News
News and Events
2024
Chi was invited by the NIH Innovation Lab to participate in a five-day close door discussions with other experts to explore innovative use of quantum computing in real world biomedical research problems. https://apply.knowinnovation.com/quantum-biomed/ 10/2024
Sha has been awarded the NIGMS R35 grant, to develop systems biology framework for dissecting the crosstalk of different cellular components in disease tissue microenvironment. 10/24
Sha has been awarded the American Cancer Society Research Scholar Grant, which will support her research focusing on breast and pancreatic cancer. 10/24
Congratulations to Chi on being awarded an R01 that uses AI-empowered wearable multimodal sensors for noninvasive monitoring of Parkinson’s disease. 09/2024
Sha presented a poster entitled “Computational methods to study metabolic variations in PDAC” at the AACR Pancreatic Cancer Meeting 2024 in Boston. 09/2024.
Sha gave a talk on “Integrating multi-omics data for sparse latent space detection” at the ICSA China in Wuhan, as well as the ISGTM conference in Xi’An. 06/2024.
The BDRL group officially launched at OHSU on July 1, 2024. We’re thrilled to embark on this next chapter in such a vibrant and supportive research environment.
A collaborator work with Dr. Xinna Zhang’s group on “Inhibition of Glutamate-to-Glutathione Flux Promotes Tumor Antigen Presentation in Colorectal Cancer Cells” was accepted by Advanced Science. 09/2024.
We announced that BDRL will move to Oregon Health and Science University (OHSU) in the fall semester of 2024. Chi Zhang and Sha Cao will be Associate Professors of Biomedical Engineering at OHSU. We will also join the Brenden-Colson Center for Pancreatic Care (BCC) group and the Center for Biomedical Data Science at OHSU Knight Cancer Institute. Multiple positions at the level of postdocs and data scientist will be opened soon. 05/2024
Jia Wang received a 10k Training Grant entitled "Computational Modeling of MHC-I antigen presentation flow in cancer cells" from IUSCCC. We appreciate the support from IUSCCC. 05/2024
Collaborative work "A highly reproducible and efficient method for retinal organoid differentiation from human pluripotent stem cells" has been accepted by PNAS, Congratulations! 05/2024
Changlin's paper "Ambiguities in neural-network-based hyperedge prediction" has been published by the Journal of Applied and Computational Topology, Congratulations! 05/2024
Xiao's paper "Bias-aware Boolean Matrix Factorization Using Disentangled Representation Learning" has been accepted by UAI 2024, Congratulations! 05/2024
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 received a Susan G Komen Foundation Research Grant with Dr. Xin Lu from Notre Dame University. This project will focus on studying metabolic heterogeneity in the TME of breast cancer. We appreciate the support from the Susan G Komen Foundation! 01/2024
Chi Zhang received a supplement award from the American Cancer Society for the RSG entitled "Computational modeling of stromal-immune cell interactions in triple-negative breast cancer". We appreciate the support from the American Cancer Society! 12/2023
A newsletter website has been developed by BDRL members. This website will be weekly updated and focus on providing recent news in AI development, funding opportunities, and key breakthroughs for biomedical researchers. 11/2023
Collaborative work "Neutrophils resist ferroptosis and promote breast cancer metastasis through aconitate decarboxylase" with Dr. Xin Lu from Norte Dame University has been published on Cell Metabolism, Congratulations! 10/2023
We announced the AI development plan at CCBB, IUSM. Chi Zhang received an 250k internal support to fund 5-10 pilot projects to boost AI-empowered biomedical research at IUSM. 10/2023
2023
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
Congratulation on Kaman So accepting her offer as IS Programmer at Brigham and Women's Hospital! 07/2023
Tingbo Guo accepted the offer from the Department of Biostatistics, IUSM, and will continue her study in BDRL. 05/2023
Xin Lu accepted the offer from the Department of Computer Science at Indiana University Bloomington and will join the lab in Aug 2023. Welcome! 05/2023
An Zheng accepted the offer from the IBMG program IUSM and will join the lab in Aug 2023. Welcome! 05/2023
Pragathi Arunkumar will join BDRL as a summer intern student. Welcome! 05/2023
Chegu Milind Lakshmi will join BDRL as a summer intern student from SEED/STEM project. Welcome! 05/2023
Singh Aayush Kartik will join BDRL as a summer intern student from SEED/STEM project. Welcome! 05/2023
Allen Qian will join BDRL as a summer intern student from SEED/STEM project. Welcome! 05/2023
Zain Sohail will conitnue his study at BDRL as a summer intern student. 05/2023
Kevin Hu will conitnue his study at BDRL as a summer intern student. 05/2023
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
Our high school trainee, Hanming Ye, was admitted by the MIT RSI summer school (90 admissions over the world). Congratulations, Hanming! 04/2023
Our high school trainee, Sandra Yang, was admitted by the MIT RSI summer school (90 admissions over the world). Congratulations, Sandra! 04/2023
Our high school trainee, Noah Meroueh, was admitted by the Engineering School of Purdue University. Congratulations, Noah! 04/2023
Our high school trainee, Shaoyang Huang received admissions from the University of Pittsburg, Purdue University, and multiple schools. Congratulations, Shaoyang! 04/2023
Our high school trainee Grace Yang received admissions from Harvard, MIT, and multiple schools. Congratulations, Grace! 04/2023
Haiqi Zhu accepted the summer internship offer from Bristol Myers Squibb. Congratulations, Haiqi! 04/2023
Pengtao Dang accepted the summer internship offer from Genentech. Congratulations, Pengtao! 04/2023
Xinyu Zhou accepted the internship offer from Boehringer Ingelheim. Congratulations, Xinyu! 04/2023
BDRL attended AACR 2023 annual meeting at Orlando. Six posters have been presented by the students:
Computational modeling of metabolic variations in tumor microenvironment
Targeting DNA Methylation in T cells to Improve the Efficacy of Immunotherapy
Computational modeling of stromal-immune cell interactions in triple-negative breast cancer.
A data-driven and AI-empowered systems biology model of MHC class I antigen presentation pathway.
Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer.
Detecting spatially clustered transcriptional regulatory relationships using sparse and spatially smooth regression
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
Haiqi Zhu and Chi Zhang were invited to attend Breast Cancer Hackathon Challenge by Susan G. Komen for the Cure at UTSW in Dallas, TX, Haiqi was mentored and received the Advocates’ Choice Award, Congrats, Haiqi. 03/2023
Chi Zhang led the TEAM 2B for soluving "Metabolic Heterogeneity in Breast Cancer" in Susan G. Komen for the Cure's Hackathon. 03/2023
Haiqi Zhu attended TEAM 2A (led by Dr. Xin Lu) for soluving "Metabolic Heterogeneity in Breast Cancer" in Susan G. Komen for the Cure's Hackathon. 03/2023
U01 Reprogramming to PDAC Stroma by Targeting Coagulation in the Tumor Microenvironment under PSRC is funded! 01/2023
Haiqi Zhu attended Cancer Immunotherapy Conference (CICON22) held by CRI-ENCI-AACR in NYC and presented the poster "Computational modeling of metabolic variations in tumor microenvironment". 10/2022
We co-hosted the CCBB 2023 retreat at Bradford Woods - Indiana University Outdoor Center. Haiqi Zhu and Pengtao Dang presented the poster "Data-Driven and AI-empowered systems biology". 10/2022
The paper "Physioxia-induced downregulation of Tet2 in hematopoietic stem cells contributes to enhanced self-renewal" was accepted by Blood. This body of work is dedicated to Hal E. Broxmeyer for his contributions to the field of hematology and his mentorship, leadership, friendship, and love for scientific discoveries. 09/2022
The paper "Combined heterozygosity of FLT3 ITD, TET2, and DNMT3A results in aggressive leukemia" was accepted by JCI Insight. Congratulations to all authors! 09/2022
Yuhui Wei joined the lab. Yuhui is a first year PhD student from the Department of BioHealth Informatics, IUPUI. Welcome! 08/2022
Xia Wang joined the lab. Xiao is a first year PhD student from the Department of Computer Science Indiana University Bloomington. Welcome! 08/2022
Jia Wang joined the lab. Jia is a first year PhD student from the Department of Computer Science Indiana University Bloomington. Welcome! 08/2022
Chi Zhang co-edited the special issue “Artificial Intelligence-Assisted Multi-Omics Applications in Solid Tumor” on Frontiers in Genetics, 08/2022
The paper "Bias Aware Probabilistic Boolean Matrix Factorization" was accepted by the 38th Conference on Uncertainty in Artificial Intelligence (UAI) 2022. Congratulations to Changlin, Sha and all other authors! 03/2022
Chi Zhang co-edited the special issue “Application of Next-generation Sequencing for Cancer Drug Repositioning” on Frontiers in Oncology, 06/2022
The paper "Provable Second-Order Riemannian Gauss-Newton Method for Low-Rank Tensor Estimation" was accepted by ICCASP2022, 05/2022.
Zain Sohail joined BDRL as a summer intern student from the future scientist project. Welcome! 05/2022
Roohi Sanka joined BDRL as a summer intern student from SEED/STEM project. Welcome! 05/2022
Alex Qu jointed BDRL as a summer intern student from SEED/STEM project. Welcome! 05/2022
The paper "Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer" was accepted by Genomics, Proteomics, Bioinformatics. Congratulations to Wennan and all other authors! 04/2022
Our high school trainee, Hanming Ye, was admitted by the ROSE summer school (120 admissions over the world). Congratulations, Hanming! 05/2022
Paveethran Swaminathan joined the lab as a part-time RA. Pavee is a second-year master's student from the Department of Computer Science, Indiana University Bloomington. Welcome! 04/2022
The paper "PLUS: Predicting cancer metastasis potential based on positive and unlabeled learning" was accepted by PLOS Computational Biology. Congratulations to Xiaoyu, Sha and all other authors! 03/2022
2022
Welcome, Yuhui Wei to joining our lab from the Bioinformatics PhD program at Indiana University, Indianapolis! 08/2022
Incoming Ph.D. students Jia Wang and Xiao Wang will join the lab in Fall 2022. Welcome to our big family! 07/2022
Our paper 'Bias Aware Probabilistic Boolean Matrix Facortization' has been accepted by UAI 2022. Congratulations to Changlin and Pengtao! 05/2022
Dr. Chi Zhang received funding from the American Cancer Society Research Scholar Award. Congratulations to Dr. Zhang! 04/15/2022
Wennan Chang, Changlin Wan, Norah Alghamdi successfully passed the final dissertation defense for Ph.D. degree. Congratulations to Dr. Chang, Dr. Wan, and Dr. Alghamdi! 04/2022
Wennan Chang accepted the offer at Kite Pharma Inc as a research scientist. 10/2021
Changlin Wan accepted the offer at Genentech as an AI scientist. 03/2022
Xiaoyu Lu accepted the offer at Bristol Myers Squibb as a bioinformatics scientist. 03/2022
Xinyu Zhou received a summer intern offer at AbbVie. 02/2022
Dr. Sha Cao has been granted an NSF CISE IIS CAREER AWARD. Congratulation to Dr. Cao! 03/12/2022
Dr. Chi Zhang has received tenure and promotion. Dr. Zhang will become a tenured Associate Professor from July 2022. Congratulation to Dr. Zhang! 03/01/2022
FluxEstimator has been lunched. scFLUX server 01/01/2022
2021
Dr. Chi Zhang and Dr. Sha Cao serve as PC members of RECOMB 2022. 09/10/2021
SRMR has been accepted by ICDM 2021 as a regular paper. (Acceptance Rate 9.9%, first-time submission of the work). Congratulation to Wennan, Pengtao and Changlin! 08/31/2021
scFEA has been highlighted by RECOMB 2021 [video], ICIBM 2021, and 2021 ICSA Applied Statistics Symposium. 08/2021
Our paper ‘Ref-1 redox activity alters cancer cell metabolism in pancreatic cancer: Exploiting this novel finding as a potential target ' has been accepted by Journal of Experimental & Clinical Cancer Research. Congratulations to the authors. 07/2021
Our paper ‘A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data’ has been accepted by Genome Research. Congratulations to Wennan and Norah! [paper] [github] 07/01/2021
Summer intern students Grace Yang, Nonah Meroueh, Shaoyang Huang, Kevin Hu, and Jonathan Yang from 2021 Indianapolis STEM program and Tendo Mubuuke from 2021 IUSM future scientist program joined BDRL. Welcome! 06/2021
BDRL organized the “Introduction of R/Python programming and bioinformatics” workshop for high school students from the STEM, SEED, Future Scientist (FSP), and IU Simon Comprehensive Cancer Center Summer Research (SRP) programs. BDRL members Pengtao Dang, Changlin Wan, Wennan Chang, Chi Zhang and Sha Cao gave 14 lectures in this workshop. [video link] [github] 06/2021
Chi Zhang serves as a Guest Editor of the special issue “‘Application of Next-generation Sequencing for Cancer Drug Repositioning” on Frontiers In Oncology. 04/2021
Chi Zhang co-organizes the special issue “Biomedical Informatics" on Medicine in Omics with Dr. Ying Xu. 04/2021
Chi Zhang’s NSF Career Award “NSF 2047631: Mining biological functions from single-cell multi-omics data” was funded by NSF DBI IIBR. Thanks for the support by NSF! 04/12/2021
Wennan Chang received a data scientist summer intern position at Kite Pharma. Changlin Wan received a summer intern offer at Memorial Sloan Kettering Cancer Center. Xiaoyu Lu received a Bioinformatics summer intern offer at Bristol-Myers Squibb and Spatial Transcriptomics fall Co-ops offer at Merck. Congratulations to Wennan, Changlin and Xiaoyu! 03/01/2021
Chi Zhang serves as a guest editor for the “Application of Next-generation Sequencing for Cancer Drug Repositioning” special issue on Frontiers in Oncology. 02/01/2021
Chi Zhang serves as a PC member of KDD. 02/01/2021
Changlin serves as a PC member of ICML 2021 IJCAI 2021 UAI 2021 NeurIPS 2021. 01/15/02021
The clinical trial of “Cabozantinib for neurofibromatosis type 1–related plexiform neurofibromas: a phase 2 trial” we have analyzed was published on Nature Medicine. 01/13/2021
2020
Wennan has past the Preliminary Examination, congratulations to Wennan. 11/20/2020
Changlin’s paper has been accepted by IEEE BIBM 2020. Congratulations to the authors. 10/30/2020
“Modulation of Immune Infiltration of Ovarian Cancer Tumor Microenvironment by Specific Subpopulations of Fibroblasts” was published on the Journal of Cancers. Congratulations to the authors. 10/09/2020
SSMD has been accepted by Briefings in Bioinformatics. [github] Congratulations to Xiaoyu and Szu-Wei! 10/11/2020
CSMR has been accepted by Briefings in Bioinformatics. [github] Congratulations to Wennan and Changlin! 10/05/2020
“MAL2 drives immune evasion in breast cancer by suppressing tumor antigen presentation” was published on the Journal of Clinical Investigation. 09/29/2020
GETF has been accepted by NeurIPS 2020 (Acceptance Rate 20%, first-time submission of the work). Congratulations to Changlin and Wennan! 09/25/2020
Our single-cell Flux Estimation Analysis (scFEA) came online. [Paper] [github] 09/01/2020
BIND has been accepted by CIKM 2020 (Acceptance Rate 26%, first-time submission of the work) Congratulations to Changlin and Wennan! 07/16/2020
Welcome to the two high school students Harsh Duvvuru and Adithya Ayanam attending the summer research internship at BDRL 05/01/2020
Chi Zhang serves as editor of IJCBDD. 05/20/2020
Changlin got the summer research internship at Amazon. Congratulations to Changlin. 05/01/2020
The clinical trial of “Selumetinib in children with inoperable plexiform neurofibromas” we have analyzed was published on the New England Journal of Medicine. 04/09/2020
The supplementary issue “Computational methods and application in medical genomics” of ICIBM2019 is released on BMC Medical Genomics. 04/03/2019
Chi Zhang serves as a program committee member of KDD 2020. 02/12/2020
2019
Changlin and Wennan’s fast boolean factorization algorithm, MEBF, has been accepted by the Association for the Advancement of Artificial Intelligence (AAAI2020). AAAI2020 is very competitive this year. The total accept rate is around 20%. Great news! Congratulations to the authors! 11/11/2019
Sha has been granted an NSF Computer and Information Science and Engineering (CISE) Research Initiation Initiative grant. Congratulations to Sha! 09/03/2019
QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data has been accepted by Bioinformatics. Congratulations! 08/29/2019
A finalized version of ICTD is available on BioRxiv: https://www.biorxiv.org/content/10.1101/426593v2. 07/15/2019
Changlin’s paper LTMG: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data has been accepted by Nucleic Acids Research, Congratulations to Changlin and other co-authors! 07/15/2019
Sha has been granted with Showalter Young Investigator Award. Congratulations to Sha! 06/15/2019
Yu’s Paper M3S: A comprehensive model selection for multi-modal single-cell RNA sequencing data has been accepted by ICIBM2019 and BMC Bioinformatics. Congratulations to Yu and other co-authors! 05/01/2019
ICTD (Identification of Cell Type and Deconvolution) is available on Github: https://github.com/changwn/ICTD 04/10/2019
SSDM (Semi-Supervised Deconvolution for Mouse data) is available on Github: https://github.com/zy26/SSMD 04/10/2019
Wennan, Changlin, Xiaoyu and Szuwei presented their posters at AACR2019 Annual Meeting 04/03/2019
Dr. Chi Zhang will serve as the Program Committee Chair of the International Conference on Intelligent Biology and Medicine (ICIBM 2019). 03/01/2019
2018
Changlin’s tean IPU achieved ~top 15 position in the dream challenge single cell transriptomics challenge: https://www.synapse.org/#!Synapse:syn17062975/wiki/586460. It is a good rank for a first year PhD Student. 11/30/2018