Sequencing technologies

Transform ELMSeq sequencing files into sequence-specific DAMRatios [link]

Generate recYnH interaction score matrix [link]

Generate transposon insertion profiles from Tn-Seq sequencing files [link]

Analysis frameworks

Framework for bacterial genome re-annotation and novel small proteins prediction [link]

Analysis framework to explore essentiality from Tn-Seq [link]

Codon optimization tool for tissue-specific gene design. [link]

Fully customizable robust Independent Component Analysis (ICA). [link]

Structural bioinformatics

Fast and quantitative estimation of interactions and stability between molecular species [link]

Predict the helical behaviour of monomeric peptides [link]

Algorithm to predict aggregation nucleating regions in proteins [link]


Mycoplasma pneumoniae functional database. Joined effort with Dpt. of General Microbiology, University of Göttingen (Germany) [link]


FoldX In silico protein engineering: From modeling to docking
I edition (2018) [link]

Tissue Engineering Course: From Stem Cells to Organoids
II edition (2018) [link]
I edition (2017) [link]

Whole-cell modeling
III edition, EMBO course (2019) [link]
II edition (2017) [link 1] [link2]
I edition (2016) [link 1] [link2]

Other Resources

Whole-cell model web of reference. By Jonathan Karr’s group at Mt. Sinai School of Medicine (US) [link]

Collaborative Project for the establishment of a Systems Biology framework to understand key features of Mycobacterium tuberculosis [link]