Below are recent publications by Informatics Institute Faculty. 

Jake Chen, Ph.D.

Regenerative Potential of Neonatal Porcine Hearts.Circulation. 2018 Jul 20. doi: 10.1161/CIRCULATIONAHA.118.034886. Wuqiang Zhu, Eric Zhang, Meng Zhao, Zechen Chong, Chengming Fan, Yawen Tang, Jervaughn D. Hunter, Anton V. Borovjagin, Gregory P. Walcott, Jake Y. Chen, Gangjian Qin, Jianyi Zhang

PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D668–D676,. doi: 10.1093/nar/gkx1040. Zongliang Yue, Qi Zheng, Michael T Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y Chen.

Simulation Study of cDNA Dataset to Investigate Possible Association of Differentially Expressed Genes of Human THP1-Monocytic Cells in Cancer Progression Affected by Bacterial Shiga Toxins. Front. Microbiol., 13 March 2018. doi: 10.3389/fmicb.2018.00380. Syed A. Muhammad, Jinlei Guo, Thanh M. Nguyen, Xiaogang Wu, Baogang Bai, X. Frank Yang and Jake Y. Chen.

Repositioning drugs by targeting network modules: a Parkinson’s disease case study. BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):532. doi: 10.1186/s12859-017-1889-0. Yue Z, Arora I, Zhang EY, Laufer V, Bridges SL, Chen JY.

Zechen Chong, Ph.D.

Structural Variant Breakpoint Detection with novoBreak. Methods Mol Biol. 2018;1833:129-141. doi: 10.1007/978-1-4939-8666-8_10. Chong Z, Chen K.

Regenerative Potential of Neonatal Porcine Hearts. Circulation. 2018 Jul 20. pii: CIRCULATIONAHA.118.034886. doi: 10.1161/CIRCULATIONAHA.118.034886. Zhu W, Zhang E, Zhao M, Chong Z, Fan C, Tang Y, Hunter JD, Borovjagin AV, Walcott GP, Chen JY, Qin G, Zhang J.

In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer. Nat Commun. 2018 Jul 16;9(1):2732. doi: 10.1038/s41467-018-04572-3. Grzeskowiak CL, Kundu ST, Mo X, Ivanov AA, Zagorodna O, Lu H, Chapple RH, Tsang YH, Moreno D, Mosqueda M, Eterovic K, Fradette JJ, Ahmad S, Chen F, Chong Z, Chen K, Creighton CJ, Fu H, Mills GB, Gibbons DL, Scott KL.

Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Hum Mutat. 2018 Jul;39(7):939-946. doi: 10.1002/humu.23537. Grochowski CM, Gu S, Yuan B, Tcw J, Brennand KJ, Sebat J, Malhotra D, McCarthy S, Rudolph U, Lindstrand A, Chong Z, Levy DL, Lupski JR, Carvalho CMB.

A murine preclinical syngeneic transplantation model for breast cancer precision medicine. Sci Adv. 2017 Apr 19;3(4):e1600957. doi: 10.1126/sciadv.1600957. Federico L, Chong Z, Zhang D, McGrail DJ, Zhao W, Jeong KJ, Vellano CP, Ju Z, Gagea M, Liu S, Mitra S, Dennison JB, Lorenzi PL, Cardnell R, Diao L, Wang J, Lu Y, Byers LA, Perou CM, Lin SY, Mills GB.

An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell. 2017 Feb 23;168(5):830-842.e7. doi: 10.1016/j.cell.2017.01.037. Liu P, Yuan B, Carvalho CM, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR.

Integrated genomic and molecular characterization of cervical cancer. Nature. 2017 Mar 16;543(7645):378-384. doi: 10.1038/nature21386. Cancer Genome Atlas Research Network (including Chong Z as a coauthor).

novoBreak: local assembly for breakpoint detection in cancer genomes. Nat Methods. 2017 Jan;14(1):65-67. doi: 10.1038/nmeth.4084. Chong Z, Ruan J, Gao M, Zhou W, Chen T, Fan X, Ding L, Lee AY, Boutros P, Chen J, Chen K.

James Cimino, M.D.

Natural Language Processing (NLP) to Identify Acute Exacerbations of COPD in Real Time: A Pilot Program. American Journal of Respiratory and Critical Care Medicine 2018;197:A4549. J.M. Wells, J.D. Osborne, J.K. Nichols, C.C. Blackburn, H. Chitkara, A. Khare, D.P. Kirkpatrick, M. Wyatt,G. Gordon, J.H. Willig, J.J. Cimino, M.T. Dransfield. 

Is Multiclass Automatic Text De-Identification Worth the Effort?Methods Inf Med 2018; 57(04): 177-184. doi: 10.3414/ME18-01-0017. Duy Duc An Bui, David T. Redden, James J. Cimino.

Chapter 31 - Clinical Research Data: Characteristics, Representation, Storage, and Retrieval. Principles and Practice of Clinical Research (Fourth Edition). 2018, Pages 547-557. doi: 10.1016/B978-0-12-849905-4.00031-9. James J.Cimino

The UAB Informatics Institute and 2016 CEGS N-GRID de-identification shared task challenge. J Biomed Inform. 2017 Nov;75S:S54-S61. doi: 10.1016/j.jbi.2017.05.001. Epub 2017 May 3. Duy Duc AnBui, Mathew Wyatt, James J.Cimino

Clinical Informatics Researcher's Desiderata for the Data Content of the Next Generation Electronic Health Record. Appl Clin Inform 2017; 08(04): 1159-1172
doi: 10.4338/ACI-2017-06-R-0101. Timothy I. Kennell Jr., James H. Willig, James J. Cimino.

A survey of practices for the use of electronic health records to support research recruitment. J Clin Transl Sci. 2017 Aug;1(4):246-252. doi: 10.1017/cts.2017.301. Jihad S. Obeid, Laura M. Beskow, Marie Rape, Ramkiran Gouripeddi, R. Anthony Black, James J. Cimino, Peter J. Embi, Chunhua Weng, Rebecca Marnocha, John B. Buse and for the Methods and Process and Informatics Domain Task Force Workgroup 

A Learning Health Care System Using Computer-Aided Diagnosis. J Med Internet Res. 2017 Mar; 19(3): e54. doi:10.2196/jmir.6663. Amos Cahan and James J Cimino

Computer-aided assessment of the generalizability of clinical trial results. Int J Med Inform. 2017 Mar;99:60-66. doi: 10.1016/j.ijmedinf.2016.12.008. Amos CahanSorel Cahan, James J.Cimino

Context-sensitive decision support (infobuttons) in electronic health records: a systematic review. J Am Med Inform Assoc. 2017 Mar 1;24(2):460-468. doi: 10.1093/jamia/ocw104. David A Cook, Miguel T Teixeira, Bret SE Heale, James J Cimino, Guilherme Del Fiol.

Improving precision medicine using individual patient data from trials. CMAJ. 2017 Feb 6;189(5):E204-E207. doi: 10.1503/cmaj.160267. Amos Cahan and James J. Cimino. 

Classifying Clinical Trial Eligibility Criteria to Facilitate Phased Cohort Identification Using Clinical Data Repositories. AMIA Annu Symp Proc. 2017; 2017: 1754–1763. Amy Y. Wang, William J. Lancaster, Matthew C. Wyatt, Luke V. Rasmussen, Daniel G. Fort and James J. Cimino.

Classification of Clinical Research Study Eligibility Criteria to Support Multi-Stage Cohort Identification Using Clinical Data Repositories. Stud Health Technol Inform. 01 Jan 2017, 245:341-345. Cimino JJ, Lancaster WJ, Wyatt MC.

Chapter 5 - Data Systems and Global Health Informatics Research. Global Health Informatics How Information Technology Can Change our Lives in a Globalized World. 2017, Pages 109-128. dio: 10.1016/B978-0-12-804591-6.00006-9. J.J.Cimino, E.Ayres, R.Pillay.

Tiago Colicchio, Ph.D., MBA

Comprehensive methodology to monitor longitudinal change patterns during EHR implementations: a case study at a large health care delivery network. J Biomed Inform. 2018 Jul;83:40-53. doi: 10.1016/j.jbi.2018.05.018. Tiago K.Colicchio, GuilhermeDel Fiol, Debra L.Scammon, Julio C.Facelli, Watson A.BowesIII, Scott P.Narus.

Evaluation of a systematic methodology to detect in near real-time performance changes during electronic health record system implementations: a longitudinal study. AMIA Annu Symp Proc. 2018 Apr 16;2017:595-604. Colicchio TK, Fiol GD, Stoddard GJ, Narus SP.

Development and classification of a robust inventory of near real-time outcome measurementsfor assessing information technology interventions in health care. J Biomed Inform. 2017 Sep;73:62-75. doi: 10.1016/j.jbi.2017.07.014. Tiago K.Colicchio, GuilhermeDel Fiol, Debra L.Scammon, Watson A.BowesIII, Julio C.Facelli, Scott P.Narusa.

John Osborne, M.D.

Natural Language Processing (NLP) to Identify Acute Exacerbations of COPD in Real Time: A Pilot Program. American Journal of Respiratory and Critical Care Medicine 2018;197:A4549. J.M. Wells, J.D. Osborne, J.K. Nichols, C.C. Blackburn, H. Chitkara, A. Khare, D.P. Kirkpatrick, M. Wyatt,G. Gordon, J.H. Willig, J.J. Cimino, M.T. Dransfield. 

CUILESS2016: a clinical corpus applying compositional normalization of text mentions. J Biomed Semantics. 2018 Jan 10;9(1):2. doi: 10.1186/s13326-017-0173-6.  and 

Alexander Rosenberg, Ph.D.

Visualizing nationwide variation in medicare Part D prescribing patterns. BMC Medical Informatics and Decision Making. 2018;18(1):103. PMID: 30454029, PMCID: PMC6245567. Rosenberg A, Fucile C, White RJ, Trayhan M, Farooq S, Quill CM, Nelson LA, Weisenthal SJ, Bush K, Zand MS.  

Understanding B-cell activation and autoantibody repertoire selection in systemic lupus erythematosus: A B-cell immunomics approach. Immunological Reviews. 2018; 284(1):120-131. NIHMSID: NIHMS962205, PMID: 29944759, PMCID: PMC6022284. Tipton CM, Hom JR, Fucile CF, Rosenberg AF, Sanz I. 

Small proline-rich protein 2B drives stress-dependent p53 degradation and fibroblast proliferation in heart failure. Proceedings of the National Academy of Sciences of the United States of America. 2018; 115(15):E3436-E3445. PMID: 29581288, PMCID: PMC5899445. Burke RM, Lighthouse JK, Quijada P, Dirkx RA Jr, Rosenberg A, Moravec CS, Alexis JD, Small EM. 

A Highly Potent and Broadly Neutralizing H1 Influenza-Specific Human Monoclonal Antibody. Scientific Reports. 2018; 8(1):4374. PMID: 29531320, PMCID:PMC5847613. Nogales A, Piepenbrink MS, Wang J, Ortega S, Basu M, Fucile CF, Treanor JJ, Rosenberg AF, Zand MS, Keefer MC, Martinez-Sobrido L, Kobie JJ. 

Identification of GB1, a gene whose constitutive over-expression increases glycinebetaine content in maize and soybean. Plant Direct. 2018 February 22; 2(2). Castiglioni P, Lund AA, Rosenberg A, Galligan M, Hinchey BS, Bauer S, Nelson D, Benson RJ.