Dr Ying Sims

Senior Bioinformatician at the Sanger Institute

 
Ying Sims is an experienced bioinformatician who has contributed to three major Sanger endeavours over a period of 14 years. This includes most recently the Darwin Tree of Life, and previously UK10k and Sanger Informatics Core Services.  She is interested in the development of methods and tools, leveraging multimodal datasets to create SOTA solutions for a diverse set of biological questions

Ying Sims, Ph.D.

Senior Bioinformatician

About My research and technical interests encompass cloud orchestration, machine learning applications in genomics (including LLM integration and Agentic Programming), and automated workflows for genome assembly and curation.

I am currently a member of the Darwin Tree of Life Project, whose goals are to create a reference genome for all species on the British Isles. My current interests and focus is on the research, design, and implementation of advanced technologies and methodology for high-throughput genome assembly, evaluation, and curation.

This includes integration of multi-platform long-read sequencing technologies (PacBio, Oxford Nanopore, Bionano Genomics) with Illumina Hi-C data to construct and evaluate novel, never before seen,  reference quality genomes across a vast array of eukaryotic species.  This includes the development of a genome evaluation platform called TreeVal, a community leading standard being used by data curation teams all around the world.  Future focus includes the use and development of large bioAI models for expanding on understanding the complex structural genomic features that current technology can not resolve (eg genomic repeats and motifs).

Previously at Sanger I was also involved with analysing functional genomic datasets as part of population and statistical genomics projects as part of UK10K.

Beyond Sanger I have been involved in numerous community opportunities to demonstrate my scientific and technical leadership such as involvement in the Google Summer of Code (GSoC).

Timeline & Background

  • 2019 – Present: Senior Bioinformatician, Tree of Life Assembly Team, Wellcome Sanger Institute
  • 2018 – 2019: Senior Bioinformatician, Genome Reference Informatics, Wellcome Sanger Institute
  • Prior Roles: Senior Bioinformatician across Sanger Institute & University of Cambridge (Supporting UK10K, BloodPharma, and Blueprint projects; Sanger Sequencing Informatics team)
  • Earlier Career: Platform Systems Engineer, Skyscanner Early Development Team
  • PhD: University of Cambridge (Focus: Natural Language Processing & Biological Text Mining for Small-Molecule Bioactivity Information)
 

My publications

Loading publications...