Apr 2025 – Aug 2025 · 4 mos

Jun 2023 – Apr 2025 · 1 yr 10 mos

Jan 2023 – Jun 2023 · 5 mos

Jul 2020 – Jan 2023 · 2 yrs 6 mos

Mar 2018 – Jun 2020 · 2 yrs 3 mos

Mar 2017 – Mar 2018 · 1 yr · Bengaluru, Karnataka, India

• Data Science (Planning)

May 2016 – Mar 2017 · 10 mos · Bengaluru, Karnataka, India

• Planning research

Dec 2015 – May 2016 · 5 mos · Bengaluru, Karnataka, India

• My primary responsibilities include identification of novel data science usecases in life sciences research and health care and drive solutions for the same. This includes implementation of data science and traditional bioinformatics approaches towards translational medicine for cancer and neurological diseases, biomarker discovery and genomic scale structure-function modeling. Lead the data science team in developing solutions for the complete spectrum of drug discovery life cycle from target discovery, lead identification and validation, QSAR-modeling and analyzing clinical data.Play leading role in defining and implementing DSP Vision Milestone 2017. Additionally responsible for exploring new algorithms for information retrieval and text mining.

Apr 2015 – Dec 2015 · 8 mos · Greater Boston

• My key responsibilities were:
• Involved in T&M project with global pharmaceutical company as consultant
• Design and implementation of enhanced data analytics with transMART
• Lead functional SME for RFP regarding implementation of chemioinformatics and computational biology processes on Cloud (AWS) based high-computing computing cluster. Complete design of functional workflow, architectural workflow, effort estimation, roster determination and pricing
• Lead solutioning for RFI regarding universal data provisioning and analytics engine encompassing all of drug-discovery life cycle. Solution included data ingestion, machine learning based data curation, Hadoop/MapReduce based data engineering and usecase specific analytics.
• Lead solutioning and implemention for a cloud based genomics platform with Galaxy for a large biotech company

Apr 2015 – Dec 2015 · 8 mos · Greater Boston

• My key responsibilities included support, maintenance and development of research IT and analytics solutions including eNotebook, SDMS and data warehousing solutions for seamless integration of research data, including development and maintenance of integrated knowledge network. Consulting with Chemistry research division regarding possible use of scaffold search algorithms towards computational therapeutic peptide design and pairing with varied statistical knowledge-based potentials and simulations. Lead project to calculate and benchmark 3D physico-chemical properties of therapeutic peptides using implicit solvent methods like Poisson-Boltzman and Generalized Born towards the goal of predicting cell permeability of designed peptide. Additional role of consulting with Biology research division for genomic pathway analysis

May 2013 – Apr 2015 · 1 yr 11 mos · Atlanta Metropolitan Area

• The primary aim of my project is to understand the role of macromolecular crowding and hydrodynamic interactions in coordinated movement of macromolecules during intricate cell processes such as macromolecular diffusion, walking of molecular motor across microfilaments and other similar molecular motors. The primary hypothesis is that the movement of macromolecular particles inside a cell is not only affected by the forces it experiences but also indirectly affected by forces acting on other molecules within the cellular environment. To this end, we are using brownian dynamics simulation methods to simulate the cellular processes using coarse-grained models. The effect of hydrodynamics is calculated at the RPY level of approximation.

Dec 2011 – May 2013 · 1 yr 5 mos · Kansas City

• Negative staining and cryo-electron microscopy based structure analysis of anthrax toxin protective antigen to monitor prepore to pore formation and lethal factor translocation across membrane bilayer. We used single particle analysis and 3D reconstrcuction techniques to elucidate 3D electron density maps from the images collected under vitrified ice.
• Worked on feasibility studies of using lipid nanodiscs as model membrane systems to study protein insertion.
• Implementation of normal mode based flexible fitting methods to fit high resolution crystal structure of protective antigen in prepore state onto low-resolution cryo-electron volumes of protective antigen pore. Finally the full length structure of the PA pore was modeled and Molecular dynamics simulations (implicit and explicit solvent) conducted to understand mechanism of ion transport and subsequently protein translocation across the beta-barrel pore of the Protective antigen.

Jan 2009 – Dec 2011 · 2 yrs 11 mos

• Developed MM-align, a structure alignment program capable of comparing protein complex structures as extension of the monomer structure alignment program TM-align.
• In collaboration with Leonardo Garma, a study was conducted to cluster all know protein complex structures currently known using MM-align and a new scoring function to measure protein complex structure similarity, rTM-score. Following clustering, a maximum probability distribution approach was used to estimate the number of unique quaternary folds possible to be present in nature.
• Development of BSpred, a neural network based algorithm capable of predicting protein-protein interface residues using only sequence information.
• Developed COTH, a protein complex structure prediction program using threading or fold recognition. The complex query sequences are threading across a protein complex structure library to find the best template guided by ab initio interface prediction from BSpred and other sequence and structural features.The templates are ranked based on Z-score.
• Development of TACOS for prediction of protein complex structure from sequence alone.TACOS uses the COTH templates, fragments and re-assembles them using a course-grained (C-alpha and Side Chain center only) grid based system and Replica exchange Monte-carlo simulations.
• Modeling of alternatively spliced protein variants in collaboration with Ambrish Roy, Rajasree Menon and Gilbert Omenn.
• Genomic scale protein structure prediction of the RIFIN family of proteins in the Plasmodium falciparum genome in collaboration with the Dr. Elisabetta Pizzi group from the Istituto Superiore di Sanità, Rome, Italy.
• Using I-TASSER models to predict nucleic acid binding interfaces along with Dr. Fabian Glaser and Dr. Yael Mandel-Gutfreund of the Israel Institute of Technology.
• Development/Maintenance of the following web-servers; MM-align, COTH, BSpred, MUSTER, LOMETS, SVMSEQ, ANGLOR and TACOS.

Aug 2007 – Dec 2011 · 4 yrs 4 mos

• Developed MM-align, a structure alignment program capable of comparing protein complex structures as extension of the monomer structure alignment program TM-align.
• In collaboration with Leonardo Garma, a study was conducted to cluster all know protein complex structures currently known using MM-align and a new scoring function to measure protein complex structure similarity, rTM-score. Following clustering, a maximum probability distribution approach was used to estimate the number of unique quaternary folds possible to be present in nature.
• Development of BSpred, a neural network based algorithm capable of predicting protein-protein interface residues using only sequence information.
• Developed COTH, a protein complex structure prediction program using threading or fold recognition. The complex query sequences are threading across a protein complex structure library to find the best template guided by ab initio interface prediction from BSpred and other sequence and structural features.The templates are ranked based on Z-score.
• Development of TACOS for prediction of protein complex structure from sequence alone.TACOS uses the COTH templates, fragments and re-assembles them using a course-grained (C-alpha and Side Chain center only) grid based system and Replica exchange Monte-carlo simulations.
• Modeling of alternatively spliced protein variants in collaboration with Ambrish Roy, Rajasree Menon and Gilbert Omenn.
• Genomic scale protein structure prediction of the RIFIN family of proteins in the Plasmodium falciparum genome in collaboration with the Dr. Elisabetta Pizzi group from the Istituto Superiore di Sanità, Italy.
• Using I-TASSER models to predict nucleic acid binding interfaces along with Dr. Fabian Glaser and Dr. Yael Mandel-Gutfreund of the Israel Institute of Technology.
• Development/Maintenance of the following web-servers; MM-align, COTH, BSpred, MUSTER, LOMETS, SVMSEQ, ANGLOR and TACOS.
• Teaching experience: 4 semesters as Graduate Teaching Assistant.

Jun 2006 – Jun 2007 · 1 yr

• I worked as a software engineer at Infosys in the mainframe domain. I worked with two clients, AETNA and Nortwestern Mutual. At AETNA i worked on the PERS system with an emphasis on DLD of ongoing maintenance projects. At NM I worked on the upgraradtion of the PL1 complier upgradation of the NM mainframe systems