Applied Research

High-throughput sequencing for diagnostics

Virus discovery/detection

HTS for virus detection in grapes

Basic research

Determine microbes associated to disease in wheat/soybean (phytobiome)

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Andres S. Espindola

Assistant Research Professor

IBMF

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.

Interests

  • Bioinformatics
  • Ecology
  • Epidemiology
  • metagenomics
  • Metatranscriptomics

Education

  • 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

Expertise

Molecular Biology

PCR, real-time PCR, cloning

Plant Microbiome

plant rhizosphere

Python

biopython, strings, arrays

R statistics

differential gene expression, RNAseq

High-throughput Sequencing

MinION, Illumina, metagenomics, metatranscriptomics

Experience

 
 
 
 
 

Assistant Research Professor

NIMFFAB

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

NIMFFAB

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

FFAR Sep 2019
Award: $220,000

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

USDA Jul 2019
$114,449

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

ODAFF Jul 2019
$87,506

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

ODAFF Jul 2018
$50,000

Detection of Grapevine viruses using high-throughput sequencing

ODAFF Apr 2018
Two years total: $99,871

Recent Publications

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New Technologies from the Microbial World: Alternatives for Biomedical Surrogate Research

Draft genome sequences of three isolates of Coniothyrium glycines, causal agent of red leaf blotch of soybean

E-probe: A new diagnostic tool for detection of Dichorhaviruses associated with Citrus leprosis syndrome

In silico detection of multiple oomycetes in metagenomic data by using E-probe Detection of Nucleic acid Analysis (EDNA)

Metagenome sequence calculator for effective pathogen detection

See all publications

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