Yucheng Zhang | Senior Bioinformatics Engineer

About Me

I am a self-motivated researcher and Senior Bioinformatics Engineer with over 2 years of experience as a senior computational scientist at HPC centers. I specialize in deploying and benchmarking scientific applications on supercomputers and possess expert knowledge in container technology (Docker, Singularity/Apptainer) and Open OnDemand application development.

With a background in Plant Pathology and ongoing studies in Computer Science, I bridge the gap between biological research and high-performance computing.

Key Competencies

HPC & DevOps

Slurm Ansible Puppet Unix/Linux Parallel Computing Kubernetes (Intermediate)

Programming

Python R C/C++ (Intermediate) CUDA MPI/OpenMP Git

Bioinformatics

Docker/Singularity Nextflow Snakemake Genome Assembly RNAseq/ChIPseq Open OnDemand

Work Experience

Senior Bioinformatics Engineer

Tufts University, TTS Research Technology | Jul 2025 – Present

Develop and maintain bioinformatics tools, pipelines, and scientific software to support research workflows.
Administer and optimize the Tufts HPC cluster and Open OnDemand research computing environment.
Provide user support, consultations, and training workshops on HPC, Nextflow, containers, and related technologies.

Bioinformatics Engineer

Tufts University, TTS Research Technology | Oct 2023 – Jun 2025

Deployed ~200 containerized bioinformatics applications, including NVIDIA NGC containers (PyTorch, TensorFlow), as HPC environment modules.
Launched the Bioinformatics Apps category on Tufts Open OnDemand and deployed 30+ interactive applications.
Managed the Tufts Galaxy bioinformatics server and key bioinformatics licenses (IPA, Geneious Prime).
Provided consultations and delivered workshops on workflows, Nextflow, and container technologies.

Senior Life Science Scientist / Computational Scientist

Purdue University, Rosen Center for Advanced Computing | Aug 2021 – Oct 2023

Built 95% of scientific applications on Purdue RCAC’s supercomputer Negishi.
Developed the containerized bioinformatics ecosystem and documentation websites for HPC applications.
Provided training workshops including "Container 101" and "Running Bioinformatics Analysis in HPC".

Bioinformatician

Indiana University, Cancer Bioinformatics Core | Sept 2020 – Aug 2021

Analyzed ~30 projects involving RNAseq, ChIPseq, ATACseq, and scRNAseq.
Provided collaborative support to researchers from IU Medical School, Purdue, and Notre Dame.
Co-authored more than 10 high-impact papers.

Post-Doctoral Researcher

University of Florida, Dept. of Plant Pathology | Aug 2016 – Aug 2020

Used comparative genomics and CRISPR-Cas9 to identify genes involved in pathogenesis.
Investigated virulence factors in Clavibacter nebraskensis using transposon mutagenesis.

Education

M.S. Computer Science	Tufts University, USA	Expected 2026
Post-Baccalaureate Cert. Computer Science	Tufts University, USA	2025
Ph.D. Plant Pathology	University of Florida, USA	2016
M.S. & B.S. Viticulture & Enology	Northwest A&F University, China	2012 / 2009

Publications

I have co-authored numerous high-impact papers in journals such as Nature (Under review), Stem Cell Research & Therapy, and Molecular Plant Pathology.

View Full List on Google Scholar

Selected Recent Work:

Bhutra, P., Zhang, Y., et al. (2023). "Scientific applications and their documentation on Purdue clusters." PEARC '23.
Zhang, Y., et al. (2022). "Containerized Bioinformatics Ecosystem for HPC." HUST22.
Liu, J., ..., Zhang, Y., et al. (2023) "SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels..." Stem Cell Research & Therapy.