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Technical reproducibility of genotyping SNP arrays used in genome-wide association studies.

PloS one

Hong H, Xu L, Liu J, Jones WD, Su Z, Ning B, Perkins R, Ge W, Miclaus K, Zhang L, Park K, Green B, Han T, Fang H, Lambert CG, Vega SC, Lin SM, Jafari N, Czika W, Wolfinger RD, Goodsaid F, Tong W, Shi L.
PMID: 22970228
PLoS One. 2012;7(9):e44483. doi: 10.1371/journal.pone.0044483. Epub 2012 Sep 07.

During the last several years, high-density genotyping SNP arrays have facilitated genome-wide association studies (GWAS) that successfully identified common genetic variants associated with a variety of phenotypes. However, each of the identified genetic variants only explains a very small...

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Hong H, Xu L, Liu J, et al. Technical reproducibility of genotyping SNP arrays used in genome-wide association studies. PLoS One. 2012;7(9):e44483doi: 10.1371/journal.pone.0044483.
Hong, H., Xu, L., Liu, J., Jones, W. D., Su, Z., Ning, B., Perkins, R., Ge, W., Miclaus, K., Zhang, L., Park, K., Green, B., Han, T., Fang, H., Lambert, C. G., Vega, S. C., Lin, S. M., Jafari, N., Czika, W., Wolfinger, R. D., Goodsaid, F., Tong, W., & Shi, L. (2012). Technical reproducibility of genotyping SNP arrays used in genome-wide association studies. PloS one, 7(9), e44483. https://doi.org/10.1371/journal.pone.0044483
Hong, Huixiao, et al. "Technical reproducibility of genotyping SNP arrays used in genome-wide association studies." PloS one vol. 7,9 (2012): e44483. doi: https://doi.org/10.1371/journal.pone.0044483
Hong H, Xu L, Liu J, Jones WD, Su Z, Ning B, Perkins R, Ge W, Miclaus K, Zhang L, Park K, Green B, Han T, Fang H, Lambert CG, Vega SC, Lin SM, Jafari N, Czika W, Wolfinger RD, Goodsaid F, Tong W, Shi L. Technical reproducibility of genotyping SNP arrays used in genome-wide association studies. PLoS One. 2012;7(9):e44483. doi: 10.1371/journal.pone.0044483. Epub 2012 Sep 07. PMID: 22970228; PMCID: PMC3436888.
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[Interpretation on 2013 updated Chinese Consensus on the Diagnosis and Treatment of Gastrointestinal Stromal Tumors].

Zhonghua wei chang wai ke za zhi = Chinese journal of gastrointestinal surgery

Shen L.
PMID: 24760633
Zhonghua Wei Chang Wai Ke Za Zhi. 2014 Apr;17(4):305-8.

The Gastrointestinal Stromal Tumor Experts Committee amended and complemented the Chinese Consensus on the Diagnosis and Treatment of Gastrointestinal Stromal Tumors(2013 version) based on the previous edition(2011 version) after broad consulation, repeat discussion on new results of clinical trials...

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Shen L. [Interpretation on 2013 updated Chinese Consensus on the Diagnosis and Treatment of Gastrointestinal Stromal Tumors]. Zhonghua Wei Chang Wai Ke Za Zhi. 2014;17(4):305-8
Shen, L. (2014). [Interpretation on 2013 updated Chinese Consensus on the Diagnosis and Treatment of Gastrointestinal Stromal Tumors]. Zhonghua wei chang wai ke za zhi = Chinese journal of gastrointestinal surgery, 17(4), 305-8.
Shen, Lin. "[Interpretation on 2013 updated Chinese Consensus on the Diagnosis and Treatment of Gastrointestinal Stromal Tumors]." Zhonghua wei chang wai ke za zhi = Chinese journal of gastrointestinal surgery vol. 17,4 (2014): 305-8.
Shen L. [Interpretation on 2013 updated Chinese Consensus on the Diagnosis and Treatment of Gastrointestinal Stromal Tumors]. Zhonghua Wei Chang Wai Ke Za Zhi. 2014 Apr;17(4):305-8. Chinese. PMID: 24760633.
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Commentary: A century of Mendelism: on Johannsen's genotype conception.

International journal of epidemiology

Falk R.
PMID: 24691954
Int J Epidemiol. 2014 Aug;43(4):1002-7. doi: 10.1093/ije/dyu065. Epub 2014 Apr 01.

No abstract available.

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Falk R. Commentary: A century of Mendelism: on Johannsen's genotype conception. Int J Epidemiol. 2014;43(4):1002-7doi: 10.1093/ije/dyu065.
Falk, R. (2014). Commentary: A century of Mendelism: on Johannsen's genotype conception. International journal of epidemiology, 43(4), 1002-7. https://doi.org/10.1093/ije/dyu065
Falk, Raphael. "Commentary: A century of Mendelism: on Johannsen's genotype conception." International journal of epidemiology vol. 43,4 (2014): 1002-7. doi: https://doi.org/10.1093/ije/dyu065
Falk R. Commentary: A century of Mendelism: on Johannsen's genotype conception. Int J Epidemiol. 2014 Aug;43(4):1002-7. doi: 10.1093/ije/dyu065. Epub 2014 Apr 01. PMID: 24691954; PMCID: PMC4258774.
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Prothrombotic genotypes and risk of venous thromboembolism in cancer.

Thrombosis research

Gran OV, Brækkan SK, Hansen JB.
PMID: 29703469
Thromb Res. 2018 Apr;164:S12-S18. doi: 10.1016/j.thromres.2017.12.025.

Venous thromboembolism (VTE) is a common and potentially life-threatening complication in cancer. Patients with cancer are at a higher risk of VTE-related complications such as major bleeding during anticoagulant treatment, recurrence and mortality. Therefore, it is important to identify...

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Gran OV, Brækkan SK, Hansen JB. Prothrombotic genotypes and risk of venous thromboembolism in cancer. Thromb Res. 2018;164:S12-S18doi: 10.1016/j.thromres.2017.12.025.
Gran, O. V., Brækkan, S. K., & Hansen, J. B. (2018). Prothrombotic genotypes and risk of venous thromboembolism in cancer. Thrombosis research, 164S12-S18. https://doi.org/10.1016/j.thromres.2017.12.025
Gran, Olga V, et al. "Prothrombotic genotypes and risk of venous thromboembolism in cancer." Thrombosis research vol. 164 (2018): S12-S18. doi: https://doi.org/10.1016/j.thromres.2017.12.025
Gran OV, Brækkan SK, Hansen JB. Prothrombotic genotypes and risk of venous thromboembolism in cancer. Thromb Res. 2018 Apr;164:S12-S18. doi: 10.1016/j.thromres.2017.12.025. PMID: 29703469.
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Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Bioinformatics (Oxford, England)

Sun C, Medvedev P.
PMID: 30032192
Bioinformatics. 2019 Feb 01;35(3):415-420. doi: 10.1093/bioinformatics/bty641.

MOTIVATION: Genotyping a set of variants from a database is an important step for identifying known genetic traits and disease-related variants within an individual. The growing size of variant databases as well as the high depth of sequencing data...

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Sun C, Medvedev P. Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. Bioinformatics. 2019;35(3):415-420doi: 10.1093/bioinformatics/bty641.
Sun, C., & Medvedev, P. (2019). Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. Bioinformatics (Oxford, England), 35(3), 415-420. https://doi.org/10.1093/bioinformatics/bty641
Sun, Chen, and Medvedev, Paul. "Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics." Bioinformatics (Oxford, England) vol. 35,3 (2019): 415-420. doi: https://doi.org/10.1093/bioinformatics/bty641
Sun C, Medvedev P. Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. Bioinformatics. 2019 Feb 01;35(3):415-420. doi: 10.1093/bioinformatics/bty641. PMID: 30032192.
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Limb girdle muscular dystrophies: classification, clinical spectrum and emerging therapies.

Current opinion in neurology

Vissing J.
PMID: 27490667
Curr Opin Neurol. 2016 Oct;29(5):635-41. doi: 10.1097/WCO.0000000000000375.

PURPOSE OF REVIEW: The aim of the study was to describe the clinical spectrum of limb girdle muscular dystrophies (LGMDs), the pitfalls of the current classification system for LGMDs, and emerging therapies for these conditions.RECENT FINDINGS: Close to half...

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Vissing J. Limb girdle muscular dystrophies: classification, clinical spectrum and emerging therapies. Curr Opin Neurol. 2016;29(5):635-41doi: 10.1097/WCO.0000000000000375.
Vissing, J. (2016). Limb girdle muscular dystrophies: classification, clinical spectrum and emerging therapies. Current opinion in neurology, 29(5), 635-41. https://doi.org/10.1097/WCO.0000000000000375
Vissing, John. "Limb girdle muscular dystrophies: classification, clinical spectrum and emerging therapies." Current opinion in neurology vol. 29,5 (2016): 635-41. doi: https://doi.org/10.1097/WCO.0000000000000375
Vissing J. Limb girdle muscular dystrophies: classification, clinical spectrum and emerging therapies. Curr Opin Neurol. 2016 Oct;29(5):635-41. doi: 10.1097/WCO.0000000000000375. PMID: 27490667.
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SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics.

Bioinformatics (Oxford, England)

Song L, Liu A, Shi J.
PMID: 30911754
Bioinformatics. 2019 Oct 15;35(20):4038-4044. doi: 10.1093/bioinformatics/btz176.

MOTIVATION: Polygenic risk score (PRS) methods based on genome-wide association studies (GWAS) have a potential for predicting the risk of developing complex diseases and are expected to become more accurate with larger training datasets and innovative statistical methods. The...

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Song L, Liu A, Shi J. SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics. Bioinformatics. 2019;35(20):4038-4044doi: 10.1093/bioinformatics/btz176.
Song, L., Liu, A., Shi, J. (2019). SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics. Bioinformatics (Oxford, England), 35(20), 4038-4044. https://doi.org/10.1093/bioinformatics/btz176
Song, Lei, et al. "SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics." Bioinformatics (Oxford, England) vol. 35,20 (2019): 4038-4044. doi: https://doi.org/10.1093/bioinformatics/btz176
Song L, Liu A, Shi J. SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics. Bioinformatics. 2019 Oct 15;35(20):4038-4044. doi: 10.1093/bioinformatics/btz176. PMID: 30911754; PMCID: PMC6931355.
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GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size.

Molecular psychiatry

Asif H, Alliey-Rodriguez N, Keedy S, Tamminga CA, Sweeney JA, Pearlson G, Clementz BA, Keshavan MS, Buckley P, Liu C, Neale B, Gershon ES.
PMID: 32066829
Mol Psychiatry. 2021 Jun;26(6):2048-2055. doi: 10.1038/s41380-020-0670-3. Epub 2020 Feb 17.

An important issue affecting genome-wide association studies with deep phenotyping (multiple correlated phenotypes) is determining the suitable family-wise significance threshold. Straightforward family-wise correction (Bonferroni) of p 

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Asif H, Alliey-Rodriguez N, Keedy S, et al. GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size. Mol Psychiatry. 2020;26(6):2048-2055doi: 10.1038/s41380-020-0670-3.
Asif, H., Alliey-Rodriguez, N., Keedy, S., Tamminga, C. A., Sweeney, J. A., Pearlson, G., Clementz, B. A., Keshavan, M. S., Buckley, P., Liu, C., Neale, B., & Gershon, E. S. (2021). GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size. Molecular psychiatry, 26(6), 2048-2055. https://doi.org/10.1038/s41380-020-0670-3
Asif, Huma, et al. "GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size." Molecular psychiatry vol. 26,6 (2021): 2048-2055. doi: https://doi.org/10.1038/s41380-020-0670-3
Asif H, Alliey-Rodriguez N, Keedy S, Tamminga CA, Sweeney JA, Pearlson G, Clementz BA, Keshavan MS, Buckley P, Liu C, Neale B, Gershon ES. GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size. Mol Psychiatry. 2021 Jun;26(6):2048-2055. doi: 10.1038/s41380-020-0670-3. Epub 2020 Feb 17. PMID: 32066829; PMCID: PMC7429341.
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Using genetic data to strengthen causal inference in observational research.

Nature reviews. Genetics

Pingault JB, O'Reilly PF, Schoeler T, Ploubidis GB, Rijsdijk F, Dudbridge F.
PMID: 29872216
Nat Rev Genet. 2018 Sep;19(9):566-580. doi: 10.1038/s41576-018-0020-3.

Causal inference is essential across the biomedical, behavioural and social sciences.By progressing from confounded statistical associations to evidence of causal relationships, causal inference can reveal complex pathways underlying traits and diseases and help to prioritize targets for intervention. Recent...

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Pingault JB, O'Reilly PF, Schoeler T, et al. Using genetic data to strengthen causal inference in observational research. Nat Rev Genet. 2018;19(9):566-580doi: 10.1038/s41576-018-0020-3.
Pingault, J. B., O'Reilly, P. F., Schoeler, T., Ploubidis, G. B., Rijsdijk, F., & Dudbridge, F. (2018). Using genetic data to strengthen causal inference in observational research. Nature reviews. Genetics, 19(9), 566-580. https://doi.org/10.1038/s41576-018-0020-3
Pingault, Jean-Baptiste, et al. "Using genetic data to strengthen causal inference in observational research." Nature reviews. Genetics vol. 19,9 (2018): 566-580. doi: https://doi.org/10.1038/s41576-018-0020-3
Pingault JB, O'Reilly PF, Schoeler T, Ploubidis GB, Rijsdijk F, Dudbridge F. Using genetic data to strengthen causal inference in observational research. Nat Rev Genet. 2018 Sep;19(9):566-580. doi: 10.1038/s41576-018-0020-3. PMID: 29872216.
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The Extended Genotype: To What Extent? A Comment on Carthey et al.

Trends in ecology & evolution

Morimoto J, Baltrus DA.
PMID: 30679064
Trends Ecol Evol. 2019 Mar;34(3):186-187. doi: 10.1016/j.tree.2018.12.010. Epub 2019 Jan 21.

No abstract available.

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Morimoto J, Baltrus DA. The Extended Genotype: To What Extent? A Comment on Carthey et al. Trends Ecol Evol. 2019;34(3):186-187doi: 10.1016/j.tree.2018.12.010.
Morimoto, J., & Baltrus, D. A. (2019). The Extended Genotype: To What Extent? A Comment on Carthey et al. Trends in ecology & evolution, 34(3), 186-187. https://doi.org/10.1016/j.tree.2018.12.010
Morimoto, Juliano, and Baltrus, David A. "The Extended Genotype: To What Extent? A Comment on Carthey et al." Trends in ecology & evolution vol. 34,3 (2019): 186-187. doi: https://doi.org/10.1016/j.tree.2018.12.010
Morimoto J, Baltrus DA. The Extended Genotype: To What Extent? A Comment on Carthey et al. Trends Ecol Evol. 2019 Mar;34(3):186-187. doi: 10.1016/j.tree.2018.12.010. Epub 2019 Jan 21. PMID: 30679064.
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A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data.

Database : the journal of biological databases and curation

Sanderson LA, Caron CT, Tan RL, Bett KE.
PMID: 34389844
Database (Oxford). 2021 Aug 14;2021. doi: 10.1093/database/baab051.

Researchers are seeking cost-effective solutions for management and analysis of large-scale genotypic and phenotypic data. Open-source software is uniquely positioned to fill this need through user-focused, crowd-sourced development. Tripal, an open-source toolkit for developing biological data web portals, uses...

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Sanderson LA, Caron CT, Tan RL, et al. A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data. Database (Oxford). 2021;2021doi: 10.1093/database/baab051.
Sanderson, L. A., Caron, C. T., Tan, R. L., & Bett, K. E. (2021). A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data. Database : the journal of biological databases and curation, 2021. https://doi.org/10.1093/database/baab051
Sanderson, Lacey-Anne, et al. "A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data." Database : the journal of biological databases and curation vol. 2021 (2021). doi: https://doi.org/10.1093/database/baab051
Sanderson LA, Caron CT, Tan RL, Bett KE. A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data. Database (Oxford). 2021 Aug 14;2021. doi: 10.1093/database/baab051. PMID: 34389844; PMCID: PMC8363843.
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The Bnapus50K array: a quick and versatile genotyping tool for Brassica napus genomic breeding and research.

G3 (Bethesda, Md.)

Xiao Q, Wang H, Song N, Yu Z, Imran K, Xie W, Qiu S, Zhou F, Wen J, Dai C, Ma C, Tu J, Shen J, Fu T, Yi B.
PMID: 34568935
G3 (Bethesda). 2021 Sep 27;11(10). doi: 10.1093/g3journal/jkab241.

Rapeseed is a globally cultivated commercial crop, primarily grown for its oil. High-density single nucleotide polymorphism (SNP) arrays are widely used as a standard genotyping tool for rapeseed research, including for gene mapping, genome-wide association studies, germplasm resource analysis,...

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Xiao Q, Wang H, Song N, et al. The Bnapus50K array: a quick and versatile genotyping tool for Brassica napus genomic breeding and research. G3 (Bethesda). 2021;11(10)doi: 10.1093/g3journal/jkab241.
Xiao, Q., Wang, H., Song, N., Yu, Z., Imran, K., Xie, W., Qiu, S., Zhou, F., Wen, J., Dai, C., Ma, C., Tu, J., Shen, J., Fu, T., & Yi, B. (2021). The Bnapus50K array: a quick and versatile genotyping tool for Brassica napus genomic breeding and research. G3 (Bethesda, Md.), 11(10), . https://doi.org/10.1093/g3journal/jkab241
Xiao, Qing, et al. "The Bnapus50K array: a quick and versatile genotyping tool for Brassica napus genomic breeding and research." G3 (Bethesda, Md.) vol. 11,10 (2021). doi: https://doi.org/10.1093/g3journal/jkab241
Xiao Q, Wang H, Song N, Yu Z, Imran K, Xie W, Qiu S, Zhou F, Wen J, Dai C, Ma C, Tu J, Shen J, Fu T, Yi B. The Bnapus50K array: a quick and versatile genotyping tool for Brassica napus genomic breeding and research. G3 (Bethesda). 2021 Sep 27;11(10). doi: 10.1093/g3journal/jkab241. PMID: 34568935; PMCID: PMC8473974.
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Showing 25 to 36 of 131 entries