Biomedical Data Research Lab
at Indiana University School of Medicine
Research Interests
Understanding the mathematical representations of biological processes, relations, and functions in omics data and developing underlying analysis principles and mathematical theories.
Developing new systems biology models and AI frameworks to maximize the understanding of biological mechanisms in omics and multi-omics data.
Representation learning of high dimensional data, with a focus on linear/non-linear low rank and local low-rank representation of matrix and high order tensor.
Understanding biochemical variations in the microenvironment cancer and inflammatory diseases.
Developing explainable graphical/network models for biomedical data and transfer learning.
Study single cell and spatial multi-omics data to infer sample-wise/spatial dependent activity of transcriptional regulation, metabolism, and signaling pathways.
Biomarker prediction and development of personal wearable sensors and other smart health-related AI and biotechnologies.
Natural language processing-based mining of biological literature data.
Nutrient and food recommendations.
News at a glance
Jia Wang accepted the summer internship offer from Genentech. Congratulations, Jia! 03/2024
Xiao Wang accepted the summer internship offer from Genentech. Congratulations, Xiao! 02/2024
Haiqi Zhu accepted the summer internship offer from Genentech. Congratulations, Haiqi! 02/2024
Chi Zhang has been appointed as the Associate Director of AI Research at the Center for Computational Biology and Bioinformatics, IUSM. We will set long-term infrastructure and strategy for AI usage and AI-empowered method development in biomedical sciences. We will also initiate AI-centric pilot funding opportunities for promoting data generation and AI methodology research. 08/2023
Chi Zhang received NIH NIGMS Maximizing Investigators’ Research Award (MIRA, R35) for Early Stage Investigators. We will focus on the development of AI-empowered systems biology and new learning paradigms for data-driven biomedical research. We appreciate the support from NIH. 08/2023
Congratulation on Yifan Sun, Ph.D. accepting his offer as Research Scientist at Takeda Pharmaceuticals! 08/2023
Sha Cao received one more year contract from FDA to develop statistical and AI-empowered methods to predict mutation trends of infectious diseases. 07/2023
Congratulations on Kaman So, Msc, accepting her offer as IS Programmer at Brigham and Women's Hospital! 07/2023
The paper "Generalized Matrix Local Low Rank Representation by Random Projection and Submatrix Propagation" was accepted by KDD 2023 (Research Track). Congratulations, Pengtao and all other authors! 05/2023
The paper "FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data" was accepted and published by Nucleic Acids Research 2023 Webserver special issue. Congratulations, Zixuan, Haiqi, Pengtao and all other authors! 05/2023
The paper "Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer" was accepted by Frontier Oncology Special Issue "Rising Stars in Cancer Genetics 2022". This paper was co-first authored by four high school trainees, Grace Yang, Shaoyang Huang, Kevin Hu and Alex Lu. Congratulations to all the authors! 05/2023
Tingbo Guo graduated from the Department of Mathematics, IUPUI with a Master’s degree in Statistics. Congratulations, Tingbo! 05/2023
Kaman So graduated from the Department of Biostatistics, IUSM with a Master’s degree in Biostatistics. Congratulations, Kaman! 05/2023
NCI R01 entitled "Metabolic flux analysis and PDX models to understand therapeutic vulnerabilities following inhibition of Ref-1 redox signaling in pancreatic cancer" is funded! We will contribute the whole Aim 1: Computational Prediction of Synthetic Lethality Associated with Ref-1 inhibition. 04/2023
Chi Zhang serves as the co-director of Biostatistics and Bioinformatics in PRSC. 04/2023
The paper "Pipeline for Characterizing Alternative Mechanisms (PCAM) based on bi-clustering to study colorectal cancer heterogeneity" was accepted by Computational and Structural Biotechnology Journal. Congratulations to all authors! 03/2023
Haiqi Zhu attended Cold Spring Harbor Conference Network Biology 2023 and presented the poster “An AI-empowered and data-driven systems biological approach to studying complex biological networks”. 03/2023
Tingbo Guo has been selected for the Outstanding Master’s in Applied Statistics Award by IUPUI. Congrats, Tingbo. 03/2023
U01 Reprogramming to PDAC Stroma by Targeting Coagulation in the Tumor Microenvironment under PSRC is funded! 01/2023
BDRL Computational Biology Tools
Try our latest method to estimate metabolic flux or perform deconvolution via the Webservers
A webserver to estimate cell-/sample-wise metabolic fluxome by using scRNA-seq or general transcriptomics data
Predict the cell type PROPORTION and data specific cell type MARKER GENES
A semi-supervised approach for a robust identification of cell types and deconvolution of mouse transcriptomics data
More methods available in R/Python
Funding Source
