experience

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.

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)

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.

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.

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.

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.

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.

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.

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.