Publications

2023

1. Dang Y, Li F, Hu X, Keloth VK, Zhang M, Fu S, Amith MF, Fan JW, Du J, Yu E, Liu H, Jiang X, Xu H, Tao C. Systematic design and data-driven evaluation of social determinants of health ontology (SDoHO). J Am Med Inform Assoc. 2023 Aug 18;30(9):1465-1473. doi: 10.1093/jamia/ocad096.. PMID: 37301740; PMCID: PMC10436148; DOI: 10.1093/jamia/ocad096
2. Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, et al. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol. 2023 Jun 30;21(6):e3002133. doi: 10.1371/journal.pbio.3002133. eCollection 2023 Jun.. PMID: 37390046; PMCID: PMC10313015; DOI: 10.1371/journal.pbio.3002133
3. Sun F, Yao J, Du S, Qian F, Appleton AA, Tao C, Xu H, Liu L, Dai Q, Joyce BT, Nannini DR, Hou L, Zhang K. Social Determinants, Cardiovascular Disease, and Health Care Cost: A Nationwide Study in the United States Using Machine Learning. J Am Heart Assoc. 2023 Mar 7;12(5):e027919. doi: 10.1161/JAHA.122.027919. Epub 2023 Feb 21.. PMID: 36802713; PMCID: PMC10111459; DOI: 10.1161/JAHA.122.027919
4. Mohtashamian M, Hu R, Abeysinghe R, Hao X, Xu H, Cui L. Automated Identification of Missing IS-A Relations in the Human Phenotype Ontology. AMIA Annu Symp Proc. 2023 Apr 29;2022:785-794. eCollection 2022.. PMID: 37128366; PMCID: PMC10148310
5. Ohno-Machado L, Jiang X, Kuo TT, Tao S, Chen L, Ram PM, Zhang GQ, Xu H. A hierarchical strategy to minimize privacy risk when linking "De-identified" data in biomedical research consortia. J Biomed Inform. 2023 Mar;139:104322. doi: 10.1016/j.jbi.2023.104322. Epub 2023 Feb 17.. PMID: 36806328; DOI: 10.1016/j.jbi.2023.104322
6. Hu Y, Keloth VK, Raja K, Xu H. Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach. Bioinformatics. 2023 Sep 5:btad542. doi: 10.1093/bioinformatics/btad542. Online ahead of print.. PMID: 37669123; DOI: 10.1093/bioinformatics/btad542
7. Li Z, Li R, Zhou Y, Rasmy L, Zhi D, Zhu P, Dono A, Jiang X, Xu H, Esquenazi Y, Zheng WJ. Prediction of Brain Metastases Development in Patients With Lung Cancer by Explainable Artificial Intelligence From Electronic Health Records. JCO Clin Cancer Inform. 2023 Apr;7:e2200141. doi: 10.1200/CCI.22.00141.. PMID: 37018650; PMCID: PMC10281421; DOI: 10.1200/CCI.22.00141
8. Liu S, Wen A, Wang L, He H, Fu S, Miller R, Williams A, Harris D, Kavuluru R, Liu M, Abu-El-Rub N, Schutte D, Zhang R, Rouhizadeh M, Osborne JD, He Y, Topaloglu U, Hong SS, Saltz JH, Schaffter T, Pfaff E, Chute CG, Duong T, Haendel MA, Fuentes R, Szolovits P, Xu H, Liu H; National COVID Cohort Collaborative (N3C) Natural Language Processing (NLP) Subgroup, National COVID Cohort Collaborative (N3C). An Open Natural Language Processing (NLP) Framework for EHR-based Clinical Research: A Case Demonstration Using the National COVID Cohort Collaborative (N3C). J Am Med Inform Assoc. 2023 Aug 9:ocad134. doi: 10.1093/jamia/ocad134. Online ahead of print.. PMID: 37555837; DOI: 10.1093/jamia/ocad134

2022

1. Ramirez AH, Sulieman L, Schlueter DJ, Halvorson A, Qian J, Ratsimbazafy F, Loperena R, Mayo K, Basford M, Deflaux N, Muthuraman KN, Natarajan K, Kho A, Xu H, Wilkins C, Anton-Culver H, Boerwinkle E, Cicek M, Clark CR, Cohn E, Ohno-Machado L, Schully SD, Ahmedani BK, Argos M, Cronin RM, O'Donnell C, Fouad M, Goldstein DB, Greenland P, Hebbring SJ, Karlson EW, Khatri P, Korf B, Smoller JW, Sodeke S, Wilbanks J, Hentges J, Mockrin S, Lunt C, Devaney SA, Gebo K, Denny JC, Carroll RJ, Glazer D, Harris PA, Hripcsak G, Philippakis A, Roden DM; All of Us Research Program. The All of Us Research Program: Data quality, utility, and diversity. Patterns (N Y). 2022 Aug 12;3(8):100570. doi: 10.1016/j.patter.2022.100570. eCollection 2022 Aug 12.. PMID: 36033590; PMCID: PMC9403360; DOI: 10.1016/j.patter.2022.100570
2. Wang L, Fu S, Wen A, Ruan X, He H, Liu S, Moon S, Mai M, Riaz IB, Wang N, Yang P, Xu H, Warner JL, Liu H. Assessment of Electronic Health Record for Cancer Research and Patient Care Through a Scoping Review of Cancer Natural Language Processing. JCO Clin Cancer Inform. 2022 Jul;6:e2200006. doi: 10.1200/CCI.22.00006.. PMID: 35917480; PMCID: PMC9470142; DOI: 10.1200/CCI.22.00006
3. Fang Y, Idnay B, Sun Y, Liu H, Chen Z, Marder K, Xu H, Schnall R, Weng C. Combining human and machine intelligence for clinical trial eligibility querying. J Am Med Inform Assoc. 2022 Jun 14;29(7):1161-1171. doi: 10.1093/jamia/ocac051.. PMID: 35426943; PMCID: PMC9196697; DOI: 10.1093/jamia/ocac051
4. Xu J, Guo Y, Wang F, Xu H, Lucero R, Bian J, Prosperi M. Protocol for the development of a reporting guideline for causal and counterfactual prediction models in biomedicine. BMJ Open. 2022 Jun 20;12(6):e059715. doi: 10.1136/bmjopen-2021-059715.. PMID: 35725267; PMCID: PMC9214357; DOI: 10.1136/bmjopen-2021-059715
5. Du XL, Song L, Schulz PE, Xu H, Chan W. Risk of Developing Alzheimer's Disease and Related Dementias in Association with Cardiovascular Disease, Stroke, Hypertension, and Diabetes in a Large Cohort of Women with Breast Cancer and with up to 26 Years of Follow-Up. J Alzheimers Dis. 2022;87(1):415-432. doi: 10.3233/JAD-215657.. PMID: 35311707; PMCID: PMC9117151; DOI: 10.3233/JAD-215657
6. Du XL, Song L, Schulz PE, Xu H, Chan W. Associations Between Vascular Diseases and Alzheimer's Disease or Related Dementias in a Large Cohort of Men and Women with Colorectal Cancer. J Alzheimers Dis. 2022;90(1):211-231. doi: 10.3233/JAD-220548.. PMID: 36093703; PMCID: PMC9661325; DOI: 10.3233/JAD-220548
7. Maghsoudi A, Nowakowski S, Agrawal R, Sharafkhaneh A, Kunik ME, Naik AD, Xu H, Razjouyan J. Sentiment Analysis of Insomnia-Related Tweets via a Combination of Transformers Using Dempster-Shafer Theory: Pre- and Peri-COVID-19 Pandemic Retrospective Study. J Med Internet Res. 2022 Dec 27;24(12):e41517. doi: 10.2196/41517.. PMID: 36417585; PMCID: PMC9822178; DOI: 10.2196/41517
8. Schutte D, Vasilakes J, Bompelli A, Zhou Y, Fiszman M, Xu H, Kilicoglu H, Bishop JR, Adam T, Zhang R. Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature. J Biomed Inform. 2022 Jul;131:104120. doi: 10.1016/j.jbi.2022.104120. Epub 2022 Jun 13.. PMID: 35709900; PMCID: PMC9335448; DOI: 10.1016/j.jbi.2022.104120
9. Xu H, Buckeridge DL, Wang F, Tarczy-Hornoch P. Novel informatics approaches to COVID-19 Research: From methods to applications. J Biomed Inform. 2022 May;129:104028. doi: 10.1016/j.jbi.2022.104028. Epub 2022 Feb 16.. PMID: 35181495; PMCID: PMC8847074; DOI: 10.1016/j.jbi.2022.104028
10. Li J, Wei Q, Ghiasvand O, Chen M, Lobanov V, Weng C, Xu H. A comparative study of pre-trained language models for named entity recognition in clinical trial eligibility criteria from multiple corpora. BMC Med Inform Decis Mak. 2022 Sep 6;22(Suppl 3):235. doi: 10.1186/s12911-022-01967-7.. PMID: 36068551; PMCID: PMC9450226; DOI: 10.1186/s12911-022-01967-7
11. Rasmy L, Nigo M, Kannadath BS, Xie Z, Mao B, Patel K, Zhou Y, Zhang W, Ross A, Xu H, Zhi D. Recurrent neural network models (CovRNN) for predicting outcomes of patients with COVID-19 on admission to hospital: model development and validation using electronic health record data. Lancet Digit Health. 2022 Jun;4(6):e415-e425. doi: 10.1016/S2589-7500(22)00049-8. Epub 2022 Apr 21.. PMID: 35466079; PMCID: PMC9023005; DOI: 10.1016/S2589-7500(22)00049-8
12. Luo C, Islam MN, Sheils NE, Buresh J, Reps J, Schuemie MJ, Ryan PB, Edmondson M, Duan R, Tong J, Marks-Anglin A, Bian J, Chen Z, Duarte-Salles T, Fernández-Bertolín S, Falconer T, Kim C, Park RW, Pfohl SR, Shah NH, Williams AE, Xu H, Zhou Y, Lautenbach E, Doshi JA, Werner RM, Asch DA, Chen Y. DLMM as a lossless one-shot algorithm for collaborative multi-site distributed linear mixed models. Nat Commun. 2022 Mar 30;13(1):1678. doi: 10.1038/s41467-022-29160-4.. PMID: 35354802; PMCID: PMC8967932; DOI: 10.1038/s41467-022-29160-4
13. Chen UI, Xu H, Krause TM, Greenberg R, Dong X, Jiang X. Factors Associated With COVID-19 Death in the United States: Cohort Study. JMIR Public Health Surveill. 2022 May 12;8(5):e29343. doi: 10.2196/29343.. PMID: 35377319; PMCID: PMC9132142; DOI: 10.2196/29343
14. He J, Li F, Hu X, Li J, Nian Y, Wang J, Xiang Y, Wei Q, Xu H, Tao C. Chemical-Protein Relation Extraction with Pre-trained Prompt Tuning. IEEE Int Conf Healthc Inform. 2022 Jun;2022:608-609. doi: 10.1109/ichi54592.2022.00120. Epub 2022 Sep 8.. PMID: 37664001; PMCID: PMC10474649; DOI: 10.1109/ichi54592.2022.00120

2021

1. Guo Y, Zhang Y, Lyu T, Prosperi M, Wang F, Xu H, Bian J. The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. J Am Med Inform Assoc. 2021 Aug 13;28(9):2050-2067. doi: 10.1093/jamia/ocab098.. PMID: 34151987; PMCID: PMC8344463; DOI: 10.1093/jamia/ocab098
2. Yuan Z, Fan X, Zhu JJ, Fu TM, Wu J, Xu H, Zhang N, An Z, Zheng WJ. Presence of complete murine viral genome sequences in patient-derived xenografts. Nat Commun. 2021 Apr 1;12(1):2031. doi: 10.1038/s41467-021-22200-5.. PMID: 33795676; PMCID: PMC8017013; DOI: 10.1038/s41467-021-22200-5
3. Kim J, Neumann L, Paul P, Day ME, Aratow M, Bell DS, Doctor JN, Hinske LC, Jiang X, Kim KK, Matheny ME, Meeker D, Pletcher MJ, Schilling LM, SooHoo S, Xu H, Zheng K, Ohno-Machado L; R2D2 Consortium. Privacy-protecting, reliable response data discovery using COVID-19 patient observations. J Am Med Inform Assoc. 2021 Jul 30;28(8):1765-1776. doi: 10.1093/jamia/ocab054.. PMID: 34051088; PMCID: PMC8194878; DOI: 10.1093/jamia/ocab054
4. Wang J, Ren Y, Zhang Z, Xu H, Zhang Y. From Tokenization to Self-Supervision: Building a High-Performance Information Extraction System for Chemical Reactions in Patents. Front Res Metr Anal. 2021 Dec 22;6:691105. doi: 10.3389/frma.2021.691105. eCollection 2021.. PMID: 35005421; PMCID: PMC8727901; DOI: 10.3389/frma.2021.691105
5. Zuo X, Li J, Zhao B, Zhou Y, Dong X, Duke J, Natarajan K, Hripcsak G, Shah N, Banda JM, Reeves R, Miller T, Xu H. Normalizing Clinical Document Titles to LOINC Document Ontology: an Initial Study. AMIA Annu Symp Proc. 2021 Jan 25;2020:1441-1450. eCollection 2020.. PMID: 33936520; PMCID: PMC8075502
6. Li X, Liu H, Kury F, Yuan C, Butler A, Sun Y, Ostropolets A, Xu H, Weng C. A Comparison between Human and NLP-based Annotation of Clinical Trial Eligibility Criteria Text Using The OMOP Common Data Model. AMIA Jt Summits Transl Sci Proc. 2021 May 17;2021:394-403. eCollection 2021.. PMID: 34457154; PMCID: PMC8378608
7. Li J, Zhou Y, Jiang X, Natarajan K, Pakhomov SV, Liu H, Xu H. Are synthetic clinical notes useful for real natural language processing tasks: A case study on clinical entity recognition. J Am Med Inform Assoc. 2021 Sep 18;28(10):2193-2201. doi: 10.1093/jamia/ocab112.. PMID: 34272955; PMCID: PMC8449609; DOI: 10.1093/jamia/ocab112
8. Dong X, Zhou Y, Shu XO, Bernstam EV, Stern R, Aronoff DM, Xu H, Lipworth L. Comprehensive Characterization of COVID-19 Patients with Repeatedly Positive SARS-CoV-2 Tests Using a Large U.S. Electronic Health Record Database. Microbiol Spectr. 2021 Sep 3;9(1):e0032721. doi: 10.1128/Spectrum.00327-21. Epub 2021 Aug 18.. PMID: 34406805; PMCID: PMC8552669; DOI: 10.1128/Spectrum.00327-21
9. Du J, Xiang Y, Sankaranarayanapillai M, Zhang M, Wang J, Si Y, Pham HA, Xu H, Chen Y, Tao C. Extracting postmarketing adverse events from safety reports in the vaccine adverse event reporting system (VAERS) using deep learning. J Am Med Inform Assoc. 2021 Jul 14;28(7):1393-1400. doi: 10.1093/jamia/ocab014.. PMID: 33647938; PMCID: PMC8279785; DOI: 10.1093/jamia/ocab014
10. Tortolero GA, Brown MR, Sharma SV, de Oliveira Otto MC, Yamal JM, Aguilar D, Gunther MD, Mofleh DI, Harris RD, John JC, de Vries PS, Ramphul R, Serbo DM, Kiger J, Banerjee D, Bonvino N, Merchant A, Clifford W, Mikhail J, Xu H, Murphy RE, Wei Q, Vahidy FS, Morrison AC, Boerwinkle E. Leveraging a health information exchange for analyses of COVID-19 outcomes including an example application using smoking history and mortality. PLoS One. 2021 Jun 3;16(6):e0247235. doi: 10.1371/journal.pone.0247235. eCollection 2021.. PMID: 34081724; PMCID: PMC8174716; DOI: 10.1371/journal.pone.0247235
11. Wang J, Abu-El-Rub N, Gray J, Pham HA, Zhou Y, Manion FJ, Liu M, Song X, Xu H, Rouhizadeh M, Zhang Y. COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model. J Am Med Inform Assoc. 2021 Jun 12;28(6):1275-1283. doi: 10.1093/jamia/ocab015.. PMID: 33674830; PMCID: PMC7989301; DOI: 10.1093/jamia/ocab015
12. Ji Z, Ghiasvand O, Wu S, Xu H. A Discrete Joint Model for Entity and Relation Extraction from Clinical Notes. AMIA Jt Summits Transl Sci Proc. 2021 May 17;2021:315-324. eCollection 2021.. PMID: 34457146; PMCID: PMC8378610
13. Wijarnpreecha K, Li F, Xiang Y, Xu X, Zhu C, Maroufy V, Wang Q, Tao W, Dang Y, Pham HA, Zhou Y, Li J, Zhang X, Xu H, Taner CB, Yang L, Tao C. Nonselective beta-blockers are associated with a lower risk of hepatocellular carcinoma among cirrhotic patients in the United States. Aliment Pharmacol Ther. 2021 Aug;54(4):481-492. doi: 10.1111/apt.16490. Epub 2021 Jul 5.. PMID: 34224163; DOI: 10.1111/apt.16490
14. Zuo X, Chen Y, Ohno-Machado L, Xu H. How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles. Brief Bioinform. 2021 Mar 22;22(2):800-811. doi: 10.1093/bib/bbaa331.. PMID: 33757278; PMCID: PMC7799277; DOI: 10.1093/bib/bbaa331

2020

1. Wu S, Roberts K, Datta S, Du J, Ji Z, Si Y, Soni S, Wang Q, Wei Q, Xiang Y, Zhao B, Xu H. Deep learning in clinical natural language processing: a methodical review. J Am Med Inform Assoc. 2020 Mar 1;27(3):457-470. doi: 10.1093/jamia/ocz200.. PMID: 31794016; PMCID: PMC7025365; DOI: 10.1093/jamia/ocz200
2. Humphreys BL, Del Fiol G, Xu H. The UMLS knowledge sources at 30: indispensable to current research and applications in biomedical informatics. J Am Med Inform Assoc. 2020 Oct 1;27(10):1499-1501. doi: 10.1093/jamia/ocaa208.. PMID: 33059366; PMCID: PMC7647371; DOI: 10.1093/jamia/ocaa208
3. Ji Z, Wei Q, Xu H. BERT-based Ranking for Biomedical Entity Normalization. AMIA Jt Summits Transl Sci Proc. 2020 May 30;2020:269-277. eCollection 2020.. PMID: 32477646; PMCID: PMC7233044
4. Rasmy L, Tiryaki F, Zhou Y, Xiang Y, Tao C, Xu H, Zhi D. Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. J Am Med Inform Assoc. 2020 Oct 1;27(10):1593-1599. doi: 10.1093/jamia/ocaa180.. PMID: 32930711; PMCID: PMC7647355; DOI: 10.1093/jamia/ocaa180
5. Li Y, Luo YH, Wampfler JA, Rubinstein SM, Tiryaki F, Ashok K 5th, Warner JL, Xu H, Yang P. Efficient and Accurate Extracting of Unstructured EHRs on Cancer Therapy Responses for the Development of RECIST Natural Language Processing Tools: Part I, the Corpus. JCO Clin Cancer Inform. 2020 May;4:383-391. doi: 10.1200/CCI.19.00147.. PMID: 32364754; PMCID: PMC7265793; DOI: 10.1200/CCI.19.00147
6. Duan R, Luo C, Schuemie MJ, Tong J, Liang CJ, Chang HH, Boland MR, Bian J, Xu H, Holmes JH, Forrest CB, Morton SC, Berlin JA, Moore JH, Mahoney KB, Chen Y. Learning from local to global: An efficient distributed algorithm for modeling time-to-event data. J Am Med Inform Assoc. 2020 Jul 1;27(7):1028-1036. doi: 10.1093/jamia/ocaa044.. PMID: 32626900; PMCID: PMC7647322; DOI: 10.1093/jamia/ocaa044
7. Li F, Du J, He Y, Song HY, Madkour M, Rao G, Xiang Y, Luo Y, Chen HW, Liu S, Wang L, Liu H, Xu H, Tao C. Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. J Am Med Inform Assoc. 2020 Jul 1;27(7):1046-1056. doi: 10.1093/jamia/ocaa058.. PMID: 32626903; PMCID: PMC7647306; DOI: 10.1093/jamia/ocaa058
8. Wei Q, Ji Z, Si Y, Du J, Wang J, Tiryaki F, Wu S, Tao C, Roberts K, Xu H. Relation Extraction from Clinical Narratives Using Pre-trained Language Models. AMIA Annu Symp Proc. 2020 Mar 4;2019:1236-1245. eCollection 2019.. PMID: 32308921; PMCID: PMC7153059
9. Raisaro JL, Marino F, Troncoso-Pastoriza J, Beau-Lejdstrom R, Bellazzi R, Murphy R, Bernstam EV, Wang H, Bucalo M, Chen Y, Gottlieb A, Harmanci A, Kim M, Kim Y, Klann J, Klersy C, Malin BA, Méan M, Prasser F, Scudeller L, Torkamani A, Vaucher J, Puppala M, Wong STC, Frenkel-Morgenstern M, Xu H, Musa BM, Habib AG, Cohen T, Wilcox A, Salihu HM, Sofia H, Jiang X, Hubaux JP. SCOR: A secure international informatics infrastructure to investigate COVID-19. J Am Med Inform Assoc. 2020 Nov 1;27(11):1721-1726. doi: 10.1093/jamia/ocaa172.. PMID: 32918447; PMCID: PMC7454652; DOI: 10.1093/jamia/ocaa172
10. Luo J, Du J, Tao C, Xu H, Zhang Y. Exploring temporal suicidal behavior patterns on social media: Insight from Twitter analytics. Health Informatics J. 2020 Jun;26(2):738-752. doi: 10.1177/1460458219832043. Epub 2019 Mar 14.. PMID: 30866708; DOI: 10.1177/1460458219832043
11. Wei Q, Ji Z, Li Z, Du J, Wang J, Xu J, Xiang Y, Tiryaki F, Wu S, Zhang Y, Tao C, Xu H. A study of deep learning approaches for medication and adverse drug event extraction from clinical text. J Am Med Inform Assoc. 2020 Jan 1;27(1):13-21. doi: 10.1093/jamia/ocz063.. PMID: 31135882; PMCID: PMC6913210; DOI: 10.1093/jamia/ocz063
12. Amith M, Lin RZ, Cui L, Wang D, Zhu A, Xiong G, Xu H, Roberts K, Tao C. Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents. BMC Med Inform Decis Mak. 2020 Dec 14;20(Suppl 4):259. doi: 10.1186/s12911-020-01267-y.. PMID: 33317519; PMCID: PMC7734717; DOI: 10.1186/s12911-020-01267-y
13. Xiang Y, Ji H, Zhou Y, Li F, Du J, Rasmy L, Wu S, Zheng WJ, Xu H, Zhi D, Zhang Y, Tao C. Asthma Exacerbation Prediction and Risk Factor Analysis Based on a Time-Sensitive, Attentive Neural Network: Retrospective Cohort Study. J Med Internet Res. 2020 Jul 31;22(7):e16981. doi: 10.2196/16981.. PMID: 32735224; PMCID: PMC7428917; DOI: 10.2196/16981
14. Wang Q, Ji Z, Wang J, Wu S, Lin W, Li W, Ke L, Xiao G, Jiang Q, Xu H, Zhou Y. A study of entity-linking methods for normalizing Chinese diagnosis and procedure terms to ICD codes. J Biomed Inform. 2020 May;105:103418. doi: 10.1016/j.jbi.2020.103418. Epub 2020 Apr 13.. PMID: 32298846; DOI: 10.1016/j.jbi.2020.103418
15. Duan R, Boland MR, Liu Z, Liu Y, Chang HH, Xu H, Chu H, Schmid CH, Forrest CB, Holmes JH, Schuemie MJ, Berlin JA, Moore JH, Chen Y. Learning from electronic health records across multiple sites: A communication-efficient and privacy-preserving distributed algorithm. J Am Med Inform Assoc. 2020 Mar 1;27(3):376-385. doi: 10.1093/jamia/ocz199.. PMID: 31816040; PMCID: PMC7025371; DOI: 10.1093/jamia/ocz199
16. Kim J, Neumann L, Paul P, Aratow M, Bell DS, Doctor JN, Hinske LC, Jiang X, Kim KK, Matheny ME, Meeker D, Pletcher MJ, Schilling LM, SooHoo S, Xu H, Zheng K, Ohno-Machado L. Privacy-Protecting, Reliable Response Data Discovery Using COVID-19 Patient Observations. medRxiv. 2020 Sep 23:2020.09.21.20196220. doi: 10.1101/2020.09.21.20196220. Preprint.. PMID: 32995818; PMCID: PMC7523159; DOI: 10.1101/2020.09.21.20196220
17. Wang Y, You L, Chyr J, Lan L, Zhao W, Zhou Y, Xu H, Noble P, Zhou X. Causal Discovery in Radiographic Markers of Knee Osteoarthritis and Prediction for Knee Osteoarthritis Severity With Attention-Long Short-Term Memory. Front Public Health. 2020 Dec 18;8:604654. doi: 10.3389/fpubh.2020.604654. eCollection 2020.. PMID: 33409263; PMCID: PMC7779681; DOI: 10.3389/fpubh.2020.604654
18. Yang X, Yang H, Lyu T, Yang S, Guo Y, Bian J, Xu H, Wu Y. A Natural Language Processing Tool to Extract Quantitative Smoking Status from Clinical Narratives. IEEE Int Conf Healthc Inform. 2020 Nov-Dec;2020:10.1109/ICHI48887.2020.9374369. doi: 10.1109/ICHI48887.2020.9374369. Epub 2021 Mar 12.. PMID: 33786419; PMCID: PMC8006894; DOI: 10.1109/ICHI48887.2020.9374369
19. Dong X, Li J, Soysal E, Bian J, DuVall SL, Hanchrow E, Liu H, Lynch KE, Matheny M, Natarajan K, Ohno-Machado L, Pakhomov S, Reeves RM, Sitapati AM, Abhyankar S, Cullen T, Deckard J, Jiang X, Murphy R, Xu H. COVID-19 TestNorm: A tool to normalize COVID-19 testing names to LOINC codes. J Am Med Inform Assoc. 2020 Jul 1;27(9):1437-1442. doi: 10.1093/jamia/ocaa145.. PMID: 32569358; PMCID: PMC7337837; DOI: 10.1093/jamia/ocaa145
20. Xu H, Li J, Jiang X, Chen Q. Electronic Health Records for Drug Repurposing: Current Status, Challenges, and Future Directions. Clin Pharmacol Ther. 2020 Apr;107(4):712-714. doi: 10.1002/cpt.1769. Epub 2020 Feb 3.. PMID: 32012237; DOI: 10.1002/cpt.1769

2019

1. Vydiswaran VGV, Zhang Y, Wang Y, Xu H. Special issue of BMC medical informatics and decision making on health natural language processing. BMC Med Inform Decis Mak. 2019 Apr 4;19(Suppl 3):76. doi: 10.1186/s12911-019-0777-0.. PMID: 30943961; PMCID: PMC6448180; DOI: 10.1186/s12911-019-0777-0
2. Xiong Y, Wang Z, Jiang D, Wang X, Chen Q, Xu H, Yan J, Tang B. A fine-grained Chinese word segmentation and part-of-speech tagging corpus for clinical text. BMC Med Inform Decis Mak. 2019 Apr 9;19(Suppl 2):66. doi: 10.1186/s12911-019-0770-7.. PMID: 30961602; PMCID: PMC6454584; DOI: 10.1186/s12911-019-0770-7
3. Si Y, Wang J, Xu H, Roberts K. Enhancing clinical concept extraction with contextual embeddings. J Am Med Inform Assoc. 2019 Nov 1;26(11):1297-1304. doi: 10.1093/jamia/ocz096.. PMID: 31265066; PMCID: PMC6798561; DOI: 10.1093/jamia/ocz096
4. Liu Z, Wang X, Chen Q, Tang B, Xu H. Temporal indexing of medical entity in Chinese clinical notes. BMC Med Inform Decis Mak. 2019 Jan 31;19(Suppl 1):17. doi: 10.1186/s12911-019-0735-x.. PMID: 30700331; PMCID: PMC6354334; DOI: 10.1186/s12911-019-0735-x
5. Shi X, Yi Y, Xiong Y, Tang B, Chen Q, Wang X, Ji Z, Zhang Y, Xu H. Extracting entities with attributes in clinical text via joint deep learning. J Am Med Inform Assoc. 2019 Dec 1;26(12):1584-1591. doi: 10.1093/jamia/ocz158.. PMID: 31550346; PMCID: PMC7647140; DOI: 10.1093/jamia/ocz158
6. Wei Q, Chen Y, Salimi M, Denny JC, Mei Q, Lasko TA, Chen Q, Wu S, Franklin A, Cohen T, Xu H. Cost-aware active learning for named entity recognition in clinical text. J Am Med Inform Assoc. 2019 Nov 1;26(11):1314-1322. doi: 10.1093/jamia/ocz102.. PMID: 31294792; PMCID: PMC6798575; DOI: 10.1093/jamia/ocz102
7. Zhang Y, Tiryaki F, Jiang M, Xu H. Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison. BMC Med Inform Decis Mak. 2019 Apr 4;19(Suppl 3):77. doi: 10.1186/s12911-019-0783-2.. PMID: 30943955; PMCID: PMC6448179; DOI: 10.1186/s12911-019-0783-2
8. Miao S, Dong X, Zhang X, Jing S, Zhang X, Xu T, Wang L, Du X, Xu H, Liu Y. Detecting pioglitazone use and risk of cardiovascular events using electronic health record data in a large cohort of Chinese patients with type 2 diabetes. J Diabetes. 2019 Aug;11(8):684-689. doi: 10.1111/1753-0407.12894. Epub 2019 Feb 5.. PMID: 30597747; PMCID: PMC6850402; DOI: 10.1111/1753-0407.12894
9. Ji Z, Wei Q, Franklin A, Cohen T, Xu H. Cost-sensitive Active Learning for Phenotyping of Electronic Health Records. AMIA Jt Summits Transl Sci Proc. 2019 May 6;2019:829-838. eCollection 2019.. PMID: 31259040; PMCID: PMC6568101
10. Xiang Y, Xu J, Si Y, Li Z, Rasmy L, Zhou Y, Tiryaki F, Li F, Zhang Y, Wu Y, Jiang X, Zheng WJ, Zhi D, Tao C, Xu H. Time-sensitive clinical concept embeddings learned from large electronic health records. BMC Med Inform Decis Mak. 2019 Apr 9;19(Suppl 2):58. doi: 10.1186/s12911-019-0766-3.. PMID: 30961579; PMCID: PMC6454598; DOI: 10.1186/s12911-019-0766-3
11. Xu J, Xiang Y, Li Z, Lee HJ, Xu H, Wei Q, Zhang Y, Wu Y, Wu S. Detect Attributes of Medical Concepts via Sequence Labeling. IEEE Int Conf Healthc Inform. 2019 Jun;2019:10.1109/ICHI.2019.8904714. doi: 10.1109/ICHI.2019.8904714. Epub 2019 Nov 21.. PMID: 32537570; PMCID: PMC7293163; DOI: 10.1109/ICHI.2019.8904714
12. Walker G, Soysal E, Xu H. Development of a Natural Language Processing Tool to Extract Radiation Treatment Sites. Cureus. 2019 Oct 28;11(10):e6010. doi: 10.7759/cureus.6010.. PMID: 31815074; PMCID: PMC6881088; DOI: 10.7759/cureus.6010
13. Chen H, Shi L, Wang N, Han Y, Lin Y, Dai M, Liu H, Dong X, Xue M, Xu H. Analysis on geographic variations in hospital deaths and endovascular therapy in ischaemic stroke patients: an observational cross-sectional study in China. BMJ Open. 2019 Jun 24;9(6):e029079. doi: 10.1136/bmjopen-2019-029079.. PMID: 31239305; PMCID: PMC6597735; DOI: 10.1136/bmjopen-2019-029079
14. Soysal E, Warner JL, Wang J, Jiang M, Harvey K, Jain SK, Dong X, Song HY, Siddhanamatha H, Wang L, Dai Q, Chen Q, Du X, Tao C, Yang P, Denny JC, Liu H, Xu H. Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. Stud Health Technol Inform. 2019 Aug 21;264:1041-1045. doi: 10.3233/SHTI190383.. PMID: 31438083; PMCID: PMC7359882; DOI: 10.3233/SHTI190383
15. Xu J, Li Z, Wei Q, Wu Y, Xiang Y, Lee HJ, Zhang Y, Wu S, Xu H. Applying a deep learning-based sequence labeling approach to detect attributes of medical concepts in clinical text. BMC Med Inform Decis Mak. 2019 Dec 5;19(Suppl 5):236. doi: 10.1186/s12911-019-0937-2.. PMID: 31801529; PMCID: PMC6894107; DOI: 10.1186/s12911-019-0937-2
16. Li Z, Yang Z, Shen C, Xu J, Zhang Y, Xu H. Integrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text. BMC Med Inform Decis Mak. 2019 Jan 31;19(Suppl 1):22. doi: 10.1186/s12911-019-0736-9.. PMID: 30700301; PMCID: PMC6354333; DOI: 10.1186/s12911-019-0736-9
17. Wang Y, Xu H, Uzuner O. Editorial: The second international workshop on health natural language processing (HealthNLP 2019). BMC Med Inform Decis Mak. 2019 Dec 5;19(Suppl 5):233. doi: 10.1186/s12911-019-0930-9.. PMID: 31801516; PMCID: PMC6894102; DOI: 10.1186/s12911-019-0930-9

2018

1. Dixit R, Rogith D, Narayana V, Salimi M, Gururaj A, Ohno-Machado L, Xu H, Johnson TR. User needs analysis and usability assessment of DataMed - a biomedical data discovery index. J Am Med Inform Assoc. 2018 Mar 1;25(3):337-344. doi: 10.1093/jamia/ocx134.. PMID: 29202203; PMCID: PMC7378884; DOI: 10.1093/jamia/ocx134
2. Vashisht R, Jung K, Schuler A, Banda JM, Park RW, Jin S, Li L, Dudley JT, Johnson KW, Shervey MM, Xu H, Wu Y, Natrajan K, Hripcsak G, Jin P, Van Zandt M, Reckard A, Reich CG, Weaver J, Schuemie MJ, Ryan PB, Callahan A, Shah NH. Association of Hemoglobin A1c Levels With Use of Sulfonylureas, Dipeptidyl Peptidase 4 Inhibitors, and Thiazolidinediones in Patients With Type 2 Diabetes Treated With Metformin: Analysis From the Observational Health Data Sciences and Informatics Initiative. JAMA Netw Open. 2018 Aug 3;1(4):e181755. doi: 10.1001/jamanetworkopen.2018.1755.. PMID: 30646124; PMCID: PMC6324274; DOI: 10.1001/jamanetworkopen.2018.1755
3. Zhang X, Wang L, Miao S, Xu H, Yin Y, Zhu Y, Dai Z, Shan T, Jing S, Wang J, Zhang X, Huang Z, Wang Z, Guo J, Liu Y. Analysis of treatment pathways for three chronic diseases using OMOP CDM. J Med Syst. 2018 Nov 13;42(12):260. doi: 10.1007/s10916-018-1076-5.. PMID: 30421323; PMCID: PMC6244882; DOI: 10.1007/s10916-018-1076-5
4. Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim HE, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone SA, Fore IM, Ohno-Machado L, Grethe JS, Xu H. DataMed - an open source discovery index for finding biomedical datasets. J Am Med Inform Assoc. 2018 Mar 1;25(3):300-308. doi: 10.1093/jamia/ocx121.. PMID: 29346583; PMCID: PMC7378878; DOI: 10.1093/jamia/ocx121
5. Du J, Zhang Y, Luo J, Jia Y, Wei Q, Tao C, Xu H. Extracting psychiatric stressors for suicide from social media using deep learning. BMC Med Inform Decis Mak. 2018 Jul 23;18(Suppl 2):43. doi: 10.1186/s12911-018-0632-8.. PMID: 30066665; PMCID: PMC6069295; DOI: 10.1186/s12911-018-0632-8
6. Wu Y, Jiang M, Xu J, Zhi D, Xu H. Clinical Named Entity Recognition Using Deep Learning Models. AMIA Annu Symp Proc. 2018 Apr 16;2017:1812-1819. eCollection 2017.. PMID: 29854252; PMCID: PMC5977567
7. Lee HJ, Zhang Y, Jiang M, Xu J, Tao C, Xu H. Identifying direct temporal relations between time and events from clinical notes. BMC Med Inform Decis Mak. 2018 Jul 23;18(Suppl 2):49. doi: 10.1186/s12911-018-0627-5.. PMID: 30066643; PMCID: PMC6069692; DOI: 10.1186/s12911-018-0627-5
8. Wang L, Zhang Y, Jiang M, Wang J, Dong J, Liu Y, Tao C, Jiang G, Zhou Y, Xu H. Toward a normalized clinical drug knowledge base in China-applying the RxNorm model to Chinese clinical drugs. J Am Med Inform Assoc. 2018 Jul 1;25(7):809-818. doi: 10.1093/jamia/ocy020.. PMID: 29635469; PMCID: PMC7647010; DOI: 10.1093/jamia/ocy020
9. Wei Q, Franklin A, Cohen T, Xu H. Clinical text annotation - what factors are associated with the cost of time?. AMIA Annu Symp Proc. 2018 Dec 5;2018:1552-1560. eCollection 2018.. PMID: 30815201; PMCID: PMC6371268
10. Wang Y, Zheng K, Xu H, Mei Q. Interactive medical word sense disambiguation through informed learning. J Am Med Inform Assoc. 2018 Jul 1;25(7):800-808. doi: 10.1093/jamia/ocy013.. PMID: 29584896; PMCID: PMC6658868; DOI: 10.1093/jamia/ocy013
11. Yi Y, Li Y, Hou A, Ge Y, Xu Y, Xiong G, Yang X, Acevedo SA, Shi L, Xu H. A Retrospective Cohort Study of Patients with Type 2 Diabetes in China: Associations of Hypoglycemia with Health Care Resource Utilization and Associated Costs. Diabetes Ther. 2018 Jun;9(3):1073-1082. doi: 10.1007/s13300-018-0409-1. Epub 2018 Apr 5.. PMID: 29623592; PMCID: PMC5984912; DOI: 10.1007/s13300-018-0409-1
12. Rasmy L, Wu Y, Wang N, Geng X, Zheng WJ, Wang F, Wu H, Xu H, Zhi D. A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. J Biomed Inform. 2018 Aug;84:11-16. doi: 10.1016/j.jbi.2018.06.011. Epub 2018 Jun 15.. PMID: 29908902; PMCID: PMC6076336; DOI: 10.1016/j.jbi.2018.06.011
13. Zhang Y, Li HJ, Wang J, Cohen T, Roberts K, Xu H. Adapting Word Embeddings from Multiple Domains to Symptom Recognition from Psychiatric Notes. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:281-289. eCollection 2018.. PMID: 29888086; PMCID: PMC5961810
14. Huang J, Duan R, Hubbard RA, Wu Y, Moore JH, Xu H, Chen Y. PIE: A prior knowledge guided integrated likelihood estimation method for bias reduction in association studies using electronic health records data. J Am Med Inform Assoc. 2018 Mar 1;25(3):345-352. doi: 10.1093/jamia/ocx137.. PMID: 29206922; PMCID: PMC7378882; DOI: 10.1093/jamia/ocx137
15. Miao S, Xu T, Wu Y, Xie H, Wang J, Jing S, Zhang Y, Zhang X, Yang Y, Zhang X, Shan T, Wang L, Xu H, Wang S, Liu Y. Extraction of BI-RADS findings from breast ultrasound reports in Chinese using deep learning approaches. Int J Med Inform. 2018 Nov;119:17-21. doi: 10.1016/j.ijmedinf.2018.08.009. Epub 2018 Aug 18.. PMID: 30342682; DOI: 10.1016/j.ijmedinf.2018.08.009
16. Soysal E, Wang J, Jiang M, Wu Y, Pakhomov S, Liu H, Xu H. CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines. J Am Med Inform Assoc. 2018 Mar 1;25(3):331-336. doi: 10.1093/jamia/ocx132.. PMID: 29186491; PMCID: PMC7378877; DOI: 10.1093/jamia/ocx132
17. Chen G, Tsoi A, Xu H, Zheng WJ. Predict effective drug combination by deep belief network and ontology fingerprints. J Biomed Inform. 2018 Sep;85:149-154. doi: 10.1016/j.jbi.2018.07.024. Epub 2018 Aug 3.. PMID: 30081101; DOI: 10.1016/j.jbi.2018.07.024
18. Wu Y, Yang X, Bian J, Guo Y, Xu H, Hogan W. Combine Factual Medical Knowledge and Distributed Word Representation to Improve Clinical Named Entity Recognition. AMIA Annu Symp Proc. 2018 Dec 5;2018:1110-1117. eCollection 2018.. PMID: 30815153; PMCID: PMC6371322

2017

1. Li H, Chen Q, Tang B, Wang X, Xu H, Wang B, Huang D. CNN-based ranking for biomedical entity normalization. BMC Bioinformatics. 2017 Oct 3;18(Suppl 11):385. doi: 10.1186/s12859-017-1805-7.. PMID: 28984180; PMCID: PMC5629610; DOI: 10.1186/s12859-017-1805-7
2. Soysal E, Warner JL, Denny JC, Xu H. Identifying Metastases-related Information from Pathology Reports of Lung Cancer Patients. AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:268-277. eCollection 2017.. PMID: 28815141; PMCID: PMC5543353
3. Velez Edwards DR, Hartmann KE, Wellons M, Shah A, Xu H, Edwards TL. Evaluating the role of race and medication in protection of uterine fibroids by type 2 diabetes exposure. BMC Womens Health. 2017 Apr 11;17(1):28. doi: 10.1186/s12905-017-0386-y.. PMID: 28399866; PMCID: PMC5387248; DOI: 10.1186/s12905-017-0386-y
4. Sun J, Wei Q, Zhou Y, Wang J, Liu Q, Xu H. A systematic analysis of FDA-approved anticancer drugs. BMC Syst Biol. 2017 Oct 3;11(Suppl 5):87. doi: 10.1186/s12918-017-0464-7.. PMID: 28984210; PMCID: PMC5629554; DOI: 10.1186/s12918-017-0464-7
5. Amith M, Manion FJ, Harris MR, Zhang Y, Xu H, Tao C. Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. Stud Health Technol Inform. 2017;245:838-842.. PMID: 29295217; PMCID: PMC6644701
6. Liu Z, Yang M, Wang X, Chen Q, Tang B, Wang Z, Xu H. Entity recognition from clinical texts via recurrent neural network. BMC Med Inform Decis Mak. 2017 Jul 5;17(Suppl 2):67. doi: 10.1186/s12911-017-0468-7.. PMID: 28699566; PMCID: PMC5506598; DOI: 10.1186/s12911-017-0468-7
7. Ohno-Machado L, Sansone SA, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj AE, Bell E, Soysal E, Zong N, Kim HE. Finding useful data across multiple biomedical data repositories using DataMed. Nat Genet. 2017 May 26;49(6):816-819. doi: 10.1038/ng.3864.. PMID: 28546571; PMCID: PMC6460922; DOI: 10.1038/ng.3864
8. Duan R, Cao M, Wu Y, Huang J, Denny JC, Xu H, Chen Y. An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies. AMIA Annu Symp Proc. 2017 Feb 10;2016:1764-1773. eCollection 2016.. PMID: 28269935; PMCID: PMC5333313
9. Wang H, Luo J, Liu C, Niu H, Wang J, Liu Q, Zhao Z, Xu H, Ding Y, Sun J, Zhang Q. Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. BMC Bioinformatics. 2017 Sep 2;18(1):388. doi: 10.1186/s12859-017-1796-4.. PMID: 28865443; PMCID: PMC5581471; DOI: 10.1186/s12859-017-1796-4
10. Zhang Y, Zhang O, Wu Y, Lee HJ, Xu J, Xu H, Roberts K. Psychiatric symptom recognition without labeled data using distributional representations of phrases and on-line knowledge. J Biomed Inform. 2017 Nov;75S:S129-S137. doi: 10.1016/j.jbi.2017.06.014. Epub 2017 Jun 15.. PMID: 28624644; PMCID: PMC5705397; DOI: 10.1016/j.jbi.2017.06.014
11. Cai R, Liu M, Hu Y, Melton BL, Matheny ME, Xu H, Duan L, Waitman LR. Identification of adverse drug-drug interactions through causal association rule discovery from spontaneous adverse event reports. Artif Intell Med. 2017 Feb;76:7-15. doi: 10.1016/j.artmed.2017.01.004. Epub 2017 Feb 10.. PMID: 28363289; PMCID: PMC6438384; DOI: 10.1016/j.artmed.2017.01.004
12. Ji Z, Zhang Y, Xu J, Chen X, Wu Y, Xu H. Comparing Cancer Information Needs for Consumers in the US and China. Stud Health Technol Inform. 2017;245:126-130.. PMID: 29295066; PMCID: PMC5805146
13. Malec SA, Wei P, Xu H, Bernstam EV, Myneni S, Cohen T. Literature-Based Discovery of Confounding in Observational Clinical Data. AMIA Annu Symp Proc. 2017 Feb 10;2016:1920-1929. eCollection 2016.. PMID: 28269951; PMCID: PMC5333204
14. Redman JS, Natarajan Y, Hou JK, Wang J, Hanif M, Feng H, Kramer JR, Desiderio R, Xu H, El-Serag HB, Kanwal F. Accurate Identification of Fatty Liver Disease in Data Warehouse Utilizing Natural Language Processing. Dig Dis Sci. 2017 Oct;62(10):2713-2718. doi: 10.1007/s10620-017-4721-9. Epub 2017 Aug 31.. PMID: 28861720; DOI: 10.1007/s10620-017-4721-9
15. Lee HJ, Wu Y, Zhang Y, Xu J, Xu H, Roberts K. A hybrid approach to automatic de-identification of psychiatric notes. J Biomed Inform. 2017 Nov;75S:S19-S27. doi: 10.1016/j.jbi.2017.06.006. Epub 2017 Jun 7.. PMID: 28602904; PMCID: PMC5705430; DOI: 10.1016/j.jbi.2017.06.006
16. Amith M, Song HY, Zhang Y, Xu H, Tao C. Lightweight predicate extraction for patient-level cancer information and ontology development. BMC Med Inform Decis Mak. 2017 Jul 5;17(Suppl 2):73. doi: 10.1186/s12911-017-0465-x.. PMID: 28699547; PMCID: PMC5506564; DOI: 10.1186/s12911-017-0465-x
17. Zhang Y, Jiang M, Wang J, Xu H. Semantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features. AMIA Annu Symp Proc. 2017 Feb 10;2016:1283-1292. eCollection 2016.. PMID: 28269926; PMCID: PMC5333340
18. Chen Y, Lask TA, Mei Q, Chen Q, Moon S, Wang J, Nguyen K, Dawodu T, Cohen T, Denny JC, Xu H. An active learning-enabled annotation system for clinical named entity recognition. BMC Med Inform Decis Mak. 2017 Jul 5;17(Suppl 2):82. doi: 10.1186/s12911-017-0466-9.. PMID: 28699546; PMCID: PMC5506567; DOI: 10.1186/s12911-017-0466-9
19. Wang Y, Zheng K, Xu H, Mei Q. Clinical Word Sense Disambiguation with Interactive Search and Classification. AMIA Annu Symp Proc. 2017 Feb 10;2016:2062-2071. eCollection 2016.. PMID: 28269966; PMCID: PMC5333264
20. Zheng WJ, Ruan J, Xu H, Zhao Z, Liu Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. BMC Syst Biol. 2017 Oct 3;11(Suppl 5):88. doi: 10.1186/s12918-017-0461-x.. PMID: 28984194; PMCID: PMC5629615; DOI: 10.1186/s12918-017-0461-x
21. Dong X, Zhang Y, Xu H. Search Datasets in Literature: A Case Study of GWAS. AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:40-49. eCollection 2017.. PMID: 28815103; PMCID: PMC5543360
22. Wu Y, Denny JC, Trent Rosenbloom S, Miller RA, Giuse DA, Wang L, Blanquicett C, Soysal E, Xu J, Xu H. A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). J Am Med Inform Assoc. 2017 Apr 1;24(e1):e79-e86. doi: 10.1093/jamia/ocw109.. PMID: 27539197; PMCID: PMC7651947; DOI: 10.1093/jamia/ocw109
23. Cohen T, Roberts K, Gururaj AE, Chen X, Pournejati S, Alter G, Hersh WR, Demner-Fushman D, Ohno-Machado L, Xu H. A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database (Oxford). 2017 Jan 1;2017:bax061. doi: 10.1093/database/bax061.. PMID: 29220453; PMCID: PMC5737202; DOI: 10.1093/database/bax061

2016

1. Kolek MJ, Graves AJ, Xu M, Bian A, Teixeira PL, Shoemaker MB, Parvez B, Xu H, Heckbert SR, Ellinor PT, Benjamin EJ, Alonso A, Denny JC, Moons KG, Shintani AK, Harrell FE Jr, Roden DM, Darbar D. Evaluation of a Prediction Model for the Development of Atrial Fibrillation in a Repository of Electronic Medical Records. JAMA Cardiol. 2016 Dec 1;1(9):1007-1013. doi: 10.1001/jamacardio.2016.3366.. PMID: 27732699; PMCID: PMC5293184; DOI: 10.1001/jamacardio.2016.3366
2. Fathiamini S, Johnson AM, Zeng J, Araya A, Holla V, Bailey AM, Litzenburger BC, Sanchez NS, Khotskaya Y, Xu H, Meric-Bernstam F, Bernstam EV, Cohen T. Automated identification of molecular effects of drugs (AIMED). J Am Med Inform Assoc. 2016 Jul;23(4):758-65. doi: 10.1093/jamia/ocw030. Epub 2016 Apr 23.. PMID: 27107438; PMCID: PMC4926748; DOI: 10.1093/jamia/ocw030
3. Xu J, Lee HJ, Zeng J, Wu Y, Zhang Y, Huang LC, Johnson A, Holla V, Bailey AM, Cohen T, Meric-Bernstam F, Bernstam EV, Xu H. Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov. J Am Med Inform Assoc. 2016 Jul;23(4):750-7. doi: 10.1093/jamia/ocw009. Epub 2016 Mar 24.. PMID: 27013523; PMCID: PMC4926744; DOI: 10.1093/jamia/ocw009
4. Xu J, Wu Y, Zhang Y, Wang J, Lee HJ, Xu H. CD-REST: a system for extracting chemical-induced disease relation in literature. Database (Oxford). 2016 Mar 25;2016:baw036. doi: 10.1093/database/baw036. Print 2016.. PMID: 27016700; PMCID: PMC4808251; DOI: 10.1093/database/baw036
5. Zhang Y, Wu HY, Du J, Xu J, Wang J, Tao C, Li L, Xu H. Extracting drug-enzyme relation from literature as evidence for drug drug interaction. J Biomed Semantics. 2016 Mar 7;7:11. doi: 10.1186/s13326-016-0052-6. eCollection 2016.. PMID: 26955465; PMCID: PMC4780188; DOI: 10.1186/s13326-016-0052-6
6. Hart T, Dider S, Han W, Xu H, Zhao Z, Xie L. Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology. Sci Rep. 2016 Feb 4;6:20441. doi: 10.1038/srep20441.. PMID: 26841718; PMCID: PMC4740793; DOI: 10.1038/srep20441
7. Zhang Y, Xu J, Chen H, Wang J, Wu Y, Prakasam M, Xu H. Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. Database (Oxford). 2016 Apr 17;2016:baw049. doi: 10.1093/database/baw049. Print 2016.. PMID: 27087307; PMCID: PMC4834204; DOI: 10.1093/database/baw049
8. Zhang Y, Wu HY, Xu J, Wang J, Soysal E, Li L, Xu H. Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. BMC Syst Biol. 2016 Aug 26;10 Suppl 3(Suppl 3):67. doi: 10.1186/s12918-016-0311-2.. PMID: 27585838; PMCID: PMC5009562; DOI: 10.1186/s12918-016-0311-2
9. Chen H, Zhang Y, Wu D, Gong C, Pan Q, Dong X, Wu Y, Zhang K, Wang S, Lei J, Xu H. Comorbidity in Adult Patients Hospitalized with Type 2 Diabetes in Northeast China: An Analysis of Hospital Discharge Data from 2002 to 2013. Biomed Res Int. 2016;2016:1671965. doi: 10.1155/2016/1671965. Epub 2016 Oct 25.. PMID: 27847807; PMCID: PMC5099493; DOI: 10.1155/2016/1671965
10. Zhang Y, Wu HY, Du J, Xu J, Wang J, Tao C, Li L, Xu H. Erratum to: Extracting drug-enzyme relation from literature as evidence for drug drug interaction. J Biomed Semantics. 2016 Apr 19;7:21. doi: 10.1186/s13326-016-0063-3. eCollection 2016.. PMID: 27099701; PMCID: PMC4837541; DOI: 10.1186/s13326-016-0063-3

2015

1. Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, Leaman R, Lu Y, Ji D, Lowe DM, Sayle RA, Batista-Navarro RT, Rak R, Huber T, Rocktäschel T, Matos S, Campos D, Tang B, Xu H, Munkhdalai T, Ryu KH, Ramanan SV, Nathan S, Žitnik S, Bajec M, Weber L, Irmer M, Akhondi SA, Kors JA, Xu S, An X, Sikdar UK, Ekbal A, Yoshioka M, Dieb TM, Choi M, Verspoor K, Khabsa M, Giles CL, Liu H, Ravikumar KE, Lamurias A, Couto FM, Dai HJ, Tsai RT, Ata C, Can T, Usié A, Alves R, Segura-Bedmar I, Martínez P, Oyarzabal J, Valencia A. The CHEMDNER corpus of chemicals and drugs and its annotation principles. J Cheminform. 2015 Jan 19;7(Suppl 1 Text mining for chemistry and the CHEMDNER track):S2. doi: 10.1186/1758-2946-7-S1-S2. eCollection 2015.. PMID: 25810773; PMCID: PMC4331692; DOI: 10.1186/1758-2946-7-S1-S2
2. Zheng K, Vydiswaran VGV, Liu Y, Wang Y, Stubbs A, Uzuner Ö, Gururaj AE, Bayer S, Aberdeen J, Rumshisky A, Pakhomov S, Liu H, Xu H. Ease of adoption of clinical natural language processing software: An evaluation of five systems. J Biomed Inform. 2015 Dec;58 Suppl(Suppl):S189-S196. doi: 10.1016/j.jbi.2015.07.008. Epub 2015 Jul 22.. PMID: 26210361; PMCID: PMC4974203; DOI: 10.1016/j.jbi.2015.07.008
3. Chen Y, Sun J, Huang LC, Xu H, Zhao Z. Classification of Cancer Primary Sites Using Machine Learning and Somatic Mutations. Biomed Res Int. 2015;2015:491502. doi: 10.1155/2015/491502. Epub 2015 Oct 11.. PMID: 26539502; PMCID: PMC4619847; DOI: 10.1155/2015/491502
4. Tang B, Feng Y, Wang X, Wu Y, Zhang Y, Jiang M, Wang J, Xu H. A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature. J Cheminform. 2015 Jan 19;7(Suppl 1 Text mining for chemistry and the CHEMDNER track):S8. doi: 10.1186/1758-2946-7-S1-S8. eCollection 2015.. PMID: 25810779; PMCID: PMC4331698; DOI: 10.1186/1758-2946-7-S1-S8
5. Zhang Y, Tang B, Jiang M, Wang J, Xu H. Domain adaptation for semantic role labeling of clinical text. J Am Med Inform Assoc. 2015 Sep;22(5):967-79. doi: 10.1093/jamia/ocu048. Epub 2015 Jun 10.. PMID: 26063745; PMCID: PMC4986662; DOI: 10.1093/jamia/ocu048
6. Liu Z, Zhang Y, Franzin L, Cormier JN, Chan W, Xu H, Du XL. Trends and variations in breast and colorectal cancer incidence from 1995 to 2011: a comparative study between Texas Cancer Registry and National Cancer Institute's Surveillance, Epidemiology and End Results data. Int J Oncol. 2015 Apr;46(4):1819-26. doi: 10.3892/ijo.2015.2881. Epub 2015 Feb 6.. PMID: 25672365; PMCID: PMC4356494; DOI: 10.3892/ijo.2015.2881
7. Xu J, Zhang Y, Wu Y, Wang J, Dong X, Xu H. Citation Sentiment Analysis in Clinical Trial Papers. AMIA Annu Symp Proc. 2015 Nov 5;2015:1334-41. eCollection 2015.. PMID: 26958274; PMCID: PMC4765697
8. Sun J, Zhao M, Jia P, Wang L, Wu Y, Iverson C, Zhou Y, Bowton E, Roden DM, Denny JC, Aldrich MC, Xu H, Zhao Z. Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput Biol. 2015 Jun 17;11(6):e1004202. doi: 10.1371/journal.pcbi.1004202. eCollection 2015 Jun.. PMID: 26083494; PMCID: PMC4470683; DOI: 10.1371/journal.pcbi.1004202
9. Chen Y, Lasko TA, Mei Q, Denny JC, Xu H. A study of active learning methods for named entity recognition in clinical text. J Biomed Inform. 2015 Dec;58:11-18. doi: 10.1016/j.jbi.2015.09.010. Epub 2015 Sep 15.. PMID: 26385377; PMCID: PMC4934373; DOI: 10.1016/j.jbi.2015.09.010
10. Dahlin A, Denny J, Roden DM, Brilliant MH, Ingram C, Kitchner TE, Linneman JG, Shaffer CM, Weeke P, Xu H, Kubo M, Tamari M, Clemmer GL, Ziniti J, McGeachie MJ, Tantisira KG, Weiss ST, Wu AC. CMTR1 is associated with increased asthma exacerbations in patients taking inhaled corticosteroids. Immun Inflamm Dis. 2015 Jul 14;3(4):350-9. doi: 10.1002/iid3.73. eCollection 2015 Dec.. PMID: 26734457; PMCID: PMC4693729; DOI: 10.1002/iid3.73
11. Tang B, Chen Q, Wang X, Wu Y, Zhang Y, Jiang M, Wang J, Xu H. Recognizing Disjoint Clinical Concepts in Clinical Text Using Machine Learning-based Methods. AMIA Annu Symp Proc. 2015 Nov 5;2015:1184-93. eCollection 2015.. PMID: 26958258; PMCID: PMC4765674
12. Wu Y, Jiang M, Lei J, Xu H. Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network. Stud Health Technol Inform. 2015;216:624-8.. PMID: 26262126; PMCID: PMC4624324
13. Chen G, Zhao J, Cohen T, Tao C, Sun J, Xu H, Bernstam EV, Lawson A, Zeng J, Johnson AM, Holla V, Bailey AM, Lara-Guerra H, Litzenburger B, Meric-Bernstam F, Jim Zheng W. Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. Database (Oxford). 2015 Apr 8;2015:bav034. doi: 10.1093/database/bav034. Print 2015.. PMID: 25858285; PMCID: PMC4390608; DOI: 10.1093/database/bav034
14. Wu Y, Xu J, Jiang M, Zhang Y, Xu H. A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text. AMIA Annu Symp Proc. 2015 Nov 5;2015:1326-33. eCollection 2015.. PMID: 26958273; PMCID: PMC4765694
15. Zhang Y, Soysal E, Moon S, Wang J, Tao C, Xu H. Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction. AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:204-8. eCollection 2015.. PMID: 26306271; PMCID: PMC4525275
16. Tao C, Sun J, Zheng WJ, Chen J, Xu H. Colorectal cancer drug target prediction using ontology-based inference and network analysis. Database (Oxford). 2015 Mar 27;2015:bav015. doi: 10.1093/database/bav015. Print 2015.. PMID: 25818893; PMCID: PMC4375358; DOI: 10.1093/database/bav015
17. Xu H, Aldrich MC, Chen Q, Liu H, Peterson NB, Dai Q, Levy M, Shah A, Han X, Ruan X, Jiang M, Li Y, Julien JS, Warner J, Friedman C, Roden DM, Denny JC. Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J Am Med Inform Assoc. 2015 Jan;22(1):179-91. doi: 10.1136/amiajnl-2014-002649. Epub 2014 Jul 22.. PMID: 25053577; PMCID: PMC4433365; DOI: 10.1136/amiajnl-2014-002649

2014

1. Zhao Z, Zhang B, Huang Y, Xu H, McDermott JE. Computational methods for omics data. Int J Comput Biol Drug Des. 2014;7(2-3):97-101. doi: 10.1504/IJCBDD.2014. Epub 2014 May 28.. PMID: 24878722; DOI: 10.1504/IJCBDD.2014
2. Lei J, Tang B, Lu X, Gao K, Jiang M, Xu H. A comprehensive study of named entity recognition in Chinese clinical text. J Am Med Inform Assoc. 2014 Sep-Oct;21(5):808-14. doi: 10.1136/amiajnl-2013-002381. Epub 2013 Dec 17.. PMID: 24347408; PMCID: PMC4147609; DOI: 10.1136/amiajnl-2013-002381
3. Tang B, Cao H, Wang X, Chen Q, Xu H. Evaluating word representation features in biomedical named entity recognition tasks. Biomed Res Int. 2014;2014:240403. doi: 10.1155/2014/240403. Epub 2014 Mar 6.. PMID: 24729964; PMCID: PMC3963372; DOI: 10.1155/2014/240403
4. McDermott JE, Huang Y, Zhang B, Xu H, Zhao Z. Integrative genomics and computational systems medicine. Biomed Res Int. 2014;2014:945253. doi: 10.1155/2014/945253. Epub 2014 Jun 15.. PMID: 25025078; PMCID: PMC4082850; DOI: 10.1155/2014/945253
5. Shang N, Xu H, Rindflesch TC, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. J Biomed Inform. 2014 Dec;52:293-310. doi: 10.1016/j.jbi.2014.07.011. Epub 2014 Jul 19.. PMID: 25046831; PMCID: PMC4261011; DOI: 10.1016/j.jbi.2014.07.011
6. Jiang M, Wu Y, Shah A, Priyanka P, Denny JC, Xu H. Extracting and standardizing medication information in clinical text - the MedEx-UIMA system. AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:37-42. eCollection 2014.. PMID: 25954575; PMCID: PMC4419757
7. Zeng J, Wu Y, Bailey A, Johnson A, Holla V, Bernstam EV, Xu H, Meric-Bernstam F. Adapting a natural language processing tool to facilitate clinical trial curation for personalized cancer therapy. AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:126-31. eCollection 2014.. PMID: 25717412; PMCID: PMC4333699
8. Gobbel GT, Garvin J, Reeves R, Cronin RM, Heavirland J, Williams J, Weaver A, Jayaramaraja S, Giuse D, Speroff T, Brown SH, Xu H, Matheny ME. Assisted annotation of medical free text using RapTAT. J Am Med Inform Assoc. 2014 Sep-Oct;21(5):833-41. doi: 10.1136/amiajnl-2013-002255. Epub 2014 Jan 15.. PMID: 24431336; PMCID: PMC4147611; DOI: 10.1136/amiajnl-2013-002255
9. Masanz J, Pakhomov SV, Xu H, Wu ST, Chute CG, Liu H. Open Source Clinical NLP - More than Any Single System. AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:76-82. eCollection 2014.. PMID: 25954581; PMCID: PMC4419764
10. Sun J, Huang LC, Xu H, Zhao Z. Network-assisted prediction of potential drugs for addiction. Biomed Res Int. 2014;2014:258784. doi: 10.1155/2014/258784. Epub 2014 Feb 9.. PMID: 24689033; PMCID: PMC3932722; DOI: 10.1155/2014/258784
11. Chen Y, Wrenn J, Xu H, Spickard A 3rd, Habermann R, Powers J, Denny JC. Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies. AMIA Annu Symp Proc. 2014 Nov 14;2014:375-84. eCollection 2014.. PMID: 25954341; PMCID: PMC4419906

2013

1. Tang B, Cao H, Wu Y, Jiang M, Xu H. Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features. BMC Med Inform Decis Mak. 2013;13 Suppl 1(Suppl 1):S1. doi: 10.1186/1472-6947-13-S1-S1. Epub 2013 Apr 5.. PMID: 23566040; PMCID: PMC3618243; DOI: 10.1186/1472-6947-13-S1-S1
2. Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H. A hybrid system for temporal information extraction from clinical text. J Am Med Inform Assoc. 2013 Sep-Oct;20(5):828-35. doi: 10.1136/amiajnl-2013-001635. Epub 2013 Apr 9.. PMID: 23571849; PMCID: PMC3756274; DOI: 10.1136/amiajnl-2013-001635
3. Van Driest SL, Shah A, Marshall MD, Xu H, Smith AH, McGregor TL, Kannankeril PJ. Opioid use after cardiac surgery in children with Down syndrome. Pediatr Crit Care Med. 2013 Nov;14(9):862-8. doi: 10.1097/PCC.0b013e31829f5d9d.. PMID: 23962833; PMCID: PMC3830692; DOI: 10.1097/PCC.0b013e31829f5d9d
4. Moon S, Berster BT, Xu H, Cohen T. Word Sense Disambiguation of clinical abbreviations with hyperdimensional computing. AMIA Annu Symp Proc. 2013 Nov 16;2013:1007-16. eCollection 2013.. PMID: 24551390; PMCID: PMC3900125
5. Wu Y, Lei J, Wei WQ, Tang B, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Zheng K, Xu H. Analyzing differences between chinese and english clinical text: a cross-institution comparison of discharge summaries in two languages. Stud Health Technol Inform. 2013;192:662-6.. PMID: 23920639; PMCID: PMC4957806

2012

1. Huang Y, Zhao Z, Xu H, Shyr Y, Zhang B (2012) Advances in Intelligent Biology and Medicine: Selected papers from 2012 ICIBM Conference. BMC Systems Biology 6 (Suppl S2):S1 (in press)
2. Zhao Z, Zhang B, Shyr Y, Huang Y, Xu H, (2012) Genomics in 2012: challenges and opportunities in the next generation sequencing era. BMC Genomics 13 (Suppl S7):S1 (in press)
3. Zhao Z, Xu H, Zhang B, Huang Y (2012) Advances in Intelligent Biology and Medicine: Selected papers from 2012 ICIBM Conference. International Journal of Computational Biology and Drug Design (IJCBDD) 5(4): (in press)
4. Liu M, Matheny ME, Hu Y, Xu H. Data mining methodologies for pharmacovigilance. ACM SIGKDD Explorations Newsletter. 2012, 14(1), 35-42.
5. Tang B, Can H, Wu Y, Jiang M, Xu H. Clinical Entity Recognition using Structural Support Vector Machines with Rich Features. ACM Sixth International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO), 2012, In Press.
6. Xu H, Stetson PD, Friedman C. Combining corpus-derived sense profiles with estimated frequency information to disambiguate clinical abbreviations. AMIA Annu Symp Proc. 2012. In Press.
7. Wu Y, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Xu H. A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. AMIA Annu Symp Proc. 2012. In Press.
8. Liu M, Shah A, Min J, Peterson NB, Dai Q, Aldrich MC, Chen Q, Bowton EA, Liu H, Denny JC, Xu H. A study of transportability of an existing smoking status detection module across institutions. AMIA Annu Symp Proc. 2012. In Press.
9. Jiang M, Denny JC, Tang B, Cao H, Xu H. Extracting semantic lexicons from discharge summaries using machine learning and c-value method. AMIA Annu Symp Proc. 2012. In Press.
10. Wu Y, Liu M, Zheng W, Zhao Z, Xu H. Ranking gene-drug relationships in biomedical literature using latent dirichlet allocation. Pac Symp Biocomput. 2012: 422-33. [PMID: 22174297]
11. Liu M, McPeek Hinz ER, Matheny ME, Denny JC, Schildcrout JS, Miller RA, Xu H. Comparative Analysis of Pharmacovigilance Methods in Detection of Adverse Drug Reactions from Electronic Medical Records. J Am Med Inform Assoc. 2012, In Press. [PMID: 23161894]
12. Xu H, Wu Y, Elhadad N, Stetson PD, Friedman C. A new clustering method for detecting rare sense of abbreviations in clinical notes. J Biomed Inform. 2012, 45(6):1075-83. [PMID: 22742938]
13. Liu M, Wu Y, Chen Y, Sun J, Zhao Z, Chen X, and Xu H. Large-scale prediction of adverse drug reaction by integrating chemical, biological, and phenotypic properties of drugs. J Am Med Inform Assoc. 2012. 19(e1): e28-e35. [PMCID:PMC3392844]
14. Denny JC, Schildcrout JS, Bowton EA, Gregg W, Pulley JM, Basford MA, Cowan J, Xu H, Ramirez AH, Crawford DC, Ritchie MD, Peterson JF, Masys DR, Wilke RA, Roden DM. Optimizing drug outcomes through pharmacogenetics: A case for preemptive genotyping. Clin Pharmacol Ther. 2012. 92(2):235-42. [PMID: 22739144]
15. Wu Y, Levy MA, Micheel CM, Yeh P, Tang B, Cantrell MJ, Cooreman SM, Xu H. Identifying the status of genetic lesions in cancer clinical trial documents using machine learning. BMC Genomics. 2012, 13 Suppl 8:S21 [PMCID: PMC3535695]
16. Han B, Chen XW, Talebizadeh Z, Xu H. Genetic studies of complex human diseases: characterizing SNP-disease associations using Bayesian networks. BMC Syst Biol. 2012. 6 Suppl 3: S14 [PMCID: PMC3524021]
17. Lu Y, Xu H, Peterson NB, Dai Q, Jiang M, Denny JC, Liu M. Extracting epidemiological exposure and outcome terms from literature using machine learning approaches. Int J Data Min Bioinform. 2012; 6(4):447-59. [PMID: 23155773]
18. Roden DM, Xu H, Denny JC, Wilke RA. Electronic Medical Records as a Tool in Clinical Pharmacology: Opportunities and Challenges. Clin Pharmacol Ther. 2012, Apr 25. [PMID:22534870]
19. Delaney JT, Ramirez AH, Bowton EA, Pulley JM, Basford MA, Schildcrout JS, Shi Y, Zink R, Oetjens M, Xu H, Cleator JH, Jahangir E, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Predicting clopidogrel response using DNA samples linked to an electronic health record. Clin Pharmacol Ther. 2012 Feb;91(2):257-63. [PMID: 22190063]
20. Birdwell KA, Grady B, Choi L, Xu H, Bian A, Denny JC, Jiang M, Vranic G, Basford M, Cowan JD, Richardson DM, Robinson MP, Ikizler TA, Ritchie MD, Stein CM, Haas DW. The use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients. Pharmacogenet Genomics. 2012 22(1):32-42. [PMCID: PMC3237759]
21. Ramirez AH, Shi Y, Schildcrout JS, Delaney JT, Xu H, Oetjens MT, Zuvich RL, Basford MA, Bowton EA, Jiang M, Speltz P, Zink R, Cowan J, Pulley JM, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Predicting warfarin dosage in European and African Americans using DNA samples linked to an electronic health record. Pharmacogenomics. 2012, 13(4):407-18. [PMCID: PMC3361510]
22. Sun J, Xu H, Zhao Z Network-assisted investigation of antipsychotic drugs and their targets. Chem Biodivers. 2012, 9(5): 900-10. [PMID:22589091]
23. Sun J, Wu Y, Xu H, Zhao Z. DTome: a web-based tool for drug-target interactome construction, BMC Bioinformatics. 2012, 13(Suppl 9): 57.
24. Carroll RJ, Thompson WK, Eyler AE, Mandelin AM, Cai T, Zink RM, Pacheco JA, Boomershine CS, Lasko TA, Xu H, Karlson EW, Perez RG, Gainer VS, Murphy SN, Ruderman EM, Pope RM, Plenge RM, Kho AN, Liao KP, Denny JC. Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J Am Med Inform Assoc. 2012 Feb 28. [PMID: 22374935]
25. Doan S, Collier N, Xu H, Pham HD, and Tu MP. Recognition of medication information from discharge summaries using ensembles of classifiers. BMC Medical Informatics and Decision Making. 2012, 12(1):36. [PMID: 22564405]
26. Chen Y, Mani S, Xu H. Applying active learning to assertion classification of concepts in clinical text. J Biomed Inform 2012, 45(2): 265-272. [PMCID: PMC3306548]
27. Sun J, Gong X, Purow B, Zhao Z. Uncovering microRNA and transcription factor mediated regulatory networks in glioblastoma. PLoS Computational Biology. 2012 8(7): e1002488
28. Sun J, Wu Y, Xu H, Zhao Z. DTome: a web-based tool for drug-target interactome construction. BMC Bioinformatics. 2012 13 (Suppl 9): 57
29. Sun J, Jayathilake K, Zhao Z, Meltzer H. Investigating association of four gene regions (GABRB3, MAOB, PAH, and SLC6A4) with five symptoms in schizophrenia. Psychiatry Research. 2012 198(2):202-206
30. Xu J, Sun J, Chen J, Helm M, Li Anna, Zhao Z, Chen X. RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia. BMC Genomics. 2012 13(Suppl 8):S2. (Co-first author)
31. Sun J, Xu H, Zhao Z. Network-assisted investigation of antipsychotic drugs and their targets. Chemistry & Biodiversity. 2012 9(5):900-910
32. Zhao M, Sun J, Zhao Z. Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PLoS One. 2012 7(8):e44175
33. Schleker S, Sun J, Raghavan B, Srnec M, Müller N, Koepfinger M, Murthy L, Zhao Z, Klein-Seetharaman J. The current Salmonella-host interactome. Proteomics - Clinical Applications. 2012 6(1-2):117-133
34. Zhao M, Sun J, Zhao Z. Comprehensive analyses of tumor suppressor genes and oncogenes in protein-protein interaction networks: a topological perspective. GENSIPS 2012:101-102.

2011

1. Xu H, Fu Z, Shah A, Chen Y, Peterson NB, Chen Q, Mani S, Levy MA, Dai Q,Denny JC. Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases. AMIA Annu Symp Proc. 2011, 1564-72. [PMCID: PMC3244156]
2. Liu M, Kawai VK, Stein CM, Denny JC, Roden DM, Xu H. Modeling drug exposure data in electronic medical records: an application to warfarin. AMIA Annu Symp Proc. 2011, 815-23. [PMCID: PMC3243123]
3. Wu Y, Rosenbloom ST, Denny JC, Miller RA, Mani S, Giuse DA, Xu H. Detecting abbreviations in discharge summaries using machine learning methods. AMIA Annu Symp Proc. 2011, 1541-9. [PMCID: PMC3243185]
4. Xu H, AbdelRahman S, Jiang M, Fan JW, Huang Y. An Initial Study of Full Parsing of Clinical Text using the Stanford Parser. International Workshop on Biomedical and Health Informatics, IEEE Conference of Bioinformatics and Biomedicine (BIBM), 2011.
5. Wilke RA, Xu H, Denny JC, Roden DM, Krauss RM, McCarty CA, Davis RL, Skaar T, Lamba J, and Savova G. The emerging role of electronic medical records in pharmacogenomics. Clin Pharmacol Ther. 2011, 89(3): 379-86. [PMCID: PMC3204342]
6. Rosenbloom ST, Denny JC, Xu H, Lorenzi N, Stead WW, Johnson KB. Data from clinical notes: a perspective on the tension between structure and flexible documentation. J Am Med Inform Assoc. 2011, 18(2):181-6. [PMCID: PMC3116264]
7. Jiang M, Chen Y, Liu M, Rosenbloom ST, Mani S, Denny JC, Xu H. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc. 2011, 18(5):601-6. [PMCID: PMC3168315]
8. Xu H, Jiang M, Oetjens M, Bowton EA, Ramirez AH, Jeff JM, Basford MA, Pulley JM, Cowan JD, Wang X, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Facilitating pharmacogenetic studies using electronic health records and natural language processing: a case study of warfarin. J Am Med Inform Assoc. 2011; 18(4): 387-91. [PMCID: PMC3128409]
9. Xu H, AbdelRahman S, Lu Y, Denny JC, Doan S. Applying semantic-based probabilistic context free grammar to medical language processing – a preliminary study on parsing medication sentences. J Biomed Inform 2011, 44(6): 1068-75. [PMCID: PMC3226929]
10. Sun J, Wan C, Jia P, Riley BP, Kendler KS, Zhao Z. Application of systems biology approach identifies and validates GRB2 as a risk gene for schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample. Schizophrenia Research. 2011 125(2-3):201-208
11. Putnam D, Sun J, Zhao Z. Exploring schizophrenia drug-gene interactions through molecular network and pathway modeling. AMIA Annu. Symp. Proc. 2011 2011:1127-1133
12. Xia J, Sun J, Jia P, Zhao Z. Do cancer proteins really interact strongly in the human protein-protein interaction network? Computational Biology and Chemistry. 2011 35(3):121-125
13. Gong X, Sun J, Zhao Z. Gene regulation in glioblastoma: a combinatorial analysis of microRNAs and transcription factors. Int. J. Comput. Biol. Drug Des. 2011 4(2):111-126

2010

1. Xu H, Doan S, Birdwell KA, Cowan JD, Vincz AJ, Haas DW, Basford MA, Denny JC. An automated approach to calculating the daily dose of tacrolimus in electronic health records. AMIA Summits Transl Sci Proc. 2010:71-5. [PMCID: PMC3041548]
2. Denny JC, Speltz P, Maddox R, Stein G, Xu H, Spickard A. Comparing Content Coverage in Medical Curriculum to Trainee-Authored Clinical Notes. AMIA Annu Symp Proc. 2010, 157-161. [PMCID: PMC3041398]
3. Doan S and Xu H. Recognizing Medication related Entities in Hospital Discharge Summaries using Support Vector Machine. COLING 2010, the 23rd International Conference on Computational Linguistics, 259-266.
4. Xu H, Lu Y, Jiang M, Liu M, Denny JC, Dai Q, Peterson NB. Mining Biomedical Literature for Terms related to Epidemiologic Exposures. AMIA Annu Symp Proc. 2010, 897-901. [PMCID: PMC3041399]
5. Xu H, Stenner SP, Doan S, Johnson KB, Waitman LR, Denny JC. MedEx – A Medication Information Extraction System for Clinical Narratives. J Am Med Inform Assoc. 2010; 17(1):19-24. [PMCID: PMC2995636]
6. Denny JC, Peterson JF, Choma NN, Xu H, Miller RA, Bastarache L, Peterson NB. Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. J Am Med Inform Assoc. 2010; 17(4): 393-8. [PMCID: PMC2815478]
7. Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H. Integrating Existing NLP Tools for Medication Extraction from Discharge Summaries. J Am Med Inform Assoc. 2010, 17:528-31. [PMCID: PMC2995674]
8. Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng: Genome3D: A view-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. BMC Bioinformatics, Sep 2; 11:444, 2010 (Highly Accessed).
9. Wei WQ, Tao C, Jiang G, Chute CG. A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes. AMIA Annual Symposium. 2010; 2010:857-61. Epub 2010 Nov 13. PMID:21347100. PMCID:3041302.
10. Sun J, Jia P, Fanous AH, van den Oord EJCG, Chen X, Riley BP, Amdur RL, Kendler KS, Zhao Z. Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. PLoS One. 2010 5(6): e11351
11. Sun J, Zhao Z. Functional features, biological pathways and protein interaction networks of addiction-related genes. Chemistry & Biodiversity. 2010 7(5):1153-1161
12. Sun J, Zhao Z. A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics. 2010 11 (Suppl 3):S5
13. Sun J, Han L, Zhao Z. Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis. Artificial Intelligence in Medicine. 2010 48(2-3):99-106
14. Jia P, Sun J, Guo AY, Zhao Z. SZGR: A comprehensive schizophrenia gene resource. Molecular Psychiatry. 2010 15(5):453-462
15. Guo AY, Sun J, Jia P, Zhao Z. A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Systems Biology. 2010 4:10
16. Guo AY, Sun J, Jia P, Zhao Z. Network analysis of ethanol-related candidate genes. Chemistry & Biodiversity. 2010 7(5):1142-1152

2009

1. Xu H, Stetson P, Friedman C. Methods for Building Sense Inventories of Abbreviations in Clinical Notes. J Am Med Inform Assoc. 2009 16(1):103-108. [PMCID: PMC2605589]
2. Sun J, Jia P, Fanous AH, Webb BT, van den Oord EJCG, Kendler KS, Zhao Z. A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases – schizophrenia as a case. Bioinformatics. 2009 25(19):2595-2602
3. Guo A, Sun J, Riley BP, Kendler KS, Zhao Z. The dystrobrevin binding protein 1 gene: features and networks. Molecular Psychiatry. 2009 14:18-29. (*Co-first author)

2008

1. Chen ES, Hripcsak G, Xu H, Markatou M, Friedman C. Automated Acquisition of Disease-Drug Knowledge from Biomedical and Clinical Documents. J Am Med Inform Assoc. 2008, 15(1):87-98. [PMCID: PMC2274872]
2. Sarah Bradshaw, W. Jim Zheng, Lam C. Tsoi, Gary S. Gilkeson, Xian K. Zhang: A role for Fli-1 in B cell proliferation: implications for SLE pathogenesis. Clinical Immunology, 129(1):19-30, 2008
3. Jingshan Huang, Jiangbo Dang, Michael N. Huhns, W. Jim Zheng: Using Artificial Neural Network to Align Biological Ontology. BMC Genomics, 9 Suppl 2:S16, 2008
4. Sun J, Kuo PH, Riley BP, Kendler KS, Zhao Z. Candidate genes for schizophrenia: a survey of association studies and gene ranking. American Journal of Medical Genetics B: Neuropsychiatric Genetics. 2008 147B(7):1173-1181

2007

1. Fan JW, Xu H, Friedman C. Using Distributional Analysis to Semantically Classify UMLS Concepts. In Proceedings of Medinfo. 2007; 519-23. [PMID: 17911771]
2. Xu H, Fan JW, Friedman C. Combine multiple evidence for gene symbol disambiguation. ACL 2007, BioNLP Workshop, p41-48.
3. Xu H, Stetson P, Friedman C. A Study of Abbreviations in Clinical Notes. AMIA Annu Symp Proc. 2007; 821-5.
4. Tulipano KP, Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier YA, Friedman C. Natural language processing and visualization in the molecular imaging domain. J Biomed Inform. 2007; 40:3, 270-281. [PMID: 17084109]
5. Fan JW, Xu H, Friedman C. Using Contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007; 8: 264. [PMCID: PMC2014782]
6. Xu H, Fan JW, Hripcsak G, Mendonça EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics, 2007 23(8):1015-1022. [PMID: 17314123]
7. Sun J, Sun Y, Ding G, Liu Q, Wang C, He Y, Shi T, Li Y, Zhao Z. InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics. 2007 8:414
8. Sun J, Zhao Z. Construction of phylogenetic profiles based on genetic distance of hundreds of genomes. Biochemical and Biophysical Research Communications. 2007 355(3):849-853
9. Sun J, Li Y, Zhao Z. Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochemical and Biophysical Research Communications. 2007 353(4):985-991

2006

1. Xu H, Markatou M, Dimova R, Liu H, Friedman C. Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinformatics. 2006; 7:334. [PMCID: PMC1550263]
2. Sun J, Xu J, Cao J, Liu Q, Guo X, Shi T, Li Y. Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans. Chinese Science Bulletin. 2006 51:1296-1305

2005

1. Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y. Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics. 2005 21(16):3409-3415
2. Sun J, Chen M, Xu J, Luo J. Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes. Journal of Molecular Evolution 2005 61(4):437-444
3. Sun J, Xu J, Li Y. Analysis and application of large-scale protein-protein interaction data sets. Chinese Science Bulletin. 2005 50:2267-2272

2004

1. Xu, H, Anderson, K, Grann, V, Friedman, C. Facilitating Cancer Research using Natural Language Processing of Pathology Reports. In Proceedings of Medinfo. 2004; 565-72. [PMID: 15360876]
2. Lee HT, Krichevsky IE, Xu H, Ota-Setlik A, D'Agati VD, Emala CW. Local anesthetics worsen renal function after ischemia-reperfusion injury in rats. Am J Physiol Renal Physiol. 2004; 286(1):F111-9. [PMID: 14519592]
3. Lee HT, Xu H, Nasr SH, Schnermann J, Emala CW. A1 adenosine receptor knockout mice exhibit increased renal injury following ischemia and reperfusion. Am J Physiol Renal Physiol. 2004; 286(2):F298-306. [PMID: 14600029]

2003

1. Lee HT, Xu H, Ota-Setlik A, Emala CW. Oxidant preconditioning protects human proximal tubular cells against lethal oxidant injury via p38 MAPK and heme oxygenase-1. Am J Nephrol. 2003; 23(5):324-33. [PMID: 12915776]
2. Lee HT, Ota-Setlik A, Xu H, D'Agati VD, Jacobson MA, Emala CW. A3 adenosine receptor knockout mice are protected against ischemia- and myoglobinuria-induced renal failure. Am J Physiol Renal Physiol. 2003; 284(2):F267-73. [PMID: 12388399]
3. Lee HT, Xu H, Siegel CD, Krichevsky IE. Local anesthetics induce human renal cell apoptosis. Am J Nephrol. 2003; 23(3):129-39. [PMID: 12586958]