Code for the paper Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates.
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Updated
Jan 20, 2017 - Jupyter Notebook
Code for the paper Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates.
Scripts to download the PacBio, ONT and MiSeq datasets used in https://www.nature.com/articles/s41598-017-03996-z and run the pipelines as described in the paper or simply download the final assemblies as generated by the authors.
An automated method to map yeast variants to proteins modifications and functional regions
An open source predictive model of protein expression in yeast, written in Python.
Collection of scripts for improving lipid constraints in yeast-GEM
Mathematica notebook to compare methods of ML for ribosom density on mRNA prediction
A Julia package to find ageing genes in S. pombe
Code-base for my ABC-selectivity paper in Current Biology
Genome-scale metabolic model of Rhodotorula toruloides
Presentations and work done for University of Pittsburgh course, Synthetic Biology.
Supplementary code and results from doi:10.1101/2020.02.20.957662
Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs | Thierry D.G.A. Mondeel, Oleksandr Ivanov, Hans V. Westerhoff, Wolfram Liebermeister and Matteo Barberis | NPJ Syst. Biol. Appl. (2020) | https://doi.org/10.1038/s41540-020-0125-0
The package is used to conduct the mutation cluster analysis with aid of protein 3D structures for yeast.
A bioinformatic analysis was carried out with the goal of identifying carbohydrate-active enzymes in 332 published yeast genomes.
Analysis of multiple yeast strains whole-genome knockout libraries 🔬📈
Metadata files for the idr0040 submission
Tools for causal inference on yeast gene expression data.
Brouwsoftware
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