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A
Numanagić I, Malikić S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer S, S Sahinalp C. Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes. Nat Commun. 2018 ;9(1):828.
Nelson DL, Ballabio A, Victoria MF, Pieretti M, Bies RD, Gibbs RA, Maley JA, Chinault AC, Webster TD, Caskey CT. Alu-primed polymerase chain reaction for regional assignment of 110 yeast artificial chromosome clones from the human X chromosome: identification of clones associated with a disease locus. Proc Natl Acad Sci U S A. 1991 ;88(14):6157-61.
Wang M, Wang Y, You M, Devereux TR. Analysis of the Par2 modifier of pulmonary adenoma formation in mice. Exp Lung Res. 2005 ;31(2):193-204.
Zhao C, Shukle R, Navarro-Escalante L, Chen M, Richards S, Stuart JJ. Avirulence gene mapping in the Hessian fly (Mayetiola destructor) reveals a protein phosphatase 2C effector gene family. J Insect Physiol. 2016 ;84:22-31.
B
Rogers J, Hixson JE. Baboons as an animal model for genetic studies of common human disease. Am J Hum Genet. 1997 ;61(3):489-93.
Sedlazeck FJ, Talloji P, von Haeseler A, Bachmair A. Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets. Genomics. 2013 ;101(3):204-9.
Rogers J, Mahaney MC, Beamer WG, Donahue LR, Rosen CJ. Beyond one gene-one disease: alternative strategies for deciphering genetic determinants of osteoporosis. Calcif Tissue Int. 1997 ;60(3):225-8.
Liu Y, Qin X, Song X-ZHenry, Jiang H, Shen Y, K Durbin J, Lien S, Kent MPeter, Sodeland M, Ren Y, Zhang L, Sodergren E, Havlak P, Worley KC, Weinstock GM, Gibbs RA. Bos taurus genome assembly. BMC Genomics. 2009 ;10:180.
C
Gelb BD, Worley KC, Griffin LD, Adams V, Chinault AC, McCabe ER. Characterization of human genomic yeast artificial chromosome inserts containing hexokinase 1 coding information on chromosome 10. Biochem Med Metab Biol. 1992 ;47(3):265-9.
Sanghvi RV, Buhay CJ, Powell BC, Tsai EA, Dorschner MO, Hong CS, Lebo MS, Sasson A, Hanna DS, McGee S, Bowling KM, Cooper GM, Gray DE, Lonigro RJ, Dunford A, Brennan CA, Cibulskis C, Walker K, Carneiro MO, Sailsbery J, Hindorff LA, Robinson DR, Santani A, Sarmady M, Rehm HL, Biesecker LG, Nickerson DA, Hutter CM, Garraway L, Muzny DM, Wagle N. Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genet Med. 2018 ;20(8):855-866.
Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SRama Srida, Purushothaman K, Saju JM, Jiang J, Mbandi SKimbung, Jonas M, Tong AHin Yan, Mwangi S, Lau D, Ngoh SYan, Liew WChang, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin C-S, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Katneni VKumar, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet. 2016 ;12(4):e1005954.
Mamun AA al, Tominaga A, Enomoto M. Cloning and characterization of the region III flagellar operons of the four Shigella subgroups: genetic defects that cause loss of flagella of Shigella boydii and Shigella sonnei. J Bacteriol. 1997 ;179(14):4493-500.
Hinojos CA, Boerwinkle E, Fornage M, Doris PA. Combined genealogical, mapping, and expression approaches to identify spontaneously hypertensive rat hypertension candidate genes. Hypertension. 2005 ;45(4):698-704.
Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AOrtlieb, Jagodic M, Tuncel J, Norin U, Beattie E, Huynh N, Miller WH, Koller DL, Alam I, Falak S, Osborne-Pellegrin M, Martinez-Membrives E, Canete T, Blazquez G, Vicens-Costa E, Mont-Cardona C, Diaz-Moran S, Tobena A, Hummel O, Zelenika D, Saar K, Patone G, Bauerfeind A, Bihoreau M-T, Heinig M, Lee Y-A, Rintisch C, Schulz H, Wheeler DA, Worley KC, Muzny DM, Gibbs RA, Lathrop M, Lansu N, Toonen P, Ruzius FPaul, de Bruijn E, Hauser H, Adams DJ, Keane T, Atanur SS, Aitman TJ, Flicek P, Malinauskas T, E Jones Y, Ekman D, Lopez-Aumatell R, Dominiczak AF, Johannesson M, Holmdahl R, Olsson T, Gauguier D, Hübner N, Fernandez-Teruel A, Cuppen E, Mott R, Flint J. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. Nat Genet. 2013 ;45(7):767-75.
Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, K Durbin J, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MAF, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005 ;15(1):1-18.
Ansari-Lari MA, Oeltjen JC, Schwartz S, Zhang Z, Muzny DM, Lu J, Gorrell JH, Chinault AC, Belmont JW, Miller W, Gibbs RA. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Res. 1998 ;8(1):29-40.
Levin ML, Chatterjee A, Pragliola A, Worley KC, Wehnert M, Zhuchenko O, Smith RF, Lee CC, Herman GE. A comparative transcription map of the murine bare patches (Bpa) and striated (Str) critical regions and human Xq28. Genome Res. 1996 ;6(6):465-77.
Matejková P, Strouhal M, Smajs D, Norris SJ, Palzkill T, Petrosino JF, Sodergren E, Norton JE, Singh J, Richmond TA, Molla MN, Albert TJ, Weinstock GM. Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol. 2008 ;8:76.
Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet. 2020 ;16(5):e1008742.
Atkinson EG, Rogers J, Mahaney MC, Cox LA, Cheverud JM. Cortical Folding of the Primate Brain: An Interdisciplinary Examination of the Genetic Architecture, Modularity, and Evolvability of a Significant Neurological Trait in Pedigreed Baboons (Genus Papio). Genetics. 2015 ;200(2):651-65.
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Raveendran M, Harris RA, Milosavljevic A, Johnson Z, Shelledy W, Cameron J, Rogers J. Designing new microsatellite markers for linkage and population genetic analyses in rhesus macaques and other nonhuman primates. Genomics. 2006 ;88(6):706-710.
Mamun AA al, Tominaga A, Enomoto M. Detection and characterization of the flagellar master operon in the four Shigella subgroups. J Bacteriol. 1996 ;178(13):3722-6.
Bardoni B, Zanaria E, Guioli S, Floridia G, Worley KC, Tonini G, Ferrante E, Chiumello G, McCabe ER, Fraccaro M. A dosage sensitive locus at chromosome Xp21 is involved in male to female sex reversal. Nat Genet. 1994 ;7(4):497-501.
Eichler EE, Lu F, Shen Y, Antonacci R, Jurecic V, Doggett NA, Moyzis RK, Baldini A, Gibbs RA, Nelson DL. Duplication of a gene-rich cluster between 16p11.1 and Xq28: a novel pericentromeric-directed mechanism for paralogous genome evolution. Hum Mol Genet. 1996 ;5(7):899-912.
E
Weinstock GM. ENCODE: more genomic empowerment. Genome Res. 2007 ;17(6):667-8.