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Items: 9

1.

VCPA: genomic Variant Calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.

Leung YY, Valladares O, Chou YF, Lin HJ, Kuzma AB, Cantwell L, Qu L, Gangadharan P, Salerno WJ, Schellenberg GD, Wang LS.

Bioinformatics. 2018 Oct 23. doi: 10.1093/bioinformatics/bty894. [Epub ahead of print]

PMID:
30351394
2.

Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation.

Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Charbonnier C, Chung J, Crane PK, Cruchaga C, Cupples LA, Dartigues JF, Debette S, Deleuze JF, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, Ikram MA, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimäki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, Pericak-Vance MA, Perola M, Psaty BM, Quenez O, Rajabli F, Redon R, Reitz C, Remes AM, Salomaa V, Sarnowski C, Schmidt H, Schmidt M, Schmidt R, Soininen H, Thornton TA, Tosto G, Tzourio C, van der Lee SJ, van Duijn CM, Vardarajan B, Wang W, Wijsman E, Wilson RK, Witten D, Worley KC, Zhang X; Alzheimer’s Disease Sequencing Project, Bellenguez C, Lambert JC, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, Destefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj AC, Fornage M, Farrer LA.

Mol Psychiatry. 2018 Aug 14. doi: 10.1038/s41380-018-0112-7. [Epub ahead of print]

PMID:
30108311
3.

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.

Naj AC, Lin H, Vardarajan BN, White S, Lancour D, Ma Y, Schmidt M, Sun F, Butkiewicz M, Bush WS, Kunkle BW, Malamon J, Amin N, Choi SH, Hamilton-Nelson KL, van der Lee SJ, Gupta N, Koboldt DC, Saad M, Wang B, Nato AQ, Sohi HK, Kuzma A, Wang LS, Adrienne Cupples L, van Duijn C, Seshadri S, Schellenberg GD, Boerwinkle E, Bis JC, Dupuis J, Salerno WJ, Wijsman EM, Martin ER, DeStefano AL.

Genomics. 2018 May 29. pii: S0888-7543(18)30281-7. doi: 10.1016/j.ygeno.2018.05.004. [Epub ahead of print]

PMID:
29857119
4.

SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads.

Hampton OA, English AC, Wang M, Salerno WJ, Liu Y, Muzny DM, Han Y, Wheeler DA, Worley KC, Lupski JR, Gibbs RA.

BMC Genomics. 2017 Oct 3;18(Suppl 6):691. doi: 10.1186/s12864-017-4021-y.

5.

Assessing structural variation in a personal genome-towards a human reference diploid genome.

English AC, Salerno WJ, Hampton OA, Gonzaga-Jauregui C, Ambreth S, Ritter DI, Beck CR, Davis CF, Dahdouli M, Ma S, Carroll A, Veeraraghavan N, Bruestle J, Drees B, Hastie A, Lam ET, White S, Mishra P, Wang M, Han Y, Zhang F, Stankiewicz P, Wheeler DA, Reid JG, Muzny DM, Rogers J, Sabo A, Worley KC, Lupski JR, Boerwinkle E, Gibbs RA.

BMC Genomics. 2015 Apr 11;16:286. doi: 10.1186/s12864-015-1479-3.

6.

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping.

English AC, Salerno WJ, Reid JG.

BMC Bioinformatics. 2014 Jun 10;15:180. doi: 10.1186/1471-2105-15-180.

7.

Rhox homeobox gene cluster: recent duplication of three family members.

MacLean JA 2nd, Lorenzetti D, Hu Z, Salerno WJ, Miller J, Wilkinson MF.

Genesis. 2006 Mar;44(3):122-9.

PMID:
16496311
8.

MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data.

Salerno WJ, Seaver SM, Armstrong BR, Radhakrishnan I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W566-8.

9.

Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding.

Kang RS, Daniels CM, Francis SA, Shih SC, Salerno WJ, Hicke L, Radhakrishnan I.

Cell. 2003 May 30;113(5):621-30.

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