Jiande Wu, Ph.D.

Data Manager / Data Scientist
Center for Public Health Modeling and Response, Clemson University

About

I work on public health data and infectious disease forecasting at the Center for Public Health Modeling and Response (CPHMR), Clemson University. My current focus is forecasting respiratory hospitalizations (COVID-19, influenza, RSV) from CDC surveillance data while accounting for reporting gaps and data-quality variation.

From 2017 to 2023 I was a Senior Bioinformatics Specialist at LSU Health Sciences Center, building reproducible workflows for RNA-seq, DNA methylation, and single-cell analyses of cancer cohorts. I earned my Ph.D. in Electrical Engineering at the University of New Orleans, where I worked on parallel and GPU-accelerated particle filtering for target tracking.

Projects

ObsAwareData

Weekly COVID-19, influenza, and RSV surveillance data for the 50 US states and DC (NHSN, NSSP, NWSS, Census), with reliability flags and source-release provenance.

Data · CC BY 4.0

ObsAwareData-pipeline

Archive of CDC data releases and the pipeline that builds ObsAwareData.

Python

TCGA breast cancer analyses

RNA-seq, miRNA, and DNA methylation analyses of TCGA breast cancer, focused on triple-negative breast cancer.

R · Bioinformatics

Pan-cancer methylation

DNA methylation workflows (DMP, DMR, survival) across TCGA BRCA, COAD, LUAD, and PRAD.

R · Bioinformatics

STAR + JUM splicing workflow

Configurable two-pass STAR and JUM workflow for RNA-seq alternative splicing analysis.

Shell · Workflow

resplens

Reliability-aware AI toolkit for US respiratory surveillance data, with MCP tools and evaluated document retrieval.

Python · AI / MCP

More on GitHub.

Publications

See also Google Scholar.

2025

  1. Wu J, Tanim S, Woo M, Ahammed T, Bleichrodt AM, Rennert L. A deep learning approach for enhancing pandemic prediction: A retrospective evaluation of transformer neural networks and multi-source data fusion for infectious disease forecasting. Epidemics 53:100865.
  2. Hossain F, Danos D, Zabaleta J, Wu XC, Del Valle L, Hicks C, Wu J, et al. Immunogenomic diversity of triple-negative breast cancers in obese and non-obese black and white women. npj Breast Cancer 11:126.

2023

  1. Mamidi YKK, Mamidi TKK, Kabir MWU, Wu J, Hoque MT, Hicks C. PCa-Clf: A classifier of prostate cancer patients into patients with indolent and aggressive tumors using machine learning. Machine Learning and Knowledge Extraction 5(4):1302–1319.
  2. Lyu H, Hou D, Liu H, Ruan S, Tan C, Wu J, Hicks C, Liu B. HER3 targeting augments the efficacy of panobinostat in claudin-low triple-negative breast cancer cells. npj Precision Oncology 7:72.
  3. Chen C, Wu J, Hicks C, Lan MS. Repurposing a plant alkaloid homoharringtonine targets insulinoma associated-1 in N-Myc-activated neuroblastoma. Cellular Signalling 109:110753.

2022

  1. Wu J, Zhang L, Kuchi A, Otohinoyi D, Hicks C. CpG site-based signature predicts survival of colorectal cancer. Biomedicines 10(12):3163.
  2. Otohinoyi D, Kuchi A, Wu J, Hicks C. Integrating genomic information with tumor-immune microenvironment in triple-negative breast cancer. International Journal of Environmental Research and Public Health 19(21):13901.
  3. Kuchi A, Wu J, Fuloria J, Hicks C. Landscape of molecular crosstalk perturbation between lung cancer and COVID-19. International Journal of Environmental Research and Public Health 19:3454.

2021

  1. Wu J, Hicks C. Breast cancer type classification using machine learning. Journal of Personalized Medicine 11(2):61.
  2. Zhang L, Hsieh MC, Rennert L, Neroda P, Wu XC, Hicks C, Wu J, Gimbel R. Diagnosis-to-surgery interval and survival for different histologies of stage I–IIA lung cancer. Translational Lung Cancer Research 10(7):3043–3058.
  3. Neroda P, Hsieh MC, Wu XC, Cartmell KB, Mayo R, Wu J, Hicks C, Zhang L. Racial disparity and social determinants in receiving timely surgery among stage I–IIIA non-small cell lung cancer patients in a U.S. southern state. Frontiers in Public Health 9:662876.
  4. Zhang L, Hsieh MC, Allison C, Devane M, Hicks C, Yu Q, Shi L, Wu J, Wu XC. Racial differences in the risk of second primary bladder cancer following radiation therapy among localized prostate cancer patients. Cancer Epidemiology 73:101967.
  5. Mamidi TKK, Wu J, Hicks C. Elucidation of the genomic-epigenomic interaction landscape of aggressive prostate cancer. BioMed Research International 2021:6641429.
  6. Dean MJ, Ochoa JB, Sanchez-Pino MD, et al. (incl. Wu J, Hicks C). Severe COVID-19 is characterized by an impaired type I interferon response and elevated levels of arginase producing granulocytic myeloid derived suppressor cells. Frontiers in Immunology 12:695972.

2020

  1. Wu J, Mamidi TKK, Zhang L, Hicks C. Unraveling the genomic-epigenomic interaction landscape in triple negative and non-triple negative breast cancer. Cancers 12(6):1559.
  2. Wu J, Mamidi TKK, Zhang L, Hicks C. Delineation of the germline and somatic mutation interaction landscape in triple-negative and non-triple-negative breast cancer. International Journal of Genomics 2020:2641370.

2019

  1. Wu J, Mamidi TKK, Zhang L, Hicks C. Deconvolution of the genomic and epigenomic interaction landscape of triple-negative breast cancer. Cancers 11(11):1692.
  2. Wu J, Mamidi TKK, Zhang L, Hicks C. Integrating germline and somatic mutation information for the discovery of biomarkers in triple-negative breast cancer. International Journal of Environmental Research and Public Health 16(6):1055.
  3. Mamidi TKK, Wu J, Hicks C. Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer. BMC Cancer 19(1):229.
  4. Mamidi TKK, Wu J, Hicks C. Interactions between germline and somatic mutated genes in aggressive prostate cancer. Prostate Cancer 2019.
  5. Mamidi TKK, Wu J, Hicks C. Mapping the germline and somatic mutation interaction landscape in indolent and aggressive prostate cancers. Journal of Oncology 2019.
  6. Nicklow E, Mamidi TKK, Wu J, Tsien F, Hicks C. Transcriptome analysis of molecular signatures and pathways modulating white blood cell count in childhood acute lymphoblastic leukemia. Biomedical Journal of Scientific & Technical Research 20(1):14693–14704.

2018

  1. Mamidi TKK, Wu J, Tchounwou PB, Miele L, Hicks C. Whole genome transcriptome analysis of the association between obesity and triple-negative breast cancer in Caucasian women. International Journal of Environmental Research and Public Health 15(11):2338.
  2. Hu Q, Shi L, Chen L, Zhang L, Truong K, Ewing A, Wu J, Scott J. Seasonality in the adverse outcomes in weight loss surgeries. Surgery for Obesity and Related Diseases 14(3):291–296.
Earlier work (2008–2015): parallel computing, particle filtering, embedded systems
  1. Jilkov VP, Wu J. Efficient GPU-accelerated implementation of particle and particle flow filters for target tracking. Journal of Advances in Information Fusion 10(1):73–88, 2015.
  2. Charalampidis D, Jilkov VP, Wu J. Implementation and performance of FPGA-accelerated particle flow filter. Signal and Data Processing of Small Targets, Proc. SPIE 9596:95960B, 2015.
  3. Wu J. Parallel computing of particle filtering algorithms for target tracking applications. Ph.D. dissertation, University of New Orleans, 2014.
  4. Jilkov VP, Wu J, Chen H. Performance comparison of GPU-accelerated particle flow and particle filters. 16th International Conference on Information Fusion, 1095–1102, 2013.
  5. Wu J, Jilkov VP. Parallel multitarget tracking particle filters using graphics processing unit. 44th Southeastern Symposium on System Theory (SSST), 151–155, 2012.
  6. Jilkov VP, Wu J. Implementation and performance of a parallel multitarget tracking particle filter. 14th International Conference on Information Fusion, 1–8, 2011.
  7. Qiu M, Wu J, Huang HC, Li W. Hardware controlled systematic approach to detect and prevent virus. Handbook of Security and Networks, 285, 2011.
  8. Jilkov VP, Wu J, Chen H. Parallel particle filter implementation on cluster computer for satellite tracking application. 4th International Conference on Neural, Parallel & Scientific Computations, 179–186, 2010.
  9. Qiu M, Liu M, Li H, Huang HC, Li W, Wu J. Energy-aware loop scheduling and assignment for multi-core, multi-functional-unit architecture. Journal of Signal Processing Systems 57(3):363–379, 2009.
  10. Qiu M, Wu J, Hu F, Liu S, Wang L. Voltage assignment for soft real-time embedded systems with continuous probability distribution. 15th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications, 413–418, 2009.
  11. Qiu M, Wu J, Hu J, He Y, Sha EHM. Dynamic and leakage power minimization with loop voltage scheduling and assignment. IEEE/IFIP International Conference on Embedded and Ubiquitous Computing, 192–198, 2008.
  12. Qiu M, Wu J, Xue CJ, Hu JA, Tseng WC, Sha EHM. Loop scheduling and assignment to minimize energy while hiding latency for heterogeneous multi-bank memory. International Conference on Field Programmable Logic and Applications, 459–462, 2008.
  13. Qiu M, Wu J, Xue CJ, Hu J, Tseng WC, Sha EHM. QoS for networked heterogeneous real-time embedded systems. ISCA PDCCS, 135–140, 2008.
  14. Qiu M, Wu J. Energy saving for memory with loop scheduling and prefetching. 18th ACM Great Lakes Symposium on VLSI, 155–158, 2008.
  15. Qiu M, Huang HC, Yang LT, Wu J. Intelligent search agent for internet computing with fuzzy approach. 11th IEEE International Conference on Computational Science and Engineering, 181–188, 2008.

Education