Research laboratory of Nadav Ahituv, PhD

Publications

  • Luizon MR, Eckalbar WL, Wang Y, Jones SL, Smith RP, Laurance M, Lin L, Gallins PJ, Etheridge AS, Wright F, Zhou Y, Molony C, Innocenti F, Yee SW, Giacomini KM, Ahituv N. Genomic Characterization of Metformin Hepatic Response. PLoS Genet. 2016 Nov 30;12(11):e1006449. PMID: 27902686. View in: PubMed

  • Eclov RJ, Kim MJ, Smith RP, Liang X, Ahituv N, Kroetz DL. In Vivo Hepatic Enhancer Elements in the Human ABCG2 Locus. Drug Metab Dispos. 2016 Nov 17. [Epub ahead of print]. PMID: 27856528. View in: PubMed

  • Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res. 2016 Nov 9. [Epub ahead of print]. PMID: 27831498. View in: PubMed

  • Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM, Nishizaki S, Muswamba-Nday C, Terhune E, Nevonen KA, Makki N, Friedrich T, VanderMeer JE, Pollard KS, Carbone L, Wall JD, Illing N, Ahituv N. Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet. 2016 [Epub ahead of print]. PMID: 27019111. View in: PubMed

  • Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N. Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PLoS Genet. 2016 Mar; 12(3):e1005738. PMID: 27019019. View in: PubMed

  • Ahituv N. Exonic enhancers: proceed with caution in exome and genome sequencing studies. Genome Med. 2016; 8(1):14. PMID: 26856702. View in: PubMed

  • Jorgenson E, Makki N, Shen L, Chen DC, Tian C, Eckalbar WL, Hinds D, Ahituv N, Avins A. A genome-wide association study identifies four novel susceptibility loci underlying inguinal hernia. Nat Commun. 2015; 6:10130. PMID: 26686553. View in: PubMed

  • Matharu N, Ahituv N. Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease. PLoS Genet. 2015 Dec; 11(12):e1005640. PMID: 26632825. View in: PubMed

  • Hesse RG, Kouklis GK, Ahituv N, Pomerantz JH. The human ARF tumor suppressor senses blastema activity and suppresses epimorphic tissue regeneration. Elife. 2015; 4. PMID: 26575287. View in: PubMed

  • Luizon MR, Ahituv N. Uncovering drug-responsive regulatory elements. Pharmacogenomics. 2015 Nov; 16(16):1829-41. PMID: 26555224. View in: PubMed

  • Yang S, Oksenberg N, Takayama S, Heo SJ, Poliakov A, Ahituv N, Dubchak I, Boffelli D. Functionally conserved enhancers with divergent sequences in distant vertebrates. BMC Genomics. 2015; 16(1):882. PMID: 26519295. View in: PubMed

  • Tapaltsyan V, Charles C, Hu J, Mindell D, Ahituv N, Wilson GM, Black BL, Viriot L, Klein OD, et al. Identification of novel Fgf enhancers and their role in dental evolution. Evol Dev. 2015 Jun 18. PMID: 26086993. View in: PubMed

  • Inoue F, Ahituv N. Decoding enhancers using massively parallel reporter assays. Genomics. 2015 Sep; 106(3):159-64. PMID: 26072433. View in: PubMed

  • Sharma S, Londono D, Eckalbar WL, Gao X, Zhang D, Mauldin K, Kou I, Takahashi A, Matsumoto M, Kamiya N, Murphy KK, Cornelia R, Herring JA, Burns D, Ahituv N, Ikegawa S, Gordon D, Wise CA. A PAX1 enhancer locus is associated with susceptibility to idiopathic scoliosis in females. Nat Commun. 2015; 6:6452. PMID: 25784220. View in: PubMed

  • Birnbaum RY, Patwardhan RP, Kim MJ, Findlay GM, Martin B, Zhao J, Bell RJ, Smith RP, Ku AA, Shendure J, Ahituv N. Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PLoS Genet. 2014 Oct; 10(10):e1004592. View in: PubMed

  • Markenscoff-Papadimitriou E, Allen WE, Colquitt BM, Goh T, Murphy KK, Monahan K, Mosley CP, Ahituv N, Lomvardas S. Enhancer interaction networks as a means for singular olfactory receptor expression. Cell. 2014 Oct 23; 159(3):543-57. View in: PubMed

  • Smith RP, Eckalbar WL, Morrissey KM, Luizon MR, Hoffmann TJ, Sun X, Jones SL, Force Aldred S, Ramamoorthy A, Desta Z, Liu Y, Skaar TC, Trinklein ND, Giacomini KM, Ahituv N. Genome-wide discovery of drug-dependent human liver regulatory elements. PLoS Genet. 2014 Oct; 10(10):e1004648. View in: PubMed

  • VanderMeer JE, Smith RP, Jones SL, Ahituv N. Genome-wide identification of signaling center enhancers in the developing limb. Development. 2014 Nov; 141(21):4194-8. View in: PubMed

  • Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol. 2014 Jun; 10(6):e1003677. View in: PubMed

  • VanderMeer JE, Lozano R, Sun M, Xue Y, Daentl D, Jabs EW, Wilcox WR, Ahituv N. A Novel ZRS Mutation Leads to Preaxial Polydactyly Type 2 in a Heterozygous Form and Werner Mesomelic Syndrome in a Homozygous Form. Hum Mutat. 2014 Aug; 35(8):945-8. View in: PubMed

  • Laurell T, Nilsson D, Hofmeister W, Lindstrand A, Ahituv N, Vandermeer J, Amilon A, Annerén G, Arner M, Pettersson M, Jäntti N, Rosberg HE, Cattini PA, Nordenskjöld A, Mäkitie O, Grigelioniene G, Nordgren A. Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease. Mol Genet Genomic Med. 2014 Sep; 2(5):402-11. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • Kim MJ, Oksenberg N, Hoffmann TJ, Vaisse C, Ahituv N. Functional characterization of SIM1-associated enhancers. Hum Mol Genet. 2014 Apr 1; 23(7):1700-8. View in: PubMed

  • Booker BM, Murphy KK, Ahituv N. Functional analysis of limb enhancers in the developing fin. Dev Genes Evol. 2013 Nov; 223(6):395-9. View in: PubMed

  • Zhao J, Shi H, Ahituv N. Classification of topological domains based on gene expression and regulation. Genome. 2013 Jul; 56(7):415-23. View in: PubMed

  • Oksenberg N, Ahituv N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet. 2013 Oct; 29(10):600-8. View in: PubMed

  • 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 Sep; 45(9):1021-8. View in: PubMed

  • 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; 14(7):R72. View in: PubMed

  • Oksenberg N, Stevison L, Wall JD, Ahituv N. Function and regulation of AUTS2, a gene implicated in autism and human evolution. PLoS Genet. 2013; 9(1):e1003221. View in: PubMed

  • Taher L, Smith RP, Kim MJ, Ahituv N, Ovcharenko I. Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. Genome Biol. 2013; 14(10):R117. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • Smith RP, Lam ET, Markova S, Yee SW, Ahituv N. Pharmacogene regulatory elements: from discovery to applications. Genome Med. 2012; 4(5):45. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • Ahituv N. Location, location, cis-mutation. Hum Mutat. 2011 Dec; 32(12):iv. View in: PubMed

  • 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. View in: PubMed

  • VanderMeer JE, Ahituv N. cis-regulatory mutations are a genetic cause of human limb malformations. Dev Dyn. 2011 May; 240(5):920-30. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • 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. View in: PubMed

  • Svenson KL, Ahituv N, Durgin RS, Savage H, Magnani PA, Foreman O, Paigen B, Peters LL. A new mouse mutant for the LDL receptor identified using ENU mutagenesis. J Lipid Res. 2008 Nov; 49(11):2452-62. View in: PubMed

  • Goren A, Kim E, Amit M, Bochner R, Lev-Maor G, Ahituv N, Ast G. Alternative approach to a heavy weight problem. Genome Res. 2008 Feb; 18(2):214-20. View in: PubMed

  • Ahituv N, Akiyama J, Chapman-Helleboid A, Fruchart J, Pennacchio LA. In vivo characterization of human APOA5 haplotypes. Genomics. 2007 Dec; 90(6):674-9. View in: PubMed

  • Costford SR, Kavaslar N, Ahituv N, Chaudhry SN, Schackwitz WS, Dent R, Pennacchio LA, McPherson R, Harper ME. Gain-of-function R225W mutation in human AMPKgamma(3) causing increased glycogen and decreased triglyceride in skeletal muscle. PLoS One. 2007; 2(9):e903. View in: PubMed

  • Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 2007 Sep; 5(9):e234. View in: PubMed

  • Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio LA. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007 Apr; 80(4):779-91. View in: PubMed

  • Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006 Nov 23; 444(7118):499-502. View in: PubMed

  • Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 4; 441(7089):87-90. View in: PubMed

  • Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Collier JM, Hébert S, Doelle H, Dent R, Pennacchio LA, McPherson R. A PYY Q62P variant linked to human obesity. Hum Mol Genet. 2006 Feb 1; 15(3):387-91. View in: PubMed

  • Ahituv N, Prabhakar S, Poulin F, Rubin EM, Couronne O. Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. Hum Mol Genet. 2005 Oct 15; 14(20):3057-63. View in: PubMed

  • Baroukh N, Ahituv N, Chang J, Shoukry M, Afzal V, Rubin EM, Pennacchio LA. Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene. Mamm Genome. 2005 Feb; 16(2):91-5. View in: PubMed

  • Ahituv N, Rubin EM, Nobrega MA. Exploiting human--fish genome comparisons for deciphering gene regulation. Hum Mol Genet. 2004 Oct 1; 13 Spec No 2:R261-6. View in: PubMed

  • Ahituv N, Erven A, Fuchs H, Guy K, Ashery-Padan R, Williams T, de Angelis MH, Avraham KB, Steel KP. An ENU-induced mutation in AP-2alpha leads to middle ear and ocular defects in Doarad mice. Mamm Genome. 2004 Jun; 15(6):424-32. View in: PubMed

  • Ahituv N, Avraham KB. Mouse models for human deafness: current tools for new fashions. Trends Mol Med. 2002 Sep; 8(9):447-51. View in: PubMed

  • Melchionda S, Ahituv N, Bisceglia L, Sobe T, Glaser F, Rabionet R, Arbones ML, Notarangelo A, Di Iorio E, Carella M, Zelante L, Estivill X, Avraham KB, Gasparini P. MYO6, the human homologue of the gene responsible for deafness in Snell's waltzer mice, is mutated in autosomal dominant nonsyndromic hearing loss. Am J Hum Genet. 2001 Sep; 69(3):635-40. View in: PubMed

  • Kiernan AE, Ahituv N, Fuchs H, Balling R, Avraham KB, Steel KP, Hrabé de Angelis M. The Notch ligand Jagged1 is required for inner ear sensory development. Proc Natl Acad Sci U S A. 2001 Mar 27; 98(7):3873-8. View in: PubMed

  • Ahituv N, Sobe T, Robertson NG, Morton CC, Taggart RT, Avraham KB. Genomic structure of the human unconventional myosin VI gene. Gene. 2000 Dec 31; 261(2):269-75. View in: PubMed

  • Ahituv N, Avraham KB. Auditory and vestibular mouse mutants: models for human deafness. J Basic Clin Physiol Pharmacol. 2000; 11(3):181-91. View in: PubMed

  • Vahava O, Morell R, Lynch ED, Weiss S, Kagan ME, Ahituv N, Morrow JE, Lee MK, Skvorak AB, Morton CC, Blumenfeld A, Frydman M, Friedman TB, King MC, Avraham KB. Mutation in transcription factor POU4F3 associated with inherited progressive hearing loss in humans. Science. 1998 Mar 20; 279(5358):1950-4. View in: PubMed

  • Ahituv N, Berman O. Devising a cooperation policy for emergency networks. J Oper Res Soc. 1987 Nov; 38(11):1015-29. View in: PubMed