Open to opportunities

Juan josé Picon

@juanjospicon

Computational biologist and bioinformatician building NGS/metagenomics pipelines for genome, transcriptome, and chromatin analysis.

Colombia

Message

What I'm looking for

I’m looking for a computational biology role where I can build and improve NGS/third-gen pipelines, analyze genome/transcriptome/chromatin data, and work on reproducible HPC workflows with a team that values clarity and scientific impact.

I’m a computational biologist focused on turning high-throughput sequencing data into clear biological insights. My work spans genome assembly and metagenomics, plus transcriptomic and chromatin openness profiling.

I specialize in NGS and third-generation workflows (ONT, PacBio HiFi), with transcriptomic profile analysis using Bulk/single-cell RNA-seq and POP-seq (prokaryote ATAC-seq). I develop reproducible pipelines on HPC systems using Python, Bash, R, and Nextflow, and I’m comfortable integrating tools across Bioconductor and modern scRNA-seq analysis with Seurat v5.

I’ve built and deployed pipelines like MITNANEX, pneumoPipe, MAUS: Metagenomic Analysis UniSeqs, and SRAMetadataExtractor, and I’ve presented at the nf-core Hackathon/Summit collaboration and ISCB. At the Stowers Institute for Medical Research, I supported pan-genome and plasmidome assembly/analysis, DESeq2-based bulk RNA-seq under NCR peptide conditions, Seurat v5 single microbe RNA-seq, and POP-seq processing for free living and bacteroids.

Experience

Work history, roles, and key accomplishments

Computational Biologist Scholar

Stowers Institute For Medical Research

Jun 2025 - Nov 2026 (1 year 5 months)

Applied third-generation sequencing (PacBio HiFi, ONT) to assemble pan-genome and construct plasmidome for 256 Sinorhizobium meliloti strains. Developed pan-genome/plasmidome pipelines and performed bulk RNA-seq (DESeq2), single-cell RNA-seq (Seurat v5), and POP-seq (prokaryote ATAC-seq) analyses.

PacBio HiFi Oxford Nanopore Pan Genomics Plasmidome Analysis Bulk RNA Seq (DESeq2)POP Seq Prokaryote ATAC Seq Nextflow

Bioinformatician Junior

Fundación Universidad de Antioquia

Aug 2024 - Dec 2024 (4 months)

Performed NGS quality control and metagenomic analyses for amplicon (16S/ITS) and shotgun sequencing datasets. Assembled and serotyped 80 new Streptococcus pneumoniae genomes from 2×150 Illumina paired-end WGS and built a processing pipeline for paired-end data.

Amplicon Sequencing (16S ITS)Pathogen Serotyping Pipeline Development BASH HPC

Genome Research (Fungus)

Eafit University

Jan 2022 - Jun 2024 (2 years 5 months)

Generated first-draft genome assembly and annotation of cadmium-resistant fungus Talaromyces santanderensis HF05 from Oxford Nanopore (MinION) and Illumina (Seq100) data. Developed MITNANEX for de novo mitogenome assembly/annotation and performed methylome analysis, and presented findings at the 12th International Mycological Congress.

Oxford Nanopore Illumina Seq100 De Novo Genome Assembly Genome Annotation Mitogenome Assembly Methylome Analysis Rust Nextflow Python DNA Extraction

Research Intern

University of Oregon

Jan 2023 - Dec 2023 (11 months)

Led a mouse social cooperation project, designing and implementing a reward-based behavioral paradigm and adapting experimental procedures. Analyzed results with Python modules and tracked animal movement in recorded videos using SLEAP.

Animal Behavior Research Reward Based Experimental Design Python SLEAP Animal Handling & Recordkeeping