L PONOOP PRASAD PATRO

Project 1: Sequence patterns and HMM profiles to predict proteome wide zinc finger motifs (ZnFs)

• Developed and co-created ZnF-Prot (https://project.iith.ac.in/znprot/), a cutting-edge web server for accurately predicting ZnF domains in protein/proteome sequences across diverse organisms.
• Designed and implemented an innovative workflow, combining Pfam HMM profile search and ZnF motif pattern search using Python scripts, resulting in highly precise predictions.
• Contributed to the development of the web server using PHP, HTML, and CSS, and ensured the quality of the research by meticulously editing and proofreading the manuscript published in "Pattern Recognition" journal.

Project 2: Structural diversity among Acinetobacter baumannii K-antigens and its implication in the in silico serotyping

• Enhanced the functionality of ABSD (https://project.iith.ac.in/ABSD/), a web server housing a comprehensive repository of 3D-structural models for all 64 K-antigens of A. baumannii, enabling accurate serotype prediction.
• Designed a robust workflow incorporating BLAST package and BASH scripts to facilitate efficient serotype predictions by comparing query sequences with a reference dataset.
• Maintained the web server's functionality using PHP, HTML, and CSS, and actively contributed to the writing and editing process of the manuscript accepted for publication in "Frontiers in Microbiology".

Project 3: CoVe-tracker: An interactive database that provides the evolution of SARS-CoV-2 (PANGO) lineages (lineage) and the concomitant variants and mutations

• Co-developed CoVe-tracker (https://project.iith.ac.in/cove-tracker/), an interactive web-GUI platform that provides real-time updates on SARS-CoV-2 proteome variants, their distribution, and evolutionary patterns.
• Designed and implemented a comprehensive workflow involving translation and analysis of over 5.7 million SARS-CoV-2 genome sequences from the GISAID web server, enabling accurate variant and lineage classifications.
• Built the protein-wise mutation distribution module of the server and utilized JSMOL scripts to visually represent recurring mutations on viral protein structures.
• Published the research findings in the esteemed "Journal of Proteome Research".

• Completed a distinguished doctoral thesis titled "Devising Methodologies for Sequence-based Characterization of Pathogens of Global Concern and Development of Web Tools for Biomacromolecular Modeling and Validation." The thesis encompassed four independent projects focusing on bacterial genome/proteome analyses and computational tool/workflow development.
• Pioneered the development of the serotype prediction and virulence prediction modules of the K-PAM (https://iith.ac.in/K-PAM/) web server, facilitating deposition of modeled three-dimensional K-antigen structure and strain identification for Klebsiella species.
• Played a crucial role in analyzing SARS-CoV-2 genome sequences since the onset of the pandemic, gaining valuable insights into the evolution and dissemination of variants and elucidating the significance of evolutionarily favorable mutation combinations in the emergence of dominant variants.
• Innovated the 3D-NuS (https://www.iith.ac.in/3dnus/) web server for automated modeling and visualization of non-canonical 3-dimensional nucleic acid structures, such as G-quadruplexes, triplexes, and Z-DNA, while also contributing to the development of STRIDER (https://iith.ac.in/strider/), a web tool for identifying steric hindrance within and between biomolecules.
• Acquired expertise in scientific literature survey, standardized protocols, and scripting languages including BASH, Python, R, FORTRAN, PHP, HTML, and CSS for data analysis, presentation, and web-GUI development.

• Assisted the principal investigator in preparing and updating course materials for advanced courses such as "Structural Bioinformatics," "Programming for Biomacromolecular Analyses," and "Biomolecular NMR" taught to post-graduate students.
• Delivered an engaging presentation as a speaker in a Department of Biotechnology mini-webinar on "Evolutionary Dynamics of SARS-CoV-2" held on October 22, 2022.
• Played a vital role in organizing two highly successful national-level workshops titled "Essential Programming for Life Scientists" (July 13-15, 2017) and "Multiscale Modeling of Biomacromolecules" (March 19, 2016) conducted by our laboratory.

CGPA: 8.56

• Received Junior Research Fellowship (JRF) offered by Ministry of Education, India for the period 2016-2018
• Received Senior Research Fellowship (SRF) offered by Ministry of Education, India for the period 2018-2021

CGPA:9.05

• Received the Post Graduate Scholarship Scheme (PGSSS) offered by the All India Council for Technical Education (AICTE)

CGPA: 8.36

• Received the Common Application for Financial Assistance Scheme (CAFAS) offered by the Government of Odisha, India