Open to opportunities

Alejandro Berrio

@alejandroberrio

Message

I build single-cell genomics pipelines to uncover developmental and disease mechanisms.

United States

Message

What I'm looking for

I'm looking to lead and contribute to computational genomics research that applies single-cell, comparative, and functional-genomics methods to questions in development, evolution, disease, and precision medicine.

At Duke University, I lead single-cell RNA-seq studies of sea urchin embryonic development and serve as the lab's primary computational lead. I created and maintain public Shiny applications for exploring single-cell gene-expression datasets.

I've developed institution-wide COVID-19 variant-classification workflows, identified regions under positive selection in SARS-CoV-2, and delivered bioinformatic pipelines supporting comparative and regulatory genomics research. My work integrates large public datasets including ENCODE, GTEx, 1000 Genomes, and the Epigenomics Roadmap.

I also mentor graduate students and postdocs in reproducible single-cell analysis, lead biosafety and environmental efforts, and bring extensive wet-lab experience spanning scRNA-seq, ChIP-seq, RNA-seq, PCR, cytogenetics, and sequencing-library preparation.

Experience

Work history, roles, and key accomplishments

Current

Research Scientist

Current

Duke University

Jan 2022 - Present (4 years 8 months)

Lead single-cell RNA-seq experiments investigating sea urchin embryonic development, from experimental design through analysis and publication. Participated in SARS-CoV-2 genomic surveillance, classified viral variants, and served as the lab's primary computational lead.

Computational Biology Genomics SARS CoV 2 Detection Shiny R Python Docker

Short-Term Consultant

Sapere Bio

Jan 2022 - Dec 2022 (11 months)

Delivered novel genetic markers involved in senescence and aging by mining and reanalyzing public scRNA-seq datasets from GEO.

ScRNA Seq GEO Data Mining Bioinformatics

Postdoctoral Associate

Duke University

Jan 2016 - Dec 2022 (6 years 11 months)

Prepared sequencing libraries and processed single-cell transcriptomic data from sea urchin embryos. Designed an automated bioinformatic workflow for COVID-19 variant classification and discovered regions under positive selection in SARS-CoV-2.

Single Cell Transcriptomics Bioinformatics SARS CoV 2 Positive Selection Docker 1000 Genomes

Assistant Instructor

University of Texas at Austin

Jan 2010 - Dec 2016 (6 years 11 months)

Created and graded assignments, facilitated discussion of primary scientific literature, and assisted in course syllabus design.

Teaching Curriculum Development

Research Assistant

University of Texas at Austin

Jan 2010 - Dec 2016 (6 years 11 months)

Developed methods to identify selection at the Avpr1a locus, prepared and analyzed ChIP-seq libraries, and assembled transcriptomes of singing mice and prairie voles. Supervised students and led biosafety and environmental efforts.

ChIP Seq Population Genetics PCR Biosafety

Research Associate

Colombian Coffee Research Center (CENICAFE)

Jan 2007 - Dec 2009 (2 years 11 months)

Developed fluorescent in situ hybridization (FISH) protocols from chromosome preparations of the coffee berry borer. Standardized cytogenetic protocols and designed PCR and qPCR assays for genotyping population markers.

FISH Cytogenetics PCR