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Jamshaid Ali, PhD

Senior Manager (Bioinformatics Operations)

+91-471-2781246

jam@rgcb.res.in

Jamshaid Ali
Jamshaid Ali

Jamshaid Ali, PhD

Senior Manager (Bioinformatics Operations)

+91-471-2781246

jam@rgcb.res.in

  • Profile

    • 2013, PhD, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
    • 2005, M.Sc Biotechnology, Aligarh Muslim University, India
    • 2003, B. Sc (Hons) Zoology, Aligarh Muslim University, India
    • Feb 2017 –Till date, Senior Manager (Bioinformatics Operations), Rajiv Gandhi Centre for Biotechnology
    • Aug 2013 – Aug 2016, Postdoctoral scientist, Department of Plant Physiology, Ruhr University, Bochum, Germany
    • 2014 Travel/accommodation support from COST (European Corporation in Science and Technology) for "SeqAhead: NGS current challenges and data analysis for plant researchers" at TGAC, Norwich, UK
    • 2012 Asia Pacific Bioinformatics Network Travel Award for attending InCoB 2012 at Bangkok, Thailand
    • Qualified GATE with 97.24 percentile
    • Qualified JRF conducted by CSIR-UGC
    • Qualified DBT sponsored M. Sc Biotechnology program
  • Research

    Computational Genomics :

    My main research interest has been genomics by improving the annotation of already sequenced organisms and by generating the genomics data where it is lacking. I improved the genome annotation of apicomplexan parasites such as Plasmodium, Toxoplasma and Cryptosporidium etc. which cause some of the deadly diseases in humans and animals (Ali J et. al., BMC Genomics 2012). I also developed a web server ApicoAlign: a tool for improving the annotation of apicomplexan proteins (Ali J et. al., BMC Genomics 2011). Later I moved from apicomplexan genomics to plant genomics and worked on different NGS (next generation sequencing) projects like GBS (Genotyping by Sequencing) of several hundred A. halleri accessions, small RNA sequencing, A. halleri genome assembly and Phylogenomics of Arabidopsis genus (Polina et. al., Nature Genetics 2016). The apicomplexan parasites already had lot of sequencing data while in case of A. halleri, it was lacking.

    At RGCB, I again move to cancer genomics from plant genomics. I believe that my programming skills and experience of NGS projects would be a nice addition to the cancer research at RGCB.

  • Publications

    1. Polina Yu. Novikova, Nora Hohmann, Viktoria Nizhynska, Takashi Tsuchimatsu, Jamshaid Ali, Graham Muir, Alessia Guggisberg, Tim Paape, Karl Schmid, Olga M. Fedorenko, Svante Holm, Torbjörn Säll, Christian Schlötterer, Karol Marhold, Alex Widmer, Jun Sese, Kentaro K. Shimizu, Detlef Weigel, Ute Krämer, Marcus A. Koch and Magnus Nordborg: Sequencing of the genus Arabidopsis reveals a complex history of non-bifurcating speciation and abundant trans-specific polymorphism. Nature Genetics 2016 , 48:1077-82.
    2. Md. Zahid Kamal, Jamshaid Ali and Nalam Madhusudhana Rao Binding of bis-ANS to Bacillus subtilis lipase: A combined computational and experimental investigation. Biochim Biophys Acta. 2013, 1834(8):1501-9.
    3. Jamshaid Ali, Shashi Rekha Thummala and Akash Ranjan The parasite specific substitution matrices improve the annotation of apicomplexan proteins. BMC Genomics 2012, 13(Suppl 8):S19.
    4. Jamshaid Ali, Umadevi Paila and Akash Ranjan ApicoAlign: An alignment and sequence search tool for apicomplexan proteins. BMC Genomics 2011, 12(Suppl 3):S6.
    5. *Jamshaid Ali and Hina Younus: Effect of succinylation of antibodies on their conformation and interaction with the antigen Biochemistry (Mosc) . 2006 Dec:71(12):1336-40. (Pubmed ID: 17223786)
    6. *Work done as part of M. Sc project.
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