Opening

Ph.D. students, Research Assistant (RA), and Postdoc or senior RA openings

Group: Dr. Yanni Sun, Electrical Engineering at City University of Hong Kong

When the human genome was sequenced more than a decade ago, people thought that we obtained the language of life. However, it turns out that this is not a language we understand! Our research goal is to apply computational models/methods to decypher the language of life. The methods/tools we use include: advanced data structures, general algorithm design, machine learning methods, applied deep learning, data mining techniques, graph theories etc. You will be trained to handle BIG genomic data and solve high-impact research problems. The training will provide you with ample career opportunities.

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Research area and projects:

• Bioinformatics: sequence analysis, plant genome annotation
• Deep learning-based virus composition analysis, virus host prediction, and virus classification.
• Metagenomic analysis: strain-level composition
• Viral haplotype reconstruction using third-generation sequencing (TGS) reads
• Accurate virus genome assembly using nanopore reads

We have on-going research projects on RNA viruses, phages, bacterial strain analysis in metagenomic data, plant genomics, etc. You can refer to the following publications for further details.

• Dehan Cai and Yanni Sun, “Reconstructing viral haplotypes using long reads”, Bioinformatics, 2022
• Xubo Tang, Jiayu Shang, and Yanni Sun, “RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data”, Briefings in Bioinformatics, 2022.
• Herui Liao, Dehan Cai, and Yanni Sun, “VirStrain : a strain identification tool for RNA viruses.”, Genome Biology, 2022. (the link of preprint: https://www.biorxiv.org/content/10.1101/2020.12.21.423722v2.full)
• Yang Li, Ning Jiang, and Yanni Sun, “AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes”, Plant Physiology, 2021.
• Jiayu Shang, Jingzhe Jiang, and Yanni Sun, “Bacteriophage classification for assembled contigs using graph convolutional network”, Bioinformatics (ISMB/ECCB 2021 Proceedings), 2021.
• Jiayu Shang, and Yanni Sun, “Predicting the hosts of prokaryotic viruses using GCN-based semi-supervised learning”, BMC Biology, 2021.

The methods/tools we use include: general algorithm design, machine learning methods, applied deep learning, data mining techniques, graph theories etc. You will be trained to handle BIG genomic data and solve high-impact research problems.

My expectations:

• You should have training from Computer Science, Data Science, Electronic Engineering, BME, Bioinformatics, Statistics, or related fields
• You need to be familiar with some programming languages/data processing pipelines. I also welcome applicants with research experiences in microbiology even though you have limited experiences in programming
• You should be highly motivated to study research problems you are interested in. I am happy to provide you with the freedom of choosing appropriate research topics.
• If you have any questions, feel free to drop me a message (yannisun@cityu.edu.hk).