Genomics and Gene Regulation @ Cardiff University

Genomics and Gene Regulation

The Genomics and Gene Regulation group at Cardiff University is interested in understanding how gene expression is regulated during both development and in a disease context; with a focus on cancer.

We use a number of computational and statistical approaches to ask and answer questions about biological systems, often in close collaboration with experimental biologists. Our research interests encompass a variety of themes, including understanding how the 3D structure around important transcription factors influences genome evolution and identifying the genomic and epigenetic features that determine whether a gene is regulated by a specific developmental signalling pathway.

News

September 2024: Kieran Howard joins the lab as a PhD student working to understand enhancer function and conservation
July 2024: FOXO-regulated DEAF1 controls muscle regeneration through autophagy is now published
May 2024: ggbulksurv: An R package for easy Drosophila and C. elegans survival analysis is now out in microPublication Biology
March 2024: Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma is now published as part of a collaboration with Dr. Yinghui Li's group at NTU, Singapore
February 2024: The Wnt Co-Receptor PTK7/Otk and Its Homolog Otk-2 in Neurogenesis and Patterning is now published - congrats QH
January 2024: The cholesterol biosynthesis enzyme FAXDC2 couples Wnt/β-catenin to RTK/MAPK signaling is now published online
December 2023: New preprint posted: The cholesterol biosynthesis enzyme FAXDC2 couples Wnt/beta-catenin to RTK/MAPK signaling
October 2022: Combining stem cell rejuvenation and senescence targeting to synergistically extend lifespan is now published
August 2022: A high-resolution map of human RNA translation is now published
June 2022:A p300/GATA6 axis determines differentiation and Wnt dependency in pancreatic cancer models is now published
June 2022:A non-canonical Raf function is required for dorsal–ventral patterning during Drosophila embryogenesis is now published
April 2022: New preprint posted: Combining Stem Cell Rejuvenation and Senescence Targeting to Synergistically Extend Lifespan as part of a collaboration with the Tolwinski and Gruber labs at Yale-NUS
April 2022: New review paper published - The importance of considering regulatory domains in genome-wide analyses – the nearest gene is often wrong!
January 2022: Wnt Signaling Rescues Amyloid Beta-Induced Gut Stem Cell Loss now published
September 2021: New preprint posted: Wnt signaling rescues amyloid beta induced stem cell loss as part of a collaboration with the Tolwinski lab at Yale-NUS
August 2021: Glenda Chin joins the lab for her capstone project
August 2021: Sara Haghani joins the lab as a Research Assistant
July 2021: New preprint posted: A Non-Canonical Raf Function Is Required for Dorsal-Ventral Patterning During Drosophila Embryogenesis as part of a collaboration with the Tolwinski lab at Yale-NUS
November 2020: Perspective on Regulation in common: Sponge to zebrafish now published in Science
November 2020: Our poster on Analyses of mutational and structural variation in a cohort of anaplastic astrocytoma has been accepted at Frontiers in Cancer Science, Singapore 2020
August 2020: Samen Yasar and Sara Haghani join the lab for their capstone projects
October 2019: Ellora Chua joins the lab as a Research Assistant
August 2019: Anjali Kannangath joins the lab for her capstone project
August 2019: Nathan presents on TADs Are Ancient Features that Coincide with Metazoan Clusters of Noncoding Conservation at (GRC) Genome Architecture in Cell Fate and Disease, Hong Kong 2019

Contact

E-mail: harmstonn (at) cardiff.ac.uk

Publications

You can find a current and complete list of publications on Google scholar.

FOXO-regulated DEAF1 controls muscle regeneration through autophagy (2024)
[manuscript @ Autophagy]
[GitHub]

Kah Yong Goh, Wen Xing Lee, Sze Mun Choy, Gopal Krishnan Priyadarshini, Kenon Chua, Qian Hui Tan, Shin Yi Low, Hui San Chin, Chee Seng Wong, Shu-Yi Huang, Nai Yang Fu, Jun Nishiyama, Nathan Harmston, Hong-Wen Tang

Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma (2024)
[manuscript @ Nature Communications]

Daniel A Ang, Jean-Michel Carter, Kamalakshi Deka, Joel HL Tan, Jianbiao Zhou, Qingfeng Chen, Wee Joo Chng, Nathan Harmston, Yinghui Li

The Wnt co-receptor PTK7/Otk and Its Homolog Otk-2 in neurogenesis and patterning (2024)
[manuscript @ Cells]
[GitHub]

Qian Hui Tan, Agimaa Otgonbaatar, Prameet Kaur, Angelica Faye Ga, Nathan P Harmston, Nicholas S Tolwinski

ggbulksurv: An R package for easy Drosophila and C. elegans survival analysis (2024)
[manuscript @ microPublication Biology]
[GitHub]

Qian Hui Tan, Nathan Harmston, Nicholas S Tolwinski

The cholesterol biosynthesis enzyme FAXDC2 couples Wnt/β-catenin to RTK/MAPK signaling (2024)
[manuscript @ JCI]
[Preprint]
[GitHub]

Babita Madan, Shawn Wadia, Siddhi Patnaik, Nathan Harmston, Emile Tan, Iain Bee Huat Tan, W. David Nes, Enrico Petretto, David M. Virshup

A high-resolution map of human RNA translation (2022)
[manuscript @ Molecular Cell ]

Sonia P Chothani, Eleonora Adami, Anissa A Widjaja, Sarah R Langley, Sivakumar Viswanathan, Chee Jian Pua, Nevin Tham Zhihao, Nathan Harmston, Giuseppe D’agostino, Nicola Whiffin, Wang Mao, John F Ouyang, Wei Wen Lim, Shiqi Lim, Cheryl QE Lee, Alexandra Grubman, Joseph Chen, JP Kovalik, Karl Tryggvason, Jose M Polo, Lena Ho, Stuart A Cook, Owen JL Rackham, Sebastian Schafer

A p300/GATA6 axis determines differentiation and Wnt dependency in pancreatic cancer models (2022)
[manuscript @ The Journal of Clinical Investigation ]

Z Zhong, N Harmston, KC Wood, B Madan, DM Virshup

Combining Stem Cell Rejuvenation and Senescence Targeting to Synergistically Extend Lifespan (2022)
[manuscript @ Ageing ]
[Preprint]
[GitHub]

Prameet Kaur, Agimaa Otgonbaatar, Anupriya Ramamoorthy, Ellora Hui Zhen Chua, Nathan Harmston, Jan Gruber, Nicholas S. Tolwinski

The importance of considering regulatory domains in genome-wide analyses – the nearest gene is often wrong! (2022)
[manuscript @ Biology Open]
[Future leader to watch – Nathan Harmston]
[GitHub]

Ellora Hui Zhen Chua, Samen Yasar, Nathan Harmston

Wnt Signaling Rescues Amyloid Beta-Induced Gut Stem Cell Loss (2022)
[manuscript @ Cells]
[preprint]
[GitHub]

Prameet Kaur, Ellora Hui Zhen Chua, Wen Kin Lim, Nathan Harmston, Nicholas S. Tolwinski

A Non-Canonical Raf Function Is Required for Dorsal-Ventral Patterning During Drosophila Embryogenesis (2022)
[manuscript @ Scientific Reports ]
[preprint]
[GitHub]

Jay B. Lusk, Ellora Hui Zhen Chua, Prameet Kaur, Isabelle Chiao Han Sung, Wen Kin Lim, Vanessa Yuk Man Lam, Nathan Harmston, Nicholas S. Tolwinski

WNT inhibition creates a BRCA‐like state in Wnt‐addicted cancer (2021)
[manuscript @ EMBO Molecular Medicine]

Amanpreet Kaur, Jun Yi Stanley Lim, Sugunavathi Sepramaniam, Siddhi Patnaik, Nathan Harmston, May Ann Lee, Enrico Petretto, David M Virshup, Babita Madan

Widespread repression of gene expression in cancer by a Wnt/β-catenin/MAPK pathway (2021)
[manuscript @ Cancer Research]

Nathan Harmston, Jun Yi Stanley Lim, Oriol Arqués, Héctor G Palmer, Enrico Petretto, David M Virshup, Babita Madan

Regulation in common: Sponge to zebrafish (2020)
[Manuscript]

Nathan Harmston

Team

Nathan Harmston

Principal investigator

I am a computational biologist who leads the Genomics and Gene Regulation group at Cardiff University.

Email: harmstonn@cardiff.ac.uk

Kieran Howard

Kieran's PhD is focused on understanding the conservation and function of regulatory elements using data-driven approaches.