Publications

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A. Books, Book Chapters, and Edited Volumes

Refereed Book Chapters

  1. Tong L., Wu H.,Wang MD, Wang G. “Introduction of medical genomics and clinical informatics integration for p-Health care.” Editor: Teplow D, Progress in Molecular Biology and Translational Science (PMBTS). 2022/7/30. Elsevier. 190(1), 1-37. Doi: 10.1016/bs.pmbts.2022.05.002. PMID: 36007995.
  2. Stokes TH, Kothari S, Cheng C, and Wang MD. “Quality control and analysis algorithms for tissue microarrays as biomarker validation tools.” Editor: Rueda L. Microarray Image and Data Analysis: Theory and Practice. 2018/9/3. CRC Press. p.283-312. Doi: 10.1201/9781315215785-16.
  3. Kaddi CD and Wang MD. “Computational methods for mass spectrometry imaging: challenges, progress, and opportunities.” In: Xu D, Wang MD, Zhou F, Cai Y, editors. Health Informatics Data Analysis: Methods and Examples. Springer; 2017. p. 37-49. Doi: 10.1007/978-3-319-44981-4.
  4. Chandramohan R, Yang C, Cai Y., and Wang MD. “Metagenomics for monitoring environmental biodiversity: challenges, progress, and opportunities.” In: Xu D, Wang MD, Zhou F, Cai Y, editors. Health Informatics Data Analysis: Methods and Examples. Springer; 2017. p. 73-87. Doi: 10.1007/978-3-319-44981-4_5.
  5. Kothari S, Hoffman RA, and Wang MD. “Biomedical imaging informatics for diagnostic imaging marker selection.” In: Xu D, Wang MD, Zhou F, Cai Y, editors. Health Informatics Data Analysis: Methods and Examples. Springer; 2017. p. 115-127. Doi: 007/978-3-319-44981-4.
  6. Cheng C and Wang MD. “Healthcare data mining, association rule mining, and applications.” In: Xu D, Wang MD, Zhou F, Cai Y, editors. Health Informatics Data Analysis: Methods and Examples. Springer; 2017. p. 201-210. Doi: 10.1007/978-3-319-44981-4.
  7. Smith AM, Wen MM, Wang MD, and Nie SM. “Size-minimized quantum dots for molecular and cellular imaging.” Nobel Symposium 138:Single Molecule Spectroscopy in Chemistry, Physics, and Biology: Nobel Symposium 138. Springer Heidelburg. Springer Series in Chemical Physics, 96(4): 187-201. 2010. Doi: 10.1007/978-3-642-02597-6. ISBN: 9783642025976; 3642025978; 9783642025969; 364202596X. (https://worldcat.org/title/864524132).
  8. Quo CF and Wang MD. “Incorporating problem-based learning (PBL) in medical image processing education.” In: Transform Science: Computational Education for Scientists. Microsoft Research; 2009. p. 176-94.
  9. Wang MD, Simons JW, and Nie SM. “Cancer nanotechnology for molecular profiling and individualized therapy.” In: Leyland-Jones B, editor. Pharmacogenetics of breast cancer: towards the individualization of therapy. 1st ed. Informa Healthcare; 2008 May 1. p.143-56. Doi: 10.1201/9780429137723.
  10. Agrawal A, Wang MD, and Nie SM. “Bioconjugated nanoparticles for ultrasensitive detection of molecular biomarkers and infectious agents.” In: Gonsalves K, Halberstadt C, Laurencin CT, and Nair LS, editors. Biomedical nanostructures. Hoboken, NJ: John Wiley & Sons, Inc.; 2007 Apr 11. p. 205-20. Doi: 10.1002/9780470185834.
  11. Phan JH, Quo CF, and Wang MD. “Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics.” Prog Brain Res (Editors: Scott E. Hemby and Sabine Bahn). 2006; 158: p. 83-108. Elsevier BV, Amsterdam. Doi: 10.1016/S0079-6123(06)58004-5. PMID: 17027692.
  12. Moffitt RA and Wang MD. “Microarray data analysis.” In: Metin A, editor. Wiley Encyclopedia of Biomedical Engineering. John Wiley & Sons, Inc.; 2006 Apr 14. p. 2270-9. Doi: 02/9780471740360.
  13. Hong JY, Allegood JC, Kelly S, Wang E, Merrill AH Jr., and Wang MD. “Computer visualization models for the de novo sphingolipid biosynthetic pathway.” In: Hirabayashi B, Igarashi Y, Merrill AH Jr., editors. Sphingolipid biology. Tokyo: Springer-Verlag; 2006. p. 493-508. Doi: 10.1007/4-431-34200-1.
  14. Schmelz EM, Wang MD, Merrill AH Jr. “Genomics, proteomics, metabolomics and systems biology approach to nutrition.” In: Bowman BA and Russell RM, editors. Present Knowledge in Nutrition. 9th ed. Washington, D.C.: ILSI Press; 2006. p. 3-19.

Edited Volumes

  1. Xu D, Wang MD, Zhou FF, and Cai YP, “Health Informatics Data Analysis: Methods and Examples,” Springer. 2017/9/8. ISBN 978-3-319-83178-7. Editor Teplow D,

Other Parts of Books

  1. Sha Y, and Wang MD. “Interpretable deep learning (DL) for advanced and transparent clinical decision support.” Chang AC. Intelligence-Based Medicine: Artificial Intelligence and Human Cognition in Clinical Medicine and Healthcare. 2020. Elsevier Academic Press; pp.131-133. Hardcover ISBN: 9780128233375. eBook ISBN: 9780128233382.

B. Refereed Journal Publications

2026

  1. Nnamdi MC, Tamo BJ, Marteau BL, Shi W, and Wang MD. “Advancing problem-based learning in biomedical engineering in the era of generative AI.” IEEE Transactions on Education (ToE). Doi: 10.1109/TE.2026.3658007. Open Access Link. (Accepted: 11/17/2025).
  2. Hornback A, Sathu H, Kim K, Wang Y, Zhu Y, Isgut M, Avula P, Khimani A, and Wang MD. “Large language models in healthcare and biomedical informatics: a comprehensive review.” Innovation and Emerging Technologies (World Scientific Connect). (Accepted: 01/06/2026).
  3. Zeng S, Zhu L, Zhang X, Chen Q, He H, Jin L, Tian Z, Xie Z, Nnamdi MC, Shi W, Tamo BJ, Wang MD, and Lu Y. “Multi-level asymmetric contrastive learning for medical image segmentation pre-training.” IEEE Journal of Biomedical and Health Informatics. 2024. Doi: 10.1109/JBHI.2026.3669549. [Impact Factor: 6.8].

2025

  1. Shi W, Zhu Y, Giuste F, Tamo BJ, Nnamdi MC, Hornback A, Singh A, Carpenter A, Hilton C, Iwinski HJ, Wattenbarger JM, and Wang MD. “Development of prediction model for patient rehabilitation outcomes after spinal deformity surgery: towards precision medicine.” Nature Communication Medicine. 2025. Doi: 10.1038/s43856-024-00726-1. Open Access Link. [Impact Factor: 5.4].
  2. Isgut M, Hornback A, Bao H, Sun Y, Choi K, Anderson BJ, Deshpande SR, Chang AC, and Wang MD. “Greater value add from electronic health records than polygenic risk scores for predicting myocardial infarction in machine learning.” Nature Communications Medicine. 2025. Doi: 10.1038/s43856-025-01138-5. Open Access Link. [Impact Factor: 5.4].
  3. Tamo BJ, Nishant C, Nnamdi MC, Yuan Y, Shreya C, Shi W, Hwang SW, Brenn BR, and Wang MD. “Causal machine learning for surgical interventions.” IEEE Big Data Mining and Analytics. 2025. Doi: 10.26599/BDMA.2025.9020093. Open Access Link. [Impact Factor: 6.2].
  4. Zeng S, Lee CH, Nnamdi MC, Shi W, Tamo BJ, He H, Zhang X, Chen Q, Wang MD, Zhu L, Lu, Y, Ren Q. “Novel extraction of discriminative fine-grained feature to improve retinal vessel segmentation.” Image and Vision Computing. 2025. Doi: 10.1016/j.imavis.2025.105729. Open Access Link. [Impact Factor: 4.2].
  5. Hornback A, Marteau BL, Tan SQY, Kim K, Patil O, Traynelis J, Zhu Y, Giuste F, and Wang MD. “FHIR in focus: enabling biomedical data harmonization for intelligent healthcare systems.” IEEE Reviews in Biomedical Engineering. 2025. Doi:10.1109/RBME.2025.3632213. Open Access Link. [Impact Factor: 12].

2024

  1. Tong L, Shi W, Isgut M, Zhong Y, Lais P, Sun J, Swain A, Giuste F, and Wang MD. “Integrating multi-omics data with ehr for precision medicine using advanced artificial Intelligence.” IEEE Review in Biomedical Engineering. 2024, Doi: 10.1109/RBME.2023.3324264. Open Access Link. [Impact Factor: 17.20].
  2. Vyshnya S, Epperson R, Giuste F, Shi W, Hornback A, and Wang MD. “Optimized clinical feature analysis for improved cardiovascular disease risk screening.” IEEE Open Journal of Engineering in Medicine and Biology. 2024. Doi: 10.1109/OJEMB.2023.3347479. Open Access Link.
  3. Wu H*, Shi W* (equal contributing authors), and Wang MD. “Developing a novel causal inference algorithm for personalized biomedical causal graph learning using meta machine learning.” BMC Medical Informatics and Decision Making. 2024. Doi: 10.1186/s12911-024-02510-6. Open Access Link.
  4. Isgut M, Giuste F, Gloster L, Swain A, Choi K, Hornback A, Deshpande SR, and Wang MD. “Identifying and characterizing disease subpopulations that most benefit from polygenic risk scores.” Nature Scientific Reports. 2024. Doi: 10.1038/s41598-024-63705-5. Open Access Link.
  5. Wu H*, Shi W* (equal contributing authors), Anirudh Choudhary, and Wang MD. “Clinical Decision Making under Uncertainty: A bootstrapped counterfactual inference approach.” BMC Medical Informatics and Decision Making. 2024. Doi: 10.1186/s12911-024-02606-z. Open Access Link.
  6. ul Haq MZ, Hornback A, Harzand A, Gutman DA, Gallaher B, Schoenberg ED, Zhu Y, Wang MD, and Anderson B. “Graph theoretic visualization of patient and provider messaging in the EHR.” Frontier in Artificial Intelligence, 2024. Doi: 10.3389/frai.2024.1422208.
  7. Wu H, Zhu Y, ShiW,Li T, and Wang MD. “Fairness in artificial intelligence in clinical decision support: mitigating effect of health disparity.” IEEE Journal of Biomedical and Health Informatics. 2024. Doi: 10.1109/JBHI.2024.3513398. [Impact Factor: 7.02].
  8. Wan C, Nnamdi MC, Shi W, Smith B, Purnell C, and Wang MD. “Advancing Sleep Disorder Diagnostics: A transformer-based EEG model for sleep stage classification and OSA prediction.” IEEE Journal of Biomedical and Health Informatics. 2024. Doi: 10.1109/JBHI.2024.3512616. [Impact Factor: 7.02].

2023

  1. Ellis CA, Sendi MSE, Zhang R, Carbajal DA, Wang MD, Miller RL, and Calhoun VD. “Novel methods for elucidating modality importance in multimodal electrophysiology classifiers.” Front Neuroinform. 2023. Doi: 10.3389/fninf.2023.1123376. PMID: 37006636; PMCID: PMC10050434. Open Access Link.
  2. Giuste FO, Sequeira R, Keerthipati V, Lais P, Mirzazadeh A, Mohseni A, Zhu Y, Shi W, Marteau B, Zhong Y, Tong L, Das B, Shehata B, Deshpande S, and Wang MD. “Explainable synthetic image generation to improve risk assessment of rare pediatric heart transplant rejection.” Journal of Biomedical Informatics. 2023 Mar;139:104303. Doi: 10.1016/j.jbi.2023.104303. Epub 2023 Feb 2. PMID: 36736449; PMCID: PMC10031799. Open Access Link.
  3. Isgut M, Song K, Ehm MG, Wang MD, and Davitte J. “Effect of case and control definitions on genome-wide association study (GWAS) findings.” Genet Epidemiol. 2023 Apr 6. Doi: 10.1002/gepi.22523. Epub ahead of print. PMID: 37021827. Open Access Link.
  4. Mermin-Bunnell K, Zhu Y, Hornback A, Damhorst G, Walker T, Robichaux C, Mathew L, Jaquemet N, Peters K, Johnson TM 2nd, Wang MD, and Anderson B. “Use of natural language processing of patient-initiated electronic health record messages to identify patients with COVID-19 infection.” JAMA Netw Open. 2023. Doi: 10.1001/jamanetworkopen.2023.22299. PMID: 37418261; PMCID: PMC10329205. Open Access Link.
  5. Giuste F, He L, Lais P, Shi W, Zhu Y, Hornback A, Tsai C, Isgut M, Anderson B, and Wang MD. “Early and fair COVID-19 outcome risk assessment using robust feature selection.” NatureScientific Report. 2023. Doi: 10.1038/s41598-023-36175-4. Open Access Link.
  6. Sun J*, Shi W*, Giuste F, Vaghani Y, Tang L, and Wang MD. “Patch perturbation-based evaluation pipeline for explainable artificial intelligence in COVID-19 X-ray image analysis.” Nature Scientific Report. 2023. Doi: 10.1038/s41598-023-46493-2. Open Access Link.

2022

  1. Zhu Y, Venugopalan J, Zhang Z, Chanani N, Maher K and Wang MD. “Domain adaptation using convolutional autoencoder and gradient boosting for adverse events prediction in the intensive care unit.” Frontiers in Artificial Intelligence – Medicine and Public Health. 2022. Doi: 10.3389/frai.2022.640926. PMID: 35481281. PMCID: PMC9036368. Open Access Link.
  2. Anklam E, Bahl MI, Ball R, Beger RD, Cohen J, Fitzpatrick S, Girard P, Halamoda-Kenzaoui B, Hinton D, Hirose A, Hoeveler A, Honma M, Hugas M, Ishida S, Kass GE, Kojima H, Krefting I, Liachenko S, Liu Y, Masters S, Marx U, McCarthy T, Mercer T, Patri A, Pelaez C, Pirmohamed M, Platz S, Ribeiro AJ, Rodricks JV, Rusyn I, Salek RM, Schoonjans R, Silva P, Svendsen CN, Sumner S, Sung K, Tagle D, Tong L, Tong W, Eijnden-van-Raaij JVD, Vary N, Wang T, Waterton J, Wang MD, Wen H, Wishart D, Yuan Y, and Slikker W Jr. Emerging technologies and their impact on regulatory science. Exp Biol Med (Maywood). 2022 Jan;247(1):1-75. Doi: 10.1177/15353702211052280. Epub 2021 Nov 16. PMID: 34783606; PMCID: PMC8749227.
  3. Zhu Y *, Sha Y *, Wu H *, (equal contribution first authors), Li M, Hoffman RA, Wang MD. “Proposing causal sequence of death by neural machine translation in public health informatics.” IEEE Journal of Biomedical and Health Informatics. 2022: 1422-1431. 2022. Doi: 10.1109/JBHI.2022.3163013. PMID: 35349461. PMCID: PMC9452006. Open Access Link. [Impact Factor: 7.02].
  4. Giuste F*, Shi W*, Zhu Y, Naren T, Isgut M, Sha Y, Tong L, Gupte M, and Wang MD. “Explainable Artificial Intelligence methods in combating pandemics: A systematic review.” IEEE Review in Biomedical Engineering. 2022. Doi: 10.1109/RBME.2022.3185953. PMID: 35737637. Open Access Link. [Impact Factor: 17.20].
  5. Isgut M, Gloster L, Choi K, Venugopalan J, and Wang MD. “Systematic review of data quality issues and advanced quality control methods for combatting COVID-19.” IEEE Review in Biomedical Engineering. 2022. Doi: 10.1109/RBME.2022.3216531. PMID: 36269930. Open Access Link. [Impact Factor: 17.20].

2021

  1. Venugopalan J, Tong L, Hassanzadeh H, and Wang MD. “Multimodal deep learning models for early detection of Alzheimer’s disease stage.” NatureScientific Reports, 11(1):1-13. 2021. Doi: 10.1038/s41598-020-74399-w. PMID: 33547343. PMCID: PMC7864942. Open Access Link.
  2. Littman AR, Janssen KM, Tong L, Wu H,Wang MD, Blum ES, and Kirsch AJ, “Did COVID-19 affect time to presentation in the setting of pediatric testicular torsion?” Pediatric Emergency Care, December 2020. 37(2): 123. 2021. Doi: 10.1097/PEC.0000000000002333. PMID: 33512891. PMCID: PMC7850557. Open Access Link.
  3. Shi W, Tong L, Zhu Y, and Wang MD. “COVID-19 automatic diagnosis with radiographic imaging: explainable attention transfer deep neural networks”, Journal of Biomedical and Health Informatics. 25(7), 2376-2387. 2021. Doi: 10.1109/JBHI.2021.3074893. PMID: 33882010. PMCID: PMC8545079. Open Access Link. [Impact Factor: 7.02].
  4. Hassanzadeh, H, and Wang MD. “An integrated deep network for cancer survival prediction using omics data.” Frontiers in big Data 4. 2021. Doi: 10.3389/fdata.2021.568352. PMID: 34337396. PMCID: PMC8322661. Open Access Link.
  5. Tong L, Wu H, and Wang MD. “Integrating multi-omics data by learning modality invariant representations for improved prediction of overall survival of cancer.” Methods. 2021. 189: 74-85. Doi: 10.3389/fdata.2021.568352. PMID: 34337396. PMCID: PMC8322661.

2020

  1. Choudhary A, Tong L, Zhu Y, and Wang MD. “Advancing medical imaging informatics by deep learning-based domain adaptation.” Yearbook of Medical Informatics. 2020; 29(01): 129-138. Doi: 10.1055/s-0040-1702009. PMID: 32823306. PMCID: PMC7442502. Open Access Link.
  2. Tong L, Mitchel J, Chatlin K, and Wang MD.  “Deep learning based feature-level integration of multi-omics data for breast cancer patients survival analysis.” BMC Medical Informatics and Decision Making. 2020. 20: 225. Doi: 10.1186/s12911-020-01225-8. PMID: 32933515. PMCID: PMC7493161. Open Access Link.
  3. Qv L, Wang L, He F, Han Y, Yang L, Wang MD, and Zhu HQ. “The landscape of micro-inversions provide clues for population genetic analysis of humans.” Interdisciplinary Sciences: Computational Life Sciences. 2020; 12(4):499-514. Doi: 10.1007/s12539-020-00392-6. PMID: 32929667. PMCID: PMC7658078. Open Access Link.
  4. Adans-Dester CP, Bamberg S, Bertacchi FP, Caulfield B, Chappie L, Demarchi D, Erb MK, Estrada J, Fabara EE, Freni M, Friedl KE, Ghaffari R, Gill G, Greenberg MS, Hoyt RW, Jovanov E, Kanzler CM, Katabi D, Kernan M, Kigin C, Lee SI, Leonhardt S, Lovell NH, Mantilla J, McCoy TH, Luo NM, Miller GA, Moore J, O’Keeffe D, Palmer J, Parisi F, Patel S, Po J, Pugliese BL, Quatieri T, Rahman T, Ramasarma N, Rogers JA, Ruiz-Esparza GU, Sapienza S, Schiurring G, Schwamm L, Shafiee H, Silacci SK, Sims NM, Talkar T, Tharion WJ, Toombs JA, Uschnig C, Vergara-Diaz GP, Wacnik P, Wang MD, Welch J, Williamson L, Zafonte R, Zai A, Zhang YT, Tearney GJ, Ahmad R, Walt DR, and Bonato P. “Can mHealth technology help mitigate the effects of the COVID-19 pandemic?” IEEE Open Journal of Engineering in Medicine and Biology. 2020. 1:243-248. [Note: This is an international task force for assessing technology solutions for combating COVID19. Four of my lab members are acknowledged for contributing to multiple subject sections in the paper supplement: Tanade C, Tong L, Wu H, and Zhu Y.]. Doi: 10.1109/OJEMB.2020.3015141. PMID: 34192282. PMCID: PMC8023427. Open Access Link.
  5. Tong L*, Wu PY*, Phan JH* (equal contribution first authors), Hassanzadeh HR, SEQC Consortium, Tong WD*, and Wang MD* (co-corresponding senior author and handling author). “Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction.” Nature Scientific Reports. 10(1): 1-20. 2020. Doi: 10.1038/s41598-020-74567-y. PMID: 33087762. PMCID: PMC7578822. Open Access Link.

2019

  1. Venugopalan J, Chanani N, Maher K, and Wang MD. “Novel data imputation for multiple types of missing data in intensive care units.”  Journal of Biomedical and Health Informatics. 2019; 23(3): 1243-1250. Doi: 10.1109/JBHI.2018.2883606. PMID: 30998482. Open Access Link. [Impact Factor: 7.02].
  2. Tong L, Wu H, and Wang MD. “CAESNet: Convolutional autoencoder based semi-supervised network for improving multi-class classification of endomicroscopic images.” Journal of American Medical Informatics Association. 2019 Nov. 26(11): 1286–1296. Doi: 10.1093/jamia/ocz089. PMID: 31260038. PMCID: PMC6798571.
  3. Cheng CW, Brown C, Venugopalan J, and Wang MD. “Towards an effective patient health engagement system using cloud-based text messaging technology.” Journal of Translational Engineering in Health and Medicine (JTEHM). 2019. Vol. 8. Doi: 10.1109/JTEHM.2018.2868358. PMID: 32974110. PMCID: PMC7508315. Open Access Link.

2018

  1. Hoffman RA, Wu H, Venugopalan J, Braun P, and Wang MD. “Intelligent mortality reporting with FHIR.” Journal of Biomedical and Health Informatics, 22 (5) 1583-1588. 2018. Doi: 10.1109/JBHI.2017.2780891. PMID: 29993991. Open Access Link. [Impact Factor: 7.02].
  2. Hogan S, Phan JH, Alvarado-Velez M, Wang MD, Bellamkonda R, Fernandez F, and LaPlaca M. “Discovery of lipidome alterations following traumatic brain injury via high-resolution metabolomics.” Journal of Proteome Research. 2018; 17(6):2131-2143. Doi: 10.1021/acs.jproteome.8b00068. PMID: 29671324. PMCID: PMC7341947.
  3. Yang C, Yang L, Zhou M, Xie H, Zhang C, Wang MD, and Zhu H, “LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning.” Bioinformatics. 2018; 34(22): 3825-3834. Doi: 10.1021/acs.jproteome.8b00068. PMID: 29671324. PMCID: PMC7341947. Open Access Link.

2017

  1. Wu PY, Cheng CW, Hoffman R, Kaddi CD, Venugopalan J, and Wang MD. “-Omic and electronic health record big data analytics for precision medicine.” IEEE Transactions on Biomedical Engineering. 2017; 64(2): 263-273. Doi: 10.1109/TBME.2016.2573285. PMID: 27740470. PMCID: PMC5859562. Open Access Link.

2016

  1. Kairdolf B, Bouras A, Kaluzova M, Sharma A, Wang MD, Hadjipanayis C, and Nie SM. “Intraoperative spectroscopy with ultrahigh sensitivity for image-guided surgery of malignant brain tumors.” Anal Chem. 2016; 88 (1): 858-867. Doi: 10.1021/acs.analchem.5b03453. PMID: 26587976. PMCID: PMC8559335.
  2. Han Z, Zhang A, Wang X, Sun Z, Wang MD, and Xie T. “In vivo use of hyperspectral imaging to develop a noncontact endoscopic diagnosis support system for malignant colorectal tumors.” Journal of Biomed Opt. 2016; 21(1), 016001. Doi: 10.1117/1.JBO.21.1.016001. PMID: 26747475. Open Access Link.
  3. Paine MRL, Bennett RV, Kim J, Parry RM, Wang MD, Matzuk MM, and Fernández FM. “Whole reproductive system Non-Negative Matrix Factorization mass spectrometry imaging of an early-stage ovarian cancer mouse model.” PLOS ONE. 2016 May; 11(5): e0154837. Doi: 10.1371/journal.pone.0154837. PMID: 27159635. PMCID: PMC4861325. Open Access Link.

2015

  1. *Wang MD, *Simons JW, and *Nie SM (co-corresponding senior authors). “Nanotechnology in personalized and predictive oncology.” US Oncol. 2006; 1(2): 92-95. Doi: 10.1586/14737140.7.6.833. PMID: 17555393. Open Access Link.
  2. Zhang W, Yu Y, (SEQC Consortium Phan JH, Wu PY, and Wang MD et al.), and Matthias Fischer. “Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.” Genome Biol. 2015; 16: 133. Doi: 10.1186/s13059-015-0694-1. PMID: 26109056. PMCID: PMC4506430. Open Access Link.
  3. Zarkogianni K, Litsa E, Mitsis K, Wu PY, Kaddi CD, Cheng C, Wang MD and Nikita KS. “A review of emerging technologies for the management of diabetes mellitus.” IEEE Trans. on Biomed Eng (TBME). 2015 Dec.; 62(12): 2735-2749. Doi: 10.1109/TBME.2015.2470521. PMID: 26292334. PMCID: PMC5859570.
  4. Kaddi CD, Bennett RV, Paine MRL, Banks MD, Weber AL, Fernández FM, and Wang MD. “DetectTLC: Automated reaction mixture screening utilizing quantitative mass spectrometry image features.” Journal of the American Society for Mass Spectrometry. 2015; 27(2): 359-365. Doi: 10.1007/s13361-015-1293-9. PMID: 26508443. PMCID: PMC5003040.
  5. Kaddi CD and Wang MD. “Models for predicting stage in head and neck squamous cell carcinoma using proteomic and transcriptomic data.” Journal of Biomedical and Health Informatics. 2015 Oct.; 21(1): 246-253. Doi: 10.1109/JBHI.2015.2489158. PMID: 26462248. PMCID: PMC4983540. Open Access Link. [Impact Factor: 7.02].

2014

  1. Okusanya OT, Madajewski B, Segal E, Judy BF, Venegas OG, Judy RP, Quatromoni JG, Wang MD, Nie S, and Singhal S. “Small portable interchangeable imager of fluorescence for fluorescence guided surgery and research.” Technol Cancer Res Treat. 2014 Apr;14(2):213-20. Doi: 10.7785/tcrt.2012.500400. PMID: 24354756. PMCID: PMC4134767.
  2. Kothari S, Phan JH, Stokes TH, Osunkoya AO, Young AN, and Wang MD. “Removing batch effects from histopathological images for enhanced cancer diagnosis.” Journal of Biomedical and Health Informatics. 2014 May; 18(3):765-772. Doi: 10.1109/JBHI.2013.2276766. PMID: 24808220. PMCID: PMC5003052. [Impact Factor: 7.02].
  3. SEQC/MAQC-III (The Microarray Quality Control Consortium-III) SEQC Project and Li S, Mason CE et. al. (Wang MD and other authors). “Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.” Nat Biotechnol. 2014 Sept; 32(9): 915-925. Doi: 10.1038/nbt.2972. PMID: 25150835. PMCID: PMC4167418. Open Access Link. [Journal h5-index: 175].
  4. SEQC/MAQC-III (The Microarray Quality Control Consortium -III) SEQC Project and Su Z, Kreil DP, Mason CE, and Shi L et. al (Wang MD, Phan JH, Wu PY, and other authors). “A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium.” Nat Biotechnol. 2014 Sep; 32(9): 903-914. Doi: 10.1038/nbt.2957. PMID: 25150838. PMCID: PMC4321899. Open Access Link. [Journal h5-index: 175].
  5. Li S, Zumbo P, Kreil D, Labaj P, Shi W, Shi L, Phan JH, Wu PY, Wang MD, Wang C, Thierry-Mieg D, Thierry-Mieg J, and Mason C. “Detecting and correcting systematic variation in large-scale RNA sequencing.” Nat Biotechnol. 2014 Sep; 32(9): 888-895. Doi: 10.1038/nbt.3000. PMID: 25150837. PMCID: PMC4160374. Open Access Link. [Journal h5-index: 175].
  6. Wu PY, Chandramohan R, Phan JH, Mahle WT, Gaynor JW, Maher KO, and Wang MD. “Cardiovascular transcriptomics and epigenomics using next-generation sequencing: challenges, progress, and opportunities.” Circ Cardiovasc Genet. 2014 Oct; 7: 701-710. Doi: 10.1161/CIRCGENETICS.113.000129. PMID: 25518043. PMCID: PMC4983435. Open Access Link.
  7. Okusanya OT, Holt D, Heitjan D, Deshpande C, Venegas O, Jiang J, Judy R, DeJesus E, Madajewski B, Oh K, Wang MD, Albelda SM, Nie S, and Singhal S. “Intraoperative near-infrared imaging can identify pulmonary nodules.” Ann Thorac Surg. 2014 Oct; 98(4): 1223-1230. Doi: 10.1016/j.athoracsur.2014.05.026. PMID: 25106680. PMCID: PMC4185369.

2013

  1. Wang MD. “In the spotlight: bioinformatics.” IEEE Rev Biomed Eng. 2013;6:3-8. Doi: 10.1109/RBME.2012.2228311. PMID: 23192635. PMCID: PMC4983422. Open Access Link.
  2. Parry RM and Wang MD. “A fast least-squares algorithm for population inference in GWAS.” BMC Bioinformatics. 2013 Jan 23; 14: 28. Doi: 10.1186/1471-2105-14-28. PMID: 23343408. PMCID: PMC3602075. Open Access Link.
  3. Parry RM, Galhena AS, Gamage CM, Bennett RV, *Wang MD (co-corresponding and handling author), and *Fernandez FM. “OmniSpect: An open MATLAB-based tool for visualization and analysis of matrix-assisted laser desorption/ionization and desorption electrospray ionization mass spectrometry images.” Journal of the American Society for Mass Spectrometry. 2013 Apr; 24(4):646-649. Doi: 10.1007/s13361-012-0572-y. PMID: 23440717. PMCID: PMC4983445.
  4. Kairdolf BA, Smith AM, Stokes TH, Wang MD, Young AN, and Nie S. “Semiconductor quantum dots for bioimaging and biodiagnostic applications.” Annual Review of Analytical Chemistry. 2013 Mar 12; 6:143-162. Doi: 10.1146/annurev-anchem-060908-155136. PMID: 23527547. PMCID: PMC3733675.
  5. Kothari S, Phan JH, Young AN, and Wang MD. “Histological image classification using biologically interpretable shape-based features.” BMC Medical Imaging. 2013 Mar 13; 13:9. Doi: 10.1186/1471-2342-13-9. PMID: 23497380. PMCID: PMC3623732. Open Access Link.
  6. Kaddi CD, Phan JH, and Wang MD. “Computational nanomedicine: modeling of nanoparticle-mediated hyperthermal cancer therapy.” Nanomedicine. 2013 Aug; 8(8): 1323-1333. Doi: 10.2217/nnm.13.117. PMID: 23914967. PMCID: PMC4983427. Open Access Link.
  7. Zhang H, Wu PY, Ma M, Ye Y, Hao Y, Yang J, Yin S, Sun C, Phan JH, Wang MD, and Xi J. “An integrative approach for the large-scale identification of human genome kinases regulating cancer metastasis.” Nanomedicine: Nanotechnology, Biology, and Medicine. 2013 Aug; 9(6): 732-736. Doi: 10.1016/j.nano.2013.05.015. PMID: 23751374. PMCID: PMC5003042.
  8. Kothari S, Phan JH, and Wang MD. “Eliminating tissue-fold artifacts in histopathological whole-slide images for improved image-based prediction of cancer-grade.” J Pathol Inform. 2013 Aug 31; 4:22. Doi: 10.4103/2153-3539.117448. PMID: 24083057. PMCID: PMC3779385. Open Access Link.
  9. Kaddi CD, Parry RM, and Wang MD. “Multivariate hypergeometric similarity measure.” IEEE/ACMTrans Comput Biol Bioinformatics. 2013 Nov; 10(6): 1505-1516. Doi: 10.1109/TCBB.2013.28. PMID: 24407308. PMCID: PMC4983430. [Journal h5-index:52].
  10. Kothari S, Phan JH, Stokes TH, and Wang MD. “Pathology imaging informatics for quantitative analysis of whole-slide images.” Journal of American Medical Information Association. 2013 Nov-Dec; 20(6):1099-1108. Doi: 10.1136/amiajnl-2012-001540. PMID: 23959844. PMCID: PMC3822114. Open Access Link (v= https://academic.oup.com/jamia/article/20/6/1099/2909332). [Journal h5-index:74].
  11. Wu PY, Phan JH, and Wang MD. “Assessing the impact of human genome annotation choice on RNA-seq expression estimates.” BMC Bioinformatics. 2013 Nov 4; 14(11):1-13. Doi:10.1186/1471-2105-14-S11-S8. PMID: 24564364; PMCID: PMC3816316. Open Access Link.
  12. Cheng C, Chanani N, Venugopalan J, Maher K, and Wang MD. “icuARM – An ICU clinical decision support system using association rule mining.” IEEE J Trans Eng Health Med. 2013 Nov; 1(1): 122-131. Doi: 10.1109/JTEHM.2013.2290113. PMID: 27170860. PMCID: PMC4847478. Open Access Link.
  13. Phan JH, Young AN, and Wang MD. “omniBiomarker: a web-based application for knowledge-driven biomarker identification.” IEEE Transactions on Biomed Eng. 2013; 60(12): 3364-3367. Doi: 10.1109/TBME.2012.2212438. PMID: 22893372. PMCID: PMC5003093.

2012

  1. Sharma Y, Moffitt RA, Stokes TH, Chaudry Q, and Wang MD. “Feasibility analysis of high resolution tissue image registration using 3-D synthetic data.” J Pathol Inform. 2012 Jan; 2: 6. Doi: 10.4103/2153-3539.92037. PMID: 22811962. PMCID: PMC3312712. Open Access Link.
  2. Parry RM, Phan JH, and Wang MD. “Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems.” BMC Bioinformatics. 2012 Mar 21; 13(Suppl 3): S7. Doi: 10.1186/1471-2105-13-S3-S7. PMID: 22536905. PMCID: PMC3485616. Open Access Link [Journal h5-index: 75].
  3. Freimuth RR, Freund ET, Schick L, Sharma MK, Stafford GA Suzek BE, Hernandez J, Hipp J, Kelley J, Rokicki K, Pan S, Buckler A, Stokes TH, Fernandez A, Fore I, Beutow K, and Klemm J. “Life sciences domain analysis model.” J Am Med Inform Assoc. 2012 Jun 28; 19(6): 1095-1102. Doi: 10.1136/amiajnl-2011-000763. PMID: 22744959. PMCID: PMC3486731. Open Access Link.
  4. Quo CF, Kaddi CD, Phan JH, Zollanvari A, Xu M, *Wang MD (co-corresponding and handling author), and *Alterovitz G. “Reverse engineering biomolecular systems using –omics data: challenges, progress, and opportunities.” Briefings in Bioinformatics. 2012 Jul; 13(4): 430-445. Doi: 10.1093/bib/bbs026. PMID: 22833495. PMCID: PMC3404400. Open Access Link. [Journal h5-index: 85].
  5. Kong KY, Marcus AI, Giannakakou P, and Wang MD. “Integrating image analysis algorithms in a web interface for the quantification of microtubule dynamics.” Int J Comput Biol Drug Des. 2012 Sept.; 5(3-4): 298-313. Doi: 10.1504/IJCBDD.2012.049211. PMID: 23013655. PMCID: PMC8645235. Open Access Link.
  6. Phan JH, Quo CF, and Wang MD. “Cardiovascular genomics: a biomarker identification pipeline.” IEEE Transactions Information Technology Biomedicine. 2012 Sep; 16(5): 809-822. Doi: 10.1109/TITB.2012.2199570. PMID: 22614726. PMCID: PMC5003026.
  7. Andras TD, Alexander TS, Gahlena A, Parry RM, Fernandez FM, Kubanek J, Wang MD, and Hay ME. “Seaweed allelopathy against coral: surface distribution of a seaweed secondary metabolite by imaging mass spectrometry.” Journal of Chemical Ecology. 2012 Oct; 38(10): 1203-1214. Doi: 10.1007/s10886-012-0204-9. PMID: 23108534. PMCID: PMC3501597.
  8. Madajewski B1, Judy BF, Mouchli A, Kapoor V, Holt D, Wang MD, Nie SM, and Singhal S. “Intraoperative near-infrared imaging of surgical wounds after tumor resections can detect residual disease.” Clinical Cancer Research. 2012 Oct 15; 18(20): 5741-5751. Doi: 10.1158/1078-0432.CCR-12-1188. PMID: 22932668. PMCID: PMC3482441. Open Access Link.
  9. Phan JH, Young AN, and Wang MD. “Robust microarray meta-analysis identifies differentially expressed genes for clinical prediction.” Scientific World Journal, Bioinformatics and Biomedical Informatics. 2012 Nov 28; 2012: 989637. Doi: 10.1100/2012/989637. PMID: 23365541. PMCID: PMC3539384. Open Access Link.
  10. Phan JH, Quo CF, Cheng C, and Wang MD. “Multi-scale integration of molecular, imaging, and clinical data in biomedical informatics.” IEEE Rev Biomed Eng. 2012 Dec 10; 5: 74-87. Doi: 10.1109/RBME.2012.2212427. PMID: 23231990. PMCID: PMC5859561.

2011

  1. Quo CF, Moffitt RA, Merrill AH Jr., and Wang MD. “Adaptive control model reveals systematic feedback and key molecules in metabolic pathway regulation.” J Comput Biol. 2011 Feb; 18(2):169-82. Doi: 10.1089/cmb.2010.0215. PMID: 21314456. PMCID: PMC3123842. Open Access Link.
  2. Moffitt RA, Yin-Goen Q, Stokes TH, Parry RM, Torrance JH, Phan JH, Young AN, and Wang MD. “caCORRECT2: improving accuracy and reliability of microarray data in the presence of artifacts.” BMC Bioinformatics. 2011 Sep 29; 12:383. Doi: 10.1186/1471-2105-12-383. PMID: 21957981. PMCID: PMC3230913. Open Access Link [Journal h5-index: 75].
  3. Wang MD. “In the spotlight: bioinformatics, computational biology and systems biology.” IEEE Rev Biomed Eng. 2011; 4:3-5. Doi: 10.1109/RBME.2011.2177935. PMID: 22273782. PMCID: PMC5003032. Open Access Link.

2010

  1. Liu J, Lau SK, Varma VA, Moffitt RA, Caldwell M, Liu T, Young AN, Petros JA, Osunkoya AO, Krogstad T, Leyland-Jones B, Wang MD, and Nie SM. “Molecular mapping of tumor heterogeneity on clinical tissue specimens with multiplexed quantum dots.” ACS Nano. 2010 Apr 8; 4(5): 2755-2765. Doi: 10.1021/nn100213v. PMID: 20377268. PMCID: PMC2923482. Open Access Link.
  2. Singhal S, Nie SM, and Wang MD. “Nanotechnology applications in surgical oncology.” Annual Review of Medicine. 2010 Aug 2. 61: 359-373. Doi: 10.1146/annurev.med.60.052907.094936. PMID: 20059343. PMCID: PMC2913871. Open Access Link.
  3. Parry RM*, Jones W*, Stokes TH* (equal contributing authors), Phan JH, Moffitt RA, Fang H, Shi L, Oberthuer A, Fischer M, Tong W, and Wang MD. “K-nearest neighbors (KNN) models for microarray gene-expression analysis and clinical outcome prediction.” Pharmacogenomics J. 2010 Aug; 10(4): 292-309. Nature Biotechnology Supplement 2010 Oct; S62-S79. Doi: 10.1038/tpj.2010.56. PMID: 20676068. PMCID: PMC2920072. Open Access Link.
  4. The Microarray Quality Control Consortium (MAQC) and Shi L et al. (Wang MD,Phan JH, Stokes TH, Parry RM,Moffitt RA, and 190 other authors). “The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray-based predictive models.” Nature Biotechnology. 2010 Aug; 28(8): 827-838. Doi: 10.1038/nbt.1665. PMID: 20676074. PMCID: PMC3315840. Open Access Link. [Journal h5-index: 175].
  5. Mohs AM, Mancini MC, Singhal S, Provenzale JM, Leyland-Jones B, Wang MD, and Nie S. “A hand-held spectroscopic device for in vivo and intraoperative tumor detection: contrast enhancement, detection sensitivity, and tissue penetration.” Anal Chem. 2010 Nov 1;82(21):9058-9065. Doi: 10.1021/ac102058k. PMID: 20925393. PMCID: PMC3030682. Open Access Link.

2009

  1. Chaudry Q, Raza SH, Young AN, and Wang MD. “Automated renal cell carcinoma subtype classification using morphological, textural and wavelets based features.” J Signal Process Syst. 2009; 55(1):15-23. Doi: 10.1007/s11265-008-0214-6. PMID: 28133502. PMCID: PMC5267341. Open Access Link.
  2. Merrill AH Jr., Stokes TH, Momin A, Park H, Portz BJ, Kelly S, Wang E, Sullards MC, and Wang MD. “Sphingolipidomics: a valuable tool for understanding the roles of sphingolipids in biology and disease.” J Lipid Res. 2009 Apr; 50(Suppl): S97-S102. Doi: 10.1194/jlr.R800073-JLR200. PMID: 19029065. PMCID: PMC2674747. Open Access Link.
  3. Lane AL, Nyadong L, Galhena A, Stout EP, Parry RM, Wang MD, Hay ME, Fernandez FM, and Kubanek J. “Desorption electrospray ionization mass spectrometry reveals surface-mediated antifungal chemical defense of a tropical seaweed.” Proc Natl Acad Sci (PNAS) USA. 2009 May 5; 106(18): 7314-7319. Doi: 10.1073/pnas.0812020106. PMID: 19366672. PMCID: PMC2678663. Open Access Link.
  4. Nyadong L, Harris GA, Belayssac S, Galhena AS, Malet-Martino M, Martino R, Parry RM, Wang MD, *Fernandez FM, and *Gilard V (co-corresponding senior authors). “Combining two-dimensional diffusion-ordered nuclear magnetic resonance spectroscopy, imaging desorption electrospray ionization mass spectrometry and direct analysis in real time mass spectrometry for the integral investigation of counterfeit pharmaceuticals.” Anal Chem. 2009 May 19; 81(12): 4803-4812. Doi: 10.1021/ac900384j. PMID: 19453162. PMCID: PMC4983440. Open Access Link.
  5. Phan JH, Moffitt RA, Stokes TH, Liu J, Young AN, *Nie SM, and *Wang MD (co-corresponding senior authors). “Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment.” Trends Biotechnol. 2009 Jun; 27(6): 350-358. Doi: 10.1016/j.tibtech.2009.02.010. PMID: 19409634. PMCID: PMC3779321. Open Access Link. [Journal h5-index: 90].
  6. Osunkoya AO, Yin-Goen Q, Phan JH, Moffitt RA, Stokes TH, Wang MD, and Young AN. “Diagnostic biomarkers for renal cell carcinoma: selection using novel bioinformatics systems for microarray data analysis.” Hum Pathol. 2009 Dec; 40(12): 1671-1678. Doi: 10.1016/j.humpath.2009.05.006. PMID: 19695674. PMCID: PMC2783948. Open Access Link.

2008

  1. Qian X, Peng XH, Ansari DO, Yin-Goen Q, Chen GZ, Shin DM, Yang L, Young AN, Wang MD, and Nie SM. “In vivo tumor targeting and spectroscopic detection with surface-enhanced Raman nanoparticle tags.” Nat Biotechnol. 2008 Jan; 26(1): 83-90. Doi: 10.1038/nbt1377. PMID: 18157119. [Journal h5-index: 175].
  2. Young AN, Master VA, Paner GP, Wang MD, and Amin MB. “Renal epithelial neoplasms: diagnostic applications of gene expression profiling.” Adv Anat Pathol. 2008 Jan; 15(1): 28-38. Doi: 10.1097/PAP.0b013e3181594720. PMID: 18156810.
  3. Agrawal A., Deo R, Wang G, *Wang MD, and *Nie SM (co-corresponding senior authors). “Nanometer-scale mapping and single molecule detection with color-coded nanoparticle probes.” Proc Natl Acad Sci USA. 2008 Mar 4; 105(9): 3298-303. Note: This paper was derived from Wang G, Agrawal A, Nie SM, and Wang MD, “Optically encoded nanoparticles for detecting single biomolecules and viruses: rapid analysis of two-color colocalization data by high-speed computing.” Proc. of IEEE 27th Annual Int. Conf. Engineering in Medicine and Biology Society (EMBC’05); pp.1739-1742. Doi: 10.1073/pnas.0712351105. PMID: 18305159. PMCID: PMC2265145. Open Access Link.
  4. Quo CF and Wang MD. “Quantitative analysis of numerical solvers for oscillatory biomolecular system models.” BMC Bioinformatics. 2008 May 28; 9(Suppl 6):S17. Doi: 10.1186/1471-2105-9-S6-S17. PMID: 18541052. PMCID: PMC2423440. Open Access Link. [Journal h5-index: 75].
  5. Stokes TH, Torrance JT, Li H, and Wang MD. “ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.” BMC Bioinformatics. 2008 May 28; 9(Suppl 6): S18. Doi: 10.1186/1471-2105-9-S6-S18. PMID: 18541053. PMCID: PMC2423441. Open Access Link. [Journal h5-index: 75].

2007

  1. Xing Y, Chaudry Q, Shen C, Kong KY, Zhau HE, Chung LW, Petros JA, O’Regan RM, Yezhelyev MV, Simons JW, *Wang MD, and *Nie SM (co-corresponding senior authors). “Bioconjugated quantum dots for multiplexed and quantitative immunohistochemistry.” Nat Protoc. 2007 May 3; 2(5):1152-1165. Doi: 10.1038/nprot.2007.107. PMID: 17546006. Open Access Link.
  2. *Stokes TH, *Moffitt RA (equal contributing authors), Phan JH, and Wang MD. “chip artifact CORRECTion (caCORRECT): A bioinformatics system for quality assurance of genomics and proteomics array data.” Ann Biomed Eng. 2007 Jun; 35(6): 1068-1680. Doi: 10.1007/s10439-007-9313-y. PMID: 17458699. Open Access Link [Journal h5-index: 52].
  3. Wang MD, Shin DM, Simons JW, and Nie SM. “Nanotechnology for targeted cancer therapy.” Expert Rev Anticancer Ther. 2007 Jun; 7(6): 833-837. Doi: 10.1586/14737140.7.6.833. PMID: 17555393.
  4. *Wang MD, *Simons JW, and *Nie SM (co-corresponding senior authors). “Biomedical nanotechnology with bioinformatics–the promise and current progress.” Proc IEEE. 2007 Jul; 95(7): 1386-1389. Open Access Link [Journal h5-index: 101].
  5. Merrill AH Jr., Wang MD, Park M, and Sullards MC. “(Glyco)sphingolipidology: an amazing challenge and opportunity for systems biology.” Trends Biochem Sci. 2007 Oct; 32(10): 457-468. Doi: 10.1016/j.tibs.2007.09.004. PMID: 17928229.

2006

  1. Yin-Goen Q, Dale J, Yang WL, Phan JH, Moffitt RA, Petros JA, Datta MW, Amin MB, Wang MD, and Young AN. “Advances in molecular classification of renal neoplasms.” Histol Histopathol. 2006 Mar; 21(3): 325-339. Doi: 10.14670/HH-21.325. PMID: 16372253. Open Access Link.
  2. Young AN, Dale J, Yin-Goen Q, Harris WB, Petros JA, Datta MW, Wang MD, Marshall FF, and Amin MB. “Current trends in molecular classification of adult renal tumors.” Urology. 2006 May; 67(5):873-880. Doi: 10.1016/j.urology.2005.11.042. PMID: 16698345.

2005

  1. *Pardo SJ, *Patel MJ (equal contributing authors), Sykes MC, Platt MO, Boyd NO, Sorescu GP, Xu M, van Loon JJ, Wang MD, and Jo H. “Simulated microgravity using the random positioning machine inhibits differentiation and alters gene expression profiles of 2T3 pre-osteoblasts.” Am J Physiol Cell Physiol. 2005 Jun; 288(6): C1211-21. Doi: 10.1152/ajpcell.00222.2004. PMID: 15689415. Open Access Link.

2003

  1. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, and Weinstein JN. “GoMiner: a resource for biological interpretation of genomic and proteomic data.” Genome Biol. 2003 Mar 25; 4(4): R28. Doi: 10.1186/gb-2003-4-4-r28. PMID: 12702209. PMCID: PMC154579. Open Access Link.

C. Refereed Conference Proceedings

2026

  1. Gu Y, Li X, Zhang C, Wang R, Huang, Cargin E, Nnamdi MC, Tamo BJ, Shi W, and Wang MD. “PKAttn: Pharmacokinetics-inspired fusion of DCE-MRl and clinical data for accurate breast cancer recurrence prediction.” 2026 IEEE 23rd International Symposium on Biomedical Imaging (ISBI). London, UK. 2026; pp. 1 – 4. [Note: Oral]
  2. Wang S, Zhong Y, Marteau BL, Tan SQY, Yuan Y, Wang Y, and Wang MD. “Rethinking model complexity: Contrastive frame embedding in transformer-based echocardiogram ejection fraction estimation.” 2026 IEEE 23rd International Symposium on Biomedical Imaging (ISBI). London, UK. 2026; pp. 1 – 4.
  3. Li J, Chen M, Nnamdi MC, Tamo BJ, Marteau BL, and Wang MD. “RobustMedSAM: degradation-resilient medical image segmentation via robust foundation model adaptation.” Computer Vision and Pattern Recognition (CVPR) 2026 Workshop CV4Clinical. Denver, Colorado. 2026; pp. 1 – 8. [Note: Oral].
  4. Liang Y, Tan SQY, Marteau BL, Hornback A, Sathu H, Pahys JM, Hwang SW, Brenn B, Hilton C, and Wang MD. “BRIDGE: A bidirectional reality and informatics data gateway for closing the clinical workflow loop in XR”. 2026 IEEE International Conference on Intelligent Reality (IEEE ICIR). Tuscany, Italy. 2026; pp. 1 – 8.
  5. Nnamdi MC, Marteau BL, Zhong Y, Tamo BJ, and Wang MD. “Tree-of-Evidence: efficient “system 2″ search for faithful multimodal grounding.” In Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (ACL 2026), Findings. San Diego, California. 2026.
  6. Lu Y, Zhao X, Tamo BJ, Nnamdi MC, Peng R, Zeng S, Hu X, Wang J, and Wang MD. “MetaBench: A multi-task benchmark for assessing llms in metabolomics.” In Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (ACL 2026). San Diego, California. 2026.

2025

  1. Chen M, Marteau B, Nnamdi MC, Tamo JB, and Wang MD. “Augmenting spline interpolated dementia EEG data with deep learning for improved multi-centric data harmonization.” IEEE International Symposium on Biomedical Imaging (ISBI 2025). 2025; pp. 1 – 4.
  2. Patil OR, Marteau B, Giuste F, and Wang MD. “Synthetic H&E generation from highly multiplexed immunofluorescence imaging using deep-learning.” IEEE International Symposium on Biomedical Imaging (ISBI 2025). 2025; pp. 1 – 4.
  3. Kim K, Sathu H, Hornback A, Isgut M, Traynelis J, and Wang MD. “Enhancing colon cancer risk prediction in machine learning models using polygenic risk scores.” In 2025 47th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Copenhagen, Denmark. 2025; pp. 1 – 7.
  4. Piazzi M, Wang Y, Hornback A, Isgut M, Sathu H, Jaishanker A, and Wang MD. “Machine learning-based prediction for stroke patient classification using polygenic risk scores.” In 2025 47th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Copenhagen, Denmark. 2025; pp. 1 – 7.
  5. Hornback A, Lewis RW, Liang WH, Effinger KE, Muthu N, Sathu, H, Zhu, Y,Marteau B, and Wang MD. “Developing semi-automated approaches for generating survivorship care plans for pediatric cancer survivors.”  2025 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI). Atlanta, GA, USA. 2025; pp. 1 – 7. (Acceptance Rate: 29.5%).
  6. Mallya BV, Nnamdi MC, Tamo JB, Chen M, Zhong Y, Shi W, and Wang MD. “ResSwinUnet3D: a residual-based model for enhanced 3D medical image segmentation.”  2025 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI). Atlanta, GA, USA. 2025; pp. 1 – 7. (Acceptance Rate: 29.5%).
  7. Muthukumaran MP, Nnamdi MC, Tamo BJ, Purnell C, and Wang MD. “Developing an attention-based deep learning framework for obstructive sleep apnea detection using single-channel oximetry signal.” 2025 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI). Atlanta, GA, USA. 2025; pp. 1 – 7. (Acceptance Rate: 29.5%).
  8. Yuan Y, Tamo JB, Nnamdi MC, Wang Y, and Wang MD. “Leveraging evidence-guided LLMs to enhance trustworthy depression diagnosis.” 2025 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI). Atlanta, GA, USA. 2025; pp. 1 – 7. (Acceptance Rate: 29.5%). [Note: Oral].
  9. Marteau BL, Hornback A, Tan SQY, Woloff J, Lowson C, and Wang MD. “An AI implementation science study to enable trustworthy AI in a large healthcare system.” 2025 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI). Atlanta, GA, USA. 2025; pp. 1 – 7. (Acceptance Rate: 29.5%).
  10. Nnamdi MC, Shi W, Wang C, Tamo BJ, Smith B, Purnell C, and Wang MD. “KindSleep: knowledge-informed diagnosis of obstructive sleep apnea from oximetry.” The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Philadelphia, USA. 2025; pp. 1 – 10. (Acceptance Rate: 19.4%). [Note: Oral].
  11. Zhong Y, Shi W, Tamo BJ, Nnamdi MC, Yuan Y, and Wang MD. “Collective reasoning in LLMs: A multi-agent framework for clinical procedure sequencing.” The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Philadelphia, USA. 2025; pp. 1 – 10. (Acceptance Rate: 19.4%). [Note: Oral].
  12. Yuan Y, Tamo JB,Shi W, Zhong Y, Nnamdi MC, Hwang SW, Brenn BR, and Wang MD. “Developing fairness-aware task decomposition to improve equity in post-spinal fusion complication prediction.” The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Philadelphia, USA. 2025; pp. 1 – 10. (Acceptance Rate: 19.4%). [Note: Oral].
  13. Tan SQY, Wang S, Wang CP, Florea A, Wang I, Agoreyo D, Speck J, Nnamdi MC, Tamo BJ, Marteau BL, Zhong Y, Poon S, and Wang MD. “A hybrid deep learning framework for automated cobb angle estimation in scoliosis assessment.” The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Philadelphia, USA. 2025; pp. 1 – 6.
  14. Patil OR, Shazand K, Marteau B, Shen Y, and Wang MD. “Data-Driven symbolic higher-order epistasis discovery with kolmogorov-arnold networks.” The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Philadelphia, USA. 2025; pp. 1 – 6.
  15. Isgut M, Hornback A, Samel K, Gloster L, Jain N, Kim K, and Wang MD. “Interpretable neural networks reveal gene interactions underlying autoimmune disease risk.” The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Philadelphia, USA. 2025; pp. 1 – 6.
  16. Chouhan NS, Tamo JB, Oankar P, Shi W, Nnamdi MC, Hwang SW, Shazand K, and Wang MD. “From association to mechanism: Causal graph-based fine-mapping of regulatory SNPs for functional validation.” The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Philadelphia, USA. 2025; pp. 1 – 6.
  17. Tan SQY*, Marteau B*, Chouhan NS, Yuan Y, Hornback A, Zhong Y, Donahue S, Chafetz R, and Wang MD. “Generative speech-to-mesh AI pipeline for personalized VR experience.” IEEE International Conference on Intelligent Reality (IEEE ICIR). Boston, MA. 2025; pp. 1 – 8.
  18. Marteau B, Tan SQY, Li J, Hornback A, Zhong Y, Wang S, Pahys JM, Hwang SW, Hilton C, and Wang MD. “EXR: An interactive immersive EHR visualization in extended reality.”  IEEE International Conference on Intelligent Reality (IEEE ICIR). Boston, MA. 2025; pp. 1 – 8.

2024

  1. Jain N, Hornback A, and Wang MD. “EMxDesign: A genetic algorithm for high affinity drug design.” In Genetic and Evolutionary Computation Conference (GECCO’24 Companion). 2024; pp. 439-442. (Acceptance Rate: 36%).
  2. Xu R*, Shi W* (equal contributing authors), Yu Y, Zhuang Y, Jin B, Wang MD, Ho JC, and Yang C. “RAM-EHR: retrieval augmentation meets clinical predictions on electronic health records.” In Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL). 2024; pp. 754-765. [Note: Oral].
  3. Xu R, Cui H, Yu Y, Kan X, Shi W, Zhuang Y, WangMD, Jin W, Ho J, and Yang C. “Knowledge-infused prompting: assessing and advancing clinical text data generation with large language models.” In Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL). 2024; pp. 15496–15523.
  4. Khimani A, Hornback A, Jain N, Avula P, Jaishankar A, and Wang MD. “Predicting cardiovascular disease risk in tobacco users using machine learning algorithms.” In 2024 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Orlando, USA. 2024; pp. 1-4. [Note: Oral]. [Note: Georgia Tech. Bioinformatics Department MS Best Student Paper Award].
  5. Jaishankar A, Jain N, Hornback A, Khimani A, Avula P, and Wang MD. “Identifying features for keloid scars subtyping using k-modes clustering.” In 2024 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Orlando, USA. 2024; pp. 1-4. [Note: Georgia Tech. Bioinformatics Department MS Best Student Paper Award].
  6. Xu R*, Shi W* (equal contributing authors), Yu Y, Zhuang Y, Zhu Y, Wang MD, Ho JC, Zhang C, and Yang C. “BMRetriever: tuning large language models as better biomedical text retrievers.” Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP). Miami, Florida, USA. 2024; pp. 1-20.
  7. Shi W*, Xu R* (equal contributing authors), Zhuang Y, Yu Y, Zhang J, Wu H, Zhu Y, Ho JC, Yang C, and Wang MD. “EHRAgent: code empowers large language models for few-shot complex tabular reasoning on electronic health records.” Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP). Miami, Florida, USA. 2024; pp. 1-25.
  8. Shi W*, Xu R*, Zhuang Y, Yu Y, Sun H, Wu H, Yang C, and Wang MD. “MedAdapter: efficient test-time adaptation of large language models towards medical reasoning.” Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP). Miami, Florida, USA. 2024; pp. 1-21.
  9. Tamo JB, Nnamdi MC, Hornback A, Chen M, Shi W, Zhu Y, Iwinski HJ, and Wang MD. “Heterogeneous treatment effects of spinal fusion surgery for adolescent idiopathic scoliosis patients.” The 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). China, Nov. 2024; pp. 1–10. (Acceptance Rate: 34.8%; Top: 17.1%). [Note: Oral]. [Note: Best Student Paper Award].
  10. Hornback A, Isgut M, Jaishankar A, Sathu H, Avula P, Marteau B, and Wang MD. “Uncovering key features of individuals who benefit from polygenic risk scores in prostate cancer prediction.” The 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), China, Nov. 2024; pp. 1–6. (Acceptance Rate: 34.8%).
  11. Nnamdi MC, Tamo JB, Shi W, Chundru V., Marteau BL, Patil OR, and Wang MD. “Confidence-calibrated clinical decision support system for reliable respiratory disease screening.” 2024 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI). Houston, TX, USA. 2024; pp. 1 – 8. (Acceptance Rate: 24.6%).
  12. Marteau B, Hornback A, Zhong Y, Lowson C, Woloff J, Smith BM, Hilton C, and Wang MD. “Improving a large healthcare system research data warehouse using OHDSI’s data quality dashboard.” 2024 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI). Houston, TX, USA. 2024; pp. 1 – 8. (Acceptance Rate: 24.6%).
  13. Marteau B, Vashista S, Chen M, Geng W, Hornback A, Nnamdi MC, Tan S, Zhong Y, Okada N, Acerbo E, Dickey AS, Drane DL, and Wang MD. “Brain digital twin combining artificial intelligence and extended reality.” IEEE International Conference on Intelligent Reality (IEEE ICIR). Coimbra, Portugal. 2024; pp. 1 – 8. [Note: Oral].
  14. Tan S, Zhong Y, Marteau B, Hornback A, Warshauer S, Courter R, Donahue S, Lottier L, Russo S, Shi W, Richardson RT, Chafetz R, and Wang MD. “VR-RAISE: virtual reality for reachability assessment using an interactive system environment.” IEEE International Conference on Intelligent Reality (IEEE ICIR). Coimbra, Portugal. 2024; pp. 1 – 8. [Note: Oral].
  15. Chundru VK, Kilinc MS, Lim A, Nnamdi MC, Zhong Y, Shi W, and Wang MD. “Quantitative explainability study of deformable convolutional neural networks using chest X-rays.” In 2024 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). 2024; pp. 1 – 6.

2023

  1. Nnamdi MC, Tamo JB, Stackpole S, Shi W, Marteau B, and Wang MD. “Model confidence calibration for reliable COVID-19 early screening via audio signal analysis.” The 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Huston, TX, USA. Sep. 2023; pp. 1–6. (Acceptance Rate: 29%). [Note: Oral].
  2. Shi W, Marteau B, Giuste F, and Wang MD. “Choice over effort: mapping and diagnosing augmented whole slide image datasets with training dynamics.” The 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Huston, TX, USA. Sep. 2023; pp. 1–6. (Acceptance Rate: 29%). [Note: Oral].
  3. Tamo JB, Shi W, Zhu Y, Nnamdi MC, Iwinski H, Wattenbarger M, and Wang MD. “Adolescent idiopathic scoliosis patient subphenotyping for surgical planning and improved patient outcomes.” The 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Houston, TX, USA. Sep. 2023; pp. 1–10. (Acceptance Rate: 29%, Top 17.2%). [Note: Oral].
  4. Nnamdi MC, Shi W, Tamo JB, Iwinski H, Wattenbarger M, and Wang MD. “Concept bottleneck model for adolescent idiopathic scoliosis patient reported outcomes prediction.” 2023 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI), Pittsburgh, Pennsylvania, USA. 2023; pp. 1-4. (Acceptance Rate: 23.6%). [Note: Oral].
  5. Han B, Deng J, Xing S, Zhong Y, Shi W, Marteau B, Das B, Shehata B, Deshpande S, and Wang MD. “Rare heart transplant rejection classification using diffusion-based synthetic image augmentation.” 2023 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI), Pittsburgh, Pennsylvania, USA. 2023; pp. 1-4. (Acceptance Rate: 23.6%). [Note: Oral].
  6. Zhu Y, and Wang MD. “Automated seizure detection using transformer models on multi-channel EEGs.” 2023 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI), Pittsburgh, Pennsylvania, USA. 2023; pp. 1-4. (Acceptance Rate: 23.6%). [Note: Oral].
  7. Hornback A, Zhu Y, Isgut M, Shi W, Nema A, Anderson B, and Wang MD. “Latent topic extraction as a source of labeling in natural language processing.” In 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). 2023; pp. 4312-4319.
  8. Tamo JB, Nnamdi MC, Lesbats L, Shi W, Zhong Y and Wang MD. “Development of Uncertainty-aware ensemble deep learning models for out-of-distribution medical imaging analysis.” In 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). 2023; pp. 4243-4250.
  9. Shi W, Murakoso M, Guo X, and Wang MD. “Development of interpretable machine learning models for COVID-19 drug target docking scores prediction.” In 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), 2023; pp. 4124-4131.
  10. Shi W, Murakoso M, Guo X, Xiong L, Chen M, and Wang MD. “Effective surrogate models for docking scores prediction of candidate drug molecules on SARS-CoV-2 protein targets.” In 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), 2023; pp. 4235-4242.
  11. Singh A, Shi W, and Wang MD. “Multi-modal deep feature integration for Alzheimer’s disease staging.” In 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). 2023; pp. 1-6. (Acceptance Rate: 19%).
  12. Li X, Zhang C, Chen W, Shi W, and Wang MD. “Identification of single-cell RNA sequencing molecular signatures for COVID-19 infection severity classification.” In 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). 2023; pp. 2044-2047. (Acceptance Rate: 19%).
  13. Ding C, Lin D, Lei Z, Myers J, Shi W, Marteau B, and Wang MD. “Personalized COVID-19 early detection using wearable data based on self-reported records.” In 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). 2023; pp. 3348-3353.

2022

  1. Marteau B, Zhu Y, Giuste F, Shi W, Carpenter A, Hilton C, Wang MD. “Accelerating multi-site health informatics with streamlined data infrastructure using OMOP-on-FHIR.” In 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) (pp. 1-4), 2022, IEEE.
  2. Zhu Y, Mahale A, Peters K, Mathew L, Giuste F, Anderson B, and Wang MD. “Using natural language processing on free-text clinical notes to identify patients with long-term covid effects.” The 13th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Chicago, IL, USA, Sep. 2022; pp. 1–10. (Acceptance Rate: 29%).
  3. Hornback A, Shi W, Giuste F, Zhu Y, Carpenter AM, Hilton C, Bijanki VN, Stahl H, Gottesman Gs, Purnell C, Iwinski HJ, Wattenbarger JM, and Wang MD. “Development of a generalizable multi-site and multi-modality clinical data cloud infrastructure for pediatric patient care.” The 13th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Chicago, IL, USA. Sep. 2022; pp. 1–10. (Acceptance Rate: 29%).
  4. Goel A, Mudge Z, Bi S, Bremmer C, Huffman N, Giuste F, Marteau B, Shi W, and Wang MD. “Identification of COVID-19 severity and associated genetic biomarkers based on scRNA-seq data.” The 13th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Chicago, IL, USA. Sep. 2022; pp. 1-5. (Acceptance Rate: 29%).
  5. Mahale A, Zhu Y, Belhareth S, Graf A, Kruger K, Krzak J, and Wang MD. “Automating treatment recommendations for children with cerebral palsy based on multi-modal clinical data.” In 2021 IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI). 2022; pp. 1-4. (Acceptance Rate: 30.2%).
  6. Li Y, Hsu JS, Bari N, Qiu X, Viswanathan M, Shi W, Giuste F, Zhong Y, Sun J, and Wang MD. “Interpretable evaluation of diabetic retinopathy grade regarding eye color fundus images.” In 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (IEEE BIBE). 2022; pp. 1-6. (Acceptance Rate: 50.5%).
  7. Lee BJ, Martirosyan ST, Khan Z, Chiu H, Wang Z, Shi W, Giuste F, Zhong Y, Sun J, and Wang MD. “Attention-based automated chest CT image segmentation method of COVID-19 lung infection.” In 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (IEEE BIBE). 2022; pp. 1-6. (Acceptance Rate: 50.5%).
  8. Prabhu SS, Berkebile JA, Rajagopalan N, Yao R, Shi W, Giuste F, Zhong Y, Sun J, and Wang MD. “Multi-Modal deep learning models for Alzheimer’s disease prediction via integration of MRI and EHR.” In 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (IEEE BIBE). 2022; pp. 1-6. (Acceptance Rate: 50.5%).
  9. Zamitalo A, Xie Q, Allam M, Philip P, Shi W, Giuste F, Marteau B, Murakoso M, and Wang MD. “Development of machine learning regression model for COVID-19 drug target prediction.” In 2022 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). 2022; pp. 1-8. (Acceptance Rate: 19%).
  10. Zhong Y, Marteau B, Hornback A, Zhu Y, Shi W, Giuste F, Krzak J, Graf A, Chafetz R, and Wang MD. “IDTVR: A novel cloud framework for an interactive digital twin in virtual reality.” In 2022 IEEE International Conference of Intelligent Reality (IEEE ICIR). 2022; pp. 1-4. [Note: Oral]. [Note: Best Paper Award].

2021

  1. Naren T, Zhu Y, and Wang MD. “COVID-19 diagnosis using model agnostic meta-learning on limited chest x-ray images.” The 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), New York, NY, USA, 2021; pp. 1–9. [Note: Oral].
  2. Shi W, Gupte M, and Wang MD. “Learning from heterogeneous data via contrastive learning: an application in multi-source COVID-19 radiography.” 2021 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), 2021; pp. 1-4.  (Acceptance Rate: 32%).
  3. Gazi A, Lis P, Mohseni A, Ompi C, Giuste F, Shi W, Inan O, and Wang MD. “Respiratory markers significantly enhance anxiety detection using multimodal physiological sensing.” 2021 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), 2021; pp. 1-4.  (Acceptance Rate: 32%). [Note: Oral].
  4. Giuste F, He L, Isgut M, Shi W, Anderson B, and Wang MD. “Automated risk assessment of COVID-19 patients at diagnosis using electronic healthcare records.” 2021 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), 2021; pp. 1-4.  (Acceptance Rate: 32%). [Note: Oral].
  5. Mirzazadeh A, Mohseni A, Ibrahim S, Giuste F, Zhu Y, Shehata B, Deshpande S, and Wang MD. “Improving heart transplant rejection classification training using progressive generative adversarial networks.” 2021 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), 2021; pp. 1-4.  (Acceptance Rate: 32%).
  6. Usanmaz C, Valancius M, White M, and Wang MD. “A novel approach to missing data imputation in physiological time-series signals.” 2021 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI), 2021; pp. 1-4.  (Acceptance Rate: 32%).
  7. Ellis CA, Zhang R, Calhoun VD, Carbajal DA, Miller RL, Wang MD. “A gradient-based approach for explaining multimodal deep learning classifiers.” The 21th IEEE International Conference on BioInformatics and BioEngineering (IEEE BIBE), 2021; pp. 1-6.
  8. Ellis CA, Zhang R, Calhoun VD, Carbajal DA, Sendi M, Wang MD, and Miller RL. “A novel local ablation approach for explaining multimodal classifiers.” In 2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (IEEE BIBE), 2021; pp. 1-6.
  9. Shi W, Giuste F, Zhu Y, Carpenter A, Iwinski H, Hilton C, Wattenbarger M, and Wang MD. “A FHIR-compliant application for multi-site and multi-modality pediatric scoliosis patient rehabilitation.” In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 1524-1527). IEEE. (Acceptance Rate: 19%).
  10. Ellis CA, Zhang R, Calhoun VD, Carbajal DA, Miller RL, Calhoun VD, and Wang MD. “Explainable sleep stage classification with multimodal electrophysiology time-series.” In 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) (pp. 2363-2366), 2021, IEEE.

2020

  1. Wu H and Wang MD. “An information theoretic learning for causal direction identification.” 2020 IEEE Computer Society Signature Conference on Computers, Software and Applications (COMPSAC). Madrid, Spain. 2020; pp. 287-294. (Acceptance Rate: 40%). [Note: Best Paper Award].
  2. Wu H and Wang MD. “Training confidence-calibrated classifier via distributionally robust learning.” 2020 IEEE Computer Society Signature Conference on Computers, Software and Applications (COMPSAC). Madrid, Spain. 2020; pp. 295-304. (Acceptance Rate: 40%).
  3. Konda R., Wu H and Wang MD. “Graph Convolutional Neural Networks to classify whole slide images.” 2020 IEEE Computer Society Signature Conference on Computers, Software and Applications (COMPSAC). Madrid, Spain. 2020; pp. 1334-1338. (Acceptance Rate: 40%).
  4. Saqib M, Zhu Y, Wang MD and Beaulieu-Jones B. ” Regularization of Deep Neural Networks for EEG seizure detection to mitigate overfitting.” 2020 IEEE Computer Society Signature Conference on Computers, Software and Applications (COMPSAC). Madrid, Spain. 2020; pp. 664-673. (Acceptance Rate: 40%).
  5. Patil SM, Tong Li, and Wang MD. “Generating region of Interests for invasive breast cancer in histopathological whole slide image.” 2020 IEEE Computer Society Signature Conference on Computers, Software and Applications (COMPSAC). Madrid, Spain. 2020; pp. 732-728. (Acceptance Rate: 40%).
  6. Giuste F, Venkatesan M, Zhao C, Tong L, Zhu Y, Deshpande S, and Wang MD. “Automated classification of acute rejection from endomyocardial biopsies.” The 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), New York, NY, USA, Sep. 2020; pp. 1–9. (Acceptance Rate: 33%). [Note: Oral].
  7. Shi W, Tong L, Zhuang Y, Zhu Y and Wang MD. “EXAM: An explainable attention-based model for COVID-19 automatic diagnosis.” The 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), New York, NY, USA, Sep. 2020; pp. 1–6. (Acceptance Rate: 33%). [Note: Oral].
  8. Jiang Y, Alford K, Ketchum F, Tong L and Wang MD. “TLSurv: Integration of multi-omics data using multi-stage transfer learning for lung cancer prognosis prediction.” The 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), New York, NY, USA, Sep. 2020; pp. 1–9. (Acceptance Rate: 33%). [Note: Oral].
  9. Zhu Y, Saqib M, Ham E, Belhareth S,Hoffman RA, Wang MD. “Mitigating patient-to-patient variation in EEG seizure detection using meta transfer learning.” The 20th IEEE International Conference on BioInformatics and BioEngineering (IEEE BIBE), 2020; pp. 548-555. [Note: Oral].

2019

  1. Zhu Y, Tong L, and Wang MD. “Improved prediction on heart transplant rejection using convolutional Autoencoder and multiple instance learning on Whole-Slide Imaging.” 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). Chicago, IL, USA. May 2019; pp. 1-4. (Acceptance Rate: 35%). [Note: Oral].
  2. Zhu Y, Wu H, and Wang MD. “Feature exploration and causal inference on mortality of epilepsy patients using insurance claims data.” 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). Chicago, IL, USA. May 2019; pp. 1-4. (Acceptance Rate: 35%). [Note: Oral].
  3. Tong L, Sha Y, and Wang MD. “Improving classification of breast cancer by utilizing the image pyramids of whole-slide imaging and multi-scale convolutional neural networks.” Conf Proc IEEE Computer Society Signature Conference on Computers, Software and Applications (COMPSAC). Milwaukee, Wisconsin, USA. July 15-19, 2019.  Vol. 1; pp. 696-703. (Acceptance Rate: 40%). [Note: Oral].
  4. Choudhary A, Wu H, Tong L, and Wang MD. “Learning to evaluate color similarity for histopathology images using triplet networks.” The 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Niagara Falls, NY, Sept 7-10, 2019; pp. 466-474. (Acceptance Rate: 28%). [Note: Oral].
  5. Vizcarra J, Place R, Tong L, Gutman D and Wang MD. “Fusion in breast cancer histology classification.” The 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Niagara Falls, NY, Sept 7-10, 2019; pp. 485-493. (Acceptance Rate: 28%). [Note: Oral].
  6. Mitchel J, Chatlin K, Tong L and Wang MD. “A translational pipeline for overall survival prediction of breast cancer patients by decision-level integration of multi-omics data.” 2019 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM) November 18-21, 2019. San Diego, CA, USA; pp. 1573-1580. ((Acceptance Rate: 45%). [Note: Oral].
  7. Tanade C, Pate N, Paljug E, Hoffman RA and Wang MD. “Hybrid modeling of Ebola propagation.” IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE). Athens, Greece. 2019; pp. 204-210. (Acceptance Rate: 48%). [Note: Oral].

2018

  1. Dooley AE,Tong L, and Wang MD. “Prediction of heart transplant rejection using histopathological whole-slide imaging.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Las Vegas, NV, USA. 2018 Mar. 4-7; pp. 251-254. (Acceptance Rate: 37%). [Note: Oral].
  2. Wu H and Wang MD. “Variance regularized counterfactual risk minimization via variational divergence minimization.” Proceedings of the 35th International Conference on Machine Learning, 2018. Stockholm, Sweden; pp. 5353-5362. (Acceptance Rate: 25%). [Note: Oral].
  3. Saqib M, Sha Y, and Wang MD. “Early prediction of sepsis in EMR records using traditional ML techniques and deep learning LSTM networks.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Honolulu, HI, USA. 2018 July 17-21; pp. 4038-4041. [Note: Oral].
  4. Qv L, Zhu H, and Wang MD. “Micro-inversions in human cancer genomes.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Honolulu, HI, USA. 2018 July 17-21; pp. 1323-1326.
  5. Hoffman RA, Venugopalan J, Li Q, Wu H, and Wang MD. Improving validity of cause of death on death certificates” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, (ACM BCB). Washington, DC, USA, 2018. Aug 29-Sep 1; pp. 178-183. (Acceptance Rate: 45%). [Note: Oral].

2017

  1. Hoffman RA, Wu H, Venugopalan J, Braun P, and Wang MD. “Intelligent mortality reporting with FHIR.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Orlando, FL, USA. 2017 Feb. 16-19; pp. 181-184. (Acceptance Rate: 39%).
  2. Tong L, Hoffman RA, Deshpande SR, and Wang MD. “Predicting heart rejection using histopathological whole-slide imaging and deep neural network with dropout.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Orlando, FL, USA. 2017 Feb. 16-19; pp. 1-4. (Acceptance Rate: 39%).
  3. Wu H, Tong L, and Wang MD. “Improving Multi-class classification for endomicroscopic images by semi-supervised learning.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Orlando, FL, USA. 2017 Feb. 16-19; pp. 5-8. (Acceptance Rate: 39%).
  4. Jiang HY, Wu H, and Wang MD. “Causes of death in the United States, 1999 to 2014.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Orlando, FL, USA. 2017 Feb. 16-19; pp. 177-180. (Acceptance Rate: 39%). [Note: Oral].
  5. Venugopalan J, LaPlaca MC, and Wang MD. “Mining standardized neurological signs and symptoms data for concussion identification.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Orlando, FL, USA. 2017 Feb. 16-19; pp. 285-288. (Acceptance Rate: 39%).
  6. Hassanzadeh HR, Sha Y, and Wang MD. “DeepDeath: Learning to predict the underlying cause of death with big data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Jeju Island, Korea. 2017 July 11-15; pp. 3373-3376.
  7. Hassanzadeh HR, Kolhe P, Isbell CL, and Wang MD. “MotifMark: Finding regulatory motifs in DNA sequences.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Jeju Island, Korea. 2017 July 11-15; pp. 3890-3893.
  8. Wu W, Venugopalan J, and Wang MD. “11C-PIB PET image analysis for Alzheimer’s diagnosis using weighted voting ensembles.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Jeju Island, Korea. 2017 July 11-15; pp. 3914-3917. [Note: Oral].
  9. Venugopalan J, Chanani N, Maher KO, and Wang MD. “Combination of static and temporal data analysis to predict mortality and readmission in the intensive care.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Jeju Island, Korea. 2017 July 11-15; pp. 2570-2573.
  10. Nair AS, DeMuth K, Cheng C, Wang MD. “Asthma Academy: Developing educational technology to improve Asthma medication adherence and intervention efficiency.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Jeju Island, Korea. 2017 July 11-15; pp. 1364-1367. [Note: Oral].
  11. Sha Y, and Wang MD. “Interpretable predictions of clinical outcomes with an attention-based Recurrent Neural Network.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Boston, MA, USA. 2017 Aug 20; pp. 233-240. (Acceptance Rate: 31%).
  12. Wu H, and Wang MD. “Infer cause of death for population health using convolutional neural network.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Boston, MA, USA. 2017 Aug 20; pp. 526-535. (Acceptance Rate: 31%).

2016

  1. Wu PY, and Wang MD. “The selection of quantification pipelines for Illumina RNA-seq data using a subsampling approach.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Las Vegas, NV, USA. 2016 Feb. 24; pp. 78-81. (Acceptance Rate: 51%).
  2. Tong L, Yang C, Wu PY and Wang MD. “Evaluating the impact of sequencing error correction for RNA-seq data with ERCC RNA spike-in controls.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Las Vegas, NV, USA. 2016 Feb. 24; pp. 74-77. (Acceptance Rate: 51%).
  3. Kothari S, Wu H, Tong L, Woods KE and Wang MD. “Automated prediction for esophageal optical endomicroscopic images.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Las Vegas, NV, USA. 2016 Feb. 24; pp. 160-163. (Acceptance Rate: 51%).
  4. Pethiyagoda T, Chanani N, Cheng C, and Wang MD. “PEPCOR—A risk prediction model for pediatric intensive care units utilizing ventilator days and length of stay.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Las Vegas, NV, USA. 2016 Feb. 24; pp. 86-89. (Acceptance Rate: 51%).
  5. Raharjo I, Burns T, Venugopalan J, and Wang MD. “Development of user-friendly and interactive data collection system for Cerebral Palsy.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Las Vegas, NV, USA. 2016 Feb. 24; pp. 406-409. (Acceptance Rate: 51%). [Note: Oral].
  6. Phan JH, Hoffman R, Kothari S, Wu PY, and Wang MD. “Integration of multi-modal biomedical data to predict cancer grade and patient survival.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Las Vegas, NV, USA. 2016 Feb. 24; pp. 577-580. (Acceptance Rate: 51%).
  7. Cheng C, Wu H, Thompson PJ, Taylor JR, Zehnbauer BA, Wilson KK, and Wang MD. “Anticoagulation manager: development of a clinical decision support mobile application for management of anticoagulants.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Orlando, FL, USA. 2016 Aug. 16; pp. 2582-2585.
  8. Wu H, and Wang MD. “Multi-view non-negative tensor factorization as relation learning in healthcare data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Orlando, FL, USA. 2016 Aug. 16; pp. 3325-3328. [Note: Oral].
  9. Mishra S, Kaddi CD, and Wang MD. “Pan-Cancer analysis for studying cancer stage using protein and gene expression data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Orlando, FL, USA. 2016 Aug. 16; pp. 2440-2443.
  10. Sha Y, Venugopalan J, and Wang MD. “A novel temporal similarity measure for patients based on irregularly measured data in electronic health records.”  ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Seattle, WA, USA. 2016 Oct 2-5; pp. 337-344. (Acceptance Rate: 44%).
  11. Cheng C, Sha Y, and Wang MD. “InterVisAR: An interactive visualization for association rule search.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Seattle, WA, USA. 2016 Oct 2-5; pp. 175-184. (Acceptance Rate: 44%).
  12. Hassanzadeh HR, and Wang MD. “DeeperBind: Enhancing prediction of sequence specificities of DNA binding proteins.” Conf Proc IEEE Bioinform Biomed, BIBM. Shenzhen, China. 2016 Dec 15-18; pp. 178-183. (Acceptance Rate: 19%).
  13. Hassanzadeh HR, Phan JH, and Wang MD. “A Multi-modal graph-based semi-supervised pipeline for predicting cancer survival.” Conf Proc IEEE Bioinform Biomed, BIBM. Shenzhen, China. 2016 Dec 15-18; pp. 184-189. (Acceptance Rate: 19%).

2015

  1. Sha Y, Phan JH, and Wang MD. “Effect of low-expression gene filtering on detection of differentially expressed genes in RNA-Seq data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Milan, Italy. 2015 Aug 25; pp. 6461-6464.
  2. Hassanzadeh HR, Phan JH, and Wang MD. “A semi-supervised method for predicting cancer survival using incomplete clinical data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Milan, Italy. 2015 Aug 25; pp. 210-213. [Note: Oral].
  3. Wu H, Phan JH, Bhatia AK, Cundiff CA, Shehata BM, and Wang MD. “Detection of blur artifacts in histopathological whole-slide images of endomyocardial biopsies.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Milan, Italy. 2015 Aug 25; pp. 727-730.
  4. Wu H, Cheng C, Han X, Huo Y, Ding W, and Wang MD. “Post-surgical complication prediction in the presence of low rank missing data with applications to post-surgical complication prediction.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Milan, Italy. 2015 Aug 25; pp. 6808-6811.
  5. Mishra S, Kaddi CD, and Wang MD.” Pan-cancer analysis for studying cancer stage using protein expression data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Milan, Italy. 2015 Aug 25; pp. 8189-8192. [Note: Oral].
  6. Kaddi CD, and Wang MD.” Developing robust predictive models for head and neck cancer across microarray and RNAseq data.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Atlanta, GA, USA. 2015 Sept. 9; pp. 393-402. (Acceptance Rate: 34%). [Note: Oral].
  7. Cheng C, and Wang MD. “Improving personalized clinical risk prediction using casuality-based association rules.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Atlanta, GA, USA. 2015 Sept. 9; pp. 386-392. (Acceptance Rate: 34%). [Note: Oral].
  8. Yang C, Wu PY, Tong L, Phan JH and Wang MD. “The impact of RNA-seq aligners on gene expression estimation.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Atlanta, GA, USA. 2015 Sept. 9; pp. 462-471. (Acceptance Rate: 34%). [Note: Oral].
  9. Kim D, Phan JH, and Wang MD, “Intra-operative tumor tracking using optical flow and fluorescent Imaging”, IFMBE International Conference on Biomedical and Health Informatics; pp. 79-84. Springer, 2015. [Note: Oral].
  10. Schwartz M, Park M, Phan JH, and Wang MD, “Integration of multimodal RNA-Seq data for prediction of kidney cancer survival.” 2015 International Conf. on Bioinformatics and Biomedicine, Washington DC, Nov. 2015; pp. 1591-1595.

2014

  1. Cheng C, Martin G, Wu PY, and Wang MD. “PHARM – Association rule mining for predictive health.” The International Conference on Health Informatics (IFMBE-ICHI‘2013), IFMBE Proc. Nov. 2013; pp. 114-117. IFMBE Proc. Vol. 42, 2014 [Note: Oral].
  2. Hoffman RA, Kothari S, Phan JH, and Wang MD. “A high resolution tile-based approach for classifying biological regions in in whole-slide histopathological images The International Conference on Health Informatics (IFMBE-ICHI‘2013), Nov. 2013; pp. 280-283. IFMBE Proc. Vol. 42, 2014
  3. Champion A, Lu G, Walker M, Kothari S, Osunkoya AO, and Wang MD. “Semantic interpretation of robust imaging features for Fuhrman grading of renal carcinoma.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Chicago, IL, USA. 2014 Aug 26; pp. 6446-6449. [Note: Oral].
  4. Harati S, Phan JH, and Wang MD. “Investigation of factors affecting RNA-seq gene expression calls.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Chicago, IL, USA. 2014 Aug 26; pp. 5232-5235. [Note: Oral].
  5. Hoffman RA, Kothari S, and Wang MD. “Comparison of normalization algorithms for cross-batch color segmentation of histopathological images.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Chicago, IL, USA. 2014 Aug 26; pp. 194-197.
  6. Kaddi CD and Wang MD. ” Models for predicting stage in head and neck squamous cell carcinoma using proteomic data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Chicago, IL, USA. 2014 Aug 26; pp. 5216-5219. [Note: Oral].
  7. Ren JC, Venugopalan J, Xu J, Kairdolf B, Durfee R, and Wang MD. “Multi-channel LED light source for fluorescent agent aided minimally invasive surgery.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Chicago, IL, USA. 2014 Aug 26; pp. 6927-6930. [Note: Oral].
  8. Sarkari S, Kaddi CD, Bennett RV, Fernandez FM, and Wang MD. “Comparison of clustering pipelines for the analysis of mass spectrometry imaging data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Chicago, IL, USA. 2014 Aug 26; pp. 4771-4774.
  9. Zachariah N, Kothari S, Ramamurthy S, Osunkoya AO, and Wang MD. “Evaluation of performance metrics for histopathological image classifier optimization.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Chicago, IL, USA. 2014 Aug 26; pp. 1933-1936. [Note: Oral].
  10. Cheng C, Chanani N, Maher K, and Wang MD. “icuARM-II: improving the reliability of personalized risk prediction in pediatric intensive care units.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Newport Beach, CA, USA. 2014 Sept. 20; pp. 211-219. [Note: Oral].
  11. Phan JH, Kothari S, and Wang MD. “omniClassifier: a desktop grid computing system for Big Data prediction modeling.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Newport Beach, CA, USA. 2014 Sept. 20; pp. 514-523. [Note: Oral].
  12. Venugopalan J, Cheng C, and Wang MD. “MotionTalk: personalized home rehabilitation system for assisting patients with impaired mobility.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Newport Beach, CA, USA. 2014 Sept. 20; pp. 455-463. [Note: Oral].
  13. Durfee RA, Venugopalan J, Ren JC, and Wang MD. “Med-Vest: A wearable sensor platform.” IEEE Healthcare Innovation Conference (Point-of-Care Technologies), HIPT. Seattle, WA, USA. 2014 Oct 8; pp. 199-202.
  14. Yang C, Wu PY, Phan JH, and Wang MD. “The Impact of RNA-seq Alignment Pipeline on Detection of Differentially Expressed Genes.” Conf Proc IEEE Global Conference on Signal and Information Processing (GlobalSIP). Atlanta, GA, USA. 2014 Dec 3; pp. 1376-1379. [Note: Oral.]

2013

  1. Kells K, Kong KY, White WB, Kaddi CD, and Wang MD. “LED light source for fluorescence endoscopy using quantum dots.” Proc IEEE EMBS Point-of-Care Healthcare Technologies, POCHT. Bangalore India. 2013 Jan 16; pp. 9-12. [Note: Oral].
  2. Kaddi CD and Wang MD. “Mathematical model of the effect of inter-cellular cooperative interactions in cancer during drug therapy.” Oak Ridge National Lab Biomedical Science and Engineering Conference (BSEC’13). 2013 May 22; pp. 1-4.
  3. Chandramohan R, Wu PY, Phan JH, and Wang MD. “Benchmarking RNA-Seq quantification tools.” Conf Proc IEEE Eng Med Biol Soc, EMBC. 2013 Jul 3; pp. 647-650.
  4. Cheng C, Brown C, Cohen L, Stokes TH, and Wang MD. “iACT – An interactive mHealth monitoring system to enhance psychotherapy for adolescents with sickle cell disease.” Conf Proc IEEE Eng Med Biol Soc, EMBC. 2013 Jul 3; pp. 2279-2283.
  5. Hubbard EN, Stokes TH, Kairdolf BA, Tran J, and Wang MD. “Unmixing of spectrally similar quantum dots using filter selection.” Conf Proc IEEE Eng Med Biol Soc, EMBC. 2013 Jul 3; pp. 3012-3015. [Note: Oral].
  6. Stokes TH, Venugopalan J, Hubbard EN, and Wang MD. “A pilot biomedical engineering course in rapid prototyping for mobile health.” Conf Proc IEEE Eng Med Biol Soc, EMBC. 2013 Jul 3; pp. 2525-2518.
  7. Venugopalan J, Cheng C, Stokes TH, and Wang MD. “Kinect-based rehabilitation system for patients with traumatic brain injury.” Conf Proc IEEE Eng Med Biol Soc, EMBC. 2013 Jul 3; pp. 4625-4628.
  8. *Poruthoor A, *Phan JH (equal contributing authors), Kothari S, and Wang MD. “Exploration of genomic, proteomic, and histopathological image data integration methods for clinical prediction.” IEEE China SIP. 2013 Jul 6; pp. 259-263.
  9. Cheng C, Burns T, and Wang MD. “Mining association rules for neurobehavioral and motor disorders in children diagnosed with cerebral palsy.” IEEE Int. Conf Healthcare Inform, ICHI. Sept. 11, 2013; pp. 258-263. [Note: Oral].
  10. Chandramohan R, Wu PY, Phan JH and Wang MD. “Systematic assessment of RNA-Seq quantification tools using simulated sequence data.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. 2013 Sept. 22; pp. 623-632. (Acceptance Rate: about 40%) [Note: Oral].
  11. Wu PY, Phan JH, and Wang MD. “A comprehensive approach for assessing RNA-seq quantification algorithms.” IEEE Int. Workshop on Genomic Signal Processing and Statistics (GENSIPS’2013), Houston, TX, USA. 2013 Nov 17; pp. 15-18. [Note: Oral].

2012

  1. Cheng C, Brown C, New T, Stokes TH, Dampier C, and Wang MD. “SickleREMOTE: A two-way text messaging system for pediatric sickle cell disease patients.” Conf Proc IEEE EMBS Biomed Health Inform, BHI. Shenzhen China. 2012 Jan 5; pp. 408-411. [Note: Oral].
  2. Chaudry Q, Sharma Y, Raza SH, and Wang MD. “Development of a novel 2D color map for interactive segmentation of histological images.” Conf Proc IEEE Int Symp Biomed Imaging, ISBI. Spain. 2012 April 30; pp. 178-181.
  3. Kothari S, Phan JH, and Wang MD. “Scale normalization of histopathological images for batch invariant cancer diagnostic models.” Conf Proc IEEE Eng Med Biol Soc, EMBC. San Diego CA. 2012 Aug 28; pp. 4406-4409.
  4. Tran JK, Hubbard EN, Stokes TH, Moffitt RA, and Wang MD. “Feasibility of multiplex quantum dot stain using primary antibodies from four distinct host animals.” Conf Proc IEEE Eng Med Biol Soc, EMBC. San Diego CA. 2012 Aug 28; pp. 6576-6579. [Note: Oral].
  5. Venugopalan J, Brown C, Cheng C, Stokes TH, and Wang MD. “Activity and school attendance monitoring system for adolescents with sickle cell disease.” Conf Proc IEEE Eng Med Biol Soc, EMBC. San Diego CA. 2012 Aug 28; pp. 2456-2459. [Note: Oral].
  6. Wu PY, Phan JH, and Wang MD. “The effect of human genome annotation complexity on RNA-seq gene expression quantification.” Conf Proc IEEE Bioinform Biomed Workshops, BIBMW. Philadelphia PA. 2012 Oct 4; pp. 712-717. [Note: Oral].
  7. Kaddi CD, Parry RM, and Wang MD. “Multivariate hypergeometric similarity measure.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Orlando FL. 2012 Oct 7; pp. 234-241. (Acceptance Rate: about 20%) [Note: Oral].
  8. Kothari S, Phan JH, Osunkoya AO, and Wang MD. “Biological interpretation of morphological patterns in histopathological whole-slide images.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Orlando FL. 2012 Oct 7; pp. 218-225. (Acceptance Rate: about 20%) [Note: Oral].
  9. Phan JH, Wu PY, and Wang MD. “Improving the flexibility of RNA-seq data analysis pipelines.” Conf Proc IEEE Int Workshop Genomic Signal Process Stat, GENSIPS. Washington DC. 2012 Dec 2; pp. 70-3. [Note: Oral].

2011

  1. Kothari S, Phan JH, Moffitt RA, Stokes TH, Hassberger SE, Chaudry Q, Young AN, and Wang MD. “Automatic batch-invariant color segmentation of histological cancer images.” Conf Proc IEEE Int Symp Biomed Imaging, ISBI. 2011 Mar 30; 657-60. (Acceptance Rate 40%). [Note: Oral].
  2. Kaddi CD, Quo CF, and Wang MD. “Analytical comparison of informatics criteria for systems biology model selection.” International Symposium on Bioinformatics Research and Applications, ISBRA. Changsha, Hunan, China. 2011 May 27; pp. 15-18. (Acceptance Rate ~33%). [Note: Oral].
  3. Parry RM, Phan JH, and Wang MD. “Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB. Chicago IL. 2011 Aug 1; pp. 29-38. (Acceptance Rate: about 20%) [Note: Oral].
  4. Cheng C, Stokes TH, and Wang MD. “caREMOTE: The design of a cancer reporting and monitoring telemedicine system for domestic care.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Boston MA. 2011 Aug 30; pp. 3168-3171. [Note: Oral].
  5. Wu P, Phan JH, and Wang MD. “Exploring the feasibility of next-generation sequencing and microarray data meta-analysis.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Boston MA. 2011 Aug 30; pp. 7618-7621. [Note: Oral].
  6. Raza SH, Parry RM, Moffitt RA, Young AN, and Wang MD. “An analysis of scale and rotation invariance in the bag-of-features method for histopathological image classification.” Med Image Comput Comput Assist Interv, MICCAI. Toronto, Canada. 2011 Sept. 18; 14(pt 3): pp. 66-74. (Acceptance Rate: about 30%).
  7. Pierrot Al, Pujol EE, Sharma Y, and Wang MD. “Autonomous point-based registration of prostate gland tissue images.” Proc Int Conf Biomed Eng Inform, BMEI. Shanghai China. 2011 Oct 15; pp. 165-169. [Note: Oral].
  8. Kaddi CD, Parry RM, and Wang MD. “Hypergeometric similarity measure for spatial analysis in tissue imaging mass spectrometry.” Conf Proc IEEE Bioinform Biomed, BIBM. Atlanta GA. 2011 Nov 12; pp. 604-607. [Note: Oral].
  9. Kong KY, Marcus AI, Giannakakou P, and Wang MD. “A web interface for the quantification of microtubule dynamics.” Conf Proc IEEE Bioinform Biomed Workshops, BIBMW. Atlanta GA. 2011 Nov 12; pp. 209-214. [Note: Oral].
  10. Kothari S, Phan JH, Young AN, and Wang MD. “Histological image feature mining reveals emergent diagnostic properties for renal cancer.” Conf Proc IEEE Bioinform Biomed, BIBM. Atlanta GA. 2011 Nov 12; pp. 422-425.
  11. Quo CF and Wang MD. “Biological interpretation of model-reference adaptive control in a mass action kinetics metabolic pathway model.” Conf Proc IEEE Bioinform Biomed, BIBM. Atlanta GA. 2011 Nov 12; pp. 265-268.
  12. Wu PY, Phan JH, Zhou F, and Wang MD. “Evaluation of normalization methods for RNA-seq gene expression estimation.” Conf Proc IEEE Bioinform Biomed Workshops, BIBMW. Atlanta GA. 2011 Nov 12; pp. 50-57.

2010

  1. Raza SH, Parry RM, Sharma Y, Chaudry Q, Moffitt RA, Young AN, and Wang MD. “Automated classification of renal cell carcinoma subtypes using bag-of-features.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Buenos Aires, Argentina. 2010 Aug 31; pp. 6749-6752. [Note: Oral].
  2. Malavé M, Zhao X, Kong KY, Marcus AI, and Wang MD. “Automatic tip selection for microtubule dynamics quantification.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Buenos Aires, Argentina. 2010 Aug 31; pp. 3142-3145. [Note: Oral].
  3. Srimani J, Moffitt RA, and Wang MD. “WebPK, a web-based tool for custom pharmacokinetic simulation.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Buenos Aires Argentina. 2010 Aug 31; pp. 1494-1497.
  4. Quo CF, Moffitt RA, Merrill AH Jr., and Wang MD. “Adaptive control model reveals systematic feedback and key molecules in metabolic pathway regulation.” International Conference on Research in Computational Molecular Biology, RECOMB. New York City NY. 2010 Nov 16; pp. 169-182. [Note: Oral].
  5. Cheng C, Stokes TH, Hang S, and Wang MD. “TissueWikiMobile: an integrative protein expression image browser for pathological knowledge sharing and annotation on a mobile device.” Conf Proc IEEE Bioinform Biomed, BIBM. Hongkong China. 2010 Dec 18; pp. 473-480. [Note: Oral].
  6. Srimani JK, Wu P, Phan JH, and Wang MD. “A distributed system for fast alignment of next-generation sequencing data.” Conf Proc IEEE Bioinform Biomed Workshops, BIBMW. Hongkong China. 2010 Dec 18; pp. 579-184. [Note: Oral].

2009

  1. Phan JH, Yin-Goen Q, *Young AN, and *Wang MD (co-corresponding senior authors). “Improving the efficiency of biomarker identification using biological knowledge.” Pac Symp Biocomput. Kona Hawaii. 2009 Jan 5; 14: pp. 427-438. (Acceptance Rate 40%). [Note: Oral].
  2. Kothari S, Chaudry Q, and Wang MD. “Automated cell counting and cluster segmentation using concavity detection and ellipse fitting techniques.” Conf Proc IEEE Int Symp Biomed Imaging, ISBI. 2009 Jun 28; pp. 795-798. (Acceptance Rate 40%). [Note: Oral].
  3. Chaudry Q, Raza SH, Lee J, Xu Y, Wulkan M, and Wang MD. “Development of a high resolution 3D infant stomach model for surgical planning.” International Conference on Computer Analysis of Images and Patterns, CAIP. 2009 Sept. 2; Lecture Notes in Computer Science, Volume 5702. Springer Berlin Heidelberg. 2009; pp. 614-621.
  4. Kothari S, Chaudry Q, and Wang MD. “Extraction of informative cell features by segmentation of densely clustered tissue images.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Minneapolis MN. 2009 Sept. 2; pp. 6706-6709. [Note: Oral].
  5. Moffitt RA, Caldwell M, Liu T, Liu J, Nie SM and Wang MD. “Quality control of highly multiplexed proteomic immunostaining with quantum dots: correction for crosstalk.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Minneapolis MN, 2009 Sept. 2; pp. 6739-6742. [Note: Oral].
  6. Parry RM, Galhena A, Fernandex F, and Wang MD. “Deblurring molecular images using desorption electrospray ionization mass spectrometry.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Minneapolis MN. 2009 Sept. 2; pp. 6731-6734. [Note: Oral].
  7. Phan JH, Yin-Goen Q, Young AN, and Wang MD. “Emerging translational bioinformatics: knowledge-guided biomarker identification for cancer diagnostics.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Minneapolis MN. 2009 Sept. 2; pp. 4162-4166. [Note: Oral].
  8. Raza SH, Sharma Y, Chaudry Q, Young AN, and Wang MD. “Automated classification of renal cell carcinoma subtypes using scale invariant feature transform.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Minneapolis MN. 2009 Sept. 2; pp. 6687-6690.
  9. Sanders TH, Stokes TH, Moffitt RA, Chaudry Q, Parry RM, and Wang MD. “Development of an automatic quantification method for cancer tissue microarray study.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Minneapolis MN. 2009 Sept. 2; pp. 3665-3668.
  10. Stokes TH and Wang MD. “SimpleVisGrid: grid Services for visualization of diverse biomedical knowledge and molecular systems data.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Minneapolis MN. 2009 Sept. 2; pp. 4178-4181. [Note: Oral].
  11. Sharma Y, Raza SH, Kong KY, Chaudry Q, Muller S, Chen ZG, and Wang MD. “Improving classification of head and neck squamous cell carcinoma using knowledge based features.” Microscopic Image Analysis with Applications in Biology, MIAAB. 2009 Sept. 2. Online Conference Proceedings(http://www.miaab.org/miaab-2009-papers/miaab-2009-18-sharma.pdf). [Note: Oral].

2008

  1. Barrett AB, Phan JH, and Wang MD. “Combining multiple microarray studies using bootstrap meta-analysis.” Conf Proc IEEE Eng Med Biol Soc, EMBC. 2008 Aug 20; pp. 5660-5663. [Note: Oral].
  2. Caldwell M, Moffitt RA, Liu J, Parry RM, Sharma Y, and Wang MD. “Simple quantification of multiplexed quantum dot staining in clinical tissue samples.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Vancouver, BC Canada. 2008 Aug 20; pp. 1907-1910. [Note: Oral].
  3. Fox B, Moffitt RA, and Wang MD. “An agent-based stochastic tumor model for predicting mitotic arrest drug response.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Vancouver, BC Canada 2008 Aug 20; pp. 5458-5461. [Note: Oral].
  4. Kaddi CD, Quo CF, and Wang MD. “Quantitative metrics for bio-modeling algorithm selection.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Vancouver, BC Canada. 2008 Aug 20; pp. 4613-4616. [Note: Oral].
  5. Kapoor S, Quo CF, Merrill AH Jr., and Wang MD. “An interactive visualization tool and data model for experimental design in systems biology.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Vancouver, BC Canada. 2008 Aug 20; pp. 2423-2426.
  6. Sharma Y, Raza SH, Kong KY, Chaudry Q, Young AN, Chen GZ, and Wang MD. “PASuite: a preprocessing algorithm suite for cellular and molecular image classification in cancer diagnosis and treatment.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Vancouver BC Canada. 2008 Aug 20; pp. 3114-3117.
  7. Chaudry Q, Raza SH, Sharma Y, Young AN, and Wang MD. “Improving renal cell carcinoma classification by automatic region of interest selection.” Conf Proc IEEE Bioinform Bioeng, BIBE. Greece. 2008 Oct 8; pp. 1-6. [Note: Oral].
  8. Kong KY, Sharma Y, Raza SH, Chen Z, Muller S, and Wang MD. “Using spiral intensity profile to quantify head and neck cancer.” Conf Proc IEEE Bioinform Bioeng, BIBE. Greece. 2008 Oct 8; pp. 1-6. [Note: Oral].
  9. Siy PW, Moffitt RA, Parry RM, Chen YF, Liu Y, Sullards MC, Merrill AH Jr., and Wang MD. “Matrix factorization techniques for analysis of imaging mass spectrometry data.” Conf Proc IEEE Bioinform Bioeng, BIBE. Greece. 2008 Oct 8; pp. 1-6. [Note: Oral].
  10. Phan JH, Moffitt RA, Barrett AB, and Wang MD. “Combining multiple microarray studies using bootstrap data combination.” International Multi-Symposiums on Computer and Computational Sciences, IMSCCS. Shanghai China. 2008 Oct 18; pp. 37-44. [Note: Oral].

2007

  1. Chaudry Q, Kong KY, Ahearn TU, Cohen V, Bostick RM, and Wang MD. “An integrated image quantification system for colorectal cancer assessment using quantum dots and molecular profiling.” Conf Proc IEEE Int Symp Biomed Imaging, ISBI. Washington DC. 2007 Apr 12; pp. 1280-1283. (Acceptance Rate: about 40%).
  2. Quo CF and Wang MD. “Quantitative comparison of numerical solvers for models of oscillatory biochemical systems.” International Multi-Symposiums on Computer and Computational Sciences, IMSCCS. Iowa City, IA. 2007 Aug 13; pp. 44-51. [Note: Oral].
  3. Stokes TH, Torrance JH, LeGoasduff N, Li H, and Wang MD. “ArrayWiki: unleashing the power of microarray data from non-collaborative public repositories.” International Multi-Symposiums on Computer and Computational Sciences, IMSCCS. Iowa City, IA, USA. 2007 Aug 13; pp. 92-99. [Note: Oral].
  4. Dhingra S, Freedenberg M, Quo CF, Merrill AH Jr., and Wang MD. “Computational modeling of a metabolic pathway in ceramide de novo synthesis.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Lyon France. 2007 Aug 23; pp. 1405-1408. [Note: Oral].
  5. Huynh KN, Phan JH,Vo TM, and Wang MD. “Improved bolstering error estimation for gene ranking.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Lyon France. 2007 Aug 23; pp. 4633-4636.
  6. Kaddi CD, Oden E, Quo CF, and Wang MD. “Exploration of quantitative scoring metrics to compare systems biology modeling approaches.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Lyon France. 2007 Aug 23; pp. 1121-1124.
  7. Shah N, Moffitt RA, and Wang MD. “Modified genetic algorithm for parameter selection of compartmental models.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Lyon France. 2007 Aug 23; pp. 143-146.
  8. Stokes TH, Han X, Moffitt RA, and Wang MD. “Extending microarray quality control and analysis algorithms to illumina chip platform.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Lyon France. 2007 Aug 23; pp. 4637-4640.
  9. Vo TM, Phan JH, Huynh KN, and Wang MD. “Reproducibility of differential gene detection across multiple microarray studies.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Lyon France. 2007 Aug 23; pp. 4231-4234. [Note: Oral].
  10. Kong KY, Marcus AI, Giannakakou P, and Wang MD. “Using particle filter to track and model microtubule dynamics.” Proc IEEE Int Conf Image Proc, ICIP. 2007 Sept. 16; 5: pp. 517-520. (Acceptance Rate: about 40%).
  11. Alberti C, Villareal JP, Delano B, Kong KY, Marcus AI, Giannakakou P, and Wang MD. “Microtubule dynamics classification using a statistical model of the movement of outer tips.” Conf Proc IEEE Bioinform Bioeng, BIBE. 2007 Oct 14; pp. 495-502. (Acceptance Rate: about 30%).
  12. *Freedenberg M, *Kaddi CD (equal contributing authors), Quo CF, and Wang MD. “Review of systems biology simulation tools for translational research.” Conf Proc IEEE Bioinform Bioeng, BIBE. 2007 Oct 14; pp. 358-365. (Acceptance Rate: about 30%). [Note: Oral].
  13. *Muir ER, *Ndiour IJ, *Le Goasduff NA (equal contributing authors), Moffitt RA, Liu Y, Sullards MC, Merrill AH Jr., *Chen Y, and *Wang MD (co-corresponding senior authors). “Multivariate analysis of imaging mass spectrometry data.” Conf Proc IEEE Bioinform Bioeng, BIBE. 2007 Oct 14; pp. 472-479. (Acceptance Rate: about 30%). [Note: Oral].
  14. Phan JH and Wang MD. “Estimating classification error to identify biomarkers in time series expression data.” Conf Proc IEEE Bioinform Bioeng, BIBE. 2007 Oct 14; pp. 172-179. (Acceptance Rate: about 30%).
  15. Phan JH, Moffitt RA, Stokes TH, and Wang MD. “Evolving biological behavior in gene-based cellular simulations.” Conf Proc IEEE Bioinform Bioeng, BIBE. 2007 Oct 14; pp. 509-516. (Acceptance Rate: about 30%).
  16. Waheed S, Moffitt RA, Chaudry Q, Young AN, and Wang MD. “Computer-aided histopathological classification of cancer subtypes.” Conf Proc IEEE Bioinform Bioeng, BIBE. 2007 Oct 14; pp. 503-508. (Acceptance Rate: about 30%).
  17. Torrance J, Moffitt RA, Stokes TH, and Wang MD. “Can we trust biomarkers? Visualization and quantification of gene set and outlier probe co-occurrence for high density oligonucleotide microarrays.” IEEE/NIH Life Sci Syst Appl Workshop, LISA. Bethesda MD. 2007 Nov 8; pp. 196-199.

2006

  1. Bostick RM, Kong KY, Ahearn TU, Chaudry Q, Cohen V, and Wang MD. “Detecting and quantifying biomarkers of risk for colorectal cancer using quantum dots and novel image analysis algorithms.” Conf Proc IEEE Eng Med Biol Soc, EMBC. New York NY. 2006 Aug 30; pp. 3313-3316.
  2. Kong KY, Marcus AI, Hong JY, Giannakakou P, and Wang MD. “Automatic microtubule tracking for QD-based cell imaging and drug efficacy study.” Conf Proc IEEE Eng Med Biol Soc, EMBC. New York NY. 2006 Aug 30; pp. 3321-3324.
  3. Phan JH, Young AN, and Wang MD. “Selecting clinically-driven biomarkers for cancer nanotechnology.” Conf Proc IEEE Eng Med Biol Soc, EMBC. New York NY. 2006 Aug 30; pp. 3317-3320. [Note: Oral].
  4. Stokes TH, Phan JH, Quo CF, Nie SM, and Wang MD. “Bio-nano-informatics: an integrated information management system for personalized oncology.” Conf Proc IEEE Eng Med Biol Soc, EMBC. New York NY. 2006 Aug 30; pp. 3325-3328. [Note: Oral].
  5. Kong KY, Marcus AI, Hong JY, Giannakakou P, and Wang MD. “Cellular imaging data analysis: microtubule dynamics in living cell.” Proc IEEE Int Conf Image Proc, ICIP. New York NY. 2006 Oct 8; pp. 155-158. (Acceptance Rate: about 40%).

2005

  1. Feng W, Wu B, Phan JH, Dale J, Young AN, and Wang MD. “An integrated cancer biomarker information system.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 2851-2854.
  2. Henning PA, Moffitt R, Allegood J, Wang E, *Merrill AH, and *Wang MD (co-corresponding senior authors). “Computationally predicting rate constants in pathway models.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 5093-5096.
  3. Kong KY, Marcus A, Hong JY, Giannakakou P, and Wang MD. “Computer assisted analysis of microtubule dynamics in living cells.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 3982-3985. [Note: Oral].
  4. Moffitt RA, Phan JH, Hemby S, and Wang MD. “Effect of outlier removal on gene marker selection using support vector machines.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 917-920. [Note: Oral].
  5. Phan JH, Moffitt RA, Dale J, Petros JA, *Young AN, and *Wang MD (co-corresponding senior authors). “Improvement of SVM algorithm for microarray analysis using intelligent parameter selection.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 4838-4841.
  6. Quo CF, Wu B, Stokes TH, and Wang MD. “Development of a laboratory information system for cancer collaboration project.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 2859-62.
  7. Stokes TH, Phan JH, Feng W, Tuteja G, and Wang MD. “GAVis: a tool for visualization and control of genetic algorithms for -omic data analysis.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 2855-2858.
  8. Wang G, Agrawal A, Nie SM, and Wang MD. “Optically encoded nanoparticles for detecting single biomolecules and viruses: rapid analysis of two-color colocalization data by high-speed computing.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 1739-1742.
  9. Young AN, Amin MB, Petros JA, Natan MJ, Nie SM, and Wang MD. “Nanomolecular histopathology for renal tumor classification.” Conf Proc IEEE Eng Med Biol Soc, EMBC. Shanghai China. 2005 Sept. 1; pp. 723-726. [Note: Oral].

2004

  1. Mukewar PS and Wang MD. “Bionano-imaging analysis in cell behavior study.” Conf Proc IEEE Int Symp Biomed Imaging, ISBI. Arlington VA. 2004 Apr 15; pp. 1520-1524. (Acceptance Rate: about 40%). [Note: Oral].
  2. Feng W, Henning PA, and Wang MD. “EGOMiner: a comprehensive genomics and proteomics data analysis and biological function interpretation system.” Conf Proc IEEE Eng Med Biol Soc, EMBC. San Francisco CA. 2004; pp. 2809-2812. [Note: Oral].
  3. Henning PA, Wang G, *Merrill AH, and *Wang MD (co-corresponding senior authors). “Dynamic pathway modeling of sphingolipid metabolism.” Conf Proc IEEE Eng Med Biol Soc, EMBC. San Francisco CA. 2004; pp. 2913-2916.[Note: Oral].
  4. Mukewar PS, Wang G, Henning PA, Bao G, and Wang MD. “Segmentation of bionano-images for understanding cell dynamics.” Conf Proc IEEE Eng Med Biol Soc, EMBC.San Francisco CA. 2004; pp. 1759-1762.
  5. Phan JH, Quo CF, and Wang MD. “Comparative study of microarray data for cancer research.” Conf Proc IEEE Eng Med Biol Soc, EMBC. San Francisco CA. 2004; pp. 2960-2963. [Note: Oral].
  6. Hong JY and Wang MD. “High speed processing of biomedical images using programmable GPU.” Proc Int Conf Image Proc, ICIP. Singapore. 2004 Oct 24; pp. 2455-2458. (Acceptance Rate: about 40%) [Note: Oral].

2003

  1. Patra, Abhirup, and Wang MD. “Volumetric medical image compression and reconstruction for interactive visualization in surgical planning.” Conf. Proc. Data Compression Conference, DCC, 2003. IEEE. 2003 Mar. 25. pp. 442-445.

D. Other Refereed Material

2026

  1. Shukla A, Yuan Y, Tamo JB, Wang Y, Nnamdi MC, Marteau BL, Tan SQY, Li J, Willingham B, and Wang MD. “Benchmarking LLM summaries of multimodal clinical time series for remote monitoring.” ICLR 2026 TSALM Workshop 2026. Rio de Janeiro, Brazil. 2026; pp. 1-5.

2024

  1. Shi W*, Ran Xu*, Zhuang Y, Yu Y, Zhang J, Wu H, Zhu Y, Ho JC, Yang C, and Wang MD. “EHRAgent: code empowers large language models for few-shot complex tabular reasoning on electronic health records.” In ICLR 2024 Workshop on Large Language Model (LLM) Agents. 2024.
  2. Hornback A, Abid A, Lewis RW, Zhu Y, Marteau B, Lovelace BK, Djachechi P, McDaniel JMS, Wang MD, Effinger KE, Muthu N, and Liang WH.  “Human-centered design and development of a novel application to semi-automate generation of cancer treatment summaries and survivorship care plans using electronic health record data.” American Medical Informatics 2024 Annual Symposium (AMIA). 2024.

2023

  1. Hornback A, Giuste F, Zhu Y, Shi W, Marteau B, Choudhary A, Chiaro BD, Purnell C, Hilton C and Wang MD. “Development of a FHIR-based application for craniofacial microsomia sub-phenotyping.” AMIA 2023 Clinical Informatics Conference. 2023.
  2. Marteau B, Hornback A, Zhu Y, Giuste F, Zhong Y, Shi W, Carpenter A, Hilton C, and Wang MD. “Healthcare infrastructure enabling multi-site data-driven clinical decision support using OMOP-on-FHIR.” AMIA 2023 Clinical Informatics Conference. 2023.
  3. Isgut M, Jain N, Hornback A, Samel K, and Wang MD. “GeneDAE: a sparse denoising autoencoder for deriving interpretable gene embeddings.” ICLR 2023 TinyPapers. 2023.
  4. Singh A, Shi W, and Wang MD. “Autonomous soft tissue retraction using demonstration-guided reinforcement learning.” The joint 17th Augmented Reality, Augmented Environments for Computer Assisted Interventions (AE-CAI) workshop at the 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). Vancouver, Canada. 2023.
  5. Shi W, Marteau B, Giuste F, and Wang MD. “Mapping and diagnosing augmented whole slide image datasets with training dynamics.” Deep Generative Models for Health Workshop NeurIPS 2023. 2023; pp.1-5. (Acceptance Rate: 30%).

2020

  1. Amini A, Chen W, Fortino G, Li Y, Pan Y, and Wang MD (Leading Senior Guest Editor). “AI-Driven informatics, sensing, imaging and big data analytics for fighting the covid-19 pandemic.” IEEE J Biomed Health Inform. 2020. 24(10: 2731-2732).

2018

  1. Kahveci T, Pozzi G, Shehu A, and Wang MD. “Guest editorial on the special issue on informatics on biomedical data learning, reasoning, and representation.” IEEE J Biomed Health Inform. 2018. 23 (1), 81-82.

2017

  1. Bhatia AK, Tong L, Hoffman RA, Wu PY, Hassanzadeh HR, Wang MD, and Deshpande SR. “Refinement of automated whole slide image analysis in pediatric heart transplants.” The Journal of Heart and Lung Transplantation 36, no. 4 (2017): S103-S104.

2016

  1. Akay M, Coatrieux G, Hao Y, Fotiadis DI, Laine A, Lo B, Nikita KS, Noury N, Rodrigues J, and Wang MD. “Guest editorial: MobiHealth 2014, IEEE HealthCom 2014, and IEEE BHI 2014.” in IEEE Journal of Biomedical and Health Informatics, vol. 20, no. 3; pp. 731-732. May 2016, Doi: 10.1109/JBHI.2016.2559138.

2015

  1. Bhatia AK, Phan JH, Kothari S, Shehata B, and Wang MD. “Automated analysis of histopathological whole slide images to diagnose pediatric heart transplant rejection.” The Journal of Heart and Lung Transplantation, 34(4): S327. 2015.
  2. Dhawan AP, Heetderks WJ, Pavel M, Acharya S, Akay M, Mairal A, Wheeler B, Dacso CC, Sunder T, Lovell N, Gerber M, Shah M, Senthilvel SG, Wang MD, and Bhargava B. “Current and future challenges in point-of-care technologies: a paradigm-shift in affordable global healthcare with personalized and preventive medicine.” IEEE J. of Translational Engineering in Health and Medicine. 2015: 1-10.

2014

  1. Tsiknakis M, Promponas VJ, Graf N, Wang MD, Wong ST, Bourbakis N, and Pattichis CS. “Guest editorial: computational solutions to large-scale data management and analysis in translational and personalized medicine.” IEEE J Biomed Health Inform. 2014 May; 18(3):720-1.
  2. Cheng CW, Maher K, Wang MD, and Chanani N. “193: Data driven personalized risk prediction in pediatric intensive care units.” Critical Care Medicine 42, no. 12. (2014): A1407.
  3. Chhangawala S, Rudy G, Wu PY, Tighe S, Wang MD, Baldwin DA, Grills G, Mason CE, Rosenfeld J, ABRF-NGS Consortium. “Longer reads do not significantly improve RNA-seq results.” Journal of Biomolecular Techniques (JBT). 2014/5; 25(Suppl): S3-S4.

2013

  1. Poon CC, Wang MD, Bonato P, and Fenstermacher DA. “Editorial: special issue on health informatics and personalized medicine.” IEEE Trans Biomed Eng. 2013; 60(1):143-6.
  2. He B, Baird R, Butera R, Datta A, George S, Hecht B, Hero A, Lazzi G, Lee RC, Liang J, Neuman M, Peng GC, Perreault EJ, Ramasubramanian M, Wang MD, Wikswo J, Yang GZ, and Zhang YT. “Grand challenges in interfacing engineering with life sciences and medicine.” IEEE Trans Biomed Eng. 2013 Mar; 60(3): 589-98.
  3. Hsu W, Markey MK, and Wang MD. “Biomedical imaging informatics in the era of precision medicine: progress, challenges, and opportunities.” J Am Med Inform Assoc. 2013; 20(6):1010-3.

E. Creative Products

2025

  1. Anand S, Liang Y, Tran V, and Tan SQY. “DRiP: White-box framework for Depression Risk Prediction.” 1st Place in Data Competition Track 1: Understanding depression risk through demographics, clinical factors & mindfulness interventions in IEEE BHI 2025. 2025.
  2. Yuan Y, Lee H, and Pranati D. “Fairness-aware Predictive and longitudinal modeling of depression outcomes in mindfulness-based interventions.” 2nd Place in Data Competition Track 1: Understanding depression risk through demographics, clinical factors & mindfulness interventions in IEEE BHI 2025. 2025.
  3. Chouhan NS, Shah V, Patel K, and Tamo BJ. “Beyond association: identifying optimal mindfulness interventions and subgroup response trajectories in clinical depression.” 3rd Place in Data Competition Track 1: Understanding depression risk through demographics, clinical factors & mindfulness interventions in IEEE BHI 2025. 2025.
  4. Wang Y, Kim K, Sathu H, Patel S, and Hornback A. “Multimodal modeling of postprandial glucose response for carbohydrate ratio prediction and personalized nutrition.” Honorable Mentions in Data Competition Track 2: Predicting macronutrient information in IEEE BHI 2025. 2025.

2024

  1. Nnamdi MC, Tamo JB, Chen M, Wijayarathne D, Patil O, and Wang MD. “A data-driven approach for understanding urban air quality.” 3rd Place in Data Competition in IEEE BHI 2024. 2024.

2023

  1. Shi W, Zhu Y, Giuste F, Hornback A, Carpenter A, Hilton C, Iwinski H, Wattenbarger M, and Wang MD. “Development of predictive models for patient rehabilitation outcomes after spinal deformity surgery: towards personalized medicine.” AMIA 2023 AI Show Case Stage I. 2023.
  2. Shi W, Zhu Y, Giuste F, Hornback A, Carpenter A, Hilton C, Iwinski H, Wattenbarger M, and Wang MD. “usability and workflow considerations of clinical decision support system for AIS patient rehabilitation outcomes prediction.” AMIA 2023 AI Show Case Stage II. 2023.
  3. Shi W, Zhu Y, Giuste F, Hornback A, Carpenter A, Hilton C, Iwinski H, Wattenbarger M, and Wang MD. “Evaluation of health impact of clinical decision support system for AIS patient rehabilitation outcomes prediction.” AMIA 2023 AI Show Case Stage III. 2023.
  4. Guo X, Singh A, Jain N, Inho L, Chen M, Murakoso M, Shi W, and Wang MD. “Effective surrogate models for docking score prediction of candidate drug molecules on SARS-CoV-2 protein targets.” 1st Place in Data Hackathon of Bioinformatics Drug Target Challenge in IEEE BHI 2023. 2023.
  5. Li X, Zhang C, Chen W, Shi W, and Wang MD. “Identification of single-cell RNA sequencing molecular signatures for COVID-19 infection severity classification.” 1st Place in Data Hackathon of Bioinformatics scRNA-Seq Challenge in IEEE BHI 2023. 2023.
  6. Nnamdi MC, Tamo JB, Shi W, Chundru V, and Wang MD. “COVID-19 early screening via audio signal analysis.” Honorable Mention in Data Hackathon of Sensor Informatics Challenge in IEEE BHI 2023. 2023.

F. Awards

Conference Paper Awards

2025

  1. Hwang S, Shi W, Tamo BJ, Nnamdi MC, Patil O, and Wang MD. “AI-enabled genetic driver identification for clinically actionable treatments in EOS.” 2025 Shriners State of Research Meeting. 2025. [Note: 3rd Place Best Poster Award].
  2. Zhong Y, Shi W, Tamo BJ, Nnamdi MC, Yuan Y, and Wang MD. “Collective reasoning in LLMs: A multi-agent framework for clinical procedure sequencing.” The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). Philadelphia, USA. 2025; pp. 1 – 10. (Acceptance Rate: 19.4%). [Note: Oral]. [Note: Best Paper Honorable Mention Award].

2024

  1. Khimani A, Hornback A, Jain N, Avula P, Jaishankar A, and Wang MD. “Predicting cardiovascular disease risk in tobacco users using machine learning algorithms.” In 2024 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Orlando, USA. 2024; pp. 1-4. [Note: Oral]. [Note: Georgia Tech. Bioinformatics Department MS Best Student Paper Award].
  2. Jaishankar A, Jain N, Hornback A, Khimani A, Avula P, and Wang MD. “Identifying features for keloid scars subtyping using k-modes clustering.” In 2024 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Orlando, USA. 2024; pp. 1-4. [Note: Georgia Tech. Bioinformatics Department MS Best Student Paper Award].
  3. Tamo JB, Nnamdi MC, Hornback A, Chen M, Shi W, Zhu Y, Iwinski HJ, and Wang MD. “Heterogeneous treatment effects of spinal fusion surgery for adolescent idiopathic scoliosis patients” The 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). China, Nov. 2024; pp. 1–10. (Acceptance Rate: 34.8%; Top: 17.1%). [Note: Oral]. [Note: Best Student Paper Award].

2023

  1. Shi W, Zhuang Y, Zhu Y, Iwinski H, Wattenbarger M, and Wang MD. “Retrieval-augmented large language models for adolescent idiopathic scoliosis patients in shared decision-making.” The 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Huston, TX, USA. Sep. 2023; pp. 1–10. (Acceptance Rate: 29%). [Note: Oral]. [Note: Best Paper Award].

2022

  1. Zhong Y, Marteau B, Hornback A, Zhu Y, Shi W, Giuste F, Krzak J, Graf A, Chafetz R, and Wang MD. “IDTVR: A novel cloud framework for an interactive digital twin in virtual reality.” In 2022 IEEE International Conference of Intelligent Reality (IEEE ICIR). 2022; pp. 1-4. [Note: Oral]. [Note: Best Paper Award].

2020

  1. Wu H and Wang MD. “An information theoretic learning for causal direction identification.” 2020 IEEE Computer Society Signature Conference on Computers, Software and Applications (COMPSAC). Madrid, Spain. 2020; pp. 287-294. (Acceptance Rate: 40%). [Note: Best Paper Award].

Conference Poster Awards

2021

  1. Giuste F, He L, Shi W, Isgut M, and Anderson B. “Automated patient risk assessment for COVID-19 complications.” IEEE Healthcare Summit: Integrating BHI and AI to Combat Pandemics 2021 (IBACP 2021). 2021. [Note: Best Poster Award].

Other Awards

2025

  1. Sathu H. President’s Undergraduate Research Award 2025.

2024

  1. Hornback A. The 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) Rising Star Award 2024. China, Nov. 2024.
  2. Hornback A. The 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) NSF Travel Award 2024. China, Nov. 2024.
  3. Nnamdi M. IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI) Travel Award 2024. Houston, TX USA. 2024.
  4. Marteau B. IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI) Travel Award 2024. Houston, TX USA. 2024.

2023

  1. Tamo JB. The 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) NSF Travel Award 2023. TX USA, 2023.
  2. Shi W. The 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) NSF Travel Award 2023. TX USA, 2023.
  3. Shi W. The 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) Rising Star Award 2023. TX USA, 2023.
  4. Nnamdi M. IEEE EMBS International Conference on Biomedical & Health Informatics (IEEE BHI) Travel Award 2023. Pittsburgh USA. 2023.

G. Software

  1. SMART-on-FHIR for CDC Mortality Reporting: An app uploaded to Cerner FHIR sandbox and shared on Github (https://github.com/smart-on-fhir/client-js). 2019.
  2. icuARM, phARM: A set of clinical decision support systems using association rule mining (ARM) to mine electronic medical record or personal health record so to predict outcomes from health conditions (either in acute ICU condition or in chronic condition). 2013-2018.
  3. PTTAdvisorPLUS: A mobile app development for prescription workflow management for chronic condition. Obtained CDC Clearance for Apple Store deployment under Anticoagulation Manager. 2018.
  4. KNNsuite and SEQCsuite: a combinatorial of pipelines for analyzing microarray data (http://hercules.bme.gatech.edu/parry/kDAP/) and next generation sequencing data (RNA-Seq) that are used by International Microarray Quality Control Consortium partners. 2008-2017.
  5. GoMiner (http://discover.nci.nih.gov/gominer/credits.jsp). Gene Ontology Miner for biological function interpretation of genomics and proteomics data. It was fully designed and implemented by May Wang team and was fully maintained by NIH/NCI (IV.C3.[3]). The publications and presentations on this tool include Genome Biology’2003 and EMBC’2014 and CSB’2014.
  6. TissueWiki (http://tissuewiki.bme.gatech.edu/index.php/Main_Page): Tissue Wikipedia – histopathology, cytopathology, Quantum Dots (QD) multiplex tissue and other microscopic imaging data management, processing, and meta information extraction for improved clinical diagnosis. It was derived from an earlier tissue image pre-processing suite PASuite (EMBC’2008). The publications and presentation on this work include J Pathol Inform’2012, CRC Press Book Chapter’2014, ACSNano’2010, BIBM’2010, BMES’2009, and BMES’2010.
  7. StealthVest and Med-Vest: a Wearable, Multi-functional, Open-source Health Monitoring System for monitoring pediatric kid cardiac function in POC’2014 and HIMSS’2012.
  8. MotionTalk: Kinect-based personalized home-based system for mobility assessment and rehabilitation. The publication and presentation include ACM-BCB’2014 and BMES’2013.
  9. omniClassifier: a desktop grid computing suite for Big Data prediction, see publication ACM-BCB’2014.
  10. omniBioMarker (http://omnibiomarker.bme.gatech.edu): omni Biomarker analysis and identification system; Received NCI/NIH caBIG silver level compatibility certification (https://cabig.nci.nih.gov/tools/Omnibiomarker). The publications and presentations relating to this tool include TMBE’2013, TITB’2012, Trends Biotechnol’2009, and Hum Pathol’2009).
  11. omniSpect: Multi-spectral image analysis for mass spectrometry imaging; enhanced from Q-IHC, which was used by Emory-GT Cancer Nanotechnology Center PIs in quantifying multi-plex quantum dots imaging in Nature Protocols’2007. Received NCI/NIH caBIG silver level compatibility certification (caBIG’2010) http://omniSpect.bme.gatech.edu It has also been used for mass spectrometry imaging and published in J of the Am Soc for Mass Spectro’2013.
  12. SickleREMOTE, iACT, SickleSAM, a set of mobile apps that are designed to monitor children with Sickle Cell Disease. The publication and presentation on Sickle Cell Disease include BHI’2012, EMBC’2012, mHealth Summit’2012, and EMBC’2013.
  13. caREMOTE: a telemedicine system for cancer remote monitoring and reporting. This is a mobile app. The publications and presentation on this work include EMBC’2011, caBIG’2010, and BMES’2012.
  14. mtDynamics: microtubule dynamics tracking and analysis system. 2012. The publications and presentation on this work include Int J Comput Biol Drug Des, EMBC’2005, EMBC’2005, ICIP’2006, ICIP’2007, and ICIP’2007.
  15. GAVia, TIMSViz, TissueViz, DetectTLC, and interVisAR: Designed and developed a set of data and information visualization tools for visualizing –omic data analysis algorithm, tissume imaging mass spectrometry data visualization (TIMSViz), whole-slide histopathological tissue images, mass spectrometry image (desorption electrospray ionization images DetectTLC), and EMR/PHR association rules (AR). The publications and presentations on visualization work include EMBC’2005, BIBE’2007, BMES’2012.
  16. caCORRECT:chip artifact CORRECTion (http://cacorrect.bme.gatech.edu), a bioinformatics tool for genomics and proteomics data quality control. Received NCI/NIH caBIG silver level compatibility certification (https://cabig.nci.nih.gov/tools/caCorrect/). caCORRECT2 was published in 2011 BMC Bioinformatics. This tool was evolved from ChipQC and PADRE. The publications and presentations on this tool include ABME’2007, Trends Biotechnol’2009, Hum Pathol’2009, and BMC Bioinfo’2011.
  17. nanoDRIVE and WebPK: nenotherapeutic Drug Response Interactive Visualization Environment, and web-based pharmacokinetic simulation tool. Used for Emory-GT CCNE project PI in designing new nanoparticle drugs. The publications and presentation on this work include BMED’2007, EMBC’2010, and BMES’2010.
  18. sphingoViz: interactive high dimensional sphingolipid pathway data visualization; hosted by Prof. Al Merrill for LipidMAPS project. The publications and presentations relating to this tools include Sphingolipid Biology’2006, J Lipid Res’2009, and EMBC’2009.
  19. ArrayWiki (http://arraywiki.bme.gatech.edu/index.php/Main_Page): MicroarrayWikipedia — data management and meta data annotation for translational bioinformatics. The publications and presentations relating to this work include BMC Bioinfo’2008, IMSCCS’2007, and BMES’2007.

H. Patents

  1. Bio-Nano-Informatics for Personalized Medicine, USPTO GTRC-No.4015, Office of Technology Transfer, Georgia Tech, Oct. 2006.
  2. Multi-Scheme Optimal Decision Making System for Cancer Molecular Genomic and Proteomic Data Analysis, USPTO GTRC-No. 2901, Office of Technology Transfer, Georgia Tech, May 2003.
  3. Using Optimization Methods in Gene Expression Pattern Classification, USPTO GTRC-No.2903, Office of Technology Transfer, Georgia Tech, May 2003.