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Multiple testing and power calculations in genetic association studies.

Cold Spring Harbor protocols

So HC, Sham PC.
PMID: 21205861
Cold Spring Harb Protoc. 2011 Jan 01;2011(1):pdb.top95. doi: 10.1101/pdb.top95.

Modern genetic association studies typically involve multiple single-nucleotide polymorphisms (SNPs) and/or multiple genes. With the development of high-throughput genotyping technologies and the reduction in genotyping cost, investigators can now assay up to a million SNPs for direct or indirect...

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So HC, Sham PC. Multiple testing and power calculations in genetic association studies. Cold Spring Harb Protoc. 2011;2011(1):pdb.top95doi: 10.1101/pdb.top95.
So, H. C., & Sham, P. C. (2011). Multiple testing and power calculations in genetic association studies. Cold Spring Harbor protocols, 2011(1), pdb.top95. https://doi.org/10.1101/pdb.top95
So, Hon-Cheong, and Sham, Pak C. "Multiple testing and power calculations in genetic association studies." Cold Spring Harbor protocols vol. 2011,1 (2011): pdb.top95. doi: https://doi.org/10.1101/pdb.top95
So HC, Sham PC. Multiple testing and power calculations in genetic association studies. Cold Spring Harb Protoc. 2011 Jan 01;2011(1):pdb.top95. doi: 10.1101/pdb.top95. PMID: 21205861.
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A novel approach for small sample size family-based association studies: sequential tests.

European journal of human genetics : EJHG

Ilk O, Rajabli F, Dungul DC, Ozdag H, Ilk HG.
PMID: 21427757
Eur J Hum Genet. 2011 Aug;19(8):915-20. doi: 10.1038/ejhg.2011.51. Epub 2011 Mar 23.

In this paper, we propose a sequential probability ratio test (SPRT) to overcome the problem of limited samples in studies related to complex genetic diseases. The results of this novel approach are compared with the ones obtained from the...

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Ilk O, Rajabli F, Dungul DC, et al. A novel approach for small sample size family-based association studies: sequential tests. Eur J Hum Genet. 2011;19(8):915-20doi: 10.1038/ejhg.2011.51.
Ilk, O., Rajabli, F., Dungul, D. C., Ozdag, H., & Ilk, H. G. (2011). A novel approach for small sample size family-based association studies: sequential tests. European journal of human genetics : EJHG, 19(8), 915-20. https://doi.org/10.1038/ejhg.2011.51
Ilk, Ozlem, et al. "A novel approach for small sample size family-based association studies: sequential tests." European journal of human genetics : EJHG vol. 19,8 (2011): 915-20. doi: https://doi.org/10.1038/ejhg.2011.51
Ilk O, Rajabli F, Dungul DC, Ozdag H, Ilk HG. A novel approach for small sample size family-based association studies: sequential tests. Eur J Hum Genet. 2011 Aug;19(8):915-20. doi: 10.1038/ejhg.2011.51. Epub 2011 Mar 23. PMID: 21427757; PMCID: PMC3172932.
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When ".

Cold Spring Harbor molecular case studies

Cassa CA, Akle S, Jordan DM, Rosenfeld JA.
PMID: 28487880
Cold Spring Harb Mol Case Stud. 2017 May;3(3):a001099. doi: 10.1101/mcs.a001099.

The expanding use of genomic sequencing promises to improve clinical diagnostics and to drive the discovery of new disease genes. Candidate genes are increasingly being identified through recurrent cases (e.g., two or more independent cases ["

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Cassa CA, Akle S, Jordan DM, et al. When ". Cold Spring Harb Mol Case Stud. 2017;3(3):a001099doi: 10.1101/mcs.a001099.
Cassa, C. A., Akle, S., Jordan, D. M., & Rosenfeld, J. A. (2017). When ". Cold Spring Harbor molecular case studies, 3(3), a001099. https://doi.org/10.1101/mcs.a001099
Cassa, Christopher A, et al. "When "." Cold Spring Harbor molecular case studies vol. 3,3 (2017): a001099. doi: https://doi.org/10.1101/mcs.a001099
Cassa CA, Akle S, Jordan DM, Rosenfeld JA. When ". Cold Spring Harb Mol Case Stud. 2017 May;3(3):a001099. doi: 10.1101/mcs.a001099. PMID: 28487880; PMCID: PMC5411689.
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Multilayer View of Pathogenic SNVs in Human Interactome through In Silico Edgetic Profiling.

Journal of molecular biology

Cui H, Zhao N, Korkin D.
PMID: 30017919
J Mol Biol. 2018 Sep 14;430(18):2974-2992. doi: 10.1016/j.jmb.2018.07.012. Epub 2018 Jul 12.

Non-synonymous mutations linked to the complex diseases often have a global impact on a biological system, affecting large biomolecular networks and pathways. However, the magnitude of the mutation-driven effects on the macromolecular network is yet to be fully explored....

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Cui H, Zhao N, Korkin D. Multilayer View of Pathogenic SNVs in Human Interactome through In Silico Edgetic Profiling. J Mol Biol. 2018;430(18):2974-2992doi: 10.1016/j.jmb.2018.07.012.
Cui, H., Zhao, N., & Korkin, D. (2018). Multilayer View of Pathogenic SNVs in Human Interactome through In Silico Edgetic Profiling. Journal of molecular biology, 430(18), 2974-2992. https://doi.org/10.1016/j.jmb.2018.07.012
Cui, Hongzhu, et al. "Multilayer View of Pathogenic SNVs in Human Interactome through In Silico Edgetic Profiling." Journal of molecular biology vol. 430,18 (2018): 2974-2992. doi: https://doi.org/10.1016/j.jmb.2018.07.012
Cui H, Zhao N, Korkin D. Multilayer View of Pathogenic SNVs in Human Interactome through In Silico Edgetic Profiling. J Mol Biol. 2018 Sep 14;430(18):2974-2992. doi: 10.1016/j.jmb.2018.07.012. Epub 2018 Jul 12. PMID: 30017919.
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Multiple testing in candidate gene situations: a comparison of classical, discrete, and resampling-based procedures.

Statistical applications in genetics and molecular biology

Elsäβer A, Victor A, Hommel G.
PMID: 22822520
Stat Appl Genet Mol Biol. 2011;10(1):Article 51. doi: 10.2202/1544-6115.1729. Epub 2012 Apr 10.

In candidate gene association studies, usually several elementary hypotheses are tested simultaneously using one particular set of data. The data normally consist of partly correlated SNP information. Every SNP can be tested for association with the disease, e.g., using...

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Elsäβer A, Victor A, Hommel G. Multiple testing in candidate gene situations: a comparison of classical, discrete, and resampling-based procedures. Stat Appl Genet Mol Biol. 2012;10(1):Article 51doi: 10.2202/1544-6115.1729.
Elsäβer, A., Victor, A., & Hommel, G. (2011). Multiple testing in candidate gene situations: a comparison of classical, discrete, and resampling-based procedures. Statistical applications in genetics and molecular biology, 10(1), Article 51. https://doi.org/10.2202/1544-6115.1729
Elsäβer, Amelie, et al. "Multiple testing in candidate gene situations: a comparison of classical, discrete, and resampling-based procedures." Statistical applications in genetics and molecular biology vol. 10,1 (2011): Article 51. doi: https://doi.org/10.2202/1544-6115.1729
Elsäβer A, Victor A, Hommel G. Multiple testing in candidate gene situations: a comparison of classical, discrete, and resampling-based procedures. Stat Appl Genet Mol Biol. 2011;10(1):Article 51. doi: 10.2202/1544-6115.1729. Epub 2012 Apr 10. PMID: 22822520.
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The ForeSee (4C) approach for integrative analysis in gene discovery.

Methods in molecular biology (Clifton, N.J.)

Guo Y, Munro RE, Kalaitzopoulos D, Grigoriadis A.
PMID: 21779990
Methods Mol Biol. 2011;760:53-71. doi: 10.1007/978-1-61779-176-5_4.

The development of high-throughput experimental techniques has made measurements for virtually all kinds of cellular components possible. Effective integration and analysis of this diverged information to produce insightful knowledge is central to biological study today. In this chapter, we...

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Guo Y, Munro RE, Kalaitzopoulos D, et al. The ForeSee (4C) approach for integrative analysis in gene discovery. Methods Mol Biol. 2011;760:53-71doi: 10.1007/978-1-61779-176-5_4.
Guo, Y., Munro, R. E., Kalaitzopoulos, D., & Grigoriadis, A. (2011). The ForeSee (4C) approach for integrative analysis in gene discovery. Methods in molecular biology (Clifton, N.J.), 76053-71. https://doi.org/10.1007/978-1-61779-176-5_4
Guo, Yike, et al. "The ForeSee (4C) approach for integrative analysis in gene discovery." Methods in molecular biology (Clifton, N.J.) vol. 760 (2011): 53-71. doi: https://doi.org/10.1007/978-1-61779-176-5_4
Guo Y, Munro RE, Kalaitzopoulos D, Grigoriadis A. The ForeSee (4C) approach for integrative analysis in gene discovery. Methods Mol Biol. 2011;760:53-71. doi: 10.1007/978-1-61779-176-5_4. PMID: 21779990.
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Discovering Pair-wise Synergies in Microarray Data.

Scientific reports

Chen Y, Cao D, Gao J, Yuan Z.
PMID: 27470995
Sci Rep. 2016 Jul 29;6:30672. doi: 10.1038/srep30672.

Informative gene selection can have important implications for the improvement of cancer diagnosis and the identification of new drug targets. Individual-gene-ranking methods ignore interactions between genes. Furthermore, popular pair-wise gene evaluation methods, e.g. TSP and TSG, are helpless for...

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Chen Y, Cao D, Gao J, et al. Discovering Pair-wise Synergies in Microarray Data. Sci Rep. 2016;6:30672doi: 10.1038/srep30672.
Chen, Y., Cao, D., Gao, J., & Yuan, Z. (2016). Discovering Pair-wise Synergies in Microarray Data. Scientific reports, 630672. https://doi.org/10.1038/srep30672
Chen, Yuan, et al. "Discovering Pair-wise Synergies in Microarray Data." Scientific reports vol. 6 (2016): 30672. doi: https://doi.org/10.1038/srep30672
Chen Y, Cao D, Gao J, Yuan Z. Discovering Pair-wise Synergies in Microarray Data. Sci Rep. 2016 Jul 29;6:30672. doi: 10.1038/srep30672. PMID: 27470995; PMCID: PMC4965793.
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HGCS: an online tool for prioritizing disease-causing gene variants by biological distance.

BMC genomics

Itan Y, Mazel M, Mazel B, Abhyankar A, Nitschke P, Quintana-Murci L, Boisson-Dupuis S, Boisson B, Abel L, Zhang SY, Casanova JL.
PMID: 24694260
BMC Genomics. 2014 Apr 03;15:256. doi: 10.1186/1471-2164-15-256.

BACKGROUND: Identifying the genotypes underlying human disease phenotypes is a fundamental step in human genetics and medicine. High-throughput genomic technologies provide thousands of genetic variants per individual. The causal genes of a specific phenotype are usually expected to be...

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Itan Y, Mazel M, Mazel B, et al. HGCS: an online tool for prioritizing disease-causing gene variants by biological distance. BMC Genomics. 2014;15:256doi: 10.1186/1471-2164-15-256.
Itan, Y., Mazel, M., Mazel, B., Abhyankar, A., Nitschke, P., Quintana-Murci, L., Boisson-Dupuis, S., Boisson, B., Abel, L., Zhang, S. Y., & Casanova, J. L. (2014). HGCS: an online tool for prioritizing disease-causing gene variants by biological distance. BMC genomics, 15256. https://doi.org/10.1186/1471-2164-15-256
Itan, Yuval, et al. "HGCS: an online tool for prioritizing disease-causing gene variants by biological distance." BMC genomics vol. 15 (2014): 256. doi: https://doi.org/10.1186/1471-2164-15-256
Itan Y, Mazel M, Mazel B, Abhyankar A, Nitschke P, Quintana-Murci L, Boisson-Dupuis S, Boisson B, Abel L, Zhang SY, Casanova JL. HGCS: an online tool for prioritizing disease-causing gene variants by biological distance. BMC Genomics. 2014 Apr 03;15:256. doi: 10.1186/1471-2164-15-256. PMID: 24694260; PMCID: PMC4051124.
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DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database.

Nucleic acids research

Xiong Y, Wei Y, Gu Y, Zhang S, Lyu J, Zhang B, Chen C, Zhu J, Wang Y, Liu H, Zhang Y.
PMID: 27899673
Nucleic Acids Res. 2017 Jan 04;45:D888-D895. doi: 10.1093/nar/gkw1123. Epub 2016 Nov 29.

The human disease methylation database (DiseaseMeth, http://bioinfo.hrbmu.edu.cn/diseasemeth/) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have...

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Xiong Y, Wei Y, Gu Y, et al. DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Res. 2016;45:D888-D895doi: 10.1093/nar/gkw1123.
Xiong, Y., Wei, Y., Gu, Y., Zhang, S., Lyu, J., Zhang, B., Chen, C., Zhu, J., Wang, Y., Liu, H., & Zhang, Y. (2017). DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic acids research, 45D888-D895. https://doi.org/10.1093/nar/gkw1123
Xiong, Yichun, et al. "DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database." Nucleic acids research vol. 45 (2017): D888-D895. doi: https://doi.org/10.1093/nar/gkw1123
Xiong Y, Wei Y, Gu Y, Zhang S, Lyu J, Zhang B, Chen C, Zhu J, Wang Y, Liu H, Zhang Y. DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Res. 2017 Jan 04;45:D888-D895. doi: 10.1093/nar/gkw1123. Epub 2016 Nov 29. PMID: 27899673; PMCID: PMC5210584.
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Improved drug therapy: triangulating phenomics with genomics and metabolomics.

Human genomics

Monte AA, Brocker C, Nebert DW, Gonzalez FJ, Thompson DC, Vasiliou V.
PMID: 25181945
Hum Genomics. 2014 Sep 01;8:16. doi: 10.1186/s40246-014-0016-9.

Embracing the complexity of biological systems has a greater likelihood to improve prediction of clinical drug response. Here we discuss limitations of a singular focus on genomics, epigenomics, proteomics, transcriptomics, metabolomics, or phenomics-highlighting the strengths and weaknesses of each...

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Monte AA, Brocker C, Nebert DW, et al. Improved drug therapy: triangulating phenomics with genomics and metabolomics. Hum Genomics. 2014;8:16doi: 10.1186/s40246-014-0016-9.
Monte, A. A., Brocker, C., Nebert, D. W., Gonzalez, F. J., Thompson, D. C., & Vasiliou, V. (2014). Improved drug therapy: triangulating phenomics with genomics and metabolomics. Human genomics, 816. https://doi.org/10.1186/s40246-014-0016-9
Monte, Andrew A, et al. "Improved drug therapy: triangulating phenomics with genomics and metabolomics." Human genomics vol. 8 (2014): 16. doi: https://doi.org/10.1186/s40246-014-0016-9
Monte AA, Brocker C, Nebert DW, Gonzalez FJ, Thompson DC, Vasiliou V. Improved drug therapy: triangulating phenomics with genomics and metabolomics. Hum Genomics. 2014 Sep 01;8:16. doi: 10.1186/s40246-014-0016-9. PMID: 25181945; PMCID: PMC4445687.
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Motile ciliopathies.

Nature reviews. Disease primers

Wallmeier J, Nielsen KG, Kuehni CE, Lucas JS, Leigh MW, Zariwala MA, Omran H.
PMID: 32943623
Nat Rev Dis Primers. 2020 Sep 17;6(1):77. doi: 10.1038/s41572-020-0209-6.

Motile cilia are highly complex hair-like organelles of epithelial cells lining the surface of various organ systems. Genetic mutations (usually with autosomal recessive inheritance) that impair ciliary beating cause a variety of motile ciliopathies, a heterogeneous group of rare...

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Wallmeier J, Nielsen KG, Kuehni CE, et al. Motile ciliopathies. Nat Rev Dis Primers. 2020;6(1):77doi: 10.1038/s41572-020-0209-6.
Wallmeier, J., Nielsen, K. G., Kuehni, C. E., Lucas, J. S., Leigh, M. W., Zariwala, M. A., & Omran, H. (2020). Motile ciliopathies. Nature reviews. Disease primers, 6(1), 77. https://doi.org/10.1038/s41572-020-0209-6
Wallmeier, Julia, et al. "Motile ciliopathies." Nature reviews. Disease primers vol. 6,1 (2020): 77. doi: https://doi.org/10.1038/s41572-020-0209-6
Wallmeier J, Nielsen KG, Kuehni CE, Lucas JS, Leigh MW, Zariwala MA, Omran H. Motile ciliopathies. Nat Rev Dis Primers. 2020 Sep 17;6(1):77. doi: 10.1038/s41572-020-0209-6. PMID: 32943623.
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FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association.

BMC genomics

Jiang L, Xiao Y, Ding Y, Tang J, Guo F.
PMID: 30598109
BMC Genomics. 2018 Dec 31;19:911. doi: 10.1186/s12864-018-5273-x.

BACKGROUND: In the process of post-transcription, microRNAs (miRNAs) are closely related to various complex human diseases. Traditional verification methods for miRNA-disease associations take a lot of time and expense, so it is especially important to design computational methods for...

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Jiang L, Xiao Y, Ding Y, et al. FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association. BMC Genomics. 2018;19:911doi: 10.1186/s12864-018-5273-x.
Jiang, L., Xiao, Y., Ding, Y., Tang, J., & Guo, F. (2018). FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association. BMC genomics, 19911. https://doi.org/10.1186/s12864-018-5273-x
Jiang, Limin, et al. "FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association." BMC genomics vol. 19 (2018): 911. doi: https://doi.org/10.1186/s12864-018-5273-x
Jiang L, Xiao Y, Ding Y, Tang J, Guo F. FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association. BMC Genomics. 2018 Dec 31;19:911. doi: 10.1186/s12864-018-5273-x. PMID: 30598109; PMCID: PMC6311941.
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Showing 1 to 12 of 22 entries