experience

Research Experience

January 2021 - Present

Postdoctoral Scholar

Molecular and Computational Biology and Bridge Institute, Dept. of Biological SciencesUniversity of Southern California, Los Angeles, USA
Advisors: Prof. Kate White (USC) and Prof. Andrej Sali (UCSF)

Cyber Infrastructure Platform for Reproducible Data-centric Modeling of the Cell

      • Developing a comprehensive cyber infrastructure platform for modeling the cell.

      • Establishing an effective socio-technical ecosystem that will allow scientists to experiment, collaborate, and disseminate reproducible experimental data and cell models.

August 2015December 2020

Ph.D. in Computational Biology and Bioinformatics

Quantitative & Computational Biology and Bridge Institute, Dept. of Biological SciencesUniversity of Southern California, Los Angeles, USA
Advisors: Prof. Frank Alber (UCLA) and Prof. Raymond C. Stevens (USC)

Pattern mining in Cryo-electron tomography

      • Mining structure, abundance, location and orientation of recurring patterns in cryo-electron tomograms which potentially correspond to macromolecular complexes.

      • Mapping detected patterns in cryo-electron tomograms to their protein compositions (macromolecular identity) by integrating Mass Spectrometry data.

Organelle distribution using Soft X-Ray tomography

      • Analyzing spatiotemporal distribution of insulin vesicles and mitochondria in INS-1E cells under various stimuli and at different time points.

      • Understanding changes in molecular densities of various organelles under different conditions.

      • Using Neural Networks to segment organelle masks

Whole-cell modeling (Spatiotemporal multi-scale model of human pancreatic β-cell)

June 2019December 2020

Visiting Graduate Researcher

Institute for Quantitative & Computational BiosciencesUniversity of California, Los Angeles, USA
Advisors: Prof. Frank Alber

Template-free Visual Proteomics

Detecting structure, abundance, location and protein composition determination of macromolecular complexes in cryo-electron tomography.

Genomic subcompartment prediction

Using graph embedding, autoencoders and neural networks to predict active and inactive genomic subcompartments from structural features of genome structures.

Jan 2019 – Present

Scientific Advisor

World In A CellWorld Building Media Lab, University of Southern California, Los Angeles, USA

World in a Cell: an artscience project

  • It is a transmedia project that uses Virtual Reality and Augmented Reality to approach the way we share and depict biological data about the human body.

  • Within mixed-reality, immersive and interactive environments, supported by a Unity Game Engine, the viewer can observe relative scale, relative geo-location, relative activity, and relative function of each constituent of pancreatic beta cell, through time and fully immersive space.

Jan 2015 - April 2015

B.Tech. in Computer Science and Eng.

Indian Institute of Technology (IIT) Roorkee, India
Advisor: Dr. Srihari Sriganesh (The University of Queensland, Australia)

Inferring synthetic lethal interactions from the mutual exclusivity of genetic events in cancer

      • Developed an approach to directly infer synthetic lethal gene interactions using mutual exclusive nature of genes alteration.

      • Across four cancer types (breast, prostate, ovarian and uterine cancer), we identified 718 genes that are frequently amplified/upregulated in cancers and are likely to be synthetic lethal with six key DNA-Damage Response genes in these cancers.

August 2014 - Dec 2014

B.Tech. in Computer Science and Eng.

Indian Institute of Technology (IIT) Roorkee, India
Advisors: Dr. Srihari Sriganesh (The University of Queensland, Australia) and Dr. Dhaval Patel (IIT Roorkee)

Undergraduate Thesis Research work

Network-based integration of genomic and gene expression datasets for breast cancer classification

      • We intend to integrate genomic copy number and gene expression datasets from TCGA to subtype breast tumors into distinct molecular and clinical subtypes.

      • The goal of the project was to link differences in molecular patterns to clinical outcomes and possibly identify novel biomarkers or drug targets in these subtypes.

May 2014 - July 2014

Research Intern

Albert-Ludwigs-University of Freiburg, Germany
Advisor: Dr. Virginie Lecaudey

Developing tools to study morphogenesis in zebrafish posterior lateral line primordium

      • Focused on CRISPR/Cas9 mediated integration of GAL4 gene in place of eGFP which is under claudinB promoter.

      • The purpose of replacing eGFP with GAL4 is to express the gene of interest under UAS promoter specifically in the lateral line primordium.

Dec 2013

Research Intern

Indian Institute of Technology (IIT) Bombay, India
Advisor: Dr. Ranjith Padinhateeri

Literature Survey on Application of Entropy in various fields

      • The focus was to understand the concept of Entropy and its application in various fields.

      • Studied various papers and understood the application of entropy in deciphering Indus script, genomic nucleosome positioning, etc.

May 2013 - July 2013

Research Intern

Tata Institute of Fundamental Research, Mumbai
Advisor: Dr. Sreelaja Nair

Analysis of the mitotic spindle apparatus during early zebrafish development

      • Focused to study the cell biological differences in the spindle apparatus between haploid, diploid and tetraploid zebrafish embryos during early developmental stages.

      • Studying spindle characteristics of diploid zebrafish enabled us to develop a basal line of reference to compare for the haploid and tetraploid data set.