Microscopy data analysis for the paper: "Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast"
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Updated
Sep 13, 2023 - MATLAB
Microscopy data analysis for the paper: "Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast"
Code-base for my ABC-selectivity paper in Current Biology
Metadata files for the idr0040 submission
SYSBIO repository of ENG4BIO group within Universitat Autònoma de Barcelona (UAB) mainly regarding K. phaffi modelling.
The package is used to conduct the mutation cluster analysis with aid of protein 3D structures for yeast.
Code for the paper Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates.
Part of MSc Biology Project (1/2). This repo contains three different analysis pipelines, which all analyse microscopy images of yeast cells. Two calculate Sfp1 NC ratios, and one calculates nuclear and whole-cell volumes.
Repo for: Avecilla et al (2022) Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics. PLOS Biology. doi:10.1371/journal.pbio.3001633
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
Molecular biology-related analysis with a focus on yeast strains used in the AcubeSAT nanosatellite
For the analysis and visualization of array-based genetic interaction screens
Phenotypic screening of a CRISPRi strain library [Smith et 2017, Mol Syst Biol (2017)13:913] for acetic acid tolerance targeting essential and respiratory essential genes in Saccharomyces cerevisiae
Using NVIDIA Deepmind's Nucleotide Transformer to generate embeddings for yeast genomes.
Repo for: Chuong et al. (2024) DNA replication errors are a major source of adaptive gene amplification
Analysis of multiple yeast strains whole-genome knockout libraries 🔬📈
A program that uses the Synteny Index algorithm to compare between Eukaryotes.
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