Dr Agnelo Furtado
Senior Research Fellow
Centre for Nutrition and Food Sciences
+61 7 334 60640
Book Chapters
Kuram Tirumala, Ravikiran, Subbaiyan, Gopala Krishnan, Singh, Ashok Kumar, Furtado, Agnelo and Henry, Robert James (2021). RNA-Seq to understand transcriptomes and application in improving crop quality. Comprehensive foodomics. (pp. 472-485) Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-100596-5.22728-5
Hasan, Sharmin, Furtado, Agnelo and Henry, Robert (2021). RNA Extraction From Plant Seeds. Comprehensive Foodomics. (pp. 451-461) edited by Alejandro Cifuentes. Oxford, United Kingdom: Elsevier. doi: 10.1016/b978-0-08-100596-5.22751-0
Furtado, Agnelo and Henry, Robert J. (2021). RNA extraction for transcriptome analysis. Comprehensive foodomics. (pp. 440-450) Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-100596-5.22727-3
Rangan, Parimalan, Furtado, Agnelo and Henry, Robert (2021). Wheat Grain Transcriptome. Comprehensive Foodomics. (pp. 501-512) Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-100596-5.22730-3
Rangan, Parimalan, Furtado, Agnelo, Henry, Robert and Gaikwad, Ambika (2021). Development of Transcriptome Analysis Methods. Comprehensive Foodomics. (pp. 462-471) Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-100596-5.22752-2
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. Rice Grain Quality. (pp. 201-240) edited by Nese Sreenivasulu. New York, NY, United States: Humana Press Inc.. doi: 10.1007/978-1-4939-8914-0_12
Furtado, Agnelo (2014). Cloning of DNA fragments: Ligation reactions in agarose gel. Cereal genomics: methods and protocols. (pp. 117-121) edited by Robert J. Henry and Agnelo Furtado. New York, United States: Humana Press. doi: 10.1007/978-1-62703-715-0_10
Healey, Adam, Furtado, Agnelo and Henry, Robert J. (2014). Structural genomics of eucalypts. Genetics, genomics and breeding of eucalypts. (pp. 103-120) edited by Robert Henry and Chittaranjan Kole. Boca Raton, FL, United States: CRC Press. doi: 10.1201/b17154
Henry, Robert J. and Furtado, Agnelo (2014). Preface. Cereal genomics: methods and protocols. (pp. v-v) New York, NY, United States: Humana Press.
Furtado, Agnelo (2014). DNA extraction from vegetative tissue for next-generation sequencing. Cereal genomics: methods and protocols. (pp. 1-5) edited by Robert J. Henry and Agnelo Furtado. New York, NY United States: Humana Press. doi: 10.1007/978-1-62703-715-0-1
Furtado, Agnelo (2014). RNA extraction from developing or mature wheat seeds. Cereal Genomics: Methods and Protocols. (pp. 23-28) edited by Robert J. Henry and Agnelo Furtado. New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-715-0-4
Journal Articles
Hasan, Sharmin, Huang, Lichun, Liu, Qiaoquan, Perlo, Virginie, O'Keeffe, Angela, Margarido, Gabriel Rodrigues Alves, Furtado, Agnelo and Henry, Robert J (2022). The long read transcriptome of rice (oryza sativa ssp. japonica var. Nipponbare) reveals novel transcripts. Rice, 15 (1) 29. doi: 10.1186/s12284-022-00577-1
Correr, Fernando Henrique, Furtado, Agnelo, Franco Garcia, Antonio Augusto, Henry, Robert James and Rodrigues Alves Margarido, Gabriel (2022). Allele expression biases in mixed-ploid sugarcane accessions. Scientific Reports, 12 (1) 8778, 8778. doi: 10.1038/s41598-022-12725-0
Hasan, Sharmin, Furtado, Agnelo and Henry, Robert (2022). Reticulate evolution in AA-genome wild rice in Australia. Frontiers in Plant Science, 13 767635, 767635. doi: 10.3389/fpls.2022.767635
Perlo, Virginie, Margarido, Gabriel R. A., Botha, Frederik C., Furtado, Agnelo, Hodgson-Kratky, Katrina, Correr, Fernando H. and Henry, Robert J. (2022). Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content. Theoretical and Applied Genetics, 135 (5), 1619-1636. doi: 10.1007/s00122-022-04058-3
Ananda, Galaihalage K. S., Norton, Sally L., Blomstedt, Cecilia, Furtado, Agnelo, Møller, Birger Lindberg, Gleadow, Roslyn and Henry, Robert J. (2022). Transcript profiles of wild and domesticated sorghum under water-stressed conditions and the differential impact on dhurrin metabolism. Planta, 255 (2) 51, 51. doi: 10.1007/s00425-022-03831-4
Nath, Onkar, Fletcher, Stephen J., Hayward, Alice, Shaw, Lindsay M., Agarwal, Rimjhim, Furtado, Agnelo, Henry, Robert J. and Mitter, Neena (2022). A comprehensive high-quality DNA and RNA extraction protocol for a range of cultivars and tissue types of the woody crop avocado. Plants, 11 (3) 242. doi: 10.3390/plants11030242
Cowan, Max, Møller, Birger Lindberg, Norton, Sally, Knudsen, Camilla, Crocoll, Christoph, Furtado, Agnelo, Henry, Robert, Blomstedt, Cecilia and Gleadow, Roslyn M. (2022). Cyanogenesis in the Sorghum Genus: From Genotype to Phenotype. Genes, 13 (1) 140, 1-17. doi: 10.3390/genes13010140
Mason, Patrick J., Hoang, Nam V., Botha, Frederik C., Furtado, Agnelo, Marquardt, Annelie and Henry, Robert J. (2022). Comparison of the root, leaf and internode transcriptomes in sugarcane (Saccharum spp. hybrids). Current Research in Biotechnology, 4, 167-178. doi: 10.1016/j.crbiot.2022.02.005
Rodrigues Alves Margarido, Gabriel, Correr, Fernando Henrique, Furtado, Agnelo, Botha, Frederik C. and Henry, Robert J. (2021). Limited allele-specific gene expression in highly polyploid sugarcane. Genome Research, 32 (2), 297-308. doi: 10.1101/gr.275904.121
Sharma, Priyanka, Murigneux, Valentine, Haimovitz, Jasmine, Nock, Catherine J., Tian, Wei, Kharabian Masouleh, Ardashir, Topp, Bruce, Alam, Mobashwer, Furtado, Agnelo and Henry, Robert J. (2021). The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding. Plant Direct, 5 (12) e364, e364. doi: 10.1002/pld3.364
O’Connor, Daniel J., Meder, Roger, Furtado, Angelo, Henry, Robert J., Wright, Graeme C. and Rachaputi, Rao C.N. (2021). Single kernel sorting of high and normal oleic acid peanuts using near infrared spectroscopy. Journal of Near Infrared Spectroscopy, 29 (6), 366-370. doi: 10.1177/09670335211053502
Sharma, Priyanka, Kharabian Masouleh, Ardashir, Topp, Bruce, Furtado, Agnelo and Henry, Robert J. (2021). Denovo
chromosome level assembly of a plant genome from long read sequence data. The Plant Journal, 109 (3), 727-736. doi: 10.1111/tpj.15583
Vanambathina, Prameela, Henry, Robert J., Rachaputi, Rao C. N. and Furtado, Agnelo (2021). Secondary genepool of Australian Cajanus species contains sources of resistance to Helicoverpa armigera (Hübner). Annals of Applied Biology, 180 (2), 259-272. doi: 10.1111/aab.12730
Al‐Dossary, Othman, Alsubaie, Bader, Kharabian‐Masouleh, Ardashir, Al‐Mssallem, Ibrahim, Furtado, Agnelo and Henry, Robert J (2021). The jojoba genome reveals wide divergence of the sex chromosomes in a dioecious plant. The Plant Journal, 108 (5), 1283-1294. doi: 10.1111/tpj.15509
Survase, Abhijeet, Furtado, Agnelo, Thengane, Ratnakar and Henry, Robert (2021). Identification of genes associated with chapatti quality using transcriptome analysis. Journal of Cereal Science, 101 103276, 1-11. doi: 10.1016/j.jcs.2021.103276
Ananda, Galaihalage, Norton, Sally, Blomstedt, Cecilia, Furtado, Agnelo, Møller, Birger, Gleadow, Roslyn and Henry, Robert (2021). Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes. The Plant Genome, 14 (3) e20123, e20123. doi: 10.1002/tpg2.20123
Bhatt, Vacha, Barvkar, Vitthal T., Furtado, Agnelo, Henry, Robert J. and Nadaf, Altafhusain (2021). Fragrance in Pandanus amaryllifolius Roxb. Despite the presence of a betaine aldehyde dehydrogenase 2. International Journal of Molecular Sciences, 22 (13) 6968, 1-18. doi: 10.3390/ijms22136968
Healey, Adam L., Shepherd, Mervyn, King, Graham J., Butler, Jakob B., Freeman, Jules S., Lee, David J., Potts, Brad M., Silva-Junior, Orzenil B., Baten, Abdul, Jenkins, Jerry, Shu, Shengqiang, Lovell, John T., Sreedasyam, Avinash, Grimwood, Jane, Furtado, Agnelo, Grattapaglia, Dario, Barry, Kerrie W., Hundley, Hope, Simmons, Blake A., Schmutz, Jeremy, Vaillancourt, René E. and Henry, Robert J. (2021). Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. Communications Biology, 4 (1) 537, 1-13. doi: 10.1038/s42003-021-02009-0
Hodgson-Kratky, K., Perlo, V., Furtado, A., Choudhary, H., Gladden, J. M., Simmons, B. A., Botha, F. and Henry, R. J. (2021). Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. Plant Molecular Biology, 106 (1-2), 173-192. doi: 10.1007/s11103-021-01136-w
Murigneux, Valentine, Rai, Subash Kumar, Furtado, Agnelo, Bruxner, Timothy J. C., Tian, Wei, Harliwong, Ivon, Wei, Hanmin, Yang, Bicheng, Ye, Qianyu, Anderson, Ellis, Mao, Qing, Drmanac, Radoje, Wang, Ou, Peters, Brock A, Xu, Mengyang, Wu, Pei, Topp, Bruce, Coin, Lachlan J. M. and Henry, Robert J. (2020). Comparison of long-read methods for sequencing and assembly of a plant genome. GigaScience, 9 (12) giaa146. doi: 10.1093/gigascience/giaa146
Mason, Patrick J., Furtado, Agnelo, Marquardt, Annelie, Hodgson-Kratky, Katrina, Hoang, Nam V., Botha, Frederik C., Papa, Gabriella, Mortimer, Jenny C., Simmons, Blake and Henry, Robert J. (2020). Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots. Biotechnology for Biofuels, 13 (1) 201, 1-19. doi: 10.1186/s13068-020-01837-2
Henry, Robert J., Furtado, Agnelo and Rangan, Parimalan (2020). Pathways of photosynthesis in non-leaf tissues. Biology, 9 (12) 438, 1-13. doi: 10.3390/biology9120438
Perlo, Virginie, Botha, Frederik C., Furtado, Agnelo, Hodgson‐Kratky, Katrina and Henry, Robert J. (2020). Metabolic changes in the developing sugarcane culm associated with high yield and early high sugar content. Plant Direct, 4 (11) e00276, e00276. doi: 10.1002/pld3.276
Moner, Ali Mohammad, Furtado, Agnelo and Henry, Robert J. (2020). Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production. BMC Plant Biology, 20 (1) 472, 1-9. doi: 10.1186/s12870-020-02689-6
Nock, Catherine J., Baten, Abdul, Mauleon, Ramil, Langdon, Kirsty S., Topp, Bruce, Hardner, Craig, Furtado, Agnelo, Henry, Robert J. and King, Graham J. (2020). Chromosome-scale assembly and annotation of the macadamia genome (Macadamia integrifolia HAES 741). G3: Genes, Genomes, Genetics, 10 (10), 3497-3504. doi: 10.1534/g3.120.401326
Correr, Fernando Henrique, Hosaka, Guilherme Kenichi, Barreto, Fernanda Zatti, Valadão, Isabella Barros, Balsalobre, Thiago Willian Almeida, Furtado, Agnelo, Henry, Robert James, Carneiro, Monalisa Sampaio and Margarido, Gabriel Rodrigues Alves (2020). Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning. BMC Genomics, 21 (1) 673, 673. doi: 10.1186/s12864-020-07091-y
Ananda, Galaihalage K. S., Myrans, Harry, Norton, Sally L., Gleadow, Roslyn, Furtado, Agnelo and Henry, Robert J. (2020). Wild sorghum as a promising resource for crop improvement. Frontiers in Plant Science, 11 1108, 1108. doi: 10.3389/fpls.2020.01108
Cheng, Bing, Smyth, Heather E., Furtado, Agnelo and Henry, Robert J. (2020). Slower development of lower canopy beans produces better coffee. Journal of Experimental Botany, 71 (14), 4201-4214. doi: 10.1093/jxb/eraa151
Feder, Daniel, McGeary, Ross P., Mitić, Natasa, Lonhienne, Thierry, Furtado, Agnelo, Schulz, Benjamin L., Henry, Robert J., Schmidt, Susanne, Guddat, Luke W. and Schenk, Gerhard (2020). Structural elements that modulate the substrate specificity of plant purple acid phosphatases: avenues for improved phosphorus acquisition in crops. Plant Science, 294 110445, 110445. doi: 10.1016/j.plantsci.2020.110445
Rangan, Parimalan, Furtado, Agnelo and Henry, Robert (2020). Transcriptome profiling of wheat genotypes under heat stress during grain-filling. Journal of Cereal Science, 91 102895, 102895. doi: 10.1016/j.jcs.2019.102895
Badro, Hayba, Furtado, Agnelo and Henry, Robert (2019). Relationships between Iraqi rice varieties at the nuclear and plastid genome levels. Plants, 8 (11) 481, 481. doi: 10.3390/plants8110481
Hodgson-Kratky, K., Papa, G., Rodriguez, A., Stavila, V., Simmons, B., Botha, F., Furtado, A. and Henry, R. (2019). Relationship between sugarcane culm and leaf biomass composition and saccharification efficiency. Biotechnology for Biofuels, 12 (1) 247, 247. doi: 10.1186/s13068-019-1588-3
Guyeux, Christophe, Charr, Jean-Claude, Tran, Hue T. M., Furtado, Agnelo, Henry, Robert J., Crouzillat, Dominique, Guyot, Romain and Hamon, Perla (2019). Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species. PLoS One, 14 (6) e0216347, e0216347. doi: 10.1371/journal.pone.0216347
Thirugnanasambandam, Prathima P., Mason, Patrick J., Hoang, Nam V., Furtado, Agnelo, Botha, Frederik C. and Henry, Robert J. (2019). Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane. BMC Plant Biology, 19 (1) 160, 160. doi: 10.1186/s12870-019-1733-y
Nirmal, Ravi C., Singh, Amit Kumar, Furtado, Agnelo and Henry, Robert J. (2019). Analysis of the expression of transcription factors and other genes associated with aleurone layer development in wheat endosperm. Journal of Cereal Science, 85, 62-69. doi: 10.1016/j.jcs.2018.11.010
Hoang, Nam V., Furtado, Agnelo, Perlo, Virginie, Botha, Frederik C. and Henry, Robert (2019). The impact of cDNA normalization on long-read sequencing of a complex transcriptome. Frontiers in Genetics, 10 (JUN) 654, 654. doi: 10.3389/fgene.2019.00654
Rangan, Parimalan, Furtado, Agnelo and Henry, Robert (2018). Differential response of wheat genotypes to heat stress during grain filling. Experimental Agriculture, 55 (5), 818-827. doi: 10.1017/s0014479718000406
Wright, G. C., Borgognone, M. G., Connor, D. J.O., Rachaputi, R. C.N., Henry, R. J., Furtado, A., Anglin, N. L. and Freischfresser, D. B. (2018). Breeding for improved blanchability in peanut: phenotyping, genotype × environment interaction and selection. Crop & Pasture Science, 69 (12), 1237-1250. doi: 10.1071/CP18156
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) 72. 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 (1) 11612, 11612. 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, 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, 45 (Pt B), 231-236. 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, 127, 475-487. 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, 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) 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, 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, 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) gix086, 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, 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, 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
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
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) 54. doi: 10.1007/s11295-017-1138-8
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, 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) 937, 937. 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) 1537. 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) 164746, 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 (1) 31721, 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 (NOV) 190, 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) 182, 1-15. doi: 10.3389/fbioe.2015.00182
Wambugu, Peterson W., Brozynska, Marta, Furtado, Agnelo, 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) 13957, 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: 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) 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, Agnelo and Henry, Robert James (2014). Direct Chloroplast sequencing: Comparison of sequencing platforms and analysis tools for whole chloroplast barcoding. PLoS One, 9 (10) e110387, 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) 21, 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, 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
Rice, Nicole, Cordeiro, Giovanni, Shepherd, Mervyn, Bundock, Peter, Bradbury, Louis, Pacey-Miller, Toni, Furtado, Agnelo and Henry, Robert (2006). DNA banks and their role in facilitating the application of genomics to plant germplasm. Plant Genetic Resources: Characterization and Utilization, 4 (01), 64-70. doi: 10.1079/pgr2006113
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
Waldron, Julie, Peace, Cameron P., Searle, Iain R., Furtado, Agnelo, Wade, Nick, Findlay, Ian, Graham, Michael W. and Carroll, Bernard J. (2003). Randomly Amplified DNA Fingerprinting: A culmination of DNA marker technologies based on arbitrarily-primed PCR amplification. Journal of Biomedicine and Biotechnology, 2 (3), 141-150. doi: 10.1155/S1110724302206026
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
Conference Papers
Thirugnanasambandam, Prathima Perumal, Kasirajan, Lakshmi, Furtado, Agnelo, Botha, Frikkie C. and Henry, Robert J. (2020). Control of sugar and fibre: insights from sugarcane transcriptome analyses. The Third International Tropical Agriculture Conference, Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036204
Perlo, Virginie, Furtado, Agnelo, Botha, Frikkie and Henry, Robert (2020). Analysis of differences in gene expression associated with variation in biomass composition in sugarcane. The Third International Tropical Agriculture Conference, Brisbane, QLD Australia, 13-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036164
Al-Dossary, Othman, Kharabian, Ardashir, Al-Mssallem, Ibrahim, Furtado, Agnelo and Henry, Robert (2020). Transcriptomics analysis for the detection of novel drought tolerance genes in Jojoba (Simmondsia Chinensis). The Third International Tropical Agriculture Conference TropAg 2019 , Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036135
Badro, Hayba, Ndjiondjop, Marie-Noelle, Furtado, Agnelo and Henry, Robert (2019). SNPs Linked to Key Traits in Hybrids between African and Asian Rice. The Third International Tropical Agriculture Conference TropAg 2019 , Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036025
Badro, Hayba, Furtado, Agnelo and Henry, Robert (2019). Relationships between Iraqi rice varieties at the nuclear and plastid genome levels. The Third International Tropical Agriculture Conference, Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI AG. doi: 10.3390/proceedings2019036024
Ananda, Galaihalage, Gleadow, Roslyn, Norton, Sally, Furtado, Agnelo and Henry, Robert (2019). Determination of Phylogenetic Relationships of the Genus Sorghum Using Nuclear and Chloroplast Genome Assembly. The Third International Tropical Agriculture Conference TropAg 2019 , Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036017
Hasan, Sharmin, Furtado, Agnelo and Henry, Robert (2019). Diversity of domestication loci in wild rice populations. The Third International Tropical Agriculture Conference TropAg 2019 , Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036014
Cooper, T., Furtado, A., Henry, R. J. and Crayn, D. (2015). Analysis of the chloroplast genome of a coffee relative from northern Australia. International Horticultural Congress, Brisbane, QLD, Australia, 17-22 August 2014. Leuven, Belgium: International Society for Horticultural Science. 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. ISSCT Molecular Biology - Genome Analysis and Molecular Physiology, Montpellier, France, 7-11 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. IVth International Workshop on Plant Biotechnology and Sustainable Development (BioVeg) 2003, Ciego de Avila, Cuba, 14-19 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. The Genome Conference 2000, Lorne, Victoria, Australia, 13 - 17 February 2000. Australia: Lorne Genome Conference.
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. Human Genome Meeting, Brisbane Convention Cen., Brisbane, 27th -30th March, 1999. Nature Publishing Co.: Nature Genetics.
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. ComBio 99, Conrad Jupiters Casino, Gold Coast, 27-30 September, 1999. Kent Town, SA: Aust. Society for Biochemistry & Molecular Biology ..
Data Collection
Furtado Agnelo (2016). Plant Genomics Sequence Data archive.. The University of Queensland. (Dataset) doi: 10.48610/a97b567