Dr Nathan Harmston
(he/him)
BSc, MSc, PhD
- Available for postgraduate supervision
Teams and roles for Nathan Harmston
Lecturer in Bioinformatics and Computational Biology
School of Biosciences
Overview
I am a computational biologist who is interested in understanding how gene expression is regulated during both development - with a focus on Drosophila - and in a disease context; specifically cancer.
My 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. My recent work has focused on better understanding the WNT signalling pathway using transcriptomic approaches.
We use a number of computational and statistical approaches to ask and answer questions about biological systems, often in close collaboration with experimental biologists.
Publication
2025
- Ang, D. A. , Harmston, N. and Li, Y. 2025. ATF4:p52 Complex activates oncogenic enhancers in multiple myeloma via p300/CBP recruitment to regulate BACH1. Cancer Letters 623 217727. (10.1016/j.canlet.2025.217727)
- Choy, S. M. et al., 2025. Exercise suppresses DEAF1 to normalize mTORC1 activity and reverse muscle aging. Proceedings of the National Academy of Sciences 122 (48) e2508893122. (10.1073/pnas.2508893122)
2024
- Ang, D. A. et al., 2024. Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma. Nature Communications 15 (1) 2513. (10.1038/s41467-024-46728-4)
- Goh, K. Y. et al., 2024. FOXO-regulated DEAF1 controls muscle regeneration through autophagy. Autophagy 20 (12), pp.2632-2654. (10.1080/15548627.2024.2374693)
- Madan, B. et al., 2024. The cholesterol biosynthesis enzyme FAXDC2 couples Wnt/β-catenin to RTK/MAPK signaling. The Journal of Clinical Investigation 134 (6) e171222. (10.1172/JCI171222)
- Tan, Q. H. et al., 2024. The Wnt co-receptor PTK7/Otk and Its Homolog Otk-2 in neurogenesis and patterning. Cells 13 (5) 365. (10.3390/cells13050365)
2022
- Chua, E. H. Z. , Yasar, S. and Harmston, N. 2022. The importance of considering regulatory domains in genome-wide analyses – the nearest gene is often wrong!. Biology Open 11 (4) bio059091. (10.1242/bio.059091)
- Kaur, P. et al., 2022. Wnt signaling rescues amyloid beta-induced gut stem cell loss. Cells 11 (2) 281. (10.3390/cells11020281)
- Kaur, P. et al., 2022. Combining stem cell rejuvenation and senescence targeting to synergistically extend lifespan. [Online].bioRXiv. (10.1101/2022.04.21.488994)Available at: https://doi.org/10.1101/2022.04.21.488994.
- Lusk, J. B. et al., 2022. A non-canonical Raf function is required for dorsal–ventral patterning during Drosophila embryogenesis. Scientific Reports 12 7684. (10.1038/s41598-022-11699-3)
- Zhong, Z. et al., 2022. A p300/GATA6 axis determines differentiation and Wnt dependency in pancreatic cancer models. Journal of Clinical Investigation 132 (12) e156305. (10.1172/JCI156305)
2021
- Harmston, N. et al. 2021. Widespread repression of gene expression in cancer by a Wnt/β-Catenin/MAPK pathway. Cancer Research 81 (2), pp.464-475. (10.1158/0008-5472.CAN-20-2129)
2020
- Kaur, A. et al., 2020. WNT inhibition creates a BRCA-like state in Wnt-addicted cancer. [Online].bioRXiv: bioRXiv. (10.1101/2020.06.17.157024)Available at: https://doi.org/10.1101/2020.06.17.157024.
- Liu, S. et al., 2020. Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation. [Online].BioRXiv. (10.1101/2020.02.09.941005)Available at: https://doi.org/10.1101/2020.02.09.941005.
- Yapp, L. et al., 2020. In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors.. Cell Reports 26 (12), pp.3231-3245. (10.1016/j.celrep.2019.02.083)
- Yu, J. et al., 2020. The functional landscape of patient derived RNF43 mutations predicts Wnt inhibitor sensitivity. [Online].bioRXiv: bioRXiv. (10.1101/2020.03.25.006999)Available at: https://doi.org/10.1101/2020.03.25.006999.
- Yu, J. et al., 2020. The functional landscape of patient-derived RNF43 mutations predicts sensitivity to Wnt inhibition. Cancer Research 80 (24), pp.5619-5632. (10.1158/0008-5472.CAN-20-0957)
2019
- Bagnati, M. et al., 2019. Systems genetics identifies a macrophage cholesterol network associated with physiological wound healing.. JCI Insight 4 (2) 2379-3708. (10.1172/jci.insight.125736)
- Bardile, C. F. et al., 2019. Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease. Proceedings of the National Academy of Sciences of the United States of America 116 (19), pp.9622-9627. (10.1073/pnas.1818042116)
- Chen, H. et al., 2019. WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.. Nature Communications 10 3616. (10.1038/s41467-019-11551-9)
- Idris, M. et al., 2019. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA 25 (12), pp.1696-1713. (10.1261/rna.071506.119)
- Ooi, J. et al., 2019. Unbiased profiling of Isogenic Huntington Disease hPSC-Derived CNS and peripheral cells reveals strong cell-type specificity of CAG length effects. Cell Reports 26 (9), pp.2494-2508. (10.1016/j.celrep.2019.02.008)
2018
- Madan, B. et al., 2018. Temporal dynamics of Wnt-dependent transcriptome reveal an oncogenic Wnt/MYC/ribosome axis.. JCI Journal of Clinical Investigation 128 (12), pp.5620-5633. (10.1172/JCI122383)
- Moreno-Moral, A. et al., 2018. Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk.. Annals of the Rheumatic Diseases 77 , pp.596-601. (10.1136/annrheumdis-2017-212454)
- Tjin, M. S. et al., 2018. Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture.. Nature Communications 9 4432. (10.1038/s41467-018-06934-3)
2017
- Alok, A. et al., 2017. Wnt proteins synergize to activate β-catenin signaling. Development 144 (10), pp.e1.1-e1.1. (10.1242/dev.154112)
- Harmston, N. et al. 2017. Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nature Communications 8 441. (10.1101/042952)
- Rackham, O. J. L. et al., 2017. A Bayesian approach for analysis of whole-genome Bisulfite sequencing data identifies disease-associated changes in DNA Methylation.. Genetics 205 (4), pp.1443–1458. (10.1534/genetics.116.195008)
- Rackham, O. J. L. et al., 2017. A Bayesian approach for analysis of whole-genome bisulphite sequencing data identifies disease-associated changes in DNA methylation. [Online].BioRXiv. (10.1101/041715)Available at: https://doi.org/10.1101/041715.
- Suresh, J. et al., 2017. An embryonic system to assess direct and indirect Wnt transcriptional targets.. Scientific Reports 7 11092. (10.1038/s41598-017-11519-z)
2016
- Madan, B. et al., 2016. Wnt addiction of genetically defined cancers reversed by PORCN inhibition.. Oncogene 35 , pp.2197-2207. (10.1038/onc.2015.280)
- Rackham, J. O. et al., 2016. Approximate Bayesian bisulphite sequencing analysis. [Online].BioRxiv. (10.1101/041715)Available at: https://doi.org/10.1101/041715.
2015
- Harmston, N. et al. 2015. GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics 16 (1) 963. (10.1186/s12864-015-2140-x)
2013
- Harmston, N. , Barešić, A. and Lenhard, B. 2013. The mystery of extreme non-coding conservation.. Philosophical Transactions of the Royal Society B: Biological Sciences 368 (1632) 20130021. (10.1098/rstb.2013.0021)
- Harmston, N. and Lenhard, B. 2013. Chromatin and epigenetic features of long-range gene regulation.. Nucleic Acids Research 41 (15), pp.7185-7199. (10.1093/nar/gkt499)
2011
- Harmston, N. , Filsell, W. and Stumpf, M. P. 2011. Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices.. Bioinformatics 28 (2), pp.254-260. (10.1093/bioinformatics/btr640)
2010
- Harmston, N. , Filsell, W. and Stumpf, M. P. 2010. What the papers say: Text mining for genomics and systems biology. Human Genomics 5 (1) 17. (10.1186/1479-7364-5-1-17)
Articles
- Alok, A. et al., 2017. Wnt proteins synergize to activate β-catenin signaling. Development 144 (10), pp.e1.1-e1.1. (10.1242/dev.154112)
- Ang, D. A. et al., 2024. Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma. Nature Communications 15 (1) 2513. (10.1038/s41467-024-46728-4)
- Ang, D. A. , Harmston, N. and Li, Y. 2025. ATF4:p52 Complex activates oncogenic enhancers in multiple myeloma via p300/CBP recruitment to regulate BACH1. Cancer Letters 623 217727. (10.1016/j.canlet.2025.217727)
- Bagnati, M. et al., 2019. Systems genetics identifies a macrophage cholesterol network associated with physiological wound healing.. JCI Insight 4 (2) 2379-3708. (10.1172/jci.insight.125736)
- Bardile, C. F. et al., 2019. Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease. Proceedings of the National Academy of Sciences of the United States of America 116 (19), pp.9622-9627. (10.1073/pnas.1818042116)
- Chen, H. et al., 2019. WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.. Nature Communications 10 3616. (10.1038/s41467-019-11551-9)
- Choy, S. M. et al., 2025. Exercise suppresses DEAF1 to normalize mTORC1 activity and reverse muscle aging. Proceedings of the National Academy of Sciences 122 (48) e2508893122. (10.1073/pnas.2508893122)
- Chua, E. H. Z. , Yasar, S. and Harmston, N. 2022. The importance of considering regulatory domains in genome-wide analyses – the nearest gene is often wrong!. Biology Open 11 (4) bio059091. (10.1242/bio.059091)
- Goh, K. Y. et al., 2024. FOXO-regulated DEAF1 controls muscle regeneration through autophagy. Autophagy 20 (12), pp.2632-2654. (10.1080/15548627.2024.2374693)
- Harmston, N. , Barešić, A. and Lenhard, B. 2013. The mystery of extreme non-coding conservation.. Philosophical Transactions of the Royal Society B: Biological Sciences 368 (1632) 20130021. (10.1098/rstb.2013.0021)
- Harmston, N. , Filsell, W. and Stumpf, M. P. 2010. What the papers say: Text mining for genomics and systems biology. Human Genomics 5 (1) 17. (10.1186/1479-7364-5-1-17)
- Harmston, N. , Filsell, W. and Stumpf, M. P. 2011. Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices.. Bioinformatics 28 (2), pp.254-260. (10.1093/bioinformatics/btr640)
- Harmston, N. et al. 2015. GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics 16 (1) 963. (10.1186/s12864-015-2140-x)
- Harmston, N. et al. 2017. Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nature Communications 8 441. (10.1101/042952)
- Harmston, N. and Lenhard, B. 2013. Chromatin and epigenetic features of long-range gene regulation.. Nucleic Acids Research 41 (15), pp.7185-7199. (10.1093/nar/gkt499)
- Harmston, N. et al. 2021. Widespread repression of gene expression in cancer by a Wnt/β-Catenin/MAPK pathway. Cancer Research 81 (2), pp.464-475. (10.1158/0008-5472.CAN-20-2129)
- Idris, M. et al., 2019. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA 25 (12), pp.1696-1713. (10.1261/rna.071506.119)
- Kaur, P. et al., 2022. Wnt signaling rescues amyloid beta-induced gut stem cell loss. Cells 11 (2) 281. (10.3390/cells11020281)
- Lusk, J. B. et al., 2022. A non-canonical Raf function is required for dorsal–ventral patterning during Drosophila embryogenesis. Scientific Reports 12 7684. (10.1038/s41598-022-11699-3)
- Madan, B. et al., 2016. Wnt addiction of genetically defined cancers reversed by PORCN inhibition.. Oncogene 35 , pp.2197-2207. (10.1038/onc.2015.280)
- Madan, B. et al., 2018. Temporal dynamics of Wnt-dependent transcriptome reveal an oncogenic Wnt/MYC/ribosome axis.. JCI Journal of Clinical Investigation 128 (12), pp.5620-5633. (10.1172/JCI122383)
- Madan, B. et al., 2024. The cholesterol biosynthesis enzyme FAXDC2 couples Wnt/β-catenin to RTK/MAPK signaling. The Journal of Clinical Investigation 134 (6) e171222. (10.1172/JCI171222)
- Moreno-Moral, A. et al., 2018. Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk.. Annals of the Rheumatic Diseases 77 , pp.596-601. (10.1136/annrheumdis-2017-212454)
- Ooi, J. et al., 2019. Unbiased profiling of Isogenic Huntington Disease hPSC-Derived CNS and peripheral cells reveals strong cell-type specificity of CAG length effects. Cell Reports 26 (9), pp.2494-2508. (10.1016/j.celrep.2019.02.008)
- Rackham, O. J. L. et al., 2017. A Bayesian approach for analysis of whole-genome Bisulfite sequencing data identifies disease-associated changes in DNA Methylation.. Genetics 205 (4), pp.1443–1458. (10.1534/genetics.116.195008)
- Suresh, J. et al., 2017. An embryonic system to assess direct and indirect Wnt transcriptional targets.. Scientific Reports 7 11092. (10.1038/s41598-017-11519-z)
- Tan, Q. H. et al., 2024. The Wnt co-receptor PTK7/Otk and Its Homolog Otk-2 in neurogenesis and patterning. Cells 13 (5) 365. (10.3390/cells13050365)
- Tjin, M. S. et al., 2018. Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture.. Nature Communications 9 4432. (10.1038/s41467-018-06934-3)
- Yapp, L. et al., 2020. In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors.. Cell Reports 26 (12), pp.3231-3245. (10.1016/j.celrep.2019.02.083)
- Yu, J. et al., 2020. The functional landscape of patient-derived RNF43 mutations predicts sensitivity to Wnt inhibition. Cancer Research 80 (24), pp.5619-5632. (10.1158/0008-5472.CAN-20-0957)
- Zhong, Z. et al., 2022. A p300/GATA6 axis determines differentiation and Wnt dependency in pancreatic cancer models. Journal of Clinical Investigation 132 (12) e156305. (10.1172/JCI156305)
Websites
- Kaur, A. et al., 2020. WNT inhibition creates a BRCA-like state in Wnt-addicted cancer. [Online].bioRXiv: bioRXiv. (10.1101/2020.06.17.157024)Available at: https://doi.org/10.1101/2020.06.17.157024.
- Kaur, P. et al., 2022. Combining stem cell rejuvenation and senescence targeting to synergistically extend lifespan. [Online].bioRXiv. (10.1101/2022.04.21.488994)Available at: https://doi.org/10.1101/2022.04.21.488994.
- Liu, S. et al., 2020. Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation. [Online].BioRXiv. (10.1101/2020.02.09.941005)Available at: https://doi.org/10.1101/2020.02.09.941005.
- Rackham, J. O. et al., 2016. Approximate Bayesian bisulphite sequencing analysis. [Online].BioRxiv. (10.1101/041715)Available at: https://doi.org/10.1101/041715.
- Rackham, O. J. L. et al., 2017. A Bayesian approach for analysis of whole-genome bisulphite sequencing data identifies disease-associated changes in DNA methylation. [Online].BioRXiv. (10.1101/041715)Available at: https://doi.org/10.1101/041715.
- Yu, J. et al., 2020. The functional landscape of patient derived RNF43 mutations predicts Wnt inhibitor sensitivity. [Online].bioRXiv: bioRXiv. (10.1101/2020.03.25.006999)Available at: https://doi.org/10.1101/2020.03.25.006999.
Teaching
I am currently involving in teaching computational biology and data analysis skills as part of the Big Data Biology MSc.
Previous teaching roles
Assistant Professor @ Yale-NUS
- Scientific Inquiry I
- Statistics for Life Sciences
- Computational and Systems Biology
- Advanced topics in Computational and Systems Biology
Biography
Academic positions
Previous positions
- Assistant Professor @ Yale-NUS, Singapore - 2019-2023
- Assistant Professor @ Duke-NUS, Singapore - 2019-2023
- Senior Research Fellow @ Duke-NUS, Singapore - 2015-2019
- Career Development Fellow @ MRC CSC (now LMS), London, 2012-2015
Education
- PhD @ Imperial College London (2008-2012)
- MSc - Bioinformatics and Theoretical Systems Biology - Imperial College London - (2007 - 2008)
- BSc (Hons) - Computer Science - University of Nottingham - (2002 - 2006)
Committees and reviewing
Reviewer for multiple journals
Member of Committee for Academic Integrity @ Yale-NUS - 2021 - 2022
Supervisions
Current supervision
Kieran Howard
Contact Details
Research themes
Specialisms
- Bioinformatics and computational biology
- Genomics and transcriptomics