Manoj Kumar, Ph.D., M.Sc.

Manoj Kumar, Ph.D., M.Sc.

  • Postdoc Researcher
Room # 124 ASI building, Dep. of Veterinary and Biomedical Sciences, Penn State University | Animal Diagnostic Laboratory, 131 Pastureview Road
University Park, PA 16802

Areas of Expertise

  • Data Integration and Research Design • Bioinformatics • Comparative & Functional Genomics for Pathogens (whole genome comparison, SNP/variant analysis, and pan-genome analysis; field vs vaccine strain differences) • Phylogenomics, Population Genomics & Genomic Epidemiology (strain typing, evolutionary analysis, and outbreak tracking of veterinary pathogens across One Health systems) • Whole Genome Sequencing (WGS) (pathogen detection, genome assembly, variant calling, and diagnostic surveillance workflows) • Metagenomics (mixed sample analysis for pathogen detection and microbial community profiling) • RNA-Seq (e.g., differential gene expression under disease vs control conditions) • GWAS / Genotype–Phenotype Association (linking genetic variation with virulence, host specificity, and antimicrobial resistance) • Structural Bioinformatics (protein-level interpretation of mutations, motif analysis, and functional impact assessment) • Antimicrobial Resistance (AMR) Profiling (resistance gene detection, gene cassette analysis, and surveillance in bacterial pathogens within a One Health framework) • One Health Genomics & Surveillance (integrating animal, environmental, and public health data for pathogen monitoring, transmission and disease prevention)

Education

  • Ph.D., Bioinformatics | Banasthali University, India
  • Master of Science (M.Sc.), Bioinformatics | Sikkim Manipal University, India
  • Bachelor of Science (B.Sc.) | University of Rajasthan, India

Professional Development Certification

Post-Graduate Program in AI and Machine Learning | 2025 | Purdue University, USA (Online via Simplilearn)

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Websites:

Special Issue Editors

Recent Publications

Full list available on [Google Scholar Profile Link]

  • Gontu, A., Sekhwal, M.K., Diaz Huemme, A., Li, L., Kutsaya, S., Ling, M., Doshi, N.K., Byukusenge, M., Nissly, R.H. 2025. Pasteurized Milk Serves as a Passive Surveillance Tool for Highly Pathogenic Avian Influenza Virus in Dairy Cattle. Viruses, 17, 1318. PMID: 41157590
  • Sekhwal M.K., Li L., Pierre T., Matthews T., Luley E., Tewari D., Kuchipudi S., Jayarao B., Byukusenge M., 2025. Molecular epidemiology of Salmonella Dublin isolated from 2011 to 2022 from veal and dairy operations in Pennsylvania. Microorganisms, 13, 400. PMID: 40005766
  • Tewari D., Sekhwal M.K., Killian ML., Zellers C., Nicholson, CW., Schroeder B., Spackman E., Hamberg A. 2024. Attribution of Human Seasonal Influenza H3N2 Virus Detection to the Collector, Not Avian Sources, During the 2022 Highly Pathogenic Avian Influenza Outbreak in Pennsylvania, USA ̶ Implications for Biosafety and Biosecurity. Zoonotic Dis., 4:315-319. https://doi.org/10.3390/zoonoticdis4040027
  • Chothe SK., Byukusenge M., Sekhwal M.K., Li L., LaBella LC., Jakka P., Palchak K., Barry R., Yon M., Nissly RH., Kelly KM., Jayarao BM., Nair MS., Kuchipudi SV. 2023. Complete Genome Sequence of a Bovine Coronavirus Isolated from a Goat in Pennsylvania, USA. Resour. Announc. 12 (6): e00122-23. PMID: 37133378.
  • Compton S., Stackpole C., Dixit A., Sekhwal M.K., Kolb T., De la Torre AR. 2023. Differences in heat tolerance, water use efficiency and growth among Douglas-fir families and varieties evidenced by GWAS and common garden studies. AoB Plants, 15 (2), 1–15. PMID: 37007611
  • Neale DB., Zimin AV., Zaman S., Scott AD., Shrestha B., Workman RE., Puiu D., Allen BJ., Sekhwal M.K., De La Torre AR., McGuire PE., Burns E., Timp W., Wegrzyn JL., Salzberg SL. 2022. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploidy origin. G3: Genes Genomes Genetics, 12: 1-13. PMID: 35100403
  • De La Torre A., Sekhwal M.K., Puiu D., Salzberg SL., Scott AD., 3, Allen B., Neale DB., Chin ARO, Buckley TN. 2022. Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia. Plant J., 109: 7-22. PMID: 34800071
  • De La Torre A., Sekhwal M.K., Neale DB. 2021. Selective sweeps and polygenic adaptation drive local adaptation along moisture and temperature gradients in natural populations of coast redwood and giant sequoia. Genes, 12(11):1826. PMID: 34828432

Book Chapter

  • Weiss M., Sekhwal M.K., Neale DB., De La Torre A. 2022. Genomics of climate adaptation in Pinus Lambertiana. The Pine Genomes. 51-65.

 Conference Presentations & Posters

  • Sekhwal M.K., Li L., Pierre T., Matthews T., Orchard L., Murgas PM., Jayarao B., Hovingh E., Byukusenge M. 2025. Genomic characterization of Salmonellaenterica from domestic and wild animals to find associations between antimicrobial resistance and mobile genetic elements. AAVLD/USAHA Annual Meeting, Aurora, CO, USA. [Poster]
  • Martins M., Webb N., Gladwin R.P., Lu H., Sekhwal M.K., Byukusenge M., Hovingh E. 2025. Unveiling Fowl Adenovirus Diversity Over the Past Decade in Pennsylvania. Presented by Martins M., Northeast Conference on Avian Diseases (NECAD), State College, PA. [Poster]
  • Martins M., Webb N., Gladwin R., Lu H., Sekhwal M.K., Byukusenge M. 2025. Circulation of All Five Classical Fowl Adenovirus Species, Including Virulent FAdV-C Serotype 4, in Pennsylvania Poultry. Presented by Martins M., AAVLD/USAHA Annual Meeting, Aurora, CO. [Poster and Oral]
  • Sekhwal M.K., Li L., Pierre T., Matthews T., Lindsey O., Doonan E., Murgas P., Hovingh E., Byukusenge M., Jayarao B. 2024. Comparative genomics of Staphylococcus aureusisolates from chickens and turkeys isolated from 2015-2016 from clinical samples in Pennsylvania. AAVLD/USAHA Annual Meeting, Nashville, Tennessee, USA. [Poster]
  • Sekhwal M.K., Li L., Pierre T., Matthews T., Tewari D., Jayarao B., Hovingh E., Byukusenge M. 2024. Whole Genome Sequence analysis to decode the association between antimicrobial resistance genes and mobile genetic elements in Salmonella Typhimurium Isolates from Pennsylvania, USA. ASM Microbe, Atlanta, GA, USA. [Poster]
  • Hoelzle, V., Sekhwal, M.K., Li, L., Byukusenge, M., Hovingh, E., Pierre, T., Matthews, T., Kolar, J., Weninger, R., & Jayarao, B. 2024. Molecular characterization of Bacillus licheniformis from milk samples. Presented by Hoelzle V. at Student Poster Competition, Pennsylvania State University, University Park, PA.
  • Sekhwal M.K., Petersen ML., Hewitt AJ., Schmidt KN., Bergholz PW. 2019. Comparison of genome-wide associations with fourteen phenotypes reveals adaptive variants that have generalized value for growth improvement. ASM Microbe, Duluth, MN, USA. [Poster]
  • Sekhwal M.K., Knight D, Adl S. 2017. Free-living N2 fixation in Saskatchewan soils. 2nd International Symposium on Innovations in Plant and Food Sciences, University of Saskatchewan, SK, Canada. [Poster]

Awards and Fellowships

  • ASM Future Leaders Mentorship Fellowship (FLMF), American Society for Microbiology | 2024 – 2025
    • Selected for a 2-year virtual program designed to develop leadership, professional networking, and career skills in the microbial sciences.
  • NSERC Visiting Fellowship, Agriculture and Agri-Food Canada (AAFC) | 2015