Pankaj Barah

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.

• Systems level modelling of stress response mechanism in plants during biotic stress.
• Role of miRNA during plant defense response.
• Exploring complexity  of network level crosstalks, during  multiple biotic and abiotic  stresses in plants.
• Genome level molecular stress response signatures among natural variants of Arabidopsis thaliana.
• Stress response signtaure during single vs. combined stresses in plants.
• Developing Network based mathematical models of Arabidopsis thaliana stress regulatory network. 

1. 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.
2.  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 and gene families.
3. 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.
4. Computation: Database creation, Gene-Ontology based annotations, data mining and bioinformatics software creation

• 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. Recieved travel fellowship from COST (European Cooperation in Science and Technology),  to present my paper in the Fourth StatSeq workshop "Statistical Challenges of the 1000€ genome sequences in plants", held in Italy, 2012.
2. Recieved travel fellowship from SPPS - Scandinavian Plant Physiology Society to present my reserach as an oral talk in  XXIV SPPS Congress, Stavanger, Norway,2011.
3. Recieved travel fellowship from Faculty of Natural Science and Technology, Norwegian Univeristy of Science and Technology to present my paper in 10th International Conference in Systems Biology held in Heidelberg, Germany, 2011. 
4. Visiting Researcher, Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark. (November 2010- February 2011).
5. Genesys  Young Scientists Runners up award and Poster Award during International Conference on Systems Biology, held in Edinburgh (UK), Oct 9-15, 2010.
6. Recieved full fellowship from Welcome Trust (UK) to attend 10 days long Welcome Trust Advance Course "Functional Genomics to Systems Biology", held at Sanger Institute, Cambridge, UK. 2010.
7. 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, 2009. 
8. Junior Research Fellowship: Department of Biotechnology, Govt. of India, Bioinformatics Centre, University of Pune, India.
9. Summer Research Fellowship, by National centre for Biological Sciences (Tata Institute of Fundamental Researches), Banglaore, India in (June-July) 2005.
10. Child scientists award 1995, in National Children's Science Congress, organised by National Council  for Science & Technology Communication (NCSTC), Govt. of India.
11. Jalaja Technologies Pvt. Ltd:  Bangalore, India, as a  Part of India's first Bioinformatics Package Geno-Cluster) having technical collaborations with Institute of Genomics and Integrative Biology (IGIB) & CSIR.

1. Jens Rohloff+, Pankaj Barah+, and Atle M. Bones,  Improving crop productivity and abiotic stress tolerance in cultivated Fragaria using omics and systems biology approach. , in "Improving Crop Resistance to Abiotic Stress: -Omics Approaches" ,  Wiley-VCH,  ISBN-10: 3527328408, 2012. (in press)
2. Pankaj Barah,  Simon Rasmussen,  Maria Cristina Suarez-Rodriguez ,  Laurent Gautier, John Mundy, Henrik Bjørn Nielsen ,Atle M Bones,  Transcriptional regulatory networks in response to single and combined  stresses in plants, Proc. of International conference on Systems Biology 2011, Heidelberg, Germany.
3. Pankaj Barah,  Simon Rasmussen,  Maria Cristina Suarez-Rodriguez ,  Laurent Gautier, John Mundy, Henrik Bjørn Nielsen ,Atle M Bones, Arabidopsis global stress regulon, Proc. of XXIV SPPS Congress, Stavanger, Norway 2011.
4. Konika Chawla*, Pankaj Barah*, Martin Kuiper, and Atle M. Bones; "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).  * Equal contribution 
5. 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.
6. Pankaj Barah and Somdatta Sinha, Studying Protein Folds using Networks, Proceeding of NCMB, January 2009.  
7. 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
8. 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.
9. Pankaj Barah and Somdatta Sinha (2008), Analysis of Protein Folds Using Protein Contacts Networks, PRAMANA: Journal of Physics, August 2008 , Vol. 71, (No.2).

1. Presented poster in The Fourth StatSeq workshop of the TD0801 COST Action "Statistical Challenges of the 1000€ genome sequences in plants" was held on the 18th and 19th April 2012, Verona, Italy.
2. Presented an invited talk in 10th Norwegian Arabidopsis Meeting (NAM),Trondheim, Norway 2012.
3. Presented an invited talk in XXIV SPPS Congress, Stavanger, Norway 2011.
4. Presented a poster in International Conference on Systems Biology, held in Heidelberg (Germany), September, 2011.
5. Presented a poster in  International Conference on Systems Biology, held in Edinburgh (UK), Oct 9-15, 2010.
6. Participated in one of the highly prestigious advance course on "Functional Genomics and Systems Biology" held at Wellcome Trust Genome Campus, Hinxton, Cambridge 2010.
7. National Symposium on Cellular and Molecular Biophysics (NCMB ),22nd-24th January, 2009, Centre for Cellular and Molecular Biology, Hyderabad, India. 
8. International Workshop and Conference on: Statistical Physics Approaches to Multi disciplinary Problems, 2008, Indian Institute of Technology, Guwahati, India.
9. International Workshop on Physics in Biology: A Synergy (IWPBS 2007), University of Hyderabad, India, December 2007. 
10. Attended 11th ADNAT symposium on Structural Biology and Structure Prediction at CCMB Hyderabad, India.22nd –25th Feb'2007.
11. Presented paper on "Pharmacogenomics" in a conference jointly organized by Association of Biological Chemist and Dept. of Biochemistry University of Madras, India, 2005. 

• Environment: Windows, MAC, UNIX / LINUX, IRIX.
• Programming : C++(Basics), PERL, MySQL, and HTML, CGI
• Statistical Programming: MATLAB and R
• Other Bioinformatics Packages:  Biosuite, Pymol, SwissPDBV, Exome, Gromacs, VMD, AutoDock, Geno-Cluster, AMBER, INSIGHT II, PHYLIP,  GCG, Pajek etc.
• Using major bioinformatics/cheminformatics databases, software & tools.
• Working experience with Silicon Graphics Altix machine, Cluster and parallel computing.

• X-ray crystallography of proteins (Demo)
• Microarray - Hands on training on sample preparation, labeling, hybridization, scanning and data analysis using Affymetrix Gene Chip, Illumina Bead arrays, Agilent Nimblegen. 
• High through put next generation sequencing : Illumina Genome Analyzer II X, Roche 454
• NMR and Mass Spectrometry for metabolite profiling: Hands on training on  LC-MS, GC-MS, HPLC, MALDI-TOF, 2D NMR, In-vivo NMR with animal models. 
• Yeast two hybrid experiment and RNAi in C.elegans

1. Participated in National Children's Science Congress, 1996.
2. I have been publishing popular science, social, ploitical, literary articles in various newspapers in Assam, India.
3. Participated in various radio and television programmes on scientific, environmental and social issues.
4. All Assam Best Debater and best Quizzer several times.
5. Working with wild life NGOs. WWF's level 1 campaigner passport holder.
6. Participated in various science exhibition, competitions and winning awards.
7. Co-ordinating a unique community based web-portal on Assamese unicode http://www.xahitya.org./
8. Active member of  community based career portal http://xomidhan.org/, and http://www.neindiaresearch.org/
9. Served as an office bearer of Assam Association in Chennai, India (2005-2006), and Indian Student's Forum, Norway (2010-2-11).
10. I have been continously visiting various schools and colleges in remotest part of Assam to organise career and technology awareness campaigns. 

1. Prof. Atle M Bones, Department of Biology, Norwegian University of Science and Technology.
2. Prof. Martin Kuiper, Department of Systems Biology, Norwegian University of Science and Technology.
3. Prof. Somdatta Sinha, Senior Scientist, Centre for Cellular and Molecular Biology, Hyderabad (at present Honorary Professor of  Biological Sciences, ISSER- Mohali, INDIA).
4. Prof. R. Sowdhamini, National center for Biological Sciences (NCBS), Bangalore, INDIA.
5. Assoc. Prof. Henrik Bjørn Nielsen, Center for Biological Sequence Analysis, Department of Systems     Biology, technical University of Denmark.