Ashwin Sivakumar

 Pre-Doc, Bioinformatics Group

BI SymbolInstitute of Biotechnology
back to group homepageReturn to Group Homepage

| Module Space | ADDA | Suprime |

Ashwin Sivakumar's official space

I want to be a wall which when hit, hits back harder... I know that the life is full of crests and troughs but I want my crests to overshadow my troughs... I want to be loved and loved by all, I want to achieve and achieve with a purpose... I want fame; a fame with a cause... I know life is finite but I want my goals to be infinite... Oh God! please show me the path.

Current Research

My research interest revolves two "diverse" themes:


Click on the hyperlinks to jump to corresponding sub-sections.

Modular Approach to study function and evolution

The drug discovery process would be helped by information on roles played by complete functional units, reactions they catalyze and residues responsible for the specificity. This information comes at the gene product level. There are number of domain classification systems, though they are very useful for structure prediction, they have limitations when it comes to function prediction. Also available are resources, which aim at classifying protein sequences from publicly available databases like UniproT and Genpept into sequence level super-families, aiming to reciprocate SCOP at the highest level of hierarchy. Nevertheless, two key issues remain an open puzzle, firstly automated function prediction of multi-domain proteins and an automated hierarchical functional classification system using only sequence data.

We are addressing these issues by proposing what would be a “modular” classification of the protein universe. Contemporary proteins exist either as composite (A protein which exists as fused gene in one or more genomes, while occurring as two or more separate homologous genes in other genomes) or component (A complete functional protein which exists as one component of a fused gene in another genome). Many composite proteins seem to be a product of unrelated gene fusions. In other words they are made by fusion of two unrelated component proteins. Here we propose an evolutionary scenario, where proteins evolved as component proteins and hypothesizing that the function of fused genes [composite proteins] are defined either by the interaction between their component proteins or as multi-functional (combination of gene products).

Our understanding and basis of the new concept comes from study of mechanistically diverse super-families like the crotonases. The crotonases (Enoyl CoA hydratase super-family)represent a diverse set of proteins sharing a common structural scaffold at a super-family level and a common catalytic strategy by catalyzing reactions that usually involve a thioester enolate anion intermediate stabilized by hydrogen bonding with two peptidic NH groups in an oxyanion hole. The crotonase sub-classes diversify to catalyse different overall reactions. There have been extensive studies on individual enzymes proposed to belong to this remarkable super-family. We performed the first comprehensive study on evolution of functional repertoire in multiple members of this super-family. Here we studied the diversity of crotonases in the bacterial and archaeal genomes. These studies helped us addressing key issues like defining sequence level super-families, defining meaningful sub-groups within super-families, characterizing putative functional fingerprints and residues.

We have recently demoposed the complete set of sequences from complete genomes into a non-redundant set of modules. We call this set as "Module Space" which is available for download. A classification of module space into super-families of homologoues sequences is currently under development. We are actively researching on using module space to address fundamental biological questions having biomedical relevance. Module space is based on enumerating and charecterising gene fusion (the term is used broadly in this context: please refer to related manuscripts) events. We are interested in studying the following key questions in detail.

  • Does the fused gene develop a new function different from their constituent component proteins?
  • Gene fusion as an effective approach to enumerate new protein-protein interactions.

Management and strategy issues in the Biotech sector

One of my parallel areas of interests along with the scientific themes which Iam addressing is a key area which can be broadly classified under the specialist area of "knowledge dissemination".Strategies adopted for disseminating knowledge is a key to interface Science, Technology and Society which in turn decides the economy of the field. Some of the key areas of my interests are:

  • Management and marketing strategies within organisation types
  • Organisational strategies and issues
  • Maximising the potential of e-commerce in the Biotech sector

I have finished writing a series of vision articles on these issues, some of them will be available in open source. Please do not hesitate to contact me if you wish to collaborate on any of my interest themes.

Selected Publications

Sivakumar A, Wilton C, Holm L (2006) From Sequences to a functional unit: Jan 3;in press, Physiological Genomics.

Heger et al. (2005) ADDA: a domain database with global coverage of the protein universe. Nucleic Acids Res 33(Database issue):D188-91.

Sivakumar A, Mallick S, Holm L (2005) Approaches to determine biological function-New functional sub-classes with the diverse crotonase super-family. submitted

Please refer to my CV for the complete list

Past research grants, awards and achievements:

  • Selected amongst top 100 young scientists and MBAs in the global life science sector 2005- Biovision and Science.
  • Nominated for AAS Excellence in Science award- Science Magazine.
  • Intelligent Systems for Molecular Biology- Conference and Travel grant- 2001
  • Research grant- Bioinformatics (Institute of Biotechnology, University of Helsinki)- 2003-till date
  • International visiting fellowship-Jospehine Paul center for comparative and molecular biology, MBL, Woodshole, MA, USA (March-July 2004)
  • Nordic Society for Bioinformatics Conference and travel grant-2003
  • Universidad de Zaragoza grant ,Conference and travel grant- 2004
  • University of Copenhagen grant, Protein Summer School, Spetses, Greece-2004
  • Research grant-Marine Biology laboratory (March-June 2004)
  • Intelligent Systems for Molecular Biology-Conference grant-2004
  • RECOMB conference travel grant-2005
  • Biovision-World life science forum grant-2005
  • Conference grant- European Conference for computational biology- 2005

Previous Positions and current activities

Related press releases

Express pharma pulse (page 16)
The Hindu, National Indian newspaper
Biospectrum I
The Hindu business line newspaper
Biospectrum Biovision nomination
UP Tech newsletter
Bioinformatics Society of India webpage

Contact details

Ashwin Sivakumar
Institute of Biotechnology
Floor 7, Biocenter 2
Institute of Biotechnology
PO Box 56
00014 University of Helsinki
office: +358 919159113/4
e-mail: firstname *dot* secondname *at* helsinki *dot* fi

Business profiles:

Free Counter
Free Counter