Coming of age: ten years of next-generation sequencing technologies

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works

RNA-Seq: a revolutionary tool for transcriptomics

Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174 · see citing works

A map of human genome variation from population-scale sequencing.

The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877 · see citing works

Genome sequencing in microfabricated high-density picolitre reactors

Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693 · see citing works

Sequencing technologies – the next generation

Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066 · see citing works

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422 · see citing works

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 · see citing works

Accurate whole human genome sequencing using reversible terminator chemistry

Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684 · see citing works

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1229 · Cited by 2,707 · see citing works

Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase.

Holland, P. M., Abramson, R. D., Watson, R., & Gelfand, D. H. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.16.7276 · Cited by 2,694 · see citing works

The contribution of de novo coding mutations to autism spectrum disorder

Iossifov, I., O’Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., Stessman, H. A., Witherspoon, K. T., Vives, L., Patterson, K. E., et al. (2014) · Nature · doi:10.1038/nature13908 · Cited by 2,585 · see citing works

An integrated map of structural variation in 2,504 human genomes

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354 · see citing works

ChIP–seq: advantages and challenges of a maturing technology

Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217 · see citing works

An integrated semiconductor device enabling non-optical genome sequencing

Rothberg, J. M., Hinz, W., Rearick, T. M., Schultz, J., Mileski, W., Davey, M. S., Leamon, J. H., Johnson, K., Milgrew, M. J., Edwards, M. M., et al. (2011) · Nature · doi:10.1038/nature10242 · Cited by 2,187 · see citing works

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

O’Roak, B. J., Vives, L., Girirajan, S., Karakoc, E., Krumm, N., Coe, B. P., Levy, R., Ko, A., Lee, C., Smith, J. D., et al. (2012) · Nature · doi:10.1038/nature10989 · Cited by 2,165 · see citing works

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

Sanders, S. J., Murtha, M. T., Gupta, A. R., Murdoch, J. D., Raubeson, M. J., Willsey, A. J., Ercan-Sencicek, A. G., DiLullo, N. M., Parikshak, N. N., Stein, J. L., et al. (2012) · Nature · doi:10.1038/nature10945 · Cited by 2,084 · see citing works

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

Quail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., & Gu, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-341 · Cited by 2,031 · see citing works

Use of a cDNA microarray to analyse gene expression patterns in human cancer

DeRisi, J. L., Penland, L., Brown, P. O., Bittner, M. L., Meltzer, P. S., Ray, M., Chen, Y.-W., Su, Y. A., & Trent, J. M. (1996) · Nature Genetics · doi:10.1038/ng1296-457 · Cited by 1,952 · see citing works

Current Protocols in Molecular Biology

Teplitz, R. L. (1989) · JAMA · doi:10.1001/jama.1989.03420090114049 · Cited by 1,848 · see citing works

Structural Variation of Chromosomes in Autism Spectrum Disorder

Marshall, C. R., Noor, A., Vincent, J. B., Lionel, A. C., Feuk, L., Skaug, J., Shago, M., Moessner, R., Pinto, D., Ren, Y., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.12.009 · Cited by 1,815 · see citing works

Continuous base identification for single-molecule nanopore DNA sequencing

Clarke, J., Wu, H., Jayasinghe, L., Patel, A., Reid, S., & Bayley, H. (2009) · Nature Nanotechnology · doi:10.1038/nnano.2009.12 · Cited by 1,813 · see citing works

Comparison of Next-Generation Sequencing Systems

Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lü, L., & Law, M. (2012) · BioMed Research International · doi:10.1155/2012/251364 · Cited by 1,605 · see citing works

Direct detection of DNA methylation during single-molecule, real-time sequencing

Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460 · see citing works

Real-time, portable genome sequencing for Ebola surveillance

Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L. A., Boré, J. A., Koundouno, F. R., Dudas, G., Mikhail, A. F. W., et al. (2016) · Nature · doi:10.1038/nature16996 · Cited by 1,450 · see citing works

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., Chen, K., Dooling, D. J., Dunford-Shore, B. H., McGrath, S. D., Hickenbotham, M. T., et al. (2008) · Nature · doi:10.1038/nature07485 · Cited by 1,415 · see citing works

Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome

Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D., & Church, G. M. (2005) · Science · doi:10.1126/science.1117389 · Cited by 1,402 · see citing works

Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations

Levene, M. J., Korlach, J., Turner, S., Foquet, M., Craighead, H. G., & Webb, W. W. (2003) · Science · doi:10.1126/science.1079700 · Cited by 1,380 · see citing works

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., Desai, T. J., Krasnow, M. A., & Quake, S. R. (2014) · Nature · doi:10.1038/nature13173 · Cited by 1,342 · see citing works

Performance comparison of benchtop high-throughput sequencing platforms

Loman, N. J., Misra, R., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J. R., & Pallen, M. J. (2012) · Nature Biotechnology · doi:10.1038/nbt.2198 · Cited by 1,334 · see citing works

Twenty-Five Years of Quantitative PCR for Gene Expression Analysis

VanGuilder, H. D., Vrana, K. E., & Freeman, W. M. (2008) · BioTechniques · doi:10.2144/000112776 · Cited by 1,246 · see citing works

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

Meissner, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki901 · Cited by 1,224 · see citing works

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., Carnevali, P., Nazarenko, I., Nilsen, G. B., Yeung, G., et al. (2010) · Science · doi:10.1126/science.1181498 · Cited by 1,212 · see citing works

Structural Variation in the Human Genome and its Role in Disease

Stankiewicz, P., & Lupski, J. R. (2010) · Annual Review of Medicine · doi:10.1146/annurev-med-100708-204735 · Cited by 1,201 · see citing works

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 1,139 · see citing works

Uncovering the roles of rare variants in common disease through whole-genome sequencing

Cirulli, E. T., & Goldstein, D. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2779 · Cited by 1,136 · see citing works

THE STRUCTURE OF DNAPreprint

Watson, J. D., & Crick, F. H. C. (1953) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1953.018.01.020 · Cited by 1,123 · see citing works

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

Dohm, J. C., Lottaz, C., Borodina, T., & Himmelbauer, H. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn425 · Cited by 1,088 · see citing works

The UK10K project identifies rare variants in health and disease

The UK10K Consortium, Writing group, Walter, K., Min, J. L., Huang, J., Crooks, L., Memari, Y., McCarthy, S., Perry, J. R. B., Xu, C., et al. (2015) · Nature · doi:10.1038/nature14962 · Cited by 1,040 · see citing works

Whole-genome analysis informs breast cancer response to aromatase inhibition

Ellis, M. J., Ding, L., Shen, D., Luo, J. R., Suman, V. J., Wallis, J. W., Tine, B. A. V., Hoog, J., Goiffon, R., Goldstein, T. C., et al. (2012) · Nature · doi:10.1038/nature11143 · Cited by 1,023 · see citing works

Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression

Rhodes, D. R., Yu, J., Sundaram, S. K., Deshpande, N., Varambally, R., Ghosh, D., Barrette, T. R., Pandey, A., & Chinnaiyan, A. M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401994101 · Cited by 1,010 · see citing works

Hybrid error correction and de novo assembly of single-molecule sequencing reads

Koren, S., Schatz, M. C., Walenz, B. P., Martin, J. V., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2280 · Cited by 993 · see citing works

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

Zhao, S., Fung‐Leung, W., Bittner, A., Ngo, K., & Liu, X. (2014) · PLoS ONE · doi:10.1371/journal.pone.0078644 · Cited by 945 · see citing works

Expandable DNA repeats and human disease

Mirkin, S. M. (2007) · Nature · doi:10.1038/nature05977 · Cited by 934 · see citing works

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations

Dressman, D. C., Yan, H., Traverso, G., Kinzler, K. W., & Vogelstein, B. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1133470100 · Cited by 845 · see citing works

A Ligase-Mediated Gene Detection Technique

Landegren, U. D., Kaiser, R., Sanders, J. Z., & Hood, L. (1988) · Science · doi:10.1126/science.3413476 · Cited by 828 · see citing works

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

Campbell, P. J., Stephens, P. J., Pleasance, E., O’Meara, S., Li, H., Santarius, T., Stebbings, L. A., Leroy, C., Edkins, S., Hardy, C. W., et al. (2008) · Nature Genetics · doi:10.1038/ng.128 · Cited by 812 · see citing works

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

Zook, J. M., Chapman, B., Wang, J., Mittelman, D., Hofmann, O., Hide, W., & Salit, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2835 · Cited by 800 · see citing works

Large-scale whole-genome sequencing of the Icelandic population

Gudbjartsson, D. F., Helgason, H., Gudjonsson, S. A., Zink, F., Oddson, A., Gylfason, A., Besenbacher, S., Magnusson, G., Halldorsson, B. V., Hjartarson, E., et al. (2015) · Nature Genetics · doi:10.1038/ng.3247 · Cited by 791 · see citing works

Resolving the complexity of the human genome using single-molecule sequencing

Chaisson, M., Huddleston, J., Dennis, M. Y., Sudmant, P. H., Malig, M., Hormozdiari, F., Antonacci, F., Surti, U., Sandstrom, R. S., Boitano, M., et al. (2014) · Nature · doi:10.1038/nature13907 · Cited by 783 · see citing works

A single-molecule long-read survey of the human transcriptome

Sharon, D., Tilgner, H., Grubert, F., & Snyder, M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2705 · Cited by 701 · see citing works

Single-Molecule DNA Sequencing of a Viral Genome

Harris, T. D., Buzby, P. R., Babcock, H. P., Beer, E., Bowers, J., Braslavsky, I., Causey, M., Colonell, J. I., Dimeo, J. J., Efcavitch, J. W., et al. (2008) · Science · doi:10.1126/science.1150427 · Cited by 692 · see citing works

Genome-wide in situ exon capture for selective resequencing

Hodges, E. C., Xuan, Z., Balija, V. S., Kramer, M., Molla, M. N., Smith, S. W., Middle, C. M., Rodesch, M. J., Albert, T. J., Hannon, G. J., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.42 · Cited by 677 · see citing works

High‐throughput DNA sequencing – concepts and limitations

Kircher, M., & Kelso, J. F. (2010) · BioEssays · doi:10.1002/bies.200900181 · Cited by 675 · see citing works

Next-Generation Sequencing Platforms

Mardis, E. R. (2013) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-062012-092628 · Cited by 674 · see citing works

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

Lam, E. T., Hastie, A. R., Lin, C. J., Ehrlich, D., Das, S. K., Austin, M. D., Deshpande, P., Cao, H., Nagarajan, N., Xiao, M., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2303 · Cited by 650 · see citing works

Improved data analysis for the MinION nanopore sequencer

Jain, M., Fiddes, I. T., Miga, K. H., Olsen, H. E., Paten, B., & Akeson, M. A. (2015) · Nature Methods · doi:10.1038/nmeth.3290 · Cited by 639 · see citing works

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

Minoche, A. E., Dohm, J. C., & Himmelbauer, H. (2011) · Genome biology · doi:10.1186/gb-2011-12-11-r112 · Cited by 631 · see citing works

Copy-number variation and association studies of human disease

McCarroll, S. A., & Altshuler, D. M. (2007) · Nature Genetics · doi:10.1038/ng2080 · Cited by 622 · see citing works

Evaluation of next generation sequencing platforms for population targeted sequencing studies

Harismendy, O., Ng, P. C., Strausberg, R. L., Wang, X., Stockwell, T. B., Beeson, K. Y., Schork, N. J., Murray, S. S., Topol, E. J., Levy, S., et al. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r32 · Cited by 614 · see citing works

ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments

Buck, M. J., & Lieb, J. D. (2004) · Genomics · doi:10.1016/j.ygeno.2003.11.004 · Cited by 608 · see citing works

Sequence-specific error profile of Illumina sequencers

Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M. C., Hirai, A. M., Takahashi, H., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr344 · Cited by 593 · see citing works

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioningPreprint

Valouev, A., Ichikawa, J. K., Tonthat, T., Stuart, J., Ranade, S., Peckham, H. E., Zeng, K., Malek, J. A., Costa, G. L., McKernan, K. J., et al. (2008) · Genome Research · doi:10.1101/gr.076463.108 · Cited by 580 · see citing works

Integrating sequencing datasets to form highly confident SNP and indel genotype calls for a whole human genomePreprint

Zook, J. M., Chapman, B., Wang, J. J., et al. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1307.4661 · Cited by 551 · see citing works

Bioinformatics challenges of new sequencing technology

Pop, M., & Salzberg, S. L. (2008) · Trends in Genetics · doi:10.1016/j.tig.2007.12.006 · Cited by 515 · see citing works

Methods and strategies for analyzing copy number variation using DNA microarrays

Carter, N. P. (2007) · Nature Genetics · doi:10.1038/ng2028 · Cited by 510 · see citing works

Assembly of large genomes using second-generation sequencingPreprint

Schatz, M. C., Delcher, A. L., & Salzberg, S. L. (2010) · Genome Research · doi:10.1101/gr.101360.109 · Cited by 502 · see citing works

Assembly and diploid architecture of an individual human genome via single-molecule technologies

Pendleton, M., Sebra, R., Pang, A. W. C., Ummat, A., Franzén, O., Rausch, T., Stütz, A. M., Stedman, W., Anantharaman, T., Hastie, A. R., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3454 · Cited by 474 · see citing works

Assuring the quality of next-generation sequencing in clinical laboratory practice

Gargis, A. S., Kalman, L. V., Berry, M. W., Bick, D. P., Dimmock, D., Hambuch, T. M., Lu, F., Lyon, E., Voelkerding, K. V., Zehnbauer, B. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2403 · Cited by 458 · see citing works

Comprehensive high-throughput arrays for relative methylation (CHARM)Preprint

Irizarry, R. A., Ladd‐Acosta, C., Carvalho, B. S., Wu, H., Brandenburg, S. A., Jeddeloh, J. A., Wen, B., & Feinberg, A. P. (2008) · Genome Research · doi:10.1101/gr.7301508 · Cited by 433 · see citing works

Ordered Restriction Maps of Saccharomyces cerevisiae Chromosomes Constructed by Optical Mapping

Schwartz, D. C., Li, X., Hernandez, L. I., Ramnarain, S. P., Huff, E. J., & Wang, Y.-K. (1993) · Science · doi:10.1126/science.8211116 · Cited by 411 · see citing works

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genomePreprint

Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M. C., & McCombie, W. R. (2015) · bioRxiv · doi:10.1101/gr.191395.115 · Cited by 377 · see citing works

Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

Sidore, C., Busonero, F., Maschio, A., Porcu, E., Naitza, S., Żołędziewska, M., Mulas, A., Pistis, G., Steri, M., Danjou, F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3368 · Cited by 376 · see citing works

Concept, Design and Implementation of a Cardiovascular Gene-Centric 50 K SNP Array for Large-Scale Genomic Association Studies

Keating, B. J., Tischfield, S. E., Murray, S. S., Bhangale, T., Price, T. S., Glessner, J., Galver, L., Barrett, J. C., Grant, S. F. A., Farlow, D., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003583 · Cited by 370 · see citing works

Genetic variation and the de novo assembly of human genomes

Chaisson, M., Wilson, R. K., & Eichler, E. E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3933 · Cited by 337 · see citing works

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

Ip, C. L. C., Loose, M., Tyson, J. R., de Cesare, M., Brown, B. L., Jain, M., Leggett, R. M., Eccles, D., Zalunin, V. V., Urban, J. M., et al. (2015) · F1000Research · doi:10.12688/f1000research.7201.1 · Cited by 317 · see citing works

Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens

Nielsen, T. O., Wallden, B., Schaper, C., Ferree, S., Liu, S., Gao, D., Barry, G. S., Dowidar, N., Maysuria, M., & Storhoff, J. J. (2014) · BMC Cancer · doi:10.1186/1471-2407-14-177 · Cited by 311 · see citing works

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Quick, J., Ashton, P., Calus, S., Chatt, C., Gossain, S., Hawker, J. I., Nair, S., Neal, K. R., Nye, K., Peters, T. M., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0677-2 · Cited by 309 · see citing works

DNA Ligases: Structure, Reaction Mechanism, and Function

Tomkinson, A. E., Vijayakumar, S., Pascal, J. M., & Ellenberger, T. (2006) · Chemical Reviews · doi:10.1021/cr040498d · Cited by 297 · see citing works

Sequence-specific identification of 18 pathogenic microorganisms using microarray technology

Wilson, W. J., Strout, C. L., DeSantis, T. Z., et al. (2002) · Molecular and Cellular Probes · doi:10.1006/mcpr.2001.0397 · Cited by 289 · see citing works

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liverPreprint

Brunner, A. L., Johnson, D. S., Kim, S. W., Valouev, A., Reddy, T. E., Neff, N. F., Anton, E., Medina, C., Nguyen, L., Chiao, E. T., et al. (2009) · Genome Research · doi:10.1101/gr.088773.108 · Cited by 283 · see citing works

Recurrent CNVs Disrupt Three Candidate Genes in Schizophrenia Patients

Vrijenhoek, T., Buizer‐Voskamp, J. E., van der Stelt, I., Strengman, E., Sabatti, C., van Kessel, A. G., Brunner, H. G., Ophoff, R. A., & Veltman, J. A. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.09.011 · Cited by 265 · see citing works

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

Carneiro, M. O., Russ, C., Ross, M. G., Gabriel, S., Nusbaum, C., & DePristo, M. A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-375 · Cited by 255 · see citing works

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies

Fedurco, M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gnj023 · Cited by 255 · see citing works

The genome sequence of the colonial chordate, Botryllus schlosseri

Voskoboynik, A., Neff, N. F., Sahoo, D., Newman, A. M., Pushkarev, D., Koh, W. L. C., Passarelli, B., Fan, H. C., Mantalas, G. L., Palmeri, K. J., et al. (2013) · eLife · doi:10.7554/elife.00569 · Cited by 245 · see citing works

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

Li, S., Tighe, S. W., Nicolet, C. M., Grove, D., Levy, S., Farmerie, W., Viale, A., Wright, C., Schweitzer, P. A., Gao, Y., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2972 · Cited by 240 · see citing works

Caenorhabditis elegans mutant allele identification by whole-genome sequencing

Sarin, S., Prabhu, S., O’Meara, M., Pe’er, I., & Hobert, O. (2008) · Nature Methods · doi:10.1038/nmeth.1249 · Cited by 237 · see citing works

Taking qPCR to a higher level: analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution

Weaver, S., Dube, S., Mir, A., Qin, J., Sun, G., Ramakrishnan, R., Jones, R. C., & Livak, K. J. (2010) · Methods · doi:10.1016/j.ymeth.2010.01.003 · Cited by 220 · see citing works

Mammary development meets cancer genomics

Prat, A., & Perou, C. M. (2009) · Nature Medicine · doi:10.1038/nm0809-842 · Cited by 214 · see citing works

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X genePreprint

Loomis, E. W., Eid, J. S., Peluso, P. S., Yin, J., Hickey, L., Rank, D. R., McCalmon, S. A., Hagerman, R. J., Tassone, F., & Hagerman, P. J. (2012) · Genome Research · doi:10.1101/gr.141705.112 · Cited by 203 · see citing works

Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy

Kim, J. B., Porreca, G. J., Song, L., Greenway, S. C., Gorham, J., Church, G. M., Seidman, C. E., & Seidman, J. G. (2007) · Science · doi:10.1126/science.1137325 · Cited by 202 · see citing works

Common variants conferring risk of schizophrenia: A pathway analysis of GWAS data

Jia, P., Wang, L., Meltzer, H. Y., & Zhao, Z. (2010) · Schizophrenia Research · doi:10.1016/j.schres.2010.07.001 · Cited by 199 · see citing works

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

McCoy, R. C., Taylor, R. W., Blauwkamp, T. A., Kelley, J. L., Kertesz, M., Pushkarev, D., Petrov, D. A., & Fiston-Lavier, A.-S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0106689 · Cited by 199 · see citing works

Optimizing Cancer Genome Sequencing and Analysis

Griffith, M., Miller, C. A., Griffith, O. L., Krysiak, K., Skidmore, Z. L., Ramu, A., Walker, J., Dang, H. X., Trani, L., Larson, D. E., et al. (2015) · Cell Systems · doi:10.1016/j.cels.2015.08.015 · Cited by 194 · see citing works

Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators

Ju, J., Kim, D. H., Bi, L., Meng, Q., Bai, X., Li, Z., Li, X., Marma, M. S., Shi, S., Wu, J. F., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609513103 · Cited by 194 · see citing works

Haplotype-resolved genome sequencing: experimental methods and applications

Snyder, M. W., Adey, A., Kitzman, J. O., & Shendure, J. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3903 · Cited by 189 · see citing works

An assessment of the sequence gaps: Unfinished business in a finished human genome

Eichler, E. E., Clark, R. A., & She, X. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1322 · Cited by 183 · see citing works

Four-color DNA sequencing with 3′- O -modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides

Guo, J., Xu, N., Li, Z., Zhang, S., Wu, J. F., Kim, D. H., Marma, M. S., Meng, Q., Cao, H., Li, X., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804023105 · Cited by 181 · see citing works

Ethics and Genomic Incidental Findings

McGuire, A. L., Joffe, S., Koenig, B. A., Biesecker, B. B., McCullough, L. B., Blumenthal‐Barby, J. S., Caulfield, T., Terry, S. F., & Green, R. C. (2013) · Science · doi:10.1126/science.1240156 · Cited by 172 · see citing works

Whole-genome haplotyping using long reads and statistical methods

Kuleshov, V., Xie, D., Chen, R., Pushkarev, D., Ma, Z., Blauwkamp, T. A., Kertesz, M., & Snyder, M. P. (2014) · Nature Biotechnology · doi:10.1038/nbt.2833 · Cited by 170 · see citing works

Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

Cao, H., Hastie, A., Cao, D., Lam, E. T., Sun, Y., Huang, H., Lin, L., Lin, L., Andrews, W., Chan, S., et al. (2014) · GigaScience · doi:10.1186/2047-217x-3-34 · Cited by 161 · see citing works

Assessing structural variation in a personal genome—towards a human reference diploid genome

English, A., Salerno, W., Hampton, O., Gonzaga-Jauregui, C., Ambreth, S., Ritter, D., Beck, C., Davis, C., Dahdouli, M., Ma, S.-E., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1479-3 · Cited by 156 · see citing works

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

Oda, M., Glass, J. L., Thompson, R. F., Mo, Y., Olivier, E. N., Figueroa, M. E., Selzer, R. R., Richmond, T., Zhang, X., Dannenberg, L. O., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp260 · Cited by 154 · see citing works

Nucleic Acid Amplification Strategies for DNA Microarray-Based Pathogen Detection

Vora, G. J., Meador, C. E., Stenger, D. A., et al. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.5.3047-3054.2004 · Cited by 148 · see citing works

A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell linesPreprint

Liang, L., Morar, N., Dixon, A. L., Lathrop, M. G., Abecasis, G. R., Moffatt, M. F., & Cookson, W. (2013) · Genome Research · doi:10.1101/gr.142521.112 · Cited by 146 · see citing works

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

Hastie, A. R., Dong, L., Smith, A. L., Finklestein, J., Lam, E. T., Huo, N., Cao, H., Kwok, P., Deal, K. R., Dvořák, J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0055864 · Cited by 145 · see citing works

A massively parallel PicoTiterPlate™ based platform for discrete picoliter‐scale polymerase chain reactions

Leamon, J. H., Lee, W. L., Tartaro, K. R., Lanza, J. R., Sarkis, G. J., deWinter, A. D., Berka, J., & Lohman, K. L. (2003) · Electrophoresis · doi:10.1002/elps.200305646 · Cited by 144 · see citing works

Virtual terminator nucleotides for next-generation DNA sequencing

Bowers, J., Mitchell, J., Beer, E., Buzby, P. R., Causey, M., Efcavitch, J. W., Jarosz, M. V., Krzymańska-Olejnik, E., Kung, L. A., Lipson, D., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1354 · Cited by 139 · see citing works

Estimating genotype error rates from high-coverage next-generation sequence dataPreprint

Wall, J., Tang, L., Zerbe, B. S., Kvale, M., Kwok, P.-Y., Schaefer, C., & Risch, N. (2014) · Genome Research · doi:10.1101/gr.168393.113 · Cited by 134 · see citing works

Genomic-scale gene expression profiling of normal and malignant immune cells

Alizadeh, A. A., & Staudt, L. M. (2000) · Current Opinion in Immunology · doi:10.1016/s0952-7915(99)00078-3 · Cited by 131 · see citing works

Nanopores Discriminate among Five C5-Cytosine Variants in DNA

Wescoe, Z. L., Schreiber, J. M., & Akeson, M. A. (2014) · Journal of the American Chemical Society · doi:10.1021/ja508527b · Cited by 102 · see citing works

Highly accurate SNP genotyping from historical and low‐quality samples

Morin, P. A., & MCCARTHY, M. (2007) · Molecular Ecology Notes · doi:10.1111/j.1471-8286.2007.01804.x · Cited by 100 · see citing works

Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients

Malapelle, U., Vigliar, E., Sgariglia, R., Bellevicine, C., Colarossi, L., Vitale, D., Pallante, P., & Troncone, G. (2014) · Journal of Clinical Pathology · doi:10.1136/jclinpath-2014-202691 · Cited by 95 · see citing works

Whole Genome Sequencing as a Diagnostic Test: Challenges and Opportunities

Chrystoja, C. C., & Diamandis, E. P. (2013) · Clinical Chemistry · doi:10.1373/clinchem.2013.209213 · Cited by 92 · see citing works

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Rieber, N., Zapatka, M., Lasitschka, B., Jones, D., Northcott, P. A., Hutter, B., Jäger, N., Kool, M., Taylor, M. D., Lichter, P., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066621 · Cited by 92 · see citing works

Clinical Utility of Droplet Digital PCR for Human Cytomegalovirus

Sedlak, R. H., Cook, L., Cheng, A., et al. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.00803-14 · Cited by 92 · see citing works

The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndromePreprint

Sailani, M. R., Makrythanasis, P., Valsesia, A., Santoni, F. A., Deutsch, S., Popadin, K. Y., Borel, C., Migliavacca, E., Sharp, A. J., Saïl, G. D., et al. (2013) · Genome Research · doi:10.1101/gr.147991.112 · Cited by 82 · see citing works

The DNA data deluge

Schatz, M. C., & Langmead, B. (2013) · IEEE Spectrum · doi:10.1109/mspec.2013.6545119 · Cited by 79 · see citing works

Development of a Next-Generation Sequencing Method for BRCA Mutation Screening

Chan, M., Ji, S. M., Yeo, Z. X., Gan, L., Yap, E. P. H., Yap, Y. S., Ng, R. C. H., Tan, P. H., Ho, G. H., Ang, P., et al. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.06.003 · Cited by 77 · see citing works

Array feature size influences nucleic acid surface capture in DNA microarrays

Dandy, D. S., Wu, P., & Grainger, D. W. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606054104 · Cited by 76 · see citing works

Cloning and screening of sequences expressed in a mouse colon tumor.

Augenlicht, L. H., & Kobrin, D. (1982) · PubMed · Cited by 75 · see citing works

Multiplexed Gene Expression and Fusion Transcript Analysis to Detect ALK Fusions in Lung Cancer

Lira, M. E., Kim, T. M., Huang, D., et al. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.08.006 · Cited by 71 · see citing works

Sequencing of the Dutch Elm Disease Fungus Genome Using the Roche/454 GS-FLX Titanium System in a Comparison of Multiple Genomics Core Facilities

Forgetta, V., Leveque, G., Dias, J., et al. (2012) · Journal of Biomolecular Techniques JBT · doi:10.7171/jbt.12-2401-005 · Cited by 63 · see citing works

Concordance Study of 3 Direct-to-Consumer Genetic-Testing Services

Imai, K., Kricka, L. J., & Fortina, P. M. (2010) · Clinical Chemistry · doi:10.1373/clinchem.2010.158220 · Cited by 62 · see citing works

Characterization of structural variants with single molecule and hybrid sequencing approaches

Ritz, A., Bashir, A., Sindi, S., Hsu, D., Hajirasouliha, I., & Raphael, B. J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu714 · Cited by 58 · see citing works

Inferring causality and functional significance of human coding DNA variants

Sunyaev, S. R. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds385 · Cited by 50 · see citing works

The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms

Larsen, P. A., Heilman, A. M., & Yoder, A. D. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-720 · Cited by 50 · see citing works

High-throughput profiling identifies clinically actionable mutations in salivary duct carcinoma

Ku, B. M., Jung, H. A., Sun, J., Ko, Y. H., Jeong, H., Son, Y., Baek, C., Park, K., & Ahn, M. (2014) · Journal of Translational Medicine · doi:10.1186/s12967-014-0299-6 · Cited by 47 · see citing works

Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing

Shen, Y., Sarin, S., Liu, Y., Hobert, O., & Pe’er, I. (2008) · PLoS ONE · doi:10.1371/journal.pone.0004012 · Cited by 45 · see citing works

Technology-specific error signatures in the 1000 Genomes Project data

Nothnagel, M., Herrmann, A., Wolf, A., Schreiber, S., Platzer, M., Siebert, R., Krawczak, M., & Hampe, J. (2011) · Human Genetics · doi:10.1007/s00439-011-0971-3 · Cited by 38 · see citing works

Personalized investigation

Dolgin, E. (2010) · Nature Medicine · doi:10.1038/nm0910-953 · Cited by 25 · see citing works

A novel low energy electron microscope for DNA sequencing and surface analysis

Maňkoš, M., Shadman, K., Persson, H. H. J., et al. (2014) · Ultramicroscopy · doi:10.1016/j.ultramic.2014.01.007 · Cited by 17 · see citing works

Towards an Understanding of DNA Recognition by the Methyl-CpG Binding Domain 1

Rauch, C., Trieb, M., Wibowo, F. R., et al. (2005) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2005.10507036 · Cited by 11 · see citing works

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing

Wang, X., Yu, X., Zhu, W., et al. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv089 · Cited by 3 · see citing works

NanoPack: visualizing and processing long-read sequencing data

De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty149 · Cited by 3,168 · see citing works

Opportunities and challenges in long-read sequencing data analysis

Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530 · see citing works

A universal SNP and small-indel variant caller using deep neural networks

Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4235 · Cited by 1,840 · see citing works

Base editing: precision chemistry on the genome and transcriptome of living cells

Rees, H. A., & Liu, D. R. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0059-1 · Cited by 1,675 · see citing works

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

Gu, W., Miller, S., & Chiu, C. Y. (2019) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-012418-012751 · Cited by 1,458 · see citing works

mRNAs, proteins and the emerging principles of gene expression control

Buccitelli, C., & Selbach, M. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0258-4 · Cited by 1,243 · see citing works

Next-Generation Sequencing Technology: Current Trends and Advancements

Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R. P., Banday, S., Mishra, A. K., Das, G., et al. (2023) · Biology · doi:10.3390/biology12070997 · Cited by 1,299 · see citing works

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., et al. (2017) · Nature Protocols · doi:10.1038/nprot.2017.066 · Cited by 1,190 · see citing works

Towards precision medicine

Ashley, E. A. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.86 · Cited by 1,116 · see citing works

Splatter: simulation of single-cell RNA sequencing data

Zappia, L., Phipson, B., & Oshlack, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1305-0 · Cited by 905 · see citing works

Structural variant calling: the long and the short of it

Mahmoud, M., Gobet, N., Cruz-Dávalos, D. I., Mounier, N., Dessimoz, C., & Sedlazeck, F. J. (2019) · Genome Biology · doi:10.1186/s13059-019-1828-7 · Cited by 725 · see citing works

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Argimón, S., Abudahab, K., Goater, R. J. E., Fedosejev, A., Bhai, J., Glasner, C., Feil, E. J., Holden, M. T. G., Yeats, C. A., Grundmann, H., et al. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000093 · Cited by 732 · see citing works

Advances in the delivery of RNA therapeutics: from concept to clinical reality

Kaczmarek, J. C., Kowalski, P. S., & Anderson, D. G. (2017) · Genome Medicine · doi:10.1186/s13073-017-0450-0 · Cited by 656 · see citing works

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0003-4 · Cited by 530 · see citing works

Molecular Digital Data Storage Using DNA

Ceze, L., Nivala, J., & Strauss, K. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0125-3 · Cited by 551 · see citing works

Roles of transposable elements in the regulation of mammalian transcription

Fueyo, R., Judd, J., Feschotte, C., & Wysocka, J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00457-y · Cited by 451 · see citing works

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1835-8 · Cited by 452 · see citing works

Ancient DNA analysis

Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411 · see citing works

Towards population-scale long-read sequencing

De Coster, W., Weissensteiner, M. H., & Sedlazeck, F. J. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00367-3 · Cited by 323 · see citing works

Cloud computing for genomic data analysis and collaboration

Langmead, B., & Nellore, A. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.113 · Cited by 310 · see citing works

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303 · see citing works

Genomic Instability of iPSCs: Challenges Towards Their Clinical Applications

Yoshihara, M., Hayashizaki, Y., & Murakawa, Y. (2017) · Stem Cell Reviews and Reports · doi:10.1007/s12015-016-9680-6 · Cited by 283 · see citing works

Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life

Acuna-Hidalgo, R., Sengul, H., Steehouwer, M., van de Vorst, M., Vermeulen, S. H., Kiemeney, L. A. L. M., Veltman, J. A., Gilissen, C., & Hoischen, A. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.05.013 · Cited by 264 · see citing works

Microbial Community-Driven Etiopathogenesis of Peri-Implantitis

Belibasakis, G. N., & Manoil, D. (2021) · Journal of Dental Research · doi:10.1177/0022034520949851 · Cited by 244 · see citing works

Emerging Approaches to DNA Data Storage: Challenges and Prospects

Doricchi, A., Platnich, C. M., Gimpel, A., Horn, F., Earle, M., Lanzavecchia, G., Cortajarena, A. L., Liz-Marzán, L. M., Liu, N., Heckel, R., et al. (2022) · ACS Nano · doi:10.1021/acsnano.2c06748 · Cited by 235 · see citing works

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Van den Berge, K., Perraudeau, F., Soneson, C., Love, M. I., Risso, D., Vert, J.-P., Robinson, M. D., Dudoit, S., & Clement, L. (2018) · Genome Biology · doi:10.1186/s13059-018-1406-4 · Cited by 228 · see citing works

Cancer proteogenomics: current impact and future prospects

Mani, D. R., Krug, K., Zhang, B., Satpathy, S., Clauser, K. R., Ding, L., Ellis, M., Gillette, M. A., & Carr, S. A. (2022) · Nature Reviews Cancer · doi:10.1038/s41568-022-00446-5 · Cited by 229 · see citing works

Paragraph: a graph-based structural variant genotyper for short-read sequence data

Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1909-7 · Cited by 196 · see citing works

A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data

Trost, B., Walker, S., Wang, Z., Thiruvahindrapuram, B., MacDonald, J. R., Sung, W. W. L., Pereira, S. L., Whitney, J., Chan, A. J. S., Pellecchia, G., et al. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.12.007 · Cited by 191 · see citing works

A Review of bioinformatics tools for bio-prospecting from metagenomic sequence data

Roumpeka, D. D., Wallace, R. J., Escalettes, F., Fotheringham, I., & Watson, M. (2017) · Frontiers in Genetics · doi:10.3389/fgene.2017.00023 · Cited by 199 · see citing works

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application

Lightbody, G., Haberland, V., Browne, F., Taggart, L., Zheng, H., Parkes, E., & Blayney, J. K. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bby051 · Cited by 173 · see citing works

A clinician's guide to microbiome analysis

Claesson, M. J., Clooney, A. G., & O'Toole, P. W. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.97 · Cited by 153 · see citing works

Realizing the potential of blockchain technologies in genomics

Ozercan, H. I., Ileri, A. M., Ayday, E., & Alkan, C. (2018) · Genome Research · doi:10.1101/gr.207464.116 · Cited by 143 · see citing works

Microalgae with Artificial Intelligence: A Digitalized Perspective on Genetics, Systems and Products

Teng, S. Y., Yew, G. Y., Sukačová, K., Show, P. L., Máša, V., & Chang, J.-S. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107631 · Cited by 145 · see citing works

Recent advances in single-cell sequencing technologies

Wen, L., & Tang, F. (2022) · Precision Clinical Medicine · doi:10.1093/pcmedi/pbac002 · Cited by 127 · see citing works

DeepOmix: a scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis

Zhao, L., Dong, Q., Luo, C., Wu, Y., Bu, D., Qi, X., Luo, Y., & Zhao, Y. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.04.067 · Cited by 127 · see citing works

Comprehensive genome analysis and variant detection at scale using DRAGEN

Behera, S., Catreux, S., Rossi, M., Truong, S., Huang, Z., Ruehle, M., Visvanath, A., Parnaby, G., Roddey, C., Onuchic, V., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02382-1 · Cited by 137 · see citing works

Designing and interpreting ‘multi-omic’ experiments that may change our understanding of biology

Haas, R., Zelezniak, A., Iacovacci, J., Kamrad, S., Townsend, S., & Ralser, M. (2017) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.08.009 · Cited by 131 · see citing works

Epigenetic programming, early life nutrition and the risk of metabolic disease

Block, T., & El-Osta, A. (2017) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2017.09.003 · Cited by 130 · see citing works

Advances in genomics for adapting crops to climate change

Scheben, A., Yuan, Y., & Edwards, D. (2016) · Current Plant Biology · doi:10.1016/j.cpb.2016.09.001 · Cited by 117 · see citing works

Group lasso regularized deep learning for cancer prognosis from multi-omics and clinical features

Xie, G., Dong, C., Kong, Y., Zhong, J. F., Li, M., & Wang, K. (2019) · Genes · doi:10.3390/genes10030240 · Cited by 102 · see citing works

High Throughput Sequencing for Detection of Foodborne Pathogens

Sekse, C., Holst-Jensen, A., Dobrindt, U., Johannessen, G. S., Li, W., Spilsberg, B., & Shi, J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02029 · Cited by 98 · see citing works

Breaking the curse of dimensionality to identify causal variants in Breeding 4

Ramstein, G. P., Jensen, S. E., & Buckler, E. S. (2019) · Theoretical and Applied Genetics · doi:10.1007/s00122-018-3267-3 · Cited by 87 · see citing works

Data Storage Based on DNA

Hao, Y., Li, Q., Fan, C., & Wang, F. (2021) · Small Structures · doi:10.1002/sstr.202000046 · Cited by 90 · see citing works

The emerging roles of bacterial proteases in intestinal diseases

Caminero, A., Guzman, M., Libertucci, J., & Lomax, A. E. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2181922 · Cited by 92 · see citing works

The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease

Study, D. (. D. I. S. A. C., Liu, J., Zhou, Y., Liu, S., Song, X., Yang, X.-Z., Fan, Y., Chen, W., Akdemir, Z. C., Yan, Z., et al. (2018) · Human Genetics · doi:10.1007/s00439-018-1910-3 · Cited by 77 · see citing works

Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage

Xu, C., Ma, B., Gao, Z., Dong, X., Zhao, C., & Liu, H. (2021) · Science Advances · doi:10.1126/sciadv.abk0100 · Cited by 79 · see citing works

Gastric Cancer Genomics: Advances and Future Directions

Katona, B. W., & Rustgi, A. K. (2017) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2017.01.003 · Cited by 78 · see citing works

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females

Huang, Y.-F., Chen, Y.-J., Fan, T.-C., Chang, N.-C., Chen, Y.-J., Midha, M. K., Chen, T.-H., Yang, H.-H., Wang, Y.-T., Yu, A. L., et al. (2018) · BMC Medical Genomics · doi:10.1186/s12920-018-0329-y · Cited by 72 · see citing works

Genomics-based approaches to identify and predict the health-promoting and safety activities of promising probiotic strains–A probiogenomics review

Castro-López, C., García, H. S., Guadalupe Martínez-Ávila, G. C., González-Córdova, A. F., Vallejo-Cordoba, B., & Hernández-Mendoza, A. (2021) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2020.12.017 · Cited by 72 · see citing works

Carbon-based archiving: current progress and future prospects of DNA-based data storage.

Ping, Z., Ma, D., Huang, X., Chen, S., Liu, L., Guo, F., Zhu, S. J., & Shen, Y. (2019) · GigaScience · doi:10.1093/gigascience/giz075 · Cited by 55 · see citing works

Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms

Amann, T., Schmieder, V., Faustrup Kildegaard, H., Borth, N., & Andersen, M. R. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.27101 · Cited by 46 · see citing works

Reading and Writing Digital Information in TNA

Yang, K., McCloskey, C. M., & Chaput, J. C. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00361 · Cited by 41 · see citing works

NetBID2 provides comprehensive hidden driver analysis

Dong, X., Ding, L., Thrasher, A., Wang, X., Liu, J., Pan, Q., Rash, J., Dhungana, Y., Yang, X., Risch, I., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38335-6 · Cited by 37 · see citing works

Glycoengineering Chinese hamster ovary cells: a short history

Donini, R., Haslam, S. M., & Kontoravdi, C. (2021) · Biochemical Society Transactions · doi:10.1042/bst20200840 · Cited by 37 · see citing works

PopHuman: the human population genomics browser

Casillas, S., Mulet, R., Villegas-Mirón, P., Hervas, S., Sanz, E., Velasco, D., Bertranpetit, J., Laayouni, H., & Barbadilla, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx943 · Cited by 29 · see citing works

Preservation and Encryption in DNA Digital Data Storage

Zhang, Y., Ren, Y., Liu, Y., Wang, F., Zhang, H., & Liu, K. (2022) · ChemPlusChem · doi:10.1002/cplu.202200183 · Cited by 28 · see citing works

Mathiomica: an integrative platform for dynamic omics

Mias, G. I., Yusufaly, T., Roushangar, R., Brooks, L. R. K., Singh, V. V., & Christou, C. (2016) · Scientific Reports · doi:10.1038/srep37237 · Cited by 27 · see citing works

RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability

Alloza, I., Goikuria, H., Idro, J. L., Triviño, J. C., Fernández Velasco, J. M., Elizagaray, E., García-Barcina, M., Montoya-Murillo, G., Sarasola, E., Vega Manrique, R., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-03687-9 · Cited by 25 · see citing works

Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool

Rozman, V., Mohar Lorbeg, P., Treven, P., Accetto, T., Golob, M., Zdovc, I., & Bogovič Matijašić, B. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2127438 · Cited by 21 · see citing works

The Genetics of Autism Spectrum Disorders

Yuen, R. K. C., Szatmari, P., & Vorstman, J. A. S. (2019) · Autism and Pervasive Developmental Disorders · doi:10.1017/9781108297769.006 · Cited by 19 · see citing works

Dynamics of chromosome organization in a minimal bacterial cell

Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1214962 · Cited by 19 · see citing works

Dynamic visualization of multi-level molecular data: The Director package in R

Icay, K., Liu, C., & Hautaniemi, S. (2018) · Computer Methods and Programs in Biomedicine · doi:10.1016/j.cmpb.2017.10.013 · Cited by 8 · see citing works

A longitudinal analysis of function annotations of the human proteome reveals consistently high biases

Phan, A., Joshi, P., Kadelka, C., & Friedberg, I. (2025) · Database · doi:10.1093/database/baaf036 · Cited by 2 · see citing works

Massively parallel functional genomic assays in endocrinology: from promise to delivery

Xu, J., Aslanzadeh, V., Kudla, G., & Semple, R. K. (2026) · Journal of Molecular Endocrinology · doi:10.1530/jme-25-0134

Genomic relationships of N-genome Triticum species

Yen, Y., & KIMBER, G. (1992) · Genome · doi:10.1139/g92-147 · Cited by 17 · see citing works

Identification of signals required for the insertion of heterologous genome segments into the reovirus genome.

Roner, M. R., Lin, P. N., Nepluev, I. V., et al. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.26.12362 · Cited by 21 · see citing works

Estimating the size of the bacterial pan-genome

Lapierre, P., & Gogarten, J. P. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.12.004 · Cited by 354 · see citing works

Differentiation and inter-genomic relationships among C, E and D genomes in the Oryzaofficinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization

Li, C., Zhang, D.-M., Ge, S., Lu, B., & De‐Yuan, H. (2001) · Theoretical and Applied Genetics · doi:10.1007/s001220100562 · Cited by 39 · see citing works

Sequencing of Chloroplast Genome in Sesame

Li, C., Zhang, H., Ju, M., et al. (2021) · Compendium of plant genomes · doi:10.1007/978-3-319-98098-0_11 · Cited by 1 · see citing works