Life Sciences Research for Lifelong Health

Fengyuan Hu

I am a PhD candidate in the Turner lab. We are interested in searching for novel small open reading frames (smORFs) and smORFencoded bioactive polypeptides in the immune system. We are building a computational pipeline to detect smORFs using NGS technology (e.g. ribosome profiling and RNAseq).

Previously I worked as a bioinformatics developer in the Micklem lab (http://www.micklemlab.org) in the Department of Genetics Cambridge, and was involved in InterMine (http://intermine.org/) project and modENCODE (http://www.modencode.org/) project.

fterwards, I moved to the Ouwehand lab in the Platelet Biology Group, Department of Haematology Cambridge as a bioinformatician. I was involved in Genomics England 100,000 Genomes Project for which we developed a NGS pipeline to process whole genome sequncing data and ThromboGenomics project as the main bioinformatics analyst.

I am interested in bioinformatics and statistical learning. I hold a MSc in Machine Learning and Bioinformatics from the University of Edinburgh.

Key Publications

1. Simeoni, Ilenia, Jonathan C. Stephens, Fengyuan Hu , Sri V. V. Deevi, Karyn Megy et al
A comprehensive high throughput sequencing test for the diagnosis of inherited bleeding, thrombotic and platelet disorders.
Blood 10.1182/blood-2015-12-688267 (2016)

2. Jänes, Jürgen*, Fengyuan Hu *, Alexandra Lewin, and Ernest Turro.
A comparative study of RNAseq analysis strategies.
Briefings in bioinformatics 16, no. 6 (2015): 932940.

3. Kalderimis, Alex, Rachel Lyne, Daniela Butano, Sergio Contrino, Mike Lyne, Joshua Heimbach, Fengyuan Hu et al
InterMine: extensive web services for modern biology.
Nucleic acids research (2014): gku301.

4. Lyne, Mike, Richard N. Smith, Rachel Lyne, Jelena Aleksic, Fengyuan Hu , Alex Kalderimis, Radek Stepan, and Gos Micklem.
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.
Database 2013 (2013): bat060.

5. Smith, Richard N., Jelena Aleksic, Daniela Butano, Adrian Carr, Sergio Contrino, Fengyuan Hu , Mike Lyne et al
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.
Bioinformatics 28, no. 23 (2012): 31633165.

6. Nikerel, Emrah, Jan Berkhout, Fengyuan Hu , Bas Teusink, Marcel JT Reinders, and Dick De Ridder.
Understanding regulation of metabolism through feasibility analysis.
PLoS ONE 7, no. 7 (2012): e39396.

7. Contrino, Sergio, Richard N. Smith, Daniela Butano, Adrian Carr, Fengyuan Hu , Rachel Lyne, Kim Rutherford et al
modMine: flexible access to modENCODE data.
Nucleic acids research 40, no. D1 (2012): D1082D1088.

Latest Publications

The RNA-binding proteins Zfp36l1 and Zfp36l2 act redundantly in myogenesis.

Bye-A-Jee H, Pugazhendhi D, Woodhouse S

Skeletal muscle
8 2044-5040:37 (2018)

PMID: 30526691

Translational repression of pre-formed cytokine-encoding mRNA prevents chronic activation of memory T cells.

Salerno F, Engels S, van den Biggelaar M

Nature immunology
1529-2916: (2018)

PMID: 29988089

Antigen phagocytosis by B cells is required for a potent humoral response.

Martínez-Riaño A, Bovolenta ER, Mendoza P

EMBO reports
1469-3178: (2018)

PMID: 29987136

Uncovering the Role of RNA-Binding Proteins in Gene Expression in the Immune System.

Díaz-Muñoz MD, Turner M

Frontiers in immunology
9 1664-3224:1094 (2018)

PMID: 29875770

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.

Nicolas A, Kenna KP, Renton AE

Neuron
97 1097-4199:1268-1283.e6 (2018)

PMID: 29566793

The RNA-binding protein PTBP1 is necessary for B cell selection in germinal centers.

Monzón-Casanova E, Screen M, Díaz-Muñoz MD

Nature immunology
1529-2916: (2018)

PMID: 29358707

RNA-binding proteins control gene expression and cell fate in the immune system.

Turner M, Díaz-Muñoz MD

Nature immunology
1529-2916: (2018)

PMID: 29348497

Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells.

Díaz-Muñoz MD, Kiselev VY, Novère NL

Nature communications
8 2041-1723:530 (2017)

PMID: 28904350

RNA-binding protein ZFP36L1 maintains posttranscriptional regulation of bile acid metabolism.

Tarling EJ, Clifford BL, Cheng J

The Journal of clinical investigation
1558-8238: (2017)

PMID: 28891815

Characterization of the B Cell Transcriptome Bound by RNA-Binding Proteins with iCLIP.

Díaz-Muñoz MD, Monzón-Casanova E, Turner M

Methods in molecular biology (Clifton, N.J.)
1623 1940-6029:159-179 (2017)

PMID: 28589356

Maintenance of the marginal-zone B cell compartment specifically requires the RNA-binding protein ZFP36L1.

Newman R, Ahlfors H, Saveliev A

Nature immunology
1529-2916: (2017)

PMID: 28394372