# Francisco Useche

> Expert Bioinformatician

Location: San Francisco Bay Area, United States
Profile: https://flows.cv/franciscouseche

Accomplished bioinformatics software engineer with extensive R&D experience supporting the development of cutting-edge NGS genomics products and analyses.

I have expertise across the bioinformatics pipeline, from primary NGS data processing and variant detection to advanced machine learning algorithms for modeling and prediction. Strong expertise in designing, implementing, and maintining computational tools to enable discovery, testing and assay development.

I am open to opportunities where bioinformatics methods and solutions are applied to complex problems in the life sciences and medicine.

## Work Experience
### Staff Bioinformatics Software Engineer @ Helix
Jan 2022 – Present | San Mateo, California, United States
• Designed and developed a variant record merging tool to integrate specialized variant calling pipelines with AWS BatchJob support (Python)
    • Variant calling performance improvement proof of principle using short read mapping to the human pangenome (Python)
    • Product improvements to a pharmacological interpretation tool (Python)

### R&D Senior Bioinformatics Software Engineer @ Agilent Technologies
Jan 2010 – Jan 2022 | Santa Clara, California, United States
Working as member of the bioinformatics group within the Genomics R&D/SW division to support development of NGS products, including library prep and target enrichment platforms SureSelect and HaloPlex.

    • Conceptualized, designed and implemented a novel machine learning based approach for the prediction of the off-target read contribution of DNA probes in a target enrichment environment
    • Collaborated in the development of novel DNA probe scoring models for target enrichment
    • Generalized probe design framework to work with arbitrary scoring models (Python)
    • Implemented analysis pipeline for dual molecular barcode data
    • Created probe design for Agilent’s exome catalog designs, custom panel designs, and first targeted methylation assay with bisulphite-treated DNA for SureSelect
    • Conducted research on probe performance improvement strategies geared toward increased genomic coverage
    • Designed and implemented a high throughput SNP/InDel detection pipeline for NGS data (GATK, SGE)
    • Designed and implemented an alignment and methylation detection pipeline for NGS data (Bismark, SGE)
    • Integrated RNA-SeQC into an analysis tool for RNAseq library prep quality control
    • Implemented diverse set of tools to support data management automation in a high throughput sequencing environment for custom data analysis (bash, python, SGE, cwl)

### Bioinformatics Software Engineer @ Proteostasis Therapeutics, Inc. (PTI)
Jan 2008 – Jan 2010 | Cambridge, Massachusetts, United States
Worked within the Systems Biology and Bioinformatics Group to support drug discovery of small molecules by integrating and designing a variety of tools and resources. Gathered requirements, solicited feedback, and generated reports on custom-developed software to support internal customers.

    • Designed and implemented web application for gene list cross reference across multiple species (Python, Pylons)
    • Predicted protein-protein interactions confidence using logistic regression (Weka)
    • Co-developed analysis and visualization tool for gene networks (Java), with multiuser, client/server architecture and a (MySQL) db for data persistence
    • Led microarray vendor evaluation using correlation, clustering, and differential gene expression analysis (R)

### Programmer Analyst III @ UC Berkeley Phylogenomics Group
Jan 2007 – Jan 2008 | Berkeley, California, United States
Main programmer for the PhyloFacts web resource, a phylogenomics encyclopedia for the tree of life.

### Bioinformatics Engineer @ Parallele Biosciences (Affymetrix)
Jan 2004 – Jan 2007 | South San Francisco, California, United States
Computational biologist within the Oncology Technology Research and Mol.Dx group. Augmented the assay design process for SNP discovery and genotyping through the integration of genomic and experimental data.
    • Designed and implemented a GUI driven/database backed framework for management and consolidation of genomic annotations used in assay development (Java/SQLServer)
    • Developed tools to streamline the SNP genotyping panel design process (Java)
    • Designed and implemented restriction enzyme and fragment selection algorithms (Java, lp_solve library)
    • Implemented Carlson SNP tagging algorithm for genotyping panel design (Java)


## Education
### M.S. in Computer Science
University of California, Santa Cruz

### M.S. in Electrical Engineering
University of Delaware

### B.S. in Electrical, Electronics and Communications Engineering
Pontifical Javeriana University, Bogotá


## Contact & Social
- LinkedIn: https://linkedin.com/in/francisco-useche

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Source: https://flows.cv/franciscouseche
JSON Resume: https://flows.cv/franciscouseche/resume.json
Last updated: 2026-04-12