Valentin Rubio
Senior Bioinformatics Engineer
Cambridge, Massachusetts, United States
Summary
🤩
Rockstar🎓
Top SchoolValentin Rubio is a Senior Bioinformatics Engineer with 13–14 years of experience building scalable DNA-seq analysis methods and reproducible pipelines, currently driving bioinformatics at Invitae after a long tenure developing GATK and germline variant-calling workflows at the Broad Institute. He combines deep computational biology and statistical expertise with hands-on software craftsmanship across Java, Python, R, C, Perl and Scala, and is fluent in workflow and container technologies like Nextflow, Cromwell/WDL, Docker and Singularity for both HPC and GCP deployments. Valentin has shepherded short-variant calling improvements and non-diploid data support into production-grade toolkits, and brings practical experience integrating Picard, BWA, SAMtools, BEDtools and IGV into robust pipelines. His background spans pathogen genomics (Plasmodium falciparum) and evolutionary bioinformatics from academic to large-scale clinical settings, underpinned by a PhD in Evolutionary Bioinformatics. Colleagues rely on him for turning complex biological problems into auditable, high-throughput software, and for bridging research methods with production engineering. Based in Cambridge, MA, he pairs a software engineer’s discipline with a computational biologist’s curiosity, often surfacing subtle statistical or assembly-based edge cases before they reach users.
13 years of coding experience
17 years of employment as a software developer
Doctor of Philosophy (PhD), Evolutionary Bioinformatics, Doctor of Philosophy (PhD), Evolutionary Bioinformatics at Trinity College DublinUPC Universitat Politècnica de CatalunyaStarted PhD in Evolutionary Bioninformatics, Started PhD in Evolutionary Bioninformatics at Maynooth UniversityHarvard Extension School
Stackoverflow
2,746reputation
216kreached
122answers
12questions
generics
top-5%
java
top-5%
Github Skills (85)
apache-spark10
hts10
throughput10
gatk10
genomics10
spark-ml10
reproducible-science10
bam10
api10
fasta10
science10
genome10
spark10
java10
jna10
Programming languages (8)
Github contributions (5)
vruano/warp
Nov 2020 - Apr 2021
WDL Analysis Research Pipelines
Contributions:1 PR, 13 pushes, 2 branches in 4 months
pipelinepipeline-frameworkanalysiswdlpipelines
vruano/jbwt
Jan 2017 - Mar 2017
Contributions:11 pushes, 1 branch in 2 months
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