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Items: 45

1.

ExtRamp: a novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or relative codon adaptiveness.

Miller JB, Brase LR, Ridge PG.

Nucleic Acids Res. 2019 Jan 15. doi: 10.1093/nar/gky1193. [Epub ahead of print]

2.

RAB10: an Alzheimer's disease resilience locus and potential drug target.

Tavana JP, Rosene M, Jensen NO, Ridge PG, Kauwe JS, Karch CM.

Clin Interv Aging. 2018 Dec 28;14:73-79. doi: 10.2147/CIA.S159148. eCollection 2019. Review.

3.

Common DNA Variants Accurately Rank an Individual of Extreme Height.

Sexton CE, Ebbert MTW, Miller RH, Ferrel M, Tschanz JAT, Corcoran CD; Alzheimer's Disease Neuroimaging Initiative , Ridge PG, Kauwe JSK.

Int J Genomics. 2018 Sep 4;2018:5121540. doi: 10.1155/2018/5121540. eCollection 2018.

4.

JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm.

Miller JB, Pickett BD, Ridge PG.

Bioinformatics. 2019 Feb 15;35(4):546-552. doi: 10.1093/bioinformatics/bty669.

5.

Mitochondria and Alzheimer's Disease: the Role of Mitochondrial Genetic Variation.

Ridge PG, Kauwe JSK.

Curr Genet Med Rep. 2018;6(1):1-10. doi: 10.1007/s40142-018-0132-2. Epub 2018 Mar 1. Review.

6.

Mendelian adult-onset leukodystrophy genes in Alzheimer's disease: critical influence of CSF1R and NOTCH3.

Sassi C, Nalls MA, Ridge PG, Gibbs JR, Lupton MK, Troakes C, Lunnon K, Al-Sarraj S, Brown KS, Medway C, Lord J, Turton J, Bras J; ARUK Consortium, Blumenau S, Thielke M, Josties C, Freyer D, Dietrich A, Hammer M, Baier M, Dirnagl U, Morgan K, Powell JF, Kauwe JS, Cruchaga C, Goate AM, Singleton AB, Guerreiro R, Hodges A, Hardy J.

Neurobiol Aging. 2018 Jun;66:179.e17-179.e29. doi: 10.1016/j.neurobiolaging.2018.01.015. Epub 2018 Feb 2.

7.

Correction to: Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience.

Ridge PG, Karch CM, Hsu S, Arano I, Teerlink CC, Ebbert MTW, Murcia JDG, Farnham JM, Damato AR, Allen M, Wang X, Harari O, Fernandez VM, Guerreiro R, Bras J, Hardy J, Munger R, Norton M, Sassi C, Singleton A, Younkin SG, Dickson DW, Golde TE, Price ND, Ertekin-Taner N, Cruchaga C, Goate AM, Corcoran C, Tschanz J, Cannon-Albright LA, Kauwe JSK; Alzheimer’s Disease Neuroimaging Initiative.

Genome Med. 2018 Jan 12;10(1):4. doi: 10.1186/s13073-018-0516-7.

8.

Assembly of 809 whole mitochondrial genomes with clinical, imaging, and fluid biomarker phenotyping.

Ridge PG, Wadsworth ME, Miller JB, Saykin AJ, Green RC; Alzheimer's Disease Neuroimaging Initiative, Kauwe JSK.

Alzheimers Dement. 2018 Apr;14(4):514-519. doi: 10.1016/j.jalz.2017.11.013. Epub 2018 Jan 5.

9.

Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience.

Ridge PG, Karch CM, Hsu S, Arano I, Teerlink CC, Ebbert MTW, Gonzalez Murcia JD, Farnham JM, Damato AR, Allen M, Wang X, Harari O, Fernandez VM, Guerreiro R, Bras J, Hardy J, Munger R, Norton M, Sassi C, Singleton A, Younkin SG, Dickson DW, Golde TE, Price ND, Ertekin-Taner N, Cruchaga C, Goate AM, Corcoran C, Tschanz J, Cannon-Albright LA, Kauwe JSK; Alzheimer’s Disease Neuroimaging Initiative.

Genome Med. 2017 Nov 29;9(1):100. doi: 10.1186/s13073-017-0486-1. Erratum in: Genome Med. 2018 Jan 12;10 (1):4.

10.

Kmer-SSR: a fast and exhaustive SSR search algorithm.

Pickett BD, Miller JB, Ridge PG.

Bioinformatics. 2017 Dec 15;33(24):3922-3928. doi: 10.1093/bioinformatics/btx538.

11.

Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches.

Ebbert MT, Wadsworth ME, Staley LA, Hoyt KL, Pickett B, Miller J, Duce J; Alzheimer’s Disease Neuroimaging Initiative, Kauwe JS, Ridge PG.

BMC Bioinformatics. 2016 Jul 25;17 Suppl 7:239. doi: 10.1186/s12859-016-1097-3.

12.

A novel approach for multi-SNP GWAS and its application in Alzheimer's disease.

Bodily PM, Fujimoto MS, Page JT, Clement MJ, Ebbert MT, Ridge PG; Alzheimer’s Disease Neuroimaging Initiative.

BMC Bioinformatics. 2016 Jul 25;17 Suppl 7:268. doi: 10.1186/s12859-016-1093-7.

13.

Variants in CCL16 are associated with blood plasma and cerebrospinal fluid CCL16 protein levels.

Ebbert MT, Staley LA, Parker J, Parker S, Bailey M; Alzheimer’s Disease Neuroimaging Initiative, Ridge PG, Goate AM, Kauwe JS.

BMC Genomics. 2016 Jun 29;17 Suppl 3:437. doi: 10.1186/s12864-016-2788-x.

14.

Variants in ACPP are associated with cerebrospinal fluid Prostatic Acid Phosphatase levels.

Staley LA, Ebbert MT, Bunker D, Bailey M; Alzheimer’s Disease Neuroimaging Initiative, Ridge PG, Goate AM, Kauwe JS.

BMC Genomics. 2016 Jun 29;17 Suppl 3:439. doi: 10.1186/s12864-016-2787-y.

15.

Genome-wide association study of prolactin levels in blood plasma and cerebrospinal fluid.

Staley LA, Ebbert MT, Parker S, Bailey M; Alzheimer’s Disease Neuroimaging Initiative, Ridge PG, Goate AM, Kauwe JS.

BMC Genomics. 2016 Jun 29;17 Suppl 3:436. doi: 10.1186/s12864-016-2785-0.

16.

ABCA7 p.G215S as potential protective factor for Alzheimer's disease.

Sassi C, Nalls MA, Ridge PG, Gibbs JR, Ding J, Lupton MK, Troakes C, Lunnon K, Al-Sarraj S, Brown KS, Medway C, Clement N, Lord J, Turton J, Bras J, Almeida MR; ARUK Consortium, Holstege H, Louwersheimer E, van der Flier WM, Scheltens P, Van Swieten JC, Santana I, Oliveira C, Morgan K, Powell JF, Kauwe JS, Cruchaga C, Goate AM, Singleton AB, Guerreiro R, Hardy J.

Neurobiol Aging. 2016 Oct;46:235.e1-9. doi: 10.1016/j.neurobiolaging.2016.04.004. Epub 2016 Apr 20.

17.

Influence of Coding Variability in APP-Aβ Metabolism Genes in Sporadic Alzheimer's Disease.

Sassi C, Ridge PG, Nalls MA, Gibbs R, Ding J, Lupton MK, Troakes C, Lunnon K, Al-Sarraj S, Brown KS, Medway C, Lord J, Turton J; ARUK Consortium, Morgan K, Powell JF, Kauwe JS, Cruchaga C, Bras J, Goate AM, Singleton AB, Guerreiro R, Hardy J.

PLoS One. 2016 Jun 1;11(6):e0150079. doi: 10.1371/journal.pone.0150079. eCollection 2016.

18.

SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences.

Pickett BD, Karlinsey SM, Penrod CE, Cormier MJ, Ebbert MT, Shiozawa DK, Whipple CJ, Ridge PG.

Bioinformatics. 2016 Sep 1;32(17):2707-9. doi: 10.1093/bioinformatics/btw298. Epub 2016 May 11.

19.

Assessment of the genetic variance of late-onset Alzheimer's disease.

Ridge PG, Hoyt KB, Boehme K, Mukherjee S, Crane PK, Haines JL, Mayeux R, Farrer LA, Pericak-Vance MA, Schellenberg GD, Kauwe JSK; Alzheimer's Disease Genetics Consortium (ADGC).

Neurobiol Aging. 2016 May;41:200.e13-200.e20. doi: 10.1016/j.neurobiolaging.2016.02.024. Epub 2016 Mar 3.

20.

Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk.

Ebbert MTW, Boehme KL, Wadsworth ME, Staley LA; Alzheimer's Disease Neuroimaging Initiative; Alzheimer's Disease Genetics Consortium, Mukherjee S, Crane PK, Ridge PG, Kauwe JSK.

Alzheimers Dement. 2016 Feb;12(2):121-129. doi: 10.1016/j.jalz.2015.08.163. Epub 2015 Oct 9.

21.

Good laboratory practice for clinical next-generation sequencing informatics pipelines.

Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM.

Nat Biotechnol. 2015 Jul;33(7):689-93. doi: 10.1038/nbt.3237. No abstract available.

PMID:
26154004
22.

Bridging the gap between statistical and biological epistasis in Alzheimer's disease.

Ebbert MT, Ridge PG, Kauwe JS.

Biomed Res Int. 2015;2015:870123. doi: 10.1155/2015/870123. Epub 2015 May 17. Review.

23.

Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli.

Gardner SG, Miller JB, Dean T, Robinson T, Erickson M, Ridge PG, McCleary WR.

BMC Genet. 2015;16 Suppl 2:S2. doi: 10.1186/1471-2156-16-S2-S2. Epub 2015 Apr 23.

24.

Genome-wide association study of CSF levels of 59 alzheimer's disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation.

Kauwe JS, Bailey MH, Ridge PG, Perry R, Wadsworth ME, Hoyt KL, Staley LA, Karch CM, Harari O, Cruchaga C, Ainscough BJ, Bales K, Pickering EH, Bertelsen S; Alzheimer's Disease Neuroimaging Initiative, Fagan AM, Holtzman DM, Morris JC, Goate AM.

PLoS Genet. 2014 Oct 23;10(10):e1004758. doi: 10.1371/journal.pgen.1004758. eCollection 2014 Oct.

25.

Population-based analysis of cholesteryl ester transfer protein identifies association between I405V and cognitive decline: the Cache County Study.

Lythgoe C, Perkes A, Peterson M, Schmutz C, Leary M, Ebbert MT, Ridge PG, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS.

Neurobiol Aging. 2015 Jan;36(1):547.e1-3. doi: 10.1016/j.neurobiolaging.2014.08.022. Epub 2014 Aug 27.

26.

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files.

Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O'Fallon BD, Kauwe JS, Ridge PG.

BMC Bioinformatics. 2014;15 Suppl 7:S12. doi: 10.1186/1471-2105-15-S7-S12. Epub 2014 May 28.

27.

Population substructure in Cache County, Utah: the Cache County study.

Sharp AR, Ridge PG, Bailey MH, Boehme KL, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS; Alzheimer's Disease Neuroimaging Initiative.

BMC Bioinformatics. 2014;15 Suppl 7:S8. doi: 10.1186/1471-2105-15-S7-S8. Epub 2014 May 28.

28.

Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging.

Ridge PG, Maxwell TJ, Foutz SJ, Bailey MH, Corcoran CD, Tschanz JT, Norton MC, Munger RG, O'Brien E, Kerber RA, Cawthon RM, Kauwe JS.

BMC Bioinformatics. 2014;15 Suppl 7:S6. doi: 10.1186/1471-2105-15-S7-S6. Epub 2014 May 28.

29.

Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease.

Cruchaga C, Karch CM, Jin SC, Benitez BA, Cai Y, Guerreiro R, Harari O, Norton J, Budde J, Bertelsen S, Jeng AT, Cooper B, Skorupa T, Carrell D, Levitch D, Hsu S, Choi J, Ryten M, Sassi C, Bras J, Gibbs RJ, Hernandez DG, Lupton MK, Powell J, Forabosco P, Ridge PG, Corcoran CD, Tschanz JT, Norton MC, Munger RG, Schmutz C, Leary M, Demirci FY, Bamne MN, Wang X, Lopez OL, Ganguli M, Medway C, Turton J, Lord J, Braae A, Barber I, Brown K; Alzheimer's Research UK (ARUK) Consortium, Pastor P, Lorenzo-Betancor O, Brkanac Z, Scott E, Topol E, Morgan K, Rogaeva E, Singleton A, Hardy J, Kamboh MI, George-Hyslop PS, Cairns N, Morris JC, Kauwe JSK, Goate AM.

Nature. 2014 Jan 23;505(7484):550-554. doi: 10.1038/nature12825. Epub 2013 Dec 11.

30.

Alzheimer's disease: analyzing the missing heritability.

Ridge PG, Mukherjee S, Crane PK, Kauwe JS; Alzheimer’s Disease Genetics Consortium.

PLoS One. 2013 Nov 7;8(11):e79771. doi: 10.1371/journal.pone.0079771. eCollection 2013.

31.

Germline mutations in NFKB2 implicate the noncanonical NF-κB pathway in the pathogenesis of common variable immunodeficiency.

Chen K, Coonrod EM, Kumánovics A, Franks ZF, Durtschi JD, Margraf RL, Wu W, Heikal NM, Augustine NH, Ridge PG, Hill HR, Jorde LB, Weyrich AS, Zimmerman GA, Gundlapalli AV, Bohnsack JF, Voelkerding KV.

Am J Hum Genet. 2013 Nov 7;93(5):812-24. doi: 10.1016/j.ajhg.2013.09.009. Epub 2013 Oct 17.

32.

Strong evidence for a genetic contribution to late-onset Alzheimer's disease mortality: a population-based study.

Kauwe JS, Ridge PG, Foster NL, Cannon-Albright LA.

PLoS One. 2013 Oct 8;8(10):e77087. doi: 10.1371/journal.pone.0077087. eCollection 2013.

33.

Mitochondrial haplotypes associated with biomarkers for Alzheimer's disease.

Ridge PG, Koop A, Maxwell TJ, Bailey MH, Swerdlow RH, Kauwe JS, Honea RA; Alzheimer’s Disease Neuroimaging Initiative.

PLoS One. 2013 Sep 11;8(9):e74158. doi: 10.1371/journal.pone.0074158. eCollection 2013.

34.

Genetics of Alzheimer's disease.

Ridge PG, Ebbert MT, Kauwe JS.

Biomed Res Int. 2013;2013:254954. doi: 10.1155/2013/254954. Epub 2013 Jul 25. Review.

35.

Population-based analysis of Alzheimer's disease risk alleles implicates genetic interactions.

Ebbert MT, Ridge PG, Wilson AR, Sharp AR, Bailey M, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JS.

Biol Psychiatry. 2014 May 1;75(9):732-7. doi: 10.1016/j.biopsych.2013.07.008. Epub 2013 Aug 13.

36.

Cystic fibrosis testing in a referral laboratory: results and lessons from a six-year period.

Ridge PG, Miller C, Bayrak-Toydemir P, Best DH, Mao R, Swensen JJ, Lyon E, Voelkerding KV.

J Clin Bioinforma. 2013 Jan 23;3(1):3. doi: 10.1186/2043-9113-3-3.

37.

A direct comparison of next generation sequencing enrichment methods using an aortopathy gene panel- clinical diagnostics perspective.

Wooderchak-Donahue WL, O'Fallon B, Furtado LV, Durtschi JD, Plant P, Ridge PG, Rope AF, Yetman AT, Bayrak-Toydemir P.

BMC Med Genomics. 2012 Nov 14;5:50. doi: 10.1186/1755-8794-5-50.

38.

Mitochondrial genomic analysis of late onset Alzheimer's disease reveals protective haplogroups H6A1A/H6A1B: the Cache County Study on Memory in Aging.

Ridge PG, Maxwell TJ, Corcoran CD, Norton MC, Tschanz JT, O'Brien E, Kerber RA, Cawthon RM, Munger RG, Kauwe JS.

PLoS One. 2012;7(9):e45134. doi: 10.1371/journal.pone.0045134. Epub 2012 Sep 17.

39.

Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting.

Crockett DK, Ridge PG, Wilson AR, Lyon E, Williams MS, Narus SP, Facelli JC, Mitchell JA.

Genome Med. 2012 May 28;4(5):48. doi: 10.1186/gm347.

40.

Composition and evolution of the vertebrate and mammalian selenoproteomes.

Mariotti M, Ridge PG, Zhang Y, Lobanov AV, Pringle TH, Guigo R, Hatfield DL, Gladyshev VN.

PLoS One. 2012;7(3):e33066. doi: 10.1371/journal.pone.0033066. Epub 2012 Mar 30.

41.

Mycobacterium chelonae-abscessus complex associated with sinopulmonary disease, Northeastern USA.

Simmon KE, Brown-Elliott BA, Ridge PG, Durtschi JD, Mann LB, Slechta ES, Steigerwalt AG, Moser BD, Whitney AM, Brown JM, Voelkerding KV, McGowan KL, Reilly AF, Kirn TJ, Butler WR, Edelstein PH, Wallace RJ Jr, Petti CA.

Emerg Infect Dis. 2011 Sep;17(9):1692-700. doi: 10.3201/eid1709.101667.

42.

Association and expression analyses with single-nucleotide polymorphisms in TOMM40 in Alzheimer disease.

Cruchaga C, Nowotny P, Kauwe JS, Ridge PG, Mayo K, Bertelsen S, Hinrichs A, Fagan AM, Holtzman DM, Morris JC, Goate AM; Alzheimer's Disease Neuroimaging Initiative.

Arch Neurol. 2011 Aug;68(8):1013-9. doi: 10.1001/archneurol.2011.155.

43.

Predicting phenotypic severity of uncertain gene variants in the RET proto-oncogene.

Crockett DK, Piccolo SR, Ridge PG, Margraf RL, Lyon E, Williams MS, Mitchell JA.

PLoS One. 2011 Mar 30;6(3):e18380. doi: 10.1371/journal.pone.0018380.

44.
45.

Phylogenies scores for exhaustive searches and parsimony scores searches.

Carroll HD, Ridge PG, Clement MJ, Snell QO.

Int J Bioinform Res Appl. 2007;3(4):493-503.

PMID:
18048315

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