(a) Genome-wide identification of P1BS in the promoter regions of genes in rice [Underway]
The objectives include: identification of Phosphate Starvation Response-1-like binding (P1BS) motif in the promoter region of whole genome sequence in rice through in silico analysis, and validation of identified genes in rice by expression analysis under various abiotic stresses (drought, salinity, heat, cold).
After all, scientists never truly rest; if we were to take a break, who would continue the pursuit of discovery?
-
-
(a) Genome Workbench Development [Underway]
Sequence to structure and dynamics to function was an established adage in protein sciences. Our results from the last two research projects demonstrate that this is true for nucleic acids as well.
Building on this, we are working on the development of a reproducible, user-friendly platform for the identification/prediction of various genic/regulatory elements using structure/energy landscapes within these regions.
(b) Biophysical fingerprinting (profiling) of eukaryotic genome elements using physicochemical properties of DNA [Completed]
Working with the hypothesis that genomic DNA sequences must convey their functional roles through their biophysical properties, we characterized eight genomic sites, including Coding Sequences, Promoters, Gene boundaries, Exon-Intron boundaries, Start/Stop Codons, ~4.6 million in number, to establish a novel structural and energetic framework for genome annotation.(c) Mentored a final year Master’s (Bioinformatics) student for a two-month summer internship (June 2024 – July 2024), with large-scale genomic data extraction and analysis.
-
(a) Development of an Intron-Exon Boundary Junction Prediction software using Physicochemical DNA features (Backbone, Base Pair (BP)-Axis, Intra BP, Inter BP, Energetics) [Completed]
Conducted the benchmarking step in two phases: our physicochemical prediction framework vs widely used DNA-level genome predictors, and our framework vs the two best-performing tools from the previous phase on non-coding datasets that didn't go into training our models.
Helped build the user-interactive command line utility at GitHub.
(b) Mentored a final year M.Tech in Molecular Engineering, Chemical Synthesis, and Analysis student.
Assisted with the project reports and presentations submitted as “Major Project: Part 1 and 2” progress in mid-semester evaluation and final evaluation. -
(a) Development of an Intron-Exon Boundary Junction Prediction software using Physicochemical DNA features (Backbone, Base Pair (BP)-Axis, Intra BP, Inter BP, Energetics) [Completed]
Compared the performance of various machine learning/deep learning (ML/DL) models over the human genome train/test/evaluation datasets.
Incorporated the genomes of mice and worms to increase the scope of the study once an exhaustive prediction pipeline was established.
Formulated the benchmarking step of the study by including widely used DNA-level genome prediction tools for a thorough performance evaluation on blind datasets.
(b) Mentored a final year M.Tech in Molecular Engineering, Chemical Synthesis, and Analysis student.
Supported with daily laboratory tasks such as Bash scripting, data handling, and data analysis. -
(a) Development of an Intron-Exon Boundary Junction Prediction software using Physicochemical DNA features (Backbone, Base Pair (BP)-Axis, Intra BP, Inter BP, Energetics) [Completed]
Performed a thorough literature review for the project.
Executed feature selection, computation, and integration into a reproducible genome annotation pipeline.
Conducted initial machine learning models training and testing.
Presented the preliminary results as part of my master's thesis defense.