My name is Amin Mohamed and I am currently a research scientist at CSIRO, Australia working on genomics (includes transcriptomics, methylomics, epigenomics) of many aquaculture marine organisms. I apply systems biology to integrate multi-omics data to understand industry-related traits in aquaculture species. During the period July 2016/2019, I conducted postdoctoral research as an OCE postdoc fellow at CSIRO with Dr James Kijas to work in the area of Atlantic salmon genomics. I used NGS technologies to integrate multiple omics data types towards mechanistic understanding of onset of puberty ' sexual maturation" in salmon with a view to provide solutions to the salmon industry. The project involved experimental photoperiod manipulation of salmon to induce puberty, followed by collection of different omics data types to profile transcriptomes, methylomes and accessible chromatin in selected tissues. Gene regulatory networks were utilised to integrate results from these multi-omic analyses towards identification of key genes and their epigenetic regulators during the onset of puberty.
I completed a PhD degree at the coral genomics lab (Miller's lab), the ARC CoE for coral reef studies of James Cook University in 2016. My PhD projects explored molecular interactions between coral host and the symbiotic algae Symbiodinium and the newly-discovered Chromera. I am really passionate about nature and love to constantly learn new things from different disciplines to unfold some of the secrets of the marine organisms.
In my research I use genomics techniques (that involves next-gen sequencing) and bioinformatics to study responses of different marine organisms at the genome, transcriptome and epigenome levels.
I am currently involved in many interesting research projects that will lead to novel ideas in different topics including: establishment of coral-algal symbioses, molecular basis of symbiotic life-style in coral symbionts, Chromera comparative transcriptomics, biology of salmon sexual maturation and resistance against diseases including Amoebic gill disease (AGD), genome functional annotation, nutri(epi)genomics.
For more information about my work, please have a look at the Research page.
- Excited to accept postdoc position at both GEOMAR and University of Kiel to work on comparative genomics of marine invertebrates (cnidarians, Ctenophores, sponges) to understand host-microbe interactions using different omics applications in genome, transcriptome assembly and annotation along with population genomics to scan for genome wide signature of selection. More than excited!
- Polarella genomes published at BMC Biology, collaboration with Dr Cheong Chan at IMB, UQ
- Chromera comparative transcriptomics paper published at Environmental Microbiology Reports
- Last week I gave a talk to a group of microbiologists in Brisbane "BrisJams" about my PhD studies entitled "Searching for genes regulating coral-algal symbioses" 12th Feb 2020 at the VIC hotel, Brisbane city.
- Dual transcriptomics of host and symbiont during establishment of coral-algal symbiosis accepted for oral talk at the 14th International Coral Reef Symposium (ICRS 2020), which will take place in Bremen, Germany, 5-10 July 2020
- Genome-wide chromatin accessibility and transcriptome profiling during onset of maturation in Atlantic salmon accepted for oral talk at the 6th International Conference of Quantitative Genetics (ICQG6) 2020 which will take place in Brsibane, Australia June 2020
- DNA methylation and transcriptomic changes involved in Atlantic Salmon sexual maturation accepted at PAG 2020 Plant and Animal Genome Conference, San Diego, USA
- New preprint is finally out, investigating Chromera diversity and comparative transcriptomics with Symbiodiniaceae. https://www.biorxiv.org/content/10.1101/825992v1.abstract
- New preprint is now out! Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels on BioRxiv!
- New funds for functional genomics for many aquaculture species at CSIRO!
- Dual transcriptomics of host and symbiont during establishment of coral-algal symbiosis, an abstract submitted for an oral talk at ICRS2020 in Germany!
- Genome-wide chromatin accessibility and transcriptome profiling during onset of maturation in Atlantic salmon, an abstract submitted for an oral talk at ICQG6 conference in Brisbane July 2020!
- DNA methylation and transcriptomic changes involved in Atlantic salmon sexual maturation, an abstract submitted for an oral talk at PAG Plant and Animal Genome conference 2020 in San Diego, USA!
- New paper on Chromera transcriptomics coming very soon. A de novo assembled transcriptome for Chromera isolated from the GBR and comparative transcriptomics and phylogenomics with the reference strain and members of the Symbiodiniaceae!
- New preprint is out! From collab with TeamCX at IMB, UQ Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium
- Excited to start a new life within CSIRO as a marine genomicist working on genomics of many aquaculture species from 1st August 2019!
- On 31th July 2019, I completed my OCE postdoctoral fellowship “Biology of salmon sexual maturation” at CSIRO, Brisbane
- I attended the 37th ISAG conference in Lleida , Spain 7-12th July2019. Presented 15 min oral talk and a poster from my current project at CSIRO on using integrated multiomics to study salmon sexual maturation
- New preprint now avail @BioRxiv, nice collab with CX team @UQ on Adaptation to cold in a dinoflagellate "Polarella" through tandem duplication of single-exon genes, Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates
- Two papers currently under review at the ISMEJ and Frontiers in Microbiology journals about symbiont gene expression changes during symbiosis and Chromera comparative transcriptomics!
- First preprint now avail @BioRxiv from my work at the miller’s lab, JCU transctiptomic insights of establishment of coral-algal symbioses from the symbiont perspective.
- What genes make Atlantic salmon in Tasmania enter puberty? Story behind the paper describing 2 GWAS results of sex maturation in Tasmanian salmon
- New work has been published @BMCgenomics. The paper is entitled "Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon"
- My first book chapter “Current Knowledge of Coral Diseases Within the Red Sea" has been published in "Oceanographic and Biological Aspects of the Red Sea" by Springer
- Attended the 7th ISAFG conference and FAANG workshop around animal functional genome annotation in 12th November 2018 in Adelaide, South Australia
- New work just published “Salmon multi-tissue transcriptome profiling” in Frontiers in Genetics. Links to the transcriptome data and summary on the CSIRO Aquaculture website
- Has been awarded 2018 award for excellence in scientific publishing (15K EGP) from Benha University for my paper published at the ISMEJ "Deciphering the nature of the coral-Chromera association"
- Two new projects have been approved: Salmon Regulatome (40K AUD) and AGD Transcriptomics (30K AUD)
- Media release @CoralCoE "Nature of coral-Chromera interaction revealed: photosynthetic symbionts are not always beneficial to corals"
- New paper out at Nature's ISME Journal "Deciphering the nature of the coral-Chromera association"
- Has been awarded 2016 Virginia Chadwick Award from @CoralCoE for the Molecular Ecology paper on the transcriptomic response of the coral during competent Symbiodinium uptake
- PhD degree has been awarded in 27th Feb 2017. Link to the PhD thesis "Transcriptomics of coral-algal interactions:novel insights into the establishment of symbiosis" at ResearchOnline@JCU
- Started postdoctoral fellowship at CSIRO, Brisbane to work on Aquaculture Genomics, August 2016
- Media Release: OIST Preparing for a New Relationship: Coral and Algae Interactions Explored
- Media Release: CGC at JCU Next-gen sequencing detects corals response to symbiosis
- Coral transcriptomic responses to symbiont uptake out at Molecular Ecology. Links to paper and data