Dr Naeem Syed


NameDr Naeem Syed
Job titleReader
Research instituteSchool of Human and Life Sciences

Research outputs

Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

Reddy, A. S. N., Huang, J., Syed, N., Ben-Hur, A., Dong, S. and Gu, L. 2020. Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochemical Society Transactions. https://doi.org/10.1042/BST20190492

Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

Jabre, I., Chaudhary, S., Guo, W., Kalyna, M., Reddy, A. S. N., Chen, W., Zhang, R., Wilson, C. and Syed, N. 2020. Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana. New Phytologist. https://doi.org/10.1111/nph.17062

Genome-wide identification of splicing quantitative trait loci (sQTLs) in diverse ecotypes of Arabidopsis thaliana

Khokhar, W., Hassan, M., Reddy, A., Chaudhary, S., Jabre, I., Byrne, L. and Syed, N. 2019. Genome-wide identification of splicing quantitative trait loci (sQTLs) in diverse ecotypes of Arabidopsis thaliana. Frontiers in Plant Science. 10 (1160). https://doi.org/10.3389/fpls.2019.01160

Alternative splicing and protein diversity: plants versus animals

Chaudhry, S., Khokhar, W., Jabre, I., Reddy, A., Byrne, L., Wilson, C. and Syed, N. 2019. Alternative splicing and protein diversity: plants versus animals. Frontiers in Plant Science. 10 (708). https://doi.org/10.3389/fpls.2019.00708

Genetic diversity and structure of northern populations of the declining coastal plant Eryngium maritimum

Ievina, B., Rostoks, N., Syed, N., Flavell, A. and Ievinsh, G. 2019. Genetic diversity and structure of northern populations of the declining coastal plant Eryngium maritimum. Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences.. 0 (0). https://doi.org/10.2478/prolas-2019-0008

Perspective on alternative splicing and proteome complexity in plants

Chaudhary, S., Jabre, I., Reddy, A., Staiger, D. and Syed, N. 2019. Perspective on alternative splicing and proteome complexity in plants. Trends in Plant Science. 24 (6), pp. 496-506. https://doi.org/10.1016/j.tplants.2019.02.006

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Jabre, I., Reddy, A., Kalyna, M., Chaudhary, S., Khokhar, W., Byrne, L., Wilson, C. and Syed, N. 2019. Does co-transcriptional regulation of alternative splicing mediate plant stress responses? Nucleic Acids Research. 47 (6), pp. 2716-2726. https://doi.org/10.1093/nar/gkz121

A comparative study between molecular and agro-morphological methods for describing genetic relationships in Tunisian faba bean populations

Syed, N. 2016. A comparative study between molecular and agro-morphological methods for describing genetic relationships in Tunisian faba bean populations. Journal of New Sciences: Agri & Biotech. 27 (8), pp. 1513-1518.

Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting

Prince, S., Joshi, T., Mutava, R., Syed, N., Joao Vitor, M., Patil, G., Song, L., Wang, J., Lin, L., Chen, W., Shannon, J., Valliyodan, B., Xu, D. and Nguyen, H. 2015. Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Plant Science. 240, pp. 65-78. https://doi.org/10.1016/j.plantsci.2015.08.017

Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean

Syed, N., Prince, S., Mutava, R., Patil, G., Li, S., Chen, W., Babu, V., Joshi, T., Khan, S. and Nguyen, H. 2015. Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erv407

Understanding abiotic stress tolerance mechanisms in soybean: a comparative evaluation of soybean response to drought and flooding stress

Mutava, R., Prince, S., Syed, N., Song, L., Valliyodan, B., Chen, W. and Nguyen, H. 2015. Understanding abiotic stress tolerance mechanisms in soybean: a comparative evaluation of soybean response to drought and flooding stress. Plant physiology and biochemistry : PPB / Société française de physiologie végétale. 86, pp. 109-20. https://doi.org/10.1016/j.plaphy.2014.11.010

Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing

Ho, T., Cardle, L., Xu, X., Bayer, M., Prince, K., Mutava, R., Marshall, D. and Syed, N. 2014. Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing. Molecular Breeding. 34 (3), pp. 977-988. https://doi.org/10.1007/s11032-014-0090-7

Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions

Syed, N. and Flavell, A. 2007. Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nature Protocols. 1 (6), pp. 2746-2752. https://doi.org/10.1038/nprot.2006.407

Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers

Sanz, A., Gonzalez, S., Syed, N., Suso, M., Saldaña, C. and Flavell, A. 2007. Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Molecular Genetics and Genomics. 278 (4), pp. 433-441. https://doi.org/10.1007/s00438-007-0261-x

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

Kalyna, M., Simpson, C., Syed, N., Lewandowska, D., Marquez, Y., Kusenda, B., Marshall, J., Fuller, J., Cardle, L., McNicol, J., Dinh, H., Barta, A. and Brown, J. 2012. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Research. 40 (6), pp. 2454-2469. https://doi.org/10.1093/nar/gkr932

Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes

James, A., Syed, N., Bordage, S., Marshall, J., Nimmo, G., Jenkins, G., Herzyk, P., Brown, J. and Nimmo, H. 2012. Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes. The Plant Cell. 24 (3), pp. 961-981. https://doi.org/10.1105/tpc.111.093948

Alternative splicing in plants – coming of age

Syed, N., Kalyna, M., Marquez, Y., Barta, A. and Brown, J. 2012. Alternative splicing in plants – coming of age. Trends in Plant Science. 17 (10), pp. 616-623. https://doi.org/10.1016/j.tplants.2012.06.001

Thermoplasticity in the plant circadian clock: how plants tell the time-perature

James, A., Syed, N., Brown, J. and Nimmo, H. 2012. Thermoplasticity in the plant circadian clock: how plants tell the time-perature. Plant Signaling & Behavior. 7 (10), pp. 1219-1223. https://doi.org/10.4161/psb.21491

Inbred lines as testers for combining ability in cotton

Syed, W., Mehdi, S. and Syed, N. 1994. Inbred lines as testers for combining ability in cotton. Pakistan Journal of Scientific Research. 46, pp. 93-95.

Genetic study of lint percentage and staple length in cotton

Syed, W., Mehdi, S. and Syed, N. 1994. Genetic study of lint percentage and staple length in cotton. Pakistan Journal of Science. 46 (3-4), pp. 123-124.

Phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.)

Syed, N., Mehdi, S. and Syed, N. 1995. Phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.). Pakistan Journal of Scientific Research. 47 (3-4), pp. 62-65.

Two cycles of phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.)

Syed, N., Mehdi, S., Khan, I. and Syed, N. 1995. Two cycles of phenotypic recurrent selection for earliness in a random mated population of sunflower (Helianthus annuus L.). Science International (Lahore). 7, pp. 201-202.

Association of agronomic and economic characters of cotton

Syed, W., Mehdi, S. and Syed, N. 1995. Association of agronomic and economic characters of cotton. Pakistan Journal of Scientific Research. 47, pp. 46-49.

Fast and reliable genotype validation using microsatellite markers in Arabidopsis thaliana

Virk, P., Pooni, H., Syed, N. and Kearsey, M. 1999. Fast and reliable genotype validation using microsatellite markers in Arabidopsis thaliana. Theoretical and Applied Genetics. 98 (3-4), pp. 462-464. https://doi.org/10.1007/s001220051092

Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters

Hart, G., Schertz, K., Peng, Y. and Syed, N. 2001. Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters. Theoretical and Applied Genetics. 103 (8), pp. 1232-1242. https://doi.org/10.1007/s001220100582

Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L.

Kiær, L., Felber, F., Flavell, A., Guadagnuolo, R., Guiatti, D., Hauser, T., Olivieri, A., Scotti, I., Syed, N., Vischi, M., Wiel, C. and Jørgensen, R. 2009. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L. Genetic Resources and Crop Evolution. 56 (3), pp. 405-419. https://doi.org/10.1007/s10722-008-9375-1

Molecular markers for the identification of resistance genes and marker-assisted selection in breeding wheat for leaf rust resistance

Vida, G., Gál, M., Uhrin, A., Veisz, O., Syed, N., Flavell, A., Wang, Z. and Bedő, Z. 2009. Molecular markers for the identification of resistance genes and marker-assisted selection in breeding wheat for leaf rust resistance. Euphytica. 170 (1-2), pp. 67-76. https://doi.org/10.1007/s10681-009-9945-0

Development of retrotransposon-based SSAP molecular marker system for study of genetic diversity in sea holly (Eryngium maritimum L.)

Levina, B., Syed, N., Flavell, A., Ievinsh, G. and Rostoks, N. 2010. Development of retrotransposon-based SSAP molecular marker system for study of genetic diversity in sea holly (Eryngium maritimum L.). Plant Genetic Resources. 8 (3), pp. 258-266. https://doi.org/10.1017/S1479262110000316

A hAT superfamily transposase recruited by the cereal grass genome

Muehlbauer, G., Bhau, B., Syed, N., Heinen, S., Cho, S., Marshall, D., Pateyron, S., Buisine, N., Chalhoub, B. and Flavell, A. 2006. A hAT superfamily transposase recruited by the cereal grass genome. Molecular Genetics and Genomics. 275 (6), pp. 553-563. https://doi.org/10.1007/s00438-006-0098-8

Genetics of quantitative traits in Arabidopsis thaliana

Kearsey, M., Pooni, H. and Syed, N. 2003. Genetics of quantitative traits in Arabidopsis thaliana. Heredity. 91 (5), pp. 456-464. https://doi.org/10.1038/sj.hdy.6800306

Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations

Syed, N., Pooni, H., Mei, M., Chen, Z. and Kearsey, M. 2004. Optimising the construction of a substitution library in Arabidopsis thaliana using computer simulations. Molecular Breeding. 13 (1), pp. 59-68. https://doi.org/10.1023/B:MOLB.0000012845.37366.b5

Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana

Syed, N. and Chen, Z. 2005. Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana. Heredity. 94 (3), pp. 295-304. https://doi.org/10.1038/sj.hdy.6800558

Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.)

Syed, N., Sureshsundar, S., Wilkinson, M., Bhau, B., Cavalcanti, J. and Flavell, A. 2005. Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theoretical and Applied Genetics. 110 (7), pp. 1195-1202. https://doi.org/10.1007/s00122-005-1948-1

Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium)

Mei, M., Syed, N., Gao, W., Thaxton, P., Smith, C., Stelly, D. and Chen, Z. 2004. Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theoretical and Applied Genetics. 108 (2), pp. 280-291. https://doi.org/10.1007/s00122-003-1433-7

A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

Syed, N., Sørensen, A., Antonise, R., Wiel, C., Linden, C., van 't Westende, W., Hooftman, D., Nijs, H. and Flavell, A. 2006. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers. Theoretical and Applied Genetics. 112 (3), pp. 517-527. https://doi.org/10.1007/s00122-005-0155-4
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