Edinburgh Research Explorer

Dr Le Yu

(Former employee or visitor)

Willingness to take Ph.D. students: Yes

Education/Academic qualification

Doctor of Engineering, Strathclyde University
Inference of Genetic Regulatory Networks Using Systems Biology and Bioinformatics approach

Area of Expertise

Research expertise• Proficient in RNASeq, miRNASeq, SNP, MeDIPSeq and BisulfiteSeq data analysis for chicken, sheep, duck and quail etc., • Brilliant computer programming and soft development capability in Perl, Unix, R/Bioconductor, C/C++, Matlab, SQL and Python environment., • Comprehensive knowledge of mathematical modelling, machine learning and pattern recognition approaches in the application of different types of biological data such as NGS and Microarray data., • Familiar with bioinformatics databases, resources and tools such as GWAS, Ensembl etc.

Biography

  • Highly professional and self-motivated individual working with Next Generation Sequencing (NGS) data ; Profound and comprehensive understanding of genomics, genome-wide genetics, pathway and network methods and their application to drug discovery and development;
  • Over 9 years research experience in bioinformatics and functional genomics, particularly in analysing complex biological systems and diseases; Experience in a large variety of whole genome analysis techniques, bioinformatics database, resources and tools for different species; Outstanding analytical and problem solving skills of handling omics data; Brilliant computer programming and software developing skills;
  • Working effectively in multidisciplinary teams with strong communication skill and excellent interpersonal skills; Scientific liaison and managing experience of a series of collaborating research projects; Establishing and maintaining strategic partnership with academic collaborators;
  • Over 20 peer-reviewed scientific publication/software patent and a number of awards since 2005.

Current Research Interests

  • Proficient in RNASeq, miRNASeq, SNP, MeDIPSeq and BisulfiteSeq data analysis for chicken, sheep, duck and quail etc.
  • Brilliant computer programming and soft development capability in Perl, Unix, R/Bioconductor, C/C++, Matlab, SQL and Python environment.
  • Comprehensive knowledge of mathematical modelling, machine learning and pattern recognition approaches in the application of different types of biological data such as NGS and Microarray data.
  • Familiar with bioinformatics databases, resources and tools such as GWAS, Ensembl etc.

My research in a nutshell

2009 -     Genomics and Genomis Division, Roslin Institute, University of Edinburgh

                           Research Fellow, SULSA LEADERS award, Part-time Lecturer

Working in a world leading genomics research group as a named researcher in a successful BBSRC grant to fund epigenetics study of seasonal regulation of gene expression in the sheep brain.

Major Project: BBSRC Pars Tuberalis (PT) project - The purpose of this project is to define dynamic seasonal changes in the methylome, and underlying transcriptional circuits of the PT, also define photoperiodic plasticity of primary cell types, including the vasculature.

Duties:

  • Design integrated genomics approaches for analysis of a broad range of genome data (RNASeq, miRNASeq, RRBS and MeDIPSeq etc.). The pipelines include quality control, alignment, assembly, clustering, statistical analysis, functional analysis, pathway analysis and alternative-splicing transcripts analysis etc.. The approaches are mainly conducted by paralleling computing in Linux systems;
  • Apply bioinformatics and functional genomics skill to develop a novel methodology for multiple samples of MeDIPSeq data to detect differential methylated regions (DMRs) from noisy data;
  • Conduct detailed analysis and visualisation for some key genes related to epigenetic remodelling;
  • Design a pipeline to annotate over 20K sheep genes using homo sapiens / Bos taurus as models;
  • Use Matlab to generate a new package for gene clustering and infected sample detection;
  • Manage both MySQL and Access databases;
  • Write up papers and present results at a series of conferences/meetings;
  • Liaise with project collaborators from external research organisations;
  • Supervise/teach/train PhD/MSc students.

 

2008 - 2009       Department of Electronic and Electrical Engineering, University of Strathclyde Postdocal Research assistant

Functional genomics and Systems biology approaches on time-course Microarray data analysis 

Duties: Model developing and validation            

Collaborative Activity

8 involved projects outwith major projects

  • Development of a high density 600K SNP genotyping array for chicken;
  • A comparison of immune responses to avian influenza infection in ducks and chickens;
  • Gene expression analysis of chicken macrophage using RNASeq;
  • CASI (cell autonomous sex identity) and development of the sexual phenotype in birds;
  • Functional genomic analysis of spleen tissues infected by IBDV;
  • SNP detection in the chicken Naked Neck mutant;
  • The evolution of avian CSF1, IL34 and CSF1 receptor genes: a functional and structural-based analysis;
  • Endogenous Retrovirus EAV-HP Linked to Blue Egg Phenotype in Mapuche Fowl.

Duties:

  • NGS re-sequencing data alignment and data analysis using BWA, samtools and picard etc.;
  • Genome assembly for specific regions using Soapdenovo, Abyss, Velvet, Mosaik etc.;
  • RNASeq alignment, annotation and statistical analysis using Tophat, edgeR, Cufflink etc..

Visiting and Research Positions

2006 - 2008       Visiting Scholar   Division of Pathway Medicine, University of Edinburgh

                   Research Topic: Modelling of Macrophage Gene Expression in the Interferon Pathway                                                   

Visiting and Research Positions

2006                   Visiting Scholar   Genomic Signal Processing Laboratory, the Department of Electrical and Computer Science, Texas A&M University, U.S.

                   Research Topic: Computational and mathematical modelling genetic regulatory network of triggering genes in Melanoma skin cancer (Part of National Human Genome Project)

Teaching

Introduction to Bioinformatics (MSc Animal Biosciences)

Research Groups

Roslin comparative genomics

Our group is one of the key teams active in the analysis of the chicken and sheep genomes. We are also involved in the evolutionary analysis of other avian species and seasonal timing in vertebrates using comparative genomics and bioinformatics.

We have particular expertise in using bioinformatics / Biomathematics for analysis of high-throughput Next Generation Sequencing data, data mining, phylogenomics, genome comparisons and gene annotation. It includes sequence alignment, gene expression analysis (RNASeq and miRNASeq), genetic variation and gene function (SNP and CNV), DNA methylation (MeDIP-seq) and genome annotation.

Group Leader: Professor David W. Burt

 

Research students

Graduated student:  Edward Leslie (MSc)

Administrative Roles

Supervisor of MSc students

ID: 7023