saccharomyces-cerevisiae

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 |

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.

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).

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.

💻 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

Code and protocol accompanying the Prestwick × S. cerevisiae phenotypic screen (PLOS Comp Biol, 2026)

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

ABBA-BABA test conducted on Saccharomyces cerevisiae strains using whole-genome alignment.

A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission

Performance and Robustness trade-offs in yeast - analysis of phenotypic data from 24 Saccharomyces cerevisiae strains grown in 29 conditions

Reproducible analysis code (R + renv) for the study: Yeast chronological-lifespan extension correlates with human senescence, not longevity (unpublished)

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.

Proposition de loi visant à créer le statut d'Aliment à Fonction Vaccinale (AFV) et à définir les conditions de son autorisation, de son étiquetage et de son consentement éclairé.