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Project Publications: University of Washington: Functional Genomics and Bioinformatics Core Laboratory

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Superfund Research Program

Functional Genomics and Bioinformatics Core Laboratory

Project Leader: Theodor K. Bammler
Co-Investigator: James W. MacDonald
Grant Number: P42ES004696
Funding Period: 2000-2023
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  • Bammler TK. Bioinformatics in Toxicology: Statistical Methods for Supervised Learning in High-Dimensional Omics Data. In: Comprehensive Toxicology, Third Edition. Elsevier,


  • Garrick JM, Cole TB, Bammler TK, MacDonald JW, Marsillach J, Furlong CE, Costa LG. 2021. Paraoxonase 2 deficiency in mice alters motor behavior and causes region-specific transcript changes in the brain. Neurotoxicol Teratol 87(14):doi:10.1016/ PMID:34216730 PMCID:PMC8440460


  • Barrett PM, Hull EA, Burkart K, Hargrave O, McLean JA, Taylor VF, Jackson BP, Gawel J, Neumann RB. 2019. Contrasting arsenic cycling in strongly- and weakly-stratified contaminated lakes: Evidence for temperature control on sediment-water arsenic fluxes. Limnology and Oceanography 64(3):1333-1346. doi:10.1002/lno.11119 PMID:31741542 PMCID:PMC6859942
  • Criswell SR, Nielsen SS, Warden MN, Flores HP, Lenox-Krug J, Racette S, Sheppard L, Checkoway H, Racette BA. 2019. MRI signal intensity and parkinsonism in manganese-exposed workers. J Occup Environ Med 61:641-645. doi:10.1097/JOM.0000000000001634 PMID:31348423
  • Zhang L, Wang H, Abel GM, Storm D, Xia Z. 2019. The effects of gene-environment interactions between cadmium exposure and apolipoprotein E4 on memory in a mouse model of alzheimer's disease. Toxicol Sci 173(1):189-201. doi:10.1093/toxsci/kfz218 PMID:31626305




  • Garrick JM, Dao K, de Laat R, Elsworth J, Cole TB, Marsillach J, Furlong CE, Costa LG. 2016. Developmental expression of paraoxonase 2. Chem Biol Interact 259(PtB):168-174. doi:10.1016/j.cbi.2016.04.001 PMID:27062895 PMCID:PMC5055469
  • Wang L, Espinoza HM, MacDonald JW, Bammler TK, Williams CR, Yeh A, Louie KW, Marcinek DJ, Gallagher EP. 2016. Olfactory transcriptional analysis of salmon exposed to mixtures of chlorpyrifos and malathion reveal novel molecular pathways of neurobehavioral injury. Toxicol Sci 149(1):145-157. doi:10.1093/toxsci/kfv223 PMID:26494550 PMCID:PMC4731405
  • Williams CR, MacDonald JW, Bammler TK, Simpson C, Paulsen M, Gallagher EP. 2016. From the cover: cadmium exposure differentially alters odorant-driven behaviors and expression of olfactory receptors in juvenile Coho salmon (Oncorhynchus kisutch). Toxicol Sci 154(2):267-277. doi:10.1093/toxsci/kfw172 PMID:27621283 PMCID:PMC5139070


  • Maryoung LA, Lavado R, Bammler TK, Gallagher EP, Stapleton PL, Beyer RP, Farin FM, Hardiman G, Schlenk D. 2015. Differential gene expression in liver, gill, and olfactory rosettes of Coho salmon (Oncorhynchus kisutch) after acclimation to salinity. Mar Biotechnol (NY) 17(6):703-717. doi:10.1007/s10126-015-9649-5 PMID:26260986 PMCID:PMC4636457
  • Nielsen SS, Checkoway H, Zhang J, Hofmann JN, Keifer M, Paulsen M, Farin FM, Cook TJ, Simpson C. 2015. Blood α-synuclein in agricultural pesticide handlers in central Washington State. Environ Res 136:75-81. doi:10.1016/j.envres.2014.10.014 PMID:25460623 PMCID:PMC4548290
  • Searles Nielsen S, Checkoway H, Criswell SR, Farin FM, Stapleton PL, Sheppard L, Racette BA. 2015. Inducible nitric oxide synthase gene methylation and parkinsonism in manganese-exposed welders. Parkinsonism Relat Disord 21(4):355-360. doi:10.1016/j.parkreldis.2015.01.007 PMID:25634431 PMCID:PMC4512640
  • Shi M, Movius J, Dator R, Aro P, Zhao Y, Pan C, Lin X, Bammler TK, Stewart T, Zabetian CP, Peskind ER, Hu S, Quinn JF, Galasko D, Zhang J. 2015. Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation. Mol Cell Proteomics 14(3):544-555. doi:10.1074/mcp.M114.040576 PMID:25556233 PMCID:PMC4349976


  • Ahmed I, Lee P, Lill CM, Nielsen SS, Artaud F, Gallagher LG, Loriot M, Mulot C, Nacfer M, Liu T, Biernacka JM, Armasu S, Anderson K, Farin FM, Lassen CF, Hansen J, Olsen JH, Bertram L, Maraganore DM, Checkoway H, Ritz B, Elbaz A. 2014. Lack of replication of the GRIN2A-by-coffee interaction in Parkinson disease. PLoS Genet 10(11):e1004788. doi:10.1371/journal.pgen.1004788 PMID:25412286 PMCID:PMC4238979
  • Cole TB, Li WF, Co AL, Hay AM, MacDonald JW, Bammler TK, Farin FM, Costa LG, Furlong CE. 2014. Repeated gestational exposure of mice to chlorpyrifos oxon is associated with paraoxonase 1 (PON1) modulated effects in maternal and fetal tissues. Toxicol Sci 141(2):409-422. doi:10.1093/toxsci/kfu144 PMID:25070982 PMCID:PMC4271046
  • Woods JS, Heyer NJ, Russo JE, Martin MD, Pillai PB, Bammler TK, Farin FM. 2014. Genetic polymorphisms of catechol-O-methyltransferase modify the neurobehavioral effects of mercury in children. J Toxicol Environ Health A 77(6):293-312. doi:10.1080/15287394.2014.867210 PMID:24593143 PMCID:PMC3967503


  • Mata IF, Checkoway H, Hutter CM, Samii A, Roberts JW, Kim H, Alvarez V, Ribacoba R, Pastor P, Lorenzo-Betancor O, Infante J, Sierra M, Gomez-Garre P, Mir P, Ritz B, Rhodes SL, Colcher A, Van Deerlin V, Chung KA, Quinn JF, Yearout D, Martizez E, Farin FM, Wan JY, Edwards KL, Zabetian CP. 2012. Common variation in the LRRK2 gene is a risk factor for Parkinson's disease. Movement Disorders 27(14):1823-1826. doi:10.1002/mds.25226 PMID:23115130 PMCID:PMC3536918
  • Nielsen SS, Checkoway H, Butler RA, Nelson HH, Farin FM, Longstreth WT, Franklin GM, Swanson PD, Kelsey KT. 2012. LINE-1 DNA methylation, smoking and risk of Parkinson's disease. J Parkinsons Dis 2(4):303-308. doi:10.3233/JPD-012129 PMID:23938260 PMCID:PMC3962286
  • Woods JS, Heyer NJ, Echeverria D, Russo JE, Martin MD, Bernardo MF, Luis HS, Vaz L, Farin FM. 2012. Modification of neurobehavioral effects of mercury by a genetic polymorphism of coproporphyrinogen oxidase in children. Neurotoxicol Teratol 34(5):513-521. doi:10.1016/ PMID:22765978 PMCID:PMC3462250


  • Tilton F, Bammler TK, Gallagher EP. 2011. Swimming impairment and acetylcholinesterase inhibition in zebrafish exposed to copper or chlorpyrifos separately, or as mixtures. Comp Biochem Physiol C Toxicol Pharmacol 153(1):9-16. doi:10.1016/j.cbpc.2010.07.008 PMID:20692364 PMCID:PMC3034093
  • Tilton F, Tilton SC, Bammler TK, Beyer RP, Stapleton PL, Scholz N, Gallagher EP. 2011. Transcriptional impact of organophosphate and metal mixtures on olfaction: Copper dominates the chlorpyrifos-induced response in adult zebrafish. Aquat Toxicol 102(3-4):205-215. doi:10.1016/j.aquatox.2011.01.012 PMID:21356183 PMCID:PMC3991301


  • Caudle W, Bammler TK, Lin YS, Pan S, Zhang J. 2010. Using 'omics' to define pathogenesis and biomarkers of Parkinson's disease. Expert Rev Neurother 10(6):925-942. doi:10.1586/ern.10.54 PMID:20518609 PMCID:PMC2913169
  • Echeverria D, Woods JS, Heyer NJ, Martin MD, Rohlman D, Farin FM, Li T. 2010. The association between serotonin transporter gene promotor polymorphism (5-HTTLPR) and elemental mercury exposure on mood and behavior in humans. J Toxicol Environ Health A 73(15):1003-1020. doi:10.1080/15287390903566591 PMID:20526950 PMCID:PMC2882654
  • Kang J, Wilkerson H, Farin FM, Bammler TK, Beyer RP, Strand SE, Doty SL. 2010. Mammalian cytochrome CYP2E1 triggered differential gene regulation in response to trichloroethylene (TCE) in a transgenic poplar. Funct Integr Genomics 10(3):417-424. doi:10.1007/s10142-010-0165-4 PMID:20213342 PMCID:PMC3050643
  • Liu J, Shi M, Hong Z, Zhang J, Bradner J, Quinn T, Beyer RP, McGeer PL, Chen S, Zhang J. 2010. Identification of ciliary neurotrophic factor receptor alpha as a mediator of neurotoxicity induced by alpha-synuclein. Proteomics 10(11):2138-2150. doi:10.1002/pmic.200900745 PMID:20340160 PMCID:PMC3013276


  • Heyer NJ, Echeverria D, Martin MD, Farin FM, Woods JS. 2009. Catechol O-methyltransferase (COMT) VAL158MET functional polymorphism, dental mercury exposure, and self-reported symptoms and mood. J Toxicol Environ Health A 72(9):599-609. doi:10.1080/15287390802706405 PMID:19296409 PMCID:PMC2866512
  • Hofmann JN, Keifer M, Furlong CE, De Roos AJ, Farin FM, Fenske RA, van Belle G, Checkoway H. 2009. Serum cholinesterase inhibition in relation to paraoxonase-1 (PON1) status among organophosphate-exposed agricultural pesticide handlers. Environ Health Perspect 117:1402-1408. PMID:19750105
  • Lefebvre KA, Tilton SC, Bammler TK, Beyer RP, Srinouanprachanh SL, Stapleton PL, Farin FM, Gallagher EP. 2009. Gene expression profiles in zebrafish brain after acute exposure to domoic acid at symptomatic and asymptomatic doses. Toxicol Sci 107(1):65-77. doi:10.1093/toxsci/kfn207 PMID:18936300 PMCID:PMC2735419
  • Shi M, Bradner J, Bammler TK, Eaton DL, Zhang J, Ye Z, Wilson AM, Montine TJ, Pan C, Zhang J. 2009. Identification of glutathione S-transferase pi as a protein involved in Parkinson disease progression. Am J Pathol 175(1):54-65. doi:10.2353/ajpath.2009.081019 PMID:19498008 PMCID:PMC2708794


  • Echeverria D, Woods JS, Heyer NJ, Martin MD, Rholman D, Farin FM, Li T. 2008. The association between serotonin transporter gene promoter polymorphism (5-HTTLPR), self-reported symptoms, and dental mercury exposure. J Toxicol Environ Health A 71(19):1318-1326. doi:10.1080/15287390802240850 PMID:18686203 PMCID:PMC2612706


  • Bekris LM, Viernes HA, Farin FM, Maier LA, Kavanagh TJ, Takaro TK. 2006. Chronic beryllium disease and glutathione biosynthesis genes. J Occup Environ Med 48(6):599-606. PMID:16766924
  • Echeverria D, Woods JS, Heyer NJ, Rohlman D, Farin FM, Li T, Garabedian CC. 2006. The association between a genetic polymorphism of coproporphyrinogen oxidase, dental mercury exposure and neurobehavioral response in humans. Neurotoxicol Teratol 28(1):39-48. PMID:16343843


  • Costa LG, Kelada SN, Costa-Mallen P, Farin FM, Viernes HA, Smith-Weller T, Franklin GM, Longstreth WT, Swanson PD, Checkoway H, Furlong CE. 2004. Paraoxonase 2 (PON2) polymorphisms and Parkinson's disease. Neurosci Res Commun 34(3):130-135.
  • Heyer NJ, Echeverria D, Bittner AC, Farin FM, Garabedian CC, Woods JS. 2004. Chronic low-level mercury exposure, BDNF polymorphism, and associations with self-reported symptoms and mood. Toxicol Sci 81(2):354-363. PMID:15254338


  • Higashi MK, Veenstra DL, Kondo LM, Wittkowsky AK, Srinouanprachanh SL, Farin FM, Rettie AE. 2002. Association between CYP2C9 genetic variants and anticoagulation-related outcomes during warfarin therapy. JAMA - Journal of the American Medical Association 287(13):1690-1698. PMID:11926893


  • Diaz D, Krejsa CM, White CC, Keener CL, Farin FM, Kavanagh TJ. 2001. Tissue specific changes in the expression of glutamate-cysteine ligase mRNAs in mice exposed to methylmercury. Toxicol Lett 122(2):119-129. PMID:11439218
  • Farin FM, Hitosis Y, Hallagan SE, Kushleika JV, Woods JS, Janssen P, Smith-Weller T, Franklin GM, Swanson PD, Checkoway H. 2001. Genetic polymorphisms of superoxide dismutase in Parkinson's disease. Movement Disorders 16(4):705-707. PMID:11481695
  • Farin FM, Janssen P, Quigley SD, Abbott D, Hassett C, Smith-Weller T, Franklin GM, Swanson PD, Longstreth WT, Omiecinski CJ, Checkoway H. 2001. Genetic polymorphisms of microsomal and soluble epoxide hydrolase and the risk of Parkinson's disease. Pharmacogenet Genomics 11(8):703-708. PMID:11692079
  • Kim HS, Newcomb PA, Ulrich CM, Keener CL, Farin FM, Bostick RM, Potter JD. 2001. Vitamin D receptor polymorphisms and the risk of colorectal adenomas: evidence of interaction with dietary vitamin D and calcium. Cancer Epidemiol Biomarkers Prev 10(8):869-874. PMID:11489753
  • Ulrich CM, Yasui Y, Storb RF, Schubert MM, Wagner JL, Bigler J, Ariail KS, Keener CL, Li S, Liu H, Farin FM, Potter JD. 2001. Pharmacogenetics of methotrexate: toxicity among marrow transplantation patients varies with the methylenetetrahydrofolate reductase C677T polymorphism. Blood 98(1):231-234. PMID:11418485
  • Winterton DL, Kaufman JD, Keener CL, Quigley SD, Farin FM, Williams PV, Koenig JQ. 2001. Genetic polymorphisms as biomarkers of sensitivity to inhaled sulfur dioxide in subjects with asthma. Ann Allergy Asthma Immunol 86(2):232-238. doi:10.1016/S1081-1206(10)62697-X PMID:11258696


  • Costa-Mallen P, Costa LG, Smith-Weller T, Franklin GM, Swanson PD, Checkoway H. 2000. Genetic polymorphism of dopamine D2 receptors in Parkinson's disease and interactions with cigarette smoking and MAO-B intron 13 polymorphism. Journal of Neurology, Neurosurgery & Psychiatry 69(4):535-7. PMID:10990520
  • Ulrich CM, Bigler J, Velicer CM, Greene EA, Farin FM, Potter JD. 2000. Searching expressed sequence tag (EST) databases: discovery and confirmation of a common polymorphism in the thymidylate synthase gene. Cancer Epidemiol Biomarkers Prev 9(12):1381-1385. PMID:11142426
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