Publications:

• Alok Das Mohapatra, Sunil Kumar, Ashok Kumar Satapathy and Balachandran Ravindran (2011). Apoptosis in a pathogenic nematode involves mitochondrial pathway. PLoS Negl Trop Dis 5(9): e1306. doi:10.1371/journal.pntd.0001306

• MHU Turabe Fazil, Sunil Kumar, Rohit Farmer, HP Pandey and DV Singh (2010). Binding efficiencies of carbohydrate ligands with different genotypes of cholera toxin B: Molecular Modeling, dynamics and Docking Simulation studies. Journal of Molecular Modeling (In Press, Springer publication).

• Biswaranjan Paital, Sunil Kumar*, Rohit Farmer, Niraj Kanti Tripathy, Gagan Bihari Nityananda Chainy (2010) In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata. Interdisciplinary Sciences: Computational Life Sciences (Accepted, Springer publication).*corresponding author.

• Chinmayee Mohapatra, Hirak Kumar Barman, Rudra Prasanna Panda, Sunil Kumar, Varsha Das, Ramya Mohanta, Shibani Mohapatra, Pallipuram Jayasankar (2010) Cloning of cDNA and prediction of peptide structure of plzf expressed in the spermatogonial cells of Labeo rohita, Mar. Genomics, doi: 10.1016/j.margen.2010.09.002. (Elsevier publication).

• MHU Turabe Fazil*, Sunil Kumar*, N Subbarao, H P Pandey and Durg V. Singh (2009) Homology Modeling of a Sensor Histidine Kinase from Aeromonas hydrophila. Journal of Molecular Modeling DOI 10.1007/s00894-009-0602-2. * Equal contribution.

• Babu A. Manjasetty, Sunil Kumar, Andrew P. Turnbull, Niraj Kanti Tripathy (2009). Homology Modeling and Analysis of Human Proteins related to Disease:Structural Investigations into Shwachman-Bodian-Diamond Syndrome (SBDS) using a Bioinformatics Approach,.InterJRI Science and Technology, Vol. 1, Issue 2,97-104

• Sunil Kumar, B B Sahu, N K Tripathy, B P Shaw (2009) In Silico Identification of Putative Proton Binding Sites of a Plasma Membrane H⁺-ATPase Isoform of Arabidopsis Thaliana, AHA1. J Proteomics Bioinform 2: 349-359. doi:10.4172/jpb.1000095.

• Sunil Kumar, N. Subbarao , Sushmita Sahu, Mamata Ray, Priyanka Das, Prosenjit Mondal, Surendra Chandra Sabat (2009). In silico Modeling of Rice CatalaseA and Docking studies with Sucrose. Poster presented at International conference on Bioinformatics (InCoB), Singapore during 7-11 Sept., 2009.

• Fazil MHU Turabe, Kumar Sunil , Singh DV (2009). In Silico Structural Analysis Of Vibrio Cholerae Luxp: Modelling, Docking And Molecular Dynamics Simulations Studies. Indo-US Conference on Infectious Disease, TIFR Mumbai, 5-8 January, 2010

• Sunil Kumar, Priya R Debata, Prakash C Supakar (2008) Prediction of 3-dimensional structure of   cathepsin L protein of Rattus norvegicus. J Proteomics Bioinform 1: 307-314.

• Sunil kumar, Binod Bihari Sahu and B P Shaw (2007). Comparative modeling of protein of Plasma membrane H+ ATPase of Sesuvium portulacastrum. Poster presented at Internationa Conference on New Horizons in Biotechnology (NHBT -2007), NIIST, Trivendrum, India from November 26-29, 2007, Poster No.  FAB-059.

• Sunil kumar (2006). A computational Identification of novel Cathepsin L like proteins inDrosophila melanogaster genome. Poster presented at 6^th International conference in Bioinformatics (InCoB 2006) organized by DBT, JNU and IIT Delhi at Hotel Ashoka New Delhi from December 18-20, 2006, Poster No. 64.

• Vikash kumar and Sunil kumar (2004), A Rapid peptide based Alignment -free method to construct Genome trees Independent of sequence annotation. Poster presented at The 15^th International Conference on Genome Informatics. "Posters and Software Demonstrations" (GIW 2004) organized by Japanese Society for Bioinformatics, Yokohama, Japan   December 13-15, Pos. No. 152.

• Sunil kumar, Swati Nayak, Snehasish Parhi and P.C.Supakar (2003), Comparative Protein Structure Modeling. Bioinformatics India. 1(3). 11-16.

 Book Chapter: 

• MHU Turabe Fazil, Sunil Kumar and Durg V singh. In Silico Analysis of Sequence Variation in Cholera Toxin B Subunit and Their Binding with Carbohydrate Ligands. In Current Topics in Biotechnology & Microbiology. Dhingra Hk, Jha PN and Bajpai P (Eds), Lap Lambert Academic publishing AG & Co. KG, Dudweller, Landstr Germany, 2011, Pg 168-177. ISBN 978-3-8443-2975-9
• Sunil Kumar. Solvent Accessibility of proteins. In Bioinformatics and Statistics in Fishries Research, 2006, Vol-III P 42-49 Published by Central Institute of Fishries and Aquaculture, Kausalyanagar, Bhubaneswar.
• Sunil Kumar. Basics in Bioinformatics. In Bioinformatics and Statistics in Fishries Research, 2005, Vol-II P 10-21 Published by Central Institute of Fishries and Aquaculture, Kausalyanagar, Bhubaneswar.

Reviewer of Scientific Journals: 

Interdisciplinary Sciences- Computational Life Sciences (Springer)

Cell Biochemistry and Biophysics (Springer)

Molecular Modeling and application and development of Bioinformatics tools
Application Server Development

• SUN Solaris UNIX, SCO UNIX, Windows 2008 Enterpris, Windows Vista Sys Admin, MAC OS Leopard System Adminand MAC X Server Administration with Clustering Solution.

• Monitoring, troubleshooting, diagnosing and administering the service delivery components which include networks, servers like Proxy, Samba, Firewall, NIS & NFS, Database on MySQL, DHCP, DNS for domain i.e. ils.res.in, Email, Apache and Kickstart working in LINUX platform.

• Handling functionality, operating and failure modes of key networking devices (routers, switches, firewalls, bridges, print server and RAS etc.).

• Creating scripts for simplifying administrative tasks and generating web-oriented statistics using perl, linux bash script, php, mysql, javascript and html.

• Website development and updation of the institute i.e.  www.ils.res.in, Database development,  Web Application development, Antivirus server updation, Graphics designing. .Net Application development. Collection and compilation  of data on medicinal plants and making web enabled database http://database.ils.res.in .

• Development of tools for bioinformatics research purpose using .NET framework technology and Visual Basic in Windows Operating  System and Perl, PHP, HTML, Eclipse, Linux Bash, Javascript and XML in Linux Operating System.

• Molecular Modeling and computerized simulation. Worked with Modeller, SPDVB, Clustalw, Phylip, MEGA, Accelrys Discover Studio etc bioinformatics software available.

Publications:

• In silico modeling and hydrogen peroxide binding study of rice catalase
  P. Nataraj Sekhar, P. B. Kavi Kishor, L. Ananda Reddy, P. Mondal, A. K. Dash, M. Kar, S. Mohanty and S. C. Sabat

Functional Genomics using Statistical and Bioinformatics tools.

Multivariate statistical analysis of synonymous codon usage bias and amino acid usages in prokaryotes and eukaryotes. Identification of evolutionary constraints in codon usage variation. Codon bias and heterologous protein expression, codon optimization, strand asymmetry, mutational bias phylogenetic relationship, SOM (self-organizing map), genomic context analysis, comparative sequence analysis for estimating selective pressures.

Publications:

• Kinshuk Chandra Nayak. Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli. Molecular Biology Reports(Springer)2011,DOI: 10.1007/s11033-011-0768-4
   

• Bijay Misra, Chittaranjan Panda, Haribhakti Seba Das,Kinshuk Chandra Nayak, Shivaram Prasad Singh. STUDY ON AWARENESS ABOUTHEPATITIS B VIRAL INFECTION IN COASTAL EASTERN INDIA.Hepatitis B Annual 2011.6:19-28..(DOI:10.4103/0972-
  9747.76902)
   

• Gaurav Sablok, Kinshuk Chandra Nayak, Franck Vazquez, Tatiana V.Tatarinova. Synonymous codon usage, GC3 and Evolutionary patterns across plastomes of three pooid model species - Emerging grass genome models for monocots.Molecular Biotechnology. 2011.DOI 10.1007/s12033-011-9383-9
   

• Shachindra K. Pandey, Kunwar Digvijay Narayan, Saumya Bandyopadhyay, Kinshuk C. Nayak and Subrata K. Das^*. 2009. Thiosulfate oxidation by Comamonas  sp. S23 isolated from a sulfur spring. Current Microbiology. 2009 58(5):516-21
   

• Sujogya K. Panda, V. Jyoti, Bhaskar Bhadra,  Kinshuk C. Nayak, Sisinthy Shivaji, Fred A. Rainey and Subrata K. Das^*. 2009.  Thiomonas bhubaneswarensis sp. nov., a novel obligately mixotrophic, moderately thermophilic, thiosulfate oxidizing bacterium. International Journal of Systematic and Evolutionary Microiology. 59: 2171-2175
   

• Kinshuk C. Nayak, Mutational bias and Gene expression level shape codon usage in Thermobifidafusca YX.  In Silico Biology(2010), 9 : 1-17.

Peer reviewer in scientific journals
1.Bioinformatics and Biology Insights(Libertas Academica )
2.Biomedical Engineering and Computational Biology(Libertas Academica )
3. Evolutionary Bioinformatics

Posters

• Bijay Misra,  Kinshuk Chandra Nayak, Haribhakti Seba Das, Chittaranjan Panda, Shivaram Prasad Singh (2009). Study on Awareness about Hepatitis B viral infection in coastal Eastern India. Department of Gastroenterology, S.C.B. Medical College, Cuttack, 753007, India, & Institute of Life Sciences, Bhubaneswar-751023, India. Poster selected for presentation at 50^th Annual Conference of ISGCON (2009) (Indian Society of Gastroenterology) organized in Association with INASL and SGEI in December, 2009, Kolkata, 9th to 13th December, 2009, Poster No. L10.  

• Kinshuk Chandra Nayak (2009). Multivariate statistical analysis of codon and amino acid usage variation in Thermobifida fusca YX. Institute of Life Sciences, Bhubaneswar. Poster selected for presentation at International Conference on Frontiers of Interface between Statistics and Sciences during 30^th December 2009 – 2^nd January 2010, Hyderabad.