The consensus GEM for Saccharomyces cerevisiae
The metabolic twin model of yeast
Saccharomyces Genome Database (SGD) REST API wrapper
Saccharomyces cerevisiae information, gene calling and ORF identification assistant
GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae | Mondeel TDGA, Crémazy F, Barberis M. | Bioinformatics | 2018 | http://doi.org/10.1093/bioinformatics/bty052 |
Performance and Robustness trade-offs in yeast - analysis of phenotypic data from 24 Saccharomyces cerevisiae strains grown in 29 conditions
https://buddy.wasko.org BUDDY - Bioinformatic web app for modelling human VUS in yeast
Costa, C. E., Romaní, A., Cunha, J. T., Johansson, B., & Domingues, L. (2017). Integrated approach for selecting efficient Saccharomyces cerevisiae for industrial lignocellulosic fermentations: Importance of yeast chassis linked to process conditions. Bioresource Technology, 227, 24–34.
My Spring 2024 term project for NYU's Applied Genomics graduate course (M.S. Biology). Using data from Brar et al, analysis of average gene expression on certain regions of baker's yeast chromosomes during traditional time course meiosis.
Repository of a genome-scale metabolic model for Saccharomyces cerevisiae
💻 A unified bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across model organisms. Combines multi-database ortholog search with Gene Ontology annotation extension. 🎓 PhD project, King's College London (2013-2019).
https://dt.wasko.org Yeast-Doubling-Time (DT) Calculator - from raw 96 well platereader data. Initially designed for Biotek Epoch 2 but can be compatible with other platereaders.
💻 Archive of my bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across five model organisms using orthology databases (eggNOG, inParanoid, Homologene etc.). 🎓 Part of my PhD project, King's College London (2013-2019).
A summarizing analysis of Fkh1,2 target genes as indicated by 6 ChIP binding studies and an overexpression and deletion study | https://doi.org/10.1016/j.csbj.2022.03.033
How PCAn point centromere calls change with assembly contiguity, read technology and sequencing depth, measured on 134 budding yeast assemblies, 69 Saccharomyces cerevisiae strain pairs and 462 read assemblies of 33 strains.
ABBA-BABA test conducted on Saccharomyces cerevisiae strains using whole-genome alignment.
Code and protocol accompanying the Prestwick × S. cerevisiae phenotypic screen (PLOS Comp Biol, 2026)
A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission
Inferring co-translational importin binding states from Selective Ribosome Profiling (SeRP) data with a three-state Gaussian Hidden Markov Model. Bachelor's thesis, Goethe University Frankfurt.
Genome-scale metabolic model for engineering ABA production in Saccharomyces cerevisiae, derived from Yeast9 v9.1.0.
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