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. Nguyen AM, Cleland CM, Dickinson LM, Barry MP, Cykert S, Duffy FD, Kuzel AJ, Lindner SR, Parchman ML, Shelley DR  et al.  Considerations Before Selecting a Stepped-Wedge Cluster Randomized Trial Design for a Practice Improvement Study.  Ann Fam Med  ;20(3):255-261. doi:10.1370/afm.2810
  2. Namjou B, Lape M, Malolepsza E, DeVore SB, Weirauch MT, Dikilitas O, Jarvik GP, Kiryluk K, Kullo IJ, Liu C  et al.  Multiancestral polygenic risk score for pediatric asthma.  J Allergy Clin Immunol  2022 May 17;. pii:S0091-6749(22)00660-1
  3. Feng YA, Stanaway IB, Connolly JJ, Denny JC, Luo Y, Weng C, Wei WQ, Weiss ST, Karlson EW, Smoller JW  Psychiatric manifestations of rare variation in medically actionable genes: a PheWAS approach.  BMC Genomics  2022 May 19;23(1):385. doi:10.1186/s12864-022-08600-x
  4. Zhao Y, Yu Y, Wang H, Li Y, Deng Y, Jiang G, Luo Y  Machine Learning in Causal Inference: Application in Pharmacovigilance.  Drug Saf  2022 May;45(5):459-476. doi:10.1007/s40264-022-01155-6
  5. Richardson JE, Rasmussen LV, Dorr DA, Sirkin JT, Shelley D, Rivera A, Wu W, Cykert S, Cohen DJ, Kho AN  Generating and Reporting Electronic Clinical Quality Measures from Electronic Health Records: Strategies from EvidenceNOW Cooperatives.  Appl Clin Inform  2022 03;13(2):485-494. doi:10.1055/s-0042-1748145
  6. Li Y, Liu Q, Zeng Z, Luo Y  Using an Unsupervised Clustering Model to Detect the Early Spread of SARS-CoV-2 Worldwide.  Genes (Basel)  2022 04 07;13(4). pii:648
  7. Zeng C, Bastarache LA, Tao R, Venner E, Hebbring S, Andujar JD, Bland ST, Crosslin DR, Pratap S, Cooley A  et al.  Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases.  JAMA Oncol  2022 Apr 21;. doi:10.1001/jamaoncol.2022.0373
  8. Ahmad FS, Luo Y, Wehbe RM, Thomas JD, Shah SJ  Advances in Machine Learning Approaches to Heart Failure with Preserved Ejection Fraction.  Heart Fail Clin  2022 Apr;18(2):287-300. pii:S1551-7136(21)00117-3
  9. Zeng Z, Li Y, Li Y, Luo Y  Statistical and machine learning methods for spatially resolved transcriptomics data analysis.  Genome Biol  2022 03 25;23(1):83. doi:10.1186/s13059-022-02653-7
  10. Hophan SL, Odnokoz O, Liu H, Luo Y, Khan S, Gradishar W, Zhou Z, Badve S, Torres MA, Wan Y  Ductal Carcinoma In Situ of Breast: From Molecular Etiology to Therapeutic Management.  Endocrinology  2022 04 01;163(4). pii:bqac027
  11. Mao C, Yao L, Luo Y  MedGCN: Medication recommendation and lab test imputation via graph convolutional networks.  J Biomed Inform  2022 03;127:104000. pii:S1532-0464(22)00016-8
  12. Yu J, Pacheco JA, Ghosh AS, Luo Y, Weng C, Shang N, Benoit B, Carrell DS, Carroll RJ, Dikilitas O  et al.  Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions.  BMC Med Inform Decis Mak  2022 01 28;22(1):23. doi:10.1186/s12911-022-01759-z
  13. Luo Y, Wunderink RG, Lloyd-Jones D  Proactive vs Reactive Machine Learning in Health Care: Lessons From the COVID-19 Pandemic.  JAMA  2022 02 15;327(7):623-624. doi:10.1001/jama.2021.24935
  14. El-Shennawy L, Hoffmann AD, Dashzeveg NK, McAndrews KM, Mehl PJ, Cornish D, Yu Z, Tokars VL, Nicolaescu V, Tomatsidou A  et al.  Circulating ACE2-expressing extracellular vesicles block broad strains of SARS-CoV-2.  Nat Commun  2022 01 20;13(1):405. doi:10.1038/s41467-021-27893-2
  15. Yu J, Wang AA, Zimmerman LP, Deng Y, Vu TT, Tedla YG, Soulakis ND, Ahmad FS, Kho AN  A Cohort Analysis of Statin Treatment Patterns Among Small-Sized Primary Care Practices.  J Gen Intern Med  2022 Jan 08;. doi:10.1007/s11606-021-07191-9
  16. 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 12;9(Suppl 1). pii:e002205
  17. Luo Y  Evaluating the state of the art in missing data imputation for clinical data.  Brief Bioinform  2022 01 17;23(1). pii:bbab489
  18. Zhong J, Wang H, Yang K, Wang H, Duan C, Ni N, An L, Luo Y, Zhao P, Gou Y  et al.  Reversibly immortalized keratinocytes (iKera) facilitate re-epithelization and skin wound healing: Potential applications in cell-based skin tissue engineering.  Bioact Mater  2022 Mar;9:523-540. doi:10.1016/j.bioactmat.2021.07.022
  19. Smith JD, Davis P, Kho AN  Community-Driven Health Solutions on Chicago's South Side.  Stanf Soc Innov Rev  2021;19(3):A27-A29. doi:10.48558/85p7-3113
  20. Tang M, Shin HJ, Metcalf-Doetsch W, Luo Y, Lindholm PF, Kwaan H, Naidech AM  Antiplatelet Medications and Biomarkers of Hemostasis May Explain the Association of Hematoma Appearance and Subsequent Hematoma Expansion After Intracerebral Hemorrhage.  Neurocrit Care  2022 06;36(3):791-796. doi:10.1007/s12028-021-01369-z
  21. Li Y, Luo Y  Optimizing the evaluation of gene-targeted panels for tumor mutational burden estimation.  Sci Rep  2021 10 26;11(1):21072. doi:10.1038/s41598-021-00626-7
  22. Zeng Z, Mao C, Vo A, Li X, Nugent JO, Khan SA, Clare SE, Luo Y  Deep learning for cancer type classification and driver gene identification.  BMC Bioinformatics  2021 Oct 25;22(Suppl 4):491. doi:10.1186/s12859-021-04400-4
  23. Murphy J, Shin HJ, Wang H, Luo Y, Jahromi B, Bleck TP, Cella D, Naidech AM  Clusters Across Multiple Domains of Health-Related Quality of Life Reveal Complex Patient Outcomes After Subarachnoid Hemorrhage.  Crit Care Explor  2021 Sep;3(9):e0533. doi:10.1097/CCE.0000000000000533
  24. 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
  25. 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 09;9(9). pii:e002627
  26. 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
  27. 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
  28. 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 06 01;4(6):e2112820. doi:10.1001/jamanetworkopen.2021.12820
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. Baman JR, Ahmad FS  Heart Failure.  JAMA  2020 09 08;324(10):1015. doi:10.1001/jama.2020.13310
  48. 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
  49. 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
  50. 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

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