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

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

  • Post-Doctoral Scholar
  • ASI Genomics Lab / PI, Dr. Bhushan Jayarao
Penn State Animal Diagnostic Laboratory
124 ASI
University Park, PA 16802

Areas of Expertise

  • Bioinformatics, GWAS, RNA-Seq, variant calling, WGS, metagenomics, microbial genomics, environmental genomics, comparative genomics, functional genomics, molecular modeling, molecular docking, Protein-protein interaction networks, large data management and analysis.

Education

  • Ph.D., Bioinformatics
  • Master of Science (M.Sc.), Bioinformatics
  • Bachelor of Science (B.Sc.)

Publications

  1. Tewari, D., Sekhwal, M.K., Killian, M.L., Zellers, C., Nicholson,C.W., Schroeder, B., Spackman, E., Hamberg, A. The 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. 2024, 4, 315–319. https://doi.org/10.3390/zoonoticdis4040027
  2. Chothe SK., Byukusenge M., Sekhwal MK., 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.
  3. Compton S., Stackpole C., Dixit A., Sekhwal MK., 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.
  4. Neale DB., Zimin AV., Zaman S., Scott AD., Shrestha B., Workman RE., Puiu D., Allen BJ., Sekhwal MK., 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.
  5. De La Torre A., Sekhwal MK., 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.
  6. De La Torre A., Sekhwal MK., 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.
  7. Xiao , Sekhwal MK., Li P., Ragupathy R., Cloutier S., Wang X., You FM. 2016. Pseudogenes and their genome-wide prediction in plants. Int. J. Mol. Sci., 17: 1991-2006. PMID: 27916797.
  8. Sekhwal MK., Li P., Lam I., Wang X., Cloutier S., You FM. 2015. Disease resistance gene analogs (RGAs) in plants. J. Mol. Sci., 16: 19248-19290. PMID: 26287177.
  9. Sekhwal MK., Swami AK., Sharma V., Sarin R. 2015. Identification of drought induced transcription factors in Sorghum bicolor using GO terms semantic similarity. Cell Mol. Biol. Lett. 20: 1-23. PMID: 26204390.
  10. Sekhwal MK., Sharma V., Sarin R. 2013. Identification of MFS proteins in sorghum using semantic similarity. Theory Biosci, 132: 105-113. PMID: 23299296.
  11. Sharma V., Sekhwal MK., Swami AK., Sarin R. 2012. Identification of drought responsive proteins using gene ontology hierarchy. Bioinformation, 8: 595–599. PMID: 22829738.
  12. Sekhwal MK, Sharma V and Sarin R: Annotation of glycoside hydrolases in Sorghum bicolor using proteins interaction approach. Journal of Proteome Science and Computational Biology 2013, 2:2. http://dx.doi.org/10.7243/2050-2273-2-2
  13. Sekhwal MK., Swami AK., Sarin R., Sharma V. 2012. Identification of salt treated proteins in sorghum using gene ontology linkage. Physiol. Biol. Plants, 18: 209-216. PMID: 23814435.

Book Chapters

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

Posters and Abstracts

  1. Sekhwal MK., Li L., Pierre T., Matthews T., Lindsey O., Doonan E., Murgas P., Hovingh E., Byukusenge M., Jayarao B. Comparative genomics of Staphylococcus aureusisolates from chickens and turkeys isolated from 2015-2016 from clinical samples in Pennsylvania. AAVLD/USAHA, 2024, Nashville, Tennessee, USA.
  2. Sekhwal MK., Li L., Pierre T., Matthews T., Tewari D., Jayarao B., Hovingh E., Byukusenge M. 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, 2024, June 13-17, 2024. Atlanta, GA, USA.
  3. Hoelzle V., Sekhwal MK., Li L., Byukusenge M., Hovingh E., Pierre T., Matthews T., Kolar J., Weninger R., Jayarao B. Molecular characterization of Bacillus licheniformis from milk samples. Penn State University.
  4. Sekhwal MK., Petersen ML., Hewitt AJ., Schmidt KN., Bergholz PW. Comparison of genome-wide associations with fourteen phenotypes reveals adaptive variants that have generalized value for growth improvement. ASM 79th annual meeting, October 25-26, 2019. Duluth, MN, USA.
  5. Sekhwal MK., Knight D, Adl Free living N2 fixation in Saskatchewan soils. 2nd International Symposium on Innovations in Plant and Food Sciences, September 8-10, 2017, University of Saskatchewan, SK, Canada.