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WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Chemistry Advanced Proteomics Techniques and Applications Open access
David Bouyssié, Pınar Altıner, Salvador Capella-Gutiérrez, José M. Fernández, Yanick Paco Hagemeijer, Peter L. Horvatovich, +12 more
2citations -
DistributedDesignOptimizer: A modular Python framework for Setup, Execution and Processing of Distributed Design Optimization2026 arXiv (Cornell University) preprint Computer Science Advanced Multi-Objective Optimization Algorithms Open access
Sebastian Ellmaier, A.J. de Wit, Akilesh Raveendran, Marc-Eric Vogt, Thomas Bäck, Anna V. Kononova
0citations -
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 -
immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Milena Pavlović, Lonneke Scheffer, Keshav Motwani, Chakravarthi Kanduri, Radmila Kompova, Nikolay Vazov, +37 more
17citations -
fluxTrAM: Integration of tracer-based metabolomics data into atomically resolved genome-scale metabolic networks for metabolic flux analysis2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
Luojiao Huang, German Preciat, Jesús Alarcón-Gil, Edinson Lucumi Moreno, Agnieszka B. Wegrzyn, Ines Thiele, +4 more
1citations -
PILOT-GM-VAE: Patient-Level Analysis of single cell Disease Atlas with Optimal Transport of Gaussian Mixture Variational Autoencoders2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, James Shiniti Nagai, Tiago Maié, Christoph Kuppe, Ivan G. Costa
0citations -
Euclid preparation. LXXIV. Euclidised observations of Hubble Frontier Fields and CLASH galaxy clusters2025 arXiv (Cornell University) preprint Physics and Astronomy Galaxies: Formation, Evolution, Phenomena Open access
C. Gouin, P. Bergamini, Massimo Meneghetti, D. Abriola, R. Gavazzi, Patrick Hudelot, +71 more
0citations -
PeakPerformance - a tool for Bayesian inference-based fitting of LC-MS/MS peaks2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Jochen Nießer, Michael Osthege, Eric von Lieres, Wolfgang Wiechert, Stephan Noack
0citations