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OmniPath: integrated knowledgebase for multi-omics analysis2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Dénes Türei, Jonathan Schaul, Nicolàs Palacio‐Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, +25 more
0citations -
Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data2021 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Attila Gábor, Ricardo Ramirez Flores, Denis Schapiro, Julio Sáez-Rodríguez
10citations -
Integrative multi-omics analysis of childhood aggressive behavior2021 medRxiv preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Fiona A. Hagenbeek, Jenny van Dongen, René Pool, Peter J. Roetman, Amy C. Harms, Jouke‐Jan Hottenga, +9 more
3citations -
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 -
Multimodal Data Integration Advances Longitudinal Prediction of the Naturalistic Course of Depression and Reveals a Multimodal Signature of Disease Chronicity2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Treatment of Major Depression Open access
Philippe C. Habets, Rajat Mani Thomas, Yuri Milaneschi, Rick Jansen, René Pool, Wouter J. Peyrot, +4 more
0citations -
Haplomics: A Snakemake pipeline for haplotype-based association analysis in multi-omics studies2025 medRxiv preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Dariush Ghasemi-Semeskandeh, Luisa Foco, Ryosuke Fujii, Johannes Rainer, Mohadeseh Feli, Markus Ralser, +3 more
0citations -
Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Chronic Kidney Disease and Diabetes Open access
Nadine Tuechler, Mira Lea Burtscher, Martín Garrido‐Rodríguez, Muzamil Majid Khan, Dénes Türei, Christian Tischer, +8 more
0citations -
Multi-omics profiling, in vitro and in vivo enhancer assays dissect the cis -regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Retinal Development and Disorders Open access
Stijn Van de Sompele, Kent W. Small, Munevver Burcu Cicekdal, Víctor López-Soriano, Eva D’haene, Fadi S. Shaya, +23 more
3citations -
Integrative cross-omics analysis identifies DNA methylation signatures associated with bilateral hippocampal volume, asymmetry and atrophy rate in the general population2024 medRxiv preprint Biochemistry, Genetics and Molecular Biology Epigenetics and DNA Methylation Open access
Dan Liu, Valentina Talevi, Juliana F. Tavares, Ruiqi L. Wang, Mohammed Aslam Imtiaz, Konstantinos Melas, +20 more
0citations -
Multi-omics characterization of breast cancer metabolism identifies new metabolic targets2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cancer, Hypoxia, and Metabolism Open access
Hanneke Leegwater, Xiaobing Zhang, Luojiao Huang, Christine Hoegen, Xuesong Wang, Agnieszka B. Wegrzyn, +6 more
0citations -
WALDO: community-Wide Annotation of γδ Lymphocytes in single-cell Data, Openly benchmarked2026 Zenodo (CERN European Organization for Nuclear Research) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Farid Keramati, Moosa Rezwani, Likai Tan, David Hamilton, Zheng Song, Tao Yang, +10 more
0citations -
‘Omic-scale quantitative HILIC-MS/MS approach for circulatory lipid phenotyping in clinical research2022 ChemRxiv preprint Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Jessica M. Medina, Rébecca Borreggine, Tony Teav, Liang Gao, Shanshan Ji, Justin Carrard, +10 more
2citations -
TbasCO: Trait-based Comparative ’Omics Identifies Ecosystem-Level and Niche- Differentiating Adaptations of an Engineered Microbiome2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Elizabeth McDaniel, Joris J.M. van Steenbrugge, Daniel R. Noguera, Katherine D. McMahon, Jos M. Raaijmakers, Marnix H. Medema, +1 more
1citations -
Atlas-scale spatially aware clustering with support for 3D and multimodal data using SpatialLeiden2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Niklas Müller‐Bötticher, Alexander Malt, Paul Kießling, Roland Eils, Christoph Kuppe, Naveed Ishaque
0citations -
Proteome modulation by opposite inotropic drugs in human engineered cardiac tissue revealed by topology-driven cross-modal integration2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Chemistry Advanced Proteomics Techniques and Applications Open access
Doroteya K. Staykova, Danique Snippert, Hans J. C. T. Wessels, R. C. Passier, Federica Conte
0citations -
AtlasOT - The Fused Unbalanced Gromov-Wasserstein for Multimodal Integration of Disease Atlases2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kai Peng, Mayra L. Ruiz Tejada Segura, Barthélémy Caron, Christoph Kuppe, James Shiniti Nagai, Ivan G. Costa
0citations -
Percolate: an exponential family JIVE model to design DNA-based predictors of drug response2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Soufiane M. C. Mourragui, Marco Loog, Mirrelijn M. van Nee, Mark A. van de Wiel, Marcel J. T. Reinders, Lodewyk F.A. Wessels
1citations -
Reduced triacylglycerols and lipid droplets are associated with resilience to Alzheimer’s disease2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Alzheimer's disease research and treatments Open access
Daan van der Vliet, Luuk E. de Vries, Xinyu Di, Marc T.C. van der Meij, Marielle van der Peet, Amy C. Harms, +5 more
0citations -
GRIDGENE: Guided Region Identification based on Density of GENEs – a transcript density-based approach to characterize tissues by spatial transcriptomics2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ana Marta Sequeira, Marieke E. Ijsselsteijn, Miguel Rocha, Jessica P Roelands, Noel F.C.C. de Miranda
3citations