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Items: 25


Best practices for benchmarking germline small-variant calls in human genomes.

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team.

Nat Biotechnol. 2019 Mar 11. doi: 10.1038/s41587-019-0054-x. [Epub ahead of print]


Detection of long repeat expansions from PCR-free whole-genome sequence data.

Dolzhenko E, van Vugt JJFA, Shaw RJ, Bekritsky MA, van Blitterswijk M, Narzisi G, Ajay SS, Rajan V, Lajoie BR, Johnson NH, Kingsbury Z, Humphray SJ, Schellevis RD, Brands WJ, Baker M, Rademakers R, Kooyman M, Tazelaar GHP, van Es MA, McLaughlin R, Sproviero W, Shatunov A, Jones A, Al Khleifat A, Pittman A, Morgan S, Hardiman O, Al-Chalabi A, Shaw C, Smith B, Neo EJ, Morrison K, Shaw PJ, Reeves C, Winterkorn L, Wexler NS; US–Venezuela Collaborative Research Group, Housman DE, Ng CW, Li AL, Taft RJ, van den Berg LH, Bentley DR, Veldink JH, Eberle MA.

Genome Res. 2017 Nov;27(11):1895-1903. doi: 10.1101/gr.225672.117. Epub 2017 Sep 8.


A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.

Eberle MA, Fritzilas E, Krusche P, Källberg M, Moore BL, Bekritsky MA, Iqbal Z, Chuang HY, Humphray SJ, Halpern AL, Kruglyak S, Margulies EH, McVean G, Bentley DR.

Genome Res. 2017 Jan;27(1):157-164. doi: 10.1101/gr.210500.116. Epub 2016 Nov 30.


Whole-genome haplotyping by dilution, amplification, and sequencing.

Kaper F, Swamy S, Klotzle B, Munchel S, Cottrell J, Bibikova M, Chuang HY, Kruglyak S, Ronaghi M, Eberle MA, Fan JB.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5552-7. doi: 10.1073/pnas.1218696110. Epub 2013 Mar 18.


Improved imputation of common and uncommon SNPs with a new reference set.

Wang Z, Jacobs KB, Yeager M, Hutchinson A, Sampson J, Chatterjee N, Albanes D, Berndt SI, Chung CC, Diver WR, Gapstur SM, Teras LR, Haiman CA, Henderson BE, Stram D, Deng X, Hsing AW, Virtamo J, Eberle MA, Stone JL, Purdue MP, Taylor P, Tucker M, Chanock SJ.

Nat Genet. 2011 Dec 27;44(1):6-7. doi: 10.1038/ng.1044. No abstract available.


Power to detect risk alleles using genome-wide tag SNP panels.

Eberle MA, Ng PC, Kuhn K, Zhou L, Peiffer DA, Galver L, Viaud-Martinez KA, Lawley CT, Gunderson KL, Shen R, Murray SS.

PLoS Genet. 2007 Oct;3(10):1827-37. Epub 2007 Aug 22.


Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome.

Eberle MA, Rieder MJ, Kruglyak L, Nickerson DA.

PLoS Genet. 2006 Sep 8;2(9):e142. Epub 2006 Jul 25.


Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus.

Mackelprang R, Livingston RJ, Eberle MA, Carlson CS, Yi Q, Akey JM, Nickerson DA.

Hum Genet. 2006 Apr;119(3):255-66. Epub 2006 Jan 20.


Genomic regions exhibiting positive selection identified from dense genotype data.

Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA.

Genome Res. 2005 Nov;15(11):1553-65.


Extensive and breed-specific linkage disequilibrium in Canis familiaris.

Sutter NB, Eberle MA, Parker HG, Pullar BJ, Kirkness EF, Kruglyak L, Ostrander EA.

Genome Res. 2004 Dec;14(12):2388-96. Epub 2004 Nov 15.


Population history and natural selection shape patterns of genetic variation in 132 genes.

Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L.

PLoS Biol. 2004 Oct;2(10):e286. Epub 2004 Sep 7.


Comment on 'Discrepancies in dbSNP confirmations rates and allele frequency distributions from varying genotyping error rates and patterns'.

Carlson CS, Reider MJ, Nickerson DA, Eberle MA, Kruglyak L.

Bioinformatics. 2005 Jan 15;21(2):141-3. Epub 2004 Aug 27. No abstract available.


Mapping complex disease loci in whole-genome association studies.

Carlson CS, Eberle MA, Kruglyak L, Nickerson DA.

Nature. 2004 May 27;429(6990):446-52. Review.


Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations.

Crawford DC, Carlson CS, Rieder MJ, Carrington DP, Yi Q, Smith JD, Eberle MA, Kruglyak L, Nickerson DA.

Am J Hum Genet. 2004 Apr;74(4):610-22. Epub 2004 Mar 10.


Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium.

Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA.

Am J Hum Genet. 2004 Jan;74(1):106-20. Epub 2003 Dec 15.


Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans.

Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglyak L, Nickerson DA.

Nat Genet. 2003 Apr;33(4):518-21. Epub 2003 Mar 24.


Sequence variation in the human T-cell receptor loci.

Mackelprang R, Carlson CS, Subrahmanyan L, Livingston RJ, Eberle MA, Nickerson DA.

Immunol Rev. 2002 Dec;190:26-39. Review.


A new susceptibility locus for autosomal dominant pancreatic cancer maps to chromosome 4q32-34.

Eberle MA, Pfützer R, Pogue-Geile KL, Bronner MP, Crispin D, Kimmey MB, Duerr RH, Kruglyak L, Whitcomb DC, Brentnall TA.

Am J Hum Genet. 2002 Apr;70(4):1044-8. Epub 2002 Feb 27.


Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion.

Ardlie K, Liu-Cordero SN, Eberle MA, Daly M, Barrett J, Winchester E, Lander ES, Kruglyak L.

Am J Hum Genet. 2001 Sep;69(3):582-9. Epub 2001 Jul 25.


Sequence variation and linkage disequilibrium in the human T-cell receptor beta (TCRB) locus.

Subrahmanyan L, Eberle MA, Clark AG, Kruglyak L, Nickerson DA.

Am J Hum Genet. 2001 Aug;69(2):381-95. Epub 2001 Jun 29.


An update on the science and therapy of obesity and its relationship to osteoarthritis.

Korner J, Eberle MA.

Curr Rheumatol Rep. 2001 Apr;3(2):101-6. Review.


An analysis of strategies for discovery of single-nucleotide polymorphisms.

Eberle MA, Kruglyak L.

Genet Epidemiol. 2000;19 Suppl 1:S29-35.


Sampling SNPs.

Yang Z, Wong GK, Eberle MA, Kibukawa M, Passey DA, Hughes WR, Kruglyak L, Yu J.

Nat Genet. 2000 Sep;26(1):13-4. No abstract available.


Acute reversible hypoxemia in systemic lupus erythematosus.

Abramson SB, Dobro J, Eberle MA, Benton M, Reibman J, Epstein H, Rapoport DM, Belmont HM, Goldring RM.

Ann Intern Med. 1991 Jun 1;114(11):941-7.


Methotrexate inhibits neutrophil function by stimulating adenosine release from connective tissue cells.

Cronstein BN, Eberle MA, Gruber HE, Levin RI.

Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2441-5.

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