Publications

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Wise Lab

  1. Gao X, Gotway G, Rathjen K, Johnston C, Sparagana S, Rios J, Wise CA. High-density microarray and genomic analyses of patients presenting with unexplained early onset scoliosis, Spine Deformity, in press.
  2. Londono D, Kou I, Johnson TA, Sharma S, Ogura Y, Tsunoda T, Takahashi A, Matsumoto M, Herring JA, Lam T, Wang X, Tam EMS, Song YQ, Fan YH, Chan D, Cheah KSE, Qiu X, Jiang H, Huang D, Japanese Scoliosis Clinical Research Group, TSRHC IS Clinical Group, International Consortium for Scoliosis Genetics, Su P, Sham P, Cheung KMC, Luk KDK, Gordon D, Qiu Y, Cheng J, Tang N, Ikegawa S, Wise CA. A meta-analysis identifies adolescent idiopathic scoliosis association with LBX1 locus in multiple ethnic groups, J Med Genet 2014;51:401-406.PMID:24721834.
  3. Kou I, Takahashi Y, Johnson TA, Takahashi A, Guo L, Dai J, Qiu X, Sharma S, Takimoto A, Ogura Y, Jiang H, Yan H, Kono K, Kawakami N, Uno K, Ito M, Minami S, Yanagida H, Taneichi H, Hosono N, Tsuji T, Suzuki T, Sudo H, Kotani T, Yonezawa I, Londono D, Gordon D, Herring JA, Watanabe K, Chiba K, Kamatani N, Jiang Q, Hiraki Y, Kubo M, Toyama Y, Tsunoda T, Wise CA, Qiu Y, Shukunami C, Matsumoto M, Ikegawa S. Genetic variants in GPR126 are associated with adolescent idiopathic scoliosis. Nat Genet. 2013;45(6):676-9. PMID: 23666238
  4. Sharma S, Gao X, Londono D, Devroy SE, Mauldin KN, Frankel JT, Brandon JM, Zhang D, Li QZ, Dobbs MB, Gurnett CA, Grant SF, Hakonarson H, Dormans JP, Herring JA, Gordon D, Wise CA. Genome-wide association studies of adolescent idiopathic scoliosis suggest candidate susceptibility genes. Human Mol Genet 2011;20(7):1456-66. PMID: 21216876
  5. Swarkar S, Wise C. Current Understanding of Genetic Factors in Idiopathic Scoliosis. In: Kenro, Dunwoodie, editors. The Genetics and Development of Scoliosis: Springer; 2010. p.167-90.
  6. Wise CA, Gao X, Shoemaker S, Gordon D, Herring JA. Understanding genetic factors in idiopathic scoliosis, a complex disease of childhood. Curr Genomics. 2008;9(1):51-9. Epub 2008/03/01. PMID: 19424484
  7. Gao X, Gordon D, Zhang D, Browne R, Helms C, Gillum J, Weber S, Devroy S, Swaney S, Dobbs M, Morcuende J, Sheffield V, Lovett M, Bowcock A, Herring J, Wise C. CHD7 gene polymorphisms are associated with susceptibility to idiopathic scoliosis. Am J Hum Genet. 2007;80(5):957-65. Epub 2007/04/17. PMID: 17436250

Solnica-Krezel Lab

  1. Carlin, D., Sepich, D., Grover, V.K., Cooper, M.K., Solnica-Krezel, L., and Inbal, A. (2012). Six3 cooperates with Hedgehog signaling to specify ventral telencephalon by promoting early expression of Foxg1a and repressing Wnt signaling. Development 139, 2614-2624.
  2. Driever, W., Solnica-Krezel, L., Schier, A.F., Neuhauss, S.C., Malicki, J., Stemple, D.L., Stainier, D.Y., Zwartkruis, F., Abdelilah, S., Rangini, Z., et al. (1996). A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123, 37-46.
  3. Gray, R.S., Wilm, T.P., Smith, J., Bagnat, M., Dale, R.M., Topczewski, J., Johnson, S.L., and Solnica-Krezel, L. (2014). Loss of col8a1a function during zebrafish embryogenesis results in congenital vertebral malformations. Dev Biol 386, 72-85.
  4. Inbal, A., Kim, S.H., Shin, J., and Solnica-Krezel, L. (2007). Six3 represses nodal activity to establish early brain asymmetry in zebrafish. Neuron 55, 407-415.
  5. Jessen, J.R., and Solnica-Krezel, L. (2004). Identification and developmental expression pattern of van gogh-like 1, a second zebrafish strabismus homologue. Gene Expr Patterns 4, 339-344.
  6. Jessen, J.R., Topczewski, J., Bingham, S., Sepich, D.S., Marlow, F., Chandrasekhar, A., and Solnica-Krezel, L. (2002). Zebrafish trilobite identifies new roles for Strabismus in gastrulation and neuronal movements. Nat Cell Biol 4, 610-615.
  7. Kim, S.H., Speirs, C.K., Solnica-Krezel, L., and Ess, K.C. (2011). Zebrafish model of tuberous sclerosis complex reveals cell-autonomous and non-cell-autonomous functions of mutant tuberin. Dis Model Mech 4, 255-267.
  8. Lin, F., Chen, S., Sepich, D.S., Panizzi, J.R., Clendenon, S.G., Marrs, J.A., Hamm, H.E., and Solnica-Krezel, L. (2009). Galpha12/13 regulate epiboly by inhibiting E-cadherin activity and modulating the actin cytoskeleton. J Cell Biol 184, 909-921.
  9. Marlow, F., Gonzalez, E.M., Yin, C., Rojo, C., and Solnica-Krezel, L. (2004). No tail co-operates with non-canonical Wnt signaling to regulate posterior body morphogenesis in zebrafish. Development 131, 203-216.
  10. Marlow, F., Topczewski, J., Sepich, D., and Solnica-Krezel, L. (2002). Zebrafish Rho kinase 2 acts downstream of Wnt11 to mediate cell polarity and effective convergence and extension movements. Curr Biol 12, 876-884.
  11. Marlow, F., Zwartkruis, F., Malicki, J., Neuhauss, S.C., Abbas, L., Weaver, M., Driever, W., and Solnica-Krezel, L. (1998). Functional interactions of genes mediating convergent extension, knypek and trilobite, during the partitioning of the eye primordium in zebrafish. Dev Biol 203, 382-399.
  12. Miller-Bertoglio, V., Carmany-Rampey, A., Furthauer, M., Gonzalez, E.M., Thisse, C., Thisse, B., Halpern, M.E., and Solnica-Krezel, L. (1999). Maternal and zygotic activity of the zebrafish ogon locus antagonizes BMP signaling. Dev Biol 214, 72-86.
  13. Myers, D.C., Sepich, D.S., and Solnica-Krezel, L. (2002). Bmp activity gradient regulates convergent extension during zebrafish gastrulation. Dev Biol 243, 81-98.
  14. Sepich, D.S., Myers, D.C., Short, R., Topczewski, J., Marlow, F., and Solnica-Krezel, L. (2000). Role of the zebrafish trilobite locus in gastrulation movements of convergence and extension. Genesis 27, 159-173.
  15. Sepich, D.S., Usmani, M., Pawlicki, S., and Solnica-Krezel, L. (2011). Wnt/PCP signaling controls intracellular position of MTOCs during gastrulation convergence and extension movements. Development 138, 543-552.
  16. Shin, J., Chen, J., and Solnica-Krezel, L. (2014). Efficient homologous recombination mediated genome engineering in zebrafish using TALE nucleases. Development in press.
  17. Shin, J., Padmanabhan, A., de Groh, E.D., Lee, J.S., Haidar, S., Dahlberg, S., Guo, F., He, S., Wolman, M.A., Granato, M., et al. (2012). Zebrafish neurofibromatosis type 1 genes have redundant functions in tumorigenesis and embryonic development. Dis Model Mech 5, 881-894.
  18. Solnica-Krezel, L., Schier, A.F., and Driever, W. (1994). Efficient recovery of ENU-induced mutations from the zebrafish germline. Genetics 136, 1401-1420.
  19. Solnica-Krezel, L., Stemple, D.L., Mountcastle-Shah, E., Rangini, Z., Neuhauss, S.C., Malicki, J., Schier, A.F., Stainier, D.Y., Zwartkruis, F., Abdelilah, S., et al. (1996). Mutations affecting cell fates and cellular rearrangements during gastrulation in zebrafish. Development 123, 67-80.
  20. Speirs, C.K., Jernigan, K.K., Kim, S.H., Cha, Y.I., Lin, F., Sepich, D.S., DuBois, R.N., Lee, E., and Solnica-Krezel, L. (2010). Prostaglandin Gbetagamma signaling stimulates gastrulation movements by limiting cell adhesion through Snai1a stabilization. Development 137, 1327-1337.
  21. Topczewski, J., Sepich, D.S., Myers, D.C., Walker, C., Amores, A., Lele, Z., Hammerschmidt, M., Postlethwait, J., and Solnica-Krezel, L. (2001). The zebrafish glypican knypek controls cell polarity during gastrulation movements of convergent extension. Dev Cell 1, 251-264.
  22. Van Raay, T.J., Coffey, R.J., and Solnica-Krezel, L. (2007). Zebrafish Naked1 and Naked2 antagonize both canonical and non-canonical Wnt signaling. Dev Biol 309, 151-168.
  23. Wilm, T.P., and Solnica-Krezel, L. (2005). Essential roles of a zebrafish prdm1/blimp1 homolog in embryo patterning and organogenesis. Development 132, 393-404.
  24. Yin, C., and Solnica-Krezel, L. (2007a). Convergence and extension movements affect dynamic notochord-somite interactions essential for zebrafish slow muscle morphogenesis. Dev Dyn 236, 2742-2756.
  25. Yin, C., and Solnica-Krezel, L. (2007b). Convergence and extension movements mediate the specification and fate maintenance of zebrafish slow muscle precursors. Dev Biol 304, 141-155.
  26. Zeng, X.X., Wilm, T.P., Sepich, D.S., and Solnica-Krezel, L. (2007). Apelin and its receptor control heart field formation during zebrafish gastrulation. Dev Cell 12, 391-402.

Ahituv Lab

  1. Evans DS, Calton MA, Kim MJ, Kwok PY, Miljkovic I, Harris T, Koster A, Liu Y, Tranah GJ, Ahituv N, Hsueh WC, Vaisse C. Genetic Association Study of Adiposity and Melanocortin-4 Receptor (MC4R) Common Variants: Replication and Functional Characterization of Non-Coding Regions. PLoS One. 2014; 9(5):e96805.
  2. Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013 Dec 12; 504(7479):306-10.
  3. Booker BM, Murphy KK, Ahituv N. Functional analysis of limb enhancers in the developing fin. Dev Genes Evol. 2013 Nov; 223(6):395-9.
  4. Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol. 2013 Jul 18;14(7):R72.
  5. Zhao J, Shi H, Ahituv N. Classification of topological domains based on gene expression and regulation. Genome. 2013 Jul; 56(7):415-23.
  6. Oksenberg N, Ahituv N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet. 2013 Oct; 29(10):600-8.
  7. Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet. 2013 Aug 28; 45(9):1021-8.
  8. Oksenberg N, Stevison L, Wall JD, Ahituv N. Function and Regulation of AUTS2, a Gene Implicated in Autism and Human Evolution. PLoS Genet. 2013 Jan; 9(1):e1003221.
  9. Kim MJ, Ahituv N. The hydrodynamic tail vein assay as a tool for the study of liver promoters and enhancers. Methods Mol Biol. 2013; 1015:279-89.
  10. Andersson LS, Larhammar M, Memic F, Wootz H, Schwochow D, Rubin CJ, Patra K, Arnason T, Wellbring L, Hjälm G, Imsland F, Petersen JL, McCue ME, Mickelson JR, Cothran G, Ahituv N, Roepstorff L, Mikko S, Vallstedt A, Lindgren G, Andersson L, Kullander K. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature. 2012 Aug 30; 488(7413):642-6.
  11. Birnbaum RY, Everman DB, Murphy KK, Gurrieri F, Schwartz CE, Ahituv N. Functional characterization of tissue-specific enhancers in the DLX5/6 locus. Hum Mol Genet. 2012 Nov 15; 21(22):4930-8.
  12. Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G. Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 2012; 8(8):e1002852.
  13. VanderMeer JE, Afzal M, Alyas S, Haque S, Ahituv N, Malik S. A novel ZRS mutation in a Balochi tribal family with triphalangeal thumb, pre-axial polydactyly, post-axial polydactyly, and syndactyly. Am J Med Genet A. 2012 Aug; 158A(8):2031-5.
  14. Lu W, Bacino CA, Richards BS, Alvarez C, VanderMeer JE, Vella M, Ahituv N, Sikka N, Dietz FR, Blanton SH, Hecht JT. Studies of TBX4 and chromosome 17q23.1q23.2: an uncommon cause of nonsyndromic clubfoot. Am J Med Genet A. 2012 Jul; 158A(7):1620-7.
  15. Smith RP, Lam ET, Markova S, Yee SW, Ahituv N. Pharmacogene regulatory elements: from discovery to applications. Genome Med. 2012; 4(5):45.
  16. Laurell T, Vandermeer JE, Wenger AM, Grigelioniene G, Nordenskjöld A, Arner M, Ekblom AG, Bejerano G, Ahituv N, Nordgren A. A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb. Hum Mutat. 2012 Jul; 33(7):1063-6.
  17. Birnbaum RY, Clowney EJ, Agamy O, Kim MJ, Zhao J, Yamanaka T, Pappalardo Z, Clarke SL, Wenger AM, Nguyen L, Gurrieri F, Everman DB, Schwartz CE, Birk OS, Bejerano G, Lomvardas S, Ahituv N. Coding exons function as tissue-specific enhancers of nearby genes. Genome Res. 2012 Jun; 22(6):1059-68.
  18. Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, Ahituv N, Pennacchio LA, Shendure J. Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol. 2012 Mar; 30(3):265-70.
  19. Ahituv N. Location, location, cis-mutation. Hum Mutat. 2011 Dec; 32(12):iv.
  20. Kim MJ, Skewes-Cox P, Fukushima H, Hesselson S, Yee SW, Ramsey LB, Nguyen L, Eshragh JL, Castro RA, Wen CC, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Relling MV, Giacomini KM, Kroetz DL, Ahituv N. Functional characterization of liver enhancers that regulate drug-associated transporters. Clin Pharmacol Ther. 2011 Apr; 89(4):571-8.
  21. VanderMeer JE, Ahituv N. cis-regulatory mutations are a genetic cause of human limb malformations. Dev Dyn. 2011 May; 240(5):920-30.
  22. Ha Choi J, Wah Yee S, Kim MJ, Nguyen L, Ho Lee J, Kang JO, Hesselson S, Castro RA, Stryke D, Johns SJ, Kwok PY, Ferrin TE, Goo Lee M, Black BL, Ahituv N, Giacomini KM. Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1. Pharmacogenet Genomics. 2009 Oct; 19(10):770-80.
  23. Kroetz DL, Ahituv N, Burchard EG, Guo S, Sali A, Giacomini KM. Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy. Pharmacogenomics. 2009 Oct; 10(10):1569-76.
  24. Yee SW, Shima JE, Hesselson S, Nguyen L, De Val S, Lafond RJ, Kawamoto M, Johns SJ, Stryke D, Kwok PY, Ferrin TE, Black BL, Gurwitz D, Ahituv N, Giacomini KM. Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2). J Pharmacol Exp Ther. 2009 Mar; 328(3):699-707.
  25. Calton MA, Ersoy BA, Zhang S, Kane JP, Malloy MJ, Pullinger CR, Bromberg Y, Pennacchio LA, Dent R, McPherson R, Ahituv N, Vaisse C. Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study. Hum Mol Genet. 2009 Mar 15; 18(6):1140-7.