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Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschleb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, Ponting CP; Mouse Genome Sequencing Consortium. (2009). Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol May 5;7(5):e1000112.

Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. (2009). Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res
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Cellamare A, Catacchio CR, Alkan C, Giannuzzi G, Antonacci F, Cardone MF, Della Valle G, Malig M, Rocchi M, Eichler EE, Ventura M. (2009). New insights into centromere organization and evolution from the white-cheeked gibbon and marmoset. Mol Biol Evol Aug;26(8):1889-900.

Zhao Y, Marotta M, Eichler EE, Eng C, Tanaka H. (2009). Linkage disequilibrium between two high-frequency deletion polymorphisms: implications for association studies involving the glutathione-S transferase (GST) genes. PLoS Genet May;5(5):e1000472.

Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. (2009). Comparative analysis of Alu repeats in primate genomes. Genome Res May;19(5):876-85.

Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, (298 authors), Zhao FQ. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science Apr 24;324(5926):522-8.

Antonacci F, Kidd JM, Marques-Bonet T, Ventura M, Siswara P, Jiang Z, Eichler EE. (2009). Characterization of six human disease-associated inversion polymorphisms. Hum Mol Genet Jul 15;18(14):2555-66.

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Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, Ventura M, Kidd JM, Siswara P, Howard JC, Eichler EE. (2009). Death and resurrection of the human IRGM gene. PLoS Genet Mar;5(3):e1000403.

Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, Alkan C, Aksay G, Girirajan S, Siswara P, Chen L, Cardone MF, Navarro A, Mardis ER, Wilson RK, Eichler EE. (2009). A burst of segmental duplications in the genome of the African great ape ancestor. Nature Feb 12;457(7231):877-81.

de Cid R, Riveira-Munoz E, Zeeuwen PL, Robarge J, Liao W, Dannhauser EN, Giardina E, Stuart PE, Nair R, Helms C, Escaramis G, Ballana E, Martin-Ezquerra G, den Heijer M, Kamsteeg M, Joosten I, Eichler EE, Lazaro C, Pujol RM, Armengol L, Abecasis G, Elder JT, Novelli G, Armour JA, Kwok PY, Bowcock A, Schalkwijk J, Estivill X. (2009). Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat Genet Feb;41(2):211-5.