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December was a very productive month for the Department of Genetics faculty, who published 30 manuscripts on a wide variety of topics.

An NLRP3 Mutation Causes Arthropathy and Osteoporosis in Humanized Mice.

Snouwaert JN, Nguyen M, Repenning PW, Dye R, Livingston EW, Kovarova M, Moy SS, Brigman BE, Bateman TA, Ting JP, Koller BH.
Cell Rep. 2016 Dec 13;17(11):3077-3088. doi: 10.1016/j.celrep.2016.11.052.
PMID: 27974218

Ticking in Place for the Microbiome to Message Out

Liang X, Bultman SJ.
Cell Metab. 2016 Dec 13;24(6):775-777. doi: 10.1016/j.cmet.2016.11.015
PMID: 27974176

Large-scale pharmacogenomic study of sulfonylureas and the QT, JT and QRS intervals: CHARGE Pharmacogenomics Working Group.

Floyd JS, Sitlani CM, Avery CL, Noordam R, Li X, Smith AV, Gogarten SM, Li J, Broer L, Evans DS, Trompet S, Brody JA, Stewart JD, Eicher JD, Seyerle AA, Roach J, Lange LA, Lin HJ, Kors JA, Harris TB, Li-Gao R, Sattar N, Cummings SR, Wiggins KL, Napier MD, Stürmer T, Bis JC, Kerr KF, Uitterlinden AG, Taylor KD, Stott DJ, de Mutsert R, Launer LJ, Busch EL, Méndez-Giráldez R, Sotoodehnia N, Soliman EZ, Li Y, Duan Q, Rosendaal FR, Slagboom PE, Wilhelmsen KC, Reiner AP, Chen YD, Heckbert SR, Kaplan RC, Rice KM, Jukema JW, Johnson AD, Liu Y, Mook-Kanamori DO, Gudnason V, Wilson JG, Rotter JI, Laurie CC, Psaty BM, Whitsel EA, Cupples LA, Stricker BH.
Pharmacogenomics J. 2016 Dec 13. doi: 10.1038/tpj.2016.90. [Epub ahead of print] PMID: 27958378

Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression.

Zhang G, Huang KC, Xu Z, Tzeng JY, Conneely KN, Guan W, Kang J, Li Y
Genet Epidemiol. 2016 May;40(4):333-40. doi: 10.1002/gepi.21969.
PMID: 27061717

Epigenetic Regulation by ATP-Dependent Chromatin-Remodeling Enzymes: SNF-ing Out Crosstalk.

Runge JS, Raab JR, Magnuson T.
Curr Top Dev Biol. 2016;117:1-13. doi: 10.1016/bs.ctdb.2015.10.009. Review.
PMID: 26969969

HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants.

Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F, Li Y, Hu M.
BMC Res Notes. 2016 Mar 11;9:159. doi: 10.1186/s13104-016-1947-0.
PMID: 26969411

CARMA3 Is a Host Factor Regulating the Balance of Inflammatory and Antiviral Responses against Viral Infection.

Jiang C, Zhou Z, Quan Y, Zhang S, Wang T, Zhao X, Morrison C, Heise MT, He W, Miller MS, Lin X.
Cell Rep. 2016 Mar 15;14(10):2389-401. doi: 10.1016/j.celrep.2016.02.031.
PMID: 26947079

Prognostic ability of EndoPredict compared to research-based versions of the PAM50 risk of recurrence (ROR) scores in node-positive, estrogen receptor-positive, and HER2-negative breast cancer. A GEICAM/9906 sub-study.

Martin M, Brase JC, Ruiz A, Prat A, Kronenwett R, Calvo L, Petry C, Bernard PS, Ruiz-Borrego M, Weber KE, Rodriguez CA, Alvarez IM, Segui MA, Perou CM, Casas M, Carrasco E, Caballero R, Rodriguez-Lescure A.
Breast Cancer Res Treat. 2016 Feb;156(1):81-9. doi: 10.1007/s10549-016-3725-z.
PMID: 26909792

One CNV Discordance in NRXN1 Observed Upon Genome-wide Screening in 38 Pairs of Adult Healthy Monozygotic Twins.

Magnusson PK, Lee D, Chen X, Szatkiewicz J, Pramana S, Teo S, Sullivan PF, Feuk L, Pawitan Y.
Twin Res Hum Genet. 2016 Apr;19(2):97-103. doi: 10.1017/thg.2016.5.
PMID: 26899349

Generating a taxonomy for genetic conditions relevant to reproductive planning.

Korngiebel DM, McMullen CK, Amendola LM, Berg JS, Davis JV, Gilmore MJ, Harding CO, Himes P, Jarvik GP, Kauffman TL, Kennedy KA, Simpson DK, Leo MC, Lynch FL, Quigley DI, Reiss JA, Richards CS, Rope AF, Schneider JL, Goddard KA, Wilfond BS.
Am J Med Genet A. 2016 Mar;170(3):565-73. doi: 10.1002/ajmg.a.37513.
PMID: 26889673

Comprehensive analysis of schizophrenia-associated loci highlights ion channel pathways and biologically plausible candidate causal genes.

Pers TH, Timshel P, Ripke S, Lent S, Sullivan PF, O’Donovan MC, Franke L, Hirschhorn JN; Schizophrenia Working Group of the Psychiatric Genomics Consortium.
Hum Mol Genet. 2016 Mar 15;25(6):1247-54. doi: 10.1093/hmg/ddw007.
PMID: 26755824

Genetics of murine craniofacial morphology: diallel analysis of the eight founders of the Collaborative Cross.

Percival CJ, Liberton DK, Pardo-Manuel de Villena F, Spritz R, Marcucio R, Hallgrímsson B.
J Anat. 2016 Jan;228(1):96-112. doi: 10.1111/joa.12382.
PMID: 26426826

Epigenome-wide association data implicates DNA methylation-mediated genetic risk in psoriasis.

Zhou F, Shen C, Xu J, Gao J, Zheng X, Ko R, Dou J, Cheng Y, Zhu C, Xu S, Tang X, Zuo X, Yin X, Cui Y, Sun L, Tsoi LC, Hsu YH, Yang S, Zhang X.
Clin Epigenetics. 2016 Dec 5;8:131.
PMID: 27980695

APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication.

Hoopes JI, Cortez LM, Mertz TM, Malc EP, Mieczkowski PA, Roberts SA.
Cell Rep. 2016 Feb 16;14(6):1273-82. doi: 10.1016/j.celrep.2016.01.021.
PMID: 26832400

Cellular Senescence Promotes Adverse Effects of Chemotherapy and Cancer Relapse.

Demaria M, O’Leary MN, Chang J, Shao L, Liu S, Alimirah F, Koenig K, Le C, Mitin N, Deal AM, Alston S, Academia EC, Kilmarx S, Valdovinos A, Wang B, de Bruin A, Kennedy BK, Melov S, Zhou D, Sharpless NE, Muss H, Campisi J.
Cancer Discov. 2016 Dec 15. pii: CD-16-0241. [Epub ahead of print] PMID: 27979832

Cardiovascular effects of exogenous adrenomedullin and CGRP in Ramp and Calcrl deficient mice.

Pawlak JB, Wetzel-Strong SE, Dunn MK, Caron KM.
Peptides. 2016 Dec 8. pii: S0196-9781(16)30238-8. doi: 10.1016/j.peptides.2016.12.002. [Epub ahead of print] PMID: 27940069

Mucopolysaccharidosis Type I Newborn Screening: Best Practices for Diagnosis and Management.

Clarke LA, Atherton AM, Burton BK, Day-Salvatore DL, Kaplan P, Leslie ND, Scott CR, Stockton DW, Thomas JA, Muenzer J.
J Pediatr. 2016 Dec 7. pii: S0022-3476(16)31265-3. doi: 10.1016/j.jpeds.2016.11.036. [Epub ahead of print] No abstract available.
PMID: 27939258

Dual Chromatin and Cytoskeletal Remodeling by SETD2.

Park IY, Powell RT, Tripathi DN, Dere R, Ho TH, Blasius TL, Chiang YC, Davis IJ, Fahey CC, Hacker KE, Verhey KJ, Bedford MT, Jonasch E, Rathmell WK, Walker CL.
Cell. 2016 Aug 11;166(4):950-62. doi: 10.1016/j.cell.2016.07.005
PMID: 27518565

Survival of children with trisomy 13 and trisomy 18: A multi-state population-based study.

Meyer RE, Liu G, Gilboa SM, Ethen MK, Aylsworth AS, Powell CM, Flood TJ, Mai CT, Wang Y, Canfield MA; National Birth Defects Prevention Network.
Am J Med Genet A. 2016 Apr;170A(4):825-37. doi: 10.1002/ajmg.a.37495.
PMID: 26663415

DeFCoM: Analysis and Modeling of Transcription Factor Binding Sites Using a Motif-centric Genomic Footprinter.

Quach B, Furey TS.
Bioinformatics. 2016 Dec 19. pii: btw740. [Epub ahead of print] PMID: 27993786

Bloom Syndrome Helicase Promotes Meiotic Crossover Patterning and Homolog Disjunction.

Hatkevich T, Kohl KP, McMahan S, Hartmann MA, Williams AM, Sekelsky J.
Curr Biol. 2016 Dec 9. pii: S0960-9822(16)31289-1. doi: 10.1016/j.cub.2016.10.055. [Epub ahead of print] PMID: 27989672

NLRX1 Sequesters STING to Negatively Regulate the Interferon Response, Thereby Facilitating the Replication of HIV-1 and DNA Viruses.

Guo H, König R, Deng M, Riess M, Mo J, Zhang L, Petrucelli A, Yoh SM, Barefoot B, Samo M, Sempowski GD, Zhang A, Colberg-Poley AM, Feng H, Lemon SM, Liu Y, Zhang Y, Wen H, Zhang Z, Damania B, Tsao LC, Wang Q, Su L, Duncan JA, Chanda SK, Ting JP.
Cell Host Microbe. 2016 Apr 13;19(4):515-28. doi: 10.1016/j.chom.2016.03.001.
PMID: 27078069

BMI loci and longitudinal BMI from adolescence to young adulthood in an ethnically diverse cohort.

Graff M, North KE, Richardson AS, Young KL, Mazul AL, Highland HM, Mohlke KL, Lange LA, Lange EM, Harris KM, Gordon-Larsen P.
Int J Obes (Lond). 2016 Dec 27. doi: 10.1038/ijo.2016.233. [Epub ahead of print] PMID: 28025578

Genome-wide association studies in East Asians identify new loci for waist-hip ratio and waist circumference.

Wen W, Kato N, Hwang JY, Guo X, Tabara Y, Li H, Dorajoo R, Yang X, Tsai FJ, Li S, Wu Y, Wu T, Kim S, Guo X, Liang J, Shungin D, Adair LS, Akiyama K, Allison M, Cai Q, Chang LC, Chen CH, Chen YT, Cho YS, Choi BY, Gao Y, Go MJ, Gu D, Han BG, He M, Hixson JE, Hu Y, Huang T, Isono M, Jung KJ, Kang D, Kim YJ, Kita Y, Lee J, Lee NR, Lee J, Wang Y, Liu JJ, Long J, Moon S, Nakamura Y, Nakatochi M, Ohnaka K, Rao D, Shi J, Sull JW, Tan A, Ueshima H, Wu C, Xiang YB, Yamamoto K, Yao J, Ye X, Yokota M, Zhang X, Zheng Y, Qi L, Rotter JI, Jee SH, Lin D, Mohlke KL, He J, Mo Z, Wu JY, Tai ES, Lin X, Miki T, Kim BJ, Takeuchi F, Zheng W, Shu XO.
Sci Rep. 2016 Jan 20;6:17958. doi: 10.1038/srep17958.
PMID: 26785701

Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs.

Below JE, Parra EJ, Gamazon ER, Torres J, Krithika S, Candille S, Lu Y, Manichakul A, Peralta-Romero J, Duan Q, Li Y, Morris AP, Gottesman O, Bottinger E, Wang XQ, Taylor KD, Ida Chen YD, Rotter JI, Rich SS, Loos RJ, Tang H, Cox NJ, Cruz M, Hanis CL, Valladares-Salgado A.
Sci Rep. 2016 Jan 19;6:19429. doi: 10.1038/srep19429.
PMID: 26780889

Concentrations of Pro-Inflammatory Cytokines Are Not Associated with Senescence Marker p16INK4a or Predictive of Intracellular Emtricitabine/Tenofovir Metabolite and Endogenous Nucleotide Exposures in Adults with HIV Infection.

Maas BM, Francis O, Mollan KR, Lee C, Cottrell ML, Prince HM, Sykes C, Trezza C, Torrice C, White N, Malone S, Hudgens MG, Sharpless NE, Dumond JB.
PLoS One. 2016 Dec 30;11(12):e0168709. doi: 10.1371/journal.pone.0168709.
PMID: 28036343

Population Pharmacokinetics Modeling of Unbound Efavirenz, Atazanavir, and Ritonavir in HIV-Infected Subjects With Aging Biomarkers.

Dumond JB, Chen J, Cottrell M, Trezza CR, Prince H, Sykes C, Torrice C, White N, Malone S, Wang R, Patterson KB, Sharpless NE, Forrest A.
CPT Pharmacometrics Syst Pharmacol. 2016 Dec 29. doi: 10.1002/psp4.12151. [Epub ahead of print] PMID: 28032946

p16INK4a , a Senescence Marker, Influences Tenofovir/Emtricitabine Metabolite Disposition in HIV-Infected Subjects.

Dumond JB, Collins JW, Cottrell ML, Trezza CR, Prince H, Sykes C, Torrice C, White N, Malone S, Wang R, Patterson KB, Sharpless NE, Forrest A.
CPT Pharmacometrics Syst Pharmacol. 2016 Dec 26. doi: 10.1002/psp4.12150. [Epub ahead of print] PMID: 28019088

Subtumoral analysis of PRINT nanoparticle distribution reveals targeting variation based on cellular and particle properties.

Roode LE, Brighton H, Bo T, Perry JL, Parrott MC, Kersey F, Luft JC, Bear JE, DeSimone JM, Davis IJ.
Nanomedicine. 2016 May;12(4):1053-62. doi: 10.1016/j.nano.2015.12.382.
PMID: 26772430