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Showing 25 to 36 of 89 entries
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DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework.

Computational and mathematical methods in medicine

Huang PJ, Chang JH, Lin HH, Li YX, Lee CC, Su CT, Li YL, Chang MT, Weng S, Cheng WH, Chiu CH, Tang P.
PMID: 32952600
Comput Math Methods Med. 2020 Sep 01;2020:7231205. doi: 10.1155/2020/7231205. eCollection 2020.

Although sequencing a human genome has become affordable, identifying genetic variants from whole-genome sequence data is still a hurdle for researchers without adequate computing equipment or bioinformatics support. GATK is a gold standard method for the identification of genetic...

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Huang PJ, Chang JH, Lin HH, et al. DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework. Comput Math Methods Med. 2020;2020:7231205doi: 10.1155/2020/7231205.
Huang, P. J., Chang, J. H., Lin, H. H., Li, Y. X., Lee, C. C., Su, C. T., Li, Y. L., Chang, M. T., Weng, S., Cheng, W. H., Chiu, C. H., & Tang, P. (2020). DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework. Computational and mathematical methods in medicine, 20207231205. https://doi.org/10.1155/2020/7231205
Huang, Po-Jung, et al. "DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework." Computational and mathematical methods in medicine vol. 2020 (2020): 7231205. doi: https://doi.org/10.1155/2020/7231205
Huang PJ, Chang JH, Lin HH, Li YX, Lee CC, Su CT, Li YL, Chang MT, Weng S, Cheng WH, Chiu CH, Tang P. DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework. Comput Math Methods Med. 2020 Sep 01;2020:7231205. doi: 10.1155/2020/7231205. eCollection 2020. PMID: 32952600; PMCID: PMC7481958.
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What Is Prudent Governance of Human Genome Editing?.

AMA journal of ethics

Schweikart SJ.
PMID: 31876467
AMA J Ethics. 2019 Dec 01;21(12):E1042-1048. doi: 10.1001/amajethics.2019.1042.

CRISPR technology has made questions about how best to regulate human genome editing immediately relevant. A sound and ethical governance structure for human genome editing is necessary, as the consequences of this new technology are far-reaching and profound. Because...

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Schweikart SJ. What Is Prudent Governance of Human Genome Editing?. AMA J Ethics. 2019;21(12):E1042-1048doi: 10.1001/amajethics.2019.1042.
Schweikart, S. J. (2019). What Is Prudent Governance of Human Genome Editing?. AMA journal of ethics, 21(12), E1042-1048. https://doi.org/10.1001/amajethics.2019.1042
Schweikart, Scott J. "What Is Prudent Governance of Human Genome Editing?." AMA journal of ethics vol. 21,12 (2019): E1042-1048. doi: https://doi.org/10.1001/amajethics.2019.1042
Schweikart SJ. What Is Prudent Governance of Human Genome Editing?. AMA J Ethics. 2019 Dec 01;21(12):E1042-1048. doi: 10.1001/amajethics.2019.1042. PMID: 31876467.
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Targeted Perturb-seq enables genome-scale genetic screens in single cells.

Nature methods

Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, Korbel JO, Merten CA, Velten L, Steinmetz LM.
PMID: 32483332
Nat Methods. 2020 Jun;17(6):629-635. doi: 10.1038/s41592-020-0837-5. Epub 2020 Jun 01.

The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive...

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Schraivogel D, Gschwind AR, Milbank JH, et al. Targeted Perturb-seq enables genome-scale genetic screens in single cells. Nat Methods. 2020;17(6):629-635doi: 10.1038/s41592-020-0837-5.
Schraivogel, D., Gschwind, A. R., Milbank, J. H., Leonce, D. R., Jakob, P., Mathur, L., Korbel, J. O., Merten, C. A., Velten, L., & Steinmetz, L. M. (2020). Targeted Perturb-seq enables genome-scale genetic screens in single cells. Nature methods, 17(6), 629-635. https://doi.org/10.1038/s41592-020-0837-5
Schraivogel, Daniel, et al. "Targeted Perturb-seq enables genome-scale genetic screens in single cells." Nature methods vol. 17,6 (2020): 629-635. doi: https://doi.org/10.1038/s41592-020-0837-5
Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, Korbel JO, Merten CA, Velten L, Steinmetz LM. Targeted Perturb-seq enables genome-scale genetic screens in single cells. Nat Methods. 2020 Jun;17(6):629-635. doi: 10.1038/s41592-020-0837-5. Epub 2020 Jun 01. PMID: 32483332; PMCID: PMC7610614.
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Systematically Prioritizing Candidates in Genome-Based Drug Repurposing.

Assay and drug development technologies

Challa AP, Lavieri RR, Lewis JT, Zaleski NM, Shirey-Rice JK, Harris PA, Aronoff DM, Pulley JM.
PMID: 31769998
Assay Drug Dev Technol. 2019 Nov/Dec;17(8):352-363. doi: 10.1089/adt.2019.950. Epub 2019 Nov 26.

Drug repurposing is the application of approved drugs to treat diseases separate and distinct from their original indications. Herein, we define the scope of all practical precision drug repurposing using DrugBank, a publicly available database of pharmacological agents, and...

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Challa AP, Lavieri RR, Lewis JT, et al. Systematically Prioritizing Candidates in Genome-Based Drug Repurposing. Assay Drug Dev Technol. 2019;17(8):352-363doi: 10.1089/adt.2019.950.
Challa, A. P., Lavieri, R. R., Lewis, J. T., Zaleski, N. M., Shirey-Rice, J. K., Harris, P. A., Aronoff, D. M., & Pulley, J. M. (2019). Systematically Prioritizing Candidates in Genome-Based Drug Repurposing. Assay and drug development technologies, 17(8), 352-363. https://doi.org/10.1089/adt.2019.950
Challa, Anup P, et al. "Systematically Prioritizing Candidates in Genome-Based Drug Repurposing." Assay and drug development technologies vol. 17,8 (2019): 352-363. doi: https://doi.org/10.1089/adt.2019.950
Challa AP, Lavieri RR, Lewis JT, Zaleski NM, Shirey-Rice JK, Harris PA, Aronoff DM, Pulley JM. Systematically Prioritizing Candidates in Genome-Based Drug Repurposing. Assay Drug Dev Technol. 2019 Nov/Dec;17(8):352-363. doi: 10.1089/adt.2019.950. Epub 2019 Nov 26. PMID: 31769998; PMCID: PMC6921094.
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The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.

Nature biotechnology

Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, Banerjee A, Kim DS, Beier T, Urban L, Kundaje A, Stegle O, Gagneur J.
PMID: 31138913
Nat Biotechnol. 2019 Jun;37(6):592-600. doi: 10.1038/s41587-019-0140-0.

No abstract available.

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Avsec Ž, Kreuzhuber R, Israeli J, et al. The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nat Biotechnol. 2019;37(6):592-600doi: 10.1038/s41587-019-0140-0.
Avsec, �. �., Kreuzhuber, R., Israeli, J., Xu, N., Cheng, J., Shrikumar, A., Banerjee, A., Kim, D. S., Beier, T., Urban, L., Kundaje, A., Stegle, O., & Gagneur, J. (2019). The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nature biotechnology, 37(6), 592-600. https://doi.org/10.1038/s41587-019-0140-0
Avsec, Žiga, et al. "The Kipoi repository accelerates community exchange and reuse of predictive models for genomics." Nature biotechnology vol. 37,6 (2019): 592-600. doi: https://doi.org/10.1038/s41587-019-0140-0
Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, Banerjee A, Kim DS, Beier T, Urban L, Kundaje A, Stegle O, Gagneur J. The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nat Biotechnol. 2019 Jun;37(6):592-600. doi: 10.1038/s41587-019-0140-0. PMID: 31138913; PMCID: PMC6777348.
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UCSC Genome Browser enters 20th year.

Nucleic acids research

Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.
PMID: 31691824
Nucleic Acids Res. 2020 Jan 08;48:D756-D761. doi: 10.1093/nar/gkz1012.

The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our...

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Lee CM, Barber GP, Casper J, et al. UCSC Genome Browser enters 20th year. Nucleic Acids Res. 2020;48:D756-D761doi: 10.1093/nar/gkz1012.
Lee, C. M., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Gonzalez, J. N., Hinrichs, A. S., Lee, B. T., Nassar, L. R., Powell, C. C., Raney, B. J., Rosenbloom, K. R., Schmelter, D., Speir, M. L., Zweig, A. S., Haussler, D., Haeussler, M., Kuhn, R. M., & Kent, W. J. (2020). UCSC Genome Browser enters 20th year. Nucleic acids research, 48D756-D761. https://doi.org/10.1093/nar/gkz1012
Lee, Christopher M, et al. "UCSC Genome Browser enters 20th year." Nucleic acids research vol. 48 (2020): D756-D761. doi: https://doi.org/10.1093/nar/gkz1012
Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ. UCSC Genome Browser enters 20th year. Nucleic Acids Res. 2020 Jan 08;48:D756-D761. doi: 10.1093/nar/gkz1012. PMID: 31691824; PMCID: PMC7145642.
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Visualization tools for human structural variations identified by whole-genome sequencing.

Journal of human genetics

Yokoyama TT, Kasahara M.
PMID: 31666648
J Hum Genet. 2020 Jan;65(1):49-60. doi: 10.1038/s10038-019-0687-0. Epub 2019 Oct 30.

Visualizing structural variations (SVs) is a critical step for finding associations between SVs and human traits or diseases. Given that there are many sequencing platforms used for SV identification and given that how best to visualize SVs together with...

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Yokoyama TT, Kasahara M. Visualization tools for human structural variations identified by whole-genome sequencing. J Hum Genet. 2019;65(1):49-60doi: 10.1038/s10038-019-0687-0.
Yokoyama, T. T., & Kasahara, M. (2020). Visualization tools for human structural variations identified by whole-genome sequencing. Journal of human genetics, 65(1), 49-60. https://doi.org/10.1038/s10038-019-0687-0
Yokoyama, Toshiyuki T, and Kasahara, Masahiro. "Visualization tools for human structural variations identified by whole-genome sequencing." Journal of human genetics vol. 65,1 (2020): 49-60. doi: https://doi.org/10.1038/s10038-019-0687-0
Yokoyama TT, Kasahara M. Visualization tools for human structural variations identified by whole-genome sequencing. J Hum Genet. 2020 Jan;65(1):49-60. doi: 10.1038/s10038-019-0687-0. Epub 2019 Oct 30. PMID: 31666648; PMCID: PMC8075883.
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Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees.

Genome research

Ullah E, Mall R, Abbas MM, Kunji K, Nato AQ, Bensmail H, Wijsman EM, Saad M.
PMID: 30514702
Genome Res. 2019 Jan;29(1):125-134. doi: 10.1101/gr.236315.118. Epub 2018 Dec 04.

Genotype imputation is widely used in genome-wide association studies to boost variant density, allowing increased power in association testing. Many studies currently include pedigree data due to increasing interest in rare variants coupled with the availability of appropriate analysis...

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Ullah E, Mall R, Abbas MM, et al. Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees. Genome Res. 2018;29(1):125-134doi: 10.1101/gr.236315.118.
Ullah, E., Mall, R., Abbas, M. M., Kunji, K., Nato, A. Q., Bensmail, H., Wijsman, E. M., & Saad, M. (2019). Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees. Genome research, 29(1), 125-134. https://doi.org/10.1101/gr.236315.118
Ullah, Ehsan, et al. "Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees." Genome research vol. 29,1 (2019): 125-134. doi: https://doi.org/10.1101/gr.236315.118
Ullah E, Mall R, Abbas MM, Kunji K, Nato AQ, Bensmail H, Wijsman EM, Saad M. Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees. Genome Res. 2019 Jan;29(1):125-134. doi: 10.1101/gr.236315.118. Epub 2018 Dec 04. PMID: 30514702; PMCID: PMC6314157.
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Genome Diagnostics: Novel Strategies for Measuring Value.

Journal of managed care & specialty pharmacy

Hayeems RZ, Luca S, Pullenayegum E, Meyn MS, Ungar WJ.
PMID: 31556822
J Manag Care Spec Pharm. 2019 Oct;25(10):1096-1101. doi: 10.18553/jmcp.2019.25.10.1096.

Genetic testing technology is rapidly evolving with the growth of personalized medicine. While test evaluation typically relies on laboratory measures of performance, tests can be costly and analytically and ethically complex. A more fulsome consideration of value is warranted...

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Hayeems RZ, Luca S, Pullenayegum E, et al. Genome Diagnostics: Novel Strategies for Measuring Value. J Manag Care Spec Pharm. 2019;25(10):1096-1101doi: 10.18553/jmcp.2019.25.10.1096.
Hayeems, R. Z., Luca, S., Pullenayegum, E., Meyn, M. S., & Ungar, W. J. (2019). Genome Diagnostics: Novel Strategies for Measuring Value. Journal of managed care & specialty pharmacy, 25(10), 1096-1101. https://doi.org/10.18553/jmcp.2019.25.10.1096
Hayeems, Robin Z, et al. "Genome Diagnostics: Novel Strategies for Measuring Value." Journal of managed care & specialty pharmacy vol. 25,10 (2019): 1096-1101. doi: https://doi.org/10.18553/jmcp.2019.25.10.1096
Hayeems RZ, Luca S, Pullenayegum E, Meyn MS, Ungar WJ. Genome Diagnostics: Novel Strategies for Measuring Value. J Manag Care Spec Pharm. 2019 Oct;25(10):1096-1101. doi: 10.18553/jmcp.2019.25.10.1096. PMID: 31556822.
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The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity.

Genome biology and evolution

Watkins WS, Feusier JE, Thomas J, Goubert C, Mallick S, Jorde LB.
PMID: 32359137
Genome Biol Evol. 2020 Jun 01;12(6):779-794. doi: 10.1093/gbe/evaa086.

Ongoing retrotransposition of Alu, LINE-1, and SINE-VNTR-Alu elements generates diversity and variation among human populations. Previous analyses investigating the population genetics of mobile element insertions (MEIs) have been limited by population ascertainment bias or by relatively small numbers of...

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Watkins WS, Feusier JE, Thomas J, et al. The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity. Genome Biol Evol. 2020;12(6):779-794doi: 10.1093/gbe/evaa086.
Watkins, W. S., Feusier, J. E., Thomas, J., Goubert, C., Mallick, S., & Jorde, L. B. (2020). The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity. Genome biology and evolution, 12(6), 779-794. https://doi.org/10.1093/gbe/evaa086
Watkins, W Scott, et al. "The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity." Genome biology and evolution vol. 12,6 (2020): 779-794. doi: https://doi.org/10.1093/gbe/evaa086
Watkins WS, Feusier JE, Thomas J, Goubert C, Mallick S, Jorde LB. The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity. Genome Biol Evol. 2020 Jun 01;12(6):779-794. doi: 10.1093/gbe/evaa086. PMID: 32359137; PMCID: PMC7290288.
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Legal reflections on the case of genome-edited babies.

Global health research and policy

Liu S.
PMID: 32435694
Glob Health Res Policy. 2020 May 14;5:24. doi: 10.1186/s41256-020-00153-4. eCollection 2020.

Human genome-editing is banned by guidelines, laws and regulations in most countries. However, the first criminal case on genome-edited babies was sentenced in China in 2019. In this commentary we discuss our legal reflections on this case. Genome-editing on...

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Liu S. Legal reflections on the case of genome-edited babies. Glob Health Res Policy. 2020;5:24doi: 10.1186/s41256-020-00153-4.
Liu, S. (2020). Legal reflections on the case of genome-edited babies. Global health research and policy, 524. https://doi.org/10.1186/s41256-020-00153-4
Liu, Shuang. "Legal reflections on the case of genome-edited babies." Global health research and policy vol. 5 (2020): 24. doi: https://doi.org/10.1186/s41256-020-00153-4
Liu S. Legal reflections on the case of genome-edited babies. Glob Health Res Policy. 2020 May 14;5:24. doi: 10.1186/s41256-020-00153-4. eCollection 2020. PMID: 32435694; PMCID: PMC7222292.
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Prediction of driver variants in the cancer genome via machine learning methodologies.

Briefings in bioinformatics

Rogers MF, Gaunt TR, Campbell C.
PMID: 33094325
Brief Bioinform. 2021 Jul 20;22(4). doi: 10.1093/bib/bbaa250.

Sequencing technologies have led to the identification of many variants in the human genome which could act as disease-drivers. As a consequence, a variety of bioinformatics tools have been proposed for predicting which variants may drive disease, and which...

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Rogers MF, Gaunt TR, Campbell C. Prediction of driver variants in the cancer genome via machine learning methodologies. Brief Bioinform. 2021;22(4)doi: 10.1093/bib/bbaa250.
Rogers, M. F., Gaunt, T. R., & Campbell, C. (2021). Prediction of driver variants in the cancer genome via machine learning methodologies. Briefings in bioinformatics, 22(4), . https://doi.org/10.1093/bib/bbaa250
Rogers, Mark F, et al. "Prediction of driver variants in the cancer genome via machine learning methodologies." Briefings in bioinformatics vol. 22,4 (2021). doi: https://doi.org/10.1093/bib/bbaa250
Rogers MF, Gaunt TR, Campbell C. Prediction of driver variants in the cancer genome via machine learning methodologies. Brief Bioinform. 2021 Jul 20;22(4). doi: 10.1093/bib/bbaa250. PMID: 33094325; PMCID: PMC8293831.
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Showing 25 to 36 of 89 entries