
4citations -
Utilizing rat kidney gene co-expression networks to enhance safety assessment biomarker identification and human translation2025 iScience article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Steven J. Kunnen, Giulia Callegaro, Jeffrey J. Sutherland, Panuwat Trairatphisan, Hugo W van Kessel, Lukas S. Wijaya, +11 more
4citations -
Cell type heterogeneity in gene co-expression networks: implications for toxicological research2025 Briefings in Bioinformatics review Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Imke B. Bruns, Yingxue Li, James L. Stevens, Bob van de Water, Giulia Callegaro
4citations -
Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequencing data analysis2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Jeroen Eggermont, Thomas Höllt, Ahmed Essam Mahfouz, Marcel J. T. Reinders, Boudewijn P. F. Lelieveldt
2citations -
Cell-type-specific damage scores reveal kidney and liver disease trajectories in single-cell and spatial transcriptomics2026 Cell Genomics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tsimafei Padvitski, Paula Unger Avila, He Chen, Cem Özel, Fabian Braun, Marie-Kristin Kroll, +16 more
1citations -
Blood N -glycomic signature of fibrosis in MASLD shows low levels of global α2,3-sialylation2024 medRxiv preprint Biochemistry, Genetics and Molecular Biology Glycosylation and Glycoproteins Research Open access
Tamás Pongrácz, Bart J. Verwer, Anne Linde Mak, Oleg A. Mayboroda, Simone Nicolardi, Marco René Bladergroen, +9 more
1citations -
Proteomic, metabolomic, and transcriptomic examination of APOE transgenic mice2020 Alzheimer s & Dementia article Medicine Alzheimer's disease research and treatments Open access
Eric G. Mohler, Janina S. Ried, Lamiaa Bahnassawy, Peter Reinhardt, Marco Rocha Curado, Margot H.M. Bakker, +6 more
1citations -
SARS-CoV-2 induces fibrosis-associated macrophage signatures and triggers pulmonary fibrosis2023 10.01 - Respiratory infections and bronchiectasis conference-abstract Medicine COVID-19 Clinical Research Studies
Daniel Wendisch, Saskia Freifrau von Stillfried, M Mittermeier, Peter Boor, Matthias Selbach, Antoine‐Emmanuel Saliba, +1 more
1citations -
Exploring transcriptomic and genomic latent variable correction approaches in differential expression analysis2026 Scientific Reports article Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Yadusayan Appulingam, John Jammal, Aminah Ali, Simon Topp, Hemali P. Phatnani, Justin Kwan, +85 more
1citations -
Spatial Transcriptomic Characterization of Novel Pathologic Niches in IPF2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis Open access
Christoph H. Mayr, Diana Santacruz, Sebastian Jarosch, Charlotte Lempp, Lavinia Neubert, Berenice Rath, +7 more
1citations -
Phagocytosis of necroptotic cells optimizes type 1 conventional dendritic cells for induction of a cytotoxic T-cell response2026 Cell Death and Differentiation article Immunology and Microbiology Immunotherapy and Immune Responses Open access
Mo D. Staal, Zhixian Wang, Douwe M. T. Bosma, Julia Busselaar, Ellen Schrama, Evert de Vries, +2 more
1citations -
Analytical choices drive toxicogenomic potency estimates: a systematic evaluation of transcriptomic points of departure2026 Toxicological Sciences article Biochemistry, Genetics and Molecular Biology Carcinogens and Genotoxicity Assessment Open access
Imke B. Bruns, Dayna R. Schultz, Emmanuel Demuynck, Friedel Dewulf, Ioannis Theologidis, Steven J. Kunnen, +12 more
0citations -
#4547 IDENTIFICATION OF GLYCOSYLATED IGF2 IN HUMAN URINARY PEPTIDOME AND ITS ASSOCIATION WITH CKD2023 Nephrology Dialysis Transplantation article Biochemistry, Genetics and Molecular Biology Glycosylation and Glycoproteins Research Open access
Sonnal Lohia, Agnieszka Latosińska, Jérôme Zoidakis, Manousos Makridakis, Harald Mischak, Griet Glorieux, +2 more
0citations