Pankaj Barah

About me:

I am Pankaj Barah, born and brought up in a small place  Borbali in the beautiful state of Assam, India. I am friendly and funloving person. I have self confidence to achieve my goals. I have a positive look to life and generally believe that all fellow beings are good at heart, so I don’t come into conflict easily. Above all I have a deep sense of feelings for mankind and feel that that the career I opted for will bring maximum happiness to them.

 

Current position:

1) PhD Fellow in Computaional Systems Biology,Department of Biology, Norwegian University of Science and technology.Working on  'Systems Biology of Host defense.'

2) Visiting Fellow , Centre for Biological Sequence Analysis, Department of Systems Biology, Technical Univeristy of Denmark (DTU), Copenhagen.

Research interests:

• Molecular and structural systems biology: Reconstruction of complex biological systems, basically transcriptional gene regulatory network, signal transduction network and metabolic pathways. To understand protein functions in complex structural systems in the level of intra-molecular and inter-molecular (protein-protein, protein-ligand, protein-DNA) interactions using graph theory.

 • Understanding the diverged protein world: Structure prediction, functional analysis and evolutionary dynamics of protein structures. I am interested in Structural Biology as well as to implement Graph theory and other machine learning methods like HMM, ANN, SVM to find an answer for the question like how the function and structure evolve in extremely divergent protein families.

• Sequence level: sequence analysis of Protein/DNA, Prediction of secondary & tertiary structure of Proteins and RNA, Motif identification, identification of SNPs responsible for adverse drug reaction, remote homology identification, evolutionary related studies using phylogenetics, domain identification, conserved orthologue identification and prediction of miRNA.

 • Computation: Database creation, data mining and bioinformatics software creation.

Education:

· M.Sc. in Bioinformatics, University of Madras, India.  2004-2006         First Class.

 · B.Sc. (Hons.) in Biology, B. Barooah College, Gauhati University, India  2000-2003     

    First class with University Rank, Distinction.

· Higher Secondary (Science), North Lakhimpur College, Assam, India 1998-2000

      First division.

· HSLC, Borbali Higher Secondary School, Assam, India  1998

      First division, With Star marks.

Honors, scholarships, fellowships, prizes:

 

 

1) Genesys  Young Scientists Runners up award and Poster Award during International Conference on Systems Biology, held in Edinburgh (UK), Oct 9-15, 2010.

 

2) Selected for Senior Research Fellowship: Selected for this prestigious fellowship given by Council of Scientific and Industrial research (CSIR), Govt. of India under Trans Disciplinary Research area, to pursue PhD, 2009. (Mathematical Modelling and Computaional Biology Group, Centre for Cellular and Molecular Biology, Hyderabad,India)

 

 3) Junior Research Fellowship: Department of Biotechnology, Govt. of India. Under this fellowship, I  worked in Bioinformatics Centre, University of Pune (Nov. 2006-July 2007under the guidance of  Prof.  Indira Ghosh, Director, Bioinformatics Centre, University of Pune.

 

4)  Summer Research Fellowship, by National centre for Biological Sciences (Tata Institute of Fundamental Researches) in (June-July) 2005. I worked in Computational Biology Group, under Dr. R. Showdhamini  to work on different tools and techniques in Protein Structure Bioinformatics.

 

5)  Child scientists award 1995, in National Children's Science Congress, organised by National Council  for Science & Technology Communication (NCSTC), Govt. of India.

 

6) Jalaja Technologies Pvt. Ltd:  Bangalore, India (a Bioinformatics Software Company), in a software development project (Proteome calculator which is a Part of India’s first Bioinformatics Package Geno-Cluster) having technical collaborations with Institute of Genomics and Integrative Biology (IGIB) & Council of Scientific and Industrial Research (CSIR). I have worked in the ‘Proteome  calculator’ project which is one of    the applications inside the package.

 

Publications:

i)   Pankaj Barah and Somdatta Sinha (2008), Analysis of Protein Folds Using Protein Contacts Networks, PRAMANA: Journal of Physics, August 2008 , Vol. 71, (No.2).

 ii)  Sandhya. S, Pankaj B, M. K. Govind, B. Offman, N. Srinivasan,and R. Sowdhamini, CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its  application in the study of large length variations., BMC Structural Biology , 2008, 8:28.

 iii)  Sankaran Sandhya, Saane Sudha Rani, Barah Pankaj, Madabosse Kande Govind, Bernard Offman, Narayanaswamy Srinivasan and Ramanathan Sowdhamini (February, 2009) Length variations amongst  protein domain superfamilies and consequences on structure and function. PLoS One , 2009;4(3):e4981

  iv) Pankaj Barah and Somdatta Sinha, Studying Protein Folds using Networks, Proceeding of NCMB, January 2009.   

v) Chawla K., Barah P., Kuiper M. and Bones AM; " Systems Biology: a promising tool to study abiotic stress responses” in "Omics and Plant Abiotic Stress Tolerance" , Bentham Publishers, USA (ISBN: No.: 978-1-60805-058-1 (in press). 2010

 

vi) Pankaj Barah, Anna Kusnierczyk , Diem Hong Tran, Per Winge, Atle M Bones, “Systems biology of host defense in Arabidopsis thaliana during insect and bacterial attack.”, iCSB '2010 conference proceeding, Edinburgh , Scotland.

Paper presented, conferences, workshop:

1.       

   International Conference on Systems Biology (iCSB2010), Edinburgh, Scotland,Oct. 2010.  (GENESYS Poster award and Runner up for Genesys Young Scientist Award)

    

2.      

   Wellcome Trust Advanced Courses: Functional Genomics and Systems Biology, Wellcome Trust Genome Campus, Hinxton, Cambridg, 14th-25th June 2010.

4.      National Symposium on Cellular and Molecular Biophysics (NCMB ),22^nd-24^th January, 2009, Centre for Cellular and Molecular Biology.
5.      International Workshop and Conference on: Statistical Physics Approaches to Multi disciplinary Problems (StatPhys'08), 2008, Indian Institute of Technology, Guwahati, India.
6.      International Workshop on Physics in Biology: A Synergy (IWPBS 2007), University of Hyderabad, India, December 2007.  
7.       Attended 11^th ADNAT symposium on Structural Biology and Structure Prediction at CCMB Hyderabad.22^nd –25^th Feb’2007.  
8.      Presented paper on “Pharmacogenomics” in a conference jointly organized by Association of Biological Chemist and Dept. of Biochemistry University of Madras, 2005.

 

Computational and bioinformatics skills:

·      Environment: Windows, UNIX / LINUX, IRIX.

·     Programming Languages: C++(Basics), PERL, R

·     Database Programming: MySQL, Oracle 8i and Web based Programming: HTML, CGI

·     Packages: MATLAB, Biosuite, Pymol, SwissPDBV, Exome, Gromacs, VMD, AutoDock, Geno-Cluster, AMBER, INSIGHT II, PHYLIP, SAS, GCG, Cytoscape, Pajek etc.

·     Using major bioinformatics/cheminformatics databases, software & tools.

·     Working experience with Silicon Graphics Altix machine, Cluster and parallel computing.

·     Computer aided drug designing: Molecular Dynamics Simulation, Energy minimization, De novo  ligand designing, Lead optimization, Docking, QSAR studies etc.

 

 Wet-lab skills:

Extraction of DNA/RNA/PROTEIN; quantitative & qualitative estimation of biomolecules; isolation of microorganism; SDS page; RAPD; restriction mapping; PCR amplification; chromatographic techniques, blotting techniques, immunological experiments, electrophoresis etc.

Specialized training:

Ø     X-ray crystallography of proteins (Demo)

WWelcome Trust Advance Course , Sanger Institute, Cambridge:

Ø Microarray - Hands on training on sample preparation, labeling, hybridization, scanning and data analysis using Affymetrix Gene Chip, Illumina Bead arrays, Agilent Nimblegen.

Ø  High through put Next Generation sequencing and data analysis : Illumina Genome Analyzer II X

Ø  NMR and Mass Spectrometry for metabolite profiling and data analysis: Hands on training on  LC-MS, GC-MS, HPLC, MALDI-TOF, 2D NMR, In-vivo NMR with animal models.

Ø     Yeast two hybrid analysis for protein-protein interaction.

Ø   RNAi experiemnts in C.elegans and mammalian cancer cell line

Extra curricular activities:

1. Participated in National Children’s Science Congress, 1996.

2. Worked as news editor and published popular science articles in various newspapers.

3. Participated in various radio programme on scientific, environmental and social issues.

4. All Assam Best Debater and best Quizzer several times.

5. Announcer for Yuba Vani programme, All India Radio, Guwahati 2002-2003.

6. Working with wild life NGOs. WWF’s level 1 campaigner passport holder.

7. Participated in various science exhibition, competitions and winning awards.