Komal Jain

EDUCATION & TRAINING

University of Pennsylvania, Master of Biotechnology, Bioinformatics (2003)
University of Delhi, Master of Science, Microbiology (1998)
University of Delhi, Bachelor of Science, Microbiology (1996)

RESEARCH INTERESTS

Solving bioinformatics problems at the crossroads of biology, statistics, and computer science
Development of diagnostic platforms for microbial detection and discovery using high-throughput platforms
Development of pipelines and analysis strategies for pathogen surveillance and discovery, biomarker detection in host response studies
Designing programs for High Performance Computer Clusters
Data analysis to detect differential gene expression in transcriptomic datasets, pathway analysis, and transcription factor binding site analysis
Characterizing sequences using evolutionary biology methods, build phylogenetic trees from multiple sequence alignments using bayesian and non-bayesian approaches
Programming in Perl, Python, R, and Shell scripting

SELECTED PUBLICATIONS

• Price A, Caciula A, Guo C, Lee B, Morrison J, Rasmussen A, Lipkin WI, Jain K. DEvis: an R package for aggregation and visualization of differential expression data. BMC Bioinformatics. 2019 Mar 4;20(1):110. doi: 10.1186/s12859-019-2702-z.
• Tokarz R, Tagliafierro T, Sameroff S, Cucura DM, Oleynik A, Che X, Jain K, Lipkin WI. Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut. Ticks Tick Borne Dis. 2019 Jun;10(4):894-900. doi:10.1016/j.ttbdis.2019.04.011.
• Mishra N, Ng TFF, Marine RL, Jain K, Ng J, Thakkar R, Caciula A, Price A, Garcia JA, Burns JC, Thakur KT, Hetzler KL, Routh JA, Konopka-Anstadt JL, Nix WA,Tokarz R, Briese T, Oberste MS, Lipkin WI. Antibodies to Enteroviruses in Cerebrospinal Fluid of Patients with Acute Flaccid Myelitis. mBio. 2019 Aug 13;10(4). pii: e01903-19. doi: 10.1128/mBio.01903-19.
• Kim KW, Horton JL, Pang CNI, Jain K, Leung P, Isaacs SR, Bull RA, Luciani F, Wilkins MR, Catteau J, Lipkin WI, Rawlinson WD, Briese T, Craig ME. Higher abundance of enterovirus A species in the gut of children with islet autoimmunity. Sci Rep. 2019 Feb 11;9(1):1749. doi: 10.1038/s41598-018-38368-8.
• Williams SH, Che X, Garcia JA, Klena JD, Lee B, Muller D, Ulrich W, Corrigan RM, Nichol S, Jain K, Lipkin WI. Viral Diversity of House Mice in New York City. mBio. 2018 Apr 17;9(2). pii: e01354-17. doi: 10.1128/mBio.01354-17.
• Anderson ME, Nagy-Szakal D, Jain K, Patrone CC, Frattini MG, Lipkin WI, Geskin LJ. Highly Sensitive Virome Capture Sequencing Technique VirCapSeq-VERT Identifies Partial Noncoding Sequences but no Active Viral Infection in Cutaneous T-Cell Lymphoma. J Invest Dermatol. 2018 Jul;138(7):1671-1673. doi:10.1016/j.jid.2018.01.024.
• Briese T, Kapoor A, Mishra N, Jain K, Kumar A, Jabado OJ, Lipkin WI. Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis. mBio. 2015 Sep 22;6(5). pii: e01491-15. doi: 10.1128/mBio.01491-15.
• Anthony SJ, Islam A, Johnson C, Navarrete-Macias I, Liang E, Jain K, Hitchens PL, Che X, Soloyvov A, Hicks AL, Ojeda-Flores R, Zambrana-Torrelio C, Ulrich W, Rostal MK, Petrosov A, Garcia J, Haider N, Wolfe N, Goldstein T, Morse SS, Rahman M, Epstein JH, Mazet JK, Daszak P, Lipkin WI. Non-random patterns in viral diversity. Nat Commun. 2015 Sep 22;6:8147. doi: 10.1038/ncomms9147.
• Tokarz R, Sameroff S, Hesse RA, Hause BM, Desai A, Jain K, Lipkin WI. Discovery of a novel nidovirus in cattle with respiratory disease. J Gen Virol. 2015 Aug;96(8):2188-93. doi: 10.1099/vir.0.000166.
• Tokarz R, Williams SH, Sameroff S, Sanchez Leon M, Jain K, Lipkin WI. Virome analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis ticks reveals novel highly divergent vertebrate and invertebrate viruses. J Virol. 2014 Oct;88(19):11480-92. doi: 10.1128/JVI.01858-14.
• Briese T, Mishra N, Jain K, Zalmout IS, Jabado OJ, Karesh WB, Daszak P, Mohammed OB, Alagaili AN, Lipkin WI. Middle East respiratory syndrome coronavirus quasispecies that include homologues of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in Saudi Arabia. mBio. 2014 Apr 29;5(3):e01146-14. doi: 10.1128/mBio.01146-14.
• Bhat N, Tokarz R, Jain K, Haq S, Weatherholtz R, Chandran A, Karron R, Reid R, Santosham M, O'Brien KL, Lipkin WI. A prospective study of agents associated with acute respiratory infection among young American Indian children. Pediatr Infect Dis J. 2013 Aug;32(8):e324-33. doi: 10.1097/INF.0b013e31828ff4bc.
• Quan PL, Williams DT, Johansen CA, Jain K, Petrosov A, Diviney SM, Tashmukhamedova A, Hutchison SK, Tesh RB, Mackenzie JS, Briese T, Lipkin WI. Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia. Virus Res. 2011 Sep;160(1-2):206-13. doi: 10.1016/j.virusres.2011.06.021.
• Kapoor A, Simmonds P, Gerold G, Qaisar N, Jain K, Henriquez JA, Firth C, Hirschberg DL, Rice CM, Shields S, Lipkin WI. Characterization of a canine homolog of hepatitis C virus. Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11608-13. doi: 10.1073/pnas.1101794108.