Superfund Research Program

Integrative Biology Core

Project Leaders: Jason H. Moore, Jason H. Moore
Grant Number: P42ES007373
Funding Period: 2008-2014

Project-Specific Links

Publications

2014

• Payne JL, Moore JH, Wagner A. 2014. Robustness, evolvability, and the logic of genetic regulation. Artif Life 20:111-126. doi:10.1162/ARTL_a_00099 PMID:23373974 PMCID:PMC4226432

2013

• Collins RL, Hu T, Wejse C, Sirugo G, Williams SM, Moore JH. 2013. Multifactor dimensionality reduction reveals a three-locus epistatic interaction associated with susceptibility to pulmonary tuberculosis. BioData Min 6:doi:10.1186/1756-0381-6-4 PMID:23418869 PMCID:PMC3618340
• Franceschini N, Fox E, Zhang Z, Edwards TL, Nalls MA. 2013. Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations. Am J Hum Genet 93:545-554. doi:10.1016/j.ajhg.2013.07.010 PMID:23972371 PMCID:PMC3769920
• Gui J, Moore JH, Williams SM, Andrews PC, Hillege HL. 2013. A simple and computationally efficient approach to multifactor dimensionality reduction analysis of gene-gene interactions for quantitative traits. PLoS One 8(6):e66545. doi:10.1371/journal.pone.0066545 PMID:23805232 PMCID:PMC3689797
• Hoen AG, Gardner SN, Moore JH. 2013. Identification of SNPs associated with variola virus virulence. BioData Min 6:doi:10.1186/1756-0381-6-3 PMID:23410064 PMCID:PMC3599518
• Hu T, Chen Y, Kiralis JW, Collins RL, Wejse C, Sirugo G, Williams SM, Moore JH. 2013. An information-gain approach to detecting three-way epistatic interactions in genetic association studies. J Am Med Inform Assoc 20:630-636. doi:10.1136/amiajnl-2012-001525 PMID:23396514 PMCID:PMC3721169
• Hu T, Chen Y, Kiralis JW, Moore JH. 2013. ViSEN: methodology and software for visualization of statistical epistasis networks. Genet Epidemiol 37(3):283-285. doi:10.1002/gepi.21718 PMID:23468157 PMCID:PMC3758133
• Huang X, Bruce B, Buchan A, Congdon CB, Cramer CL. 2013. No-boundary thinking in bioinformatics research. BioData Min 6:doi:10.1186/1756-0381-6-19 PMID:24192339 PMCID:PMC3827872
• Malley JD, Dasgupta A, Moore JH. 2013. The limits of p-values for biological data mining. BioData Min 6(1):10. doi:10.1186/1756-0381-6-10 PMID:23663551 PMCID:PMC3668262
• Malley JD, Moore JH. 2013. The disconnect between classical biostatistics and the biological data mining community. BioData Min 6:doi:10.1186/1756-0381-6-12 PMID:23880104 PMCID:PMC3726458
• Monda KL, Chen GK, Taylor KC, Palmer C, Edwards TL. 2013. A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry. Nat Genet 45:690-696. doi:10.1038/ng.2608 PMID:23583978 PMCID:PMC3694490
• Moore JH, Ritchie MD. 2013. The central role of biological data mining in connecting diverse disciplines. BioData Min 6:doi:10.1186/1756-0381-6-14 PMID:23937773 PMCID:PMC3765075
• Pan Q, Hu T, Moore JH. 2013. Epistasis, complexity, and multifactor dimensionality reduction. Methods Mol Biol 1019:465-477. doi:10.1007/978-1-62703-447-0_22 PMID:23756906
• Pechenick DA, Moore JH, Payne JL. 2013. The influence of assortativity on the robustness and evolvability of gene regulatory networks upon gene birth. Journal of Theoretical Biology 330:26-36. doi:10.1016/j.jtbi.2013.03.019 PMID:23542384 PMCID:PMC3672371
• Penrod NM, Moore JH. 2013. Key genes for modulating information flow play a temporal role as breast tumor coexpression networks are dynamically rewired by letrozole. BMC Med Genomics 6(Suppl2):doi:10.1186/1755-8794-6-S2-S2 PMID:23819860 PMCID:PMC3654875
• Rudd J, Moore JH, Urbanowicz RJ. 2013. A multi-core parallelization strategy for statistical significance testing in learning classifier systems. Evol Intell 6:127-134. doi:10.1007/s12065-013-0092-0 PMID:24358057 PMCID:PMC3864178
• Samuels DC, Li C, Li B, Song Z, Torstenson E. 2013. Recurrent tissue-specific mtDNA mutations are common in humans. PLoS Genet 9:doi:10.1371/journal.pgen.1003929 PMID:24244193 PMCID:PMC3820769
• Shen L, Thompson PM, Potkin SG, Bertram L, Farrer L. 2013. Genetic analysis of quantitative phenotypes in AD and MCI: imaging, cognition and biomarkers. Brain Imaging Behav doi:10.1007/s11682-013-9262-z PMID:24092460 PMCID:PMC3976843
• Tsongalis GJ, Chao E, Hagenkord JM, Hambuch T, Moore JH. 2013. ioinformatics: what the clinical laboratorian needs to know and prepare for. Clin Chem 59:1301-1305. doi:10.1373/clinchem.2012.198226 PMID:23723312
• Warren CA, van Opstal EJ, Riggins MS, Li Y, Moore JH. 2013. Vancomycin treatment's association with delayed intestinal tissue injury, clostridial overgrowth, and recurrence of Clostridium difficile infection in mice. Antimicrobial Agents and Chemotherapy 57:689-696. doi:10.1128/AAC.00877-12 PMID:23147742 PMCID:PMC3553708
• Williams SM, Moore JH. 2013. Big data analysis on autopilot. BioData Min 6:doi:10.1186/1756-0381-6-22 PMID:24314297 PMCID:PMC3878969

2011

• Cowper-Sallari R, Cole MD, Karagas MR, Lupien M, Moore JH. 2011. Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 3:513-526. doi:10.1002/wsbm.132 PMID:21197657 PMCID:PMC3062944
• Gilbert-Diamond D, Moore JH. 2011. Analysis of gene-gene interactions. Chapter 1 in: Current Protocols in Human Genetics. Wiley,
• Gui J, Andrew AS, Andrews PC, Nelson HH, Kelsey KT, Karagas MR, Moore JH. 2011. A robust multifactor dimensionality reduction method for detecting gene-gene interactions with application to the genetic analysis of bladder cancer susceptibility. Annals of Human Genetics 75(1):20-28. doi:10.1111/j.1469-1809.2010.00624.x PMID:21091664 PMCID:PMC3057873 (Completed with ARRA Funds)
• Hu T, Sinnott-Armstrong NA, Kiralis JW, Andrew AS, Karagas MR, Moore JH. 2011. Characterizing genetic interactions in human disease association studies using statistical epistasis networks. BMC Bioinformatics 12:364. doi:10.1186/1471-2105-12-364 PMID:21910885 PMCID:PMC3215301 (Completed with ARRA Funds)

2010

• Greene CS, Himmelstein DS, Moore JH. 2010. A model free method to generate human genetics datasets with complex gene-disease relationships. Lecture Notes in Computer Science 6023:74-85. doi:10.1007/978-3-642-12211-8_7
• Greene CS, Himmelstein DS, Nelson HH, Kelsey KT, Williams SM, Andrew AS, Karagas MR, Moore JH. 2010. Enabling personal genomics with an explicit test of epistasis. Pac Symp Biocomput 327-36. doi:10.1142/9789814295291_0035 PMID:19908385 PMCID:PMC2916690
• Greene CS, Sinnott-Armstrong NA, Himmelstein DS, Park PJ, Moore JH, Harris BT. 2010. Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. Bioinformatics 26(5):694-695. doi:10.1093/bioinformatics/btq009 PMID:20081222 PMCID:PMC2828117
• Marsit CJ, Houseman EA, Christensen BC, Gagne LA, Wrensch MR, Nelson HH, Wiemels JL, Zheng S, Wiencke JK, Andrew AS, Schned AR, Karagas MR, Kelsey KT. 2010. Identification of methylated genes associated with aggressive bladder cancer. PLoS One 5:e12334. doi:10.1371/journal.pone.0012334 PMID:20808801 PMCID:PMC2925945

2009

• Andrew AS, Gui J, Sanderson A, Mason RA, Morlock EV, Schned AR, Kelsey KT, Marsit CJ, Moore JH, Karagas MR. 2009. Bladder cancer SNP panel predicts susceptibility and survival. Hum Genet 125(5-6):527-539. doi:10.1007/s00439-009-0645-6 PMID:19252927 PMCID:PMC2763504
• Greene CS, Gilmore JM, Kiralis J, Andrews PC, Moore JH. 2009. Optimal use of expert knowledge in ant colony optimization for the analysis of epistasis in human disease. Lecture Notes in Computer Science 5483/2009:92-103. doi:10.1007/978-3-642-01184-9_9
• Greene CS, Penrod NM, Kiralis J, Moore JH. 2009. Spatially uniform relieff (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min 2(1):5. doi:10.1186/1756-0381-2-5 PMID:19772641 PMCID:PMC2761303
• Greene CS, Penrod NM, Williams SM, Moore JH. 2009. Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS One 4(6):e5639. doi:10.1371/journal.pone.0005639 PMID:19503614 PMCID:PMC2685469
• Jackson BP, Taylor VF, Baker RA, Miller EK. 2009. Low-level mercury speciation in freshwaters by isotope dilution GC-ICP-MS. Environ Sci Technol 43(7):2463-9. doi:10.1021/es802656p PMID:19452902 PMCID:PMC2692077
• Pattin KA, Moore JH. 2009. Role for protein-protein interaction databases in human genetics. Expert Rev Proteomics 6(6):647-659. doi:10.1586/epr.09.86 PMID:19929610 PMCID:PMC2813729
• Sinnott-Armstrong NA, Greene CS, Cancare F, Moore JH. 2009. Accelerating epistasis analysis in human genetics with consumer graphics hardware. BMC Res Notes 2:149. doi:10.1186/1756-0500-2-149 PMID:19630950 PMCID:PMC2732631
• Sloan CD, Andrew AS, Duell EJ, Williams SM, Karagas MR, Moore JH. 2009. Genetic population structure analysis in New Hampshire reveals Eastern European ancestry. PLoS One 4(9):e6928. doi:10.1371/journal.pone.0006928 PMID:19738909 PMCID:PMC2734429

2008

• Andrew AS, Jewell DA, Mason RA, Whitfield ML, Moore JH, Karagas MR. 2008. Drinking-water arsenic exposure modulates gene expression in human lymphocytes from a US population. Environ Health Perspect 116(4):524-531. doi:10.1289/ehp.10861 PMID:18414638 PMCID:PMC2290973
• Schned AR, Andrew AS, Marsit CJ, Kelsey KT, Zens MS, Karagas MR. 2008. Histological classification and stage of newly diagnosed bladder cancer in a population-based study from the Northeastern United States. Scand J Urol Nephrol 42(3):237-42. PMID:18432530