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[Bioinformatics and Next -generation Sequencing].

Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti

Krejčí A, Müller P, Vojtěšek B.
PMID: 26374164
Klin Onkol. 2015;28:2S91-6. doi: 10.14735/amko20152s91.

Next-generation sequencing technologies are currently well-established in the research field and progressively find their way towards clinical applications. Sequencers produce vast amounts of data and therefore bioinformatics methods are needed for processing. Without computational methods, sequencing would not be...

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Krejčí A, Müller P, Vojtěšek B. Bioinformatika a sekvenování nové generace. [Bioinformatics and Next -generation Sequencing]. Klin Onkol. 2015;28:2S91-6doi: 10.14735/amko20152s91.
Krejčí, A., Müller, P., & Vojtěšek, B. (2015). Bioinformatika a sekvenování nové generace. [Bioinformatics and Next -generation Sequencing]. Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti, 282S91-6. https://doi.org/10.14735/amko20152s91
Krejčí, A, et al. "Bioinformatika a sekvenování nové generace." [Bioinformatics and Next -generation Sequencing]. Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti vol. 28 (2015): 2S91-6. doi: https://doi.org/10.14735/amko20152s91
Krejčí A, Müller P, Vojtěšek B. Bioinformatika a sekvenování nové generace. [Bioinformatics and Next -generation Sequencing]. Klin Onkol. 2015;28:2S91-6. doi: 10.14735/amko20152s91. Czech. PMID: 26374164.
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AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing.

Bioinformatics (Oxford, England)

Shin S, Lee H, Son H, Paik S, Kim S.
PMID: 29126106
Bioinformatics. 2018 Apr 01;34(7):1232-1234. doi: 10.1093/bioinformatics/btx719.

SUMMARY: Ion Torrent sequencing is one of the most frequently used platforms in healthcare research and industry. Despite many advantages, platform-specific artifacts complicate efficient separation of true variants from errors, especially in variants with lower allele frequencies (

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Shin S, Lee H, Son H, et al. AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing. Bioinformatics. 2018;34(7):1232-1234doi: 10.1093/bioinformatics/btx719.
Shin, S., Lee, H., Son, H., Paik, S., & Kim, S. (2018). AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing. Bioinformatics (Oxford, England), 34(7), 1232-1234. https://doi.org/10.1093/bioinformatics/btx719
Shin, Sunguk, et al. "AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing." Bioinformatics (Oxford, England) vol. 34,7 (2018): 1232-1234. doi: https://doi.org/10.1093/bioinformatics/btx719
Shin S, Lee H, Son H, Paik S, Kim S. AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing. Bioinformatics. 2018 Apr 01;34(7):1232-1234. doi: 10.1093/bioinformatics/btx719. PMID: 29126106.
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Production and analytic bioinformatics for next-generation DNA sequencing.

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

Allcock RJ.
PMID: 24870128
Methods Mol Biol. 2014;1168:17-29. doi: 10.1007/978-1-4939-0847-9_2.

The bioinformatics requirements within the clinical environment are very specific, and analytic techniques need to be fit for purpose, robust, and predictable. At the same time, the bewildering amount of information produced during these analyses needs to be carefully...

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Allcock RJ. Production and analytic bioinformatics for next-generation DNA sequencing. Methods Mol Biol. 2014;1168:17-29doi: 10.1007/978-1-4939-0847-9_2.
Allcock, R. J. (2014). Production and analytic bioinformatics for next-generation DNA sequencing. Methods in molecular biology (Clifton, N.J.), 116817-29. https://doi.org/10.1007/978-1-4939-0847-9_2
Allcock, Richard James Nigel. "Production and analytic bioinformatics for next-generation DNA sequencing." Methods in molecular biology (Clifton, N.J.) vol. 1168 (2014): 17-29. doi: https://doi.org/10.1007/978-1-4939-0847-9_2
Allcock RJ. Production and analytic bioinformatics for next-generation DNA sequencing. Methods Mol Biol. 2014;1168:17-29. doi: 10.1007/978-1-4939-0847-9_2. PMID: 24870128.
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NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data.

BMC genomics

Kim NK, Jayatillake RV, Spouge JL.
PMID: 23706083
BMC Genomics. 2013 May 25;14:349. doi: 10.1186/1471-2164-14-349.

BACKGROUND: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.RESULTS: We propose a rigorous...

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Kim NK, Jayatillake RV, Spouge JL. NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Genomics. 2013;14:349doi: 10.1186/1471-2164-14-349.
Kim, N. K., Jayatillake, R. V., & Spouge, J. L. (2013). NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC genomics, 14349. https://doi.org/10.1186/1471-2164-14-349
Kim, Nak-Kyeong, et al. "NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data." BMC genomics vol. 14 (2013): 349. doi: https://doi.org/10.1186/1471-2164-14-349
Kim NK, Jayatillake RV, Spouge JL. NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Genomics. 2013 May 25;14:349. doi: 10.1186/1471-2164-14-349. PMID: 23706083; PMCID: PMC3672025.
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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing.

Journal of visualized experiments : JoVE

Lv X, Zhao M, Yi Y, Zhang L, Guan Y, Liu T, Yang L, Chen R, Ma J, Yi X.
PMID: 28872127
J Vis Exp. 2017 Aug 24;(126). doi: 10.3791/56342.

The analysis of circulating tumor DNA (ctDNA) using next-generation sequencing (NGS) has become a valuable tool for the development of clinical oncology. However, the application of this method is challenging due to its low sensitivity in analyzing the trace...

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Lv X, Zhao M, Yi Y, et al. Detection of Rare Mutations in CtDNA Using Next Generation Sequencing. J Vis Exp. 2017;(126)doi: 10.3791/56342.
Lv, X., Zhao, M., Yi, Y., Zhang, L., Guan, Y., Liu, T., Yang, L., Chen, R., Ma, J., & Yi, X. (2017). Detection of Rare Mutations in CtDNA Using Next Generation Sequencing. Journal of visualized experiments : JoVE, (126), . https://doi.org/10.3791/56342
Lv, Xiaoxing, et al. "Detection of Rare Mutations in CtDNA Using Next Generation Sequencing." Journal of visualized experiments : JoVE vol. ,126 (2017). doi: https://doi.org/10.3791/56342
Lv X, Zhao M, Yi Y, Zhang L, Guan Y, Liu T, Yang L, Chen R, Ma J, Yi X. Detection of Rare Mutations in CtDNA Using Next Generation Sequencing. J Vis Exp. 2017 Aug 24;(126). doi: 10.3791/56342. PMID: 28872127; PMCID: PMC5614374.
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Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

Briefings in functional genomics

Smith DR.
PMID: 27339634
Brief Funct Genomics. 2017 May 01;16(3):156-162. doi: 10.1093/bfgp/elw026.

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated...

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Smith DR. Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science. Brief Funct Genomics. 2017;16(3):156-162doi: 10.1093/bfgp/elw026.
Smith, D. R. (2017). Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science. Briefings in functional genomics, 16(3), 156-162. https://doi.org/10.1093/bfgp/elw026
Smith, David Roy. "Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science." Briefings in functional genomics vol. 16,3 (2017): 156-162. doi: https://doi.org/10.1093/bfgp/elw026
Smith DR. Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science. Brief Funct Genomics. 2017 May 01;16(3):156-162. doi: 10.1093/bfgp/elw026. PMID: 27339634; PMCID: PMC5439286.
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Oxford Nanopore announcement sets sequencing sector abuzz.

Nature biotechnology

Eisenstein M.
PMID: 22491260
Nat Biotechnol. 2012 Apr 10;30(4):295-6. doi: 10.1038/nbt0412-295.

No abstract available.

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Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol. 2012;30(4):295-6doi: 10.1038/nbt0412-295.
Eisenstein, M. (2012). Oxford Nanopore announcement sets sequencing sector abuzz. Nature biotechnology, 30(4), 295-6. https://doi.org/10.1038/nbt0412-295
Eisenstein, Michael. "Oxford Nanopore announcement sets sequencing sector abuzz." Nature biotechnology vol. 30,4 (2012): 295-6. doi: https://doi.org/10.1038/nbt0412-295
Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol. 2012 Apr 10;30(4):295-6. doi: 10.1038/nbt0412-295. PMID: 22491260.
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Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies.

Applied and environmental microbiology

Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG, Kleerebezem M.
PMID: 22492454
Appl Environ Microbiol. 2012 Jun;78(12):4141-8. doi: 10.1128/AEM.00470-12. Epub 2012 Apr 06.

RNA sequencing is starting to compete with the use of DNA microarrays for transcription analysis in eukaryotes as well as in prokaryotes. The application of RNA sequencing in prokaryotes requires additional steps in the RNA preparation procedure to increase...

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Leimena MM, Wels M, Bongers RS, et al. Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Appl Environ Microbiol. 2012;78(12):4141-8doi: 10.1128/AEM.00470-12.
Leimena, M. M., Wels, M., Bongers, R. S., Smid, E. J., Zoetendal, E. G., & Kleerebezem, M. (2012). Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Applied and environmental microbiology, 78(12), 4141-8. https://doi.org/10.1128/AEM.00470-12
Leimena, Milkha M, et al. "Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies." Applied and environmental microbiology vol. 78,12 (2012): 4141-8. doi: https://doi.org/10.1128/AEM.00470-12
Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG, Kleerebezem M. Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Appl Environ Microbiol. 2012 Jun;78(12):4141-8. doi: 10.1128/AEM.00470-12. Epub 2012 Apr 06. PMID: 22492454; PMCID: PMC3370542.
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Verification of systems biology research in the age of collaborative competition.

Nature biotechnology

Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.
PMID: 21904331
Nat Biotechnol. 2011 Sep 08;29(9):811-5. doi: 10.1038/nbt.1968.

No abstract available.

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Meyer P, Alexopoulos LG, Bonk T, et al. Verification of systems biology research in the age of collaborative competition. Nat Biotechnol. 2011;29(9):811-5doi: 10.1038/nbt.1968.
Meyer, P., Alexopoulos, L. G., Bonk, T., Califano, A., Cho, C. R., de la Fuente, A., de Graaf, D., Hartemink, A. J., Hoeng, J., Ivanov, N. V., Koeppl, H., Linding, R., Marbach, D., Norel, R., Peitsch, M. C., Rice, J. J., Royyuru, A., Schacherer, F., Sprengel, J., Stolle, K., Vitkup, D., & Stolovitzky, G. (2011). Verification of systems biology research in the age of collaborative competition. Nature biotechnology, 29(9), 811-5. https://doi.org/10.1038/nbt.1968
Meyer, Pablo, et al. "Verification of systems biology research in the age of collaborative competition." Nature biotechnology vol. 29,9 (2011): 811-5. doi: https://doi.org/10.1038/nbt.1968
Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G. Verification of systems biology research in the age of collaborative competition. Nat Biotechnol. 2011 Sep 08;29(9):811-5. doi: 10.1038/nbt.1968. PMID: 21904331.
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High throughput sequencing methods and analysis for microbiome research.

Journal of microbiological methods

Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G.
PMID: 24029734
J Microbiol Methods. 2013 Dec;95(3):401-14. doi: 10.1016/j.mimet.2013.08.011. Epub 2013 Sep 09.

High-throughput sequencing technology is rapidly improving in quality, speed and cost. It is therefore becoming more widely used to study whole communities of prokaryotes in many niches. This review discusses these techniques, including nucleic acid extraction from different environments,...

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Di Bella JM, Bao Y, Gloor GB, et al. High throughput sequencing methods and analysis for microbiome research. J Microbiol Methods. 2013;95(3):401-14doi: 10.1016/j.mimet.2013.08.011.
Di Bella, J. M., Bao, Y., Gloor, G. B., Burton, J. P., & Reid, G. (2013). High throughput sequencing methods and analysis for microbiome research. Journal of microbiological methods, 95(3), 401-14. https://doi.org/10.1016/j.mimet.2013.08.011
Di Bella, Julia M, et al. "High throughput sequencing methods and analysis for microbiome research." Journal of microbiological methods vol. 95,3 (2013): 401-14. doi: https://doi.org/10.1016/j.mimet.2013.08.011
Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G. High throughput sequencing methods and analysis for microbiome research. J Microbiol Methods. 2013 Dec;95(3):401-14. doi: 10.1016/j.mimet.2013.08.011. Epub 2013 Sep 09. PMID: 24029734.
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Variants from the deep.

Nature methods

Nawy T.
PMID: 30377361
Nat Methods. 2018 Nov;15(11):861. doi: 10.1038/s41592-018-0209-6.

No abstract available.

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Nawy T. Variants from the deep. Nat Methods. 2018;15(11):861doi: 10.1038/s41592-018-0209-6.
Nawy, T. (2018). Variants from the deep. Nature methods, 15(11), 861. https://doi.org/10.1038/s41592-018-0209-6
Nawy, Tal. "Variants from the deep." Nature methods vol. 15,11 (2018): 861. doi: https://doi.org/10.1038/s41592-018-0209-6
Nawy T. Variants from the deep. Nat Methods. 2018 Nov;15(11):861. doi: 10.1038/s41592-018-0209-6. PMID: 30377361.
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Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing.

PloS one

Sabir SH, Krishnamurthy S, Gupta S, Mills GB, Wei W, Cortes AC, Mills Shaw KR, Luthra R, Wallace MJ.
PMID: 29281680
PLoS One. 2017 Dec 27;12(12):e0189651. doi: 10.1371/journal.pone.0189651. eCollection 2017.

PURPOSE: Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel.MATERIALS AND METHODS: All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel...

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Sabir SH, Krishnamurthy S, Gupta S, et al. Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing. PLoS One. 2017;12(12):e0189651doi: 10.1371/journal.pone.0189651.
Sabir, S. H., Krishnamurthy, S., Gupta, S., Mills, G. B., Wei, W., Cortes, A. C., Mills Shaw, K. R., Luthra, R., & Wallace, M. J. (2017). Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing. PloS one, 12(12), e0189651. https://doi.org/10.1371/journal.pone.0189651
Sabir, Sharjeel H, et al. "Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing." PloS one vol. 12,12 (2017): e0189651. doi: https://doi.org/10.1371/journal.pone.0189651
Sabir SH, Krishnamurthy S, Gupta S, Mills GB, Wei W, Cortes AC, Mills Shaw KR, Luthra R, Wallace MJ. Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing. PLoS One. 2017 Dec 27;12(12):e0189651. doi: 10.1371/journal.pone.0189651. eCollection 2017. PMID: 29281680; PMCID: PMC5744968.
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Showing 1 to 12 of 136 entries