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Publications

Browse the list below to see the latest scientific publications stemming from our center faculty’s work. To view publications of specific CHIP faculty, please visit About Us and select a profile link.

  1. Chen S, Lastra RO, Paunesku T, Antipova O, Li L, Deng J, Luo Y, Wanzer MB, Popovic J, Li Y  et al.  Development of Multi-Scale X-ray Fluorescence Tomography for Examination of Nanocomposite-Treated Biological Samples.  Cancers (Basel)  2021 Sep 06;13(17). pii:4497
  2. Bhavani SV, Luo Y, Miller WD, Sanchez-Pinto LN, Han X, Mao C, Sandikci B, Peek ME, Coopersmith CM, Michelson KN  et al.  Simulation of Ventilator Allocation in Critically Ill Patients with COVID-19.  Am J Respir Crit Care Med  2021 Sep 09;. doi:10.1164/rccm.202106-1453LE
  3. Bayless NL, Bluestone JA, Bucktrout S, Butterfield LH, Jaffee EM, Koch CA, Roep BO, Sharpe AH, Murphy WJ, Villani AC  et al.  Development of preclinical and clinical models for immune-related adverse events following checkpoint immunotherapy: a perspective from SITC and AACR.  J Immunother Cancer  2021 Sep;9(9). pii:e002627
  4. Li Y, Luo Y  Performance-weighted-voting model: An ensemble machine learning method for cancer type classification using whole-exome sequencing mutation.  Quant Biol  2020 Dec 24;8(4):347-358. doi:10.1007/s40484-020-0226-1
  5. Furmanchuk A, Liu M, Song X, Waitman LR, Meurer JR, Osinski K, Stoddard A, Chrischilles E, McClay JC, Cowell LG  et al.  Effect of the Affordable Care Act on diabetes care at major health centers: newly detected diabetes and diabetes medication management.  BMJ Open Diabetes Res Care  2021 06;9(1). pii:e002205
  6. Liu G, Shi M, Mosley JD, Weng C, Zhang Y, Lee MTM, Jarvik GP, Hakonarson H, Namjou-Khales B, Sleiman P  et al.  A Mendelian Randomization Approach Using 3-HMG-Coenzyme-A Reductase Gene Variation to Evaluate the Association of Statin-Induced Low-Density Lipoprotein Cholesterol Lowering With Noncardiovascular Disease Phenotypes.  JAMA Netw Open  2021 Jun 01;4(6):e2112820. doi:10.1001/jamanetworkopen.2021.12820
  7. Walunas TL, Ghosh AS, Pacheco JA, Mitrovic V, Wu A, Jackson KL, Schusler R, Chung A, Erickson D, Mancera-Cuevas K  et al.  Evaluation of structured data from electronic health records to identify clinical classification criteria attributes for systemic lupus erythematosus.  Lupus Sci Med  2021 04;8(1). pii:e000488
  8. Ding M, Luo Y  Unsupervised phenotyping of sepsis using nonnegative matrix factorization of temporal trends from a multivariate panel of physiological measurements.  BMC Med Inform Decis Mak  2021 04 09;21(Suppl 5):95. doi:10.1186/s12911-021-01460-7
  9. Walunas TL, Ye J, Bannon J, Wang A, Kho AN, Smith JD, Soulakis N  Does coaching matter? Examining the impact of specific practice facilitation strategies on implementation of quality improvement interventions in the Healthy Hearts in the Heartland study.  Implement Sci  2021 03 31;16(1):33. doi:10.1186/s13012-021-01100-8
  10. Kou W, Carlson DA, Baumann AJ, Donnan E, Luo Y, Pandolfino JE, Etemadi M  A deep-learning-based unsupervised model on esophageal manometry using variational autoencoder.  Artif Intell Med  2021 02;112:102006. pii:S0933-3657(20)31271-9
  11. Klann JG, Estiri H, Weber GM, Moal B, Avillach P, Hong C, Tan ALM, Beaulieu-Jones BK, Castro V, Maulhardt T  et al.  Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data.  J Am Med Inform Assoc  2021 07 14;28(7):1411-1420. doi:10.1093/jamia/ocab018
  12. Ye J, Yao L, Shen J, Janarthanam R, Luo Y  Predicting mortality in critically ill patients with diabetes using machine learning and clinical notes.  BMC Med Inform Decis Mak  2020 12 30;20(Suppl 11):295. doi:10.1186/s12911-020-01318-4
  13. Yeh P, Pan Y, Sanchez-Pinto LN, Luo Y  Hyperchloremia in critically ill patients: association with outcomes and prediction using electronic health record data.  BMC Med Inform Decis Mak  2020 12 15;20(Suppl 14):302. doi:10.1186/s12911-020-01326-4
  14. Geng F, Lu GF, Luo YJ, Dominguez S, Kong DY, Shen LH, Luo XM, Yang X, Hu M, Lai WS  et al.  The emerging role of the MiR-1272-ADAM9-CDCP1 signaling pathway in the progression of glioma.  Aging (Albany NY)  2020 11 26;13(1):894-909. doi:10.18632/aging.202196
  15. Wang H, Li Y, Khan SA, Luo Y  Prediction of breast cancer distant recurrence using natural language processing and knowledge-guided convolutional neural network.  Artif Intell Med  2020 11;110:101977. pii:S0933-3657(20)31242-2
  16. Ma Y, Jiang H, Shah SJ, Arnett D, Irvin MR, Luo Y  Genetic-Based Hypertension Subtype Identification Using Informative SNPs.  Genes (Basel)  2020 10 27;11(11). pii:E1265
  17. Xu J, Wang F, Xu Z, Adekkanattu P, Brandt P, Jiang G, Kiefer RC, Luo Y, Mao C, Pacheco JA  et al.  Data-driven discovery of probable Alzheimer's disease and related dementia subphenotypes using electronic health records.  Learn Health Syst  2020 Oct;4(4):e10246. doi:10.1002/lrh2.10246
  18. Brandt PS, Kiefer RC, Pacheco JA, Adekkanattu P, Sholle ET, Ahmad FS, Xu J, Xu Z, Ancker JS, Wang F  et al.  Toward cross-platform electronic health record-driven phenotyping using Clinical Quality Language.  Learn Health Syst  2020 Oct;4(4):e10233. doi:10.1002/lrh2.10233
  19. Zeng Z, Amin A, Roy A, Pulliam NE, Karavites LC, Espino S, Helenowski I, Li X, Luo Y, Khan SA  Preoperative magnetic resonance imaging use and oncologic outcomes in premenopausal breast cancer patients.  NPJ Breast Cancer  2020;6:49. doi:10.1038/s41523-020-00192-7
  20. Byrd TF, Ahmad FS, Liebovitz DM, Kho AN  Defragmenting Heart Failure Care: Medical Records Integration.  Heart Fail Clin  2020 Oct;16(4):467-477. pii:S1551-7136(20)30043-X
  21. Wehbe RM, Khan SS, Shah SJ, Ahmad FS  Predicting High-Risk Patients and High-Risk Outcomes in Heart Failure.  Heart Fail Clin  2020 Oct;16(4):387-407. pii:S1551-7136(20)30036-2
  22. Eickelberg G, Sanchez-Pinto LN, Luo Y  Predictive modeling of bacterial infections and antibiotic therapy needs in critically ill adults.  J Biomed Inform  2020 09;109:103540. pii:S1532-0464(20)30168-4
  23. Sanchez-Pinto LN, Stroup EK, Pendergrast T, Pinto N, Luo Y  Derivation and Validation of Novel Phenotypes of Multiple Organ Dysfunction Syndrome in Critically Ill Children.  JAMA Netw Open  2020 08 03;3(8):e209271. doi:10.1001/jamanetworkopen.2020.9271
  24. Luo Y, Eran A, Palmer N, Avillach P, Levy-Moonshine A, Szolovits P, Kohane IS  A multidimensional precision medicine approach identifies an autism subtype characterized by dyslipidemia.  Nat Med  2020 09;26(9):1375-1379. doi:10.1038/s41591-020-1007-0
  25. Baman JR, Ahmad FS  Heart Failure.  JAMA  2020 09 08;324(10):1015. doi:10.1001/jama.2020.13310
  26. Zeng Z, Vo A, Li X, Shidfar A, Saldana P, Blanco L, Xuei X, Luo Y, Khan SA, Clare SE  Somatic genetic aberrations in benign breast disease and the risk of subsequent breast cancer.  NPJ Breast Cancer  2020;6:24. doi:10.1038/s41523-020-0165-z
  27. Ahmad FS, Ricket IM, Hammill BG, Eskenazi L, Robertson HR, Curtis LH, Dobi CD, Girotra S, Haynes K, Kizer JR  et al.  Computable Phenotype Implementation for a National, Multicenter Pragmatic Clinical Trial: Lessons Learned From ADAPTABLE.  Circ Cardiovasc Qual Outcomes  2020 06;13(6):e006292. doi:10.1161/CIRCOUTCOMES.119.006292
  28. Ma Y, Luo Y, Jiang H  A novel normalization and differential abundance test framework for microbiome data.  Bioinformatics  2020 07 01;36(13):3959-3965. doi:10.1093/bioinformatics/btaa255
  29. Ahmad FS, Rasmussen LV, Persell SD, Richardson JE, Liss DT, Kenly P, Chung I, French DD, Walunas TL, Schriever A  et al.  Challenges to electronic clinical quality measurement using third-party platforms in primary care practices: the healthy hearts in the heartland experience.  JAMIA Open  2019 Dec;2(4):423-428. doi:10.1093/jamiaopen/ooz038
  30. Persell SD, Liss DT, Walunas TL, Ciolino JD, Ahmad FS, Brown T, French DD, Hountz R, Iversen K, Lindau ST  et al.  Effects of 2 Forms of Practice Facilitation on Cardiovascular Prevention in Primary Care: A Practice-randomized, Comparative Effectiveness Trial.  Med Care  2020 04;58(4):344-351. doi:10.1097/MLR.0000000000001260
  31. McHugh M, Brown T, Liss DT, Persell SD, Garrett M, Walunas TL  Qualitative evaluation of a cardiovascular quality improvement programmereveals sizable data inaccuracies in small primary care practices.  BMJ Open Qual  2019;8(4):e000702. doi:10.1136/bmjoq-2019-000702
  32. Wu T, Chen C, Spagna A, Wu X, Mackie MA, Russell-Giller S, Xu P, Luo YJ, Liu X, Hof PR  et al.  The functional anatomy of cognitive control: A domain-general brain network for uncertainty processing.  J Comp Neurol  2020 06;528(8):1265-1292. doi:10.1002/cne.24804
  33. Yeh P, Pan Y, Sanchez-Pinto LN, Luo Y  Using Machine Learning to Predict Hyperchloremia in Critically Ill Patients.  Proceedings (IEEE Int Conf Bioinformatics Biomed)  2019 Nov;2019:1703-1707. doi:10.1109/bibm47256.2019.8982933
  34. Stroup EK, Luo Y, Sanchez-Pinto LN  Phenotyping Multiple Organ Dysfunction Syndrome Using Temporal Trends in Critically Ill Children.  Proceedings (IEEE Int Conf Bioinformatics Biomed)  2019 Nov;2019:968-972. doi:10.1109/bibm47256.2019.8983126
  35. Hong N, Wen A, Stone DJ, Tsuji S, Kingsbury PR, Rasmussen LV, Pacheco JA, Adekkanattu P, Wang F, Luo Y  et al.  Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries.  J Biomed Inform  2019 11;99:103310. pii:S1532-0464(19)30229-1
  36. Shang N, Liu C, Rasmussen LV, Ta CN, Caroll RJ, Benoit B, Lingren T, Dikilitas O, Mentch FD, Carrell DS  et al.  Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network.  J Biomed Inform  2019 11;99:103293. pii:S1532-0464(19)30212-6
  37. Walunas TL, Ghosh AS, Pacheco JA, Jackson KL, Chung AH, Erickson DL, Mancera-Cuevas K, Ramsey-Goldman R, Kho AN  Assessing the Concordance of Clinical Classification Criteria for Lupus Between Electronic Health Records and a Physician Curated Registry.  Stud Health Technol Inform  2019 Aug 21;264:1466-1467. doi:10.3233/SHTI190487
  38. Zeng Z, Zhao Y, Sun M, Vo AH, Starren J, Luo Y  Rich Text Formatted EHR Narratives: A Hidden and Ignored Trove.  Stud Health Technol Inform  2019 Aug 21;264:472-476. doi:10.3233/SHTI190266
  39. Xu Z, Luo Y, Adekkanattu P, Ancker JS, Jiang G, Kiefer RC, Pacheco JA, Rasmussen LV, Pathak J, Wang F  Stratified Mortality Prediction of Patients with Acute Kidney Injury in Critical Care.  Stud Health Technol Inform  2019 Aug 21;264:462-466. doi:10.3233/SHTI190264
  40. Wang H, Li Y, Ning H, Wilkins J, Lloyd-Jones D, Luo Y  Using Machine Learning to Integrate Socio-Behavioral Factors in Predicting Cardiovascular-Related Mortality Risk.  Stud Health Technol Inform  2019 Aug 21;264:433-437. doi:10.3233/SHTI190258
  41. Sun M, Baron J, Dighe A, Szolovits P, Wunderink RG, Isakova T, Luo Y  Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes and Structured Multivariate Physiological Measurements.  Stud Health Technol Inform  2019 Aug 21;264:368-372. doi:10.3233/SHTI190245
  42. Chao G, Mao C, Wang F, Zhao Y, Luo Y  Supervised Nonnegative Matrix Factorization to Predict ICU Mortality Risk.  Proceedings (IEEE Int Conf Bioinformatics Biomed)  2018 Dec;2018:1189-1194. doi:10.1109/BIBM.2018.8621403
  43. Zeng Z, Vo AH, Mao C, Clare SE, Khan SA, Luo Y  Cancer classification and pathway discovery using non-negative matrix factorization.  J Biomed Inform  2019 08;96:103247. pii:S1532-0464(19)30166-2
  44. Xu Z, Feng Y, Li Y, Srivastava A, Adekkanattu P, Ancker JS, Jiang G, Kiefer RC, Lee K, Pacheco JA  et al.  Predictive Modeling of the Risk of Acute Kidney Injury in Critical Care: A Systematic Investigation of The Class Imbalance Problem.  AMIA Jt Summits Transl Sci Proc  2019;2019:809-818
  45. Ahmad FS, Kallen MA, Schifferdecker KE, Carluzzo KL, Yount SE, Gelow JM, McCullough PA, Kimmel SE, Fisher ES, Cella D  Development and Initial Validation of the PROMIS®-Plus-HF Profile Measure.  Circ Heart Fail  2019 06;12(6):e005751. doi:10.1161/CIRCHEARTFAILURE.118.005751
  46. Sharma H, Mao C, Zhang Y, Vatani H, Yao L, Zhong Y, Rasmussen L, Jiang G, Pathak J, Luo Y  Developing a portable natural language processing based phenotyping system.  BMC Med Inform Decis Mak  2019 04 04;19(Suppl 3):78. doi:10.1186/s12911-019-0786-z
  47. Yao L, Mao C, Luo Y  Clinical text classification with rule-based features and knowledge-guided convolutional neural networks.  BMC Med Inform Decis Mak  2019 04 04;19(Suppl 3):71. doi:10.1186/s12911-019-0781-4
  48. Mao C, Eran A, Luo Y  Efficient Genomic Interval Queries Using Augmented Range Trees.  Sci Rep  2019 03 25;9(1):5059. doi:10.1038/s41598-019-41451-3
  49. Zhang X, He L, Chen K, Luo Y, Zhou J, Wang F  Multi-View Graph Convolutional Network and Its Applications on Neuroimage Analysis for Parkinson's Disease.  AMIA Annu Symp Proc  2018;2018:1147-1156
  50. Zheng N, Hou J, Zhao H, Wu J, Luo Y, Bai H, Rogers JA, Zhao Q, Xie T  Mechano-Plastic Pyrolysis of Dynamic Covalent Polymer Network toward Hierarchical 3D Ceramics.  Adv Mater  2019 Mar;31(11):e1807326. doi:10.1002/adma.201807326

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