Bioinformatician & Cell Biologist · Postdoc / ATER @ IBGC, Université de Bordeaux
I work at the intersection of experimental and computational biology, using code to understand how cells grow, adapt, and evolve.
LNClassifier · @cbib
A research project to benchmark and improve machine learning tools for classifying long non-coding RNAs (lncRNAs) vs. mRNAs. The key challenge: current tools disagree on ~45% of transcripts, pointing to genuine biological ambiguity rather than algorithmic failure. The project integrates underexplored genomic features — transposable elements and non-B DNA motifs — to build more robust, interpretable classifiers. All pipelines are built with Snakemake.
| Repository | Description |
|---|---|
| uncertainty_aware_lnclassifier | Benchmarks 8 classification tools with inter-tool agreement and per-transcript uncertainty quantification |
| rep_extraction_pipeline | Extracts repetitive element features from transcript sequences using RepeatMasker |
| nbd_extraction_pipeline | Extracts non-B DNA motif features (G-quadruplexes, Z-DNA, triplex, etc.) using gfa and G4Discovery |
| beta_vae_lnclassifier | Deep learning classifier integrating sequence, repeat, and non-B DNA features for lncRNA/mRNA discrimination, by my amazing colleage @mikageorges |
An open-source web platform for designing and documenting molecular cloning experiments. Supports a wide range of cloning strategies with a visual, history-preserving interface. Built with React + Python/FastAPI.
Python library for simulating DNA assembly — Gibson assembly, homologous recombination, restriction cloning, and more. A core tool in the synthetic biology Python ecosystem (226 ⭐).
- García-Ruano D. et al. Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA–lncRNA classification. bioRxiv (2026)
- García-Ruano D.*, Jain A.*, et al. Long-term evolution of proliferating cells using the eVOLVER platform. Open Biology (2023)
- García-Ruano D. et al. Fluorescence exclusion — a rapid, accurate and powerful method for measuring yeast cell volume. J Cell Sci (2022)
- García-Ruano D. et al. Engineering heterothallic strains in fission yeast. Yeast (2024)
* Equal contribution · Full list on ORCID
Machine learning · RNA-seq · Genome analysis · Experimental evolution · Microscopy image analysis
Bioinformatician at @cbib · Bordeaux, France