Dr Ramil Mauleon

Ramil Mauleon


Senior Research Fellow

t: +61 2 6620 3932 
e: ramil.mauleon@scu.edu.au


Google Scholar: https://scholar.google.com/citations?user=crWy8lUAAAAJ

Research Gate:  https://www.researchgate.net/profile/Ramil_Mauleon




PhD in Genetics, with cognates in Computer Science and Molecular Biology & Biotechnology (University of the Philippines Los Baños, Philippines)
MSc in Genetics with cognate in Microbiology (University of the Philippines Los Baños, Philippines)
BSc in Biology, specializing in Genetics (University of the Philippines Los Baños, Philippines) 

Research interests/background

My bioinformatics research interests include adoption, creation, and implementation of integrative analyses methods for high-density omics-type (transcriptomics, genomics, metabolomics) and genetic data in crop plants leading to candidate gene discovery and marker development for breeding applications. On the computing technology side, my interests are in the development and implementation of re-usable analysis software workflows for high throughput datasets with high computational resource demand, and exploring/ implementing technologies for embedding into data and information systems (biological databases, web applications) to be FAIR (Findable, Accessible, interoperable, Reusable) compliant with focus on data systems infrastructure creation, ontologies/controlled vocabulary development, and Application Programming Interface high-level design. I am also interested in exploring digital methodologies for phenotype measurements such as computer vision and machine learning, with the aim of establishing a low-cost phenotyping platform for Southern Cross Plant Science focus crops.

Before I joined SCPS, I was a bioinformatics scientist at the International Rice Research Institute engaging in institute-specific and global projects. I was a core scientific team member of the 3,000 Rice Genomes Project, characterizing the genomic diversity and population structure of the largest, sequenced representative collection of a crop species to date, and am the co-first author of the main publication for the project (Wang, Mauleon, Chebotarov, et al, Nature 2018). I have also coordinated the development of the bioinformatic components of international projects for genotype data management and breeding analyses (International Rice Informatics Consortium, Genomic Open-source Breeding Informatics Initiative, Excellence in Breeding – Galaxy, Rice Galaxy) and continue to actively engage in global initiatives for the development of data and interoperability standards for agricultural data (Crop Ontology, Rice Data Interoperability Working Group).

Recent Publications

Refereed Journal Articles

  • Fuentes, RR ,D Chebotarov, J Duitama, S Smith, JF De la Hoz, M Mohiyuddin, RA. Wing, KL. McNally, T Tatarinova, A Grigoriev, R Mauleon, and N Alexandrov. (2019). Structural variants in 3000 rice genomes. Genome Research 29 (1–11).doi:10.1101/gr.241240.118.
  • Juanillas, VM., A. Dereeper, … Mauleon (2019). Rice Galaxy: an open resource for plant science. Gigascience 8(5). doi:10.1093/gigascience/giz028.
  • Tonnessen, BW, AM Bossa-Castro, R Mauleon, N Alexandrov, J Leach (2019). Shared cis-regulatory architecture identified across defence response genes is associated with broad-spectrum quantitative resistance in rice. Scientific reports. 9(1536). Doi:10.1038/s41598-018-38195-x
  • Zaw, H., C Raghavan, A Pocsedio, B. P. M Swamy, ML Jubay, RK Singh, J Bonifacio, R Mauleon, JE. Hernandez, MS. Mendioro, GB. Gregorio & H Leung (2019). Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population. Sci Rep 9 (19605). doi:10.1038/s41598-019-55357-7.
  • Karim, S., RR McNally, AS Nasaruddin, A DeReeper, R Mauleon, AO Charkowski, JE Leach, A Ben-Hur, LR Triplett (2019). Development of automated primer design workflow Uniqprimer and diagnostic primers for the broad host range plant pathogen Dickeya dianthicola. Plant Disease. Doi: 10.1094/PDIS-10-18-1819-RE.
  • Roman-reyna, V, Pinili, D, Borja, FN, Quibod, I. …, Mauleon, R and Oliva, R (2019). The Rice Leaf Microbiome Has a Conserved Community Structure Controlled by Complex Host-Microbe Interactions (May 4, 2019). CELL-HOST-MICROBE-D-19-00340. Doi: 10.2139/ssrn.3382544
  • Scheben, A., CKK Chan, L Mansueto, R Mauleon, P Larmande, …, D. Edwards. (2018). Progress in single-access information systems for wheat and rice crop improvement. Briefings in bioinformatics 20(2). doi:10.1093/bib/bby016 .
  • Wang W., R Mauleon, Z Hu, D Chebotarov, S Tai, Z Wu, M Li, T Zheng, ... H. Leung. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557 (43–49), doi:10.1038/s41586-018-0063-9.
  • Stein, JC., Y Yu, D Copetti, DJ Zwickl, …, Mauleon, ... R. Wing. (2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics 50(285–296), doi:10.1038/s41588-018-0040-0.
  • Descalsota GIL, Swamy BPM, Zaw H, Inabangan-Asilo MA, Amparado A, Mauleon R, Chadha-Mohanty P, Arocena EC, Raghavan C, Leung H, Hernandez JE, Lalusin AB, Mendioro MS, Diaz MGQ and Reinke R (2018) Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification. Front. Plant Sci. 9:1347. doi: 10.3389/fpls.2018.01347
  • Xiao G, FN Borja, R Mauleon, J Padilla, MJ Telebanco-Yanoria, J Yang, G. Lu, M Dionisio-Sese, B Zhou. (2017). Identification of resistant germplasm containing novel resistance genes at or tightly linked to the Pi2/9 locus conferring broad-spectrum resistance against rice blast. Rice 10 (1), 37
  • Swamy BPM, NAA Shamsudin, SNA Rahman, R Mauleon, W Ratnam, MT Sta Cruz, A Kumar. (2017). Association mapping of yield and yield-related traits under reproductive stage drought stress in rice (Oryza sativa). Rice 10 (1), 21
  • Thomson MJ, N Singh, MS Dwiyanti, DR Wang, MH Wright, FA Perez, G DeClerck, JH Chin, GA Malitic-Layaoen, VM Juanillas, CJ Dilla-Ermita, R Mauleon, T Kretzschmar, SR McCouch. (2017). Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications. Rice 10 (1), 40
  • Raghavan C, R Mauleon, V Lacorte, M Jubay, H Zaw, J Bonifacio, RK Singh, BE Huang, H Leung. (2017). Approaches in characterizing genetic structure and mapping in a rice multiparental population. G3: Genes, Genomes, Genetics 7 (6), 1721-1730
  • Mansueto L, RR Fuentes, FN Borja, J Detras, JM Abriol-Santos, D Chebotarov, M Sanciangco, K Palis, D Copetti, A Poliakov, I Dubchak, V Solovyev, RA Wing, R Sackville Hamilton, R Mauleon, KL McNally, N Alexandrov. 2017. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic acids research 45 (D1), D1075-D1081
  • Mansueto, L, Fuentes ,RR, Chebotarov, D , Borja , FN, Detras , J, Abriol-Santos, JM , Palis, K, Poliakov , A, Dubchak , I, Solovyev ,V, Sackville Hamilton, R , McNally , KL., Alexandrov, N, Mauleon , R (2016). SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa. Current Plant Biology, Vol 7–8, Pages 16-25, doi: 10.1016/j.cpb.2016.12.003.
  • Kim, SR, J Ramos, M Ashikari, PS. Virk, EA. Torres, E Nissila, SL Hechanova, R Mauleon and KK. Jena (2016). Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa Rice 9:12 DOI: 10.1186/s12284-016-0084-7.
  • Ereful, NC, Liu, LY, Tsai, E, Kao, SM, Dixit, S, Mauleon, R, Malabanan, K, Thomson, M, Laurena, A, Lee, D & others (2016). Analysis of allelic imbalance in rice hybrids under water stress and association of asymmetrically expressed genes with drought-response QTLs. Rice, 9, 50.