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Page 1
The DNA sequence of the human X chromosome.
Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP, Frankish A, Lovell FL, Howe KL, Ashurst JL, Fulton RS, Sudbrak R, Wen G, Jones MC, Hurles ME, Andrews TD, Scott CE, Searle S, Ramser J, Whittaker A, Deadman R, Carter NP, Hunt SE, Chen R, Cree A, Gunaratne P, Havlak P, Hodgson A, Metzker ML, Richards S, Scott G, Steffen D, Sodergren E, Wheeler DA, Worley KC, Ainscough R, Ambrose KD, Ansari-Lari MA, Aradhya S, Ashwell RI, Babbage AK, Bagguley CL, Ballabio A, Banerjee R, Barker GE, Barlow KF, Barrett IP, Bates KN, Beare DM, Beasley H, Beasley O, Beck A, Bethel G, Blechschmidt K, Brady N, Bray-Allen S, Bridgeman AM, Brown AJ, Brown MJ, Bonnin D, Bruford EA, Buhay C, Burch P, Burford D, Burgess J, Burrill W, Burton J, Bye JM, Carder C, Carrel L, Chako J, Chapman JC, Chavez D, Chen E, Chen G, Chen Y, Chen Z, Chinault C, Ciccodicola A, Clark SY, Clarke G, Clee CM, Clegg S, Clerc-Blankenburg K, Clifford K, Cobley V, Cole CG, Conquer JS, Corby N, Connor RE, David R, Davies J, Davis C, Davis J, Delgado O, Deshazo D, Dhami P, Ding Y, Dinh H, Dodsworth S, Draper H, Dugan-Rocha S, Dunham A, Dunn M, Durbin KJ, Dutta I, Eades T, Ellwood M, Eme… See abstract for full author list ➔ Ross MT, et al. Among authors: shen h. Nature. 2005 Mar 17;434(7031):325-37. doi: 10.1038/nature03440. Nature. 2005. PMID: 15772651 Free PMC article.
The finished DNA sequence of human chromosome 12.
Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Montgomery KT, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Lovering RC, Wheeler DA, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clerc-Blankenburg KP, Davis C, Delgado O, Dinh HH, Draper H, Gonzalez-Garay ML, Havlak P, Jackson LR, Jacob LS, Kelly SH, Li L, Li Z, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Pasternak S, Perez LM, Plopper FJ, Santibanez J, Shen H, Tabor PE, Verduzco D, Waldron L, Wang Q, Williams GA, Zhang J, Zhou J, Allen CC, Amin AG, Anyalebechi V, Bailey M, Barbaria JA, Bimage KE, Bryant NP, Burch PE, Burkett CE, Burrell KL, Calderon E, Cardenas V, Carter K, Casias K, Cavazos I, Cavazos SR, Ceasar H, Chacko J, Chan SN, Chavez D, Christopoulos C, Chu J, Cockrell R, Cox CD, Dang M, Dathorne SR, David R, Davis CM, Davy-Carroll L, Deshazo DR, Donlin JE, D'Souza L, Eaves KA, Simons R, Emery-Cohen AJ, Escotto M, Flagg N, Forbes LD, Gabisi AM, Garza … See abstract for full author list ➔ Scherer SE, et al. Among authors: shen h. Nature. 2006 Mar 16;440(7082):346-51. doi: 10.1038/nature04569. Nature. 2006. PMID: 16541075
The DNA sequence, annotation and analysis of human chromosome 3.
Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJ, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. Muzny DM, et al. Among authors: shen h, shen y. Nature. 2006 Apr 27;440(7088):1194-8. doi: 10.1038/nature04728. Nature. 2006. PMID: 16641997 Free article.
Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF.
Bourgogne A, Garsin DA, Qin X, Singh KV, Sillanpaa J, Yerrapragada S, Ding Y, Dugan-Rocha S, Buhay C, Shen H, Chen G, Williams G, Muzny D, Maadani A, Fox KA, Gioia J, Chen L, Shang Y, Arias CA, Nallapareddy SR, Zhao M, Prakash VP, Chowdhury S, Jiang H, Gibbs RA, Murray BE, Highlander SK, Weinstock GM. Bourgogne A, et al. Among authors: shen h. Genome Biol. 2008;9(7):R110. doi: 10.1186/gb-2008-9-7-r110. Epub 2008 Jul 8. Genome Biol. 2008. PMID: 18611278 Free PMC article.
Somatic mutations affect key pathways in lung adenocarcinoma.
Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Ding L, et al. Among authors: shen h. Nature. 2008 Oct 23;455(7216):1069-75. doi: 10.1038/nature07423. Nature. 2008. PMID: 18948947 Free PMC article.
Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.
Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, Wang Q, Shen H, Holder M, Villasana D, Nazareth LV, Cree A, Courtney L, Veizer J, Kotkiewicz H, Cho TJ, Koutseva N, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Hughes JF, et al. Among authors: shen h. Nature. 2012 Feb 22;483(7387):82-6. doi: 10.1038/nature10843. Nature. 2012. PMID: 22367542 Free PMC article.
Fully resolved assembly of Cryptosporidium parvum.
Menon VK, Okhuysen PC, Chappell CL, Mahmoud M, Mahmoud M, Meng Q, Doddapaneni H, Vee V, Han Y, Salvi S, Bhamidipati S, Kottapalli K, Weissenberger G, Shen H, Ross MC, Hoffman KL, Cregeen SJ, Muzny DM, Metcalf GA, Gibbs RA, Petrosino JF, Sedlazeck FJ. Menon VK, et al. Among authors: shen h. Gigascience. 2022 Feb 15;11:giac010. doi: 10.1093/gigascience/giac010. Gigascience. 2022. PMID: 35166336 Free PMC article.
Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism.
Chander V, Mahmoud M, Hu J, Dardas Z, Grochowski CM, Dawood M, Khayat MM, Li H, Li S, Jhangiani S, Korchina V, Shen H, Weissenberger G, Meng Q, Gingras MC, Muzny DM, Doddapaneni H, Posey JE, Lupski JR, Sabo A, Murdock DR, Sedlazeck FJ, Gibbs RA. Chander V, et al. Among authors: shen h. Hum Mutat. 2022 Dec;43(12):2033-2053. doi: 10.1002/humu.24461. Epub 2022 Sep 24. Hum Mutat. 2022. PMID: 36054313 Free PMC article.
A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus.
Pellerin D, Del Gobbo GF, Couse M, Dolzhenko E, Nageshwaran SK, Cheung WA, Xu IRL, Dicaire MJ, Spurdens G, Matos-Rodrigues G, Stevanovski I, Scriba CK, Rebelo A, Roth V, Wandzel M, Bonnet C, Ashton C, Agarwal A, Peter C, Hasson D, Tsankova NM, Dewar K, Lamont PJ, Laing NG, Renaud M, Houlden H, Synofzik M, Usdin K, Nussenzweig A, Napierala M, Chen Z, Jiang H, Deveson IW, Ravenscroft G, Akbarian S, Eberle MA, Boycott KM, Pastinen T; All of Us Research Program Long Read Working Group; Brais B, Zuchner S, Danzi MC. Pellerin D, et al. Nat Genet. 2024 Jul;56(7):1366-1370. doi: 10.1038/s41588-024-01808-5. Epub 2024 Jun 27. Nat Genet. 2024. PMID: 38937606
Phenotypic expansion in KIF1A-related dominant disorders: A description of novel variants and review of published cases.
Montenegro-Garreaud X, Hansen AW, Khayat MM, Chander V, Grochowski CM, Jiang Y, Li H, Mitani T, Kessler E, Jayaseelan J, Shen H, Gezdirici A, Pehlivan D, Meng Q, Rosenfeld JA, Jhangiani SN, Madan-Khetarpal S, Scott DA, Abarca-Barriga H, Trubnykova M, Gingras MC, Muzny DM, Posey JE, Liu P, Lupski JR, Gibbs RA. Montenegro-Garreaud X, et al. Among authors: shen h. Hum Mutat. 2020 Dec;41(12):2094-2104. doi: 10.1002/humu.24118. Epub 2020 Oct 8. Hum Mutat. 2020. PMID: 32935419 Free PMC article. Review.
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