Dr Agnelo Furtado

Subbaiyan, Gopala Krishnan, Masouleh, Ardashir K., Furtado, Agnelo, Waters, Daniel L. E. and Henry, Robert J. (2019). Re-sequencing resources to improve starch and grain quality in rice. In Nese Sreenivasulu (Ed.), Rice Grain Quality (pp. 201-240) New York, NY, United States: Humana Press Inc.. doi:10.1007/978-1-4939-8914-0_12

Healey, Adam, Furtado, Agnelo and Henry, Robert J. (2014). Structural genomics of eucalypts. In Robert Henry and Chittaranjan Kole (Ed.), Genetics, genomics and breeding of eucalypts (pp. 103-120) Boca Raton, FL, United States: CRC Press. doi:10.1201/b17154

Furtado, Agnelo (2014). RNA extraction from developing or mature wheat seeds. In Robert J. Henry and Agnelo Furtado (Ed.), Cereal Genomics: Methods and Protocols (pp. 23-28) New York, NY, United States: Humana Press. doi:10.1007/978-1-62703-715-0

Furtado, Agnelo (2014). Cloning of DNA fragments: Ligation reactions in agarose gel. In Robert J. Henry and Agnelo Furtado (Ed.), Cereal genomics: methods and protocols (pp. 117-121) New York, United States: Humana Press. doi:10.1007/978-1-62703-715-0_10

Furtado, Agnelo (2014). DNA extraction from vegetative tissue for next-generation sequencing. In Robert J. Henry and Agnelo Furtado (Ed.), Cereal genomics: methods and protocols (pp. 1-5) New York, NY United States: Humana Press. doi:10.1007/978-1-62703-715-0-1

Tran, Hue T. M., Furtado, Agnelo, Vargas, Carlos Alberto Cordero, Smyth, Heather, Lee, L. Slade and Henry, Robert (2018) SNP in the Coffea arabica genome associated with coffee quality. Tree Genetics & Genomes, 14 5: . doi:10.1007/s11295-018-1282-9

Kasirajan, Lakshmi, Hoang, Nam V., Furtado, Agnelo, Botha, Frederik C. and Henry, Robert J. (2018) Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content. Scientific Reports, 8 . doi:10.1038/s41598-018-30033-4

Cheng, Bing, Furtado, Agnelo and Henry, Robert J. (2018) The coffee bean transcriptome explains the accumulation of the major bean components through ripening. Scientific Reports, 8 1: 11414. doi:10.1038/s41598-018-29842-4

Henry, Robert J., Furtado, Agnelo and Rangan, Parimalan (2018) Wheat seed transcriptome reveals genes controlling key traits for human preference and crop adaptation. Current Opinion in Plant Biology, . doi:10.1016/j.pbi.2018.05.002

Mohammad Moner, Ali, Furtado, Agnelo and Henry, Robert J (2018) Chloroplast phylogeny of AA genome rice species. Molecular Phylogenetics and Evolution, . doi:10.1016/j.ympev.2018.05.002

Moner, Ali M., Furtado, Agnelo, Chivers, Ian, Fox, Glen, Crayn, Darren and Henry, Robert J. (2018) Diversity and evolution of rice progenitors in Australia. Ecology and Evolution, 8 8: 4360-4366. doi:10.1002/ece3.3989

Hoang, Nam V., Furtado, Agnelo, Thirugnanasambandam, Prathima P., Botha, Frederik C. and Henry, Robert J. (2018) De novo assembly and characterizing of the culm-derived meta-transcriptome from the polyploid sugarcane genome based on coding transcripts. Heliyon, 4 3: e00583. doi:10.1016/j.heliyon.2018.e00583

Tran, Hue T. M., Ramaraj, Thiruvarangan, Furtado, Agnelo, Lee, L. Slade and Henry, Robert J. (2018) Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content. Plant Biotechnology Journal, 16 10: 1756-1766. doi:10.1111/pbi.12912

Healey, Adam, Lee, David J., Furtado, Agnelo and Henry, Robert J. (2018) Evidence of inter-sectional chloroplast capture in Corymbia among sections Torellianae and Maculatae. Australian Journal of Botany, 66 5: 369-378. doi:10.1071/BT18028

Singh, Amit Kumar, Furtado, Agnelo, Brozynska, Marta, Mishra, Neeti Sanan and Henry, Robert J (2017) Phylogeny and Molecular Evolution of miR820 and miR396 microRNA Families in Oryza AA Genomes. Tropical Plant Biology, 11 1-2: 1-16. doi:10.1007/s12042-017-9197-4

Thirugnanasambandam, Prathima P, Hoang, Nam V, Furtado, Agnelo, Botha, Frederick C and Henry, Robert J (2017) Association of variation in the sugarcane transcriptome with sugar content. BMC genomics, 18 909: 1-22. doi:10.1186/s12864-017-4302-5

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert J. (2017) The transcriptome of the developing grain: A resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat. BMC Genomics, 18 1: 766-776. doi:10.1186/s12864-017-4154-z

Nirmal, Ravi C., Furtado, Agnelo, Rangan, Parimalan and Henry, Robert J. (2017) Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat. Scientific Reports, 7 1: 12539. doi:10.1038/s41598-017-12845-y

Tikapunya, Tiparat, Zou, Wei, Yu, Wenwen, Powell, Prudence O., Fox, Glen P., Furtado, Agnelo, Henry, Robert J. and Gilbert, Robert G. (2017) Molecular structures and properties of starches of Australian wild rice. Carbohydrate Polymers, 172 213-222. doi:10.1016/j.carbpol.2017.05.046

Cheng, Bing, Furtado, Agnelo and Henry, Robert J (2017) Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts. GigaScience, 6 11: 1-13. doi:10.1093/gigascience/gix086

Shamloo, Maryam, Babawale, Elizabeth A., Furtado, Agnelo, Henry, Robert J., Eck, Peter K. and Jones, Peter J. H. (2017) Effects of genotype and temperature on accumulation of plant secondary metabolites in Canadian and Australian wheat grown under controlled environments. Scientific Reports, 7 1: 9133. doi:10.1038/s41598-017-09681-5

Hoang, Nam V., Furtado, Agnelo, O'Keeffe, Angela J., Botha, Frederik C. and Henry, Robert J. (2017) Association of gene expression with biomass content and composition in sugarcane. PLoS One, 12 8: e0183417. doi:10.1371/journal.pone.0183417

Henry, Robert J., Rangan, Parimalan, Furtado, Agnelo, Busch, Florian A. and Farquhar, Graham D. (2017) Does C-4 Photosynthesis Occur in Wheat Seeds?. Plant Physiology, 174 4: 1994-1995.

Henry, Robert J., Rangan, Parimalan and Furtado, Agnelo (2017) Does C-4 Photosynthesis Occur in Wheat Seeds?. Plant Physiology, 174 4: 1992-1993. doi:10.1104/pp.17.00837

Wambugu, Peterson, Ndjiondjop, Marie-Noelle, Furtado, Agnelo and Henry, Robert (2017) Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice. Plant Biotechnology Journal, 16 1: 100-110. doi:10.1111/pbi.12752

Tran, Hue T. M., Vargas, Carlos Alberto Cordero, Lee, L. Slade, Furtado, Agnelo, Smyth, Heather and Henry, Robert (2017) Variation in bean morphology and biochemical composition measured in different genetic groups of arabica coffee (Coffea arabica L.). Tree Genetics and Genomes, 13 3: . doi:10.1007/s11295-017-1138-8

Brozynska, Marta, Copetti, Dario, Furtado, Agnelo, Wing, Rod A., Crayn, Darren, Fox, Glen, Ishikawa, Ryuji and Henry, Robert J. (2017) Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnology Journal, 15 6: 765-774. doi:10.1111/pbi.12674

Survase, Abhijeet, Furtado, Agnelo, Thengane, Ratnakar, Fox, Glen, Taylor, Terence and Henry, Robert (2017) Comparison of chapatti and breadmaking quality of wheat genotypes. Cereal Chemistry, 94 3: 409-416. doi:10.1094/CCEM-04-16-0090-R

Hoang, Nam V., Furtado, Agnelo, Mason, Patrick J., Marquardt, Annelie, Kasirajan, Lakshmi, Thirugnanasambandam, Prathima P., Botha, Frederik C. and Henry, Robert J. (2017) A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics, 18 1: 395. doi:10.1186/s12864-017-3757-8

Hoang, Nam V., Furtado, Agnelo, Donnan, Laura, Keeffe, Eloise C., Botha, Frederik C. and Henry, Robert J. (2016) High-throughput profiling of the fiber and sugar composition of sugarcane biomass. Bioenergy Research, 10 2: 1-17. doi:10.1007/s12155-016-9801-8

Cheng, Bing, Furtado, Agnelo, Smyth, Heather E. and Henry, Robert J. (2016) Influence of genotype and environment on coffee quality. Trends in Food Science and Technology, 57 A: 20-30. doi:10.1016/j.tifs.2016.09.003

Nock, Catherine J., Baten, Abdul, Barkla, Bronwyn J., Furtado, Agnelo, Henry, Robert J. and King, Graham J. (2016) Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae). BMC Genomics, 17 1: . doi:10.1186/s12864-016-3272-3

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert J. (2016) Commentary: new evidence for grain specific C4 photosynthesis in wheat. Frontiers in Plant Science, 7 OCTOBER2016: . doi:10.3389/fpls.2016.01537

Nirmal, Ravi C., Furtado, Agnelo, Wrigley, Colin and Henry, Robert J. (2016) Influence of gene expression on hardness in wheat. PLoS ONE, 11 10: e0164746. doi:10.1371/journal.pone.0164746

Rangan, Parimalan, Furtado, Agnelo and Henry, Robert J. (2016) New evidence for grain specific C4 photosynthesis in wheat. Scientific Reports, 6 31721. doi:10.1038/srep31721

Tran, Hue T. M., Lee, L. Slade, Furtado, Agnelo, Smyth, Heather and Henry, Robert J. (2016) Advances in genomics for the improvement of quality in coffee. Journal of the Science of Food and Agriculture, 96 10: 3300-3312. doi:10.1002/jsfa.7692

Henry, Robert J., Rangan, Parimalan and Furtado, Agnelo (2016) Functional cereals for production in new and variable climates. Current Opinion in Plant Biology, 30 11-18. doi:10.1016/j.pbi.2015.12.008

Tikapunya, Tiparat, Fox, Glen, Furtado, Agnelo and Henry, Robert (2016) Grain physical characteristics of the Australian wild rices. Plant Genetic Resources, 15 5: 1-12. doi:10.1017/S1479262116000083

Healey, Adam L., Lee, David J., Furtado, Agnelo, Simmons, Blake A. and Henry, Robert J. (2015) Efficient eucalypt cell wall deconstruction and conversion for sustainable lignocellulosic biofuels. Frontiers in Bioengineering and Biotechnology, 3 190.1-190.14. doi:10.3389/fbioe.2015.00190

Hoang, Nam V., Furtado, Agnelo, Botha, Frederik C., Simmons, Blake A. and Henry, Robert J. (2015) Potential for genetic improvement of sugarcane as a source of biomass for biofuels. Frontiers in Bioengineering and Biotechnology, 3 NOV: 1-15. doi:10.3389/fbioe.2015.00182

Wambugu, Peterson W., Brozynska, Marta, Furtado, Angelo, Waters, Daniel L. and Henry, Robert J. (2015) Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Scientific Reports, 5 Art No.: 13957: . doi:10.1038/srep13957

Brozynska, Marta., Furtado, Agnelo. and Henry, Robert J. (2015) Genomics of crop wild relatives: Expanding the gene pool for crop improvement. Plant Biotechnology Journal, 14 4: 1070-1085. doi:10.1111/pbi.12454

Hoang, Nam V., Furtado, Agnelo, McQualter, Richard B. and Henry, Robert J. (2015) Next Generation Sequencing of total DNA from sugarcane provides no evidence for chloroplast heteroplasmy. New Negatives in Plant Science, 1-2 33-45. doi:doi:10.1016/j.neps.2015.10.001

Furtado, A., Bundock, P. C., Banks, P. M., Fox, G., Yin, X. and Henry, R. J. (2015) A novel highly differentially expressed gene in wheat endosperm associated with bread quality. Scientific Reports, 5 10446: 1-14. doi:10.1038/srep10446

Henry, Robert J., Rangan, Parimalan and Furtado, Agnelo (2015) Developing cereals acceptable to consumers for production in new and variable climates. Procedia Environmental Sciences, 29 9-10. doi:10.1016/j.proenv.2015.07.128

Furtado, Agnelo, Lupoi, Jason S., Hoang, Nam V., Healey, Adam, Singh, Seema, Simmons, Blake A. and Henry, Robert J. (2014) Modifying plants for biofuel and biomaterial production. Plant Biotechnology Journal, 12 9: 1246-1258. doi:10.1111/pbi.12300

Brozynska, Marta, Omar, Ernnie Syafika, Furtado, Agnelo, Crayn, Darren, Simon, Bryan, Ishikawa, Ryuji and Henry, Robert James (2014) Chloroplast genome of novel rice germplasm identified in Northern Australia. Tropical Plant Biology, 7 3-4: 111-120. doi:10.1007/s12042-014-9142-8

Brozynska, Marta, Furtado, Angelo and Henry, Robert James (2014) Direct Chloroplast sequencing: Comparison of sequencing platforms and analysis tools for whole chloroplast barcoding. PLoS One, 9 10: e110387.1-e110387.10. doi:10.1371/journal.pone.0110387

Healey, Adam, Furtado, Agnelo, Cooper, Tal and Henry, Robert J. (2014) Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods, 10 1: 1-8. doi:10.1186/1746-4811-10-21

Wambugu, Peterson W., Furtado, Agnelo, Le Waters, Daniel, Nyamongo, Desterio O. and Henry, Robert J. (2013) Conservation and utilization of African Oryza genetic resources. Rice, 6 1: 29.1-29.13. doi:10.1186/1939-8433-6-29

Gillies, Susan A., Futardo, Agnelo and Henry, Robert J. (2012) Gene expression in the developing aleurone and starchy endosperm of wheat. Plant Biotechnology Journal, 10 6: 668-679. doi:10.1111/j.1467-7652.2012.00705.x

Furtado, Agnelo, Henry, Robert J. and Pellegrineschi, Alessandro (2009) Analysis of promoters in transgenic barley and wheat. Plant Biotechnology Journal, 7 3: 240-253. doi:10.1111/j.1467-7652.2008.00394.x

Furtado, Agnelo, Henry, Robert J. and Takaiwa, Fumio (2008) Comparison of promoters in transgenic rice. Plant Biotechnology Journal, 6 7: 679-693. doi:10.1111/j.1467-7652.2008.00352.x

Furtado, Agnelo and Henry, Robert James (2005) The wheat Em promoter drives reporter gene expression in embryo and aleurone tissue of transgenic barley and rice. Plant Biotechnology Journal, 3 4: 421-434. doi:10.1111/j.1467-7652.2005.00135.x

Furtado, A, Henry, R, Scott, K and Meech, S (2003) The promoter of the asi gene directs expression in the maternal tissues of the seed in transgenic barley. PLANT MOLECULAR BIOLOGY, 52 4: 787-799. doi:10.1023/A:1025097218768

Furtado, A and Henry, R (2002) Measurement of green fluorescent protein concentration in single cells by image analysis. ANALYTICAL BIOCHEMISTRY, 310 1: 84-92. doi:10.1016/S0003-2697(02)00281-6

Cooper, T., Furtado, A., Henry, R. J. and Crayn, D. (2015). Analysis of the chloroplast genome of a coffee relative from northern Australia. In: Proceedings of the IV International Symposium on Plant Genetic Resources. International Horticultural Congress, Brisbane, QLD, Australia, (177-182). 17-22 August 2014. doi:10.17660/ActaHortic.2015.1101.27

Furtado, A., Piperidus, G., Croft, B. J., Cox, M., Mcintyre, C. L., Smith, G. R. and Brumbley, S. M. (2003). Identification of molecular markers to smut resistance in sugarcane. In: IVth International Workshop on Plant Biotechnology and Sustainable Development (BioVeg) 2003, Ciego de Avila, Cuba, (). 14-19 April 2003.

Furtado, A., Piperidus, G., Croft, B. J., Cox, M., Mcintyre, C. L., Smith, G. R. and Brumbley, S. M. (2003). Identification of molecular markers to smut resistance in sugarcane. In: ISSCT Molecular Biology - Genome Analysis and Molecular Physiology, Montpellier, France, (). 7-11 April 2003.

Reyes, M., Waldron, J., Furtado, A., Klimyuk, V., Jones, J. D., Wang, J. S., Scott, K. J. and Carroll, B. J. (2000). Transposon tagging of DNA sequences for alleviating transgene silencing. In: 21st Annual Conference on the Organisation and Expression of the Genome. The Genome Conference 2000, Lorne, Victoria, Australia, (202). 13 - 17 February 2000.

Waldron, J., Reyes, M., Furtado, A., Klimyuk, V., Wang, J. S., Godwin, I. D., Scott, K. J., Jones, J. D. and Carroll, B. J. (1999). Transposon tagging of chromosomal regions responsible for alleviating transgene silencing. In: HGM'99. Human Genome Meeting, Brisbane Convention Cen., Brisbane, (83). 27th -30th March, 1999.

Carroll, B. J., Reyes, M., Waldron, J., Furtado, A., Klimyuk, V., Wang, J. S., Scott, K. J. and Jones, J. D. (1999). Transposon tagging or DNA sequences for alleviating transgene silencing. In: Combined Conference Abstracts: 43rd Annual ASBMB, 18th Annual ANZSCDB and 39th Annual ASPP. ComBio 99, Conrad Jupiters Casino, Gold Coast, (Pos-Wed-06). 27-30 September, 1999.

Dr Agnelo Furtado

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