Publications
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Clinical assessment incorporating a personal genome.
Ashley EA,
Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB.
Lancet.
2010;
375
(9725):
1525-35
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Likelihood ratios for genome medicine.
Morgan AA,
Chen R, Butte AJ.
Genome Med.
2010;
2
(5):
30
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Proline: the distribution, frequency, positioning, and common functional roles of proline and polyproline sequences in the human proteome.
Morgan AA,
Rubenstein E.
PLoS One.
2013;
8
(1):
e53785
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Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction.
Morgan AA,
Pyrgos VJ, Nadeau KC, Williamson PR, Butte AJ.
J Am Med Inform Assoc.
2012 Mar-Apr;
19
(2):
284-8
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Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays.
Morgan AA,
Chen R, Butte AJ.
J Am Med Inform Assoc.
2012;
19
(e1):
e21-7
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Coanalysis of GWAS with eQTLs reveals disease-tissue associations.
Kang HP,
Morgan AA, Chen R, Schadt EE, Butte AJ.
AMIA Summits Transl Sci Proc.
2012:
2012
35-41
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Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes.
Kodama K,
Horikoshi M, Toda K, Yamada S, Hara K, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ.
Proc Natl Acad Sci U S A.
2012;
109
(18):
7049-54
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FoxO6 regulates memory consolidation and synaptic function.
Salih DA,
Rashid AJ, Colas D, de la Torre-Ubieta L, Zhu RP, Morgan AA, Santo EE, Ucar D, Devarajan K, Cole CJ, Madison DV, Shamloo M, Butte AJ, Bonni A, Josselyn SA, Brunet A.
Genes Dev.
2012;
26
(24):
2780-801
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Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.
Chen R,
Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ.
PLoS Genet.
2012;
8
(4):
e1002621
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Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.
Dudley JT,
Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ.
Sci Transl Med.
2011;
3
(96):
96ra76
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Discovery and preclinical validation of drug indications using compendia of public gene expression data.
Sirota M,
Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ.
Sci Transl Med.
2011;
3
(96):
96ra77
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Identification of an IFN-γ/mast cell axis in a mouse model of chronic asthma.
Yu M,
Eckart MR, Morgan AA, Mukai K, Butte AJ, Tsai M, Galli SJ.
J Clin Invest.
2011;
121
(8):
3133-43
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ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.
Engreitz JM,
Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ.
Bioinformatics.
2011;
27
(23):
3317-8
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Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants.
Morgan AA,
Khatri P, Jones RH, Sarwal MM, Butte AJ.
BMC Bioinformatics.
2010:
11 Suppl 9
S6
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Content-based microarray search using differential expression profiles.
Engreitz JM,
Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ.
BMC Bioinformatics.
2010:
11
603
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Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
Chen R,
Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal MM, Butte AJ.
PLoS Comput Biol.
2010;
6
(9)
-
Dynamism in gene expression across multiple studies.
Morgan AA,
Dudley JT, Deshpande T, Butte AJ.
Physiol Genomics.
2010;
40
(3):
128-40
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Translational bioinformatics in the cloud: an affordable alternative.
Dudley JT,
Pouliot Y, Chen R, Morgan AA, Butte AJ.
Genome Med.
2010;
2
(8):
51
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Validating pathophysiological models of aging using clinical electronic medical records.
Chen DP,
Morgan AA, Butte AJ.
J Biomed Inform.
2010;
43
(3):
358-64
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FoxO3 regulates neural stem cell homeostasis.
Renault VM,
Rafalski VA, Morgan AA, Salih DA, Brett JO, Webb AE, Villeda SA, Thekkat PU, Guillerey C, Denko NC, Palmer TD, Butte AJ, Brunet A.
Cell Stem Cell.
2009;
5
(5):
527-39
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FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease.
Chen R,
Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ.
Genome Biol.
2008;
9
(12):
R170
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Overview of BioCreative II gene normalization.
Morgan AA,
Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L.
Genome Biol.
2008:
9 Suppl 2
S3
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Unsupervised method for automatic construction of a disease dictionary from a large free text collection.
Xu R,
Supekar K, Morgan A, Das A, Garber A.
AMIA Annu Symp Proc.
2008:
820-4
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Rapidly retargetable approaches to de-identification in medical records.
Wellner B,
Huyck M, Mardis S, Aberdeen J, Morgan A, Peshkin L, Yeh A, Hitzeman J, Hirschman L.
J Am Med Inform Assoc.
2007 Sep-Oct;
14
(5):
564-73
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Automating document classification for the Immune Epitope Database.
Wang P,
Morgan AA, Zhang Q, Sette A, Peters B.
BMC Bioinformatics.
2007:
8
269
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Evaluating the automatic mapping of human gene and protein mentions to unique identifiers.
Morgan AA,
Wellner B, Colombe JB, Arens R, Colosimo ME, Hirschman L.
Pac Symp Biocomput.
2007:
281-91
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BioCreAtIvE task 1A: gene mention finding evaluation.
Yeh A,
Morgan A, Colosimo M, Hirschman L.
BMC Bioinformatics.
2005:
6 Suppl 1
S2
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Data preparation and interannotator agreement: BioCreAtIvE task 1B.
Colosimo ME,
Morgan AA, Yeh AS, Colombe JB, Hirschman L.
BMC Bioinformatics.
2005:
6 Suppl 1
S12
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Overview of BioCreAtIvE task 1B: normalized gene lists.
Hirschman L,
Colosimo M, Morgan A, Yeh A.
BMC Bioinformatics.
2005:
6 Suppl 1
S11
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Gene name identification and normalization using a model organism database.
Morgan AA,
Hirschman L, Colosimo M, Yeh AS, Colombe JB.
J Biomed Inform.
2004;
37
(6):
396-410
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Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup.
Yeh AS,
Hirschman L, Morgan AA.
Bioinformatics.
2003:
19 Suppl 1
i331-9
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Rutabaga by any other name: extracting biological names.
Hirschman L,
Morgan AA, Yeh AS.
J Biomed Inform.
2002;
35
(4):
247-59
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