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 highthroughput sequencing test for the diagnosis of inherited bleeding, thrombotic and platelet disorders.
Blood http://dx.doi.org/10.1182/blood201512688267 (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

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

Cell cycle RNA regulons coordinating early lymphocyte development.

Galloway A, Turner M

Wiley interdisciplinary reviews. RNA
1757-7012: (2017)

PMID: 28231639

RNA-binding proteins mind the GAPs.

Turner M, Monzón-Casanova E

Nature immunology
18 1529-2916:146-148 (2017)

PMID: 28102216

The RNA-binding protein TTP is a global post-transcriptional regulator of feedback control in inflammation.

Tiedje C, Diaz-Muñoz MD, Trulley P

Nucleic acids research
1362-4962: (2016)

PMID: 27220464

RNA-binding proteins ZFP36L1 and ZFP36L2 promote cell quiescence.

Galloway A, Saveliev A, Łukasiak S

Science (New York, N.Y.)
352 1095-9203:453-9 (2016)

PMID: 27102483

MicroRNA-155 controls affinity-based selection by protecting c-MYC+ B cells from apoptosis.

Nakagawa R, Leyland R, Meyer-Hermann M

The Journal of clinical investigation
1558-8238: (2015)

PMID: 26657861

GIMAP1 Is Essential for the Survival of Naive and Activated B Cells In Vivo.

Webb LM, Datta P, Bell SE

Journal of immunology (Baltimore, Md. : 1950)
1550-6606: (2015)

PMID: 26621859

Generation of functionally distinct isoforms of PTBP3 by alternative splicing and translation initiation.

Tan LY, Whitfield P, Llorian M

Nucleic acids research
1362-4962: (2015)

PMID: 25940628