2008
Moore, J.H., Andrews, P.C., Barney, N., White, B.C. Development and
evaluation of an open-ended computational evolution system for the
genetic analysis of susceptibility to common human diseases. Lecture
Notes in Computer Science 4973, 129-140 (2008).
Wilke, R.A., Mareedu, R.K., Moore, J.H. The pathway less traveled:
Moving from candidate genes to candidate pathways in the analysis of
genome-wide data from large scale pharmacogenetic association
studies. Current Pharmacogenomics and Personalized Medicine, in
press (2008).
Moore, J.H. Analysis of gene-gene interactions. In: Dracopoli,
N.C., Haines, J.L., Korf, B.R., Moir, D.T., Morton, C.C.,
Seidman, C.E., Seidman, J.G., Smith, D.R. (eds), Current Protocols in
Human Genetics, Wiley-Liss, Inc., New York, 2nd Ed., in press (2008).
Moore, J.H., Karagas, M.R., Andrew, A.S. Novel analytical methods for
association studies. In: Rebbeck, T., Ambrosone, C.B., Shields, P.G.
(Eds.) Molecular Epidemiology: Applications in Cancer and Other Human
Diseases. Informa Healthcare USA, Inc., in press (2008).
Moore, J.H. The critical need for computational intelligence in human genetics. Computing Reviews, in press (2008).
Arehart, E., Stitham, J., Asselbergs, F.W., Douville, K., MacKenzie,
T., Fetalvero, K.M., Gleim, S., Kasza, Z., Rao, Y., Martel, L., Segel,
S., Robb, J., Kaplan, A., Simons, M., Powell, R.J., Moore, J.H., Rimm,
E.B., Martin, K.A., Hwa, J. Acceleration of cardiovascular disease by a
dysfunctional prostacyclin receptor mutation, potential implications
for COX-2 inhibition. Circulation Research, in press (2008).
Andrew, A.S., Jewell, D., Mason, R., Whitfield, M., Moore, J.H.,
Karagas, M.R. Drinking water arsenic exposure modulates gene expression
in human lymphocytes. Environmental Health Perspectives, in press
(2008).
Berretta, L., Cappiello, J.H., Moore, J.H., Scorza, R. IL-1 gene
complex single nucleotide polymorphisms in systemic sclerosis: A
further step ahead. Human Immunology, in press (2008).
Berretta, L., Cappiello, J.H., Moore, J.H., Greene, C.S., Barili, M.,
Scorza, R. Epistatic interactions of cytokine single nucleotide
polymorphisms predict susceptibility to disease subsets in systemic
sclerosis patients. Arthritis Care and Research, in press (2008).
Reif, D.M., McKinney, B.A., Motsinger, A., Chanock, S.J., Edwards,
K.M., Rock, M.T., Moore, J.H., Crowe, J.E. Jr. Genetic basis for
adverse events following smallpox vaccination. Journal of Infectious
Diseases, in press (2008).
Moore,
J.H. Bases, bits and disease: A mathematical theory for human genetics.
European Journal of Human Genetics 16, 143-144 (2008). [PubMed]
Moore,
J.H., Barney, N., White, B.C. Solving complex problems in human
genetics using genetic programming: The importance of
theorist-practitioner-computer interaction. In: Riolo, R., Soule, T., Worzel, B. (eds.) Genetic
Programming Theory and Practice V, Springer (2008). [Springer] [Amazon]
Moore, J.H. Bioinformatics. In: Wild, C., Vineis, P., Garte, S. (eds.) Molecular
Epidemiology of Chronic Diseases, Wiley, in press (2008). [Wiley] [Amazon.com]
Moore, J.H., Karagas, M., Andrew, A.S. Statistical analysis of complex
datasets. In: Wild, C., Vineis, P., Garte, S. (eds.) Molecular
Epidemiology of Chronic Diseases, Wiley, in press (2008). [Wiley] [Amazon.com]
Marchiori, E., Moore, J.H. (eds.) Evolutionary
Computation, Machine Learning and Data Mining in Bioinformatics.
Lecture Notes in Computer Science 4974, Springer (2008). [Springer]
Sloan, C., Sayarath, V., Moore, J.H. Systems genetics of alcoholism. Alcohol Research and Health, in press (2008).
Duell,
E.J., Moore, J.H., Bracci, P.M., Burk, R.D., Kelsey, K.T., Holly, E.A.
Detecting complex, pathway-based gene-gene and gene-environment
interactions in pancreatic cancer. Carcinogenesis, in press (2008).
Thornton-Wells, T.A., Moore, J.H., Haines, J.L. Confronting complexity
in late-onset Alzheimer disease: Application of two-stage analysis
approach addressing heterogeneity and epistasis. Genetic Epidemiology,
in press (2008). [PubMed]
Andrew, A.S., Karagas, M.R., Nelson, H.H., Guarrera, S., Polidoro, S.,
Gamberini, S., Sacerdote, C., Moore, J.H., Kelsey, K.T., Vineis, P.,
Matullo, G. Assessment of multiple DNA repair gene polymorphisms and
bladder cancer susceptibility in a joint Italian and U.S. population: a
comparison of alternative analytic approaches. Human Heredity 65,
105-118 (2008). [PubMed]
2007
Williams,
S.M., Canter, J.A., Crawford, D.C., Moore, J.H., Ritchie, M.D., Haines,
J.L. Problems with genome-wide association studies. Science 316,
1840-1842 (2007). [PubMed]
Moore, J.H. Bioinformatics. Journal of Cellular Physiology 213, 365-369 (2007). [PubMed]
Greene,
C.S., White, B.C., Moore, J.H. An expert knowledge-guided mutation
operator for genome-wide genetic analysis using genetic programming.
Lecture Notes in Bioinformatics 4774, 30-40 (2007). [Springer]
McKinney, B.A., Reif, D.M., White, B.C., Crowe, J.E., Moore, J.H.
Evaporative cooling feature selection for genotypic data involving
interactions. Bioinformatics 23, 2113-2120 (2007). [PubMed]
Moore,
J.H., Barney, N., Tsai, C.T., Chiang, F.T., Gui, J., White, B.C.
Symbolic modeling of epistasis. Human Heredity 63, 120-133 (2007). [PubMed]
Moore,
J.H., White, B.C. Tuning ReliefF for genome-wide genetic
analysis. Lecture Notes in Computer Science 4447, 166-175 (2007). [Springer]
Moore,
J.H. Genome-wide analysis of epistasis using multifactor dimensionality
reduction: feature selection and construction in the domain of human
genetics. In: Knowledge Discovery and Data Mining: Challenges and
Realities with Real World Data, IGI Global, pp. 17-30 (2007). [IGI] [Amazon.com]
Moore,
J.H., White, B.C. Genome-wide genetic analysis using genetic
programming: The critical need for expert knowledge. In: Riolo, R., Soule, T., Worzel, B. (eds.) Genetic
Programming Theory and Practice IV, Springer (2007). [Amazon.com] [Springer]
Eppstein,
M.J., Payne, J.L., White, B.C., Moore, J.H. Genomic mining for complex
disease traits with “random chemistry”. Genetic Programming
and Evolvable Machines 8, 395-411 (2007). [Springer]
Velez, D.R., White, B.C., Motsinger,
A.A., Bush, W.S., Ritchie, M.D., Williams, S.M., Moore, J.H.
A balanced accuracy metric for epistasis modeling in imbalanced datasets
using
multifactor dimensionality reduction. Genetic
Epidemiology 31, 306-315 (2007). [PubMed]
Asselbergs, F.W., Williams, S.M., Hebert, P.R., Coffey, C.S., Hillege,
H.L., de Jong, P.E., Vaughan, D.E., van Gilst, W.H., Moore, J.H.
The effects of polymorphisms in genes from the renin-angiotensin,
bradykinin, and fibrinolytic systems on plasma t-PA and PAI-1 levels
are dependent on environmental context. Human Genetics 122,
275-281(2007). [PubMed]
Asselbergs,
F.W., Williams, S.M., Hebert, P.R., Coffey, C.S., Hillege, H.L., de
Jong, P.E., Vaughan, D.E., van Gilst, W.H., Moore, J.H. Epistatic
effects of genes from the fibrinolytic, renin-angiotensin, and
bradykinin systems on plasma PAI-1 and t-PA levels. Genomics 89, 362-9
(2007). [PubMed]
Asselbergs, F.W., Williams, S.M., Hebert, P.R., Coffey,
C.S., Hillege, H.L., de Jong, P.E., Vaughan, D.E., van Gilst, W.H.,
Moore, J.H. Gender-specific correlations between PAI-1 and t-PA
levels and cardiovascular-related traits in the general population.
Journal of Thrombosis and Haemostasis 5, 313-20 (2007). [PubMed]
Williams, S.M.,
Poku, K., Brown, N.J., Vaughan, D.E., Moore, J.H. Design of a
population-based study of the genetic architecture of plasma t-PA and
PAI-1 in Blacks from Ghana. Ethnicity and Disease 17, 492-497 (2007) [PubMed]
Reif DM,
Israel MA, Moore JH. Exploratory visual analysis of statistical results
from microarray experiments comparing high and low grade glioma.
Cancer Informatics 2, 19-24 (2007). [Libertas Academica] [PDF]
Ritchie, M.D., Motsinger, A.A., Coffey, C.S., Moore, J.H. Genetic programming neural
networks: a powerful bioinformatics tools for human genetics. Applied
Soft Computing 7, 471-479 (2007). [Elsevier]
Heim, K.E., White-Branco, K.A., Deng, D., Tomlinson, C.R., Moore, J.H.,
Freemantle, S.J., Spinella, M.J. Selective repression of retinoic
acid target genes by RIP140 during induced tumor cell differentiation
of pluripotent human embryonal carcinoma cells. Molecular Cancer 19, 57
(2007). [PubMed]
Gaur, A.B.,
Jewell, D.A., Liang, Y., Ridzon, D., Moore,
J.H., Chen, C., Ambros, V.R., Israel, M.A. Characterization of microRNA
expression levels and their biological correlates in human cancer cell
lines. Cancer Research 67, 2456-2468
(2007). [PubMed]
Garcia-Barcelo, M., Miao, X., Lui, V.C.-H., So, M.T., Ngan, E.S.-W., Leon,
Y., Lau, D.K., Liu, T., Ao, X.,
Guo, W., Holden, W., Moore, J.H., Tam, P.K. Correlation between genetic
variations in hox clusters and Hirschsprung’s disease. Annals of Human Genetics 71, 526-536 (2007). [PubMed]
Coutinho
AM, Sousa I, Martins M, Correia C, Morgadinho T, Bento C, Marques C,
Ataide A, Miguel TS, Moore JH, Oliveira G, Vicente AM. Evidence for
epistasis between SLC6A4 and ITGB3 in autism etiology and in the
determination of platelet serotonin levels. Human Genetics 121, 243-256
(2007). [PubMed]
Garcia-Barcelo, M., King, S.K., Miao, X., So, M., Holden, W., Moore,
J.H., Sutcliffe, J.R., Hutson, J.M., Tam, P.K.H. Application of HapMap
data to the evaluation of 8 candidate genes for pediatric slow transit
constipation. Journal of Pediatric Surgery 42, 666-671 (2007). [PubMed]
Julia, T., Moore, J.H., Marsal, S. Identification of a two-loci
epistatic interaction associated with susceptibility to rheumatoid
arthritis through reverse engineering and multifactor dimensionality
reduction. Genomics 90, 6-13 (2007). [PubMed]
Tsai,
C.-T., Hwang, J.-J., Ritchie, M.D., Moore, J.H., Chiang, F.T., Lai,
L.-P., Hsu, K.-L., Tseng, C.-D., Liau, C.-Suong., Lin, J.-L., Tseng,
Y.-Z. Renin-angiotensin system gene polymorphisms and coronary artery
disease in a large angiographic cohort: Detection of gene-gene
interactions. Atherosclerosis 195, 172-180 (2007). [PubMed]
Lind, J.M.,
Hutcheson-Dilks, H.B., Williams, S.M., Moore, J.H., Essex, M.,
Ruiz-Pesini, E., Wallace, D.C., Tishkoff, S.A., O’Brien, S.J., Smith,
M.W. Elevated male European and female African contributions to the
genomes of African Americans. Human Genetics 120:713-22 (2007). [PubMed]
Raj, J.U., Aliferis, C., Caprioli, R.M., Cowley, A.W., Davies, P.F.,
Duncan, M.W., Erle, D.J., Erzurum, S.C., Finn, P.W., Ischiropoulos, H.,
Kaminski, N., Kleeberg, S.R., Leikauf, G.D., Lloyd, J.E., Martin, T.R.,
Matalon, S., Moore, J.H., Quackenbush, J., Sabo-Attwood, T., Shapiro,
S.D., Schitzer, J.E. Scwartz, D.A., Schwiebert, L.M., Sheppard, D.,
Ware, L.B., Weiss, S.T., Whitsett, J.A., Wurfel, M.M. Genomics and
proteomics of lung disease: Conference summary. American Journal of
Physiology 293, L45-51 (2007). [PubMed]
Canter, J.A., Norris, P.R., Moore, J.H., Jenkins, J.M., Morris, J.A.
Specific polymorphic variation in the mitochondrial genome and
increased mortality following severe trauma. Annals of Surgery 246, 406-411 (2007). [PubMed]
Nordgard, S.H., Ritchie, M.D., Jensrud, S.D., Motsinger, A.A., Alnaes,
G.I., Lemmon, G., Berg, M., Geisler, S., Moore, J.H., Lonning, P.E.,
Borresen-Dale, A.L., Kristensen, V.N. ABCB1 and GST polymorphisms
associated with TP53 status in breast cancer. Pharmacogenetics and
Genomics 17, 127-136 (2007). [PubMed]
Moore, J.H., Barney, N., White, B.C. Towards human-human-computer
interaction for biologically-inspired problem solving in human
genetics. Proceedings of the Genetic and Evolutionary Computing
Conference. ACM Press, p. 432 (2007). [ACM]
Keitzer, M., Moore, J.H., et al. (Eds.) Proceedings of the Genetic and
Evolutionary Computing Conference. ACM
Press, New York (2007). [GECCO'07]
Marchiori, E., Moore, J.H., Rajapakse, J. (Eds.) Evolutionary
Computation, Machine Learning and Data Mining in Bioinformatics.
Lecture Notes in Computer Science 4447, Springer (2007). [Springer]
Moore, J.H.
Multiclass cancer classification using semisupervised ellipsoid ARTMAP
and particle swarm optimization with gene expression data. Computing
Reviews #CR70033 (2007). [ACM]
2006
Moore, J.H., Gilbert, J.C., Tsai, C.-T., Chiang, F.T., Holden, W.,
Barney, N., White, B.C. A flexible computational framework for
detecting, characterizing, and interpreting statistical patterns of
epistasis in genetic studies of human disease susceptibility. Journal
of Theoretical Biology 241, 252-261 (2006). [PDF] [PubMed]
Moore,
J.H., White, B.C. Exploiting expert knowledge in genetic programming
for genome-wide genetic analysis. In: Runarsson et al. (eds), Lecture
Notes in Computer Science 4193, 969-977 (2006). [Springer]
Reif, D.M., Moore, J.H. Visual analysis of statistical results
from microarray studies of human breast cancer. Oncology Reports
14, 1043-1047 (2006). [PubMed]
Thornton-Wells, T.A., Moore, J.H., Haines, J.L. Comparison of three
clustering methods for dissecting trait heterogeneity in genotypic
data. BMC Bioinformatics 7, 204 (2006). [PDF] [PubMed]
Chittenden,
T.W., Sherman, J.A., Xiong, F., Hall, A.E., Lanahan, A., Taylor, J.M.,
Pearlman, J., Moore, J.H., Schwartz, S., Simons, M. Transcriptional
regulation in coronary artery disease: Indications for novel markers of
coronary collateralization. Circulation 114, 1811-20 (2006). [PubMed]
Asselbergs,
F.W., Williams, S.M., Hebert, P.R., Coffey, C.S., Hillege, H.L., de
Jong, P.E., Vaughan, D.E., van Gilst, W.H., Moore, J.H. The
gender-specific role of polymorphisms from the fibrinolytic,
renin-angiotensin, and bradykinin systems in determining plasma PAI-1
and t-PA levels. Thrombosis and Haemostasis 96, 471-477 (2006). [PubMed]
Reif, D.M.,
Motsinger, A.A., McKinney, B.A., Crowe Jr, J., Moore, J.H. Feature
selection using random forests for the integrated analysis of multiple
data types. Proceedings of the 2006 IEEE Symposium on Computational
Intelligence in Bioinformatics and Computational Biology (2006). [IEEE]
Moore, J.H. Quantitative trait linkage analysis. In:
Haines, J.L. and Pericak-Vance, M.A. (eds), Genetic Analysis of Complex
Disease, 2nd Ed., Wiley-Liss, Inc., New York, pp. 237-253 (2006). [Wiley] [Amazon]
McKinney, B., Reif, D.M., Ritchie, M.D., Moore, J.H. Machine
learning for detecting gene-gene interactions. Applied Bioinformatics
5, 77-88 (2006). [PubMed]
Kidd, L.R., Martin R.C., Moore, J.H., Hein D.W. Genetic
polymorphism of N-acetyltransferase genes as risk modifiers of
colorectal cancer from consumption of well-done meat. In: Choi, S.-W.,
Friso, S. (eds), Nutrient-Gene Interactions in Cancer, CRC Press, New
York, pp 189-212 (2006). [CRC Press] [Amazon]
Sanada, H., Yatabe, J., Midorikawa, S., Hashimoto, S., Watanabe, T.,
Ritchie, M.D., Moore, J.H., Williams, S.M., Eisner, G.M., Jose, P.A.,
Felder, R.A. Single-nucleotide polymorphisms for diagnosis of
salt-sensitive hypertension. Clinical Chemistry 52, 352-360 (2006). [PubMed]
Martin, E.R. Hahn, L.W., Bass, M., Ritchie, M.D., Moore, J.H. A
combined multifactor dimensionality reduction and pedigree
disequilibrium test (MDR-PDT) approach for detecting gene-gene
interactions in pedigrees. Genetic Epidemiology 30, 111-23 (2006). [PubMed]
McKinney, B.A., Barney, N., Crooke, P.S., Crowe, J.E. Jr., Moore,
J.H. Hybrid grammar-based approach to nonlinear dynamical system
identification from biological time series. Physical Review E 73,
021912 (2006). [PubMed]
McKinney, B.A., Reif, D.M., Rock, M.T., Edwards, K.N., Kingsmore, S.F.,
Moore, J.H., Crowe, J.E. Jr. Cytokine expression patterns associated
with systemic adverse events following smallpox vaccination.
Journal of Infectious Disease 194, 444-53 (2006). [PDF] [PubMed]
Andrew, A.S., Nelson, H.N., Kelsey, K.T., Moore, J.H., Meng, A.,
Casella, D.P., Tosterson, T.D., Schned, A.R., Karagas, M.R. Concordance
of multiple analytical approaches demonstrates a complex relationship
between DNA repair gene SNPs, smoking, and bladder cancer
susceptibility. Carcinogenesis 27, 1030-1037 (2006). [PubMed]
Huang, C., Kim, Y., Moore, J.H., Walker, P.C., Rich, S., Mychaleckyi,
J., Mauer, M. Diabetic nephropathy is associated with gene expression
levels of oxidative phosphorylation and related pathways.
Diabetes 55, 1826-1831 (2006). [PubMed]
Asselbergs, F.W., Moore, J.H., van den Berg, M.P., Rimm, E.B., de Boer,
R.A., Dullaart, R.P., Navis, G., van Gilst, W.H. A role for CETP
TaqB polymorphism in determining susceptibility to atrial fibrillation:
a nested case control study. BMC Medical Genetics 7, 39 (2006). [PDF] [PubMed]
Rothlauf, F., Branke, J., Cagnoni, S., Costa, E.; Cotta, C., Drechsler,
R., Lutton, E., Machado, P., Moore, J.H., Romero, J., Smith, G.D.,
Squillero, G., Takagi, H. (Eds.). Applications of Evolutionary
Computing: Lecture Notes in Computer Science 3907. Springer (2006). [Springer]
Moore, J.H. Joint classification and pairing of human chromosomes. Computing Reviews, #CR132587, March 22 (2006). [ACM]
Keitzer, M., Moore, J.H., et al. (Eds.) Proceedings of the Genetic and
Evolutionary Computing Conference. ACM
Press (2006).
[ACM]
2005
Wilke, R., Reif, D.M., Moore, J.H. Combinatorial pharmacogenetics. Nature Reviews Drug Discovery 4, 911-8 (2005). [PubMed]
Moore, J.H. A global view of epistasis. Nature Genetics 37, 13-14 (2005). [PubMed]
Moore,
J.H., Williams, S.M. Traversing the conceptual divide between
biological and statistical epistasis: Systems biology and a more modern
synthesis. BioEssays 27, 637-646 (2005). [PubMed]
Skaar, D.A., Shao, Y., Haines, J.L., Stenger, J.E., Jaworski, J.,
Martin, E.R., Delong, G.R., Moore, J.H., McCauley, J.L., Sutcliffe,
J.S., Ashley-Koch, A.E., Cuccaro, M.L., Folstein, S.E., Gilbert, J.R.,
Pericak-Vance, M.A. Analysis of the RELN gene as a genetic risk factor
for autism. Molecular Psychiatry 10, 563-71 (2005). [PubMed]
Reif, D.M., Dudek, S.M., Shaffer, C.M., Wang, J., Moore, J.H.
Exploratory visual analysis of pharmacogenomic results. Pacific
Symposium on Biocomputing 296-307 (2005). [PubMed]
Moore, J.H., Boczko, E., Summar, M. Connecting the dots between genes,
biochemistry, and disease susceptibility: Systems biology modeling in
human genetics. Molecular Genetics and Metabolism 84:104-111 (2005). [PubMed]
Fox, R.M., Von Stetina, S.E., Barlow, S.J., Shaffer, C., Olszewski,
K.L., Moore, J.H., Dupuy, D., Vidal, M., Miller, D.M. A gene expression
fingerprint of C. elegans embryonic motor neurons. BMC Genomics
6, 42 (2005). [PubMed]
Wilke, R.A., Moore, J.H., Burmester, J.K. Relative impact of CYP3A
genotype and concomitant medication on the severity of
atorvastatin-induced myopathy. Pharmacogenetics and Genomics 15,
415-421 (2005). [PubMed]
Schwartz, S.A., Weil, R.J, Thompson, R.C., Shyr, Y., Moore, J.H., Toms
S.A., Johnson, M.D., Caprioli, R.C. Proteomic-based prognosis of brain
tumor patients using direct-tissue matrix-assisted laser desorption
ionization mass spectrometry. Cancer Research 65, 7674-81 (2005). [PubMed]
White, B.C., Gilbert, J.C., Reif, D.M., Moore, J.H. A statistical
comparison of grammatical evolution strategies in the domain of human
genetics. Proceedings of the IEEE Congress on Evolutionary
Computing, 676-682 (2005). [IEEE]
White, B.C., Moore, J.H. A complete BNF grammar for systems biology
thought experiments in human genetics using artificial life and
biologically inspired computing. Proceedings of the IEEE Congress
on Evolutionary Computing, 491-497 (2005). [IEEE]
Moore, J.H. Tumor suppressor gene networks as molecular targets for
developing new cancer treatments. Computing Reviews, #CR131430, June 27
(2005). [ACM]
Xu, J., Lowey, J., Wiklund, F., Sun, J., Lindmark, F., Hsu, F.-C.,
Dimitrov, L., Chang, B., Turner, A.R., Adami, H.-O., Suh, E., Moore,
J.H., Zheng, S.L., Isaacs, W.B., Trent, J.M., Gronberg, H. The
interaction of four inflammatory genes significantly predicts prostate
cancer risk. Cancer Epidemiology Biomarkers and Prevention 14,
2563-8 (2005). [PubMed]
2004
Moore, J.H., Ritchie, M.D. The challenges of whole-genome approaches to common diseases. JAMA 291, 1642-3 (2004). [PDF] [PubMed]
Thornton-Wells,
T.A., Moore, J.H., Haines, J.L. Genetics, statistics and human disease:
analytical retooling for complexity. Trends in Genetics 20, 640-47
(2004). [PubMed]
Moore, J.H. Computational analysis of gene-gene
interactions in common human diseases using multifactor dimensionality
reduction. Expert Review of Molecular Diagnostics 4, 795-803 (2004). [PubMed]
Moore, J.H., Hahn, L.W. Evaluation of a discrete dynamic systems
approach for modeling the hierarchical relationship between genes,
biochemistry, and disease susceptibility. Discrete and Continuous
Dynamical Systems: Series B 4, 275-87 (2004). [DCDS]
Aune, T.A., Maas, K., Parker, J., Moore, J.H., Olsen, N.J. Profiles of
gene expression in human autoimmune disease. Cell Biochemistry
and Biophysics 40, 81-96 (2004). [PubMed]
Williams, S.M., Haines, J.L., Moore, J.H. The use of animal models in
the study of complex disease. BioEssays 26, 170-9 (2004). [PubMed]
Coffey, C.S., Hebert, P.R., Krumholz, H.M., Morgan, T.M., Williams,
S.M., Moore, J.H. Reporting of model validation procedures in
human studies of genetic interactions. Nutrition 20, 69-73 (2004). [PubMed]
Moore, J.H., Hahn, L.W., Ritchie, M.D., Thornton, T.A., White,
B.C. Routine discovery of high-order epistasis models for
simulation studies in human genetics. Applied Soft Computing 4, 79-86
(2004).
Cho, Y.M., Ritchie, M.D., Moore, J.H., Kim, M., Yoon, K.H., Sung,
Y.-A., Jang, H.C., Park, J.Y., Lee, K.-U., Shin, H.D., Kim, S.Y., Lee,
H.K., Park, K.S. Multifactor dimensionality reduction reveals
interactions among the UCP2 and PPAR? genes in type 2 diabetes.
Diabetologia 47, 549-54 (2004). [PubMed]
Tsai, C.-T., Lai, L.-P., Chiang, F.-T., Fallin, D., Hwang, J.-J.,
Ritchie, M.D., Moore, J.H., Hsu, K.-L., Tseng, C.-D., Liau, C.S., Lin,
J.-L., Tseng, Y.-Z. Renin-angiotensin system gene polymorphisms and
atrial fibrillation. Circulation 109, 1640-46 (2004). [PubMed]
Williams, S.M., Ritchie, M.D., Phillips, J.A., Dawson, E., Prince, M.,
Dzhura, E., Willis, A., Summar, M., White, B.C., Addy, J.H., Wong,
L.-J., Felder, R.A., Jose, P.A., Moore, J.H. Multilocus analysis
of hypertension: A hierarchical approach. Human Heredity 57,
28-38 (2004). [PubMed]
Roodi, N., Dupont, W.D., Moore, J.H., Parl, F.F. Association of
homozygous wild-type glutothione S-transferase m1 genotype with
increased breast cancer risk. Cancer Research 64, 1233-6 (2004). [PDF] [PubMed]
Olsen, N.J., Sokka, T., Seehorn, C.L., Kraft, B., Maas. K., Moore,
J.H., Aune, T.M. A gene expression signature for recent onset
rheumatoid arthritis in peripheral blood mononuclear cells.
Annals of the Rheumatic Diseases 63, 1387-92 (2004). [PubMed]
Olsen, N.J., Moore, J.H., Aune, T.M. Gene expression signatures
for autoimmune disease in peripheral blood mononuclear cells.
Arthritis Research and Therapy 6, 120-8 (2004). [PDF] [PubMed]
Hahn L.W., Moore J.H. Ideal discrimination of discrete clinical
endpoints using multilocus genotypes. In Silico Biology 4, 0016 (2004). [PubMed]
Reif, D.M., White, B.C., Moore, J.H. Integrated analysis of genetic,
genomic, and proteomic data. Expert Review of Proteomics 1, 67-75
(2004). [PubMed]
Aune, T.M., Parker, J.S., Maas, K., Olsen, N., Moore, J.H.
Co-localization of differentially expressed genes and shared
susceptibility loci in human autoimmunity. Genetic Epidemiology 27,
162-172 (2004). [PubMed]
Moore, J.H., Hahn, L.W. An improved grammatical evolution strategy for
Petri net modeling of complex genetic systems. In: Raidl, G.R.,
Cagnoni, S., Branke, J., Corne, D.W., Rolf, D., Jin, Y., Johnson, C.,
Machado, P., Marchiori, E., Rothlauf, F., Smith, G.D., Squillero, G.
(eds), Lecture Notes in Computer Science 3005, 62-71, Springer-Verlag,
Berlin (2004). [Springer]
Moore, J.H., Hahn, L.W. Systems biology modeling in human genetics
using Petri nets and grammatical evolution. In: Deb, K., Poli,
R., Banzhaf, W., Beyer, H.-G., Burke, E., Darwen, P., Dasgupta, D.,
Floreano, D., Foster, J., Harman, M., Holland, O., Lanzi, P.L.,
Spector, L., Tettamanzi, A., Thierens, D., Tyrrell, A. (eds), Lecture
Notes in Computer Science 3102, 392-401, Springer, New York (2004). [Springer]
Ritchie, M.D., Coffey, C.S., Moore, J.H. Genetic programming neural
networks as a bioinformatics tool in human genetics. In: Deb, K.,
Poli, R., Banzhaf, W., Beyer, H.-G., Burke, E., Darwen, P., Dasgupta,
D., Floreano, D., Foster, J., Harman, M., Holland, O., Lanzi, P.L.,
Spector, L., Tettamanzi, A., Thierens, D., Tyrrell, A. (eds), Lecture
Notes in Computer Science 3102, 438-448, Springer, New York (2004). [Springer]
White, B.C., Moore, J.H. Systems biology thought experiments in human
genetics using artificial life and grammatical evolution. In:
Pollack, J., Bedau, M., Husbands, P., Ikegami, T., Watson, R.A. (eds),
Artificial Life IX. The MIT Press, Cambridge, pp 581-86 (2004). [Amazon]
Coffey, C.S., Hebert, P.R., Ritchie, M.D., Krumholz, H.M., Morgan,
T.M., Gaziano, J.M., Ridker, P.M., and Moore, J.H. An application
of conditional logistic regression and multifactor dimensionality
reduction for detecting gene-gene interactions on risk of myocardial
infarction: The importance of model validation. BMC Bioinformatics 5,
49 (2004). [PDF] [PubMed]
Osipovich, A., White-Grindley, E.K., Hicks, G.G., Roshon, M.J.,
Shaffer, C., Moore, J.H., Ruley, H.E. Activation of cryptic 3’
splice sites within introns of cellular genes following gene
entrapment. Nucleic Acids Research 32, 2912-24 (2004). [PDF] [PubMed]
Smith, M.W., Patterson, N.J., Lautenberger, J.A., Truelove, A.L.,
McDonald, G.J., Kessing, B.D., Yi, Z., de The, G., Essex, M., Kanki,
P.J., Phair, J.P., Goedert, J.J., Vlahov, D., Ferrell, R.E., Moore,
J.H., Williams, S.M., Tishkoff, S.A., Winkler, C.A., De La Vega, F.,
Woodage, T., Altshuler, D., Sninsky, J.J., Gilbert, D.A., Hafler, D.A.,
O’Brien, S.J., Reich, D.E. A high density map for disease
gene discovery in African Americans. American Journal of Human
Genetics 74, 1001-13 (2004). [PDF] [PubMed]
Kardia, S.L.R., Turner, S.T., Schwartz, G.L., and Moore, J.H.
Linear dynamic features of ambulatory blood pressure in a
population-based study. Blood Pressure Monitoring 9, 259-67
(2004). [PubMed]
2003
Moore, J.H. The
ubiquitous nature of epistasis in determining susceptibility to common
human diseases. Human Heredity 56, 73-82 (2003). [PubMed]
Moore, J.H. Cross validation consistency for the assessment of genetic
programming results in microarray studies. In: Raidl, G., Meyer,
J.-A., Middendorf, M., Cagnoni, S., Cardalda, J.J.R., Corne, D.W.,
Gottlieb, J., Guillot, A., Hart, E., Johnson, C.G., Marchiori, E.,
(eds) Lecture Notes in Computer Science 2611, pp 99-106,
Springer-Verlag, Berlin (2003). [Springer]
Moore, J.H. Analysis of gene-gene interactions. In: Dracopoli, N.C., Haines, J.L., Korf, B.R., Moir, D.T., Morton, C.C., Seidman, C.E., Seidman, J.G., Smith, D.R. (eds), Current Protocols in Human Genetics, Wiley-Liss, Inc., New York, pp. 1.14.1-1.14.11 (2003). [Wiley]
Reif,
D.M., White, B.C., Olsen, N.J., Aune, T.A., Moore, J.H. Complex
function sets improve symbolic discriminant analysis of microarray
data. In: Cantu-Paz, E. et al. (eds) Lecture Notes in Computer Science
2724, pp 2277-2287, Springer-Verlag, Berlin (2003). [Springer]
Barr,
F.E., Beverley, H., VanHook, K., Cermack, E., Christian, K.,
Drinkwater, D., Dyer, K., Raggio, N.T., Scott, N., Moore, J.H.,
Christman, B. and Summar, M. The effect of cardiopulmonary bypass
on urea cycle intermediates and nitric oxide levels after congenital
heart surgery. Journal of Pediatrics 142, 26-30 (2003). [PubMed]
Moore,
J.H., Hahn, L.W. Grammatical evolution for the discovery of Petri net
models of complex genetic systems. In: Cantu-Paz, E. et al. (eds)
Lecture Notes in Computer Science 2724, pp 2412-2413, Springer-Verlag,
Berlin (2003). [Springer]
Moore,
J.H. Quantitative traits. In: Robinson, R. (ed), Genetics,
Macmillan Science Library, New York, Volume 4, pp 1-3 (2003). [Macmillan]
Moore, J.H. Statistics. In: Robinson, R. (ed), Genetics, Macmillan Science Library, New York, Volume 4, pp 95-97 (2003). [Macmillan]
Moore,
J.H. Statistical geneticist. In: Robinson, R. (ed), Genetics,
Macmillan Science Library, New York, Volume 4, 93-94 (2003). [Macmillan]
Moore, J.H., Thornton, T.A., Ritchie, M.D. Basic statistics. In: Dracopoli, N.C., Haines, J.L.,
Korf, B.R., Moir, D.T., Morton, C.C., Seidman, C.E., Seidman, J.G.,
Smith, D.R. (eds), Current Protocols in Human Genetics, Wiley-Liss,
Inc., New York, pp. A.3M.1-A.3M.10 (2003). [Wiley]
Ritchie,
M.D., Hahn, L.W. and Moore, J.H. Power of multifactor
dimensionality reduction for detecting gene-gene interactions in the
presence of genotyping error, missing data, phenocopy, and genetic
heterogeneity. Genetic Epidemiology 24, 150-157 (2003). [PubMed]
Hahn,
L.W., Ritchie, M.D., and Moore, J.H. Multifactor dimensionality
reduction software for detecting gene-gene and gene-environment
interactions. Bioinformatics 19, 376-382 (2003). [PDF] [PubMed]
Moore, J.H.,
Hahn, L.W. Petri net modeling of high-order genetic systems using
grammatical evolution. BioSystems 72, 177-86 (2003). [PubMed]
Tarumi, T., Kravtsov, D., Moore, J.H., Williams, S.M., Gailani, D. Common single nucleotide
polymorphisms in the promoter region of the human factor XI gene.
Journal of Thrombosis and Haemostasis 1, 1854-6 (2003). [PubMed]
Aune, T.A., Mass, K., Moore, J.H., Olsen, N.J. Gene expression profiles in human autoimmune disease. Current Pharmaceutical Design 9, 1905-17 (2003). [PubMed]
Yamagata, N., Shyr, Y., Yanagisawa, K., Dang, T.P., Gonzalez, A., Nadaf, S., Larsen, P., Roberts,
J.R., Nesbitt, J.C., Jensen, R., Levy, S., Moore, J.H., Minna, J.D.,
Carbone, D.P. A training-testing approach to the molecular
classification of resected non-small cell lung cancer. Clinical Cancer
Research 9, 4695-704 (2003). [PubMed]
Egan, K.M., Thompson, P.A., Titus-Ernstoff, L., Moore, J.H., Ambrosone, C.B. MnSOD polymorphism and breast cancer in a population-based case-control study. Cancer Letters 199, 27-33 (2003). [PubMed]
Yanagisawa,
K., Shyr, Y., Xu, B.J., Massion, P.P., Larsen, P., White, B.C.,
Roberts, J.R., Gonzalez, A., Nadaf, S., Moore, J.H., Caprioli, R.M.,
Carbone, D.P. Proteomic patterns and tumour subsets in non-small cell
lung cancer. Lancet 362, 433-9 (2003). [PubMed]
Ritchie, M.D., White, B.C., Parker, J.S., Hahn, L.W., and Moore, J.H. Optimization of neural
network architecture using genetic programming improves detection and
modeling of gene-gene interactions in studies of human diseases. BMC
Bioinformatics 4, 28-42 (2003). [PDF] [PubMed]
2002
Moore, J.H. and Hahn, L.W. A cellular
automata approach to detecting interactions among single-nucleotide
polymorphisms in complex multifactorial diseases. Pacific
Symposium on Biocomputing 7, 53-64 (2002). [PubMed]
Moore, J.H., Hahn, L.W., Ritchie, M.D., Thornton, T.A., White,
B.C. Application of genetic algorithms to the discovery of
complex models for simulation studies in human genetics. In:
W.B.Langdon, E. Cantu-Paz, K. Mathias, R. Roy, D. Davis, R. Poli, K.
Balakrishnan, V. Honavar, G. Rudolph, J. Wegener, L. Bull, M.A. Potter,
A.C. Schultz, J.F. Miller, E. Burke, and N. Jonoska (eds). Proceedings
of the Genetic and Evolutionary Computation Conference, Morgan Kaufmann
Publishers, San Francisco, pp 1150-55 (2002). [ACM]
Moore, J.H., Hahn, L.W. Cellular automata and genetic algorithms
for parallel problem solving in human genetics. In: Merelo, J.J.,
Panagiotis, A., Beyer, H.-G. (eds) Lecture Notes in Computer Science
2439, pp 821-830, Springer-Verlag, Berlin (2002). [Springer]
Moore, J.H. and Williams, S.M. New strategies for identifying
gene-gene interactions in hypertension. Annals of Medicine 34,
88-95 (2002). [PubMed]
Moore, J.H., Lamb, J.M., Brown, N.J., Vaughan, D.E. A comparison of
combinatorial partitioning and linear regression for the detection of
epistatic effects of the ACE I/D and PAI-1 4G/5G polymorphisms on
plasma PAI-1 levels. Clinical Genetics 62, 74-79 (2002). [PubMed]
Moore, J.H., Smolkin, M.E., Lamb, J.M., Brown, N.J., Vaughan,
D.E. The relationship between plasma t-PA and PAI-1 levels is
dependent on epistatic effects of the ACE I/D and PAI-1 4G/5G
Polymorphisms. Clinical Genetics 62, 53-59 (2002). [PubMed]
Moore, J.H., Parker, J.S., Olsen, N.J., Aune, T. Symbolic
discriminant analysis of microarray data in autoimmune disease.
Genetic Epidemiology 23, 57-69 (2002). [PubMed]
Maas, K., Chan, S., Parker, J., Slater, A., Moore, J.H., Olsen, N., and
Aune, T.M. Cutting edge: molecular portrait of human
autoimmunity. Journal of Immunology 169, 5-9 (2002). [PubMed]
Landau, R., Xie, H.-G., Dishy, V., Stein, C.M., Wood, A.J.J., Moore,
J.H., Emala, C.W., and Smiley, R.M. B2-adrenergic receptor
genotype and preterm delivery. American Journal of Obstetrics and
Gynecology 187, 1294-8 (2002). [PubMed]
2001
Ritchie,
M.D., Hahn, L.W., Roodi, N., Bailey, L.R., Dupont, W.D., Parl, F.F. and
Moore, J.H. Multifactor dimensionality reduction reveals high-order
interactions among estrogen metabolism genes in sporadic breast
cancer. American Journal of Human Genetics 69, 138-147 (2001). [PDF] [PubMed]
Moore,
J.H., Parker, J.S. and Hahn, L.W. Symbolic discriminant analysis for
mining gene expression patterns. In: De Raedt, L., Flach, P. (eds)
Lecture Notes in Artificial Intelligence 2167, pp 372-381,
Springer-Verlag, Berlin (2001). [Springer]
Moore, J.H. and Parker, J.S.
Evolutionary computation in microarray data analysis. In Lin, S. and
Johnson, K. (eds), Methods of Microarray Data Analysis, Kluwer Academic
Publishers, Boston, pp 23-35 (2001). [Amazon]
Moore, J.H. Improved power
of sib-pair linkage analysis using measures of complex trait dynamics.
Human Heredity 52, 113-115 (2001). [PubMed]
Parker, J.S. and Moore, J.H. Dynamics based pattern recognition
and parallel genetic algorithms for the analysis of multivariate gene
expression data. In: Proceedings of the Genetic and Evolutionary
Computation Conference Workshop Program, San Francisco, pp 433-436
(2001). [BBase]
Moore, J.H. and Hahn, L.W. Multilocus pattern recognition using
cellular automata and parallel genetic algorithms. In: Spector,
L., Goodman, E.D., Wu, A., Langdon, W.B., Voigt, H.-M., Gen, M., Sen,
S., Dorigo, M., Pezeshk, S., Garzon, M.H., Burke, E. (eds) Proceedings
of the Genetic and Evolutionary Computation Conference, Morgan Kaufmann
Publishers, San Francisco, p 1452 (2001). [BBase]
2000
Schwartz,
G.L., Turner, S.T., Moore, J.H. and Sing, C.F. Predictors of
interindividual variation in ambulatory blood pressure and their time
and/or activity dependence. American Journal of Hypertension 13,
52-60 (2000). [PubMed]
Moore, J.H. Detection of linear and nonlinear
dependencies in time series using the method of surrogate data in
S-PLUS. Computer Methods and Programs in Biomedicine, 63, 117-121
(2000). [PubMed]
Schwartz, G.L., Turner, S.T., Moore, J.H. and Sing, C.F. Effect
of time of day on intraindividual variability in ambulatory blood
pressure. American Journal of Hypertension, 13, 1203-1209 (2000). [PubMed]
1999
Moore, J.H. Bootstrapping, permutation testing and the method of
surrogate data. Physics in Medicine and Biology 44, L11-L12 (1999). [PubMed]
1997
Moore, J.H., Reilly, S.L., Ferrell, R.E. and Sing, C.F. The role
of the apolipoprotein E polymorphism in the prediction of
coronary artery disease age of onset. Clinical Genetics 51, 22-25
(1997). [PubMed]
1995
Bongiorno,
P.F., Al-Kasspooles, M., Lee, S.W., Rachwal, W.J., Moore, J.H., Whyte,
R.I., Orringer, M.B., and Beer, D.G. E-cadherin expression in
primary and metastatic thoracic neoplasms and in Barrett’s
oesophagus. British Journal of Cancer 71, 166-172 (1995). [PubMed]
Moore, J.H. Artificial intelligence programming with LabVIEW:
Genetic algorithms for instrumentation control and optimization.
Computer Methods and Programs in Biomedicine 47, 73-79 (1995). [PubMed]
1994
Moore, J.H., Lesser, E.J., Erdody, D.H., Natale,
R.B., Orringer, M.B., and Beer, D.G. Intestinal differentiation and p53
gene alterations in Barrett’s esophagus and esophageal
adenocarcinoma. International Journal of Cancer 56, 487-493
(1994). [PubMed]
Bongiorno, P.F., Whyte, R.I., Lesser, E.J., Moore, J.H., Orringer,
M.B., and Beer, D.G.Alterations of K-ras, p53 and erbB-2/neu in human
lung adenocarcinomas. Journal of Thoracic and Cardiovascular
Surgery 107, 590-595 (1994). [PubMed]
1993
Al-Kasspooles, M., Moore, J.H., Orringer, M.B.,
and Beer, D.G. Amplification and overexpression of the EGFR
and erbB-2 genes in human esophageal adenocarcinomas.
International Journal of Cancer 54, 213-219 (1993). [PubMed]
Wu, G.D., Beer, D.G., Moore, J.H., Orringer, M.B., Appelman, H.D., and
Traber, P.G. Sucrase-isomaltase gene expression in Barrett’s
esophagus and adenocarcinoma. Gastroenterology 105, 837-844 (1993). [PubMed]
Last updated March 2, 2008 by JHM