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iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Damien Olivier‐Jimenez, Rico J. E. Derks, Oscar Harari, Carlos C Cruchaga, Muhammad Asri Mohd Ali, Alessandro Ori, +5 more
0citations -
A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Decision Sciences Scientific Computing and Data Management Open access
Anna Niehues, Casper de Visser, Fiona A. Hagenbeek, Purva Kulkarni, René Pool, Naama Karu, +7 more
1citations -
Integrative analysis of CAKUT multi-omics data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Jumamurat R. Bayjanov, Cenna Doornbos, Ozan Özışık, Woosub Shin, Núria Queralt-Rosiñach, Daphne Wijnbergen, +7 more
0citations -
A comprehensive and centralized database for exploring omics data in Autoimmune Diseases2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Jordi Martorell‐Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro Dominguez, Juan Antonio Villatoro-García, Guillermo Barturen, +10 more
1citations -
XomicsToModel: Omics data integration and generation of thermodynamically consistent metabolic models2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
German Preciat, Agnieszka B. Wegrzyn, Ines Thiele, Thomas Hankemeier, Ronan M. T. Fleming
10citations -
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Aurélien J. F. Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Kristina Bennet Emdal, Dorte B. Bekker‐Jensen, +7 more
16citations -
Multi-omic data fusion reveals the in vivo enzyme kinetics of Vibrio natriegens at the genome-scale2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
St. Elmo Wilken, Martin Beyß, Miroslav Kratochvíl, Alexa Grebel, Karen Methling, Anja Stefanski, +7 more
0citations -
Multimodal evidence for impaired glymphatic brain clearance as a mediator of “inflammaging” in schizophrenia – integrating insights from in vivo neuroimaging, omics, and post-mortem single nucleus-RNA-Seq data2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Cerebrospinal fluid and hydrocephalus Open access
Xiaolin Tan, Malte Simon, Daniel Rosebrock, Mariia M Firulyova, Doris Gruber-Schoffnegger, Marisa Fuerst, +7 more
0citations -
Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies2023 arXiv (Cornell University) preprint Computer Science Research Data Management Practices Open access
Yu-Ning Huang, Michael I. Love, Cynthia Ronkowski, Dhrithi Deshpande, Lynn M. Schriml, Annie Wong‐Beringer, +9 more
2citations -
Semi-automated background removal limits loss of data and normalises the images for downstream analysis of imaging mass cytometry data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Marieke E. Ijsselsteijn, Antonios Somarakis, Boudewijn P. F. Lelieveldt, Thomas Höllt, Noel F.C.C. de Miranda
2citations -
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Stavros Makrodimitris, Bram Pronk, Tamim Abdelaal, Marcel J. T. Reinders
3citations -
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data2024 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ping‐Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien‐Yu Chen, +3 more
0citations -
scTopoGAN: unsupervised manifold alignment of single-cell data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Akash Kumar Singh, Marcel J. T. Reinders, Ahmed Essam Mahfouz, Tamim Abdelaal
1citations -
Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint 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
28citations -
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio‐Escat, Olga Ivanova, Attila Gábor, +3 more
36citations -
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 -
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