Arif_MohammadMohammad Arif, PhD is currently a Research Associate in the Department of Plant Pathology at Kansas State University, United States.  Dr. Arif obtained his B.S. in Agriculture and M.S. in Molecular Biology & Biotechnology from G. B. Plant University of Agriculture & Technology, Pantnagar, India. During his masters program, he worked on population genetics of Fusarium sp. associated with malformation disease in mango (Mangifera indica). He finished his PhD in Biosciences at Jamia Millia Islamia, New Delhi. His doctoral research focused on molecular marker assisted screening for disease susceptibility in shisham seeds and pathogenic variability in Fusarium solani. He was the recipient of a merit scholarship during his masters and fellowship during his doctoral program from the Department of Biotechnology, Govt. of India. He also worked as Research Associate at the Central Rice Research Institute on allele mining and expression profiling of resistance, and avirulence-genes of the Rice-Blast pathosystem seeking the development of race non-specific disease resistance.

During his postdoctoral research at the National Institute for Microbial Forensics & Food and Agricultural Biosecurity (NIMFFAB; Oklahoma State University) and Washington State University; he worked to develop novel detection-discrimination methods based on next generation sequencing (NGS), real time qPCR, endpoint PCR, isothermal amplification and macroarray. He conducted research on population genetics of important fungal pathogens. He also conducted research on PCR thermodynamic parameters seeking increasing sensitivity of traditional assays. Dr. Arif is a creative researcher and has developed new methods to improve the PCR based methods. He has research experience on microbial forensics, plant biosecurity, population genetics, molecular diagnostics, comparative genomics, environmental microbiology and bioinformatics. He has published more than 25 peer-reviewed publications and 35 abstracts. He is member of American Phytopathological Society (APS), American Society for Microbiology (ASM) and American Association for the Advancement of Science (AAAS), and he is the reviewer of more than 15 journals.

Currently, Dr. Arif is working in collaboration with Plant Biosecurity Cooperative Research Centre, Canberra, Australia on a high consequence pathogen, Rathayibacter toxicus. He is working on whole genome based comparative genomics, population genetics, evolution, genome-informed diagnostics and CRISPR-CAS system of R. toxicus.

Publications (last 3 years)


Arif M, Busot G, Mann R, Rodoni B, Liu S, Stack JP (2015) Emergence of new population of the Select Agent Rathayibacter toxicus: an ecologically complex; geographically isolated bacterium. PLoS ONE (in revision)

Arif M, Busot G, Mann R, Rodoni B, Liu S, Stack JP (2015) Complete genome sequence of the select agent Rathayibacter toxicus strain WAC3373 from Western Australia. Stand Genomic Sci (commnicated)

Arif M, Opit G, Yerbafría A, Dobhal S, Li Z, Kucerova Z, Ochoa-Corona FM (2015) Array of synthetic oligonucleotides to generate unique multi target artificial positive control and molecular probes based discrimination of Liposcelis. PLoS ONE, 10(6): e0129810

Arif M, Zaidi NW, Haq QMR, Singh YP, Taj G, Kar CS, Singh US (2015) Morphological and comparative genomic analysis of pathogenic and non-pathogenic Fusarium solani isolated from Dalbergia sissoo. Mol Biol Rep, 42 (6), 1107-1122

Dobhal S, Olsen J, Arif M, Garcia-Suarez JA, Ochoa-Corona FM (2015) A simplified strategy for sensitive detection of Rose rosette virus compatible with three RT-PCR chemistries. J Virol Methods (in press)

Rayar JK, Arif M, Singh US (2015) Relative efficiency of RAPD and ISSR markers in assessment of DNA polymorphism and genetic diversity among Pseudomonas Afr J Biotech, 14 (13), 1096-1106

Dobhal S, Arif M, Olsen J, Mendoza-Yerbafría A, Aguilar-Moreno GS, Perez-Garcia M, Ochoa-Corona FM (2015) Sensitive detection and discrimination method for studying multiple infections of five major plant viruses infecting ornamental plants in nursery environments. Ann Appl Biol, 166, 286-296


Arif M, Aguilar-Moreno GS, Wayadande A, Fletcher J, Ochoa-Corona FM (2014) Primer modification improves rapid and sensitive in vitro and field deployable assays for detection of High plains virus variants. Appl Environ Microbiol, 80 (1), 320-327

Arif M, Dobhal S, Garrido PA, Orquera GK, Epindola A, Young CA, Ochoa-Corona FM, Marek SM, Garzon CD (2014) Highly sensitive end-point PCR and SYBR Green qPCR detection of Phymatotrichopsis omnivora, causal fungus of cotton root rot. Plant Dis, 98 (9), 1205-1212


Arif M, Zaidi NW, Haq QMR, Singh YP, Khan S, Singh US (2013) Molecular phylogeny and pathotyping of Fusarium solani: a causal agent of Dalbergia sissoo. Forest Pathol, 43 (6), 478–487

Arif M, Fletcher J, Marek S, Melcher U, Ochoa-Corona FM (2013) Development of a rapid, sensitive and field deployable Razor Ex BioDetection System and qPCR assay for detection of Phymatotrichopsis omnivora using multiple gene targets. Appl Environ Microbiol, 79 (7), 2312-2320

*Ouyang P, *Arif M, Fletcher J, Melcher U, Ochoa-Corona FM (2013) Enhanced reliability and accuracy for field deployable bioforensic detection and discrimination of Xylella fastidiosa pauca, causal agent of citrus variegated chlorosis using Razor Ex technology and TaqMan quantitative PCR. PLoS ONE, 8 (11), e81647  *Both should be consider as first author

Arif M, Ochoa-Corona FM (2013) Comparative assessment of 5’ A/T-rich overhang sequences with optimal and sub-optimal primers to increase PCR yields and sensitivity. Mol Biotechnol, 55 (1), 17-26

Cassi DRJ, Arif M, Payton M, Melcher U, Winder L, Ochoa-Corona FM (2013) A multi-target, non-infectious and clonable artificial positive control for routine PCR-based assays. J Microbiol Methods, 95 (2), 229-234


Research gate

Google Scholar

Lab activities and updates for the J Stack Lab at Kansas State University

%d bloggers like this: