Lijun Yao

About Lijun Yao

Highly skilled computational biologist with over 8 years of research experience in cancer…

Experience

1. Senior Scientist

   Genentech

   May 2023 — Present

   Baseline prognostic biomarker discovery (project lead) 1) Identified an effector T cell population enriched in treatment-responding patients via single-cell multi-omic profiling of bone marrow samples from a T-cell bispecific (TCB) clinical trial. 2) Translated a domain specific question into an ML-feasible problem. Implemented and deployed a searchable single cell foundation model (SCimilarity) to identify the effector T cell population associated with improved survival and developed a random forest model to provide novel biomarkers generalizable to other clinical applications. 3) Led cross functional collaborations with interdisciplinary teams including clinical scientists and molecular biologists to understand biological questions and design analysis strategies.• Single-cell foundation model and CAR-T target discovery (project lead) 1) Direct experience of model implementation with real world data. Built a foundation model of multiple myeloma (MM) bone marrow cell atlas with over 4.5 million cells from clinical samples. 2) Developed a pipeline to discover dual targets for CAR-T therapies to improve treatment efficacy for heterogeneous MM tumor populations.• Clinical Pharmacodynamics (PD) studies 1) Uncovered key mechanism of action (MoA), mechanisms of resistance (MoR) and PD changes from a Phase 1b TCB trial in breast cancer using single-cell tumor profiling. 2) Supervised and mentored a junior scientist, a summer PhD intern, on characterizing PD changes during B cell development in an MM TCB clinical trial.Skills:Single-cell (scRNA-seq, CITE-seq, TCR-seq, CyTOF)| NGS (WES, WGS, RNA-seq, miRNA-seq)| Variant analysis | Random forest | Foundation models | Neural networks | TensorFlow | PyTorch | Scanpy | Seurat | Python | R | C++| Docker | Snakemake | HPC | Google Cloud | AWS