Chenfu's personal page

About Me

My name is Chenfu and I am a PostDoctoral Researchers currently working at the University of Manchester. I am currently working in Gisela Orozco’s lab in the Centre for Genetics and Genomics Versus Arthritis.

My work involves analysing large scale biological datasets to improve our understanding of complex autoimmune diseases. I focus on developing pipelines and software to process data and I have particular interest in using neural networks in practical applications.

I did my undergraduate degree at the University of Trento (Italy) in Biomolecular Sciences and Technologies.

In my free time I enjoy building and flying planes and drones (possibly 3d printed).

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Current research

In the last decade genetic studies (e.g. GWAS) have linked a large number of variants to complex diseases such as Psoriatic Arthritis. These variants, however, do not usually affect the coding sequence of proteins but rather non-coding regulatory regions often with unknown targets.

In my project I work as a Bioinformatician integrating functional genomics data such as RNA-seq, ChIP-seq and chromatin conformation to direct the search of target genes that are potentially influenced by disease associated variants.

In my work I have also developed pipelines and software when necessary to process, analyse and integrate the available datasets.
Recently, I have developed an interest in using Deep Learning techniques to improve the analysis of chromatin conformation maps. These maps have many features that are visible to the human eye but really difficult to describe in the form of a statistical test.

Some of my work is available on GitHub

Publications

HiChIP-Peaks: A HiChIP peak calling algorithm
Chenfu Shi, Magnus Rattray, Gisela Orozco
Bioinformatics, Volume 36, Issue 12, 15 June 2020, Pages 3625–3631; DOI: https://doi.org/10.1093/bioinformatics/btaa202

Using functional genomics to advance the understanding of psoriatic arthritis
Chenfu Shi, Magnus Rattray, Anne Barton, John Bowes, Gisela Orozco
Rheumatology, keaa283, 10 August 2020; DOI: https://doi.org/10.1093/rheumatology/keaa283

Chromatin looping links target genes with genetic risk loci for dermatological traits
Chenfu Shi, Helen Ray-Jones, James Ding, Kate Duffus, Yao Fu, Vasanthi Priyadarshini Gaddi, Oliver Gough, Jenny Hankinson, Paul Martin, Amanda Mcgovern, Annie Yarwood, Patrick Gaffney, Steve Eyre, Magnus Rattray, Richard Warren, Gisela Orozco
Journal of Investigative Dermatology 2021; DOI: https://doi.org/10.1016/j.jid.2021.01.015

Functional genomics in primary T cells and monocytes identifies mechanisms by which genetic susceptibility loci influence systemic sclerosis risk David González-Serna, Chenfu Shi, Martin Kerick, Jenny Hankinson, James Ding, Amanda McGovern, Mauro Tutino, Norberto Ortego-Centeno, José Luis Callejas, Javier Martin & Gisela Orozco medRxiv 2022.05.08.22274711; DOI: https://doi.org/10.1101/2022.05.08.22274711

Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability Xiangyu Ge, Mojca Frank-Bertoncelj, Kerstin Klein, Amanda McGovern, Tadeja Kuret, Miranda Houtman, Blaž Burja, Raphael Micheroli, Chenfu Shi, Miriam Marks, Andrew Filer, Christopher D Buckley, Gisela Orozco, Oliver Distler, Andrew P Morris, Paul Martin, Stephen Eyre, Caroline Ospelt Genome Biol 22, 247 (2021); DOI: https://doi.org/10.1186/s13059-021-02460-6

Germline intergenic duplications at Xq26.1 underlie Bazex-Dupré-Christol syndrome, an inherited basal cell carcinoma susceptibility condition Yanshan Liu, Siddharth Banka, Yingzhi Huang, Jonathan Hardman-Smart, Derek Pye, Antonio Torrelo, Glenda M. Beaman, Marcelo G. Kazanietz, Martin J Baker, Carlo Ferrazzano, Chenfu Shi, Gisela Orozco, Stephen Eyre, Michel van Geel, Anette Bygum, Judith Fischer, Zosia Miedzybrodzka, Faris Abuzahra, Albert Rübben, Sara Cuvertino, Jamie M. Ellingford, Miriam J. Smith, D. Gareth Evans, Lizelotte J.M.T Weppner-Parren, Maurice A.M. van Steensel, Iskander H. Chaudhary, D. Chas Mangham, John T. Lear, Ralf Paus, Jorge Frank, William G. Newman, Xue Zhang MedRxiv, 2 (2022); DOI: https://doi.org/10.1101/2022.02.12.22270762

Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
Helen Ray-Jones, Kate Duffus, Amanda McGovern, Paul Martin, Chenfu Shi, Jenny Hankinson, Oliver Gough, Annie Yarwood, Andrew P Morris, Antony Adamson, Christopher Taylor, James Ding, Vasanthi Priyadarshini Gaddi, Yao Fu, Patrick Gaffney, Gisela Orozco, Richard B Warren, Steve Eyre
BMC Biol 18, 47 (2020); DOI: https://doi.org/10.1186/s12915-020-00779-3

Exploring the overlap between rheumatoid arthritis susceptibility loci and long non-coding RNA annotations
James Ding, Chenfu Shi, John Bowes, Stephen Eyre, Gisela Orozco
PLoS ONE 15(3): e0223939; DOI: https://doi.org/10.1371/journal.pone.0223939

Combined genetic analysis of juvenile idiopathic arthritis clinical subtypes identifies novel risk loci, target genes and key regulatory mechanisms
López-Isac E, Smith SL, Marion MC, Wood A, Sudman M, Yarwood A, Shi C, Gaddi VP, Martin P, Prahalad S, Eyre S, Orozco G, Morris AP, Langefeld CD, Thompson SD, Thomson W, Bowes J.
Ann Rheum Dis. 2020 Oct 26;80(3):321–8. DOI: https://doi.org/10.1136/annrheumdis-2020-218481