Prathiksha Ramesh

Elucidata

11.2024 - Current

Processed and harmonized 1000+ bulk and single-cell RNA-seq samples using Polly an ingested in the Atlas for clients including Insmed, MolPartners, Trex, Alnylam, CZI, and Owkin, ensuring high-quality multi-omics data integration and 99% data integrity.
Ran and troubleshot Nextflow pipelines, improving workflow efficiency by 30%, and reproduced scRNA-seq datasets from publications, contributing to data standardization and reproducibility.
Contributed to the development of in-house single-cell foundational models, leveraging curated datasets to enhance scalability and downstream research applications.
Managed metadata analysis, data ingestion, and quality control (FastQC, MultiQC), resolving 50+ JIRA tickets and ensuring seamless bioinformatics pipeline execution.
Recognized for accuracy in client deliverables, earning appreciation from management, and acknowledged for metadata analysis and deck preparation for CZI, enhancing data reporting and decision-making.

University of Pennsylvania

06.2024 - 09.2024

Focused on RNA sequencing (RNA-Seq) analysis, gaining hands-on experience with large-scale transcriptomics datasets and bioinformatics tools.
Developed expertise in bulk RNA-seq and single-cell RNA-seq workflows, enhancing data preprocessing, analysis, and visualization.
Applied R and Python for RNA-seq data manipulation, differential expression analysis, and functional genomics integration.
Performed quality control assessments using FastQC and MultiQC, ensuring data accuracy and integrity for downstream applications.

RWTH Aachen University

09.2023 - 03.2024

Designed and executed a DAAD-funded research project to address missing data in gene expression datasets using machine learning (ML) and deep learning (DL) techniques.
Developed and optimized data imputation models, improving the reliability and completeness of transcriptomic analyses.
Conducted an extensive literature review, identifying key gaps in existing imputation methods for gene expression studies.
Collaborated with computational biologists, machine learning experts, and data scientists, enhancing interdisciplinary research outcomes.

Indian Institute of Technology Gandhinagar

07.2022 - 08.2023

Provided academic support to 50+ students, mentoring them in Journal Writing, Energy & Matter Laboratory, and World of Engineering courses.
Guided students in research methodology, data analysis, and technical writing, strengthening their critical thinking and scientific communication skills.
Led hands-on practical projects, helping students apply theoretical concepts to real-world applications.
Assisted in designing and assessing coursework, ensuring effective learning outcomes.

Summary