Yulia
Nuzhnenko

Yuliia Nuzhnenko

I am a Bioengineer and Data Specialist combining a strong medical and biological background (MSc) with advanced professional certifications from Harvard University, Johns Hopkins, and the University of Michigan.

I combine this clinical intuition with modern computing to build high-performance bioinformatics pipelines (Nextflow / WDL), interactive web platforms, and smart AI agentic workflows. My core expertise covers RNA-Seq, Single-cell transcriptomics, and Structural Biology (3D Protein visualization).

By bridging deep domain knowledge in life sciences with data-driven workflows, I help research labs and BioTech companies accelerate their data analysis and deliver publication-ready insights without compromising on scientific accuracy.

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Yulia Nuzhnenko

My Capabilities

Transcriptomics (RNA-Seq)

Differential Expression Analysis (DESeq2/limma), Pathway Enrichment (GSEA/KEGG), and custom high-res visualizations (Volcano plots, Heatmaps).

Single-Cell Analysis

Unsupervised clustering, UMAP/t-SNE dimensionality reduction, and cell type annotation using Scanpy and Seurat.

HPC Cloud Pipelines

Scalable cloud-native workflow generation using Nextflow and WDL/Cromwell for AWS and Google Cloud environments.

Clinical Variant Annotation

Parsing VCF files, prioritizing pathogenic somatic/germline variants via Ensembl VEP, and pharmacogenomics reporting.

Antimicrobial Resistance (AMR)

Detecting resistance genes in bacterial genomes using CARD/ResFinder databases and generating epidemiological reports.

AI Scientific Assistant (RAG)

Deploying Large Language Models (LLMs) and RAG architecture for automated PubMed literature mining and systematic reviews.

3D Protein Modeling

Structural bioinformatics and Cheminformatics. Visualizing AlphaFold models and molecular drug-binding pockets.

Metagenomics & Microbiome

Analyzing 16S rRNA taxonomic abundances, calculating Alpha/Beta diversity, and modeling dysbiosis via 3D PCoA.

Featured Scientific Platforms

🤖 Flagship Open-Source Framework

Bioinformatics & Scientific AI Agent Skills

An open-source library of ready-to-use AI Agent Skills, tool specifications, and prompt protocols for single-cell, AlphaFold, VCF annotation, and drug discovery. Compatible with Cursor, Claude Code CLI, and Antigravity.

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Single-Cell Scanpy UMAP Python

Single-Cell RNA-Seq Analysis: Clustering & Biomarker Discovery

Advanced scRNA-seq pipeline on PBMC uncovering cellular heterogeneity and annotating distinct cell populations.

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Data Viz Python R

Publication-Ready Bioinformatics Data Visualization

A comprehensive suite of publication-ready visualizations created for complex biological and clinical datasets.

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Spatial Autocorrelation

Spatial Transcriptomics Atlas

Processing framework for 10x Genomics Visium spatial tissue coordinates. Computes spatial weight matrices and Moran's I spatial autocorrelation per gene.

10x Visium Moran's I
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Structural PAE Evaluator

AlphaFold DB PAE Evaluator

Parses predicted aligned error (PAE) matrices from EMBL-EBI AlphaFold DB API (UniProt P04637). Evaluates structured core domains vs intrinsically disordered regions.

AlphaFold DB PAE Matrix
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Splicing Dynamics Solver

Single-Cell RNA Velocity Engine

Single-cell mRNA splicing dynamics solver based on scVelo pancreas benchmark. Fits linear degradation constant gamma and computes velocity vectors.

scVelo Splicing Kinetics
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Antimicrobial Resistance Profiling

Processed bacterial genomes to detect AMR genes. Delivered comprehensive heatmaps mapping resistance mechanisms to drug classes.

Genomics
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Automated Systematic Reviews

Leveraged LLM/RAG architecture connected to the PubMed API to autonomously extract data and summarize cohorts for a clinical meta-analysis.

NLP / RAG
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Gene Expression Profiling

Processed raw RNA-seq counts to identify DEGs. Delivered publication-ready interactive Volcano plots and clustered heatmaps.

RNA-Seq
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Single-Cell Subpopulation Discovery

Performed clustering on 10X Genomics scRNA-seq data to map immune cell trajectories and discover novel rare cell biomarkers.

scRNA-Seq
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3D Protein Binding Pocket Analysis

Visualized AlphaFold predicted structures to evaluate the impact of clinical missense mutations on drug binding affinity.

AlphaFold DB
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Clinical VCF Variant Annotation

Filtered human Whole Exome Sequencing (WES) VCF files using Ensembl VEP to prioritize pathogenic variants for oncology targeted therapy.

Clinical
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Interactive Genomics Viewer (IGV)

Integrated IGV technology to visually verify BAM/VCF somatic mutations across hg38 human reference assemblies.

IGV.js
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NCBI GEO Mining & Pathway Enrichment

Automated microarray data retrieval and generated GSEA ridge plots mapping significantly enriched KEGG pathways in tumor samples.

GSEA
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Cloud-Native Bioinformatics Pipelines

Designed a scalable Cromwell WDL pipeline for GATK Somatic Variant Calling, ready for deployment on AWS Batch / Google Cloud Life Sciences.

Pipelines
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Metagenomic Dysbiosis Profiling

Calculated Alpha/Beta diversity from 16S microbiome ASV tables, delivering interactive 3D PCoA projections and taxonomy bar charts.

16S rRNA
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About This Project
Delivered Value
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