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Showing 1 to 8 of 8 entries
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Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.

Genome medicine

O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ.
PMID: 23537139
Genome Med. 2013 Mar 27;5(3):28. doi: 10.1186/gm432. eCollection 2013.

BACKGROUND: To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear...

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O'Rawe J, Jiang T, Sun G, et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013;5(3):28doi: 10.1186/gm432.
O'Rawe, J., Jiang, T., Sun, G., Wu, Y., Wang, W., Hu, J., Bodily, P., Tian, L., Hakonarson, H., Johnson, W. E., Wei, Z., Wang, K., & Lyon, G. J. (2013). Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome medicine, 5(3), 28. https://doi.org/10.1186/gm432
O'Rawe, Jason, et al. "Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing." Genome medicine vol. 5,3 (2013): 28. doi: https://doi.org/10.1186/gm432
O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013 Mar 27;5(3):28. doi: 10.1186/gm432. eCollection 2013. PMID: 23537139; PMCID: PMC3706896.
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SparkText: Biomedical Text Mining on Big Data Framework.

PloS one

Ye Z, Tafti AP, He KY, Wang K, He MM.
PMID: 27685652
PLoS One. 2016 Sep 29;11(9):e0162721. doi: 10.1371/journal.pone.0162721. eCollection 2016.

BACKGROUND: Many new biomedical research articles are published every day, accumulating rich information, such as genetic variants, genes, diseases, and treatments. Rapid yet accurate text mining on large-scale scientific literature can discover novel knowledge to better understand human diseases...

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Ye Z, Tafti AP, He KY, et al. SparkText: Biomedical Text Mining on Big Data Framework. PLoS One. 2016;11(9):e0162721doi: 10.1371/journal.pone.0162721.
Ye, Z., Tafti, A. P., He, K. Y., Wang, K., & He, M. M. (2016). SparkText: Biomedical Text Mining on Big Data Framework. PloS one, 11(9), e0162721. https://doi.org/10.1371/journal.pone.0162721
Ye, Zhan, et al. "SparkText: Biomedical Text Mining on Big Data Framework." PloS one vol. 11,9 (2016): e0162721. doi: https://doi.org/10.1371/journal.pone.0162721
Ye Z, Tafti AP, He KY, Wang K, He MM. SparkText: Biomedical Text Mining on Big Data Framework. PLoS One. 2016 Sep 29;11(9):e0162721. doi: 10.1371/journal.pone.0162721. eCollection 2016. PMID: 27685652; PMCID: PMC5042555.
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Mapping Splicing Quantitative Trait Loci in RNA-Seq.

Cancer informatics

Jia C, Hu Y, Liu Y, Li M.
PMID: 25733796
Cancer Inform. 2015 Feb 16;14:45-53. doi: 10.4137/CIN.S24832. eCollection 2015.

BACKGROUND: One of the major mechanisms of generating mRNA diversity is alternative splicing, a regulated process that allows for the flexibility of producing functionally different proteins from the same genomic sequences. This process is often altered in cancer cells...

Cite
Jia C, Hu Y, Liu Y, et al. Mapping Splicing Quantitative Trait Loci in RNA-Seq. Cancer Inform. 2015;14:45-53doi: 10.4137/CIN.S24832.
Jia, C., Hu, Y., Liu, Y., & Li, M. (2015). Mapping Splicing Quantitative Trait Loci in RNA-Seq. Cancer informatics, 1445-53. https://doi.org/10.4137/CIN.S24832
Jia, Cheng, et al. "Mapping Splicing Quantitative Trait Loci in RNA-Seq." Cancer informatics vol. 14 (2015): 45-53. doi: https://doi.org/10.4137/CIN.S24832
Jia C, Hu Y, Liu Y, Li M. Mapping Splicing Quantitative Trait Loci in RNA-Seq. Cancer Inform. 2015 Feb 16;14:45-53. doi: 10.4137/CIN.S24832. eCollection 2015. PMID: 25733796; PMCID: PMC4333812.
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Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress.

Genome medicine

Lyon GJ, Wang K.
PMID: 22830651
Genome Med. 2012 Jul 26;4(7):58. doi: 10.1186/gm359. eCollection 2012.

The pace of exome and genome sequencing is accelerating, with the identification of many new disease-causing mutations in research settings, and it is likely that whole exome or genome sequencing could have a major impact in the clinical arena...

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Lyon GJ, Wang K. Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Med. 2012;4(7):58doi: 10.1186/gm359.
Lyon, G. J., & Wang, K. (2012). Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome medicine, 4(7), 58. https://doi.org/10.1186/gm359
Lyon, Gholson J, and Wang, Kai. "Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress." Genome medicine vol. 4,7 (2012): 58. doi: https://doi.org/10.1186/gm359
Lyon GJ, Wang K. Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Med. 2012 Jul 26;4(7):58. doi: 10.1186/gm359. eCollection 2012. PMID: 22830651; PMCID: PMC3580414.
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Whole-genome sequencing in an autism multiplex family.

Molecular autism

Shi L, Zhang X, Golhar R, Otieno FG, He M, Hou C, Kim C, Keating B, Lyon GJ, Wang K, Hakonarson H.
PMID: 23597238
Mol Autism. 2013 Apr 18;4(1):8. doi: 10.1186/2040-2392-4-8.

BACKGROUND: Autism spectrum disorders (ASDs) represent a group of childhood neurodevelopmental disorders that affect 1 in 88 children in the US. Previous exome sequencing studies on family trios have implicated a role for rare, de-novo mutations in the pathogenesis...

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Shi L, Zhang X, Golhar R, et al. Whole-genome sequencing in an autism multiplex family. Mol Autism. 2013;4(1):8doi: 10.1186/2040-2392-4-8.
Shi, L., Zhang, X., Golhar, R., Otieno, F. G., He, M., Hou, C., Kim, C., Keating, B., Lyon, G. J., Wang, K., & Hakonarson, H. (2013). Whole-genome sequencing in an autism multiplex family. Molecular autism, 4(1), 8. https://doi.org/10.1186/2040-2392-4-8
Shi, Lingling, et al. "Whole-genome sequencing in an autism multiplex family." Molecular autism vol. 4,1 (2013): 8. doi: https://doi.org/10.1186/2040-2392-4-8
Shi L, Zhang X, Golhar R, Otieno FG, He M, Hou C, Kim C, Keating B, Lyon GJ, Wang K, Hakonarson H. Whole-genome sequencing in an autism multiplex family. Mol Autism. 2013 Apr 18;4(1):8. doi: 10.1186/2040-2392-4-8. PMID: 23597238; PMCID: PMC3642023.
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Discovering epistasis in large scale genetic association studies by exploiting graphics cards.

Frontiers in genetics

Chen GK, Guo Y.
PMID: 24348518
Front Genet. 2013 Dec 03;4:266. doi: 10.3389/fgene.2013.00266.

Despite the enormous investments made in collecting DNA samples and generating germline variation data across thousands of individuals in modern genome-wide association studies (GWAS), progress has been frustratingly slow in explaining much of the heritability in common disease. Today's...

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Chen GK, Guo Y. Discovering epistasis in large scale genetic association studies by exploiting graphics cards. Front Genet. 2013;4:266doi: 10.3389/fgene.2013.00266.
Chen, G. K., & Guo, Y. (2013). Discovering epistasis in large scale genetic association studies by exploiting graphics cards. Frontiers in genetics, 4266. https://doi.org/10.3389/fgene.2013.00266
Chen, Gary K, and Guo, Yunfei. "Discovering epistasis in large scale genetic association studies by exploiting graphics cards." Frontiers in genetics vol. 4 (2013): 266. doi: https://doi.org/10.3389/fgene.2013.00266
Chen GK, Guo Y. Discovering epistasis in large scale genetic association studies by exploiting graphics cards. Front Genet. 2013 Dec 03;4:266. doi: 10.3389/fgene.2013.00266. PMID: 24348518; PMCID: PMC3848199.
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Mapping Splicing Quantitative Trait Loci in RNA-Seq.

Cancer informatics

Jia C, Hu Y, Liu Y, Li M.
PMID: 25452687
Cancer Inform. 2014 Oct 15;13:35-43. doi: 10.4137/CIN.S13971. eCollection 2014.

BACKGROUND: One of the major mechanisms of generating mRNA diversity is alternative splicing, a regulated process that allows for the flexibility of producing functionally different proteins from the same genomic sequences. This process is often altered in cancer cells...

Cite
Jia C, Hu Y, Liu Y, et al. Mapping Splicing Quantitative Trait Loci in RNA-Seq. Cancer Inform. 2014;13:35-43doi: 10.4137/CIN.S13971.
Jia, C., Hu, Y., Liu, Y., & Li, M. (2014). Mapping Splicing Quantitative Trait Loci in RNA-Seq. Cancer informatics, 1335-43. https://doi.org/10.4137/CIN.S13971
Jia, Cheng, et al. "Mapping Splicing Quantitative Trait Loci in RNA-Seq." Cancer informatics vol. 13 (2014): 35-43. doi: https://doi.org/10.4137/CIN.S13971
Jia C, Hu Y, Liu Y, Li M. Mapping Splicing Quantitative Trait Loci in RNA-Seq. Cancer Inform. 2014 Oct 15;13:35-43. doi: 10.4137/CIN.S13971. eCollection 2014. PMID: 25452687; PMCID: PMC4218654.
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Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement.

Genome medicine

Wang K, Kim C, Bradfield J, Guo Y, Toskala E, Otieno FG, Hou C, Thomas K, Cardinale C, Lyon GJ, Golhar R, Hakonarson H.
PMID: 23889995
Genome Med. 2013 Jul 26;5(7):67. doi: 10.1186/gm471. eCollection 2013.

BACKGROUND: Whole-exome sequencing has identified the causes of several Mendelian diseases by analyzing multiple unrelated cases, but it is more challenging to resolve the cause of extremely rare and suspected Mendelian diseases from individual families. We identified a family...

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Wang K, Kim C, Bradfield J, et al. Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement. Genome Med. 2013;5(7):67doi: 10.1186/gm471.
Wang, K., Kim, C., Bradfield, J., Guo, Y., Toskala, E., Otieno, F. G., Hou, C., Thomas, K., Cardinale, C., Lyon, G. J., Golhar, R., & Hakonarson, H. (2013). Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement. Genome medicine, 5(7), 67. https://doi.org/10.1186/gm471
Wang, Kai, et al. "Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement." Genome medicine vol. 5,7 (2013): 67. doi: https://doi.org/10.1186/gm471
Wang K, Kim C, Bradfield J, Guo Y, Toskala E, Otieno FG, Hou C, Thomas K, Cardinale C, Lyon GJ, Golhar R, Hakonarson H. Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement. Genome Med. 2013 Jul 26;5(7):67. doi: 10.1186/gm471. eCollection 2013. PMID: 23889995; PMCID: PMC3971341.
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Showing 1 to 8 of 8 entries