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The Chiu Lab is an interdisciplinary team affiliated with the UPMC Hillman Cancer Center and Department of Medicine at the University of Pittsburgh. Our mission is to bridge cutting-edge computational algorithms to unmet needs in precision medicine. Read more about the PI.
Research Highlights
Mapping gene-drug interactions using large language models (GPT-4o and Gemini)
Mapping gene-drug interactions using large language models (GPT-4o and Gemini)
GeneRxGPT is an automated large language model (LLM) pipeline that integrates real-time PubMed literature to infer drug–gene relationships in cancer with improved accuracy and reduced hallucination. By systematically combining literature retrieval with advanced LLM reasoning, GeneRxGPT enables rapid, evidence-grounded discovery of therapeutic targets and drug repurposing opportunities across diverse cancer types. Read the article.
Highlight at AACR 2024: GPT-4 and gene-drug interactions
Highlight at AACR 2024: GPT-4 and gene-drug interactions
Michael's presentation at the American Association for Cancer Research (AACR) Annual Meeting 2024 has been selected as a highlight by the NCI Division of Cancer Biology (DCB; @NCICancerBio). In this study, we prototyped an efficient and accurate GPT-4 tool for analyzing gene-drug interactions through scientific literature in collaboration. Watch the DCB's interview with Michael and read the abstract.
shinyDeepDR is a user-friendly tool designed for predicting anti-cancer drug sensitivity using deep learning. With the tool, users can effortlessly perform an in silico screening of 265 approved and investigational compounds by uploading mutation and/or gene expression data from a cancer sample. Read the article.
DepLink is a web server to identify genetic and pharmacologic perturbations that induce similar effects on cell viability or molecular changes. It integrates heterogeneous datasets of genome-wide CRISPR screens, high-throughput drug screens, and gene expression signatures of perturbations. Read the article.
News
4/2024. GeneRxGPT has been published in Cancer Research Communications! This study was selected for simultaneous publication alongside our presentation at the AACR Annual Meeting 2025. Check out the paper and tool. Big applause for Ying-Ju and Li-Ju!
4/2025. Tyler is giving a talk on our digital pathology study of hepatocellular carcinoma at the American Society for Investigative Pathology (ASIP) Annual Meeting 2025 @ Portland, OR (abstract).
4/2025. We have three poster presentations at the American Association for Cancer Research (AACR) Annual Meeting 2025 @ Chicago, IL! Check out Chien-Hung's study on pathway-informed cancer dependency prediction (abstract), Yibing's context-aware gene set interpretation using large language models (abstract), and Ying-Ju's work on mapping drug-gene interactions with large language models (abstract).
3/2025. A new paper is now online in Analytical Chemistry! In collaboration with Dr. Yu-Chih Chen, we have developed a hybrid empirical and in silico drug screening method to inhibit polyploid giant cancer cells, which are major drivers of breast cancer metastasis. Kudos to Chien-Hung!
11/2024. Dr. Chiu received the Rising Star Award from the IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) 2024 @ Houston, TX.
11/2024. Dr. Chiu serves as an Organizing Committee Member and the Publication Co-chair at the IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) 2024 @ Houston, TX.
10/2024. Dr. Chiu is invited to give talks in the GenAI/GPT and Computational AI/Multi-Omic Sessions at the International Conference on Intelligent Biology and Medicine Program (ICIBM) 2024 @ Houston, TX. Ying-Ju and Yanhao are also presenting posters on our GPT studies!
9/2024. Dr. Chiu receives a 5-year R35 Maximizing Investigators' Research Award (MIRA) from the NIH/NIGMS. Kudos to all lab members!! Read the news and NIH Reporter.
7/2024. Li-Ju will be presenting our GPT-4 framework for drug-gene relationship inference at ISMB 2024.
5/2024. Dr. Chiu is invited to give a talk and join the panel discussion at the Special Session: Computational Approaches for Spatial Omics at the Great Lakes Bioinformatics (GLBIO) Conference 2024.
1/2024. shinyDeepDR has been published in Patterns! Check out the paper and tool. Huge shoutout to Li-Ju, Michael N, and Michael K!
More News
4/2024. We will be presenting at AACR 2024 @ San Diego, CA. Come to visit our posters #4921 and #5412.
4/2024. Dr. Chiu is invited to give a talk at the GI Research Grand Rounds at Pitt.
3/2024. Dr. Chiu is invited to present a talk at the Taiwan Oncology Society Annual Meeting at Kaohsiung, Taiwan.
2/2024. The preprint of reguloGPT is now available online. This method, developed in collaboration with Dr. Yufei Huang, leverages GPT and prompt engineering to construct knowledge graphs for gene regulation.
2/2024. Dr. Chiu is invited to give talks at the Seminar in Precision Medicine at UTHealth Houston, and T32 CATER Seminar (Cellular Approaches to Tissue Engineering and Regeneration) and Computational & Systems Biology Seminar at Pitt.
1/2024. Dr. Chiu is invited to give talks at the Human Genetics Seminar at Pitt.
12/2023. Our new tool, GeneRxGPT, is available for open testing! GeneRxGPT is a GPT-powered R Shiny app for cancer gene-drug relationship inference.
12/2023. Our new tool, shinyDeepDEP, is available for open testing! shinyDeepDEP is a user-friendly web tool designed to prioritize genetic dependencies in cancer using our DeepDEP deep learning model.
10/2023. Dr. Chiu serves as an Organizing Committee Member and the Educational Activity Co-chair at the IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) 2023 @ Pittsburgh.
9/2023. Dr. Chiu receives an Administrative Supplement award from the NIH Office of the Director to develop computational frameworks that enhance AI-readiness of multi-omics data!
9/2023. Dr. Chiu receives an R03 award from the NIH Office of the Director to collaborate with Dr. Yinan Gong (MPI) to study therapeutic strategies by modulating immune surveillance adaptation!
9/2023. Dr. Chiu has been nominated by the University of Pittsburgh for the Searle Scholars Program, which recognizes exceptional young faculty in the biomedical sciences and chemistry.
7/2023. Dr. Chiu receives a two-year New Investigator Research Grant from the Leukemia Research Foundation to develop intelligent therapeutic strategies for acute myeloid leukemia.
7/2023. We will be presenting at ISMB/ECCB 2023 @ Lyon, France on our newest web server that predicts anti-cancer drug responses.
6/2023. DepLink has now been published in Bioinformatics Advances! Check out the paper and tool. Kudos to Tapsya and Li-Ju!
5/2023. We will be presenting at GLBIO 2023 @ Montreal, Canada. Dr. Chiu is giving a talk about our newest web tool DepLink, which systematically links genetic vulnerabilities to drug responses using high-throughput screening data.
4/2023. Dr. Chiu receives the Pittsburgh Liver Research Center (PLRC) Pilot & Feasibility Grant to team up with Dr. Paul Monga to study and predict drug responses of hepatocellular carcinoma.
4/2023. We will be presenting at AACR 2023 @ Orlando, FL. Come to check out our posters #2094 and #3175.
2/2023. We will be presenting at San Antonio Pediatric Cancer Symposium @ San Antonio, TX.
1/2023. Dr. Chiu receives a pilot award from the UPMC Hillman Cancer Center Developmental Pilot Program with Dr. Yu-Chih Chen (MPI) to implement an intelligent drug screening device for single cancer cells.
12/2022. We will be presenting at AACR-JCA Joint Conference 2022 @ Maui, HI.
11/2022. Dr. Chiu is invited to present in the "BHI Technical and Educational Lecture" organized by the IEEE EMBS Community on Biomedical & Health Informatics (BHI).
9/2022. Dr. Chiu is selected as the "2022 Hillman Early Career Fellow for Innovative Cancer Research" by the Hillman Foundation.
8/2022. We will be presenting at ICIBM 2022 @ Philadelphia, PA. Dr. Chiu is co-chairing the session “Artificial Intelligence on Big Data: Promise for Early-stage Trainees.”
7/2022. We will be presenting at ISMB 2022 @ Madison, WI.
7/2022. Grand Opening of our lab at Pitt!
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Our lab is located at The Assembly – where history, innovation, technology, and medicine meet!
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