Dr Nathan Harmston
(e/fe)
BSc, MSc, PhD
- Ar gael fel goruchwyliwr ôl-raddedig
Timau a rolau for Nathan Harmston
Darlithydd mewn Biowybodeg a Bioleg Gyfrifiadurol
Ysgol y Biowyddorau
Trosolwyg
Rwy'n fiolegydd cyfrifiannol sydd â diddordeb mewn deall sut mae mynegiant genynnau yn cael ei reoleiddio yn ystod y ddau ddatblygiad - gyda ffocws ar Drosophila - ac yng nghyd-destun clefyd; Yn enwedig canser.
Mae fy niddordebau ymchwil yn cwmpasu amrywiaeth o themâu, gan gynnwys deall sut mae'r strwythur 3D o amgylch ffactorau trawsgrifio pwysig yn dylanwadu ar esblygiad genom a nodi'r nodweddion genomig ac epigenetig sy'n penderfynu a yw genyn yn cael ei reoleiddio gan lwybr signalau datblygiadol penodol. Mae fy ngwaith diweddar wedi canolbwyntio ar ddeall llwybr signalau WNT yn well gan ddefnyddio dulliau trawsgrifio.
Rydym yn defnyddio nifer o ddulliau cyfrifiadurol ac ystadegol i ofyn ac ateb cwestiynau am systemau biolegol, yn aml mewn cydweithrediad agos â biolegwyr arbrofol.
Cyhoeddiad
2024
- 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)
- 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), article number: 2513. (10.1038/s41467-024-46728-4)
- 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), article number: e171222. (10.1172/JCI171222)
- Tan, Q. H., Otgonbaatar, A., Kaur, P., Ga, A. F., Harmston, N. P. and Tolwinski, N. S. 2024. The Wnt co-receptor PTK7/Otk and Its Homolog Otk-2 in neurogenesis and patterning. Cells 13(5), article number: 365. (10.3390/cells13050365)
2022
- Zhong, Z., Harmston, N., Wood, K. C., Madan, B. and Virshup, M. 2022. A p300/GATA6 axis determines differentiation and Wnt dependency in pancreatic cancer models. Journal of Clinical Investigation 132(12), article number: e156305. (10.1172/JCI156305)
- Lusk, J. B. et al. 2022. A non-canonical Raf function is required for dorsal–ventral patterning during Drosophila embryogenesis. Scientific Reports 12, article number: 7684. (10.1038/s41598-022-11699-3)
- Kaur, P., Otgonbaatar, A., Ramamoorthy, A., Chua, E. H. Z., Harmston, N., Gruber, J. and Tolwinski, N. S. 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
- 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), article number: bio059091. (10.1242/bio.059091)
- Kaur, P., Chua, E. H. Z., Lim, W. K., Liu, J., Harmston, N. and Tolwinski, N. 2022. Wnt signaling rescues amyloid beta-induced gut stem cell loss. Cells 11(2), article number: 281. (10.3390/cells11020281)
2021
- Harmston, N., Lim, S. Y. J., Arqués, O., Palmer, H. G., Petretto, E., Virshup, D. M. and Madan, B. 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
- 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)
- 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
- Yu, J., Yuso, P. . A. B. M., Goh, P., Harmston, N., Epstein, D. M., Virship, D. M. and Madan, B. 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
- 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)
- 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
2019
- Idris, M., Harmston, N., Petretto, E., Madan, B. and Virshup, D. M. 2019. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA 25(12), pp. 1696-1713. (10.1261/rna.071506.119)
- Chen, H. et al. 2019. WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.. Nature Communications 10, article number: 3616. (10.1038/s41467-019-11551-9)
- 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)
- 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)
- Bagnati, M. et al. 2019. Systems genetics identifies a macrophage cholesterol network associated with physiological wound healing.. JCI Insight 4(2), article number: 2379-3708. (10.1172/jci.insight.125736)
2018
- Madan, B., Harmston, N., Nallan, G., Montoya, A., Faull, P., Petretto, E. and Virshup, D. M. 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)
- Tjin, M. S. et al. 2018. Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture.. Nature Communications 9, article number: 4432. (10.1038/s41467-018-06934-3)
- 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)
2017
- Suresh, J. et al. 2017. An embryonic system to assess direct and indirect Wnt transcriptional targets.. Scientific Reports 7, article number: 11092. (10.1038/s41598-017-11519-z)
- Harmston, N., Ing-Simmons, E., Tan, G., Perry, M., Merkenschlager, M. and Lenhard, B. 2017. Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nature Communications 8, article number: 441. (10.1101/042952)
- 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)
- 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
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., Ing-Simmons, E., Perry, M., Barešić, A. and Lenhard, B. 2015. GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics 16(1), article number: 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), article number: 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), article number: 17. (10.1186/1479-7364-5-1-17)
Erthyglau
- 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)
- 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), article number: 2513. (10.1038/s41467-024-46728-4)
- 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), article number: e171222. (10.1172/JCI171222)
- Tan, Q. H., Otgonbaatar, A., Kaur, P., Ga, A. F., Harmston, N. P. and Tolwinski, N. S. 2024. The Wnt co-receptor PTK7/Otk and Its Homolog Otk-2 in neurogenesis and patterning. Cells 13(5), article number: 365. (10.3390/cells13050365)
- Zhong, Z., Harmston, N., Wood, K. C., Madan, B. and Virshup, M. 2022. A p300/GATA6 axis determines differentiation and Wnt dependency in pancreatic cancer models. Journal of Clinical Investigation 132(12), article number: e156305. (10.1172/JCI156305)
- Lusk, J. B. et al. 2022. A non-canonical Raf function is required for dorsal–ventral patterning during Drosophila embryogenesis. Scientific Reports 12, article number: 7684. (10.1038/s41598-022-11699-3)
- 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), article number: bio059091. (10.1242/bio.059091)
- Kaur, P., Chua, E. H. Z., Lim, W. K., Liu, J., Harmston, N. and Tolwinski, N. 2022. Wnt signaling rescues amyloid beta-induced gut stem cell loss. Cells 11(2), article number: 281. (10.3390/cells11020281)
- Harmston, N., Lim, S. Y. J., Arqués, O., Palmer, H. G., Petretto, E., Virshup, D. M. and Madan, B. 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)
- 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)
- 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)
- Idris, M., Harmston, N., Petretto, E., Madan, B. and Virshup, D. M. 2019. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA 25(12), pp. 1696-1713. (10.1261/rna.071506.119)
- Chen, H. et al. 2019. WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.. Nature Communications 10, article number: 3616. (10.1038/s41467-019-11551-9)
- 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)
- 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)
- Bagnati, M. et al. 2019. Systems genetics identifies a macrophage cholesterol network associated with physiological wound healing.. JCI Insight 4(2), article number: 2379-3708. (10.1172/jci.insight.125736)
- Madan, B., Harmston, N., Nallan, G., Montoya, A., Faull, P., Petretto, E. and Virshup, D. M. 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)
- Tjin, M. S. et al. 2018. Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture.. Nature Communications 9, article number: 4432. (10.1038/s41467-018-06934-3)
- 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)
- Suresh, J. et al. 2017. An embryonic system to assess direct and indirect Wnt transcriptional targets.. Scientific Reports 7, article number: 11092. (10.1038/s41598-017-11519-z)
- Harmston, N., Ing-Simmons, E., Tan, G., Perry, M., Merkenschlager, M. and Lenhard, B. 2017. Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nature Communications 8, article number: 441. (10.1101/042952)
- 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)
- 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)
- 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)
- Harmston, N., Ing-Simmons, E., Perry, M., Barešić, A. and Lenhard, B. 2015. GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics 16(1), article number: 963. (10.1186/s12864-015-2140-x)
- 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), article number: 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)
- 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., Filsell, W. and Stumpf, M. P. 2010. What the papers say: Text mining for genomics and systems biology. Human Genomics 5(1), article number: 17. (10.1186/1479-7364-5-1-17)
Gwefannau
- Kaur, P., Otgonbaatar, A., Ramamoorthy, A., Chua, E. H. Z., Harmston, N., Gruber, J. and Tolwinski, N. S. 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
- 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
- Yu, J., Yuso, P. . A. B. M., Goh, P., Harmston, N., Epstein, D. M., Virship, D. M. and Madan, B. 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
- 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, 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
- Rackham, J. O. et al. 2016. Approximate Bayesian bisulphite sequencing analysis. [Online]. BioRxiv. (10.1101/041715) Available at: https://doi.org/10.1101/041715
Addysgu
Ar hyn o bryd rwy'n ymwneud ag addysgu bioleg gyfrifiadurol a sgiliau dadansoddi data fel rhan o'r MSc Bioleg Data Mawr.
Rolau addysgu blaenorol
Athro Cynorthwyol @ Yale-NUS
- Ymchwiliad Gwyddonol I
- Ystadegau ar gyfer Gwyddorau Bywyd
- Bioleg Gyfrifiadurol a Systemau
- Pynciau Uwch mewn Bioleg Gyfrifiadurol a Systemau
Bywgraffiad
Safleoedd academaidd blaenorol
Swyddi blaenorol
- Athro Cynorthwyol @ Yale-NUS, Singapôr - 2019-2023
- Athro Cynorthwyol @Duke-NUS, Singapôr - 2019-2023
- Uwch Gymrawd Ymchwil @Duke-NUS, Singapore - 2015-2019
- Cymrawd Datblygu Gyrfa @ MRC CSC (LMS bellach), Llundain, 2012-2015
Addysg
- PhD @ Imperial College Llundain (2008-2012)
- MSc - Biowybodeg a Bioleg Systemau Damcaniaethol - Coleg Imperial Llundain - (2007 - 2008)
- BSc (Anrh) - Cyfrifiadureg - Prifysgol Nottingham - (2002 - 2006)
Pwyllgorau ac adolygu
adolygydd ar gyfer cylchgronau lluosog
Aelod o'r Pwyllgor Uniondeb Academaidd @ Yale-NUS - 2021 - 2022
Meysydd goruchwyliaeth
Goruchwyliaeth gyfredol
Kieran Howard
Contact Details
Themâu ymchwil
Arbenigeddau
- Biowybodeg a bioleg gyfrifiadurol
- Genomeg a thrawsgrifiadau