I'm a computational biologist and bioinformatician working on histone post-translational modifications (hPTMs) in plants, with a special focus on lysine methylation and acetylation marks in Arabidopsis thaliana.
Currently finishing my PhD at the University of Oviedo (FPI fellowship PRE2019-091395), building the EpiProfile_PLANTS ecosystem for reproducible plant histone proteomics. Previously at the Spanish National Cancer Research Centre (CNIO) in the Computational Cancer Genomics Group.
This account hosts my thesis work, analysis pipelines, teaching materials, and everything in between.
| Area | Description |
|---|---|
| Plant epigenomics | Chromatin regulation and histone PTM landscapes in Arabidopsis, Marchantia, Chlamydomonas |
| Histone marks in plants | Characterising methylation and acetylation states across development and stress |
| Histone proteomics | Quantitative workflows for propionylation-based bottom-up MS |
| Epitranscriptomics | Nanopore direct RNA-seq and m6A modification detection |
| Reproducible pipelines | FAIR-compliant, containerised workflows from raw data to figures |
| Teaching | Making bioinformatics accessible to wet-lab biologists |
A central piece of my PhD: an end-to-end platform for plant histone proteomics, from vendor files to publication-ready figures.
WIFF/RAW ──▶ mzML ──▶ MS1/MS2 ──▶ EpiProfile_PLANTS ──▶ hDP/hPF/hPTM ──▶ Dashboard ──▶ Figures
│ │ │ │ │ │
│ msconvert xtract_xml MATLAB core 3-tier model Dash/Plotly
│ (Docker) (workflow) (species bundles) (audit-ready) (7 tabs)
▼ ▼ ▼ ▼ ▼ ▼
PRIDE centroided text files AT / MP / CR QC artifacts interactive
|
Core MATLAB code. Species-specific histone peptide catalogs and layouts for Arabidopsis, Marchantia, and Chlamydomonas. Three-tier data model: hDP (peptides) / hPF (peptideforms) / hPTM (site-level). RT reference system, T1-T4 audit provenance. |
Docker + Snakemake preprocessing pipeline. PRIDE FTP download, msconvert to centroided mzML, MS1/MS2 extraction. Processed 220 raw files / 123 GB across 3 datasets (PXD046034, PXD046788, PXD014739). |
Interactive Dash/Plotly dashboard with 7 tabs: Histone Ratios, Single PTMs, QC Dashboard, PSM Explorer, Sample Browser, Comparisons, Correlations. Heatmaps, PCA, dendrograms, mass accuracy QC. |
Keen Comprehensive High-throughput Omics Pipeline Organizer - a 9-stage Snakemake + Docker pipeline for Oxford Nanopore direct RNA-seq with emphasis on epitranscriptomics. Named after the Asturian cachopo - layers upon layers.
graph LR
A["1. Basecalling<br/>Dorado / Guppy"] --> B["2. Filtering<br/>NanoFilt"]
B --> C["3. Read QC<br/>NanoPlot"]
C --> D["4. Alignment<br/>Minimap2"]
D --> E["5. Align QC<br/>samtools"]
E --> F["6. Isoforms<br/>FLAIR / StringTie2"]
F --> G["7. Epitranscriptomics<br/>ELIGOS2 / m6Anet"]
G --> H["8. Diff. Expression<br/>DESeq2"]
H --> I["9. Report<br/>MultiQC"]
style A fill:#a78bfa,stroke:#7c3aed,color:#fff
style B fill:#22d3ee,stroke:#06b6d4,color:#000
style C fill:#22d3ee,stroke:#06b6d4,color:#000
style D fill:#39ff73,stroke:#22c55e,color:#000
style E fill:#22d3ee,stroke:#06b6d4,color:#000
style F fill:#f59e0b,stroke:#d97706,color:#000
style G fill:#f472b6,stroke:#ec4899,color:#000
style H fill:#ef4444,stroke:#dc2626,color:#fff
style I fill:#e2e8f0,stroke:#94a3b8,color:#000
Currently applied to an Arabidopsis thaliana 2x2 factorial experiment (WT vs anac017-1 mutant x Control vs Antimycin A):
| Wild Type (WT) | anac017-1 Mutant | |
|---|---|---|
| Control | 3 replicates | 3 replicates |
| Antimycin A | 3 replicates | 1 replicate |
Results: 20,958 isoforms quantified | 435 DEGs by genotype | 266 DEGs by treatment
My thesis combines four chapters spanning methods, biology, and synthesis:
| Ch. | Topic | Approach |
|---|---|---|
| 1 | EpiProfile_PLANTS methods | Software validation, species-specific catalogs, QC framework |
| 2 | Arabidopsis rosette ontogeny | Developmental gradient (YNG / BOT / FLOR / SEN) histone PTM profiling |
| 3 | Re-analysis of public datasets | Genotoxic stress datasets from PRIDE (PXD010102, PXD046034, etc.) |
| 4 | Target-mark synthesis | Behaviour of the studied marks across development and stress-related contexts |
|
Vision-Integrated Diagnostic Imaging Orchestrator Multi-modal biomedical image analysis for retinal imaging, histopathology (OpenSlide), radiology (DICOM/NIfTI), and spatial transcriptomics (H5AD). Built on Falcon WSGI, PyTorch/MONAI, OpenCV, with 5-stage pipeline and TCGA integration. |
Teaching materials Linux/WSL2/Docker for scientific computing, introductory Python and R/Bioconductor for omics, and small hands-on projects connecting code with real biological questions. Courses delivered at IAAP, University of Oviedo, City Council of Oviedo, FORMACAL, and ARTEAULA. |
Across all repositories I follow a consistent philosophy:
raw_wiff/ # Vendor files, PXD accessions documented
mzML/ # Converted with msconvert (Docker)
MS1_MS2/ # Extracted text files
EpiProfile_output/ # Quantification matrices
layouts/ # Species-specific peptide catalogs
phenodata/ # Sample metadata
R/ # Downstream statistics
docs/ # Documentation and manifests
- Every analysis links back to explicit PXD accessions
- Complete reproduction from WIFF/RAW to figures in a single command
- FAIR principles: findable, accessible, interoperable, reusable
- GPL-family licences with citable documentation
| Year | Title | Venue |
|---|---|---|
| 2026 | RNA Sequencing Platforms and Bioinformatics Tools | Book chapter |
| 2017 | Clusterization in head and neck squamous carcinomas based on lncRNA expression | Clinical Epigenetics |
University of Oviedo ███████████████████████████░░░ PhD (FPI) · Plant epigenomics · 2020–present
CNIO ████████████████░░░░░░░░░░░░░ Computational Cancer Genomics · lncRNA / NGS
Teaching (IAAP & more) ██████████████████████░░░░░░░ Linux, Python, R, Docker for biologists
GeoAI / ICM / FSP ████████████░░░░░░░░░░░░░░░░░ Data analysis, geospatial AI, healthcare
A growing project to teach bioinformatics and computational biology to biologists from scratch:
- Step-by-step notebooks and slides with real biological data
- Recorded sessions and screencasts
- Reusable templates for academic and public administration courses
- Material linked from biopelayo.github.io
If you work on plant epigenomics, histone proteomics, reproducible omics workflows, or are interested in re-analysing PRIDE datasets related to chromatin, feel free to open an issue or reach out.
Suggestions, discussions, and pull requests are very welcome.
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