About
I am a computational biologist, with over a decade of academic research in life sciences. Using computational tools, I have systematically assimilated and analysed data of varied structures. With strong background in statistical and analytical approaches, I am looking to transition to avenues of application.
I am currently pursuing computational transcriptomics with special focus on cell to cell transdifferentiation. My area of expertise can be broadly described as computational biology, through which I have tackled problems in a wide spectrum of areas including protein biophysics, cell biology, evolution and neuroscience.
For my doctoral dissertation, I asked several questions on the interrelationship between the function, dynamics and structure of protein kinases. I also identified the specificity conferring residues in all known protein kinase families, which can potentially render modularity to the kinase superfamily. I defended my doctoral thesis on "Dynamics of protein kinases: Its relationship to functional sites and states" in May 2017.
At the undergraduate level, I was trained as an engineer in Biotechnology. After the 4-year programme, I took to full-time research as a Ph.D. student.
I am originally from Chennai, India. My current inspirations include Elon Musk, Kurzgesagt, Veritasium and Tim Urban.
Research experience
Identification of kinase-specific functional sites
Analysed 107 protein kinase families; Calculated an integrated score for every residue in each family indicative of functional specificity; Validated the identified family-specific sites in the light of relatedness, substrate-recognition and specific protein-protein interactions.
Molecular dynamics simulations of protein kinases
Simulated different functional forms of kinase catalytic domains; Characterised the differences in mobility of speicific structural motifs and scrutinised its correlation with the functional state of the kinase; Investigated the effect of bound ligand and activation loop phosphorylation on the differential mobility between kinase functional states.
Tight coupling of structural fluctuations and functions in protein kinases
Analysed the correspondence of normal mode analysis perceived structural fluctuations to the functional state of kinases; Established the conservation and conservative substitution of structural fluctuations in homologous protein kinases.
Neuronal encoding of image segmentation in primate visual brain
Jan 2011 – Jul 2013
Carried out primate neurophysiology experiments to understand image segmentation and recognition in inferotemporal (IT) cortex; Studied various perceptual phenomena including figure-ground perception, occlusion, perception of holes and ambiguous contours.
Perceived visual blurriness as a function of spatial frequency and eccentricity using human psychophysics
Nov 2010 – Apr 2011
Varied spatial frequency and eccentricity of stimuli with respect to fovea in classical psychophysics study; Used MATLAB to quantitatively assess the psychometric function of blurriness as perceived by human subjects.
Simulation of feedback mechanisms and effects in single neuron firing
Feb 2011 – Apr 2011
Analysed different temporal patterns of feedback signal to single neurons and characterised their effects in establishing homeostatic firing rates; Used MATLAB and NEURON simulation environments.
Prediction of circumvention of mycolic acid biosynthesis pathway in Isoniazid-resistant M.tuberculosis
Nov 2009 – Mar 2010
Used computation to postulate a feasible circumvention pathway in Isoniazid-resistant M.tuberculosis.
Quantification of gene copy numbers in strains of Pichia pastoris using real time PCR
Summer 2009
Used different molecular biology techniques for quantification of an expressed gene product; Quantified lipase B expression in various strains of Pichia pastoris using real time PCR.
Cloning and expression of recombinant lipase B in Pichia pastoris
Summer 2008
Selected strains of Pichia pastoris with high expression of cloned gene product; Cloned and expressed lipase B in fermentable concentrations.
Publications
Conferences
Computer skills
References
The following people may be contacted for reference.
Prof. N. Srinivasan
Molecular Biophysics Unit
Indian Institute of Science
Bangalore, India
Lab webpage, Personal page
iiscsrinivasan@gmail.com
Dr. Alexandre G. de Brevern
Senior Researcher
French Institute for Health and Medical Research (INSERM)
Dynamique des Structures et Interactions des Macromolécules
Biologiques (DSIMB)
University Paris Diderot, Sorbonne Paris Cite (UP7)
National Institute for Blood Transfusion (INTS)
Paris, France
Lab webpage, Personal page
alexandre.debrevern@univ-paris-diderot.fr
Alexandre.De-Brevern@inserm.fr
Prof. R. Sowdhamini
National centre for biological sciences (NCBS)
Bangalore, India
Lab webpage
mini@ncbs.res.in