Computational Biologist · Virologist
Marcos Ribeiro-Junior, Ph.D.
Sequencing-Based Diagnostics for Plant, Zoonotic & Human Pathogens.
About
Dr. Marcos Roberto Ribeiro-Junior is a computational biologist and virologist specializing in the development and validation of sequencing-based diagnostic platforms for the detection of plant, zoonotic, and human pathogens.
He holds a Ph.D. in Agronomy (Plant Protection) from São Paulo State University (UNESP), with a collaborative research period at Oklahoma State University (OSU), and has accumulated over a decade of experience in molecular diagnostics, high-throughput sequencing (Nanopore and Illumina), and bioinformatics pipeline development.
Currently, Dr. Ribeiro-Junior serves as Postdoctoral Researcher at the Institute for Biosecurity and Microbial Forensics (IBMF), Department of Entomology and Plant Pathology, Oklahoma State University. His work centers on pathogen detection, portable genomics, and bioinformatics.
Alma mater
São Paulo State University (UNESP)
University of Marília (UNIMAR)
Known for
EDNA-MiFi® e-probe diagnostics for plant, zoonotic, and human pathogens; global soybean virus screening; tick-borne pathogen surveillance
Fields
Plant pathology · Molecular diagnostics · Microbial forensics · Bioinformatics · Genomics · Phylogenetics
Institution
Oklahoma State University (OSU) — Institute for Biosecurity and Microbial Forensics (IBMF), Department of Entomology and Plant Pathology
Publications
30 peer-reviewed articles · 4 book chapters · 39 conference presentations
Current Appointments
Postdoctoral Researcher
Institute for Biosecurity and Microbial Forensics (IBMF), Dept. of Entomology & Plant Pathology, Oklahoma State University
Current Project
Microbe Finder (MiFi®) for Early Detection and Diagnosis of Tick-Borne Pathogens
This project develops and validates MiFi®-based genomic diagnostics for the early detection of tick-borne pathogens in tick, human, and animal samples. Leveraging EDNA-MiFi® e-probe technology and Oxford Nanopore sequencing, the project targets a curated panel of more than 68 clinically and epidemiologically relevant pathogens — including bacteria, viruses, and protozoa. The workflow integrates field sample collection, nucleic acid extraction, library preparation, and bioinformatics analysis within a standardized surveillance framework applicable to public health and veterinary diagnostic settings.
Selected Publications
First-author and representative co-authored works. For a complete list see Google Scholar.
2026
Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFi®)
Frontiers in Microbiology
2025
An attempt toward the global screening of soybean viruses using EDNA-MiFi®-based electronic probes
PhytoFrontiers™
2025
Development and validation of a suite of e-probes for EDNA to detect 20 graft-transmissible pathogens of citrus using MiFi® and blind ring testing among novice users
PhytoFrontiers™
2024
Molecular identification of thrips species in Brazilian agroecosystems
Phytoparasitica
2022
Molecular and biological characterization of an isolate of the potyvirus Passiflora virus Y naturally infecting soybean (Glycine max) in Brazil
Archives of Virology
Skills & Technologies
Sequencing Platforms
Oxford Nanopore Technologies (ONT) · Illumina
Molecular Biology
DNA/RNA extraction · PCR, RT-PCR, RPA · Primer design · NGS library preparation · Sanger sequencing
Bioinformatics
BLAST · MAFFT · MEGA · Minimap2 · Bowtie · Geneious · CLC Genomics Workbench
Diagnostics Platform
EDNA-MiFi® · E-probe design & curation · In silico validation · SPAdes / metaSPAdes · Diamond · Kraken2 · Bracken
Programming & HPC
Bash · Python · R / ggplot2 · Linux · SLURM · AWS · Git / GitHub
Phylogenetics
Bayesian inference · Maximum Likelihood · Phylogenetic network analysis
Experience
Oct 2023 – Sep 2024
Postdoctoral Fellow, Dept. of Plant Protection
São Paulo State University (UNESP) · Botucatu, SP, Brazil
- Molecular characterization of orthotospoviruses infecting soybean and thrips insects.
- DNA/RNA extraction and library preparation for Illumina sequencing.
- Mentored undergraduate and graduate students in molecular diagnostics.
May – Jul 2023
Consultant, PFI MiFi for Citrus Project
University of California Riverside (UCR) & Oklahoma State University (OSU) · Remote
- Designed and validated e-probes for pathogen detection in citrus.
- Conducted beta testing and data analysis using MiFi® diagnostic systems.
Jul – Dec 2022
Postdoctoral Researcher, IBMF
Oklahoma State University (OSU) · Stillwater, OK, USA
- Developed e-probes for pathogen detection in citrus using high-throughput sequencing.
- Conducted HTS data analysis for virus, viroid, and bacteria identification.
Jan – Dec 2021
Ph.D. Internship, IBMF
Oklahoma State University (OSU) · Stillwater, OK, USA
- Conducted Nanopore NGS library preparation and sequencing.
- Created and curated e-probes to detect global soybean viruses.
Mar 2018 – Jun 2022
Graduate Research Assistant (Ph.D.) & Temporary Lecturer
São Paulo State University (UNESP) · Botucatu, SP, Brazil
- Molecular identification of thrips and whitefly species using PCR and Sanger sequencing.
- Developed molecular markers for thrips detection; surveyed plant viruses in soybean fields.
- Delivered lectures on crop disease management and supervised student projects.
Mar 2016 – Feb 2018
Graduate Research Assistant (M.S.)
São Paulo State University (UNESP) · Botucatu, SP, Brazil
- Biological, serological, and molecular identification of plant viruses.
- Established virus detection methods in lettuce and chard.
Additional Information
Languages
Portuguese (Native) · English (Fluent) · Spanish (Intermediate)
Interests
Virology · Molecular diagnostics · High-throughput sequencing · Genomics · Bioinformatics · Portable diagnostics
Education
Ph.D. Agronomy (Plant Protection) — UNESP, 2022
M.S. Agronomy (Plant Protection) — UNESP, 2018
B.Sc. Agricultural Engineering — UNIMAR, 2016
Contact
Address
127 Noble Research Center
Oklahoma State University
Stillwater, OK 74078, USA
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