Publication

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

Publications associées (28)

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

The Replica Project: Co-Designing a Discovery Engine for Digital Art History

Isabella Di Lenardo

This article explains how the Replica project is a particular case of different professionals coming together to achieve the digitization of a historical photographic archive, intersecting complementary knowledge specific to normally unconnected communitie ...

2022

Digitised Newspapers – A New Eldorado for Historians? Reflections on Tools, Methods and Epistemology

Maud Ehrmann, Frédéric Clavert

The application of digital technologies to historical newspapers has changed the research landscape historians were used to. An Eldorado? Despite undeniable advantages, the new digital affordance of historical newspapers also transforms research practices ...

De Gruyter2022

Strategic Insights into Engineering Parameters Affecting Cell Type-Specific Uptake of DNA-Based Nanomaterials

Maartje Martina Cornelia Bastings, Alice Comberlato, Hugo José Rodriguez Franco, Marianna Mainardi Koga

DNA-based nanomaterials are gaining popularity as uniform and programmable bioengineering tools as a result of recent solutions to their weak stability under biological conditions. The DNA nanotechnology platform uniquely allows decoupling of engineering p ...

American Chemical Society2022

An optimized high throughput platform, from genetic transformation to fermentation, to screen for secreted laccases in Aspergillus niger

Laure Marie Colette Leynaud-Kieffer Curran

Many challenges are faced in the conversion of biomass into advanced biofuels, one of which is finding the correct organism for the job. The filamentous fungus Aspergillus niger has been chosen as a biocatalyst for cellulose, hemicellulose, and lignin degr ...

EPFL2021

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Vassily Hatzimanikatis, Jasmin Maria Hafner, Victor Luc Etienne Viterbo, Anastasia Sveshnikova

Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

Nature Portfolio2022

Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications

Sebastian Maerkl, Ragunathan Bava Ganesh

Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of t ...

FRONTIERS MEDIA SA2022

Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"

Vassily Hatzimanikatis, Homa Mohammadi Peyhani, Anastasia Sveshnikova

Supplementary datasets accompanying the manuscript "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds" published in the Metabolic Engineering Journal (https://doi.org/10.1016/j.ymben.2022.03.013). In line w ...

Zenodo2022