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AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Advanced Electron Microscopy Techniques and Applications Open access cited by 1 patent
Shawn Q. Zheng, Georg Wolff, Garrett A. Greenan, Zhen Chen, Frank G. A. Faas, Montserrat Bárcena, +3 more
134citations -
ProteoBench: the community-curated platform for comparing proteomics data analysis workflows2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Chemistry Advanced Proteomics Techniques and Applications Open access
Robbe Devreese, Caroline Jachmann, Bart Van Puyvelde, Holda A. Anagho, Witold Wolski, Henry Emanuel Webel, +44 more
5citations -
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 -
Ais: streamlining segmentation of cryo-electron tomography datasets2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Advanced Electron Microscopy Techniques and Applications Open access
Mart G.F. Last, Leoni Abendstein, Lenard M. Voortman, Thomas Harry Sharp
3citations -
The Network Zoo: a multilingual package for the inference and analysis of biological networks2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Marouen Ben Guebila, Tian Wang, Camila M. Lopes‐Ramos, Viola Fanfani, Deborah A. Weighill, Rebekka Burkholz, +17 more
1citations -
A NEST-based framework unlocks massively parallel simulation of networks of multicompartment neurons with customizable subcellular dynamics2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Neural dynamics and brain function Open access
Willem A. M. Wybo, Leander Ewert, Charl Linssen, Pooja N. Babu, Elena Pastorelli, Pier Stanislao Paolucci, +1 more
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 -
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods2025 eLife preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Ziv Rafael Yaniv, Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando Arroyo-Mejías, Rebecca T. Beuschel, Katy Börner, +55 more
0citations -
FLAG-X: Hybrid machine learning workflows for automated gating of clinical flow cytometry data2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Paul Martini, Marziyeh Mohammadi, Michael Christoph Thrun, David B. Blumenthal, Stefan W. Krause
0citations -
mzQuality: A tool for quality monitoring and reporting of targeted mass spectrometry measurements2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Marielle van der Peet, Pascal Maas, Agnieszka B. Wegrzyn, Lieke Lamont, Ronan M. T. Fleming, Amy C. Harms, +2 more
5citations