Cited by 275Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsSingle-cell and spatial transcriptomics

The DOI matches its Crossref record; 86 of the 88 references it cites were found in a registry or an index.

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

Open access

Lister, Ryan, Gregory, Brian D, Ecker, Joseph R·2009·Current Opinion in Plant Biology

DOI 10.1016/j.pbi.2008.11.004PMC PMC2723731

Open this paper in CoChat — free account

Abstract

The sudden availability of DNA sequencing technologies that rapidly produce vast amounts of sequence information has triggered a paradigm shift in genomics, enabling massively parallel surveying of complex nucleic acid populations. The diversity of applications to which these technologies have already been applied demonstrates the immense range of cellular processes and properties that can now be studied at the single-base resolution. These include genome resequencing and polymorphism discovery, mutation mapping, DNA methylation, histone modifications, transcriptome sequencing, gene discovery, alternative splicing identification, small RNA profiling, DNA-protein, and possibly even protein-protein interactions. Thus, these deep sequencing technologies offer plant biologists unprecedented opportunities to increase the understanding of the functions and dynamics of plant cells and populations.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1016/j.pbi.2008.11.004

Cites

86 of 86 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
A novel genetic system to detect protein–protein interactions
Fields, S., & Song, O.-K. (1989) · Nature · doi:10.1038/340245a0 · Cited by 6,152
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations.
Michelmore, R. W., Paran, I., & Kesseli, R. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.21.9828 · Cited by 4,551
Next-generation DNA sequencing
Shendure, J., & Ji, H. (2008) · Nature Biotechnology · doi:10.1038/nbt1486 · Cited by 4,509
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
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
Li, E., Bestor, T. H., & Jaenisch, R. (1992) · Cell · doi:10.1016/0092-8674(92)90611-f · Cited by 3,984
Serial Analysis of Gene Expression
Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995) · Science · doi:10.1126/science.270.5235.484 · Cited by 3,713

Show all 88 references

Sorted by citations

Research on plant abiotic stress responses in the post‐genome era: past, present and future
Hirayama, T., & Shinozaki, K. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04124.x · Cited by 1,215
Computational methods for transcriptome annotation and quantification using RNA-seq
Garber, M., Grabherr, M. G., Guttman, M., & Trapnell, C. (2011) · Nature Methods · doi:10.1038/nmeth.1613 · Cited by 1,042
Biofuels from algae: Challenges and potential
Hannon, M., Gimpel, J., Tran, M., Rasala, B., & Mayfield, S. (2010) · Biofuels · doi:10.4155/bfs.10.44 · Cited by 813
SHOREmap: simultaneous mapping and mutation identification by deep sequencing
Schneeberger, K., Ossowski, S., Lanz, C., Juul, T., Petersen, A. H., Nielsen, K. L., Jørgensen, J.-E., Weigel, D., & Andersen, S. U. (2009) · Nature Methods · doi:10.1038/nmeth0809-550 · Cited by 606
Shade tolerance: when growing tall is not an option
Gommers, C. M. M., Visser, E. J. W., Onge, K. R. S., Voesenek, L. A. C. J., & Pierik, R. (2012) · Trends in Plant Science · doi:10.1016/j.tplants.2012.09.008 · Cited by 548
RNA-seq: from technology to biology
Marguerat, S., & Bähler, J. (2009) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-009-0180-6 · Cited by 566
The development of Arabidopsis as a model plant
Koornneef, M., & Meinke, D. W. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2009.04086.x · Cited by 490
Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry
Xu, L., Zhu, L., Tu, L., Liu, L., Yuan, D., Jin, L., Long, L., & Zhang, X. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/err245 · Cited by 485
Progress Toward Understanding Heterosis in Crop Plants
Schnable, P. S., & Springer, N. M. (2013) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042110-103827 · Cited by 469
An epigenetic view of plant cells cultured in vitro: Somaclonal variation and beyond
Miguel, C., & Marum, L. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/err155 · Cited by 395
Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses
Li, P., & Brutnell, T. P. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/err096 · Cited by 394
Abiotic Stress - Plant Responses and Applications in Agriculture
Vahdati, K., & Leslie, C. A. (2013) · InTech eBooks · doi:10.5772/45842 · Cited by 385
Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana
Bergelson, J. M., & Roux, F. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2896 · Cited by 365
Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
Cavagnaro, P. F., Senalik, D. A., Yang, L., Simon, P. W., Harkins, T. T., Kodira, C. D., Huang, S., & Weng, Y. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-569 · Cited by 346
Next‐generation mapping of Arabidopsis genes
Austin, R. S., Vidaurre, D. P., Stamatiou, G., Breit, R., Provart, N. J., Bonetta, D. T., Zhang, J., Fung, P., Gong, Y., Wang, P. W., et al. (2011) · The Plant Journal · doi:10.1111/j.1365-313x.2011.04619.x · Cited by 305
Moving micronutrients from the soil to the seeds: Genes and physiological processes from a biofortification perspective
Waters, B. M., & Sankaran, R. P. (2010) · Plant Science · doi:10.1016/j.plantsci.2010.12.003 · Cited by 301
Designing future crops: challenges and strategies for sustainable agriculture
Tian, Z., Wang, J., Li, J., & Han, B. (2020) · The Plant Journal · doi:10.1111/tpj.15107 · Cited by 275
Genome-WideMedicago truncatulaSmall RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules
Lelandais‐Brière, C., Naya, L., Sallet, E., Calenge, F., Frugier, F., Hartmann, C., Gouzy, J., & Crespi, M. D. (2009) · The Plant Cell · doi:10.1105/tpc.109.068130 · Cited by 255
Using next-generation sequencing to isolate mutant genes from forward genetic screens
Schneeberger, K. (2014) · Nature reviews genetics · doi:10.1038/nrg3745 · Cited by 233
Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms
Yamamoto, T., Nagasaki, H., Yonemaru, J., Ebana, K., Nakajima, M., Shibaya, T., & Yano, M. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-267 · Cited by 239
Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions
Mochida, K., & Shinozaki, K. (2011) · Plant and Cell Physiology · doi:10.1093/pcp/pcr153 · Cited by 239
Targeted enrichment strategies for next‐generation plant biology
Cronn, R., Knaus, B. J., Liston, A., Maughan, P. J., Parks, M., Syring, J. V., & Udall, J. A. (2012) · American Journal of Botany · doi:10.3732/ajb.1100356 · Cited by 218
Linking genotype to phenotype using the Arabidopsis unimutant collection
O’Malley, R. C., & Ecker, J. R. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04119.x · Cited by 209
Self-citation
RNA ‐Seq transcriptome analysis to identify genes involved in metabolism‐based diclofop resistance in Lolium rigidum
Gaines, T. A., Lorentz, L., Figge, A., Herrmann, J., Maiwald, F., Ott, M., Han, H., Busi, R., Yu, Q. P., Powles, S. B., et al. (2014) · The Plant Journal · doi:10.1111/tpj.12514 · Cited by 212
Genome‐wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal
Zhou, Z., Zeng, H., Liu, Z. P., & Yang, Z. M. (2011) · Plant Cell & Environment · doi:10.1111/j.1365-3040.2011.02418.x · Cited by 205
Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium
Zhou, Z., Song, J., & Yang, Z. M. (2012) · Journal of Experimental Botany · doi:10.1093/jxb/ers136 · Cited by 205
The Epigenome and Plant Development
He, G., Elling, A. A., & Deng, X. W. (2011) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042110-103806 · Cited by 198
Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology
Dalziel, A. C., Rogers, S. M., & Schulte, P. M. (2009) · Molecular Ecology · doi:10.1111/j.1365-294x.2009.04427.x · Cited by 198
The role of QTLs in the breeding of high-yielding rice
Miura, K., Ashikari, M., & Matsuoka, M. (2011) · Trends in Plant Science · doi:10.1016/j.tplants.2011.02.009 · Cited by 190
Ppe TAC 1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species
Dardick, C., Callahan, A., Horn, R., Ruiz, K. B., Zhebentyayeva, T., Hollender, C., Whitaker, M., Abbott, A., & Scorza, R. (2013) · The Plant Journal · doi:10.1111/tpj.12234 · Cited by 184
What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research
Bräutigam, A., & Gowik, U. (2010) · Plant Biology · doi:10.1111/j.1438-8677.2010.00373.x · Cited by 183
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
Horner, D. S., Pavesi, G., Castrignanò, T., Meo, P. D. D., Liuni, S., Sammeth, M., Picardi, E., & Pesole, G. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp046 · Cited by 183
deepBase: a database for deeply annotating and mining deep sequencing data
Yang, J., Shao, P., Zhou, H., Chen, Y., & Qu, L. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp943 · Cited by 163
Evolutionary history and stress regulation of the lectin superfamily in higher plants
Jiang, S., Ma, Z., & Ramachandran, S. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-79 · Cited by 167
NGS technologies for analyzing germplasm diversity in genebanks*
Kilian, B., & Graner, A. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/elr046 · Cited by 159
Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
Franssen, S. U., Shrestha, R. P., Bräutigam, A., Bornberg‐Bauer, E., & Weber, A. P. M. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-227 · Cited by 158
microRNAs and genetic diseases
Meola, N., Gennarino, V. A., & Banfi, S. (2009) · PathoGenetics · doi:10.1186/1755-8417-2-7 · Cited by 158
RNA sequencing on Solanum lycopersicum trichomes identifies transcription factors that activate terpene synthase promoters
Spyropoulou, E. A., Haring, M. A., & Schuurink, R. C. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-402 · Cited by 149
Light signal transduction: an infinite spectrum of possibilities
Chory, J. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2009.04105.x · Cited by 139
Towards the Understanding of Complex Traits in Rice: Substantially or Superficially?
Yamamoto, T., Yonemaru, J., & Yano, M. (2009) · DNA Research · doi:10.1093/dnares/dsp006 · Cited by 138
Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing
Wang, Y., Xu, L., Chen, Y., Shen, H., Gong, Y., Limera, C., & Liu, L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066539 · Cited by 137
Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics
Schilmiller, A. L., Miner, D. P., Larson, M. D., McDowell, E. T., Gang, D. R., Wilkerson, C. G., & Last, R. L. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.157214 · Cited by 136
The Integrated Phenotype
Murren, C. J. (2012) · Integrative and Comparative Biology · doi:10.1093/icb/ics043 · Cited by 136
Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems
Yang, S. S., Tu, Z. J., Cheung, F., Xu, W. W., Lamb, J. F., Jung, H. G., Vance, C. P., & Gronwald, J. W. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-199 · Cited by 132
Genetic improvement of C4 grasses as cellulosic biofuel feedstocks
Jakob, K., Zhou, F., & Paterson, A. H. (2009) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/s11627-009-9214-x · Cited by 129
Darwinian agriculture: how understanding evolution can improve agriculture
Denison, R. (2012) · Choice Reviews Online · doi:10.5860/choice.50-2063 · Cited by 125
Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae
Kellar, P. R., Hertweck, K. L., Mayfield, D. R., McKain, M. R., Leebens‐Mack, J., & Pires, J. C. (2012) · American Journal of Botany · doi:10.3732/ajb.1100491 · Cited by 125
Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing
Miyao, A., Nakagome, M., Ohnuma, T., Yamagata, H., Kanamori, H., Katayose, Y., Takahashi, A., Matsumoto, T., & Hirochika, H. (2012) · Plant and Cell Physiology · doi:10.1093/pcp/pcr172 · Cited by 135
Differential transcriptome analysis of leaves of tea plant (Camellia sinensis) provides comprehensive insights into the defense responses to Ectropis oblique attack using RNA-Seq
Wang, Y., Tang, L., Hou, Y., Wang, P., Yang, H., & Wei, C. (2016) · Functional & Integrative Genomics · doi:10.1007/s10142-016-0491-2 · Cited by 113
Poplar and Pathogen Interactions: Insights fromPopulusGenome-Wide Analyses of Resistance and Defense Gene Families and Gene Expression Profiling
Duplessis, S., Major, I. T., Martin, F. M., & Séguin, A. (2009) · Critical Reviews in Plant Sciences · doi:10.1080/07352680903241063 · Cited by 113
Signaling between Chloroplasts and the Nucleus: Can a Systems Biology Approach Bring Clarity to a Complex and Highly Regulated Pathway?
Jung, H.-S., & Chory, J. (2009) · PLANT PHYSIOLOGY · doi:10.1104/pp.109.149070 · Cited by 111
Identification of EMS-Induced Causal Mutations in a Non-Reference Arabidopsis thaliana Accession by Whole Genome Sequencing
Uchida, N., Sakamoto, T., Kurata, T., & Tasaka, M. (2011) · Plant and Cell Physiology · doi:10.1093/pcp/pcr029 · Cited by 111
Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore
Knaus, B. J., Cronn, R., Liston, A., Pilgrim, K. L., & Schwartz, M. K. (2011) · BMC Ecology · doi:10.1186/1472-6785-11-10 · Cited by 107
Abiotic Stress Responses in Plants: Unraveling the Complexity of Genes and Networks to Survive
Sofia, A., de Almeida, A. M., da Silva, A. B., da Silva, J. M., Paula, A., Santos, D., Fevereiro, P., & Sousa Araujo, S. D. (2013) · Abiotic Stress - Plant Responses and Applications in Agriculture · doi:10.5772/52779 · Cited by 106
Low-temperature tolerance in land plants: Are transcript and membrane responses conserved?
Raju, S. K. K., Barnes, A. C., Schnable, J. C., & Roston, R. (2018) · Plant Science · doi:10.1016/j.plantsci.2018.08.002 · Cited by 101
Novel Genomic Tools and Modern Genetic and Breeding Approaches for Crop Improvement
Varshney, R. K., & Dubey, A. (2009) · Journal of Plant Biochemistry and Biotechnology · doi:10.1007/bf03263311 · Cited by 100
Trigenomic Bridges forBrassicaImprovement
Chen, S., Nelson, M. N., Chèvre, A., Jenczewski, E., Li, Z., Mason, A. S., Meng, J., Plummer, J. A., Pradhan, A., Siddique, K. H. M., et al. (2011) · Critical Reviews in Plant Sciences · doi:10.1080/07352689.2011.615700 · Cited by 100
High throughput DNA sequencing: The new sequencing revolution
Delseny, M., Han, B., & Hsing, Y. I. (2010) · Plant Science · doi:10.1016/j.plantsci.2010.07.019 · Cited by 102
Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique
Gao, Y., Xu, H., Shen, Y., & Wang, J. (2013) · Plant Molecular Biology · doi:10.1007/s11103-013-0009-4 · Cited by 94
Global analysis of the Gossypium hirsutum L. Transcriptome during leaf senescence by RNA-Seq
Lin, M., Pang, C., Fan, S., Song, M., Wei, H., & Yu, S. (2015) · BMC Plant Biology · doi:10.1186/s12870-015-0433-5 · Cited by 93
De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers
Mudalkar, S., Ramesh, G., Ghatty, S., & Reddy, A. R. (2013) · Plant Molecular Biology · doi:10.1007/s11103-013-0125-1 · Cited by 89
SOLiD-SAGE of Endophyte-Infected Red Fescue Reveals Numerous Effects on Host Transcriptome and an Abundance of Highly Expressed Fungal Secreted Proteins
Ambrose, K. V., & Belanger, F. C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0053214 · Cited by 89
Plant stress biology in epigenomic era
Perrone, A. F., & Martinelli, F. (2019) · Plant Science · doi:10.1016/j.plantsci.2019.110376 · Cited by 88
Plant systems biology: insights, advances and challenges
Sheth, B. P., & Thaker, V. S. (2014) · Planta · doi:10.1007/s00425-014-2059-5 · Cited by 89
Digital Gene Expression Signatures for Maize Development
Eveland, A. L., Satoh‐Nagasawa, N., Goldshmidt, A., Meyer, S., Beatty, M. K., Sakai, H., Ware, D., & Jackson, D. P. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.159673 · Cited by 87
De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.)
Xu, L., Wang, Y., Liu, W., Wang, J., Zhu, X., Zhang, K., Yu, R., Wang, R., Xie, Y., Zhang, W., et al. (2015) · Plant Science · doi:10.1016/j.plantsci.2015.04.015 · Cited by 87
Evolution of Genome Size in Duckweeds (Lemnaceae)
Wang, W., Kerstetter, R. A., & Michael, T. P. (2011) · Journal of Botany · doi:10.1155/2011/570319 · Cited by 86
ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass)
Gardin, J., Gouzy, J., Carrère, S., & Délye, C. (2015) · BMC Genomics · doi:10.1186/s12864-015-1804-x · Cited by 86
Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies
Parra-González, L., Aravena-Abarzúa, G. A., Navarro, C., Udall, J. A., Maughan, J., Peterson, L. M., Salvo-Garrido, H., & Maureira‐Butler, I. J. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-425 · Cited by 83
Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis
Yakovlev, I., Lee, Y., Rotter, B., Olsen, J. E., Skrøppa, T., Johnsen, Ø., & Fossdal, C. G. (2014) · Tree Genetics & Genomes · doi:10.1007/s11295-013-0691-z · Cited by 81
A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis
Hou, X., Li, L., Peng, Z., Wei, B., Tang, S., Ding, M., Liu, J., Zhang, F., Zhao, Y., Gu, H., et al. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04277.x · Cited by 82
Deep mRNA Sequencing for In Vivo Functional Analysis of Cardiac Transcriptional Regulators
Matkovich, S. J., Zhang, Y., Booven, D. J. V., & Dorn, G. W. (2010) · Circulation Research · doi:10.1161/circresaha.110.217513 · Cited by 80
T ranscriptome Profiling Reveals Auxin and Cytokinin Regulating Somatic Embryogenesis in Different Sister Lines of Cotton Cultivar CCRI24
Xu, Z., Zhang, C., Zhang, X., Liu, C., Wu, Z., Yang, Z., Zhou, K., Yang, X., & Li, F. (2013) · Journal of Integrative Plant Biology · doi:10.1111/jipb.12073 · Cited by 79
A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions
PACURAR, D. I., Păcurar, M. L., Street, N. R., Bussell, J. D., Pop, T. I., Gutierrez, L., & Bellini, C. (2012) · Journal of Experimental Botany · doi:10.1093/jxb/err422 · Cited by 79
DNA Methylation and Its Implications and Accessibility for Neuropsychiatric Therapeutics
Day, J. J., Kennedy, A. J., & Sweatt, J. D. (2015) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124527 · Cited by 78
Biodiversity assessment: State‐of‐the‐art techniques in phylogenomics and species identification
Kellar, P. R., & Pires, J. C. (2011) · American Journal of Botany · doi:10.3732/ajb.1000296 · Cited by 78
The Legume Root Nodule: From Symbiotic Nitrogen Fixation to Senescence
Dupont, L., Alloing, G., Pierre, O., El, S., Hopkins, J., Hrouart, D., & Frendo, P. (2012) · InTech eBooks · doi:10.5772/34438 · Cited by 77
High-throughput sequencing of black pepper root transcriptome
Gordo, S. M. D. C., Pinheiro, D. G., Moreira, E. C. O., Rodrigues, S. D. M., Poltronieri, M. C., de Lemos, O. F., da Silva, I. T., Ramos, R. T. J., Silva, A., Schneider, H., et al. (2012) · BMC Plant Biology · doi:10.1186/1471-2229-12-168 · Cited by 75
DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data
Nagasaki, H., Mochizuki, T., Kodama, Y., Saruhashi, S., Morizaki, S., Sugawara, H., Ohyanagi, H., Kurata, N., Okubo, K., Takagi, T., et al. (2013) · DNA Research · doi:10.1093/dnares/dst017 · Cited by 73
Transcriptomic Signatures of Ash (Fraxinus spp.) Phloem
Bai, X., Rivera-Vega, L. J., Mamidala, P., Bonello, P., Herms, D. A., & Mittapalli, O. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016368 · Cited by 71
Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean
Song, X., Wei, H., Cheng, W., Yang, S., Zhao, Y., Li, X., Luo, D., Zhang, H., & Feng, X. (2015) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.022780 · Cited by 71
Identification of differentially expressed genes in flax (Linum usitatissimum L.) under saline–alkaline stress by digital gene expression
Yu, Y., Huang, W., Chen, H., Wu, G., Yuan, H., Song, X., Kang, Q., Zhao, D., Jiang, W., Liu, Y., et al. (2014) · Gene · doi:10.1016/j.gene.2014.07.053 · Cited by 70
RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit
García‐Seco, D., Zhang, Y., Gutiérrez‐Mañero, F. J., Martin, C. R., & Ramos‐Solano, B. (2015) · BMC Genomics · doi:10.1186/s12864-014-1198-1 · Cited by 70
Update on Chloroplast Research: New Tools, New Topics, and New Trends
Armbruster, U., Pesaresi, P., Pribil, M., Hertle, A. P., & Leister, D. (2010) · Molecular Plant · doi:10.1093/mp/ssq060 · Cited by 67
Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in Caenorhabditis elegans
Doitsidou, M., Jarriault, S., & Poole, R. J. (2016) · Genetics · doi:10.1534/genetics.115.186197 · Cited by 64
Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing
Villarino, G., Bombarely, A., Giovannoni, J. J., Scanlon, M. J., & Mattson, N. S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0094651 · Cited by 58
Genome-Wide Mining, Characterization and Development of Microsatellite Markers in Gossypium Species
Wang, Q., Fang, L., Chen, J., Hu, Y., Si, Z., Wang, S., Chang, L., Guo, W., & Zhang, T. (2015) · Scientific Reports · doi:10.1038/srep10638 · Cited by 59
Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review
Muthuramalingam, P., Jeyasri, R., Rakkammal, K., Satish, L., Shamili, S., Karthikeyan, A., Valliammai, A., Priya, A., Selvaraj, A., Gowri, P., et al. (2022) · Biology · doi:10.3390/biology11071022 · Cited by 58
Biochemical Genomics for Gene Discovery in Benzylisoquinoline Alkaloid Biosynthesis in Opium Poppy and Related Species
Dang, T. T., Onoyovwi, A., Farrow, S. C., & Facchini, P. J. (2012) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-394290-6.00011-2 · Cited by 58
The use of high-throughput sequencing methods for plant microRNA research
Ma, X., Tang, Z., Qin, J., & Meng, Y. (2015) · RNA Biology · doi:10.1080/15476286.2015.1053686 · Cited by 56
De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat
Zhang, J., Liu, W., Han, H., Song, L., Bai, L., Gao, Z., Zhang, Y., Yang, X., Li, X., Gao, A., et al. (2015) · Genomics · doi:10.1016/j.ygeno.2015.04.003 · Cited by 56
TILLING, high-resolution melting (HRM), and next-generation sequencing (NGS) techniques in plant mutation breeding
Taheri, S., Abdullah, T. L., Jain, S. M., Sahebi, M., & Azizi, P. (2017) · Molecular Breeding · doi:10.1007/s11032-017-0643-7 · Cited by 55
Viral induction and suppression of RNA silencing in plants
Shimura, H., & Pantaleo, V. (2011) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.04.005 · Cited by 57
Bulk Segregant Analysis of an Induced Floral Mutant Identifies aMIXTA-Like R2R3MYBControlling Nectar Guide Formation inMimulus lewisii
Yuan, Y., Sagawa, J. M., Stilio, V. S. D., & Bradshaw, H. D. (2013) · Genetics · doi:10.1534/genetics.113.151225 · Cited by 53
More than the sum of its parts – How to achieve a specific transcriptional response to abiotic stress
Vaahtera, L., & Brosché, M. (2010) · Plant Science · doi:10.1016/j.plantsci.2010.11.009 · Cited by 50
DNA Fingerprinting, DNA Barcoding, and Next Generation Sequencing Technology in Plants
Sucher, N. J., Hennell, J. R., & Carles, M. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-609-8_2 · Cited by 51
Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster
Kang, H., Weng, Y., Yang, Y., Zhang, Z., Zhang, S., Mao, Z., Cheng, G., Gu, X., Huang, S., & Xie, B. (2010) · Theoretical and Applied Genetics · doi:10.1007/s00122-010-1487-2 · Cited by 48
Investigating the mechanisms of glyphosate resistance in goosegrass (Eleusine indica (L.) Gaertn.) by RNA sequencing technology
Chen, J., Huang, H., Wei, S., Huang, Z., Wang, X., & Zhang, C. (2016) · The Plant Journal · doi:10.1111/tpj.13395 · Cited by 48
ncRNAimprint: A comprehensive database of mammalian imprinted noncoding RNAs
Zhang, Y., Guan, D.-G., Yang, J., Shao, P., Zhou, H., & Qu, L. (2010) · RNA · doi:10.1261/rna.2226910 · Cited by 46
Transcriptome sequencing and comparative analysis of the gametophyte thalli of Pyropia tenera under normal and high temperature conditions
Choi, S., Hwang, M. S., Im, S., Kim, N., Jeong, W.-J., Park, E., Gong, Y.-G., & Choi, D. (2012) · Journal of Applied Phycology · doi:10.1007/s10811-012-9921-2 · Cited by 46

Authors: Lister, R., Gregory, B. D., & Ecker, J. R.
Affiliations: Salk Institute for Biological Studies (US)
Corresponding author: Ecker, Joseph R
ORCID: Lister, Ryan
Gregory, Brian D
Ecker, Joseph R
Venue: Current Opinion in Plant Biology
Publisher: Elsevier BV
Published: 2009-04
Volume: 12
Issue: 2
Pages: 107-118
ISSN: 1369-5266 (ISSN-L)
DOI: 10.1016/j.pbi.2008.11.004
PMC: PMC2723731
OpenAlex: W2067360806
Cited by: 274
References: 88
Citations by year: 2026: 1 · 2025: 1 · 2024: 3 · 2023: 2 · 2022: 5 · 2021: 7 · 2020: 5 · 2019: 8 · 2018: 13 · 2017: 16 · 2016: 13 · 2015: 17 · 2014: 30 · 2013: 29 · 2012: 29
FWCI: 3.16
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Current Opinion in Plant Biology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
UWA Profiles and Research Repository (UWA) (submittedVersion)
Funders: Damon Runyon Cancer Research Foundation
Mary K. Chapman Foundation
National Institute of Environmental Health Sciences (U01ES017166)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords: next-generation sequencing, DNA sequencing technologies, genome resequencing, mutation mapping, DNA methylation, histone modifications, transcriptome sequencing, gene discovery, alternative splicing, small RNA profiling, protein-DNA interactions, plant genomics
MeSH terms: Polymorphism, Genetic, Sequence Analysis, DNA, Genome, Plant, RNA, Plant, DNA Methylation, Gene Expression Profiling

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks