Publications

Recent Publications

Clinical Informatics | Bioinformatics | Clinical Epidemiology | Health Information Management

Clinical Informatics

Racial and ethnic differences in clinical outcome trajectories for care managed patients.

Quiñones AR1, Ramsey K, Newsom JT, Dorr DA. Med Care. 2014 Nov;
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BCR-ABL1 promotes leukemia by converting p27 into a cytoplasmic oncoprotein.

Agarwal A, Mackenzie RJ, Besson A, Jeng S, Carey A, LaTocha DH, Fleischman AG, Duquesnes N, Eide CA, Vasudevan KB, Loriaux MM, Firpo E, Cortes JE, McWeeney S, O'Hare T, Roberts JM, Druker BJ, Deininger MW. Blood. 2014 Oct 7
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Participation in EHR based simulation improves recognition of patient safety issues.

Stephenson LS, Gorsuch A, Hersh WR, Mohan V, Gold JA1. BMC Med Educ. 2014 Oct 21
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Meaningful use: how did we do, where are we now, where do we go from here?

Lim MC, Chiang MF, Boland MV, McCannel CA, Wedemeyer L, Epley KD, Silverstone DE, Saini A, Lum F. Ophthalmology. 2014 Sep;
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Clinical interpretation of CNVs with cross-species phenotype data

Kohler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA, Robinson PN. J Med Genet. 2014 Oct 3. pii: jmedgenet-2014-102633
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Focus article: report of the NIH task force on research standards for chronic low back pain

Deyo RA, Dworkin SF, Amtmann D, Andersson G, Borenstein D, Carragee E, Carrino J, Chou R, Cook K, DeLitto A, Goertz C, Khalsa P, Loeser J, Mackey S, Panagis J, Rainville J, Tosteson T, Turk D, Von Korff M, Weiner DK. Eur Spine J. 2014 Oct;23(10):2028-45. doi: 10.1007/s00586-014-3540-3.
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Report of the National Institutes of Health task force on research standards for chronic low back pain.

Deyo RA, Dworkin SF, Amtmann D, Andersson G, Borenstein D, Carragee E, Carrino J, Chou R, Cook K, DeLitto A, Goertz C, Khalsa P, Loeser J, Mackey S, Panagis J, Rainville J, Tosteson T, Turk D, Von Korff M, Weiner DK; J Manipulative Physiol Ther. 2014 Sep;
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Implementing a Paradigm Shift: Incorporating Pain Management Competencies into Pre-Licensure Curricula

Arwood E, Rowe JM, Singh NS, Carr DB, Herr KA, Chou R. Pain Med. 2014 Sep 22. doi: 10.1111/pme.12563.
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Response to katz and krantz letter to the editor

Chou R. J Pain. 2014 Sep;15(9):977. doi: 10.1016/j.jpain.2014.06.006.
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Functional and genomic context in pathway analysis of GWAS data

Mooney MA, Nigg JT, McWeeney SK, Wilmot B. Trends Genet. 2014 Aug 22. pii: S0168-9525(14)00116-4. doi: 10.1016/j.tig.2014.07.004.
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Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology

Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. J Biomed Semantics. 2014 Aug 11;5:34. doi: 10.1186/2041-1480-5-34
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Development of an electronic breast pathology database in a community health system.

Nelson HD, Weerasinghe R, Martel M, Bifulco C, Assur T, Elmore JG, Weaver DL. J Pathol Inform. 2014 Jul 30;5:26. doi: 10.4103/2153-3539.137730. eCollection 2014.
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Second opinion in breast pathology: policy, practice and perception

Geller BM, Nelson HD, Carney PA, Weaver DL, Onega T, Allison KH, Frederick PD, Tosteson AN, Elmore JG. J Clin Pathol. 2014 Jul 22. pii: jclinpath-2014-202290. doi: 10.1136/jclinpath-2014-202290
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Depression Drug Treatment Outcomes in Pregnancy and the Postpartum Period: A Systematic Review and Meta-analysis

McDonagh MS, Matthews A, Phillipi C, Romm J, Peterson K, Thakurta S, Guise JM. Obstet Gynecol. 2014 Jul 7
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Meaningful Use: How Did We Do, Where Are We Now, Where Do We Go from Here?

Lim MC, Chiang MF, Boland MV, McCannel CA, Wedemeyer L, Epley KD, Silverstone DE, Saini A, Lum F.
Ophthalmology. 2014 Jul 24.
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Low back pain in primary care.

Deyo RA, Jarvik JG, Chou R. BMJ. 2014 Jul 16
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Vitamin D and falls-fitting new data with current guidelines.

LeBlanc ES, Chou R. 2015 May;175(5):712-3. doi: 10.1001/jamainternmed.2015.0248.

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Reassuring patients about low back pain.

Chou R.  2015 May;175(5):743-4. doi: 10.1001/jamainternmed.2015.0252.
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Twelve recommendations for integrating existing systematic reviews into new reviews: EPC guidance.

Robinson KA, Chou R, Berkman ND, Newberry SJ, Fu R, Hartling L, Dryden D, Butler M, Foisy M, Anderson J, Motu'apuaka M, Relevo R, Guise JM, Chang S
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Use of semantic workflows to enhance transparency and reproducibility in clinical omics.

Zheng CL, Ratnakar V, Gil Y, McWeeney SK
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Methylomic analysis of salivary DNA in childhood ADHD identifies altered DNA methylation in VIPR2.

Wilmot B, Fry R, Smeester L, Musser ED, Mill J, Nigg JT
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Vitamin D Supplements and the Risk of Falls-Reply.

LeBlanc ES, Chou R
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Next-generation diagnostics and disease-gene discovery with the Exomiser.

Smedley D, Jacobsen JO, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN

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Automated confidence ranked classification of randomized controlled trial articles: an aid to evidence-based medicine.

Cohen AM, Smalheiser NR, McDonagh MS, Yu C, Adams CE, Davis JM, Yu PS
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Aggregator: a machine learning approach to identifying MEDLINE articles that derive from the same underlying clinical trial.

Shao W, Adams CE, Cohen AM, Davis JM, McDonagh MS, Thakurta S, Yu PS, Smalheiser NR

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IL-10 and integrin signaling pathways are associated with head and neck cancer progression.

Bornstein S, Schmidt M, Choonoo G, Levin T, Gray J, Thomas CR Jr, Wong M, McWeeney S

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Treatment of muscle-invasive bladder cancer: A systematic review.

Chou R, Selph SS, Buckley DI, Gustafson KS, Griffin JC, Grusing SE, Gore JL

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Intranasal or transdermal nicotine for the treatment of postoperative pain.

Matthews AM, Fu R, Dana T, Chou R.

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A Prospective Evaluation of an Automated Classification System to Support Evidence-based Medicine and Systematic Review.

Cohen AM, Ambert K, McDonagh M

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Mammography Screening in a Large Health System Following the U.S. Preventive Services Task Force Recommendations and the Affordable Care Act.

Nelson HD, Weerasinghe R, Wang L, Grunkemeier G

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Intranasal or transdermal nicotine for the treatment of postoperative pain.

Matthews AM, Fu R, Dana T, Chou R.

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Plasma Exosomal miRNAs in Persons with and without Alzheimer Disease: Altered Expression and Prospects for Biomarkers.

Lugli G, Cohen AM, Bennett DA, Shah RC, Fields CJ, Hernandez AG, Smalheiser NR

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Pediatric Airway Management and Prehospital Patient Safety: Results of a National Delphi Survey by the Children's Safety Initiative-Emergency Medical Services for Children.

Hansen M, Meckler G, OʼBrien K, Engle P, Dickinson C, Dickinson K, Jui J, Lambert W, Cottrell E, Guise JM

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Interventions to reduce childhood antibiotic prescribing for upper respiratory infections: systematic review and meta-analysis.

Hu Y, Walley J, Chou R, Tucker JD, Harwell, Wu, Yin , Zou , Wei X

Twelve recommendations for integrating existing systematic reviews into new reviews: EPC guidance.

Robinson KA, Chou R, Berkman ND, Newberry SJ, Fu R, Hartling L, Dryden D, Butler M, Foisy M, Anderson J, Motu'apuaka M, Relevo R, Guise JM, Chang S

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Treatment of muscle-invasive bladder cancer: A systematic review.

Chou R, Selph SS, Buckley DI, Gustafson KS, Griffin JC, Grusing SE, Gore JL

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Emergency Medical Services Provider Pediatric Adverse Event Rate Varies by Call Origin Pediatric Emergency Care.

Jones D, Hansen M, Van Otterloo J, Dickinson C, Guise JM

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Paramedic assessment and treatment of upper airway obstruction in pediatric patients: an exploratory analysis by the Children's Safety Initiative-Emergency Medical Services.

Hansen M, Meckler G, Lambert W, Dickinson C, Dickinson K, Guise JM

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Are current standards of reporting quality for clinical trials sufficient in addressing important sources of bias?

Mills EJ, Ayers D, Chou R, Thorlund K

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2015 Updated Method Guideline for Systematic Reviews in the Cochrane Back and Neck Group.

Furlan AD, Malmivaara A, Chou R, Maher CG, Deyo RA, Schoene M, Bronfort G, van Tulder MW; Editorial Board of the Cochrane Back, Neck Group

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Team Mentoring for Interdisciplinary Team Science: Lessons From K12 Scholars and Directors.

Guise JM, Geller S, Regensteiner JG, Raymond N, Nagel J; Building Interdisciplinary Research Careers in Women's Health Program Leadership.

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IL-10 and integrin signaling pathways are associated with head and neck cancer progression.

Bornstein S, Schmidt M, Choonoo G, Levin T, Gray J, Thomas CR Jr, Wong M, McWeeney S

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The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus.

McDermott JE, Mitchell HD, Gralinski LE, Eisfeld AJ, Josset L, Bankhead A, Neumann G, Tilton SC, Schäfer A, Li C, Fan S, McWeeney S, Baric RS, Katze MG, Waters KM

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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ

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Paramedic assessment and treatment of upper airway obstruction in pediatric patients: an exploratory analysis by the Children's Safety Initiative-Emergency Medical Services.

Hansen M, Meckler G, Lambert W, Dickinson C, Dickinson K, Guise JM

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Emergency Medical Services Provider Pediatric Adverse Event Rate Varies by Call Origin Pediatric Emergency Care.

Jones D, Hansen M, Van Otterloo J, Dickinson C, Guise JM

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American Gastroenterological Association Institute Technical Review on the Management of Crohn's Disease After Surgical Resection.

Regueiro M, Velayos F, Greer JB, Bougatsos C, Chou R, Sultan S, Singh S

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Statins for Prevention of Cardiovascular Disease in Adults: Evidence Report and Systematic Review for the US Preventive Services Task Force.

Chou R, Dana T, Blazina I, Daeges M, Jeanne TL

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Patient safety events in out-of-hospital paediatric airway management: a medical record review by the CSI-EMS.

Hansen M, Meckler G, Lambert W, Dickinson C, Dickinson K, Van Otterloo J, Guise JM

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Intravesical Therapy for the Treatment of Nonmuscle Invasive Bladder Cancer: A Systematic Review and Meta-Analysis.

Chou R, Selph S, Buckley DI, Fu R, Griffin JC, Grusing S, Gore JL

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Primary Care-Based Models for the Treatment of Opioid Use Disorder: A Scoping Review

Korthuis PT, McCarty D, Weimer M, Bougatsos C, Blazina I, Zakher B, Grusing S, Devine B, Chou R

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Statins for Prevention of Cardiovascular Disease in Adults: Evidence Report and Systematic Review for the US Preventive Services Task Force.

Chou R, Dana T, Blazina I, Daeges M, Jeanne TL

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Management of Postoperative Pain: A Clinical Practice Guideline From the American Pain Society, the American Society of Regional Anesthesia and Pain Medicine, and the American Society of Anesthesiologists' Committee on Regional Anesthesia, Executive Committee, and Administrative Council.

Chou R, Gordon DB, de Leon-Casasola OA, Rosenberg JM, Bickler S, Brennan T, Carter T, Cassidy CL, Chittenden EH, Degenhardt E, Griffith S, Manworren R, McCarberg B, Montgomery R, Murphy J, Perkal MF, Suresh S, Sluka K, Strassels S, Thirlby R, Viscusi E, Walco GA, Warner L, Weisman SJ, Wu CL

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Research Gaps in Practice Guidelines for Acute Postoperative Pain Management in Adults: Findings From a Review of the Evidence for an American Pain Society Clinical Practice Guideline.

Gordon DB, de Leon-Casasola OA, Wu CL, Sluka KA, Brennan TJ, Chou R.

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The Association Between Hospital Capacity Strain and Inpatient Outcomes in Highly Developed Countries: A Systematic Review.

Eriksson CO, Stoner RC, Eden KB, Newgard CD, Guise JM

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Vaginal birth after cesarean: neonatal outcomes and United States birth setting.

Tilden EL, Cheyney M, Guise JM, Emeis C, Lapidus J, Biel FM, Wiedrick J, Snowden JM.

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REST corepressors RCOR1 and RCOR2 and the repressor INSM1 regulate the proliferation-differentiation balance in the developing brain.

Monaghan CE, Nechiporuk T, Jeng S, McWeeney SK, Wang J, Rosenfeld MG, Mandel G

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Effects of selection for ethanol preference on gene expression in the nucleus accumbens of HS-CC mice.

Colville AM, Iancu OD, Oberbeck DL, Darakjian P, Zheng CL, Walter NA, Harrington CA, Searles RP, McWeeney S, Hitzemann RJ

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A MicroRNA Screen Identifies the Wnt Signaling Pathway as a Regulator of the Interferon Response during Flavivirus Infection.

Smith JL, Jeng S, McWeeney SK, Hirsch AJ

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Does Articaine Provide an Advantage over Lidocaine in Patients with Symptomatic Irreversible Pulpitis? A Systematic Review and Meta-analysis.

Kung J, McDonagh M, Sedgley CM

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Bioinformatics and Computational Biology

HitWalker2: visual analytics for precision medicine and beyond.

Bottomly D, McWeeney SK, Wilmot B

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Identification and Characterization of Tyrosine Kinase Nonreceptor 2 Mutations in Leukemia through Integration of Kinase Inhibitor Screening and Genomic Analysis.

Maxson JE, Abel ML, Wang J, Deng X, Reckel S, Luty SB, Sun H, Gorenstein J, Hughes SB, Bottomly D, Wilmot B, McWeeney SK, Radich J, Hantschel O, Middleton RE, Gray NS, Druker BJ, Tyner JW.

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Splicing landscape of the eight collaborative cross founder strains.

Zheng CL, Wilmot B, Walter NA, Oberbeck D, Kawane S, Searles RP, McWeeney SK, Hitzemann R

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Research Gaps in Practice Guidelines for Acute Postoperative Pain Management in Adults: Findings From a Review of the Evidence for an American Pain Society Clinical Practice Guideline.

Gordon DB, de Leon-Casasola OA, Wu CL, Sluka KA, Brennan TJ, Chou R

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Influenza vaccination of pregnant women: attitudes and behaviors of Oregon physician prenatal care providers.

Arao RF, Rosenberg KD, McWeeney S, Hedberg K.

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Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.

Ochs C, Perl Y, Geller J, Haendel M, Brush M, Arabandi S, Tu S.; J Biomed Inform. 2015 Jun 3.
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Clinical interpretation of CNVs with cross-species phenotype data.

Khler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA, Robinson PN. J Med Genet. 2014 Nov;
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Screening and routine supplementation for iron deficiency anemia: a systematic review.

McDonagh MS, Blazina I, Dana T, Cantor A, Bougatsos C. , Pediatrics. 2015 Apr;
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Therapeutically Targetable ALK Mutations in Leukemia.

Maxson JE, Davare MA, Luty SB, Eide CA, Chang BH, Loriaux MM, Tognon CE, Bottomly D, Wilmot B, McWeeney SK, Druker BJ, Tyner JW., Cancer Res. 2015 Jun 1;
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Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations.

Iancu OD, Colville A, Oberbeck D, Darakjian P, McWeeney SK, Hitzemann R. , Front Genet. 2015 May 13;
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Gene set analysis: A step-by-step guide.

Mooney MA, Wilmot B., Am J Med Genet B Neuropsychiatr Genet. 2015 Jun 8.
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Digitized whole slides for breast pathology interpretation: current practices and perceptions.

Onega T, Weaver D, Geller B, Oster N, Tosteson AN, Carney PA, Nelson H, Allison KH, O'Malley FP, Schnitt SJ, Elmore JG. J Digit Imaging. 2014 Oct;
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Gene set analysis: A step-by-step guide.

Mooney MA, Wilmot B. Am J Med Genet B, Neuropsychiatr Genet. 2015 Jun 8.
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The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Groza T, Kˆhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. Am J Hum Genet. 2015 June 25;
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Disease insights through cross-species phenotype comparisons.

Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Kˆhler S, Lewis SE, Robinson PN, Smedley D. Mamm Genome. 2015 Jun 20.
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Cytomegalovirus miRNAs target secretory pathway genes to facilitate formation of the virion assembly compartment and reduce cytokine secretion.

Hook LM, Grey F, Grabski R, Tirabassi R, Doyle T, Hancock M, Landais I, Jeng S, McWeeney S, Britt W, Nelson JA., Cell Host Microbe, 2014 Mar 12
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Challenges in secondary analysis of high throughput screening data

Blucher AS, McWeeney SK. Pac Symp Biocomput. 2014:114-24.
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The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology

Thacker RW, Daz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ. J Biomed Semantics. 2014 Sep 8;5(1):39. doi: 10.1186/2041-1480-5-39
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Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

Zemojtel T, Khler S, Mackenroth L, Jger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krger U, Frommer G, Fischer B, Kornak U, Flttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN. Sci Transl Med. 2014 Sep 3;6(252):252ra123
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Functional and genomic context in pathway analysis of GWAS data

Mooney MA, Nigg JT, McWeeney SK, Wilmot B. Trends Genet. 2014 Aug 22. pii: S0168-9525(14)00116-4. doi: 10.1016/j.tig.2014.07.004.
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Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology

Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. J Biomed Semantics. 2014 Aug 11;5:34. doi: 10.1186/2041-1480-5-34
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A framework for evaluating diagnostic discordance in pathology discovered during research studies.

Feng S, Weaver DL, Carney PA, M Reisch L, M Geller B, Goodwin A, Rendi MH, Onega T, Allison KH, Tosteson AN, Nelson HD, Longton G, Pepe M, Elmore JG.
Arch Pathol Lab Med. 2014 Jul;
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Influenza Vaccination of Pregnant Women: Attitudes and Behaviors of Oregon Physician Prenatal Care Providers

Arao RF, Rosenberg KD, McWeeney S, Hedberg K. Matern Child Health J. 2014 Jul 18
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A proposed approach may help systematic reviews retain needed expertise while minimizing bias from nonfinancial conflicts of interest.

Viswanathan M, Carey TS, Belinson SE, Berliner E, Chang SM, Graham E, Guise JM, Ip S, Maglione MA, McCrory DC, McPheeters M, Newberry SJ, Sista P, White CM. J Clin Epidemiol. 2014 Jul 9. pii: S0895-4356(14)00211-X. doi: 10.1016/j.jclinepi.2014.02.023.
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PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases.

Use of model organism and disease databases to support matchmaking for human disease gene discovery.

Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA.
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Does Articaine Provide an Advantage over Lidocaine in Patients with Symptomatic Irreversible Pulpitis? A Systematic Review and Meta-analysis.

Kung J, McDonagh M, Sedgley CM
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Effect of Laparoscopic-Assisted Resection vs Open Resection of Stage II or III Rectal Cancer on Pathologic Outcomes: The ACOSOG Z6051 Randomized Clinical Trial.

Fleshman J, Branda M, Sargent DJ, Boller AM, George V, Abbas M, Peters WR Jr, Maun D, Chang G, Herline A9, Fichera A, Mutch M, Wexner S, Whiteford M, Marks J, Birnbaum E, Margolin D, Larson D, Marcello P16, Posner M, Read T, Monson J, Wren SM, Pisters PW, Nelson H
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Mammography Screening and Overdiagnosis.

Nelson HD
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Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.

Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D
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Use of Digital Whole Slide Imaging in Dermatopathology.

Onega T, Reisch LM, Frederick PD, Geller BM, Nelson HD, Lott JP, Radick AC, Elder DE, Barnhill RL Piepkorn MW, Elmore JG
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How concerns and experiences with medical malpractice affect dermatopathologists' perceptions of their diagnostic practices when interpreting cutaneous melanocytic lesions.

Carney PA, Frederick PD, Reisch LM, Knezevich S, Piepkorn MW, Barnhill RL, Elder DE, Geller BM, Titus L, Weinstock MA, Nelson HD, Elmore JG
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Medical malpractice concerns and defensive medicine: a nationwide survey of breast pathologists.

Reisch LM, Carney PA, Oster NV, Weaver DL, Nelson HD, Frederick PD, Elmore JG
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Reproducibility and conflicts in immune epitope data.

Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B

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Sequestrectomy Versus Conventional Microdiscectomy for the Treatment of a Lumbar Disc Herniation: A Systematic Review.

Azarhomayoun A, Chou R, Shirdel S, Lakeh MM, Vaccaro AR, Rahimi-Movaghar V

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Out-of-hospital pediatric airway management in the United States.

Hansen M, Lambert W, Guise JM, Warden CR, Mann NC, Wang H

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Paramedic assessment and treatment of upper airway obstruction in pediatric patients: an exploratory analysis by the Children's Safety Initiative-Emergency Medical Services.

Hansen M, Meckler G, Lambert W, Dickinson C, Dickinson K, Guise JM

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Intranasal or transdermal nicotine for the treatment of postoperative pain.

Matthews AM, Fu R, Dana T, Chou R

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Treatment of muscle-invasive bladder cancer: A systematic review.

Chou R, Selph SS, Buckley DI, Gustafson KS, Griffin JC, Grusing SE, Gore JL

Screening for Impaired Visual Acuity in Older Adults: Updated Evidence Report and Systematic Review for the US Preventive Services Task Force.

Chou R, Dana T, Bougatsos C, Grusing S, Blazina I.

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Understanding the value of mixed methods research: the Children's Safety Initiative-Emergency Medical Services.

Hansen M, O'Brien K, Meckler G, Chang AM, Guise JM

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Patient Safety Perceptions in Pediatric Out-of-Hospital Emergency Care: Children's Safety Initiative.

Guise JM, Meckler G, O'Brien K, Curry M, Engle P, Dickinson C, Dickinson K, Hansen M, Lambert W

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Impact of simulation and team training on postpartum hemorrhage management in non-academic centers.

Marshall NE, Vanderhoeven J, Eden KB, Segel SY, Guise JM.

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Next-generation diagnostics and disease-gene discovery with the Exomiser.

Smedley D, Jacobsen JO, Jäger M, Köhler S2 Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN

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Advancing knowledge of rapid reviews: an analysis of results, conclusions and recommendations from published review articles examining rapid reviews.

Featherstone RM, Dryden DM, Foisy M, Guise JM, Mitchell MD, Paynter RA, Robinson KA, Umscheid CA, Hartling L

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Human Cytomegalovirus miR-UL112-3p Targets TLR2 and Modulates the TLR2/IRAK1/NFκB Signaling Pathway.

Landais I, Pelton C, Streblow D, DeFilippis V, McWeeney S, Nelson JA

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Expert Diagnosis of Plus Disease in Retinopathy of Prematurity From Computer-Based Image Analysis.

Campbell JP, Ataer-Cansizoglu E, Bolon-Canedo V, Bozkurt A, Erdogmus D, Kalpathy-Cramer J, Patel SN, Reynolds JD, Horowitz J, Hutcheson K, Shapiro M, Repka MX, Ferrone P, Drenser K, Martinez-Castellanos MA, Ostmo S, Jonas K, Chan RV, Chiang MF; Imaging and Informatics in ROP (i-ROP) Research Consortium

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Treatment of muscle-invasive bladder cancer: A systematic review.

Chou R, Selph SS, Buckley DI, Gustafson KS, Griffin JC, Grusing SE, Gore JL

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Emergency Medical Services Provider Pediatric Adverse Event Rate Varies by Call Origin Pediatric Emergency Care.

Jones D, Hansen M, Van Otterloo J, Dickinson C, Guise JM

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Paramedic assessment and treatment of upper airway obstruction in pediatric patients: an exploratory analysis by the Children's Safety Initiative-Emergency Medical Services.

Hansen M, Meckler G, Lambert W, Dickinson C, Dickinson K, Guise JM

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Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H, Mabee PM, Muller HM, Mungall CJ, Sternberg PW, Van Auken K, Vinyard CJ, Williams SH, Wall CE

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A Systematic Review of PCSK9 Inhibitors Alirocumab and Evolocumab.

McDonagh M, Peterson K, Holzhammer B, Fazio S

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Use of semantic workflows to enhance transparency and reproducibility in clinical omics.

Zheng CL, Ratnakar V, Gil Y, McWeeney SK

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How concerns and experiences with medical malpractice affect dermatopathologists' perceptions of their diagnostic practices when interpreting cutaneous melanocytic lesions.

Carney PA, Frederick PD, Reisch LM, Knezevich S, Piepkorn MW, Barnhill RL, Elder DE, Geller BM, Titus L, Weinstock MA, Nelson HD, Elmore JG

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Mammography Decision Aid Reduces Decisional Conflict for Women in Their Forties Considering Screening.

Eden KB, Scariati P, Klein K, Watson L, Remiker M, Hribar M, Forro V, Michaels L, Nelson HD

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Gene set analysis: A step-by-step guide.

Mooney MA, Wilmot B

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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ

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Reproducibility and conflicts in immune epitope data.

Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B

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Disease insights through cross-species phenotype comparisons.

Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D

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A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Smedley D, Schubach M, Jacobsen JO, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall CJ, Lewis SE, Groza T, Valentini G, Robinson PN

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Navigating the Phenotype Frontier: The Monarch Initiative.

McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA

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Treatment of muscle-invasive bladder cancer: A systematic review.

Chou R, Selph SS, Buckley DI, Gustafson KS, Griffin JC, Grusing SE, Gore JL

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The influence of tumor regression, solar elastosis, and patient age on pathologists' interpretation of melanocytic skin lesions.

Titus L, Barnhill RL, Lott JP, Piepkorn MW, Elder DE, Frederick PD, Nelson HD, Carney PA, Knezevich SR, Weinstock MA, Elmore JG

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The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA

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Bayesian Network Inference Modeling Identifies TRIB1 as a Novel Regulator of Cell-Cycle Progression and Survival in Cancer Cells.

Gendelman R, Xing H, Mirzoeva OK, Sarde P, Curtis C, Feiler HS, McDonagh P, Gray JW, Khalil I, Korn WM

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Clinical Epidemiology

Mammography Screening in a Large Health System Following the U.S. Preventive Services Task Force Recommendations and the Affordable Care Act.

Nelson HD, Weerasinghe R, Wang L, Grunkemeier G., PLoS One. 2015 Jun 29;
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Fully Automated Assessment of the Severity of Parkinson's Disease from Speech.

Bayestehtashk A, Asgari M, Shafran I, McNames J., Comput Speech Lang. 2015 Jan
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Kreuzschmerzen in der Primärversorgung

Deyo RA, Jarvik JG, Chou R. Praxis (Bern 1994). 2014 Nov 1
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Focus Article Report of the NIH Task Force on Research Standards for Chronic Low Back Pain.

Deyo RA, Dworkin SF, Amtmann D, Andersson G, Borenstein D, Carragee E, Carrino J, Chou R, Cook K, DeLitto A, Goertz C, Khalsa P, Loeser J, Mackey S, Panagis J, Rainville J, Tosteson T, Turk D, Von Korff M, Weiner DK. Clin J Pain. 2014 Aug;
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Influenza Vaccination of Pregnant Women: Attitudes and Behaviors of Oregon Physician Prenatal Care Providers

Arao RF, Rosenberg KD, McWeeney S, Hedberg K. Matern Child Health J. 2014 Jul 18
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A proposed approach may help systematic reviews retain needed expertise while minimizing bias from nonfinancial conflicts of interest.

Viswanathan M, Carey TS, Belinson SE, Berliner E, Chang SM, Graham E, Guise JM, Ip S, Maglione MA, McCrory DC, McPheeters M, Newberry SJ, Sista P, White CM. J Clin Epidemiol. 2014 Jul 9. pii: S0895-4356(14)00211-X. doi: 10.1016/j.jclinepi.2014.02.023.
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Patient Safety Perceptions in Pediatric Out-of-Hospital Emergency Care: Children's Safety Initiative.

Guise JM, Meckler G, O'Brien K, Curry M, Engle P, Dickinson C, Dickinson K, Hansen M, Lambert W
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Comparative risk of harm associated with the use of targeted immunomodulators- A systematic review.

Desai RJ, Thaler KJ, Mahlknecht P, Gartlehner G, McDonagh MS, Mesgarpour B, Mazinanian A, Glechner A, Gopalakrishnan C, Hansen RA

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Paramedic assessment and treatment of upper airway obstruction in pediatric patients: an exploratory analysis by the Children's Safety Initiative-Emergency Medical Services.

Hansen M, Meckler G, Lambert W, Dickinson C, Dickinson K, Guise JM

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Out-of-hospital pediatric airway management in the United States.

Hansen M, Lambert W, Guise JM, Warden CR, Mann NC, Wang H

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Pathway analysis in attention deficit hyperactivity disorder: An ensemble approach.

Mooney MA, McWeeney SK, Faraone SV, Hinney A, Hebebrand J; IMAGE2 Consortium; German ADHD GWAS Group, Nigg JT, Wilmot B

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The Influence of Disease Severity of Preceding Clinical Cases on Pathologists' Medical Decision Making.

Frederick PD, Nelson HD, Carney PA, Brunyé TT, Allison KH, Weaver DL, Elmore JG

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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ

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Disease insights through cross-species phenotype comparisons.

Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D

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Consequences of Increasing Time to Colonoscopy Examination After Positive Result From Fecal Colorectal Cancer Screening Test.

Meester RG, Zauber AG, Doubeni CA, Jensen CD, Quinn VP, Helfand M, Dominitz JA, Levin TR, Corley DA, Lansdorp-Vogelaar I

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Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease.

Mulder N, Nembaware V, Adekile A, Anie KA, Inusa B, Brown B, Campbell A, Chinenere F, Chunda-Liyoka C, Derebail VK, Geard A, Ghedira K, Hamilton CM, Hanchard NA, Haendel M, Huggins W, Ibrahim M, Jupp S, Kamga KK, Knight-Madden J, Lopez-Sall P, Mbiyavanga M, Munube D, Nirenberg D, Nnodu O, Ofori-Acquah SF, Ohene-Frempong K, Opap KB, Panji S, Park M, Pule G, Royal C, Sangeda R, Tayo B, Treadwell M, Tshilolo L, Wonkam A

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Identification and Characterization of Tyrosine Kinase Nonreceptor 2 Mutations in Leukemia through Integration of Kinase Inhibitor Screening and Genomic Analysis.

Maxson JE, Abel ML, Wang J, Deng X, Reckel S, Luty SB, Sun H, Gorenstein J, Hughes SB, Bottomly D, Wilmot B, McWeeney SK, Radich J, Hantschel O, Middleton RE, Gray NS, Druker BJ, Tyner JW

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Evaluation of 12 strategies for obtaining second opinions to improve interpretation of breast histopathology: simulation study.

Elmore JG, Tosteson AN, Pepe MS, Longton GM, Nelson HD, Geller B, Carney PA, Onega T, Allison KH, Jackson SL, Weaver DL

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Screening for Syphilis: Updated Evidence Report and Systematic Review for the US Preventive Services Task Force.

Cantor AG, Pappas M, Daeges M, Nelson HD

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Mammography Screening and Overdiagnosis.

Nelson HD

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Consequences of Increasing Time to Colonoscopy Examination After Positive Result From Fecal Colorectal Cancer Screening Test.

Meester RG, Zauber AG, Doubeni CA, Jensen CD, Quinn VP, Helfand M, Dominitz JA, Levin TR, Corley DA, Lansdorp-Vogelaar I

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Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H, Mabee PM, Muller HM, Mungall CJ, Sternberg PW, Van Auken K, Vinyard CJ, Williams SH, Wall CE

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Nitrofurantoin vs other prophylactic agents in reducing recurrent urinary tract infections in adult women: a systematic review and meta-analysis.

Price JR, Guran LA, Gregory WT, McDonagh MS

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Does the Urinary Microbiome Play a Role in Urgency Urinary Incontinence and Its Severity?

Karstens L, Asquith M, Davin S, Stauffer P, Fair D, Gregory WT, Rosenbaum JT, McWeeney SK, Nardos R

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The health care and life sciences community profile for dataset descriptions.

Dumontier M, Gray AJ, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A

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Drivers of maternity care in high-income countries: can health systems support woman-centred care?

Shaw D, Guise JM, Shah N, Gemzell-Danielsson K, Joseph KS, Levy B, Wong F, Woodd S, Main EK

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Sequestrectomy Versus Conventional Microdiscectomy for the Treatment of a Lumbar Disc Herniation: A Systematic Review.

Azarhomayoun A, Chou R, Shirdel S, Lakeh MM, Vaccaro AR, Rahimi-Movaghar V.

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Interventions to optimise the care continuum for chronic viral hepatitis: a systematic review and meta-analyses.

Zhou K, Fitzpatrick T, Walsh N, Kim JY, Chou R, Lackey M, Scott J, Lo YR, Tucker JD

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Long-acting opioids for chronic noncancer pain were linked to mortality.

Chou R

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Consequences of Increasing Time to Colonoscopy Examination After Positive Result From Fecal Colorectal Cancer Screening Test.

Meester RG, Zauber AG, Doubeni CA, Jensen CD, Quinn VP, Helfand M, Dominitz JA, Levin TR, Corley DA, Lansdorp-Vogelaar I

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Diagnostic Reproducibility: What Happens When the Same Pathologist Interprets the Same Breast Biopsy Specimen at Two Points in Time?

Jackson SL, Frederick PD, Pepe MS, Nelson HD, Weaver DL, Allison KH, Carney PA, Geller BM, Tosteson AN, Onega T, Elmore JG

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The Human Phenotype Ontology in 2017.

Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN

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Predictive Utility of the Total Glasgow Coma Scale Versus the Motor Component of the Glasgow Coma Scale for Identification of Patients With Serious Traumatic Injuries.

Chou R, Totten AM, Carney N, Dandy S, Fu R, Grusing S, Pappas M, Wasson N, Newgard CD

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Health Information Management

Electronic health record impact on productivity and efficiency in an academic pediatric ophthalmology practice.

Redd TK, Read-Brown S, Choi D, Yackel TR, Tu DC, Chiang MF. J AAPOS. 2014 Dec;
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The Resource Identification Initiative: A Cultural Shift in Publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N

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Outcomes From Health Information Exchange: Systematic Review and Future Research Needs.

Hersh WR, Totten AM, Eden KB, Devine B, Gorman P, Kassakian SZ, Woods SS, Daeges M, Pappas M, McDonagh MS.

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Reproducibility and conflicts in immune epitope data.

Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B

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The Matchmaker Exchange: a platform for rare disease gene discovery.

Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME2, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL

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Use of model organism and disease databases to support matchmaking for human disease gene discovery.

Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA

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PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases.

Buske OJ, Girdea M, Dumitriu S, Gallinger B, Hartley T, Trang H, Misyura A, Friedman T, Beaulieu C, Bone WP, Links AE, Washington NL, Haendel MA, Robinson PN, Boerkoel CF, Adams D, Gahl WA, Boycott KM, Brudno M

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Implementation of Recovery Programming on an Inpatient Acute Psychiatric Unit and Its Impact on Readmission.

Koval RD, Mcdonagh J, Grubaugh A, Young W, Corcoran B, Lee A, Dumas B, Edlund B.

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The Resource Identification Initiative: A Cultural Shift in Publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N

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User survey finds rapid evidence reviews increased uptake of evidence by Veterans Health Administration leadership to inform fast-paced health-system decision-making.

Peterson K, Floyd N, Ferguson L, Christensen V, Helfand M

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Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H Mabee PM, Muller HM, Mungall CJ, Sternberg PW, Van Auken K, Vinyard CJ, Williams SH, Wall CE

Read the Article

Disease insights through cross-species phenotype comparisons.

Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D

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Reproducibility and conflicts in immune epitope data.

Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B

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Barriers and facilitators to exchanging health information: a systematic review.

Eden KB, Totten AM, Kassakian SZ, Gorman PN, McDonagh MS, Devine B, Pappas M, Daeges M, Woods S, Hersh WR

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Understanding the value of mixed methods research: the Children's Safety Initiative-Emergency Medical Services.

Hansen M, O'Brien K, Meckler G, Chang AM, Guise JM

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