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ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation.

PloS one

Sante T, Vergult S, Volders PJ, Kloosterman WP, Trooskens G, De Preter K, Dheedene A, Speleman F, De Meyer T, Menten B.
PMID: 25503062
PLoS One. 2014 Dec 12;9(12):e113800. doi: 10.1371/journal.pone.0113800. eCollection 2014.

Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist...

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Sante T, Vergult S, Volders PJ, et al. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLoS One. 2014;9(12):e113800doi: 10.1371/journal.pone.0113800.
Sante, T., Vergult, S., Volders, P. J., Kloosterman, W. P., Trooskens, G., De Preter, K., Dheedene, A., Speleman, F., De Meyer, T., & Menten, B. (2014). ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PloS one, 9(12), e113800. https://doi.org/10.1371/journal.pone.0113800
Sante, Tom, et al. "ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation." PloS one vol. 9,12 (2014): e113800. doi: https://doi.org/10.1371/journal.pone.0113800
Sante T, Vergult S, Volders PJ, Kloosterman WP, Trooskens G, De Preter K, Dheedene A, Speleman F, De Meyer T, Menten B. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLoS One. 2014 Dec 12;9(12):e113800. doi: 10.1371/journal.pone.0113800. eCollection 2014. PMID: 25503062; PMCID: PMC4264741.
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Unfixed endogenous retroviral insertions in the human population.

Journal of virology

Marchi E, Kanapin A, Magiorkinis G, Belshaw R.
PMID: 24920817
J Virol. 2014 Sep 01;88(17):9529-37. doi: 10.1128/JVI.00919-14. Epub 2014 Jun 11.

UNLABELLED: One lineage of human endogenous retroviruses (HERVs), HERV-K(HML2), is upregulated in many cancers, some autoimmune/inflammatory diseases, and HIV-infected cells. Despite 3 decades of research, it is not known if these viruses play a causal role in disease, and...

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Marchi E, Kanapin A, Magiorkinis G, et al. Unfixed endogenous retroviral insertions in the human population. J Virol. 2014;88(17):9529-37doi: 10.1128/JVI.00919-14.
Marchi, E., Kanapin, A., Magiorkinis, G., & Belshaw, R. (2014). Unfixed endogenous retroviral insertions in the human population. Journal of virology, 88(17), 9529-37. https://doi.org/10.1128/JVI.00919-14
Marchi, Emanuele, et al. "Unfixed endogenous retroviral insertions in the human population." Journal of virology vol. 88,17 (2014): 9529-37. doi: https://doi.org/10.1128/JVI.00919-14
Marchi E, Kanapin A, Magiorkinis G, Belshaw R. Unfixed endogenous retroviral insertions in the human population. J Virol. 2014 Sep 01;88(17):9529-37. doi: 10.1128/JVI.00919-14. Epub 2014 Jun 11. PMID: 24920817; PMCID: PMC4136357.
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HTSeq--a Python framework to work with high-throughput sequencing data.

Bioinformatics (Oxford, England)

Anders S, Pyl PT, Huber W.
PMID: 25260700
Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep 25.

MOTIVATION: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed.RESULTS: We present HTSeq, a Python library to facilitate...

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Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014;31(2):166-9doi: 10.1093/bioinformatics/btu638.
Anders, S., Pyl, P. T., & Huber, W. (2015). HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics (Oxford, England), 31(2), 166-9. https://doi.org/10.1093/bioinformatics/btu638
Anders, Simon, et al. "HTSeq--a Python framework to work with high-throughput sequencing data." Bioinformatics (Oxford, England) vol. 31,2 (2015): 166-9. doi: https://doi.org/10.1093/bioinformatics/btu638
Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep 25. PMID: 25260700; PMCID: PMC4287950.
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[Genomic medicine].

Ugeskrift for laeger

Nielsen FC.
PMID: 30950375
Ugeskr Laeger. 2019 Apr 01;181(7).

Genomic medicine refers to genomics and bioinformatics in the context of clinical care and diagnostics. Due to the generic and technology-based nature of the field, genomic medicine relates to a broad variety of medical specialities. Genomic medicine is fuelled...

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Nielsen FC. [Genomic medicine]. Ugeskr Laeger. 2019;181(7)
Nielsen, F. C. (2019). [Genomic medicine]. Ugeskrift for laeger, 181(7), .
Nielsen, Finn Cilius. "[Genomic medicine]." Ugeskrift for laeger vol. 181,7 (2019).
Nielsen FC. [Genomic medicine]. Ugeskr Laeger. 2019 Apr 01;181(7). Danish. PMID: 30950375.
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Naming Genes for Dystonia: DYT-z or Ditzy?.

Tremor and other hyperkinetic movements (New York, N.Y.)

Mencacci NE, Jinnah HA.
PMID: 31523486
Tremor Other Hyperkinet Mov (N Y). 2019 Aug 28;9. doi: 10.7916/tohm.v0.710. eCollection 2019.

Dystonias are a clinically and etiologically diverse group of disorders. Numerous genes have now been associated with different dystonia syndromes, and multiple strategies have been proposed for how these genes should be lumped and split into meaningful categories. The...

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Mencacci NE, Jinnah HA. Naming Genes for Dystonia: DYT-z or Ditzy?. Tremor Other Hyperkinet Mov (N Y). 2019;9doi: 10.7916/tohm.v0.710.
Mencacci, N. E., & Jinnah, H. A. (2019). Naming Genes for Dystonia: DYT-z or Ditzy?. Tremor and other hyperkinetic movements (New York, N.Y.), 9. https://doi.org/10.7916/tohm.v0.710
Mencacci, Niccolo E, and Jinnah, H A. "Naming Genes for Dystonia: DYT-z or Ditzy?." Tremor and other hyperkinetic movements (New York, N.Y.) vol. 9 (2019). doi: https://doi.org/10.7916/tohm.v0.710
Mencacci NE, Jinnah HA. Naming Genes for Dystonia: DYT-z or Ditzy?. Tremor Other Hyperkinet Mov (N Y). 2019 Aug 28;9. doi: 10.7916/tohm.v0.710. eCollection 2019. PMID: 31523486; PMCID: PMC6714488.
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Shared decision making: Implications for return of results from whole-exome and whole-genome sequencing.

Translational behavioral medicine

Vadaparampil ST, Cragun D.
PMID: 29385585
Transl Behav Med. 2018 Jan 29;8(1):80-84. doi: 10.1093/tbm/ibx048.

In this issue, Kaphingst and colleagues report on young breast cancer patient's preferences for learning about various results from genomic sequencing. In our commentary, we discuss the results in light of the burgeoning clinical use of whole-exome and whole-genome...

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Vadaparampil ST, Cragun D. Shared decision making: Implications for return of results from whole-exome and whole-genome sequencing. Transl Behav Med. 2018;8(1):80-84doi: 10.1093/tbm/ibx048.
Vadaparampil, S. T., & Cragun, D. (2018). Shared decision making: Implications for return of results from whole-exome and whole-genome sequencing. Translational behavioral medicine, 8(1), 80-84. https://doi.org/10.1093/tbm/ibx048
Vadaparampil, Susan T, and Cragun, Deborah. "Shared decision making: Implications for return of results from whole-exome and whole-genome sequencing." Translational behavioral medicine vol. 8,1 (2018): 80-84. doi: https://doi.org/10.1093/tbm/ibx048
Vadaparampil ST, Cragun D. Shared decision making: Implications for return of results from whole-exome and whole-genome sequencing. Transl Behav Med. 2018 Jan 29;8(1):80-84. doi: 10.1093/tbm/ibx048. PMID: 29385585.
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The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery.

Genomics, proteomics & bioinformatics

Sun J, Zhang Y, Wang M, Guan Q, Yang X, Ou JX, Yan M, Wang C, Zhang Y, Li ZH, Lan C, Mao C, Zhou HW, Hao B, Zhang Z.
PMID: 32827758
Genomics Proteomics Bioinformatics. 2020 Oct;18(5):516-524. doi: 10.1016/j.gpb.2019.05.004. Epub 2020 Aug 19.

Identification of genetic variants via high-throughput sequencing (HTS) technologies has been essential for both fundamental and clinical studies. However, to what extent the genome sequence composition affects variant calling remains unclear. In this study, we identified 63,897 multi-copy sequences...

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Sun J, Zhang Y, Wang M, et al. The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery. Genomics Proteomics Bioinformatics. 2020;18(5):516-524doi: 10.1016/j.gpb.2019.05.004.
Sun, J., Zhang, Y., Wang, M., Guan, Q., Yang, X., Ou, J. X., Yan, M., Wang, C., Zhang, Y., Li, Z. H., Lan, C., Mao, C., Zhou, H. W., Hao, B., & Zhang, Z. (2020). The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery. Genomics, proteomics & bioinformatics, 18(5), 516-524. https://doi.org/10.1016/j.gpb.2019.05.004
Sun, Jing, et al. "The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery." Genomics, proteomics & bioinformatics vol. 18,5 (2020): 516-524. doi: https://doi.org/10.1016/j.gpb.2019.05.004
Sun J, Zhang Y, Wang M, Guan Q, Yang X, Ou JX, Yan M, Wang C, Zhang Y, Li ZH, Lan C, Mao C, Zhou HW, Hao B, Zhang Z. The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery. Genomics Proteomics Bioinformatics. 2020 Oct;18(5):516-524. doi: 10.1016/j.gpb.2019.05.004. Epub 2020 Aug 19. PMID: 32827758; PMCID: PMC8377240.
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Detecting inherited and novel structural variants in low-coverage parent-child sequencing data.

Methods (San Diego, Calif.)

Spence M, Banuelos M, Marcia RF, Sindi S.
PMID: 31271880
Methods. 2020 Feb 15;173:61-68. doi: 10.1016/j.ymeth.2019.06.025. Epub 2019 Jul 02.

Structural variants (SVs) are a class of genomic variation shared by members of the same species. Though relatively rare, they represent an increasingly important class of variation, as SVs have been associated with diseases and susceptibility to some types...

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Spence M, Banuelos M, Marcia RF, et al. Detecting inherited and novel structural variants in low-coverage parent-child sequencing data. Methods. 2019;173:61-68doi: 10.1016/j.ymeth.2019.06.025.
Spence, M., Banuelos, M., Marcia, R. F., & Sindi, S. (2020). Detecting inherited and novel structural variants in low-coverage parent-child sequencing data. Methods (San Diego, Calif.), 17361-68. https://doi.org/10.1016/j.ymeth.2019.06.025
Spence, Melissa, et al. "Detecting inherited and novel structural variants in low-coverage parent-child sequencing data." Methods (San Diego, Calif.) vol. 173 (2020): 61-68. doi: https://doi.org/10.1016/j.ymeth.2019.06.025
Spence M, Banuelos M, Marcia RF, Sindi S. Detecting inherited and novel structural variants in low-coverage parent-child sequencing data. Methods. 2020 Feb 15;173:61-68. doi: 10.1016/j.ymeth.2019.06.025. Epub 2019 Jul 02. PMID: 31271880.
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Statistics in the Genomic Era.

Genes

Jiang H, He K.
PMID: 32325634
Genes (Basel). 2020 Apr 18;11(4). doi: 10.3390/genes11040443.

In recent years, technology breakthroughs have greatly enhanced our ability to understand the complex world of molecular biology [...].

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Jiang H, He K. Statistics in the Genomic Era. Genes (Basel). 2020;11(4)doi: 10.3390/genes11040443.
Jiang, H., & He, K. (2020). Statistics in the Genomic Era. Genes, 11(4), . https://doi.org/10.3390/genes11040443
Jiang, Hui, and He, Kevin. "Statistics in the Genomic Era." Genes vol. 11,4 (2020). doi: https://doi.org/10.3390/genes11040443
Jiang H, He K. Statistics in the Genomic Era. Genes (Basel). 2020 Apr 18;11(4). doi: 10.3390/genes11040443. PMID: 32325634; PMCID: PMC7230157.
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Editorial overview: Diving into the Genome.

Current opinion in genetics & development

Bystricky K, Merkenschlager M.
PMID: 32950132
Curr Opin Genet Dev. 2020 Apr;61:iii-vi. doi: 10.1016/j.gde.2020.06.001.

No abstract available.

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Bystricky K, Merkenschlager M. Editorial overview: Diving into the Genome. Curr Opin Genet Dev. 2020;61:iii-vidoi: 10.1016/j.gde.2020.06.001.
Bystricky, K., & Merkenschlager, M. (2020). Editorial overview: Diving into the Genome. Current opinion in genetics & development, 61iii-vi. https://doi.org/10.1016/j.gde.2020.06.001
Bystricky, Kerstin, and Merkenschlager, Matthias. "Editorial overview: Diving into the Genome." Current opinion in genetics & development vol. 61 (2020): iii-vi. doi: https://doi.org/10.1016/j.gde.2020.06.001
Bystricky K, Merkenschlager M. Editorial overview: Diving into the Genome. Curr Opin Genet Dev. 2020 Apr;61:iii-vi. doi: 10.1016/j.gde.2020.06.001. PMID: 32950132.
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Review of Altered inheritance: CRISPR and the ethics of human genome editing by Françoise Baylis.

Monash bioethics review

Sun BZ.
PMID: 32314277
Monash Bioeth Rev. 2020 May;38(1):91-93. doi: 10.1007/s40592-020-00106-0.

No abstract available.

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Sun BZ. Review of Altered inheritance: CRISPR and the ethics of human genome editing by Françoise Baylis. Monash Bioeth Rev. 2020;38(1):91-93doi: 10.1007/s40592-020-00106-0.
Sun, B. Z. (2020). Review of Altered inheritance: CRISPR and the ethics of human genome editing by Françoise Baylis. Monash bioethics review, 38(1), 91-93. https://doi.org/10.1007/s40592-020-00106-0
Sun, Bob Z. "Review of Altered inheritance: CRISPR and the ethics of human genome editing by Françoise Baylis." Monash bioethics review vol. 38,1 (2020): 91-93. doi: https://doi.org/10.1007/s40592-020-00106-0
Sun BZ. Review of Altered inheritance: CRISPR and the ethics of human genome editing by Françoise Baylis. Monash Bioeth Rev. 2020 May;38(1):91-93. doi: 10.1007/s40592-020-00106-0. PMID: 32314277.
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Progress, Challenges, and Surprises in Annotating the Human Genome.

Annual review of genomics and human genetics

Zerbino DR, Frankish A, Flicek P.
PMID: 32421357
Annu Rev Genomics Hum Genet. 2020 Aug 31;21:55-79. doi: 10.1146/annurev-genom-121119-083418. Epub 2020 May 18.

Our understanding of the human genome has continuously expanded since its draft publication in 2001. Over the years, novel assays have allowed us to progressively overlay layers of knowledge above the raw sequence of A's, T's, G's, and C's....

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Zerbino DR, Frankish A, Flicek P. Progress, Challenges, and Surprises in Annotating the Human Genome. Annu Rev Genomics Hum Genet. 2020;21:55-79doi: 10.1146/annurev-genom-121119-083418.
Zerbino, D. R., Frankish, A., & Flicek, P. (2020). Progress, Challenges, and Surprises in Annotating the Human Genome. Annual review of genomics and human genetics, 2155-79. https://doi.org/10.1146/annurev-genom-121119-083418
Zerbino, Daniel R, et al. "Progress, Challenges, and Surprises in Annotating the Human Genome." Annual review of genomics and human genetics vol. 21 (2020): 55-79. doi: https://doi.org/10.1146/annurev-genom-121119-083418
Zerbino DR, Frankish A, Flicek P. Progress, Challenges, and Surprises in Annotating the Human Genome. Annu Rev Genomics Hum Genet. 2020 Aug 31;21:55-79. doi: 10.1146/annurev-genom-121119-083418. Epub 2020 May 18. PMID: 32421357; PMCID: PMC7116059.
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Showing 13 to 24 of 89 entries