Qingzhou Zhang

AI-Driven Systems Biology & Predictive Modelling: Machine learning, network-based modelling, and interpretable AI approaches for multi-omic integration, biological system simulation, and hypothesis generation. Single-Cell & Spatial Multi-Omics: Lineage reconstruction, cell-state dynamics, and transcriptomic integration (scRNA-seq, CITE-seq, scATAC-seq).

Epigenomics & Chromatin Biology: Chromatin accessibility, histone modification profiling, and transcription factor network inference.

Proteomics & Interactomics: AP-MS/MS confidence scoring, protein complex reconstruction, and cellular system dynamics.

Research Software Engineering: Designing reproducible workflow architectures for high-throughput biological data.

Postdoctoral Fellow at University of New Brunswick, Canada (Gagarinova Lab) (2024-04 – Present)

• Lead the computational modeling strategy for a high-throughput bacterial systems biology project, integrating multi-omic datasets (genomic, transcriptomic, and proteomic) to infer gene-regulatory networks.
• Programmed ComplexMap, an interactive visual framework to discover functional protein assemblies and cluster modules.
• Engineered automated quality control (QC) and network visualization pipelines to support collaborative manuscript preparation and hypothesis generation.

Collaborative Bioinformatics Consultant at Independent Academic & Clinical Collaborations (2021-10 – Present)

• Provide end-to-end computational support for principal investigators, transforming raw genomic and proteomic sequence data into validated figures, statistical reports, and raw data deposits for peer-reviewed manuscripts.
• Standardize custom pipeline scripts into robust, reproducible pipelines to enable consistent analytical replication across multi-institutional consortia.

Postdoctoral Fellow at Ottawa Hospital Research Institute, Canada (Brand Lab) (2021-10 – 2024-03)

• Programmed single-cell multi-omic pipelines to analyze haematopoiesis differentiation lineages, integrating surface protein markers (CITE-seq) with transcriptomic profiles (scRNA-seq).
• Developed and open-sourced Epi-Flow, a Conda and Docker pipeline for reproducible analysis of ATAC-seq, ChIP-seq, and CUT&RUN assays, currently deployed across multi-lab collaborations.
• Developed ShinyCITExpresso, an interactive R/Shiny visualization application that allows wet-lab collaborators to independently query expression patterns, accelerating target discovery and validation cycles.
• Developed and published the open-source Python library SingleCellFeatureProfiler to automate statistical feature profiling for single-cell gene expression datasets.

Translational Genomics & Pipeline Architecture at Independent Research Consultant (2013-09 – 2015-12)

• Provided remote bioinformatics support, custom pipeline scripting, and statistical analysis for academic research teams investigating mammalian model organisms.
• Designed pipelines for processing targeted panel sequencing, bulk RNA-seq, and array-based genomics.

Head of Bioinformatics, Co-Founder at 3D Medicines (3DMed) (2011-01 – 2013-09)

• Co-founded translational genomics startup, remotely designing computational workflows during MSc studies before serving in full-time leadership.
• Established high throughput functional genomics screening pipelines to translate academic genomic models into clinical cancer diagnostic workflows.

Bioinformatics Engineer at Abmart Shanghai (2007-11 – 2008-10)

• Developed database schemas, internal metadata tracking systems, and user interfaces to support high-throughput antibody production and research pipelines.

PhD in Biochemistry (Bioinformatics) – University of Regina (2016-01 – 2021-10)

MSc in Bioinformatics – University of Manchester (2009-09 – 2011-12)

BSc in Biotechnology – Nanjing Agricultural University (2004-09 – 2008-06)