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Hiren Karathia
Present Address
Affiliation: Ph.D scholar
Dept. Ciencies Mediques Basiques
Universidad de Lleida
Montserrat Roig 2
25008 Lleida
Spain
email: hiren@cmb.udl.cat |
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Education-
(i)M.Sc (Bioinformatics) from Sikkim Manipal University with Ist Div. in 2004
(ii)M.Sc (Biomedical Technology) from Gujarat University with Ist Div. in 2001
(iii)B.Sc. (Biochemistry) from Saurashtra University, Rajkot with Ist div. in 1999
(iv)Higher Diploma in Software Engineer from Aptech Education Ltd. in 1998
RESEARCH EXPERIENCE-
Present status-
Working as Ph.D student in Faculty of Medicine at the University of Lleida, Spain, under the guidance of Dr. Rui Alves, since June, 2008 with a scholar title provided by AGAUR (Cataluña, Spain).
Title of project: “Development and application of computational methodologies for Integrated Molecular Systems Biology”.
Previous status-
Working as Lecturer and Research scientist in Biotechnology dept., AMITY University; Noida (U.P), India. Work profile is taking lectures on Computational Biology, Bioinformatics Algorithms, Recombinant technology, Cell Signaling pathways, Microarray analysis & doing research on HIV induced signal pathways: from Aug. 2006 to May. 2008.
Worked as Research Scientist & Technical team member in Institute of Bioinformatics (IOB); Bangalore, collaborated with Pandey’s Lab at Johns Hopkins University; USA: from Mar. 2005 to Aug. 2006.
Worked as Technical consultants & Bioinformatics Course Coordinator at Applitech Education Ltd.; Ahmedabad. Work profiles were to design & development the tools for data mining over the mechanisms of RNA splicing and Proteomics, from Sep. 2004 to Mar. 2005.
Worked as Lecturer in Biotechnology and Medical Laboratory Technology dept., Virani Science College affiliated with Saurashtra University, from July 2001 to Aug 2002.
Previous project-
Worked on creation of the signal transduction pathways to gather the Knowledge of interaction and pattern of transcription associated with the development of AIDS and HIV induced dementia between host and HIV at AMITY Institute of Biotechnology (AIB) by using technologies i.e., Perl, Oracle 9i, GenMapp, ZOPE, Photoshop and Dream-viewer since (Oct. 2006 – Dec. 2007).
Worked in developing a Database - Human Protein Reference Database (HPRD) in Institute of Bioinformatics (IOB), by using technologies: Python, Oracle 8i, ZOPE, DTML, XML, HTML, Javascript, Photoshop and Dream-viewer for seven months (Apr-to-Oct. 2005). This database is integrated within NCBI database to get the reference for human proteins. (http://hprd.org)
Worked in designing a Tool for Annotation of human proteins, entitled as “Bio-Builder 2.0”, in Institute of Bioinformatics (IOB), by using technologies: Python, Oracle 8i, ZOPE, DTML, XML, HTML, JavaScript, Photoshop and Dreamviewer. This tool is used for annotation of HPRD (Human Protein Reference Database). http://bioibuilder.ibioinformatics.org
Worked in revamping the database - “Plasma Protein Database (PPD)”: transformed the Object Oriented model into Relational model, by using technologies: Python, Oracle 8i, PERL, ZOPE, and XML, at Institute of Bioinformatics (IOB) for two months (Nov-to-Dec. 2005). http://plasmaproteomedatabase.org
Worked in a project, conceptualized as “Dynamic graphical representation of Protein-Protein interactome available in HPRD” at Institute of Bioinformatics, by using technologies: Python, ‘PIL.Image’ package of Python, Oracle 8i, ZOPE, Photoshop for one month (Dec to Jan. 2005). http://hprd.org
Worked on a project, conceptualized as Knowledge discovery from HPRD (Human Protein Reference Database), by clustering the human proteins over different dimensional views of HPRD: Protein localization, Protein expression, protein interactions, protein post-translational modification etc. in Institute of Bioinformatics (IOB) for 2 months (Jan-Feb, 2006). The purpose of this project was to standardize the protocol for designing Knowledge- ware for human proteomics and association of it with Microarray.
Worked in a project entitled as “Networks and pathways” and conceptualized as “Curation of protein complex (Ligand-Receptor) induced signal transduction pathway in human”, designed based on BioPax (Biological Pathway Exchange) and PSI MI standards, in Institute of Bioinformatics, by using technologies; Python, PERL, GenMapp, Photoshop, XML, Excel, DreamViewer. Enriched information on proteins is: Protein-protein Interactions; post translation modifications (PTMs); transportation, Activation/Inhibition; Controls; Gene regulations (Receptor signal induced Up-regulation or Down-regulation) and Recruitments. The duration of this project is 4 months (Feb-to-June 2006). http://netpath.org
Academic work Experience-
Completed dissertation for the partial fulfillment of M.Sc in Biomedical Technology program, entitled as “Arsenic induced Genotoxicity on Human Blood Cultures” in School of sciences, Zoology Department; Gujarat University; Ahmedabad during Jan 2001 to June 2001.
Completed project for the partial fulfillment of M.Sc in Bioinformatics program, entitled as “Human Homologous Protein prediction of SnRNP from Rice [Oryza sativa (spp. Indica)]” at Sikkim Manipal University, Extended center; Ahmedabad for 4 months during April 2004 to July 2004.
Worked as a guide in a project for partial fulfillment of P.G. Diploma students of Bioinformatics, entitled as “Designing a Data mining tool for the discovery of Alternative splicing mechanism induced by snRNP” at Applitech Education Ltd., for 3 months during September 2004 to November 2004.
Other Project work Experience-
Completed project work for the partial fulfillment of Higher Diploma Software Engineering (HDSE), entitled as “Inventory system for Hotel management” at APTECH Education Ltd.; Rajkot for 3 months during June 1996 to August 1996, by using language – ‘C’.
PUBLICATION:
Karathia H. M, Rui Alves S.cerevisiae as a model organism: Strengths and limitations (In preparation).
Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G, Kumar HG, Nagini M, Kumar GS, Jose R, Deepthi P, Mohan SS, Gandhi TK, Harsha HC, Deshpande KS, Sarker M, Prasad TS, Pandey A (2006). Human protein reference database--2006 update. Nucleic Acids Res. 2006 Jan 1;34 (Database issue):D411-4. PMID: 16381900.
ABSTRACTS/PROCEEDINGS OF MEETINGS:
Hiren Karathia*, Gajendra Aseri, Neelam Jain, Sandeep K. Shrivastava. Discovery of targets for nano-particle tagged antibodies specific to cancer biomarkers. Seminar-cum-Workshop on Application of Nanotechnology in Microbial and Herbal Product Development, March 23 – 25, 2007. Amity Institute of Microbial Technology, New Delhi, India.
Paper in process- “Arsenic Induced genotoxicity on Human Blood cultures by using technique - PBLC (Peripheral Blood Lymphocyte Cultures)”.
ADVANCED TRAINING/SHORT COURSES ATTENDED-
Traning in Flow Cytometry, Cytochemistry, ELISA (Enzyme Linked Immuno Sorbant Assay), Histological Slide analysis for Breast cancer, BCRA-2 protein analysis, analysis of apoptosis responsible proteins by immuno-cytochemistry, Other techniques learned were PCR applications, and Blotting Techniques at M.P. Shah Cancer Institute, Civil Hospital, Ahmedabad; Gujarat.
HANDS ON EXPERIENCE-
Knowledge Domains
Broadly three domains – Biomedical Technology, Bioinformatics (Proteomics, Signal transduction pathways & DNA microarray) & Information Technology (IT).
(A) BIOMEDICAL TECHNOLOGY
DNA & RNA isolation and qualitatively as well as quantitatively estimation
cDNA library construction for the purpose of Microarray experiments
Sothern Blotting, Restriction Mapping, PCR & other Recombinant Technology experiments.
Electrophoresis: Agarose Gel and SDS-PAGE.
Chromosomes isolation, staining & karyotyping.
Cytogenetic & Genotoxic analysis on Peripheral Lymphocyte Blood Culture (PBLC)
Microscopy: Light Microscopy, Electron microscopy.
ELISA and RIA techniques: for bio-molecule and antigens/antibody estimation.
Slide preparation & analysis for Histology & Pathology, Hematology and Immunology.
(B) BIOINFORMATICS
Proteomics and Genomics: Annotation, tool development for microarray analysis.
Biology database: design and development of data modelling over Relational and Object oriented Database.
Data mining: strategy design and tool development
Protein based signal transduction pathways: Annotation and analysis with relative interpretation of Gene regulations.
Computational Biology based on Homology modelling, HMM (Hidden Markov Model), SVM (Support Vector Machine) & Dynamic programming for Sequence analysis.
DNA microarray: Annotation and analysis by using statistical language i.e., ‘R’.
(C) IN KNOWLEDGE DISCOVERY-
Biostatistics: Hypothesis testing, multivariate analysis. Hands on experience on solving the patterns of heterogeneous data by applying ANOVA and regression analysis. Evaluating Microarray data using statistical language i.e., ‘R’.
Data warehousing: Theoretical knowledge over star and snow-flake protocol to develop knowledge-ware. Hands on experience on application of business rule on Proteomics problems to optimize the designing of Knowledge-ware.
(D) INFORMATION TECHNOLOGY
Languages: C, C++, Java, Visual Basic, PERL, Python, PL/SQL, XML, HTML, DTML, R.
Operating Systems: Windows 2000, XP and Linux.
RDBMS: Oracle 8i & 9i, MySQL, MS Access.
System Administration: Software installation, Windows O/S, Linux installation.
Database Administration: Oracle 8i and MySQL database administration.
Network Administration: Intranet traffic management.
Advance Multimedia: Flash-MX, Photoshop, Dream-Viewer MX, Adobe illustrator.
(E) IN ADMINISTRATION
Coordinating in life cycle of projects.
Organizing events for team motivations.
Mediator for proposing problems and responding solutions of problems in between two various state of mind teams.
Knowledge on developing team for Data ware-housing project. |
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