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Datasets

AMR is a global problem. We therefore embrace the principles of open science and collaboration, and are proud to publish our data, so that scientists around the world can see, expand and build on our work.


Dataset – Single-cell segmentation in bacterial biofilms with an optimized deep learning method enables tracking of cell lineages and measurements of growth rates

https://zenodo.org/record/7704410
https://zenodo.org/record/8192357
https://zenodo.org/record/7709693
https://zenodo.org/record/8182800
https://zenodo.org/record/818280


Dataset – Computational identification of a systemic antibiotic for gram-negative bacteria

https://www.ebi.ac.uk/pdbe/entry/pdb/7t3h
https://www.ebi.ac.uk/pdbe/entry/pdb/7r1v
https://www.ebi.ac.uk/pdbe/entry/pdb/7r1w


Dataset – reComBat: batch-effect removal in large-scale multi-source gene-expression data integration

https://github.com/BorgwardtLab/reComBat
https://github.com/BorgwardtLab/batchCorrectionPublicData
https://zenodo.org/record/8155099
https://zenodo.org/record/8154663


Dataset – Antibiotic persistence of intracellular Brucella abortus

doi:10.1371/journal.pntd.0010635.s005
doi:10.5281/zenodo.7043646


Dataset – Combining CRISPRi and metabolomics for functional annotation of compound libraries

https://www.nature.com/articles/s41589-022-00970-3#Sec32
https://www.ebi.ac.uk/pride/archive/projects/PXD024133
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA776168
https://zenodo.org/record/8214736


Dataset – CRISPRi-seq for genome-wide fitness quantification in bacteria

https://github.com/veeninglab/CRISPRi-seq
https://github.com/veeninglab/2FAST2Q/tree/V2.5.0
https://pypi.org/project/fast2q/
doi:10.5281/zenodo.7012813
https://zenodo.org/record/8124288


Dataset – Dynamic persistence of intracellular bacterial communities of uropathogenic Escherichia coli in a human bladder-chip model of urinary tract infections

doi:10.5281/zenodo.5028262


Dataset – Early invasion of the bladder wall by solitary bacteria protects uropathogenic E. coli from antibiotics and neutrophil swarms in an organoid model

doi:10.5281/zenodo.4772819


Dataset – The antibiotic darobactin mimics a beta-strand to inhibit outer membrane insertase

doi:10.2210/pdb7nre/pdb
doi:10.2210/pdb7nrf/pdb
doi:10.2210/pdb7nri/pdb
EMD-12546
doi:10.6084/m9.figshare.12179784
https://github.com/hiller-lab/kaur-jakob-2021
https://zenodo.org/record/8154971