Computational Structural Biology Lab

Department of Biotechnology
Indian Institute of Technology Kharagpur

NITHIN C, Research Scholar

Profile

ACADEMICS

  1. Pursuing PhD in Bioinformatics & Computational Biology at Indian Institute of Technology, Kharagpur (2012-)
  2. Master of Technology in  Biotechnology and Biochemical Engineering from Indian Institute of Technology, Kharagpur (2010-2012).
  3. Bachelor of Technology in Biotechnology and Biochemical Engineering from Sree Chitra Thirunal College of Engineering , University of Kerala (2006-2010).

PUBLICATIONS


Number of citations : 51
h-index             : 04
i10-index           : 02
Source              :  Google Scholar.
  1. Title  : A non‐redundant protein–RNA docking benchmark version 2.0
Authors: Nithin C, Mukherjee S and Bahadur RP
Journal: Proteins: Structure, Function, and Bioinformatics 85(2), 256–267 (2012).
  2. Title  : Targeting non-coding RNAs in Plants with the CRISPR-Cas technology is a challenge yet worth accepting
Authors: Basak J and Nithin C
Journal: Frontiers in Plant Science 6, 1001 (2015).
  3. Title  : Probing binding hot spots at protein-RNA recognition sites
Authors: Barik A+, Nithin C+, Karampudi NBR, Mukherjee S and Bahadur RP (+Joint first authors)
Journal: Nucleic Acids Research doi: 10.1093/nar/gkv876 (2015).  
  4. Title  : Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures
Authors: Nithin C+, Patwa N+, Thomas A+, Bahadur RP and Basak (+Equal contributors)
Journal: BMC Plant Biology 15(140), 1-16 (2015).  
  5. Title  : Molecular architecture of protein-RNA interfaces
Authors: Barik A, Nithin C, Pilla SP, Bahadur RP
Journal: Journal of Biomolecular Structure and Dynamics 6(1), (2015).
  6. Title  : A protein-RNA docking benchmark (I): Non-redundant cases
Authors: Barik A, Nithin C, Manasa P, Bahadur RP
Journal: Proteins: Structure, Function, and Bioinformatics 80(7), 1866-1871 (2012).

CONFERENCES

  1. Conference          : From Functional Genomics to Systems Biology (Nov 2016)
Mode of Presentation: Poster
Title               : A multi-class SVM classifier using single sequence repeat signatures to distinguish between ncRNA types
Authors             : Nithin C, Mukherjee S and Bahadur RP
Venue               : EMBL Heidelberg, Germany
  2. Conference          : 4th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2016) (Apr 2016)
Mode of Presentation: Poster
Title               : A mathematical model for the accurate prediction of protein-RNA binding affinity using structural and physiochemical parameters
Authors             : Nithin C, Mukherjee S and Bahadur RP
Venue               : Science Faculty, University of Granada, Granada
  3. Conference          : Keystone Symposia on Molecular and Cellular Biology - Small RNA Silencing: Little Guides, Big Biology (A6) (Jan 2016)
Mode of Presentation: Abstract
Title               : An effective computational strategy for predicting miRNAs in plants: Discovering new miRNAs and their targets in Phaseolus vulgaris
Authors             : Nithin C, Patwa N, Thomas A, Bahadur RP, Basak J.
Venue               : Keystone Resort, Keystone, Colorado, USA.
  4. Conference          : EMBO/EMBL Symposium: The Non-Coding Genome (Oct 2015)
Mode of Presentation: Poster
Title               : Computational identification of miRNAs and lncRNAs in Cajanus cajan.
Authors             : Nithin C, Thomas A, Basak J, Bahadur RP.
Venue               : EMBL Heidelberg, Germany
  5. Conference          : National Symposium on Biophysics and Golden Jubilee Meeting of Indian Biophysical Society (Feb 2015)
Mode of Presentation: Oral
Title               : Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures
Authors             : Nithin C, Thomas A, Bahadur RP, Basak J.
Venue               : Jamia Millia Islamia, New Delhi, India.
  6. Conference          : Annual Conference of Indian Biophysical Society entitled Molecular Architecture, Dynamics and Assembly in Living Systems (Jan 2014)
Mode of Presentation: Poster
Title               : A structure based binding affinity benchmark for Protein-RNA complexes
Authors             : Nithin C, Bahadur RP
Venue               : Saha Institute of Nuclear Physics, Kolkata, India.
  7. Conference          : International conference on biomolecular forms and functions (Jan 2013)
Mode of Presentation: Poster
Title               : A structure based binding affinity benchmark for Protein-RNA complexes
Authors             : Nithin C, Bahadur RP
Venue               : Indian Institute of Science Bangalore, India
  8. Conference          : 100th Indian Science Congress, Kolkata (Jan 2013)
Mode of Presentation: Poster
Title               : A Protein-RNA Docking Benchmark
Authors             : Barik A, Nithin C, Manasa P, Bahadur RP
Venue               : Kolkata India
  9. Conference          : International Interdisciplinary Science Conference (Nov 2011)
Mode of Presentation: Poster
Title               : A Protein-RNA Docking Benchmark
Authors             : Barik A, Nithin C, Manasa P, Bahadur RP
Venue               : Jamia Millia Islamia, New Delhi.

COMPUTATIONAL SKILLS

  1. Bioinformatics skills : BLAST, CLUSTAL, GROMACS, NACCESS, DALI, BOWTIE, HBPLUS, DSSP, VMD, PYMOL, RASMOL, MODELLER, MIRDEEP, ViennaRNA.

  2. Programming skills    : C++ (C++11/14, STL, BOOST), Python, Bash, MATLAB.
  3. Others                : Microsoft Office, Linux Desktop.

RESEARCH PROJECTS

  1. PhD     :  Interactions of RNA with proteins and their structural analysis
  2. M. Tech : Analysis on conformational changes of antigen-antibody interactions.
  3. B. Tech : Analysis of Catalase enzyme and comparison with peroxidase enzyme

STRENGTHS

Hard working
Determined and patient
Good written and verbal communications skills
Ability to learn new concepts quickly and utilize same in productive manner.

WORKSHOPS

  1. Topic          : Scaling Applications on Many Core Processor Clusters with GPU Accelerators & Co-processors
Organizers     : Dept. of Metallurgical & Materials Engineering, IIT, Kharagpur and Centre for Development of Advanced Computing (C-DAC), Pune
Month and Year : Aug 2015
  2. Topic          : Machine Learning and Complex Networks
Organizers     : Department of Computer Science, IIT Kharagpur
Month and Year : Feb 2015
  3. Topic          : GPU Programming & Applications
Organizers     : CUDA Center of Excellence, IIT Bombay
Month and Year : Feb 2014
  4. Topic          : High Performance Computing
Organizers     : Bose Institute Kolkata
Month and Year : July 2013

FELLOWSHIPS

TRAVEL GRANTS

ACHIEVEMENTS

MEMBERSHIPS

TEACHING ASSISTANCE

Teaching Assistance Classes taken for Under Graduate Students at IIT Kharagpur.