Keyword Connections

•  Joshua Denny

•  Stephen Camarata

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Publications

• Automated identification of postoperative complications within an electronic medical record using natural language processing.
  Murff HJ, FitzHenry F, Matheny ME, Gentry N, Kotter KL, Crimin K, Dittus RS, Rosen AK, Elkin PL, Brown SH, Speroff T
  (2011) JAMA 306: 848-55
• A scheme for assessing measurement sensitivity in program evaluation and other applied research.
  Lipsey MW
  (1983) Psychol Bull 94: 152-65
• Programming biological models in Python using PySB.
  Lopez CF, Muhlich JL, Bachman JA, Sorger PK
  (2013) Mol Syst Biol 9: 646
• TM4SF20 ancestral deletion and susceptibility to a pediatric disorder of early language delay and cerebral white matter hyperintensities.
  Wiszniewski W, Hunter JV, Hanchard NA, Willer JR, Shaw C, Tian Q, Illner A, Wang X, Cheung SW, Patel A, Campbell IM, Gelowani V, Hixson P, Ester AR, Azamian MS, Potocki L, Zapata G, Hernandez PP, Ramocki MB, Santos-Cortez RL, Wang G, York MK, Justice MJ, Chu ZD, Bader PI, Omo-Griffith L, Madduri NS, Scharer G, Crawford HP, Yanatatsaneejit P, Eifert A, Kerr J, Bacino CA, Franklin AI, Goin-Kochel RP, Simpson G, Immken L, Haque ME, Stosic M, Williams MD, Morgan TM, Pruthi S, Omary R, Boyadjiev SA, Win KK, Thida A, Hurles M, Hibberd ML, Khor CC, Van Vinh Chau N, Gallagher TE, Mutirangura A, Stankiewicz P, Beaudet AL, Maletic-Savatic M, Rosenfeld JA, Shaffer LG, Davis EE, Belmont JW, Dunstan S, Simmons CP, Bonnen PE, Leal SM, Katsanis N, Lupski JR, Lalani SR
  (2013) Am J Hum Genet 93: 197-210
• Functional disruption in the organization of the brain for reading in dyslexia.
  Shaywitz SE, Shaywitz BA, Pugh KR, Fulbright RK, Constable RT, Mencl WE, Shankweiler DP, Liberman AM, Skudlarski P, Fletcher JM, Katz L, Marchione KE, Lacadie C, Gatenby C, Gore JC
  (1998) Proc Natl Acad Sci U S A 95: 2636-41
• The perceptual reality of synesthetic colors.
  Palmeri TJ, Blake R, Marois R, Flanery MA, Whetsell W
  (2002) Proc Natl Acad Sci U S A 99: 4127-31
• Dyslexia: bridging the gap between hearing and reading.
  Wallace MT
  (2009) Curr Biol 19: R260-2
• Neural systems for compensation and persistence: young adult outcome of childhood reading disability.
  Shaywitz SE, Shaywitz BA, Fulbright RK, Skudlarski P, Mencl WE, Constable RT, Pugh KR, Holahan JM, Marchione KE, Fletcher JM, Lyon GR, Gore JC
  (2003) Biol Psychiatry 54: 25-33
• Subcortical vascular dementia: integrating neuropsychological and neuroradiologic data.
  Price CC, Jefferson AL, Merino JG, Heilman KM, Libon DJ
  (2005) Neurology 65: 376-82
• Individual common variants exert weak effects on the risk for autism spectrum disorders.
  Anney R, Klei L, Pinto D, Almeida J, Bacchelli E, Baird G, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Casey J, Conroy J, Correia C, Corsello C, Crawford EL, de Jonge M, Delorme R, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Gilbert J, Gillberg C, Glessner JT, Green A, Green J, Guter SJ, Heron EA, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Jacob S, Kenny GP, Kim C, Kolevzon A, Kustanovich V, Lajonchere CM, Lamb JA, Law-Smith M, Leboyer M, Le Couteur A, Leventhal BL, Liu XQ, Lombard F, Lord C, Lotspeich L, Lund SC, Magalhaes TR, Mantoulan C, McDougle CJ, Melhem NM, Merikangas A, Minshew NJ, Mirza GK, Munson J, Noakes C, Nygren G, Papanikolaou K, Pagnamenta AT, Parrini B, Paton T, Pickles A, Posey DJ, Poustka F, Ragoussis J, Regan R, Roberts W, Roeder K, Roge B, Rutter ML, Schlitt S, Shah N, Sheffield VC, Soorya L, Sousa I, Stoppioni V, Sykes N, Tancredi R, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Vorstman JA, Wallace S, Wing K, Wittemeyer K, Wood S, Zurawiecki D, Zwaigenbaum L, Bailey AJ, Battaglia A, Cantor RM, Coon H, Cuccaro ML, Dawson G, Ennis S, Freitag CM, Geschwind DH, Haines JL, Klauck SM, McMahon WM, Maestrini E, Miller J, Monaco AP, Nelson SF, Nurnberger JI, Oliveira G, Parr JR, Pericak-Vance MA, Piven J, Schellenberg GD, Scherer SW, Vicente AM, Wassink TH, Wijsman EM, Betancur C, Buxbaum JD, Cook EH, Gallagher L, Gill M, Hallmayer J, Paterson AD, Sutcliffe JS, Szatmari P, Vieland VJ, Hakonarson H, Devlin B
  (2012) Hum Mol Genet 21: 4781-92
• Simultaneous event-related potential and near-infrared spectroscopic studies of semantic processing.
  Horovitz SG, Gore JC
  (2004) Hum Brain Mapp 22: 110-5
• An adaptive semantic matching paradigm for reliable and valid language mapping in individuals with aphasia.
  Wilson SM, Yen M, Eriksson DK
  (2018) Hum Brain Mapp 39: 3285-3307
• An event-related functional MRI study of the stroop color word interference task.
  Leung HC, Skudlarski P, Gatenby JC, Peterson BS, Gore JC
  (2000) Cereb Cortex 10: 552-60
• The functional neural architecture of components of attention in language-processing tasks.
  Shaywitz BA, Shaywitz SE, Pugh KR, Fulbright RK, Skudlarski P, Mencl WE, Constable RT, Marchione KE, Fletcher JM, Klorman R, Lacadie C, Gore JC
  (2001) Neuroimage 13: 601-12
• Adaptive paradigms for mapping phonological regions in individual participants.
  Yen M, DeMarco AT, Wilson SM
  (2019) Neuroimage 189: 368-379
• White matter microstructural differences linked to left perisylvian language network in children with dyslexia.
  Rimrodt SL, Peterson DJ, Denckla MB, Kaufmann WE, Cutting LE
  (2010) Cortex 46: 739-49
• Disorders of speech and language: aphasia, apraxia and dysarthria.
  Jordan LC, Hillis AE
  (2006) Curr Opin Neurol 19: 580-5
• edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
  Robinson MD, McCarthy DJ, Smyth GK
  (2010) Bioinformatics 26: 139-40
• GEL: a novel genotype calling algorithm using empirical likelihood.
  Nicolae DL, Wu X, Miyake K, Cox NJ
  (2006) Bioinformatics 22: 1942-7
• Increased healthcare resource utilization for acute respiratory illness among Latino infants.
  Valet RS, Gebretsadik T, Carroll KN, Minton PA, Woodward KB, Liu Z, Hayes R, Hartert TV
  (2013) J Pediatr 163: 1186-91
• Letter processing in the visual system: different activation patterns for single letters and strings.
  James KH, James TW, Jobard G, Wong AC, Gauthier I
  (2005) Cogn Affect Behav Neurosci 5: 452-66
• An early electrophysiological response associated with expertise in letter perception.
  Wong AC, Gauthier I, Woroch B, DeBuse C, Curran T
  (2005) Cogn Affect Behav Neurosci 5: 306-18
• Identifying lupus patients in electronic health records: Development and validation of machine learning algorithms and application of rule-based algorithms.
  Jorge A, Castro VM, Barnado A, Gainer V, Hong C, Cai T, Cai T, Carroll R, Denny JC, Crofford L, Costenbader KH, Liao KP, Karlson EW, Feldman CH
  (2019) Semin Arthritis Rheum 49: 84-90
• Multivariate Approaches to Understanding Aphasia and its Neural Substrates.
  Wilson SM, Hula WD
  (2019) Curr Neurol Neurosci Rep 19: 53
• Comprehensive knowledge of HIV among women in rural Mozambique: development and validation of the HIV knowledge 27 scale.
  Ciampa PJ, Skinner SL, Patricio SR, Rothman RL, Vermund SH, Audet CM
  (2012) PLoS One 7: e48676
• A quick aphasia battery for efficient, reliable, and multidimensional assessment of language function.
  Wilson SM, Eriksson DK, Schneck SM, Lucanie JM
  (2018) PLoS One 13: e0192773
• Integrating functional and diffusion magnetic resonance imaging for analysis of structure-function relationship in the human language network.
  Morgan VL, Mishra A, Newton AT, Gore JC, Ding Z
  (2009) PLoS One 4: e6660
• RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite.
  Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D
  (2011) PLoS One 6: e20161
• Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences.
  Fan JW, Yang EW, Jiang M, Prasad R, Loomis RM, Zisook DS, Denny JC, Xu H, Huang Y
  (2013) J Am Med Inform Assoc 20: 1168-77
• Development and evaluation of an ensemble resource linking medications to their indications.
  Wei WQ, Cronin RM, Xu H, Lasko TA, Bastarache L, Denny JC
  (2013) J Am Med Inform Assoc 20: 954-61
• Automated extraction of clinical traits of multiple sclerosis in electronic medical records.
  Davis MF, Sriram S, Bush WS, Denny JC, Haines JL
  (2013) J Am Med Inform Assoc 20: e334-40
• Hiding in plain sight: use of realistic surrogates to reduce exposure of protected health information in clinical text.
  Carrell D, Malin B, Aberdeen J, Bayer S, Clark C, Wellner B, Hirschman L
  (2013) J Am Med Inform Assoc 20: 342-8
• "Understanding" medical school curriculum content using KnowledgeMap.
  Denny JC, Smithers JD, Miller RA, Spickard A
  (2003) J Am Med Inform Assoc 10: 351-62
• Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin.
  Xu H, Jiang M, Oetjens M, Bowton EA, Ramirez AH, Jeff JM, Basford MA, Pulley JM, Cowan JD, Wang X, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC
  (2011) J Am Med Inform Assoc 18: 387-91
• Assisted annotation of medical free text using RapTAT.
  Gobbel GT, Garvin J, Reeves R, Cronin RM, Heavirland J, Williams J, Weaver A, Jayaramaraja S, Giuse D, Speroff T, Brown SH, Xu H, Matheny ME
  (2014) J Am Med Inform Assoc 21: 833-41
• A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries.
  Jiang M, Chen Y, Liu M, Rosenbloom ST, Mani S, Denny JC, Xu H
  (2011) J Am Med Inform Assoc 18: 601-6
• MedEx: a medication information extraction system for clinical narratives.
  Xu H, Stenner SP, Doan S, Johnson KB, Waitman LR, Denny JC
  (2010) J Am Med Inform Assoc 17: 19-24
• Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality.
  Xu H, Aldrich MC, Chen Q, Liu H, Peterson NB, Dai Q, Levy M, Shah A, Han X, Ruan X, Jiang M, Li Y, Julien JS, Warner J, Friedman C, Roden DM, Denny JC
  (2015) J Am Med Inform Assoc 22: 179-91
• Integrating existing natural language processing tools for medication extraction from discharge summaries.
  Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H
  (2010) J Am Med Inform Assoc 17: 528-31