Publications

David M Geiser, Frank N Martin, Andres S Espindola, Judith K Brown, Terrence H Bell, Yinong Yang, Seogchan Kang (2023). Knowledge Gaps, Research Needs, and Opportunities in Plant Disease Diagnostic Assay Development and Validation. PhytoFrontiers™.

Ana M Bocsanczy, Andres S Espindola, Kitty Cardwell, David J Norman (2023). Development and Validation of E-Probes with the MiFi System for Detection of Ralstonia solanacearum Species Complex in Blueberries. PhytoFrontiers™.

Sai Narayanan, Andres S Espindola, Jerry Malayer, Kitty Cardwell, Akhilesh Ramachandran (2023). Development and evaluation of Microbe Finder (MiFi)®: a novel in silico diagnostic platform for pathogen detection from metagenomic data. J. Med. Microbiol..

Fernanda Proaño-Cuenca, Andres S Espindola, Carla D Garzon (2023). Detection of Phytophthora, Pythium, Globisporangium, Hyaloperonospora and Plasmopara species in High-Throughput Sequencing data by in silico and in vitro analysis using Microbe Finder (MiFi®). PhytoFrontiers™.

Tyler Dang, Huizi Wang, Andrés S Espı́ndola, Joshua Habiger, Georgios Vidalakis, Kitty Cardwell (2022). Development and statistical validation of e-probe diagnostic nucleic acid analysis (EDNA) detection assays for the detection of citrus pathogens from raw high throughput sequencing data. PhytoFrontiers™.

Andres S Espindola, Kitty Cardwell, Frank N Martin, Peter R Hoyt, Stephen M Marek, William Schneider, Carla D Garzon (2022). A Step Towards Validation of High-Throughput Sequencing for the Identification of Plant Pathogenic Oomycetes. Phytopathology.

Tyler Dang, Andres Espindola, Georgios Vidalakis, Kitty Cardwell (2022). An In Silico Detection of a Citrus Viroid from Raw High-Throughput Sequencing Data. Viroids: Methods and Protocols.

Andres S Espindola, Daniela Sempertegui-Bayas, Danny F Bravo-Padilla, Viviana Freire-Zapata, Francisco Ochoa Corona, Kitty F Cardwell (2021). TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics. Viruses.

Rachel Rattner, Shree Prasad Thapa, Tyler Dang, Fatima Osman, Vijayanandraj Selvaraj, Yogita Maheshwari, Deborah Pagliaccia, Andres S Espindola, Subhas Hajeri, Jianchi Chen, Gitta Coaker, Georgios Vidalakis, Raymond Yokomi (2021). Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors. BMC Genomics.

Andres S Espindola, Kitty F Cardwell (2021). Microbe Finder (MiFi$^®$): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data. Plants.

Martha M Malapi-Wight, Kitty F Cardwell, Andres Espindola (2020). IDEA CAFE: Detection of plant pathogens in metagenomics datasets using Microbe Finder (MiFi). Plant Health 2020 Online.

Huizi Wang, Joshua Habiger, Andres Espindola, Kitty F Cardwell, Tyler Dang, Georgios Vidalakis, Avijit Roy (2020). Determining Limit of Detection of High Throughput Sequencing Diagnostics with MiFi®. Plant Health 2020 Online.

Trenna Blagden, Andres Espindola, Kitty Cardwell, Alejandro Ortega-Beltran, Ranajit Bandyopadhyay (2019). Draft Genome Sequences of Three Isolates of Coniothyrium glycines, Causal Agent of Red Leaf Blotch of Soybean. Microbiol Resour Announc.

Ana Maria Bocsanczy, Andres S Espindola, David J Norman (2019). Whole-Genome Sequences of Ralstonia solanacearum Strains P816, P822, and P824, Emerging Pathogens of Blueberry in Florida. Microbiol Resour Announc.

Francisco Ochoa Corona, Kitty Cardwell, Andres S Espindola (2019). New Technologies from the Microbial World: Alternatives for Biomedical Surrogate Research. Advances in Biotechnology and Microbiology.

Andres Espindola, Kitty F Cardwell (2019). Microbe Finder (MiFi): Pathogen detection in metagenomic sequence data. Plant Health, APS Annual Meeting.

Andres Espindola, Joshua Habiger, Kitty F Cardwell (2019). Metagenome sequence calculator for effective pathogen detection. Phytopathology.

Andres Espindola, Avijit Roy, Vessela A Mavrodieva, Kitty F Cardwell (2019). E-probe: A new diagnostic tool for detection of Dichorhaviruses associated with Citrus leprosis syndrome. Phytopathology.

Andres Espindola, Viviana Freire-Zapata, Luı́s Fernando Maranho Watanabe, Francisco Ochoa Corona, Kitty F Cardwell (2019). Detecting viruses and bacteria of grapevine with Microbe Finder (MiFi$^®$) and an Oxford Nanopore sequencer. Phytopathology.

Andres S Espindola, William Schneider, Kitty F Cardwell, Yisel Carrillo, Peter R Hoyt, Stephen M Marek, Hassan A Melouk, Carla D Garzon (2018). Inferring the presence of aflatoxin-producing textitAspergillus flavus strains using RNA sequencing and electronic probes as a transcriptomic screening tool. PLoS One.

Maria Fernanda Proano, Andres Espindola, Carla D Garzon (2018). Detection of multiple oomycetes in metagenomic data by Using E-probe Detection of Nucleic Analysis (EDNA). International Congress of Plant Pathology (ICPP) 2018: Plant Health in A Global Economy.

Andres Espindola, Kitty Cardwell (2018). Third generation sequencing and EDNA for detection of aflatoxin production in the soil. Phytopathology.

Lizbeth Pena Zuniga, Jon Daniels, Andres Espindola, Francisco Ochoa Corona (2018). EDNA-Water, using deep sequencing and bioinformatics approach for water-borne plant virus detection. International Congress of Plant Pathology (ICPP) 2018: Plant Health in A Global Economy.

Ana Maria Bocsanczy, Andres Espindola, David J Norman, Kitty F Cardwell (2018). E-probes development for rapid, sensitive and specific pathogen detection in blueberries. International Congress of Plant Pathology (ICPP) 2018: Plant Health in A Global Economy.

Andres Espindola, William Schneider, Hassan A Melouk, Stephen M Marek, Kitty F Cardwell, Carla D Garzon (2017). Unassembled transcriptome analysis to infer aflatoxin production in Aspergillus flavus strains infecting corn using EDNA. 2017 APS Annual Meeting.

Lizbeth Pena Zuniga, Andres Espindola, Hassan A Melouk, Akhtar Ali, Kitty F Cardwell, Francisco Ochoa Corona (2017). Detection of cucurbit viruses in Oklahoma combining EDNA with Multiplex RT-PCR coupled with High Resolution Melting. Phytopathology.

Andres S Espindola (2016). Eukaryotic Plant Pathogen Detection Through High Throughput DNA/RNA Sequencing Data Analysis.

Jerry E Weiland, Patricia Garrido, Zhian N Kamvar, Andrés S Espı́ndola, Stephen M Marek, Niklaus J Grünwald, Carla D Garzon (2015). Population Structure of Pythium irregulare, P. ultimum, and P. sylvaticum in Forest Nursery Soils of Oregon and Washington. Phytopathology.

A S Espindola, W Schneider, H Melouk, S Marek, C D Garzón (2015). The draft genome of Sclerotinia minor. American Phytopathological Society Meeting 2015.

Andres Espindola, William Schneider, Peter R Hoyt, Stephen M Marek, Carla Garzon (2015). A new approach for detecting fungal and oomycete plant pathogens in next generation sequencing metagenome data utilising electronic probes. Int. J. Data Min. Bioinform..

M Arif, S Dobhal, P A Garrido, G K Orquera, A S Espı́ndola, C A Young, F M Ochoa-Corona, S M Marek, C D Garzón (2014). Highly Sensitive End-Point PCR and SYBR Green qPCR Detection of Phymatotrichopsis omnivora, Causal Fungus of Cotton Root Rot. Plant Dis..

Anthony H Stobbe, Jon Daniels, Andres S Espindola, Ruchi Verma, Ulrich Melcher, Francisco Ochoa Corona, Carla Garzon, Jacqueline Fletcher, William Schneider (2013). E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics. J. Microbiol. Methods.

Andres Espindola (2013). Massively parallel sequencing (MPS) as a diagnostic and forensic analysis tool for important fungi and chromista plant pathogens. Oklahoma State University.

J Daniels, A Stobbe, A Espindola, W Schneider, J Sallee, T Blagden, F Ochoa-Corona, C Garzon, J Fletcher (2013). CSI in a tomato disease plot: Engaging 4-H youth and educators in STEM through investigative plant pathology. Phytopathology.

W Schneider, R Verma, A Stobbe, J Daniels, A Espindola, T Blagden, J Fletcher, F M Ochoa-Corona, C Garzon, U Melcher (2013). Bioinformatics strategies for microbial forensics. PHYTOPATHOLOGY.

A S Espindola, C D Garzón, J Fletcher, W L Schneider (2012). Validation of EDNA, a newly developed bioinformatics tool, for detection of Phakopsora pachyrhizi from metagenomic samples. PHYTOPATHOLOGY.

W L Schneider, A H Stobbe, J Daniels, A S Espindola, R Verma, T Blagden, J Fletcher, F Ochoa-Corona, C Garzon, P R Hoyt, Others (2012). Next-generation diagnostics: Eliminating the excessive sequence processing associated with next-generation sequencing using EDNA. PHYTOPATHOLOGY.

A H Stobbe, J Daniels, A Espindola, W L Schneider, J Fletcher, U K Melcher (2011). Use of massively parallel sequencing as a diagnostic tool. Phytopathology.

J Daniels, T Stobbe, A Espindola, W Schneider, J Fletcher, F Ochoa-Corona (2011). In silico simulation of massively parallel sequencing as a diagnostic tool for bacterial phytopathogens. PHYTOPATHOLOGY.

A S Espindola, A H Stobbe, J Daniels, J Fletcher, C D Garzón, W L Schneider (2011). Design and validation of queries for the detection of Phytophthora ramorum in simulated metagenomes. Phytopathology.

Andrés Sebastian Espindola Camacho (2009). Remoción de arsénico de un medio liquido a nivel de laboratorio mediante la utilización de un consorcio y una cepa axenica de cianobacterias en suspensión aisladas a partir de las hojas de polylepis pauta de bosques nativos del páramo de Papallacta, Ecuad. Revista Ciencia ESPE.