Kannan Sankar
http://www.public.iastate.edu/~ksankar/
108 Office & Lab Building, Ames, IA 50011, USA
ksankar@iastate.edu | Off: 515-294-5445 | kannantvm31@gmail.com | Cell: 515-708-7774
SUMMARY
PhD candidate in the field of Bioinformatics and Computational biology seeking
entry level positions in the biotech/pharma industry starting summer 2016 | 5 years
of research experience in structural bioinformatics including industrial internship experience in the Antibody Engineering deptartment at Genentech.
Interests: Computational structural biology | Protein-protein interaction networks |
Protein structure and dynamics | Protein-protein docking | Antibody Engineering
EDUCATION
Iowa State University, Ames, IA
Summer 2016
Ph.D, Bioinformatics & Computational Biology (GPA: 4.00/4.00)
Birla Institute of Technology and Science (BITS), Pilani, India
2011
Integrated Master of Science (Hons.), Biological Sciences (GPA: 9.29/10.00)
Bachelor of Engineering (Hons.), Computer Science (Dual Major)
WORK
EXPERIENCE
Genentech | Computational Biology Intern
June-Aug 2015
Antibody Engineering Department, Genentech Inc., South San Francisco Campus, CA
Advisor: Dr. Qing Zhang
• Developed an in silico method for prediction of amino acid liabilities on therapeutic monoclonal antibodies using machine learning (random forests). [manuscript
in preparation]
• Computationally predicted epitopes on antigens for candidate monoclonal antibodies using a combination of homology modeling & protein-protein docking
(using Schrodinger Biologics suite)
USDA-ARS | Research Intern @ MaizeGDB
May-Aug 2014
Crop Genome Informatics Laboratory, Ames, IA
Advisor: Dr. Taner Z. Sen
• Developed machine learning based methods for the computational prediction
of a protein-protein interaction network (PPIN) in Maize using interacting homologous genes (interologs) in other genomes such as Arabidopsis & yeast.
NCBS | Bioinformatics Research Intern
Jul 2010 - Jun 2011
National Centre for Biological Sciences (NCBS), Bangalore, India
Advisor: Dr. R. Sowdhamini (all works published - Please refer to Publications)
• Homology modeled olfactory receptors (ORs) from selected model organisms
using MODELLER to investigate dimerization and deposited them in the form
a database of olfactory receptors (DOR): http://caps.ncbs.res.in/DOR/.
• Developed Perl based software (using PerlTk & BioPerl) called TM-MOTIF for
the interactive visualization of transmembrane regions and motifs in G-Protein
Coupled Receptor (GPCR) proteins.
• Developed an algorithm called DockScore (in Perl) for scoring docking predictions of protein-protein complexes; now available as a server: http://caps.
ncbs.res.in/dockscore/
• Designed a sequence based scoring scheme using functional templates & cysteine
residue positions to analyze conservation of ligand binding sites in proteins.
CURRENT
RESEARCH
Graduate Research Assistant
Aug 2011 - present
Advisors: Prof. Robert L. Jernigan & Prof. Drena L. Dobbs,Iowa State University
• Combining knowledge-based potential functions and coarse-grained model based
entropy functions to construct free energy landscapes for conformational transitions in proteins and predict effect of mutations [published in J. Chem. Phys:
Link]
• Characterization of amino acid contact changes during conformational changes
in proteins to improve predictive models of protein dynamics (elastic network
models)
• Molecular dynamics analysis of diverse proteins including:
- conformational switching in cadherins
- mechanisms of ligand transport in multi-drug transporter proteins.
SOFTWARE
SKILLS
Biomolecular Structure analysis: Molecular visualization (PyMOL), molecular
dynamics (VMD, NAMD), energy calculations (SYBYL-Tripos), small-molecule
docking (GLIDE, AutoDock), homology modeling with specialized experience in
antibody modeling (MOE, Schrodinger) and membrane protein (GPCR) modeling
(MODELLER, I-TASSER) and antibody-antigen docking (PIPER/ClusPro)
Sequence Analysis: Analysis of Next-Gen Sequencing (NGS) data: Genome
Assembly (de novo - Velvet, Ray) & Transcriptome Assembly, Assignment to reference genomes (GSNAP), Differential Expression Analysis (HTSeq), RNA-Seq (Trinity
package), SNP analysis
Biological network analysis: Measuring network properties, motifs and aligning
networks using CytoScape and igraph package in R
Programming: Significant experience in working in a UNIX/LINUX environment
Strong skills in C/C++, Perl (including BioPerl + PerlTk) and MATLAB
Database management and Wed-development using MySQL and phpMyAdmin
Machine learning: Supervised (classification, association rule mining) and Unsupervised learning methods (clustering, outlier detection, etc) with R & Weka
Statistics: Significant experience in coding in R, handling high dimensional data
with multivariate methods: principal component analysis (PCA), multi-dimernsional
scaling, clustering, multivariate regression, etc.
LABORATORY
SKILLS
Genomics: Both sequencng by Sanger’s technique & Next-Gen Sequencing (Illumina)
Genetics & Molecular Biology: Fully proficient in techniques including genomic
DNA & plasmid extraction, PCR, recombinant DNA techniques (gene cloning, transformation, etc.) agarose gel electrophoresis, SDS-PAGE and Western blotting
Biochemistry: Significant experience in biochemical methods such as estimation of
protein & DNA conc., protein purification (FPLC) & autoradiography
Microbiology: Significant experience in microbial culture (E. coli & Lactobacillus),
streak plating, antibiotic assays (disc-plate method), & phage titrations
AWARDS &
FELLOWSHIPS
James Cornette Research Fellowship in Bioinformatics & Computational Biology, Iowa State University (2014)
Fellowship of The Office of Biotechnology, Iowa State University (2011-12)
Kishore Vaigyanik Protsahan Yojna (KVPY) Fellowship, a prestigious science fellowship by Dept. of Science & technology, Govt. of India (2007-11)
National Talent Search (NTS) Scholarship Award, Govt of India (2004-11)
St. Thomas Scholar Award, St. Thomas Residential School (2004-06)
CONFERENCE
TALKS
Intellignent Systems for Molecular Biology (ISMB) & 3DSig, 2014, Boston, MA
Sankar, K., Walia, R. R., Mann, C. M., Jernigan, R. L., Honavar V. G., Dobbs, D.
(2014) Analysis of Conformational Changes in RNA-binding Proteins (Talk + Poster)
International Symposium on Bioinformatics Research & Applications (ISBRA) 2012
Sankar, K., Zimmermann, M. T., & Jernigan, R. L. (2012) Investigations on Elastic
Network Models of Coarse-Grained Membrane Proteins (Talk)
PUBLICATIONS Sankar, K., Liu, J., Wang Y. & Jernigan, R. L. (2015) Distributions of experimental
protein structures on coarse-grained free Energy landscapes, J. Chem. Phys 143 (24):
243153. Link
Sankar, K., Walia R. R., Mann C. M., Jernigan, R. L., Honavar V. G., Dobbs D.
(2014) An analysis of conformational changes upon RNA-protein binding, Proc. 5th
ACM Conf. on Bioinf., Comp. Biol. and Health Inf. 592-593. Link
Katebi, Ataur R., Sankar, K., Jia, K. & Jernigan, R. L. (2015) The Use of Experimental Structures to Model Protein Dynamics. Molecular Modeling of Proteins,
Meth. Mol. Biol. 1215. Springer New York, 213-236. Link
Malhotra, S., Sankar, K., & Sowdhamini, R. (2014). Structural Interface Parameters
Are Discriminatory in Recognizing Near-Native Poses of Protein-Protein interactions.
PLoS ONE 9(2): e80255. Link
Nagarathnam, B., Karpe, S. D., Harini, K., Sankar, K., Iftekhar, M., Rajesh, D.,
Giji, S., Archunan, G., Balakrishnan, V., Gromiha, M. M., Nemoto, W., Fukui,
K., Sowdhamini, R. (2014) DOR - A Database of Olfactory Receptors - integrated
repository for sequence and secondary structural information of olfactory receptors
in selected eukaryotic genomes, Bioinformatics & Biology Insights 8: 147-158. Link
Manoharan, M., Sankar, K., Offmann, B., & Sowdhamini, R. (2013). Association of
putative Members to Family of Mosquito Odorant Binding proteins: scoring scheme
Using Fuzzy Functional Templates and Cys Residue positions. Bioinformatics and
Biology Insights 7: 231-251. Link
Harini, K., Sankar, K., Nemoto, W., Fukui, K., & Sowdhamini, R. (2012). Residue
conservation and dimer-interface analysis of olfactory receptor molecular models.
Journal of Molecular Biochemistry 1(3): 161-170. Link
Nagarathnam, B., Sankar, K., Dharnidharka, V., Balakrishnan, V., Archunan, G.,
& Sowdhamini, R. (2011). TM-MOTIF: an alignment viewer to annotate predicted
transmembrane helices and conserved motifs in aligned set of sequences. Bioinformation 7(5): 214-221. Link
Nagarathnam, B., Sankar, K., Dharnidharka, V., Balakrishnan, V., Archunan, G.,
& Sowdhamini, R. (2011). Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, the fly and the worm GPCR clusters.
Bioinformation 7(1): 15-20. Link
TEACHING
EXPERIENCE
Teaching Assistant, Fund. of Genome Informatics (BCB 567)
Fall 2015
BCB, Iowa State University
• Work closely with instructor to create, post and grade assignments
• Take review sessions before exams as well as selected lecture classes on topics
such as brute-force search algorithms, clustering algorithms and divide and
conquer approaches to programming.
Teaching Assistant, Computational & Functional Genomics & Systems
Biology (BCB 570)
Spring 2015
BCB, Iowa State University
• Teach lab sessions on network analysis using Cytoscape & ’graph’ package in R
• Work closely with instructor to create, post and grade assignments
• Take review sessions before exams as well as selected lecture classes
Teaching Assistant, Survey of Biochemistry (BBMB 301)
Fall 2014
BBMB dept., Iowa State University
• Prepare and deliver review sessions on basic biochemical metabolic pathways
• Mentor students during office hours & help them prepare for exams
PROFESSIONAL Professional fluency in English
SKILLS
Excellent written and verbal communication skills
Significant team-work and leadership experience
Other languages: Native Fluency in Tamil & Malayalam
EXTRACURRICULAR
ACTIVITIES
Projects Coordinator, Bioinformatics and Computational Biology Graduate Student
Organization: Guided several students on multiple projects
(2015)
Volunteer Judge, Science & Technology Fair of Iowa
(2015)
Volunteer Judge, Protein Modeling Competition, Ames High School
(2015)
Coordinator, 10th Human Frontier Science Program (HFSP) Awardees Meeting (2010)
Joint Coordinator, Biological Association, BITS Pilani
(2009)
School Prefect, St. Thomas Residential School
(2000-04)
REFERENCES
Available upon request.