News & Events


  • Incoming Ph.D students Jia Wang and Xiao Wang will join the lab in Fall 2022. Welcome to our big family! 07/2022
  • Dr. Chi Zhang received funding from American Cancer Society Research Scholar Award. Congratulation to Dr. Zhang! 04/15/2022
  • Wennan Chang, Changlin Wan, Norah Alghamdi successfully passed final dissertation defense for Ph.D. degree. Congratulation to Dr. Chang, Dr. Wan, and Dr. Alghamdi! 04/2022
  • Wennan Chang accepted offer at Kite Pharma Inc as research scientist. 10/2021
  • Changlin Wan accepted offer at Genentech as AI scientist. 03/2022
  • Xiaoyu Lu accepted offer at Bristol Myers Squibb as 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
  • scFLUX has been lunched. scFLUX server 01/01/2022


  • Dr. Chi Zhang and Dr. Sha Cao serves as a PC member 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, 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


  • Wennan has past the Preliminary Examination, congratulations to Wennan. 11/20/2020
  • Changlin’s paper has been accepted by IEEE BIBM 2020. Congratulations to authors. 10/30/2020
  • “Modulation of Immune Infiltration of Ovarian Cancer Tumor Microenvironment by Specific Subpopulations of Fibroblasts” was publised on the Journal of Cancers. Congratulations to 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 for 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 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 program committee member of KDD 2020. 02/12/2020


  • Changlin and Wennan’s fast boolean factorization algorithm, MEBF, has been accepted by 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 authors! 11/11/2019
  • Sha has been granted with 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 algorithms for analyses and interpretatin of large-scale RNA-Seq data has been accepted by Bioinformatics. Congratulations! 08/29/2019
  • A finalized version of ICTD is available on BioRxiv: 07/15/2019
  • Changlin’ 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: 04/10/2019
  • SSDM (Semi-Supervised Deconvolution for Mouse data) is available on Github: 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 International Conference on Intelligent Biology and Medicine (ICIBM 2019). 03/01/2019