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scTopoGAN: unsupervised manifold alignment of single-cell data2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Kirti Biharie, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
6citations -
Community-driven ELIXIR activities in single-cell omics2022 F1000Research article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Paulo Czarnewski, Ahmed Essam Mahfouz, Raffaele Calogero, Patricia M. Palagi, Laura Portell-Silva, Asier Gonzalez‐Uriarte, +21 more
11citations -
Hyperpathway: visualizing organization of pathway-molecule enriched interactions in omics studies via hyperbolic bipartite network embedding2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Ilyes Abdelhamid, Ziheng Liao, Yuchi Liu, Armel Lefebvre, Carlo Vittorio Cannistraci
0citations -
Multi-omic analyses in immune cell development with lessons learned from T cell development2023 Frontiers in Cell and Developmental Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Martijn Cordes, Karin Pike‐Overzet, Erik B. van den Akker, Frank J. T. Staal, Kirsten Canté-Barrett
9citations -
Dynamic data-driven meta-analysis for prioritisation of host genes implicated in COVID-192020 Scientific Reports article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Nick Parkinson, Natasha Rodgers, Max Head Fourman, Bo Wang, Marie Zechner, Maaike C. Swets, +5 more
50citations -
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data2022 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Ricardo O. Ramirez Flores, Attila Gábor, Denis Schapiro, Julio Sáez-Rodríguez
291citations -
OmniPath: integrated knowledgebase for multi-omics analysis2025 Nucleic Acids Research article 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
23citations -
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics2023 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders
12citations -
Integration of epidemiologic, pharmacologic, genetic and gut microbiome data in a drug–metabolite atlas2020 Nature Medicine article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Jun Liu, Lies Lahousse, Michel Guillaume Nivard, Mariska Bot, Lianmin Chen, Jan Bert van Klinken, +41 more
82citations -
Multi-omics subgroups associated with glycaemic deterioration in type 2 diabetes: an IMI-RHAPSODY Study2024 Frontiers in Endocrinology article Medicine Diabetes, Cardiovascular Risks, and Lipoproteins Open access
Shiying Li, Iulian Dragan, Van Du T. Tran, Chun Ho Fung, Michael K. Hansen, Joline W. J. Beulens, +11 more
7citations -
Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models2023 Nature Biotechnology article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Rosa Lundbye Allesøe, Agnete Troen Lundgaard, Ricardo Hernández Medina, Alejandro Aguayo‐Orozco, Joachim Johansen, Jakob Nybo Nissen, +94 more
109citations -
Integrative Multi-omics Analysis of Childhood Aggressive Behavior2022 Behavior Genetics article 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
24citations -
#894 Dynamic multi-omics and mechanistic modelling approach provides deeper insight into kidney fibrosis progression2024 Nephrology Dialysis Transplantation article Medicine Chronic Kidney Disease and Diabetes Open access
Nadine Tuechler, Mira Lea Burtscher, Martin Garrido Rodriguez-Cordoba, Muzamil Majid Khan, Dénes Türei, Rafael Kramann, +3 more
0citations -
Network integration and modelling of dynamic drug responses at multi-omics levels2020 Communications Biology article Medicine Chemotherapy-induced cardiotoxicity and mitigation Open access cited by 1 patent
Nathalie Selevsek, Florian Caiment, Ramona Nudischer, Hans Gmuender, Irina V. Agarkova, Francis L. Atkinson, +37 more
51citations