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Hire Ayush S.

United States

USD 70 /hr

Senio Bioinformatics Analyst

Profile Summary

Senior bioinformatics analyst with experience building and operating scalable analysis pipelines for single-cell and epigenomic sequencing data, including scRNA-seq, scATAC-seq, DNA methylation, and gene expression analyses in cancer and translational research settings. I develop and maintain computational tools that take raw sequencing data to reliable, decision-ready results, with a focus on reproducibility and performance. I am the developer of Tranquillyzer, a deep learning-based framework for annotating and demultiplexing single-cell long-read RNA-seq data, benchmarked against 10x Genomics datasets and used in automated pipelines. I work closely with experimental and computational collaborators at the Van Andel Institute and the University of Michigan, contributing to TCGA epigenomic analyses, methylation tool benchmarking, and method development for single-cell long-read technologies.

Subject Matter Expertise

• ☆ Computational Biology
• ☆ Molecular Biology
• ☆ Chromatin
• ☆ Epigenetics
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ Gene Expression Analysis
• ☆ Genome Sequencing
• ☆ RNA Sequencing
• ☆ ChIP-Seq
• ☆ Data Analysis
• ☆ Algorithm Design
• ☆ Data Processing
• ☆ Data Exploration
• ☆ Cluster Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Data Manipulation
• ☆ Machine Learning
• ☆ Data Cleaning
• ☆ Natural Language Processing
• ☆ Data Architecture
• ☆ Neural Networks
• ☆ Artificial Intelligence
• ☆ Deep Learning
• ☆ Computer Vision
• ☆ Bioinformatics
• ☆ Python
• ☆ R
• ☆ Software Development
• ☆ Cloud Application Development

Services

• Research
• Data & AI
• Product Development

Research Scientific and Technical Research, Systematic Literature Review

Data & AI Predictive Modeling, Statistical Analysis, Algorithm Design-Non ML, Algorithm Design-ML, Data Visualization, Data Mining, Data Cleaning, Data Processing, Data Insights

Product Development Product Evaluation, Quality Assurance & Control (QA/QC), Packaging Design, Prototyping

Work Experience

Bioinformatics Analyst II

Van Andel Institute

July 2023 - Present

Bioinformatics Analyst

Van Andel Research Institute

October 2021 - Present

Bioinformatics Analyst I

Van Andel Institute

February 2019 - July 2023

Education

MS in Bioinformatics

Georgia Institute of Technology

August 2017 - December 2018

MS (Bioinformatics)

Georgia Tech Research Institute

August 2017 - December 2018

Certifications

• Certification details not provided.

Publications

PREPRINT

Ayush Semwal, Jacob Morrison, Ian Beddows, Theron Palmer, Mary F. Majewski, H. Josh Jang, Benjamin K. Johnson, Hui Shen (2025). Tranquillyzer: A Flexible Neural Network Framework for Structural Annotation and Demultiplexing of Long-Read Transcriptomes .