张小蕾 Xiaolei Zhang

Xiaolei Zhang 张小蕾

I am passionate about advancing healthcare using computational and statistical approaches. I am currently a Postdoctoral Fellow based at European Bioinformatics Institute (Hinxton, UK). I am also awared as a Borysiewicz Interdisplinary Fellow (University of Cambridge) and Junior Research Fellow (Darwin College, University of Cambridge). Previously I studied Computational Biology and Bioinformatics in University of Science and Technology of China, ETH Zurich and finished my PhD in Imperial College London in the study of statistical methods for clinical genome interpretation with specific application in inherited cardiac conditions.

Publications

10.X Zhang, PI Theotokis, N Li, C Wright, KE Samocha, N Whiffin, JS Ware Genetic constraint at single amino acid resolution improves missense variant prioritisation and gene discovery medRxiv [DOI]

9. X Zhang, M Wakeling, J Ware, N Whiffin Annotating high-impact 5’untranslated region variants with the UTRannotator Bioinformatics [DOI] [UTRannotator]

8. X Zhang et al. Disease-specific variant pathogenicity prediction significantly improves clinical variant interpretation in inherited cardiac conditions. Genetics in Medicine [DOI] [CardioBoost]

7. N Whiffin, KJ Karczewski, X Zhang, S Chothani, et al. Characterising the loss-of-function impact of 5' untranslated region variants in whole genome sequence data from 15,708 individuals. Nature Communications [DOI] [Code]

6. R Yao, M Heinrich,Y Zou, E Reich, X Zhang, Y Chen, CS Weckerle. Quality Variation of Goji (Fruits of Lycium spp.) in China: A Comparative Morphological and Metabolomic Analysis. Frontiers in pharmacology [DOI]

5. N Whiffin, R Walsh, R Govind, M Edwards, M Ahmad, X Zhang et al. CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation.Genetics In Medicine [DOI]

4. X Zhang, E Minikel, A O’Donnell-Luria, D MacArthur, J Ware, B Weisburd. ClinVar Data Parsing . Wellcome Open Research [DOI][Code]

3. M Maiolo, X Zhang, M Gil, M Anisimova. Progressive multiple sequence alignment With indel evolution. BMC bioinformatics [DOI]

2. X Zhang Analysis of Bias and Reliability of Progressive Poisson Indel Process Algorithm. Master Thesis, ETH Zurich. [PDF]

1. Y Dong, X Zhang^*, M Xie, B Arefnezhad et al. Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC genomics [DOI] (* co-first author)

Projects

Here is a collection of some interesting projects I've worked on

A list of selected awesome resources to learn Machine learning for Healthcare including courses, key publications and conferences.
Reproduce HilbertCNN: An image representation based convolutional network for DNA classification.
ClinVar Data Parsing: an automatic data retreival pipeline of ClinVar database for variant interpretation study
5' UTR Annotator: an VEP plugin to annoate 5' UTR variant effect
Parsing the Massive Pfam Stockholm Alignment file