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SURESH KUMAR
PhD student, Univeristy of Vienna, Austria
e-mail: sureshtnau(at)yahoo(dot)co(dot)in
Website: Bioinformatics Web

EDUCATION
2006-Present - PhD in Bioinformatics, University of Vienna, Austria
2003-2005- MSc in Bioinformatics, Bharathiar University, India
1998-2002- BSc in Agriculture, Tamil Nadu Agricultural University, India

RESEARCH EXPERIENCE
Ph.D thesis work
Topic: Likelihood of protein structure determination
Supervisors: Prof.Oliviero Carugo (advisor), Prof.Kristina Djinovic (accessor),
University of Vienna, Austria
Abstract: Increasing attention is devoted to bioinformatics analyses of amino acidic sequences in order to predict if a protein can correctly fold into a stable and functional three dimensional structure that can be determined experimentally. Several factors can hamper the production of protein samples that need to be homogenous and monodispersed, including conformational disorder, improper selection of domain boundaries, and solubility. Another aspect is the requirement of other molecules in order to fold into a functional supra-molecular assembly. A protein chain can correspond to a monomeric protein or it can form, together with other chains, oligomeric assemblies, which can be either homo-oligomers or hetero-oligomers. In the latter case, it must be avoided to determine the 3D structure of a single protomer, since it will not be functional and it will also be probably extremely difficult to express in a soluble form. Our aim of study, to interface several prediction methods and to develop novel techniques to predict the level of structural organization of a protein construct on the basis of its amino acidic sequence focusing on unstructure protein, protein quaternary status, protein domain selection and metalloprotein prediction.

Research training
Topic: Implementation of Computational Pipeline for Musa ESTs analysis
Position: Bioinformatician
Supervisor: Dr.Nicolas Roux, Coordinator of global Musa consortium, INIBAP, France
Completion date: July 2005 – December 2005
Abstract: The primary objective of this project making Musa ESTs publicly available by developing basic genomics tools for plant genome researchers. The main part of this project includes reducing the sequencing error and redundancy of ESTs by clustering based on Open Sputnik pipeline by using bio-moby technology.

M.Sc thesis work
Topic: Molecular Biodiversity and Banana Genomics: Anonymous markers, Gene
Analysis and Access
Supervisor: Prof. (Pat) J.S. Heslop-Harrison, University of Leicester, UK
Completion date: January - May 2005
M.Sc summer training
Topic: Remote homolog identification of GAGA protein in Mouse
Supervisor: Dr.Rakesh Mishra, Centre for cellular and Molecular Biology, India
Completion date: May -July 2004

PROFESSIONAL EXPERIENCE
2005 (July - December) – Bioinformatician, Musa Genome Project, International
Network for the Improvement of Banana and Plantain (INIBAP), France
2005 (January – May) - Visiting researcher, Department of Biology, University of
Leicester, U.K
2004 (May- July) – summer trainee, Centre for Cellular & Molecular Biology, India

HONORS/AWARDS/FELLOWSHIPS
2006- Present - International PhD fellowship from Austrian Genome Programme (GENAU),
Bioinformatics Integration Network (BIN-II)
2009 (July) -The European Science Foundation summer school scholarship for Plant
Bioinformatics, Systems and Synthetic Biology Summer School, University of
Nottingham, UK (declined)
2005 (June – December) - Generation Challenge Programme training fellowship
2005 (September) – GCP travel grant
2005 (January – May) – Generation challenge Programme visiting researcher fellowship

SKILLS
Computer Skills
OS: Windows 98 / XP/NT, UNIX / LINUX, SOLARIS
C, PERL, HTML, Java script, Oracle, PHP , Dream weaver MX, Flash MX, Fireworks
MX, MS-office
Bioinformatics software’s & tools
Working knowledge on all major sequence, structure database and analysis tools
Molecular Visualization Software: Rasmol, Pymol, Cn3d, VMD, SwissPdbviewer
Molceular modelling & Docking Software: Modeller, Hex, GRAMM
Genetics software: Power marker, structure, Arlequin
Machine learning: Weka package

AFFILIATIONS
Member of International society of Computational Biology
Member of Bioinformatics Society of India

PRESENTATIONS AND CONFERENCES
2nd International Conference on Bioinformatics Research and Development
(BIRD’08), July 2008, Technical University of Vienna, Austria
[Poster] Discriminating protein hetro-oligomeric state from amino acid sequences
Structure and Interaction of Biological Macromolecules meeting, MFPL, Vienna,
Austria, 2008
[Poster] Structural Bioinformatics at the MFPL
2nd BIN II PhD workshop-2008, IMP, Vienna, Austria
[Oral & Poster] Discriminating protein hetero-oligomeric state from aminoacid sequences
1st BIN II PhD workshop-2007, IMP, Vienna, Austria
[Oral & Poster] Prediction of crystallizability of gene products
Intrinsically Unfolded Proteins (IUP): Biophysical Characterization and Biological
Significance, 2007, Budapest, Hungary
GCP annual research meeting- 2005, Rome, Italy
[Oral] Implementation of Computational Pipeline for Musa ESTs analysis
[Poster] Validation of conserved orthologous Markers: conserved Genes and Universal
Primers in Bananas and Plantains

Thesis/reports
Molecular Biodiversity and Banana Genomics: Anonymous markers, Gene Analysis
and Access (Master thesis)
Implementation of Computational Pipeline for Musa ESTs analysis (GCP technical
report)
Remote homolog identification of GAGA protein in Mouse (summer training technical
report)

Publications
Kumar, S. and O. Carugo (2008). “Consensus prediction of protein conformational
disorder from amino acidic sequence.” Open Biochem J 2: 1-5.
Kirillova, S., S. Kumar, et al. (2009). “Protein domain boundary predictions: a structural
biology perspective.” Open Biochem J 3: 1-8.

REFERENCE: Available on request