Andres S. Espindola

Assistant Research Professor


Oklahoma State University

Plant Pathologists and Bioinformatician at Oklahoma State University. I currently work with DNA/RNA sequencing data to develop bioinformatic tools to improve speed of plant pathogen detection. I am interested in fast and innovative tools that help plant pathologists detecting known and emerging pests. By using High-throughput Sequencing we aim to develop the appropriate protocols to detect any pathogen in any plant sample. Currently I am using Oxford Nanopore Technologies (ONT) minION sequencer to validate portability of sequencing devices for diagnostics.


  • Bioinformatics
  • Ecology
  • Epidemiology
  • metagenomics
  • Metatranscriptomics


  • PhD in Plant Pathology, 2016

    Oklahoma State University

  • Bioinformatics Certificate, 2016

    Oklahoma State University

  • MS in Entomology and Plant Pathology, 2013

    Oklahoma State University

  • Biotechnology Engineering, 2009

    Army Polytechnic School ESPE - Ecuador


Molecular Biology

PCR, real-time PCR, cloning

Plant Microbiome

plant rhizosphere


biopython, strings, arrays

R statistics

differential gene expression, RNAseq

High-throughput Sequencing

MinION, Illumina, metagenomics, metatranscriptomics



Assistant Research Professor


Nov 2018 – Present Stilwater, OK
Responsibilities include:

  • Develop Microbe Finder (MiFi) MinION for Plant Pathogens, Animal pathogens and forensics.
  • Graphical User Interface of MiFi (http://bioinfo.okstate.edu)
  • Grapevine virus detection with MinION and MiFi
  • Rose virus detection in a single shot with MinION and MiFi
  • Citrus virus and bacteria detection with MinION and MiFi.
  • E-probe design and validation for the detection of Ralstonia species in blueberry

Postdoctoral Fellow


Jan 2017 – Nov 2018 Stilwater, OK
Responsibilities include:

  • EDNA MinION for Plant Pathogens
  • Oxford Nanopore Sequencing (MinION) validation for plant pathogen detection in Grapes, Roses, Cucurbits.
  • Use RNA sequencing and eprobes to determine Aspergillus flavus presence in soil.
  • MinION sequencing for Grapevine pathogen detection.

Research Assistant and Teaching Assistant

Oklahoma State University

Jan 2011 – Dec 2016 Oklahoma
Developed bioinformatic tools for plant pathogen detection using high-throughput sequencing Responsibilities include: * Analyze the genome and transcriptome of Sclerotinia minor and Aspergillus flavus by using next-generation sequencing. * Conduct a profound statistical analysis in R for molecular biology projects including PCR, qPCR and sequencing

Extramural Funding

Metagenomic probes for the rapid identification of the microbiome community in a wheat rhizosphere model system

Award: $220,000

E-probe Diagnostic Nucleic acid Analysis (EDNA) for quarantine detection and discrimination of Poaceae viruses


Detection of detrimental viruses and viroids in high value chrysanthemums in Oklahoma


Electronic Diagnostic Nucleic Acid Analysis (EDNA) for accurate detection and discrimination of Rose Viruses


Detection of Grapevine viruses using high-throughput sequencing

Two years total: $99,871

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