About Me

Hi! My name is Yunrui Lu. I’m a Bioengineering PhD student at Caltech. I’m interested in developing ML and statistical methods, using spatial transcriptomics, single cell and multiomics to explore tumor heterogeneity and cell cell communication in tumor immune microenvironment.

Previously, I worked at Cedars Sinai and Dartmouth Hitchcock Medical Center as research associate. I graduated from Dartmouth College in 2022 with Master degree in Quantitative Biomedical Science, and from Xiamen University, China in 2021 with Bachelor degrees in German Language and Literature and Mathematical Economics.

I’m always happy to connect and collaborate with researchers who are interested in computational biology, deep learning, spatial transcriptomics, single cell and digital pathology. I have mentored master students and undergrads. Feel free to reach out and would love to chat about potential opportunities.

Selected Publications

• Integration of Elemental Imaging and Spatial Transcriptomic Profiling for Proof-of-Concept Metals-Based Pathway Analysis of Colon Tumor Microenvironment
  Yunrui Lu, Serin Han, Aruesha Srivastava, Neha Shaik, Matthew Chan, Alos Diallo, Naina Kumar, Nishita Paruchuri, Hrishikesh Deosthali, Vismay Ravikumar, Kevin Cornell, Elijah Stommel, Tracy Punshon, Brian Jackson, Fred Kolling IV, Linda Vahdat, Louis Vaickus, Jonathan Marotti, Sunita Ho, Joshua Levy
  Bioinformatics Advances, 2025

• An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology
  Michael Y Fatemi*, Yunrui Lu*, Alos B Diallo, Gokul Srinivasan, Zarif L Azher, Brock C Christensen, Lucas A Salas, Gregory J Tsongalis, Scott M Palisoul, Laurent Perreard, Fred W Kolling IV, Louis J Vaickus, Joshua J Levy
  Briefings in Bioinformatics, 2024

• Feasibility of Inferring Spatial Transcriptomics from Single-Cell Histological Patterns for Studying Colon Cancer Tumor Heterogeneity
  Michael Y Fatemi*, Yunrui Lu*, Cyril Sharma, Eric Feng, Zarif L Azher, Alos B Diallo, Gokul Srinivasan, Grace M Rosner, Kelli B Pointer, Brock C Christensen, Lucas A Salas, Gregory J Tsongalis, Scott M Palisoul, Laurent Perreard, Fred W Kolling IV, Louis J Vaickus, Joshua J Levy
  BIOSTEC 2025

• HiTAIC: hierarchical tumor artificial intelligence classifier traces tissue of origin and tumor type in primary and metastasized tumors using DNA methylation
  Ze Zhang, Yunrui Lu, Soroush Vosoughi, Joshua J Levy, Brock C Christensen, Lucas A Salas
  NAR Cancer, 2023

• Development of an interactive web dashboard to facilitate the reexamination of pathology reports for instances of underbilling of CPT codes
  Jack Greenburg, Yunrui Lu, Shuyang Lu, Uhuru Kamau, Robert Hamilton, Jason Pettus, Sarah Preum, Louis Vaickus, Joshua Levy
  Journal of Pathology Informatics, 2023

(*equal contribution)

Out of lab

I spend a lot of time playing basketball, swim, randomly work out, travel, eat a lot, drink some and sleep a lot.