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Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

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Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

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Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers

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Herbaceous energy crop development: recent progress and future prospects

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Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)

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Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

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Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

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High-throughput SNP discovery and assay development in common bean

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De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties

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Insertion-deletion polymorphisms (indels) as genetic markers in natural populations

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Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery

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Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation

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Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

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Single-Molecule DNA Amplification and Analysis Using Microfluidics

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Quantification of rare allelic variants from pooled genomic DNA

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Global gene expression analysis of the shoot apical meristem of maize ( Zea mays L.)

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Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array

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Targeted sequence capture as a powerful tool for evolutionary analysis1

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Development and mapping of SNP assays in allotetraploid cotton

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Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea

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Transcriptomics of a Giant Freshwater Prawn (Macrobrachium rosenbergii): De Novo Assembly, Annotation and Marker Discovery

Jung, H., Lyons, R. E., Dinh, H., Hurwood, D. A., McWilliam, S. M., & Mather, P. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027938 · Cited by 140 · see citing works

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

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High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.)

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Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing

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Large SNP arrays for genotyping in crop plants

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Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next‐generation sequencing and Sequenom iPLEX MassARRAY genotyping

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High-Throughput SNP Discovery and Genotyping for Constructing a Saturated Linkage Map of Chickpea (Cicer arietinum L.)

Gaur, R. K., Azam, S., Jeena, G., Khan, A. W., Choudhary, S., Jain, M., Yadav, G., Tyagi, A. K., Chattopadhyay, D., & Bhatia, S. (2012) · DNA Research · doi:10.1093/dnares/dss018 · Cited by 133 · see citing works

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 · see citing works

Discovering genetic polymorphisms in next‐generation sequencing data

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Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

Wang, S., Chen, J., Zhang, W., Hu, Y., Chang, L., Fang, L., Wang, Q., Lv, F., Wu, H., Si, Z., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0678-1 · Cited by 127 · see citing works

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

Castaño-Sánchez, C., Smith, T. P. L., Wiedmann, R. T., Vallejo, R. L., Salem, M., Yao, J., & Rexroad, C. E. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-559 · Cited by 126 · see citing works

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 124 · see citing works

Quality assessment parameters for EST-derived SNPs from catfish

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Transcriptome sequencing of wild chickpea as a rich resource for marker development

Jhanwar, S., Priya, P., Garg, R., Parida, S. K., Tyagi, A. K., & Jain, M. (2012) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2012.00712.x · Cited by 122 · see citing works

Shedding light on an extremophile lifestyle through transcriptomics

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Sequence-based marker development in wheat: Advances and applications to breeding

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Genic and nongenic contributions to natural variation of quantitative traits in maizePreprint

Li, X., Zhu, C., Yeh, C., Wu, W., Takacs, E. M., Petsch, K. A., Tian, F., Bai, G., Buckler, E. S., Muehlbauer, G. J., et al. (2012) · Genome Research · doi:10.1101/gr.140277.112 · Cited by 121 · see citing works

Sympatric Speciation in the Post “Modern Synthesis” Era of Evolutionary Biology

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Extreme‐phenotype genome‐wide association study ( XP ‐ GWAS ): a method for identifying trait‐associated variants by sequencing pools of individuals selected from a diversity panel

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A set of EST-SNPs for map saturation and cultivar identification in melon

Deleu, W., Esteras, C., Roig, C., González, M., Fernández-Silva, I., González‐Ibeas, D., Blanca, J., Aranda, M. A., Arús, P., Nuez, F., et al. (2009) · BMC Plant Biology · doi:10.1186/1471-2229-9-90 · Cited by 118 · see citing works

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

O’Neil, S. T., Dzurisin, J. D. K., Carmichael, R., Lobo, N. F., Emrich, S., & Hellmann, J. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-310 · Cited by 117 · see citing works

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

Ashrafi, H., Hill, T. A., Stoffel, K. M., Kozik, A., Yao, J., Reyes-Chin-Wo, S., & Deynze, A. V. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-571 · Cited by 117 · see citing works

Single-Nucleotide Polymorphisms (SNPs) under Diversifying Selection Provide Increased Accuracy and Precision in Mixed-Stock Analyses of Sockeye Salmon from the Copper River, Alaska

Ackerman, M. W., Habicht, C., & Seeb, L. W. (2011) · Transactions of the American Fisheries Society · doi:10.1080/00028487.2011.588137 · Cited by 117 · see citing works

Advances in molecular technology and their impact on fisheries genetics

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Genetic control of morphometric diversity in the maize shoot apical meristem

Leiboff, S., Li, X., Hu, H.-C., Todt, N. R., Yang, J., Li, X., Yu, X., Muehlbauer, G. J., Timmermans, M. C. P., Yu, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms9974 · Cited by 112 · see citing works

Genomics of Fungal Disease Resistance in Tomato

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Next‐generation sequencing applications for wheat crop improvement

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Transcript Profiling by 3′-Untranslated Region Sequencing Resolves Expression of Gene Families

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Characterizing the mouse ES cell transcriptome with Illumina sequencing

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Transcriptomic, Proteomic, Metabolomic and Functional Genomic Approaches for the Study of Abiotic Stress in Vegetable Crops

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Genome-Wide SNP Calling Using Next Generation Sequencing Data in Tomato

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Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics

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Single nucleotide polymorphism discovery from wheat next‐generation sequence data

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High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

Grattapaglia, D. G., Silva‐Junior, O. B., Kirst, M., de Lima, B. M., de Faria, D. A., & Pappas, G. J., Jr. (2011) · BMC Plant Biology · doi:10.1186/1471-2229-11-65 · Cited by 104 · see citing works

SNP Mining from Maize 454 EST SequencesPreprint

Barbazuk, W. B., Emrich, S., & Schnable, P. S. (2007) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot4786 · Cited by 11 · see citing works

SNP Discovery by Transcriptome Pyrosequencing

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Gene discovery and annotation using LCM-454 transcriptome sequencingPreprint

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Large‐Scale Discovery of Gene‐Enriched SNPs

Gore, M. A., Wright, M. H., Ersoz, E. S., Bouffard, P., Szekeres, E. S., Jarvie, T. P., Hurwitz, B. L., Narechania, A., Harkins, T. T., Grills, G. S., et al. (2009) · The Plant Genome · doi:10.3835/plantgenome2009.01.0002 · Cited by 62 · see citing works

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

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