PhD candidate / guest
Shardul Paricharak is in the final phase of his PhD in cheminformatics at Cambridge University (UK) and Leiden University, where he develops and applies in silico data-driven methods to improve activity modeling and efficiency of high-throughput screens.
I started my undergraduate training as an experimental biologist (at Leiden University and TU Delft), but soon discovered my interest for the computational side of biology, during an Erasmus exchange program at Lund University (Sweden) where I underwent a 6-month training in bioinformatics. Fascinated by in silico approaches, I then gained further experience in bioinformatics (gene expression analysis, software development, database programming) during an undergraduate internship at the Leiden Academic Centre for Drug Research (LACDR), and a summer job at Galapagos B.V.
During my master in pharmaceutical sciences at Utrecht University, I did another bioinformatics internship at UMC Utrecht, where I worked on genome sequencing data. During this master, I also got an opportunity to do an internship at Cambridge University (UK), where I worked on cheminformatics (QSAR, PCM). I then received a personal grant for a PhD at Cambridge University and Leiden University, during which I planned to further delve into the intricacies of cheminformatics (data analysis, machine learning). During my PhD, I worked for Novartis (Switzerland), where I worked on applying computational methods to improve the efficiency of high-throughput screens, and discovered my current passion for data science.
My research has led to 7 peer-reviewed publications so far, with more envisaged by the end of my PhD. In addition, I have obtained a personal grant (NWO Mosaic), and several scholarships/prizes (Prins Bernhard Cultuurfonds Pieter Beijer scholarship, Hendrik Muller Vaderlandsch Fonds scholarship, Huygens Scholarship, Fundatie van Renswoude grant, ECHO award 2009 nominee).
- Paricharak S.A. (9 February 2017), Transforming data into knowledge for intelligent decision-making in early drug discovery (PhD thesis. Leiden Academic Centre for Drug Research (LACDR), Science, Leiden University). Supervisor(s) and Co-supervisor(s): IJzerman, A.P., Bender, A.
- Paricharak S.A., Méndez-Lucio O., Chavan Ravindranath A., Bender A., IJzerman A.P. & Westen G.J. van (2018), Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening, Briefings in bioinformatics 19(2): 277-285.
- Mohan C.D., Srinivasa V., Rangappa S., Mervin L., Mohan S., Paricharak S.A., Baday S., Li F., Shanmugam M.K., Chinnathambi A., Zayed M.E., Alharbi S.A., Bender A., Sethi G. & Basappa Rangappa K.S. (2016), Trisubstituted-Imidazoles Induce Apoptosis in Human Breast Cancer Cells by Targeting the Oncogenic PI3K/Akt/mTOR Signaling Pathway, PLoS ONE 11(4): e0153155.
- Paricharak S., IJzerman A.P., Bender A. & Nigsch F. (2016), Analysis of Iterative Screening with Stepwise Compound Selection Based on Novartis In-house HTS Data, ACS Chemical Biology 11: 1255-1264.
- Kumar K.H., Paricharak S., Mohan C.D., Bharathkumar H., Nagabhushana G.P., Rajashekar D.K., Chandrappa G.T., Bender A. & Basappa Rangappa K.S. (2016), Nano-MoO3-mediated synthesis of bioactive thiazolidin-4-ones acting as anti-bacterial agents and their mode-of-action analysis using in silico target prediction, docking and similarity searching, New Journal of Chemistry 40(3): 2189-2199.
- Anusha S., Baburajeev C.P., Mohan C.D., Mathai J., Rangappa S., Mohan S., Paricharak S., Mervin L., Fuchs J.E., Mahedra M., Bender A. & Basappa Rangappa K.S. (2015), A Nano-MgO and Ionic Liquid-Catalyzed ‘Green’ Synthesis Protocol for the Development of Adamantyl-Imidazolo- Thiadiazoles as Anti-Tuberculosis Agents Targeting Sterol 14α-Demethylase (CYP51), PLoS ONE 10(10): e0139798.
- Paricharak S., Cortés-Ciriano I., IJzerman A.P., Malliavin T.E. & Bender A. (2015), Proteochemometric modelling coupled to in silico target prediction:: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules, Journal of Cheminformatics 7.
- Neelgundmath M., Dinesh K.R., Mohan C.D., Li F., Dai X., Siveen K.S., Paricharak S., Mason D.J., Fuchs J.E., Sethi G., Bender A., Rangappa K.S., Kotresh O. & Basappa (2015), Novel synthetic coumarins that targets NF-κB in Hepatocellular carcinoma, Bioorganic and Medicinal Chemistry Letters 25: 893-897.
- Bharathkumar H., Paricharak S., Dinesh K.R., Siveen K.S., Fuchs J.E., Rangappa S., Mohan C.D., Mohandas N., Kumar A.P., Sethi G., Bender A. & Basappa Rangappa K.S. (2014), Synthesis, biological evaluation and in silico and in vitro mode-of-action analysis of novel dihydropyrimidones targeting PPAR-γ, RSC Advances 4: 45143-45146.
- Bharathkumar H., Sundaram M.S., Jagadish S., Paricharak S.A., Hemshekhar M., Mason D., Kemparaju K., Girish K.S., Basappa Bender A. & Rangappa K.S. (2014), Novel Benzoxazine-Based Aglycones Block Glucose Uptake In Vivo by Inhibiting Glycosidases, PLoS ONE 9(7): e102759.
- Paricharak S., Klenka T., Augustin M., Patel U.A. & Bender A. (2013), Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases, 5(49): 49-68.
- Koutsoukas A., Paricharak S., Galloway W.R.J.D., Spring D.R., IJzerman A.P., Glen R.C., Marcus D. & Bender A. (2014), How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space, Journal of Chemical Information and Modeling 54(1): 230-242.
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