Major Projects: 1. PhD Thesis : Taxono-genomics, a strategy incorporating genomic data into the taxonomic description of human bacteria Supervisor : Prof. Pierre-Edouard Fournier Project Tenure : Nov 2011 – will finish by Nov 2014 Place : Aix-Marseille University, URMITE, Faculty de Medicine, Marseille, France Accomplished : more than 10 publications including two review, learned Next generation sequencing, de novo assembly, developed a pipeline which the lab uses. 2. Project Title: Transgenic Overexpression of mouse expressing 12R-Lipoxygenase and Phylogenetic Studies of Lipoxygenase gene family. Supervisor : Prof. P Reddanna Project Tenure : May 2006 – Oct 2010 Place : Hyderabad Central University, Animal Science Department, Hyderabad, India Accomplished : poster presentation accepted in European Conference on Computational Biology at Ghent , Belgium - September 26-29, 2010, Learned the techniques of cell culture and embryonic stem cell culture. 3. Project Title: Sequencing, Annotation and Phylogenetic studies of full-length molecular clone of HIV-1 Subtype C. Supervisor : Dr. Udaykumar Ranga Project Tenure : Oct 2004 – Feb 2006 Place : Jawaharlal Nehru Centre for Advanced Scientific Research, Molecular Virology Laboratory, Molecular Biology and Genetics Unit. Bangalore, India Accomplished : co authored an article in journal Retrovirology, done several HIV viral assembly and annotation , developed lab website. 4. Thesis Title : Identification of dispersed repeat families in genome. Course : Advanced Post Graduate Diploma in Bioinformatics. Supervisor : Prof Alok Bhattacharya Project Tenure : Jan 2004 – April 2004. Place : Bioinformatics Center, JNU, New Delhi, India. Accomplished : learned programming in perl, bioperl, unix shell scripting. Developed a script to identify and classify the dispersed repeat elements. 5. Thesis Title : Screening of marine algae for Hemagglutinins and the detection of Hemagglutination titre. Course : M.Sc in Marine Biotechnology. Supervisor : Dr. Urmila Barros. Project Tenure : July 2001 – April 2002. Place : Department of Marine Sciences and Biotechnology, Goa University, Goa, India. Minor Projects (In Bioinformatics) 1. Microarray analysis of data and clustering by using K-mean technique and visualization by Principle Component Analysis (PCA). 2. Find out coding and non-coding region using 1st order Markov model. 3. Making a relational database using Oracle8i. 4. Identification of gene families in microbial genomes.

Coordonnées

rosaak@gmail.com
rosaak@gmail.com

Expérience professionelle

Type de contrat : CDD
Organisme de rattachement ou entreprise : Institut des Maladies Métaboliques et Cardiovasculaires.
Ville : Toulouse
Pays : FRANCE

Adresse professionnelle

URMITE - UMR CNS 6236, IRD 198 Université de la Méditerranée Unités Rickettsies - Centre de Référence Faculté de Médecine 27, Boulevard Jean Moulin 13005 Marseille
+337811289352

Techniques maîtrisées

Domain Specific Knowledge Analysis of Next Generation Sequence Data [Illumina , SOLiD, 454] for metagenomics as well as whole genome assembly. Hands on experience in Roche/454 Sequencing. de novo assembly tools - Velvet, Newbler, Mira, CLC. Setting up and maintaining local database for Handling NGS Data, Blast database etc. Knowledge of the algorithms behind BLAST, BLAT, OrthoMCL etc. Developing pipelines for Phylogenomics [MAGI : Developed a pipeline for whole genome comparison (manuscript under preparation) ]. Large Scale Genome Analysis using Galaxy browser. Intermediate level Linux Administration. And an in depth knowledge of a large number of tools, resources and databases available over the WWW for biological sequence analysis. Familiar with the following Bioinformatics tools BLAST [standalone, web] BLAT DNASTAR EMBOSS CLUSTAL-W Phylogentic softwares like Phylip,PhyML,MEGA DAMBE Oligo6 for Primer designing Phred, Phrap, Consed HMMER RasMol,MSI(Insight) ADT,VMD,NAMD Repeat Finder Swiss PDB Viewer Large Scale Genome Analysis by Galaxy browser And an in depth knowledge of a large number of tools, resources and databases available over the WWW for biological analysis. Statistical Softwares : MINITAB, Octave,R Molecular Biology tools and techniques Genomic DNA, RNA isolation Plasmid DNA isolation Molecular Cloning / Recombineering. PCR (Hot start, Nested PCR, RT-PCR) cDNA Library construction. mouse ES cell /Animal Cell culture MALDI-TOF, SDS PAGE, ELISA, Western /Southern Blotting Protein purification techniques Reporter gene assay [SEAP Assay, -gal assay]. DNA Sequencing [ABI, Roche/454]. Tissue Culture techniques Growth and maintenance of cell lines (HaCaT,CHO,BSF, HEK293) Culturing of mouse Embryonic Stem Cells (R19) Fibroblast cell line (BSF and HaCat cell lines) Electroporation of knockout vectors Making Embryoid Bodies by Hanging drop

Compétences

Bioinformatics , Genomics, Phylogentics, Scientific Programming in Perl and Python

Doctorat

Intitulé : Biologie-Santé - Spécialité Maladies Infectieuses
1ère inscription en thèse : November 2011
École doctorale : Sciences de la Vie et de la Santé
Date de soutenance de la thèse : 8 December 2014
Sujet : Taxono-génomique, une stratégie intégrant les données génomiques dans la description taxonomique des bactéries humaines
Directeur de thèse : Pierre-Edouard FOURNIER
Co-directeur :
Unité de recherche : URMITE - Unité de Recherche sur les Maladies Infectieuses et Tropicales
Intitulé de l'équipe : Unité des Rickettsies et des pathogènes émergents

Master

Intitulé : Goa Univeristy
April 2002 - Goa Univeristy

Langues vivantes

Anglais : B2 - Intermédiaire supérieur
Hindi : B2 - Intermédiaire supérieur
Malayalam : C2 - Maternel

Production scientifique

  • Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov.
    Stand. Genomic Sci. 2013
    Roshan Padmanabhan1, Jean-Christophe Lagier1, Nicole Prisca Makaya Dangui1, Caroline Michelle1, Carine Couderc1, Didier Raoult1, Pierre-Edouard Fournier1*
    http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4077819/945
  • Genomics and Metagenomics in Medical Microbiology
    Journal of Microbiological Methods 2013
    Roshan Padmanabhan, Ajay Kumar Mishra , Didier Raoult, Pierre-Edouard Fournier*
    http://www.sciencedirect.com/science/article/pii/S0167701213003217
  • Non-contiguous finished genome sequence and description of Clostridium dakarense sp. nov.
    Standards in Genomic Sciences 2013
    Cheikh Ibrahima Lo1, Ajay Kumar Mishra1, Roshan Padhmanabhan1, Bissoume Samb, Ba2, Amy Gassama Sow2, Catherine Robert1, Carine Couderc1, Ngor Faye3, Didier Raoult1, Pierre-Edouard Fournier1, Florence Fenollar1*
    http://standardsingenomics.org/index.php/sigen/article/view/sigs.4097825/969
  • ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation), a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
    Antimicrobial Agents and Chemotherapy 2013
    Sushim Kumar Gupta1, Babu Roshan Padmanabhan1, Seydina M. Diene1, Rafael Lopez-Rojas2, Marie Kempf3, Luce Landraud4 and Jean-Marc Rolain1*
    ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation), a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
  • Non contiguous-finished genome sequence and description of Gorillabacterium massiliensis gen. nov, sp. nov., a new member of the Family Paenibacillaceae
    Standards in Genomic Sciences 2013
    Mamadou Bhoye Keita, Roshan Padhmanabhan, Aurelia Caputo, Catherine Robert, Eric Delaporte, Didier Raoult, Pierre-Edouard Fournier, Fadi Bittar
    http://standardsingenomics.org/index.php/sigen/article/view/519/1126
  • Non contiguous-finished genome sequence and description of Paenibacillus gorillae sp. nov.
    Standards in Genomic Sciences 2013
    Mamadou Bhoye Keita, Roshan Padhmanabhan, Aurelia Caputo, Catherine Robert, Eric Delaporte, Didier Raoult, Pierre-Edouard Fournier, Fadi Bittar
    http://standardsingenomics.org/index.php/sigen/article/view/518/1125
  • A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species
    International Journal of Systematic and Evolutionary Microbiology 2014
    Dhamodharan Ramasamy, Ajay Kumar Mishra, Jean-Christophe Lagier, Roshan Padhmanabhan, Morgane Rossi, Erwin Sentausa, Didier Raoult and Pierre-Edouard Fournier
    http://ijs.sgmjournals.org/content/64/Pt_2/384.full.pdf+html