Publications

  1. Huang P, Wei G, Kirkpatrick JD, Lin Y, Tan L, Matta H, Nasser I, Huang M, Chen L, Petitjean M, Skelton-Badlani D, Gao W, Vaid K, Zhao S, Lugovskoy A, Alenzi M, Chen X, Gores GJ, Popov YV. Transposon-based oncogene integration in Abcb4(Mdr2)(-/-) mice recapitulates high susceptibility to cholangiocarcinoma in primary sclerosing cholangitis. J Hepatol. 2025 Jan; 82 (1):84-96 Epub 2024 July 30
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  2. Abou Chaar MK, Grigsby-Rocca G, Huang M, Blackmon SH. ChatGPT vs Expert-Guided Care Pathways for Postesophagectomy Symptom Management. Ann Thorac Surg Short Rep. 2024 Dec; 2 (4):674-679 Epub 2024 June 25
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  3. Kelpin S, Brockman TA, Decker PA, Young A, Boehmer K, Nguyen A, Kamath C, St Sauver J, Sinicrope PS, Sharma P, McCoy R, Allen S, Huang M, Pritchett J, Esterov D, Lampman M, Petersen C, Cheville A, Patten CA. Increasing digital equity to promote online smoking cessation program engagement among rural adults: a randomized controlled pilot trial. Commun Med (Lond). 2024 Oct 8; 4 (1):194 Epub 2024 Oct 08
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  4. Ren Y, Wu Y, Fan JW, Khurana A, Fu S, Wu D, Liu H, Huang M. Automatic uncovering of patient primary concerns in portal messages using a fusion framework of pretrained language models. J Am Med Inform Assoc. 2024 Aug 1; 31 (8):1714-1724
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  5. Lv C, Xue X, Huang M, Yang Z, Chen X, Koo CW. The dynamic contrast enhanced-magnetic resonance imaging and diffusion-weighted imaging features of alveolar soft part sarcoma. Quant Imaging Med Surg. 2023 Oct 1; 13 (10):7269-7280 Epub 2023 Sept 11
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  6. Pritchett JC, Borah BJ, Dholakia R, Moriarty JP, Ahn HH, Huang M, Khera N, Wilshusen L, Dronca RS, Ticku J, Leppin AL, Tilburt JC, Paludo J, Haddad TC. Patient- and Provider-Level Factors Associated With Telehealth Utilization Across a Multisite, Multiregional Cancer Practice From 2019 to 2021. JCO Oncol Pract. 2023 Sep; 19 (9):750-758 Epub 2023 June 19
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  7. Kumar A, Taghi Khani A, Duault C, Aramburo S, Sanchez Ortiz A, Lee SJ, Chan A, McDonald T, Huang M, Lacayo NJ, Sakamoto KM, Yu J, Hurtz C, Carroll M, Tasian SK, Ghoda L, Marcucci G, Gu Z, Rosen ST, Armenian S, Izraeli S, Chen CW, Caligiuri MA, Forman SJ, Maecker HT, Swaminathan S. Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia. J Immunother Cancer. 2023 May; 11 (5)
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  8. Patten CA, Koller KR, Sinicrope PS, Prochaska JJ, Young C, Resnicow K, Decker PA, Hughes CA, Merritt ZT, McConnell CR, Huang M, Thomas TK. Facebook Intervention to Connect Alaska Native People With Resources and Support to Quit Smoking: CAN Quit Pilot Randomized Controlled Trial. Nicotine Tob Res. 2023 Mar 22; 25 (4):803-813
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  9. Fan JW, Wang W, Huang M, Liu H, Hooten WM. Retrospective content analysis of consumer product reviews related to chronic pain. Front Digit Health. 2023; 5:958338 Epub 2023 Apr 24
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  10. Chen Z, Yang R, Fu S, Zong N, Liu H, Huang M. Detecting Reddit users with depression using a hybrid neural network SBERT-CNN. Proceedings - 2023 IEEE 11th International Conference on Healthcare Informatics, ICHI 2023. 2023; 193-9
  11. Miller K, Agnikula Kshatriya BS, Nunez NA, Gardea-Resendez M, Ryu E, Coombes BJ, Fu S, Frye MA, Biernacka J, Huang M, Wang Y. Identifying major depressive disorder from clinical notes using neural language models with distant supervision. Proceedings - 2023 IEEE 11th International Conference on Healthcare Informatics, ICHI 2023. 2023; 183-92
  12. Ren Y, Wu D, Khurana A, Mastorakos G, Fu S, Zong N, Fan J, Liu H, Huang M. Classification of patient portal messages with BERT-based language models. Proceedings - 2023 IEEE 11th International Conference on Healthcare Informatics, ICHI 2023. 2023; 176-82
  13. Omranian S, Zolnoori M, Huang M, Campos-Castillo C, McRoy S. Predicting Patient Satisfaction With Medications for Treating Opioid Use Disorder: Case Study Applying Natural Language Processing to Reviews of Methadone and Buprenorphine/Naloxone on Health-Related Social Media. JMIR Infodemiology. 2023; 3:e37207 Epub 2023 Jan 23
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  14. Wu D, Kasson E, Singh AK, Ren Y, Kaiser N, Huang M, Cavazos-Rehg PA. Topics and Sentiment Surrounding Vaping on Twitter and Reddit During the 2019 e-Cigarette and Vaping Use-Associated Lung Injury Outbreak: Comparative Study. J Med Internet Res. 2022 Dec 13; 24 (12):e39460
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  15. Huang M, Wen A, He H, Wang L, Liu S, Wang Y, Zong N, Yu Y, Prigge JE, Costello BA, Shah ND, Ting HH, Doubeni C, Fan JW, Liu H, Patten CA. Midwest rural-urban disparities in use of patient online services for COVID-19. J Rural Health. 2022 Sep; 38 (4):908-915 Epub 2022 Mar 08
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  16. Patten C, Brockman T, Kelpin S, Sinicrope P, Boehmer K, St Sauver J, Lampman M, Sharma P, Reinicke N, Huang M, McCoy R, Allen S, Pritchett J, Esterov D, Kamath C, Decker P, Petersen C, Cheville A. Interventions for Increasing Digital Equity and Access (IDEA) among rural patients who smoke: Study protocol for a pragmatic randomized pilot trial. Contemp Clin Trials. 2022 Aug; 119:106838 Epub 2022 June 25
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  17. Zong N, Li N, Wen A, Ngo V, Yu Y, Huang M, Chowdhury S, Jiang C, Fu S, Weinshilboum R, Jiang G, Hunter L, Liu H. BETA: a comprehensive benchmark for computational drug-target prediction. Brief Bioinform. 2022 Jul 18; 23 (4)
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  18. Zong N, Wen A, Moon S, Fu S, Wang L, Zhao Y, Yu Y, Huang M, Wang Y, Zheng G, Mielke MM, Cerhan JR, Liu H. Computational drug repurposing based on electronic health records: a scoping review. NPJ Digit Med. 2022 Jun 14; 5 (1):77 Epub 2022 June 14
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  19. Huang M, Khurana A, Mastorakos GM, Fan J. Identification of Transportation Barriers in Patient Portal Messages via Deep Semantic Embeddings and Clustering. Stud Health Technol Inform. 2022 Jun 6; 290:794-798
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  20. Huang M, Khurana A, Mastorakos G, Wen A, He H, Wang L, Liu S, Wang Y, Zong N, Prigge J, Costello B, Shah N, Ting H, Fan J, Patten C, Liu H. Patient Portal Messaging for Asynchronous Virtual Care During the COVID-19 Pandemic: Retrospective Analysis. JMIR Hum Factors. 2022 May 5; 9 (2):e35187 Epub 2022 May 05
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  21. Huang M, Fan J, Prigge J, Shah ND, Costello BA, Yao L. Characterizing Patient-Clinician Communication in Secure Medical Messages: Retrospective Study. J Med Internet Res. 2022 Jan 11; 24 (1):e17273
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  22. Huang M, Khurana A, Mastorakos G, Wen A, He H, Wang L, Liu S, Wang Y, Zong N, Prigge J, Costello B, Shah N, Ting H, Fan J, Patten C, Liu H. Patient portal messaging for asynchronous virtual care during the COVID-19 pandemic: retrospective analysis. JMIR Human Factors. 2022; 9 (2):e35187
  23. Ren Y, Wu D, Singh A, Kasson E, Huang M, Cavazos-Rehg P. Automated Detection of Vaping-Related Tweets on Twitter During the 2019 EVALI Outbreak Using Machine Learning Classification. Front Big Data. 2022; 5:770585 Epub 2022 Feb 10
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  24. Zhou J, Arriaga RI, Liu H, Huang M. A tale of two perspectives: harvesting system views and user views to understand patient portal engagement. Proceedings - 2022 IEEE 10th International Conference on Healthcare Informatics, ICHI 2022. 2022; 373-83
  25. Miller K, Fu S, Abah K, Escarria AM, Peterson K, Liu H, Hart L, Tan N, Huang M. Aspect-based sentiment analysis of radiology patient experience surveys: a cohort study. Proceedings - 2022 IEEE 10th International Conference on Healthcare Informatics, ICHI 2022. 2022; 90-6
  26. Kasson E, Singh AK, Huang M, Wu D, Cavazos-Rehg P. Using a mixed methods approach to identify public perception of vaping risks and overall health outcomes on Twitter during the 2019 EVALI outbreak. Int J Med Inform. 2021 Nov; 155:104574 Epub 2021 Sept 14
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  27. De A, Huang M, Feng T, Yue X, Yao L. Analyzing Patient Secure Messages Using a Fast Health Care Interoperability Resources (FIHR)-Based Data Model: Development and Topic Modeling Study. J Med Internet Res. 2021 Jul 30; 23 (7):e26770 Epub 2021 July 30
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  28. Zong N, Ngo V, Stone DJ, Wen A, Zhao Y, Yu Y, Liu S, Huang M, Wang C, Jiang G. Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study. JMIR Med Inform. 2021 May 25; 9 (5):e23586
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  29. Zong N, Wong RSN, Yu Y, Wen A, Huang M, Li N. Drug-target prediction utilizing heterogeneous bio-linked network embeddings. Brief Bioinform. 2021 Jan 18; 22 (1):568-580
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  30. Zong N, Stone DJ, Sharma DK, Wen A, Wang C, Yu Y, Huang M, Liu S, Liu H, Shi Q, Jiang G. Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. Int J Med Inform. 2021 Jan; 145:104308 Epub 2020 Oct 22
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  31. Mastorakos G, Khurana A, Huang M, Fu S, Tafti AP, Fan J, Liu H. Probing Patient Messages Enhanced by Natural Language Processing: A Top-Down Message Corpus Analysis. Health Data Sci. 2021; 2021:1504854 Epub 2021 May 18
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  32. Wen A, Wang L, He H, Liu S, Fu S, Sohn S, Kugel JA, Kaggal VC, Huang M, Wang Y, Shen F, Fan J, Liu H. An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. J Biomed Inform. 2021 Jan; 113:103660 Epub 2020 Dec 13
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  33. Seligson ND, Warner JL, Dalton WS, Martin D, Miller RS, Patt D, Kehl KL, Palchuk MB, Alterovitz G, Wiley LK, Huang M, Shen F, Wang Y, Nguyen KA, Wong AF, Meric-Bernstam F, Bernstam EV, Chen JL. Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity. J Am Med Inform Assoc. 2020 Nov 1; 27 (11):1808-1812
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  34. Kasson E, Cao L, Huang M, Wu D, Cavazos-Rehg P. Leveraging Twitter Data to Explore the Feasibility of Detecting Negative Health Outcomes Related to Vaping International Conference on Human-Computer Interaction. 2020; 464-468.
  35. Yu Y, Ruddy K, Mansfield A, Zong N, Wen A, Tsuji S, Huang M, Liu H, Shah N, Jiang G. Detecting and Filtering Immune-Related Adverse Events Signal Based on Text Mining and Observational Health Data Sciences and Informatics Common Data Model: Framework Development Study. JMIR Med Inform. 2020 Jun 12; 8 (6):e17353 Epub 2020 June 12
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  36. Huang M, Shah ND, Yao L. Evaluating global and local sequence alignment methods for comparing patient medical records. BMC Med Inform Decis Mak. 2019 Dec 19; 19 (Suppl 6):263
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  37. Zolnoori M, Huang M, Patten CA, Balls-Berry JE, Goudarzvand S, Brockman TA, Sagheb E, Yao L. Mining news media for understanding public health concerns. J Clin Transl Sci 2019 Oct 23; 5 (1):e1
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  38. Zolnoori M, Balls-Berry JE, Brockman TA, Patten CA, Huang M, Yao L. A Systematic Framework for Analyzing Patient-Generated Narrative Data: Protocol for a Content Analysis. JMIR Res Protoc. 2019 Aug 26; 8 (8):13914
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  39. He K, Wu J, Ma X, Zhang C, Huang M, Li C, Yao L. Extracting Kinship from Obituary to Enhance Electronic Health Records for Genetic Research Proceedings of the Fourth Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task. 2019; 1-10.
  40. Huang M, Zolnoori M, Balls-Berry JE, Brockman TA, Patten CA, Yao L. Multimedia Appendix Correction: Technological Innovations in Disease Management: Text Mining US Patent Data From 1995 to 2017. J Med Internet Res. 2019 Jul 5; 21 (7):e14678 Epub 2019 July 05
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  41. He K, Hong N, Lapalme-Remis S, Lan Y, Huang M, Li C, Yao L. Understanding the patient perspective of epilepsy treatment through text mining of online patient support groups. Epilepsy Behav. 2019 May; 94:65-71 Epub 2019 Mar 17
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  42. Huang M, Zolnoori M, Balls-Berry JE, Brockman TA, Patten CA, Yao L. Technological Innovations in Disease Management: Text Mining US Patent Data From 1995 to 2017. J Med Internet Res. 2019 Apr 30; 21 (4):e13316
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  43. Huang M, Zolnoori M, Shah N, Yao L. Temporal sequence alignment in electronic health records for computable patient representation. The 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2018.
  44. Li X, Deng P, Huang M, Li D, Wang H. DP _DETECTION: An outlier detection algorithm based on density of big data Data Science and Knowledge Engineering for Sensing Decision Support. 2018; 534-554.
  45. Li D, Huang M, Li X, Ruan Y, Yao L. MfeCNN: Mixture Feature Embedding Convolutional Neural Network for Data Mapping. IEEE Trans Nanobioscience. 2018 Jul; 17 (3):165-171 Epub 2018 May 28
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  46. Huang M, ElTayeby O, Zolnoori M, Yao L. Public Opinions Toward Diseases: Infodemiological Study on News Media Data. J Med Internet Res. 2018 May 8; 20 (5):e10047 Epub 2018 May 08
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  47. Li D, Liu P, Huang M, Gu Y, Zhang Y, Li X, Dean D, Liu X, Xu J, Lei H, Ruan Y. Mapping client messages to a unified data model with mixture feature embedding convolutional neural network 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2017.
  48. Huang M, Dissanayake T, Kuechler E, Radak BK, Lee TS, Giese TJ, York DM. A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations. J Chem Theory Comput. 2017 Sep 12; 13 (9):3975-3984 Epub 2017 Aug 17
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  49. Yue Q, Zhen H, Huang M, Zheng X, Feng L, Jiang B, Yang M, Wu W, Liu X, Guo D. Proteasome inhibition contributed to the cytotoxicity of arenobufagin after its binding with Na, K-ATPase in human cervical carcinoma HeLa cells PloS One. 2016; 11:e0159034.
  50. Huang M, Giese TJ, York DM. Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models Journal of Computational Chemistry. 2015; 36(18):1370-1389.
  51. Radak BK, Romanus M, Lee T, Chen H, Huang M, Treikalis A, Balasubramanian V, Jha S, York DM. Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations Journal of Chemical Theory and Computation. 2015; 11(2):373-377.
  52. Chen H, Giese TJ, Huang M, Wong K, Harris ME, York DM. Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions Chemistry-A European Journal. 2014; 20(44):14336-14343.
  53. Giese TJ, Huang M, Chen H, York DM. Recent advances toward a general purpose linear-scaling quantum force field Accounts of Chemical Research. 2014; 47(9):2812-2820.
  54. Li C, Wang L, Zhang J, Huang M, Wong F, Liu X, Liu F, Cui X, Yang G, Chen J, Liu Y, Wang J, Liao S, Gao M, Hu X, Shu X, Wang Q, Yin Z, Tang Z, Liu M. CERKL interacts with mitochondrial TRX2 and protects retinal cells from oxidative stress-induced apoptosis. Biochim Biophys Acta. 2014 Jul; 1842 (7):1121-9 Epub 2014 Apr 13
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  55. Huang M, York DM. Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations Physical Chemistry Chemical Physics. 2014; 16(30):15846-15855.
  56. Huang M, Giese TJ, Lee T, York DM. Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods Journal of Chemical Theory and Computation. 2014; 10(4):1538-1545.
  57. Giese TJ, Chen H, Huang M, York DM. Parametrization of an orbital-based linear-scaling quantum force field for noncovalent interactions Journal of Chemical Theory and Computation. 2014; 10(3):1086-1098.
  58. Lee T, Radak BK, Huang M, Wong K, York DM. Roadmaps through free energy landscapes calculated using the multidimensional vFEP approach Journal of Chemical Theory and Computation. 2014; 10(1):24-34.
  59. Giese TJ, Chen H, Dissanayake T, Giambasu GM, Heldenbrand H, Huang M, Kuechler ER, Lee T, Panteva MT, Radak BK, York DM. A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields Journal of Chemical Theory and Computation. 2013; 9(3):1417-1427.
  60. Liu M, Yang SC, Sharma S, Luo J, Cui X, Peebles KA, Huang M, Sato M, Ramirez RD, Shay JW, Minna JD, Dubinett SM. EGFR signaling is required for TGF-beta 1 mediated COX-2 induction in human bronchial epithelial cells. Am J Respir Cell Mol Biol. 2007 Nov; 37 (5):578-88 Epub 2007 June 28
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