The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Next-Generation DNA Sequencing Methods
Abstract
Recent scientific discoveries that resulted from the application of next-generation DNA sequencing technologies highlight the striking impact of these massively parallel platforms on genetics. These new methods have expanded previously focused readouts from a variety of DNA preparation protocols to a genome-wide scale and have fine-tuned their resolution to single base precision. The sequencing of RNA also has transitioned and now includes full-length cDNA analyses, serial analysis of gene expression (SAGE)-based methods, and noncoding RNA discovery. Next-generation sequencing has also enabled novel applications such as the sequencing of ancient DNA samples, and has substantially widened the scope of metagenomic analysis of environmentally derived samples. Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge.
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Cites
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Self-citationThe gut microbiota as an environmental factor that regulates fat storage
Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245
Obesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176
Host-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Development of the Human Infant Intestinal Microbiota
Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050177 · Cited by 2,877
Archaea predominate among ammonia-oxidizing prokaryotes in soils
Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G. W., Prosser, J. I., Schuster, S. C., & Schleper, C. (2006) · Nature · doi:10.1038/nature04983 · Cited by 2,497
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
Cited by
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Real-Time DNA Sequencing from Single Polymerase Molecules
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., et al. (2009) · Science · doi:10.1126/science.1162986 · Cited by 3,732
ChIP–seq: advantages and challenges of a maturing technology
Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217
Characterization of the gut microbiome using 16S or shotgun metagenomics
Jovel, J., Patterson, J., Wang, W., Hotte, N., O'Keefe, S., Mitchel, T., Perry, T., Kao, D., Mason, A. L., Madsen, K. L., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00459 · Cited by 942
Field guide to next‐generation DNA sequencers
GLENN, T. C. (2011) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2011.03024.x · Cited by 940
Sequencing technologies and genome sequencing
Pareek, C. S., Smoczynski, R., & Tretyn, A. (2011) · Journal of Applied Genetics · doi:10.1007/s13353-011-0057-x · Cited by 868
Systems biology and multi-omics integration: viewpoints from the metabolomics research community
Pinu, F. R., Beale, D. J., Paten, A. M., Kouremenos, K., Swarup, S., Schirra, H. J., & Wishart, D. (2019) · Metabolites · doi:10.3390/metabo9040076 · Cited by 723
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
Baym, M., Kryazhimskiy, S., Lieberman, T. D., Chung, H., Desai, M. M., & Kishony, R. (2015) · PLOS ONE · doi:10.1371/journal.pone.0128036 · Cited by 685
A new view of the fish gut microbiome: advances from next-generation sequencing
Ghanbari, M., Kneifel, W., & Domig, K. J. (2015) · Aquaculture · doi:10.1016/j.aquaculture.2015.06.033 · Cited by 669
Synthetic spike-in standards for RNA-seq experiments
Jiang, L., Schlesinger, F., Davis, C. A., Zhang, Y., Li, R., Salit, M., Gingeras, T. R., & Oliver, B. (2011) · Genome Research · doi:10.1101/gr.121095.111 · Cited by 653
The impact of next-generation sequencing on genomics
Zhang, J., Chiodini, R., Badr, A., & Zhang, G. (2011) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2011.02.003 · Cited by 577
“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”
BackgroundLee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Ferrante, T. C., Terry, R., Turczyk, B. M., Yang, J. L., Lee, H. S., Aach, J., et al. (2015) · Nature Protocols · doi:10.1038/nprot.2014.191 · Cited by 529
Next generation sequencing and its applications in forensic genetics
Børsting, C., & Morling, N. (2015) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2015.02.002 · Cited by 460
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Yu, Y., Fuscoe, J. C., Zhao, C., Guo, C., Jia, M., Qing, T., Bannon, D. I., Lancashire, L., Bao, W., Du, T., et al. (2014) · Nature Communications · doi:10.1038/ncomms4230 · Cited by 395
Fouhy, F., Clooney, A. G., Stanton, C., Claesson, M. J., & Cotter, P. D. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0738-z · Cited by 310
Genomic views of STAT function in CD4+ T helper cell differentiation
O'Shea, J. J., Lahesmaa, R., Vahedi, G., Laurence, A., & Kanno, Y. (2011) · Nature Reviews Immunology · doi:10.1038/nri2958 · Cited by 295
Application of 'next-generation' sequencing technologies to microbial genetics
MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2088 · Cited by 293
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond
Lister, R., Gregory, B. D., & Ecker, J. R. (2009) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2008.11.004 · Cited by 274
De novo assembly of short sequence reads
Paszkiewicz, K., & Studholme, D. J. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq020 · Cited by 204
Global Analysis of the Evolution and Mechanism of Echinocandin Resistance in Candida glabrata
Singh-Babak, S. D., Babak, T., Diezmann, S., Hill, J. A., Xie, J. L., Chen, Y.-L., Poutanen, S. M., Rennie, R. P., Heitman, J., & Cowen, L. E. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002718 · Cited by 205
“Developments in sequencing technology [9–11] now enable this question to be addressed on a genome-wide scale to reveal the identity of mutations that either confer drug resistance in a clinically relevant context or that modify the fitness consequences of resistance mutations.”
BackgroundRoles of small regulatory RNAs in determining neuronal identity
Li, X., & Jin, P. (2010) · Nature Reviews Neuroscience · doi:10.1038/nrn2739 · Cited by 151
Brown, S. D., Nagaraju, S., Utturkar, S., De Tissera, S., Segovia, S., Mitchell, W., Land, M. L., Dassanayake, A., & Köpke, M. (2014) · Biotechnology for Biofuels · doi:10.1186/1754-6834-7-40 · Cited by 145
Massively Parallel Sequencing for Genetic Diagnosis of Hearing Loss: The New Standard of Care
Shearer, A. E., & Smith, R. J. H. (2015) · Otolaryngology–Head and Neck Surgery · doi:10.1177/0194599815591156 · Cited by 144
Fusion genes and chromosome translocations in the common epithelial cancers
Edwards, P. A. (2010) · The Journal of Pathology · doi:10.1002/path.2632 · Cited by 126
Wood, S. H., Craig, T., Li, Y., Merry, B., & de Magalhães, J. P. (2013) · AGE · doi:10.1007/s11357-012-9410-1 · Cited by 105
Han, L., Zi, X., Garmire, L. X., Wu, Y., Weissman, S. M., Pan, X., & Fan, R. (2014) · Scientific Reports · doi:10.1038/srep06485 · Cited by 83
Optimization of DNA Recovery and Amplification from Non-Carbonized Archaeobotanical Remains
Wales, N., Andersen, K., Cappellini, E., Ávila-Arcos, M. C., & Gilbert, M. T. P. (2014) · PLoS ONE · doi:10.1371/journal.pone.0086827 · Cited by 80
First insights into the metagenome of Egyptian mummies using next-generation sequencing
Khairat, R., Ball, M., Chang, C.-C. H., Bianucci, R., Nerlich, A. G., Trautmann, M., Ismail, S., Shanab, G. M. L., Karim, A. M., Gad, Y. Z., et al. (2013) · Journal of Applied Genetics · doi:10.1007/s13353-013-0145-1 · Cited by 72
Neverov, A., & Chumakov, K. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012537107 · Cited by 68
Hardt, O., Wild, S., Oerlecke, I., Hofmann, K., Luo, S., Wiencek, Y., Kantelhardt, E., Vess, C., Smith, G. P., Schroth, G. P., et al. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.06.010 · Cited by 64
Hu, H., Wrogemann, K., Kalscheuer, V., Tzschach, A., Richard, H., Haas, S. A., Menzel, C., Bienek, M., Froyen, G., Raynaud, M., et al. (2009) · The HUGO Journal · doi:10.1007/s11568-010-9137-y · Cited by 49
Genome‐wide survey of transcriptional initiation in the pathogenic fungus, Candida glabrata
Aoyama, T., Nakayama, H., Ueno, K., Inukai, T., Tanabe, K., Nagi, M., Bard, M., & Chibana, H. (2014) · Genes to Cells · doi:10.1111/gtc.12147 · Cited by 12
Impact of Next-Generation Sequencing Technology in Plant–Microbe Interaction Study
Kumari, A., Sumer, S., Jalan, B., Nongbri, P. L., & Laskar, M. A. (2017) · Microbial Applications Vol.1 · doi:10.1007/978-3-319-52666-9_13 · Cited by 13
Fundamental Methods in Molecular Biology
Ijaz, S., & Hassan, S. (2026) · Molecular Biology Methods · doi:10.1007/978-981-92-2642-9_1
Metadata
- Authors
- Mardis, E. R.
- Venue
- Annual Review of Genomics and Human Genetics
- Publisher
- Annual Reviews
- Published
- 2008-09-01
- Volume
- 9
- Issue
- 1
- Pages
- 387-402
- ISSN
- 1527-8204 (ISSN-L)
- 1545-293X
- OpenAlex
- W2103903744
- Cited by
- 2,369
- References
- 14
- FWCI
- 8.51
- Type
- journal article
- Language
- en
- Open access
- closed
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