Colin Semple

Search results

• 2024

  Protein structural context of cancer mutations reveals molecular mechanisms and candidate driver genes

  Chillón, D., Badonyi, M., Semple, C. A. & Marsh, J. A., 22 Oct 2024, (E-pub ahead of print) In: Cell Reports.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Oncogene 100%
  • Structural Protein 100%
  • Tumor Suppressor Protein 66%
  • Missense Mutation 33%
  • Protein Structure 33%

• Regionally enriched rare deleterious exonic variants in the UK and Ireland

  Halachev, M., Gountouna, V-E., Meynert, A. M., Tzoneva, G., Shuldiner, A. R., Semple, C. A. & Wilson, J. F., 2 Oct 2024, In: Nature Communications.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Genetic Divergence 100%
  • Exome Sequencing 50%
  • Genetic Variation 50%
  • Genetics 50%
  • Genetic Screening 50%

• Strand-resolved mutagenicity of DNA damage and repair

  Liver Cancer Evolution Consortium, 12 Jun 2024, In: Nature.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Transcription 100%
  • Mutagenesis 100%
  • Polymerase 100%
  • Nucleotide Excision Repair 100%
  • Excision Repair 100%
• 2023

  IMPROVE-DD: Integrating Multiple Phenotype Resources Optimises Variant Evaluation in genetically determined Developmental Disorders

  Aitken, S., Firth, H. V., Wright, C. F., Hurles, M. E., FitzPatrick, D. R. & Semple, C. A., 12 Jan 2023, In: Human Genetics and Genomics Advances. 4, 1, 9 p., 100162.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Evaluation Study 100%
  • Developmental Disorder 100%
  • Phenotype 100%
  • Evaluation 100%
  • Gene 71%
• 2022

  Multiomic characterisation of high grade serous ovarian carcinoma enables high resolution patient stratification

  Hollis, R., Meynert, A. M., Michie, C. O., Rye, T., Churchman, M., Hallas-Potts, A., Croy, I., McCluggage, G. W., R Williams, A., Bartos, C., Iida, Y., Okamoto, A., Dougherty, B., Barrett, C. J., March, R., Matakidou, A., Roxburgh, P., Semple, C. A., D. Harkin, P., Kennedy, R., & 2 othersHerrington, C. S. & Gourley, C., 13 Jun 2022, In: Clinical Cancer Research.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Gene Co-Expression Network Analysis Identifies Vitamin D-Associated Gene Modules in Adult Normal Rectal Epithelium Following Supplementation

  Blackmur, J. P., Vaughan-Shaw, P. G., Donnelly, K., Harris, B. T., Svinti, V., Ochocka-Fox, A-M., Freile, P., Walker, M., Gurran, T., Reid, S., Semple, C. A., Din, F. V. N., Timofeeva, M., Dunlop, M. G. & Farrington, S. M., 4 Jan 2022, In: Frontiers in Genetics. 12, p. 783970 783970.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Vitamin D 100%
  • Nested Gene 100%
  • RNA Metabolism 8%
  • Rectum Mucosa 8%
  • Hormone Metabolism 8%
• 2021

  Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome

  Deciphering Developmental Disorders Study, 1 Oct 2021, In: Genome Research.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Binding Site 100%
  • Regulatory Site 100%
  • Human Genome 100%
  • Spermatogonium 100%
  • Transcription Factor 83%

• ISGylation drives basal breast tumour progression by promoting EGFR recycling and Akt signalling

  Bolado-carrancio, A., Lee, M., Ewing, A., Muir, M., Macleod, K. G., Gallagher, W. M., Nguyen, L. K., Carragher, N. O., Semple, C. A., Brunton, V. G., Caswell, P. T. & Von Kriegsheim, A., 23 Sept 2021, (E-pub ahead of print) In: Oncogene.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Drive 100%
  • ISG15 100%
  • Tumor Progression 100%
  • Akt Signaling 100%
  • Interferon 25%

• Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

  Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-sueki, H., Frith, M., Abugessaisa, I., Aitken, S., & 471 othersAken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Archer, J., Archibald, A. L., Arner, E., Arner, P., Asai, K., Ashoor, H., Astrom, G., Babina, M., Baillie, J. K., Bajic, V. B., Bajpai, A., Baker, S., Baldarelli, R. M., Balic, A., Bansal, M., Batagov, A. O., Batzoglou, S., Beckhouse, A. G., Beltrami, A. P., Beltrami, C. A., Bertin, N., Bhattacharya, S., Bickel, P. J., Blake, J. A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J. B., Bult, C. J., Burroughs, A. M., Burt, D. W., Busch, A., Caglio, G., Califano, A., Cameron, C. J., Cannistraci, C. V., Carbone, A., Carlisle, A. J., Carninci, P., Carter, K. W., Cesselli, D., Chang, J., Chen, J. C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E. L., Coskun, M., Dalby, M., Dalla, E., Daub, C. O., Davis, C. A., De Hoon, M. J. L., De Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A. D., Dieterich, L. C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-carson, M. C., Faulkner, G. J., Favorov, A., Fernandes, A. M., Ferrai, C., Forrest, A. R. R., Forrester, L. M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T. C., Frith, M., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T. B. H., Ghosh, S., Ghosheh, Y., Gingeras, T. R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A. J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T. J., Haberle, V., Hale, P., Hallstrom, B. M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hasegawa, A., Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Hayashizaki, Y., Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K. J., Sui, S. H., ’t Hoen, P. A. C., Hon, C. C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Itoh, M., Ivshina, A. V., Jankovic, B. R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A. S., Kasukawa, T., Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y. I., Kawasaki, S., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S. P., Kloppmann, E., Knox, A. J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V. A., Kwon, T. J., Larouche, M., Lassmann, T., Law, A., Le-cao, K., Lecellier, C., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G. K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y. A., Meehan, T. F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A. K., Mummery, C. L., Mungall, C. J., Murakawa, Y., Muramatsu, M., Murata, M., Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakamura, Y., Nakazawa, T., Nason, G. P., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Nishida, K., Nishiguchi, K. M., Nishiyori, H., Nitta, K., Noguchi, S., Noma, S., Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G. S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S. P., Park, S., Pascarella, G., Passier, R., Persson, H., Philippens, I. H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T. M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X., Quackenbush, J., Rackham, O., Ramilowski, J., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M. B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E. A., Schulze-tanzil, G., Semple, C. A., Seno, S., Seo, W., Sese, J., Severin, J., Sheng, G., Shi, J., Shimoni, Y., Shin, J. W., Simonsanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G. S., Stoiber, M. H., Sugiyama, D., Summers, K. M., Suzuki, A. M., Suzuki, H., Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D. J., Swoboda, R. K., Tagami, M., Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K. T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M. S., Terada, A., Terao, Y., Testa, A. C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E. T., Toyoda, H., Tsang, H. G., Tsujikawa, M., Uhlén, M., Valen, E., Van De Wetering, M., Van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-seerup, K., Von Feilitzen, K., Voolstra, C. R., Vorontsov, I. E., Wahlestedt, C., Wasserman, W. W., Watanabe, K., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R. S., Yu, N. Y., Yumoto, N., Zabierowski, S. E., Zhang, P. G., Zucchelli, S., Zwahlen, M., Chatelain, C., Carninci, P., De Hoon, M. J. L., Wasserman, W. W., Bréhélin, L. & Lecellier, C., 2 Jun 2021, In: Nature Communications. 12, 1

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Microsatellite DNA 100%
  • Transcription Initiation 100%
  • Short Tandem Repeat 100%
  • Gene Expression 33%
  • Transcription 22%

• Integrated molecular characterisation of endometrioid ovarian carcinoma identifies opportunities for stratification

  Hollis, R., Stanley, B., Thomson, J. P., Churchman, M., Croy, I., Rye, T., Bartos, C., Nussey, F., Mackean, M. J., Meynert, A. M., Semple, C. A., Gourley, C. & Herrington, C. S., 2 Jun 2021, (E-pub ahead of print) In: npj Precision Oncology .

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Krukenberg Tumor 100%
  • Survival 42%
  • Mutant 42%
  • Patient 42%
  • Receptor Expression 28%

• Structural variants at the BRCA1/2 loci are a common source of homologous repair deficiency in high grade serous ovarian carcinoma

  Ewing, A., Meynert, A. M., Churchman, M., Grimes, G. R., Hollis, R., Herrington, C. S., Rye, T., Bartos, C., Croy, I., Ferguson, M., Lennie, M., McGoldrick, T., McPhail, N., Siddiqui, N., Dowson, S., Glasspool, R., MacKean, M., Nussey, F., McDade, B., Ennis, D., & 11 othersThe Scottish Genomes Partnership, McMahon, L., Matakidou, A., Dougherty, B., March, R., Barrett, J. C., A. McNeish, I., V. Biankin, A., Roxburgh, P., Gourley, C. & Semple, C. A., 1 Jun 2021, In: Clinical Cancer Research.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Functional brain defects in a mouse model of a chromosomal t(1;11) translocation that disrupts DISC1 and confers increased risk of psychiatric illness

  Bonneau, M., O'Sullivan, S. T., Gonzalez-Lozano, M. A., Baxter, P., Gautier, P., Marchisella, E., Hardingham, N. R., Chesters, R. A., Singh, Y., Didier, M., Koopmans, F., Semple, C. A., McIntosh, A. M., Volkmer, H., Loos, M., Fox, K., Hardingham, G., Vernon, A. C., Porteous, D. J., Smit, A. B., & 2 othersPrice, D. & Millar, J. K., 19 Feb 2021, In: Translational Psychiatry.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2020

  Molecular stratification of endometrioid ovarian carcinoma predicts clinical outcome

  Hollis, R., Thomson, J., Stanley, B., Churchman, M., Meynert, A. M., Rye, T., Bartos, C., Iida, Y., Croy, I., Mackean, M. J., Nussey, F., Okamoto, A., Semple, C. A., Gourley, C. & Herrington, C. S., 5 Oct 2020, (E-pub ahead of print) In: Nature Communications. 11, 10, 4995.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Krukenberg Tumor 100%
  • Mutation 66%
  • Diagnosis 33%
  • ARID1A 16%
  • DNA Mismatch Repair 16%

• Functional annotation of human long noncoding RNAs via molecular phenotyping

  Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J-C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Ooi, J. L. C., Ouyang, J. F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I. V., Arner, E., Bonetti, A., Bono, H., & 96 othersBorsari, B., Brombacher, F., Cameron, C. J. F., Cannistraci, C. V., Cardenas, R., Cardon, M., Chang, H., Dostie, J., Ducoli, L., Favorov, A., Fort, A., Garrido, D., Gil, N., Gimenez, J., Guler, R., Handoko, L., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, K., Hayatsu, N., Heutink, P., Hirose, T., Imada, E. L., Itoh, M., Kaczkowski, B., Kanhere, A., Kawabata, E., Kawaji, H., Kawashima, T., Kelly, S. T., Kojima, M., Kondo, N., Koseki, H., Kouno, T., Kratz, A., Kurowska-Stolarska, M., Kwon, A. T. J., Leek, J., Lennartsson, A., Lizio, M., López-Redondo, F., Luginbühl, J., Maeda, S., Makeev, V. J., Marchionni, L., Medvedeva, Y. A., Minoda, A., Müller, F., Muñoz-Aguirre, M., Murata, M., Nishiyori, H., Nitta, K. R., Noguchi, S., Noro, Y., Nurtdinov, R., Okazaki, Y., Orlando, V., Paquette, D., Parr, C. J. C., Rackham, O. J. L., Rizzu, P., Sánchez Martinez, D. F., Sandelin, A., Sanjana, P., Semple, C. A. M., Shibayama, Y., Sivaraman, D. M., Suzuki, T., Szumowski, S. C., Tagami, M., Taylor, M. S., Terao, C., Thodberg, M., Thongjuea, S., Tripathi, V., Ulitsky, I., Verardo, R., Vorontsov, I. E., Yamamoto, C., Young, R. S., Baillie, J. K., Forrest, A. R. R., Guigó, R., Hoffman, M. M., Hon, C. C., Kasukawa, T., Kauppinen, S., Kere, J., Lenhard, B., Schneider, C., Suzuki, H., Yagi, K., de Hoon, M. J. L., Shin, J. W. & Carninci, P., 27 Jul 2020, (E-pub ahead of print) In: Genome Research. 30, p. 1060-1072

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Long Noncoding RNA 100%
  • Phenotype 100%
  • Gene Expression 60%
  • Introspection 20%
  • Deep Sequencing 20%

• Pervasive lesion segregation shapes cancer genome evolution

  Aitken, S. J., Anderson, C. J., Connor, F., Pich, O., Sundaram, V., Feig, C., Rayner, T. F., Lukk, M., Aitken, S., Luft, J., Kentepozidou, E., Arnedo-Pac, C., Beentjes, S. V., Davies, S. E., Drews, R. M., Ewing, A., Kaiser, V. B., Khamseh, A., Lopez-Arribillaga, E., Redmond, A. M., & 9 othersSantoyo-Lopez, J., Sentís, I., Talmane, L., Yates, A. D., Semple, C. A., López-Bigas, N., Flicek, P., Odom, D. T. & Taylor, M. S., 9 Jul 2020, In: Nature. 583, p. 265–270 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Mutation 100%
  • Genome Evolution 100%
  • DNA Damage 100%
  • Mouse 50%
  • Evolution 50%

• Pan-cancer analysis of whole genomes

  ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium & Semple, C., 5 Feb 2020, (E-pub ahead of print) In: Nature. 578, 7793, p. 82-93 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Coding 100%
  • Mutation 66%
  • Somatic Mutation 66%
  • Point Mutation 66%
  • Fusion Gene 33%
• 2019

  Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions

  Scottish Genomes Partnership, 25 Nov 2019, (E-pub ahead of print) In: PLoS Genetics. 15, 11, p. 1-29 30 p., e1008480.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Regulatory Region 100%
  • Genetic Drift 100%
  • Founder Effect 50%
  • Sample 50%
  • Negative Selection (Natural Selection) 50%

• Zebrafish MITF-low melanoma subtype models reveal transcriptional subclusters and MITF-independent residual disease

  Travnickova, J., Wojciechowska, S., Khamseh, A., Gautier, P., Brown, D. V., Lefevre, T., Brombin, A., Ewing, A., Capper, A., Spitzer, M., Dilshat, R., Semple, C. A., Mathers, M. E., Lister, J. A., Steingrimsson, E., Voet, T., Ponting, C. P. & Patton, E. E., Nov 2019, In: Cancer Research. 79, 22, p. 5769-5784 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Nodular Melanoma 100%
  • Minimal Residual Disease 100%
  • Melanocyte 100%
  • Transcription Factor 100%
  • Zebra Fish 100%

• An actionable KCNH2 Long QT Syndrome variant detected by sequence and haplotype analysis in a population research cohort

  Kerr, S., Klaric, L., Halachev, M., Hayward, C., Boutin, T., Meynert, A. M., Semple, C. A., Tuiskula, A. M., Swan, H., Santoyo-Lopez, J., Vitart, V., Haley, C., Dean, J., Miedzybrodzka, Z., Aitman, T. J. & Wilson, J. F., 29 Jul 2019, In: Scientific Reports. 9, 10964.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Haplotype 100%
  • Protein Sequencing 100%
  • Population Research 100%
  • Long QT Syndrome 100%
  • Phenotype 40%

• Clinical and molecular characterization of ovarian carcinoma displaying isolated lymph node relapse

  Hollis, R. L., Carmichael, J., Meynert, A. M., Churchman, M., Hallas-Potts, A., Rye, T., MacKean, M., Nussey, F., Semple, C. A., Herrington, C. S. & Gourley, C., 2 May 2019, (E-pub ahead of print) In: American Journal of Obstetrics & Gynecology (AJOG).

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Modeling double strand break susceptibility to interrogate structural variation in cancer

  Ballinger, T. J., Bouwman, B. A. M., Mirzazadeh, R., Garnerone, S., Crosetto, N. & Semple, C. A., 8 Feb 2019, (E-pub ahead of print) In: Genome Biology. 20, 28 .

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Mutation 100%
  • Enhancer Region 50%
  • Negative Selection (Natural Selection) 50%
  • DNA 50%
  • Introspection 50%
• 2018

  DISC1 regulates N-methyl-D-aspartate receptor dynamics: abnormalities induced by a Disc1 mutation modelling a translocation linked to major mental illness

  Malavasi, E. L. V., Economides, K. D., Grünewald, E., Makedonopoulou, P., Gautier, P., Mackie, S., Murphy, L. C., Murdoch, H., Crummie, D., Ogawa, F., McCartney, D. L., O'Sullivan, S. T., Burr, K., Torrance, H. S., Phillips, J., Bonneau, M., Anderson, S. M., Perry, P., Pearson, M., Constantinides, C., & 16 othersDavidson-Smith, H., Kabiri, M., Duff, B., Johnstone, M., Polites, H. G., Lawrie, S. M., Blackwood, D. H., Semple, C. A., Evans, K. L., Didier, M., Chandran, S., McIntosh, A. M., Price, D. J., Houslay, M. D., Porteous, D. J. & Millar, J. K., 6 Sept 2018, In: Translational Psychiatry. 8, 1, 184.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Mutation 100%
  • DISC1 100%
  • Dynamics 100%
  • Aspartic Acid 100%
  • Eicosanoid Receptor 100%

• Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

  Vacca, A., Itoh, M., Kawaji, H., Arner, E., Lassmann, T., Daub, C., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., FANTOM consortium, T., Aitken, J. & Semple, C., 8 Aug 2018, In: Open Biology.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline

  Kaiser, V. B. & Semple, C. A., 30 Jul 2018, In: Genome Biology. 19, 101.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • CTCF 100%
  • Chromatin 100%
  • Genome Instability 100%
  • Germline 100%
  • Single-Nucleotide Polymorphism 75%

• Enhanced response rate to pegylated liposomal doxorubicin in high grade serous ovarian carcinomas harbouring BRCA1 and BRCA2 aberrations

  Hollis, R. L., Meynert, A. M., Churchman, M., Rye, T., Mackean, M., Nussey, F., Arends, M. J., Sims, A. H., Semple, C. A., Herrington, C. S. & Gourley, C., 3 Jan 2018, In: BMC Cancer. 18, 1, p. 16

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • BRCA1 100%
  • Doxorubicin 100%
  • Krukenberg Tumor 100%
  • Aberration 100%
  • Patient 53%
• 2017

  The circadian dynamics of small nucleolar RNA in the mouse liver

  Aitken, J. & Semple, C., 3 May 2017, In: Journal of the Royal Society. Interface.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Mouse 100%
  • Small Nucleolar RNA 100%
  • Ribosomal RNA 100%
  • Dynamics 100%
  • Regulatory Mechanism 57%
• 2016

  Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types

  Kaiser, V. B., Taylor, M. S. & Semple, C. A., 4 Aug 2016, In: PLoS Genetics. 12, 8, 19 p., e1006207.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Binding Site 100%
  • Drive 100%
  • Regulatory Site 100%
  • Mutation 71%
  • Transcription Factor 57%
• 2015

  Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

  FANTOM Consortium, Fraser, J., Ferrai, C., Chiariello, A. M., Schueler, M., Rito, T., Laudanno, G., Barbieri, M., Moore, B. L., Kraemer, D. C., Aitken, S., Xie, S. Q., Morris, K. J., Itoh, M., Kawaji, H., Jaeger, I., Hayashizaki, Y., Carninci, P., Forrest, A. R., Semple, C. A., & 3 othersDostie, J., Pombo, A. & Nicodemi, M., 28 Dec 2015, In: Molecular Systems Biology. 11, 12, p. 852 14 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Tree 100%
  • Chromosome 100%
  • Cellular Differentiation 100%
  • Scale up 33%
  • DNA 33%

• The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

  Hurst, L. D., Ghanbarian, A. T., Forrest, A. R. R., FANTOM consortium & Huminiecki, L., 18 Dec 2015, In: PLoS Biology. 13, 12, e1002315.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Genes 100%
  • X Chromosome 100%
  • Shape 100%
  • Haploidy 100%
  • Nested Gene 100%

• Homozygous loss-of-function variants in European cosmopolitan and isolate populations

  Generation Scotland, UK10K, Kaiser, V. B., Svinti, V., Prendergast, J. G., Chau, Y-Y., Campbell, A., Patarcic, I., Barroso, I., Joshi, P. K., Hastie, N. D., Miljkovic, A., Taylor, M. S., Enroth, S., Memari, Y., Kolb-Kokocinski, A., Wright, A. F., Gyllensten, U., Durbin, R., Rudan, I., & 11 othersCampbell, H., Polašek, O., Johansson, Å., Sauer, S., Porteous, D. J., Fraser, R. M., Drake, C., Vitart, V., Hayward, C., Semple, C. A. & Wilson, J. F., 14 Jul 2015, In: Human Molecular Genetics.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Nested Gene 100%
  • Gene Function 75%
  • Human 50%
  • Loss of Function Mutation 50%
  • Sample 25%

• Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization

  Moore, B. L., Aitken, S. & Semple, C. A., 27 May 2015, In: Genome Biology. 16, 1, 110.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Chromatin 100%
  • Enhancer Region 16%
  • DNA-binding Protein 16%
  • Transcription Factor YY1 16%
  • Transcription Factor CTCF 16%

• Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

  FANTOM Consortium, Aitken, J., Magi, S., Alhendi, A. M. N., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Arner, E., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Khachigian, L. M., Okada-Hatakeyama, M. & Semple, C. A., 17 Apr 2015, In: PLoS Computational Biology. 11, 4, e1004217.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Non-Coding RNA 100%
  • Dynamics 100%
  • Time 100%
  • Immediate Early Gene 83%
  • Chromatin 33%
• 2014

  Sequence level mechanisms of human epigenome evolution

  Prendergast, J. G. D., Chambers, E. V. & Semple, C. A. M., 24 Jun 2014, In: Genome Biology and Evolution. 6, 7, p. 1758-1771

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Evolution 100%
  • Epigenome 100%
  • DNA Methylation 75%
  • Chromatin 62%
  • Alu Element 25%

• Abundant local interactions in the 4p16.1 region suggest functional mechanisms underlying SLC2A9 associations with human serum uric acid

  Wei, W., Guo, Y., Kindt, A. S. D., Merriman, T. R., Semple, C. A., Wang, K. & Haley, C. S., 12 May 2014, In: Human Molecular Genetics. E-pub 12 May

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Single Nucleotide Polymorphism 100%
  • Association 100%
  • SLC2A9 100%
  • Uric Acid Blood Level 100%
  • Cohort Study 42%

• A promoter-level mammalian expression atlas

  FANTOM Consortium & RIKEN PMI CLST DGT, 27 Mar 2014, In: Nature. 507, 7493, p. 462-470 9 p.

  Research output: Contribution to journal › Article › peer-review

  • Promoter Region 100%
  • Transcription Initiation Site 75%
  • Nested Gene 50%
  • Sample 25%
  • Mouse 25%
• 2013

  Lsh regulates LTR retrotransposon repression independently of Dnmt3b function

  Dunican, D. S., Cruickshanks, H. A., Suzuki, M., Semple, C. A., Davey, T., Arceci, R. J., Greally, J., Adams, I. R. & Meehan, R. R., 24 Dec 2013, In: Genome Biology. 14, 12, p. R146

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • DNA Methylation 100%
  • Defense Mechanism 100%
  • Retrotransposon 100%
  • Chromatin 50%
  • Helicase 25%

• Corrigendum of 'High throughput analysis of epistasis in genome-wide association studies with BiForce'

  Gyenesei, A., Semple, C. A. M., Haley, C. S. & Wei, W-H., 15 Oct 2013, In: Bioinformatics. 29, 20, p. 2667-2668 2 p.

  Research output: Contribution to journal › Article › peer-review

• Properties of local interactions and their potential value in complementing genome-wide association studies

  Wei, W., Gyenesei, A., Semple, C. A. M. & Haley, C. S., 5 Aug 2013, In: PLoS ONE. 8, 8, p. e71203

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Genome-Wide Association Study 100%
  • Electric Potential 100%
  • Genome Wide Association Study 100%
  • Single Nucleotide Polymorphism 37%
  • Birth 25%

• Side effects: substantial non-neutral evolution flanking regulatory sites

  Prendergast, J. G. D. & Semple, C. A., May 2013, In: PLoS Genetics. 9, 5, p. e1003528

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

  Chambers, E. V., Bickmore, W. A. & Semple, C. A., Apr 2013, In: PLoS Computational Biology. 9, 4, e1003017.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Mouse 100%
  • Evolution 100%
  • Chromatin Structure 100%
  • Nested Gene 75%
  • Species 25%

• The genomic signature of trait-associated variants

  Kindt, A. S. D., Navarro, P., Semple, C. A. M. & Haley, C. S., 18 Feb 2013, In: BMC Genomics. 14, 15 p., ARTN 108.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Single Nucleotide Polymorphism 100%
  • Genomic Signature 100%
  • Association 60%
  • Genome-Wide Association Study 20%
  • Regulatory Region 20%
• 2012

  BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies

  Gyenesei, A., Moody, J., Laiho, A., Semple, C. A. M., Haley, C. S. & Wei, W., 1 Jul 2012, In: Nucleic Acids Research. 40, W1, p. W628-W632

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Genome-Wide Association Study 100%
  • Gene Interaction 100%
  • Nested Gene 100%
  • High Throughput 100%
  • Wide Association Study 100%

• Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk

  The Colorectal Tumour Gene Identification (CORGI) Consortium, The Swedish Low-Risk Colorectal Cancer Study Group, The COIN Collaborative Group & Tomlinson, I., Jul 2012, In: Nature Genetics. 44, 7, p. 770-776 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Genome-Wide Association Study 100%
  • Introspection 100%
  • Genetic Architecture 100%

• Genome-wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway

  Nimmo, E. R., Prendergast, J. G., Aldhous, M. C., Kennedy, N. A., Henderson, P., Drummond, H. E., Ramsahoye, B. H., Wilson, D. C., Semple, C. A. & Satsangi, J., May 2012, In: Inflammatory Bowel Diseases. 18, 5, p. 889-899 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Epigenetics 100%
  • Host Resistance 100%
  • Regulatory Mechanism 100%
  • Methylation 100%
  • NOD2 25%

• Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

  Schroder, K., Irvine, K. M., Taylor, M. S., Bokil, N. J., Le Cao, K-A., Masterman, K-A., Labzin, L. I., Semple, C. A., Kapetanovic, R., Fairbairn, L., Akalin, A., Faulkner, G. J., Baillie, J. K., Gongora, M., Daub, C. O., Kawaji, H., McLachlan, G. J., Goldman, N., Grimmond, S. M., Carninci, P., & 5 othersSuzuki, H., Hayashizaki, Y., Lenhard, B., Hume, D. A. & Sweet, M. J., 17 Apr 2012, In: Proceedings of the National Academy of Sciences (PNAS). 109, 16, p. E944-E953

  Research output: Contribution to journal › Article › peer-review

  • Macrophage 100%
  • Mouse 100%
  • Gene Expression 100%
  • TLR4 100%
  • Lipopolysaccharide 80%

• A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

  Prendergast, J. G., Tong, P., Hay, D. C., Farrington, S. M. & Semple, C. A., 2012, In: Epigenetics and Chromatin. 5, 1, p. 6

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Histone Modification 100%
  • Embryonic Stem Cell 100%
  • Allele 100%
  • DNA Methylation 28%
  • Chromatin Structure 14%

• High throughput analysis of epistasis in genome-wide association studies with BiForce

  Gyenesei, A., Moody, J., Semple, C. A. M., Haley, C. S. & Wei, W., 2012, In: Bioinformatics. 28, 15, p. 1957-1964

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Genome-Wide Association Study 100%
  • Single Nucleotide Polymorphism 100%
  • Epistasis 100%
  • Memory 16%
  • Comprehension 16%
• 2011

  A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

  Diez-Roux, G., Banfi, S., Sultan, M., Geffers, L., Anand, S., Rozado, D., Magen, A., Canidio, E., Pagani, M., Peluso, I., Lin-Marq, N., Koch, M., Bilio, M., Cantiello, I., Verde, R., De Masi, C., Bianchi, S. A., Cicchini, J., Perroud, E., Mehmeti, S., & 48 othersDagand, E., Schrinner, S., Nuernberger, A., Schmidt, K., Metz, K., Zwingmann, C., Brieske, N., Springer, C., Hernandez, A. M., Herzog, S., Grabbe, F., Sieverding, C., Fischer, B., Schrader, K., Brockmeyer, M., Dettmer, S., Helbig, C., Alunni, V., Battaini, M-A., Mura, C., Henrichsen, C. N., Garcia-Lopez, R., Echevarria, D., Puelles, E., Garcia-Calero, E., Kruse, S., Uhr, M., Kauck, C., Feng, G., Milyaev, N., Ong, C. K., Kumar, L., Lam, M., Semple, C., Gyenesei, A., Mundlos, S., Radelof, U., Lehrach, H., Sarmientos, P., Reymond, A., Davidson, D. R., Dolle, P., Antonarakis, S. E., Yaspo, M-L., Martinez, S., Baldock, R., Eichele, G. & Ballabio, A., Jan 2011, In: PLoS Biology. 9, 1, p. 1-13 13 p., e1000582.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Transcriptome 100%
  • Mouse 100%
  • Gene 100%
  • Nested Gene 100%
  • Tissues 28%

• Human β-defensin 3 affects the activity of pro-inflammatory pathways associated with MyD88 and TRIF

  Semple, F., MacPherson, H., Webb, S., Cox, S. L., Mallin, L. J., Tyrrell, C., Grimes, G. R., Semple, C. A., Nix, M. A., Millhauser, G. L. & Dorin, J. R., 2011, In: European Journal of Immunology. 41, 11, p. 3291-300 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Macrophage 100%
  • TRIF 100%
  • Defensin 100%
  • Nested Gene 75%
  • TLR4 75%

• Opening sequence: computational genomics in the era of high-throughput sequencing

  Chambers, E. V., Kindt, A. S. & Semple, C. A., 2011, In: Genome Biology. 12, 12, p. 310

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • High Throughput Sequencing 100%
  • Computational Genomics 100%