Publications

2013 Publications

Aiyegbo MS, Sapparapu G, Spiller BW, Eli IM, Williams DR, Kim R, Lee DE, Liu T, Li S, Woods VL Jr, Nannemann DP, Meiler J, Stewart PL, Crowe JE Jr. Human Rotavirus VP6-Specific Antibodies Mediate Intracellular Neutralization by Binding to a Quaternary Structure in the Transcriptional Pore. PLoS One 2013;8(5):e61101 PMID: 23671563 

Blum JM, Stentz MJ, Maile MD, Jewell E, Raghavendran K, Engoren M, Ehrenfeld JM. Automated Alerting and Recommendations for the Management of Patients with Preexisting Hypoxia and Potential Acute Lung Injury: A Pilot Study. Anesthesiology 2013 May 15; PMID: 23681144 

Bow HC, Dattilo JR, Jonas AM, Lehmann CU. A Crowdsourcing Model for Creating Preclinical Medical Education Study Tools. Acad Med 2013 Apr 24; PMID: 23619061 

Bush WS, Boston J, Pendergrass SA, Dumitrescu L, Goodloe R, Brown-Gentry K, Wilson S, McClellan B, Torstenson E, Basford MA, Spencer KL, Ritchie MD, Crawford DC. Enabling high-throughput genotype-phenotype associations in the epidemiologic architecture for genes linked to environment (eagle) project as part of the population architecture using genomics and epidemiology (page) study. Pac Symp Biocomput 2013;:373-84 PMID: 23424142 

Butkiewicz M, Lowe EW, Mueller R, Mendenhall JL, Teixeira PL, Weaver CD, Meiler J. Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database. Molecules 2013 Jan 8;18(1):735-56 PMID: 23299552 

Chen Q, Chen MH, Ohlssen D, Ibrahim JG. Bayesian modeling and inference for clinical trials with partial retrieved data following dropout. Stat Med 2013 Apr 26; PMID: 23620446 

Chen Y, Cao H, Mei Q, Zheng K, Xu H. Applying active learning to supervised word sense disambiguation in MEDLINE. J Am Med Inform Assoc 2013 Jan 30; PMID: 23364851 

Combs SA, Deluca SL, Deluca SH, Lemmon GH, Nannemann DP, Nguyen ED, Willis JR, Sheehan JH, Meiler J. Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc 2013 Jun 6;8(7):1277-98 PMID: 23744289 

Connor RE, Codreanu SG, Marnett LJ, Liebler DC. Targeted protein capture for analysis of electrophile-protein adducts. Methods Mol Biol 2013;987:163-76 PMID: 23475677 

Cox ZL, McCoy AB, Matheny ME, Bhave G, Peterson NB, Siew ED, Lewis J, Danciu I, Bian A, Shintani A, Ikizler TA, Neal EB, Peterson JF. Adverse Drug Events during AKI and Its Recovery. Clin J Am Soc Nephrol 2013 Mar 28; PMID: 23539228 

Deluca SH, Rathmann D, Beck-Sickinger AG, Meiler J. The activity of prolactin releasing peptide correlates with its helicity. Biopolymers 2013 May;99(5):314-25 PMID: 23426574 

Dennis BM, Eckert MJ, Gunter OL, Morris JA Jr, May AK. Safety of Bedside Percutaneous Tracheostomy in the Critically Ill: Evaluation of More than 3,000 Procedures. J Am Coll Surg 2013 Feb 8; PMID: 23403139 

Douglas S, Cartmill R, Brown R, Hoonakker P, Slagle J, Schultz Van Roy K, Walker JM, Weinger M, Wetterneck T, Carayon P. The Work of Adult and Pediatric Intensive Care Unit Nurses. Nurs Res 2013 Jan;62(1):50-58 PMID: 23222843 

Ferluga ED, Sathe NA, Krishnaswami S, McPheeters ML. Surgical intervention for feeding and nutrition difficulties in cerebral palsy: a systematic review. Dev Med Child Neurol 2013 Jun 5; PMID: 23738903 

Fitzhenry F, Murff HJ, Matheny ME, Gentry N, Fielstein EM, Brown SH, Reeves RM, Aronsky D, Elkin PL, Messina VP, Speroff T. Exploring the Frontier of Electronic Health Record Surveillance: The Case of Postoperative Complications. Med Care 2013 Jun;51(6):509-516 PMID: 23673394 

Gregory KJ, Nguyen ED, Reiff SD, Squire EF, Stauffer SR, Lindsley CW, Meiler J, Conn PJ. Probing the Metabotropic Glutamate Receptor 5 (mGlu5) Positive Allosteric Modulator (PAM) Binding Pocket: Discovery of Point Mutations that Engender a "Molecular Switch" in PAM Pharmacology. Mol Pharmacol 2013 Feb 26; PMID: 23444015 

Heatherly RD, Loukides G, Denny JC, Haines JL, Roden DM, Malin BA. Enabling Genomic-Phenomic Association Discovery without Sacrificing Anonymity. PLoS One 2013;8(2):e53875 PMID: 23405076 

Ho YX, Chen Q, Nian H, Johnson KB. An assessment of pharmacists' readiness for paperless labeling: a national survey. J Am Med Inform Assoc 2013 Mar 23; PMID: 23523874 

Holman JD, Dasari S, Tabb DL. Informatics of Protein and Posttranslational Modification Detection via Shotgun Proteomics. Methods Mol Biol 2013;1002:167-79 PMID: 23625403 

Janz DR, Bastarache JA, Peterson JF, Sills G, Wickersham N, May AK, Roberts LJ 2nd, Ware LB. Association Between Cell-Free Hemoglobin, Acetaminophen, and Mortality in Patients With Sepsis: An Observational Study. Crit Care Med 2013 Jan 10; PMID: 23314583 

Jeff JM, Ritchie MD, Denny JC, Kho AN, Ramirez AH, Crosslin D, Armstrong L, Basford MA, Wolf WA, Pacheco JA, Chisholm RL, Roden DM, Hayes MG, Crawford DC. Generalization of Variants Identified by Genome-Wide Association Studies for Electrocardiographic Traits in African Americans. Ann Hum Genet 2013 Mar 28; PMID: 23534349 

Leman JK, Mueller R, Karakas M, Woetzel N, Meiler J. Simultaneous prediction of protein secondary structure and trans-membrane spans. Proteins 2013 Jan 24; PMID: 23349002 

Liebler DC, Zimmerman LJ. Targeted Quantitation of Proteins by Mass Spectrometry. Biochemistry 2013 Mar 27; PMID: 23517332 

Lindegren ML, Krishnaswami S, Reimschisel T, Fonnesbeck C, Sathe NA, McPheeters ML. A Systematic Review of BH4 (Sapropterin) for the Adjuvant Treatment of Phenylketonuria. JIMD Rep 2013;8:109-19 PMID: 23430527 

Liu Q, Halvey PJ, Shyr Y, Slebos RJ, Liebler DC, Zhang B. Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation. Mol Cell Proteomics 2013 Apr 2; PMID: 23550052 

Lorenzi N. Safe and secure. Integration is key in evaluating technologies. Health Facil Manage 2013 Jan;26(1):39-42 PMID: 23387105 

Lorenzi N. Chiller up: technology advances drive major efficiency gains for hospitals. Health Facil Manage 2013 Mar;26(3):39-42 PMID: 23577512 

Mascaux C, Feser WJ, Lewis MT, Barón AE, Coldren CD, Merrick DT, Kennedy TC, Eckelberger JI, Rozeboom LM, Franklin WA, Minna JD, Bunn PA, Miller YE, Keith RL, Hirsch FR. Endobronchial miRNAs as Biomarkers in Lung Cancer Chemoprevention. Cancer Prev Res (Phila) 2013 Jan 15; PMID: 23268837 

Morris JA Jr, Diaz J, Fildes J, May AK, Britt LD, Meredith JW. A research agenda for emergency general surgery: Clinical trials. J Trauma Acute Care Surg 2013 Jan;74(1):329-333 PMID: 23271107 

Morris JA Jr, Fildes J, May AK, Diaz J, Britt LD, Meredith JW. A research agenda for emergency general surgery: Health policy and basic science. J Trauma Acute Care Surg 2013 Jan;74(1):322-8 PMID: 23271106 

Mulherin DP, Zimmerman CR, Chaffee BW. National standards for computerized prescriber order entry and clinical decision support: the case of drug interactions. Am J Health Syst Pharm 2013 Jan 1;70(1):59-64 PMID: 23261902 

Nesbitt JC, St Julien J, Absi TS, Ahmad RM, Grogan EL, Balaguer JM, Lambright ES, Deppen SA, Wu H, Putnam JB. Tissue-based coronary surgery simulation: Medical student deliberate practice can achieve equivalency to senior surgery residents. J Thorac Cardiovasc Surg 2013 Mar 14; PMID: 23499474 

Novak LL, Holden RJ, Anders SH, Hong JY, Karsh BT. Using a sociotechnical framework to understand adaptations in health IT implementation. Int J Med Inform 2013 Apr 2; PMID: 23562140 

Oetjens MT, Denny JC, Ritchie MD, Gillani NB, Richardson DM, Restrepo NA, Pulley JM, Dilks HH, Basford MA, Bowton E, Masys DR, Wilke RA, Roden DM, Crawford DC. Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records. Pharmacogenomics 2013 May;14(7):735-44 PMID: 23651022 

Osborn CY, Wallston KA, Shpigel A, Cavanaugh K, Kripalani S, Rothman RL. Development and validation of the General Health Numeracy Test (GHNT). Patient Educ Couns 2013 Feb 20; PMID: 23433635 

Pekow J, Dougherty U, Huang Y, Gometz E, Nathanson J, Cohen G, Levy S, Kocherginsky M, Venu N, Westerhoff M, Hart J, Noffsinger AE, Hanauer SB, Hurst RD, Fichera A, Joseph LJ, Liu Q, Bissonnette M. Gene Signature Distinguishes Patients with Chronic Ulcerative Colitis Harboring Remote Neoplastic Lesions. Inflamm Bowel Dis 2013 Feb 6; PMID: 23388545 

Preininger AM, Meiler J, Hamm H. Conformational flexibility and structural dynamics in GPCR-mediated G protein activation: a perspective. J Mol Biol 2013 Apr 16; PMID: 23602809 

Raphemot R, Weaver CD, Denton JS. High-throughput Screening for Small-molecule Modulators of Inward Rectifier Potassium Channels. J Vis Exp 2013 Jan 27;(71) PMID: 23381507 

Ritchie MD, Denny JC, Zuvich RL, Crawford DC, Schildcrout JS, Bastarache L, Ramirez AH, Mosley JD, Pulley JM, Basford MA, Bradford Y, Rasmussen LV, Pathak J, Chute CG, Kullo IJ, McCarty CA, Chisholm RL, Kho AN, Carlson CS, Larson EB, Jarvik GP, Sotoodehni Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk. Circulation 2013 Apr 2;127(13):1377-85 PMID: 23463857 

Rosenbloom ST, Miller RA, Adams P, Madani S, Khan N, Shultz EK. Implementing an interface terminology for structured clinical documentation. J Am Med Inform Assoc 2013 Feb 5; PMID: 23384817 

Smith AH, Gay JC, Patel NR. Trends in Resource Utilization Associated with the Inpatient Treatment of Neonatal Congenital Heart Disease. Congenit Heart Dis 2013 Jun 5; PMID: 23734574 

Theobald CN, Stover DG, Choma NN, Hathaway J, Green JK, Peterson NB, Sponsler KC, Vasilevskis EE, Kripalani S, Sergent J, Brown NJ, Denny JC. The Effect of Reducing Maximum Shift Lengths to 16 Hours on Internal Medicine Interns' Educational Opportunities. Acad Med 2013 Feb 19; PMID: 23425987 

Wang D, Dasari S, Chambers MC, Holman JD, Chen K, Liebler DC, Orton DJ, Purvine SO, Monroe ME, Chung CY, Rose KL, Tabb DL. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates. Genomics Proteomics Bioinformatics 2013 Mar 7; PMID: 23499924 

Wang J, Duncan D, Shi Z, Zhang B. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res 2013 May 23; PMID: 23703215 

Wang Q, Jia P, Zhao Z. VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data. PLoS One 2013;8(5):e64465 PMID: 23717618 

Wei WQ, Cronin RM, Xu H, Lasko TA, Bastarache L, Denny JC. Development and evaluation of an ensemble resource linking medications to their indications. J Am Med Inform Assoc 2013 Apr 10; PMID: 23576672 

Weiner BE, Woetzel N, KarakaÅŸ M, Alexander N, Meiler J. BCL::MP-Fold: Folding Membrane Proteins through Assembly of Transmembrane Helices. Structure 2013 May 29; PMID: 23727232 

Weiss JB, Berner ES, Johnson KB, Giuse DA, Murphy BA, Lorenzi NM. Recommendations for the Design, Implementation and Evaluation of Social Support in Online Communities, Networks, and Groups. J Biomed Inform 2013 Apr 10; PMID: 23583424 

Willis JR, Briney BS, Deluca SL, Crowe JE Jr, Meiler J. Human germline antibody gene segments encode polyspecific antibodies. PLoS Comput Biol 2013 Apr;9(4):e1003045 PMID: 23637590 

Zhao Z, Xu H, Zhang B, Huang Y. Advances in intelligent biology and medicine. Int J Comput Biol Drug Des 2013;6(1-2):1-4 PMID: 23428469