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Genome-wide association analysis confirms and extends the association of SLC2A9 with serum uric acid levels to Mexican Americans.

Frontiers in genetics

Voruganti VS, Kent JW, Debnath S, Cole SA, Haack K, Göring HH, Carless MA, Curran JE, Johnson MP, Almasy L, Dyer TD, Maccluer JW, Moses EK, Abboud HE, Mahaney MC, Blangero J, Comuzzie AG.
PMID: 24379826
Front Genet. 2013 Dec 16;4:279. doi: 10.3389/fgene.2013.00279. eCollection 2013.

Increased serum uric acid (SUA) is a risk factor for gout and renal and cardiovascular disease (CVD). The purpose of this study was to identify genetic factors that affect the variation in SUA in 632 Mexican Americans participants of...

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Voruganti VS, Kent JW, Debnath S, et al. Genome-wide association analysis confirms and extends the association of SLC2A9 with serum uric acid levels to Mexican Americans. Front Genet. 2013;4:279doi: 10.3389/fgene.2013.00279.
Voruganti, V. S., Kent, J. W., Debnath, S., Cole, S. A., Haack, K., Göring, H. H., Carless, M. A., Curran, J. E., Johnson, M. P., Almasy, L., Dyer, T. D., Maccluer, J. W., Moses, E. K., Abboud, H. E., Mahaney, M. C., Blangero, J., & Comuzzie, A. G. (2013). Genome-wide association analysis confirms and extends the association of SLC2A9 with serum uric acid levels to Mexican Americans. Frontiers in genetics, 4279. https://doi.org/10.3389/fgene.2013.00279
Voruganti, Venkata Saroja, et al. "Genome-wide association analysis confirms and extends the association of SLC2A9 with serum uric acid levels to Mexican Americans." Frontiers in genetics vol. 4 (2013): 279. doi: https://doi.org/10.3389/fgene.2013.00279
Voruganti VS, Kent JW, Debnath S, Cole SA, Haack K, Göring HH, Carless MA, Curran JE, Johnson MP, Almasy L, Dyer TD, Maccluer JW, Moses EK, Abboud HE, Mahaney MC, Blangero J, Comuzzie AG. Genome-wide association analysis confirms and extends the association of SLC2A9 with serum uric acid levels to Mexican Americans. Front Genet. 2013 Dec 16;4:279. doi: 10.3389/fgene.2013.00279. eCollection 2013. PMID: 24379826; PMCID: PMC3863993.
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A general approach for combining diverse rare variant association tests provides improved robustness across a wider range of genetic architectures.

European journal of human genetics : EJHG

Greco B, Hainline A, Arbet J, Grinde K, Benitez A, Tintle N.
PMID: 26508571
Eur J Hum Genet. 2016 May;24(5):767-73. doi: 10.1038/ejhg.2015.194. Epub 2015 Oct 28.

The widespread availability of genome sequencing data made possible by way of next-generation technologies has yielded a flood of different gene-based rare variant association tests. Most of these tests have been published because they have superior power for particular...

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Greco B, Hainline A, Arbet J, et al. A general approach for combining diverse rare variant association tests provides improved robustness across a wider range of genetic architectures. Eur J Hum Genet. 2015;24(5):767-73doi: 10.1038/ejhg.2015.194.
Greco, B., Hainline, A., Arbet, J., Grinde, K., Benitez, A., & Tintle, N. (2016). A general approach for combining diverse rare variant association tests provides improved robustness across a wider range of genetic architectures. European journal of human genetics : EJHG, 24(5), 767-73. https://doi.org/10.1038/ejhg.2015.194
Greco, Brian, et al. "A general approach for combining diverse rare variant association tests provides improved robustness across a wider range of genetic architectures." European journal of human genetics : EJHG vol. 24,5 (2016): 767-73. doi: https://doi.org/10.1038/ejhg.2015.194
Greco B, Hainline A, Arbet J, Grinde K, Benitez A, Tintle N. A general approach for combining diverse rare variant association tests provides improved robustness across a wider range of genetic architectures. Eur J Hum Genet. 2016 May;24(5):767-73. doi: 10.1038/ejhg.2015.194. Epub 2015 Oct 28. PMID: 26508571; PMCID: PMC4930097.
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Effects on linkage analyses of different Affymetrix expression measures as quantitative trait phenotypes.

BMC proceedings

Peralta JM, Almasy L.
PMID: 18466503
BMC Proc. 2007;1:S158. doi: 10.1186/1753-6561-1-s1-s158. Epub 2007 Dec 18.

We compared results from linkage analyses of different phenotype measurements from the same gene expression traits and found that the strongest signals were detected by all expression measures that we considered. On average, that meant that the same quantitative...

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Peralta JM, Almasy L. Effects on linkage analyses of different Affymetrix expression measures as quantitative trait phenotypes. BMC Proc. 2007;1:S158doi: 10.1186/1753-6561-1-s1-s158.
Peralta, J. M., & Almasy, L. (2007). Effects on linkage analyses of different Affymetrix expression measures as quantitative trait phenotypes. BMC proceedings, 1S158. https://doi.org/10.1186/1753-6561-1-s1-s158
Peralta, Juan Manuel, and Almasy, Laura. "Effects on linkage analyses of different Affymetrix expression measures as quantitative trait phenotypes." BMC proceedings vol. 1 (2007): S158. doi: https://doi.org/10.1186/1753-6561-1-s1-s158
Peralta JM, Almasy L. Effects on linkage analyses of different Affymetrix expression measures as quantitative trait phenotypes. BMC Proc. 2007;1:S158. doi: 10.1186/1753-6561-1-s1-s158. Epub 2007 Dec 18. PMID: 18466503; PMCID: PMC2367575.
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MM Algorithms for Geometric and Signomial Programming.

Mathematical programming

Lange K, Zhou H.
PMID: 24634545
Math Program. 2014 Feb 01;143(1):339-356. doi: 10.1007/s10107-012-0612-1.

This paper derives new algorithms for signomial programming, a generalization of geometric programming. The algorithms are based on a generic principle for optimization called the MM algorithm. In this setting, one can apply the geometric-arithmetic mean inequality and a...

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Lange K, Zhou H. MM Algorithms for Geometric and Signomial Programming. Math Program. 2014;143(1):339-356doi: 10.1007/s10107-012-0612-1.
Lange, K., & Zhou, H. (2014). MM Algorithms for Geometric and Signomial Programming. Mathematical programming, 143(1), 339-356. https://doi.org/10.1007/s10107-012-0612-1
Lange, Kenneth, and Zhou, Hua. "MM Algorithms for Geometric and Signomial Programming." Mathematical programming vol. 143,1 (2014): 339-356. doi: https://doi.org/10.1007/s10107-012-0612-1
Lange K, Zhou H. MM Algorithms for Geometric and Signomial Programming. Math Program. 2014 Feb 01;143(1):339-356. doi: 10.1007/s10107-012-0612-1. PMID: 24634545; PMCID: PMC3950732.
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Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test.

BMC proceedings

Peralta JM, Almeida M, Abraham LJ, Moses E, Blangero J.
PMID: 27980619
BMC Proc. 2016 Oct 18;10:103-108. doi: 10.1186/s12919-016-0013-1. eCollection 2016.

We present a novel approach to detect potential

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Peralta JM, Almeida M, Abraham LJ, et al. Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test. BMC Proc. 2016;10:103-108doi: 10.1186/s12919-016-0013-1.
Peralta, J. M., Almeida, M., Abraham, L. J., Moses, E., & Blangero, J. (2016). Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test. BMC proceedings, 10103-108. https://doi.org/10.1186/s12919-016-0013-1
Peralta, Juan Manuel, et al. "Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test." BMC proceedings vol. 10 (2016): 103-108. doi: https://doi.org/10.1186/s12919-016-0013-1
Peralta JM, Almeida M, Abraham LJ, Moses E, Blangero J. Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test. BMC Proc. 2016 Oct 18;10:103-108. doi: 10.1186/s12919-016-0013-1. eCollection 2016. PMID: 27980619; PMCID: PMC5133489.
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Constrained multivariate association with longitudinal phenotypes.

BMC proceedings

Melton PE, Peralta JM, Almasy L.
PMID: 27980657
BMC Proc. 2016 Oct 18;10:329-332. doi: 10.1186/s12919-016-0051-8. eCollection 2016.

BACKGROUND: The incorporation of longitudinal data into genetic epidemiological studies has the potential to provide valuable information regarding the effect of time on complex disease etiology. Yet, the majority of research focuses on variables collected from a single time...

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Melton PE, Peralta JM, Almasy L. Constrained multivariate association with longitudinal phenotypes. BMC Proc. 2016;10:329-332doi: 10.1186/s12919-016-0051-8.
Melton, P. E., Peralta, J. M., & Almasy, L. (2016). Constrained multivariate association with longitudinal phenotypes. BMC proceedings, 10329-332. https://doi.org/10.1186/s12919-016-0051-8
Melton, Phillip E, et al. "Constrained multivariate association with longitudinal phenotypes." BMC proceedings vol. 10 (2016): 329-332. doi: https://doi.org/10.1186/s12919-016-0051-8
Melton PE, Peralta JM, Almasy L. Constrained multivariate association with longitudinal phenotypes. BMC Proc. 2016 Oct 18;10:329-332. doi: 10.1186/s12919-016-0051-8. eCollection 2016. PMID: 27980657; PMCID: PMC5133503.
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Minimal Relationship between Local Gyrification and General Cognitive Ability in Humans.

Cerebral cortex (New York, N.Y. : 1991)

Mathias SR, Knowles EEM, Mollon J, Rodrigue A, Koenis MMC, Alexander-Bloch AF, Winkler AM, Olvera RL, Duggirala R, Göring HHH, Curran JE, Fox PT, Almasy L, Blangero J, Glahn DC.
PMID: 32037459
Cereb Cortex. 2020 May 18;30(6):3439-3450. doi: 10.1093/cercor/bhz319.

Previous studies suggest that gyrification is associated with superior cognitive abilities in humans, but the strength of this relationship remains unclear. Here, in two samples of related individuals (total N = 2882), we calculated an index of local gyrification...

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Mathias SR, Knowles EEM, Mollon J, et al. Minimal Relationship between Local Gyrification and General Cognitive Ability in Humans. Cereb Cortex. 2020;30(6):3439-3450doi: 10.1093/cercor/bhz319.
Mathias, S. R., Knowles, E. E. M., Mollon, J., Rodrigue, A., Koenis, M. M. C., Alexander-Bloch, A. F., Winkler, A. M., Olvera, R. L., Duggirala, R., Göring, H. H. H., Curran, J. E., Fox, P. T., Almasy, L., Blangero, J., & Glahn, D. C. (2020). Minimal Relationship between Local Gyrification and General Cognitive Ability in Humans. Cerebral cortex (New York, N.Y. : 1991), 30(6), 3439-3450. https://doi.org/10.1093/cercor/bhz319
Mathias, Samuel R, et al. "Minimal Relationship between Local Gyrification and General Cognitive Ability in Humans." Cerebral cortex (New York, N.Y. : 1991) vol. 30,6 (2020): 3439-3450. doi: https://doi.org/10.1093/cercor/bhz319
Mathias SR, Knowles EEM, Mollon J, Rodrigue A, Koenis MMC, Alexander-Bloch AF, Winkler AM, Olvera RL, Duggirala R, Göring HHH, Curran JE, Fox PT, Almasy L, Blangero J, Glahn DC. Minimal Relationship between Local Gyrification and General Cognitive Ability in Humans. Cereb Cortex. 2020 May 18;30(6):3439-3450. doi: 10.1093/cercor/bhz319. PMID: 32037459; PMCID: PMC7233007.
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Independent test assessment using the extreme value distribution theory.

BMC proceedings

Almeida M, Blondell L, Peralta JM, Kent JW, Jun G, Teslovich TM, Fuchsberger C, Wood AR, Manning AK, Frayling TM, Cingolani PE, Sladek R, Dyer TD, Abecasis G, Duggirala R, Blangero J.
PMID: 27980644
BMC Proc. 2016 Oct 18;10:245-249. doi: 10.1186/s12919-016-0038-5. eCollection 2016.

The new generation of whole genome sequencing platforms offers great possibilities and challenges for dissecting the genetic basis of complex traits. With a very high number of sequence variants, a naïve multiple hypothesis threshold correction hinders the identification of...

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Almeida M, Blondell L, Peralta JM, et al. Independent test assessment using the extreme value distribution theory. BMC Proc. 2016;10:245-249doi: 10.1186/s12919-016-0038-5.
Almeida, M., Blondell, L., Peralta, J. M., Kent, J. W., Jun, G., Teslovich, T. M., Fuchsberger, C., Wood, A. R., Manning, A. K., Frayling, T. M., Cingolani, P. E., Sladek, R., Dyer, T. D., Abecasis, G., Duggirala, R., & Blangero, J. (2016). Independent test assessment using the extreme value distribution theory. BMC proceedings, 10245-249. https://doi.org/10.1186/s12919-016-0038-5
Almeida, Marcio, et al. "Independent test assessment using the extreme value distribution theory." BMC proceedings vol. 10 (2016): 245-249. doi: https://doi.org/10.1186/s12919-016-0038-5
Almeida M, Blondell L, Peralta JM, Kent JW, Jun G, Teslovich TM, Fuchsberger C, Wood AR, Manning AK, Frayling TM, Cingolani PE, Sladek R, Dyer TD, Abecasis G, Duggirala R, Blangero J. Independent test assessment using the extreme value distribution theory. BMC Proc. 2016 Oct 18;10:245-249. doi: 10.1186/s12919-016-0038-5. eCollection 2016. PMID: 27980644; PMCID: PMC5133519.
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A quantitative trait locus on chromosome 5p influences d-dimer levels in the san antonio family heart study.

International journal of vascular medicine

Diego VP, Almasy L, Rainwater DL, Mahaney MC, Comuzzie AG, Cole SA, Tracy RP, Stern MP, Maccluer JW, Blangero J.
PMID: 21151504
Int J Vasc Med. 2010;2010:490241. doi: 10.1155/2010/490241. Epub 2010 Jun 27.

Background. D-dimer is associated with increasing severity of atherosclerosis and with increased risk of a cardiovascular disease (CVD). Methods and Results. To better understand this risk factor, we performed a genome scan on 803 (301 males and 502 females)...

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Diego VP, Almasy L, Rainwater DL, et al. A quantitative trait locus on chromosome 5p influences d-dimer levels in the san antonio family heart study. Int J Vasc Med. 2010;2010:490241doi: 10.1155/2010/490241.
Diego, V. P., Almasy, L., Rainwater, D. L., Mahaney, M. C., Comuzzie, A. G., Cole, S. A., Tracy, R. P., Stern, M. P., Maccluer, J. W., & Blangero, J. (2010). A quantitative trait locus on chromosome 5p influences d-dimer levels in the san antonio family heart study. International journal of vascular medicine, 2010490241. https://doi.org/10.1155/2010/490241
Diego, V P, et al. "A quantitative trait locus on chromosome 5p influences d-dimer levels in the san antonio family heart study." International journal of vascular medicine vol. 2010 (2010): 490241. doi: https://doi.org/10.1155/2010/490241
Diego VP, Almasy L, Rainwater DL, Mahaney MC, Comuzzie AG, Cole SA, Tracy RP, Stern MP, Maccluer JW, Blangero J. A quantitative trait locus on chromosome 5p influences d-dimer levels in the san antonio family heart study. Int J Vasc Med. 2010;2010:490241. doi: 10.1155/2010/490241. Epub 2010 Jun 27. PMID: 21151504; PMCID: PMC2989697.
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Bayesian Gaussian Mixture Models for High-Density Genotyping Arrays.

Journal of the American Statistical Association

Sabatti C, Lange K.
PMID: 21572926
J Am Stat Assoc. 2008 Mar 01;103(481):89-100. doi: 10.1198/016214507000000338..

Affymetrix's SNP (single-nucleotide polymorphism) genotyping chips have increased the scope and decreased the cost of gene-mapping studies. Because each SNP is queried by multiple DNA probes, the chips present interesting challenges in genotype calling. Traditional clustering methods distinguish the...

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Sabatti C, Lange K. Bayesian Gaussian Mixture Models for High-Density Genotyping Arrays. J Am Stat Assoc. 2008;103(481):89-100doi: 10.1198/016214507000000338..
Sabatti, C., & Lange, K. (2008). Bayesian Gaussian Mixture Models for High-Density Genotyping Arrays. Journal of the American Statistical Association, 103(481), 89-100. https://doi.org/10.1198/016214507000000338.
Sabatti, Chiara, and Lange, Kenneth. "Bayesian Gaussian Mixture Models for High-Density Genotyping Arrays." Journal of the American Statistical Association vol. 103,481 (2008): 89-100. doi: https://doi.org/10.1198/016214507000000338.
Sabatti C, Lange K. Bayesian Gaussian Mixture Models for High-Density Genotyping Arrays. J Am Stat Assoc. 2008 Mar 01;103(481):89-100. doi: 10.1198/016214507000000338.. PMID: 21572926; PMCID: PMC3092390.
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A cross-population extended haplotype-based homozygosity score test to detect positive selection in genome-wide scans.

Statistics and its interface

Zhong M, Zhang Y, Lange K, Fan R.
PMID: 26097641
Stat Interface. 2011;4(1):51-63. doi: 10.4310/SII.2011.v4.n1.a6.

In this article, we developed a cross-population comparison test statistic to detect chromosome regions in which there is no significant excess homozygosity in one population but homozygosity remains high in the other. We treated an extended stretch of homozygosity...

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Zhong M, Zhang Y, Lange K, et al. A cross-population extended haplotype-based homozygosity score test to detect positive selection in genome-wide scans. Stat Interface. 2011;4(1):51-63doi: 10.4310/SII.2011.v4.n1.a6.
Zhong, M., Zhang, Y., Lange, K., & Fan, R. (2011). A cross-population extended haplotype-based homozygosity score test to detect positive selection in genome-wide scans. Statistics and its interface, 4(1), 51-63. https://doi.org/10.4310/SII.2011.v4.n1.a6
Zhong, Ming, et al. "A cross-population extended haplotype-based homozygosity score test to detect positive selection in genome-wide scans." Statistics and its interface vol. 4,1 (2011): 51-63. doi: https://doi.org/10.4310/SII.2011.v4.n1.a6
Zhong M, Zhang Y, Lange K, Fan R. A cross-population extended haplotype-based homozygosity score test to detect positive selection in genome-wide scans. Stat Interface. 2011;4(1):51-63. doi: 10.4310/SII.2011.v4.n1.a6. PMID: 26097641; PMCID: PMC4470573.
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A robust GWSS method to simultaneously detect rare and common variants for complex disease.

PloS one

Kao CF, Liu JR, Hung H, Kuo PH.
PMID: 25880329
PLoS One. 2015 Apr 16;10(4):e0120873. doi: 10.1371/journal.pone.0120873. eCollection 2015.

The rapid advances in sequencing technologies and the resulting next-generation sequencing data provide the opportunity to detect disease-associated variants with a better solution, in particular for low-frequency variants. Although both common and rare variants might exert their independent effects...

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Kao CF, Liu JR, Hung H, et al. A robust GWSS method to simultaneously detect rare and common variants for complex disease. PLoS One. 2015;10(4):e0120873doi: 10.1371/journal.pone.0120873.
Kao, C. F., Liu, J. R., Hung, H., & Kuo, P. H. (2015). A robust GWSS method to simultaneously detect rare and common variants for complex disease. PloS one, 10(4), e0120873. https://doi.org/10.1371/journal.pone.0120873
Kao, Chung-Feng, et al. "A robust GWSS method to simultaneously detect rare and common variants for complex disease." PloS one vol. 10,4 (2015): e0120873. doi: https://doi.org/10.1371/journal.pone.0120873
Kao CF, Liu JR, Hung H, Kuo PH. A robust GWSS method to simultaneously detect rare and common variants for complex disease. PLoS One. 2015 Apr 16;10(4):e0120873. doi: 10.1371/journal.pone.0120873. eCollection 2015. PMID: 25880329; PMCID: PMC4399906.
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Showing 1 to 12 of 25 entries