![Matthew Mort](https://profiles-cardiff.imgix.net/attachments/5538?w=200&h=200&auto=format&crop=faces&fit=crop&q=90")
Dr Matthew Mort
Senior Data Scientist & Informatics Manager for the Human Gene Mutation Database
- MortM@cardiff.ac.uk
- +44 29207 45116
- Institute of Medical Genetics Building, University Hospital of Wales, Heath Park, Cardiff, CF14 4XN
Overview
Senior Data Scientist & Informatics Manager for the Human Gene Mutation Database (HGMD).
- Extensive expertise in precision medicine within medical genetics.
- Focussed on bioinformatics, data science and clinical AI including machine learning.
I am passionate about life long learning, team working, productivity, leadership and executive coaching.
I have contributed to over 100 peer reviewed publications published in high impact journals including Nature and Science.
Extensive track record of collaborations with external organizations including: NHS, Qiagen and leading universities in the USA, Europe and Asia.
AI champion for the School of Medicine.
Digital Productivity and AI in the workplace:
https://intranet.cardiff.ac.uk/staff/training-and-development/staff-courses-and-programmes/all-courses/digital-productivity-including-ai-in-the-workplace
Please contact me:
- If you wish to collaborate on any projects together.
- Have any questions about the HGMD resource.
- Have any questions relating to implementing AI in your work.
- Are intrested in being coached by myself.
Publication
2024
- Lopes-Marques, M., Mort, M., Carneiro, J., Azevedo, A., Amaro, A. P., Cooper, D. N. and Azevedo, L. 2024. Meta-analysis of 46,000 germline de novo mutations linked to human inherited disease. Human Genomics 18(1), article number: 20. (10.1186/s40246-024-00587-8)
- Duffy, ?. et al. 2024. Development of a human genetics-guided priority score for 19,365 genes and 399 drug indications. Nature Genetics 56(1), pp. 51-59. (10.1038/s41588-023-01609-2)
2023
- Fan, C. et al. 2023. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Human Genetics 142, pp. 245-274. (10.1007/s00439-022-02500-6)
2021
- Neville, M. D. et al. 2021. A platform for curated products from novel Open Reading Frames (nORFs) prompts reinterpretation of disease variants. Genome Research 31(2), pp. 327-336. (10.1101/gr.263202.120)
- Thomas, L. E. et al. 2021. Duodenal adenomas and cancer in MUTYH-associated polyposis: an international cohort study. Gastroenterology 160(3), pp. 952-954. (10.1053/j.gastro.2020.10.038)
- Bacolla, A. et al. 2021. Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin. Nucleic Acids Research 49(1), pp. 221-243. (10.1093/nar/gkaa1120)
2020
- Pejaver, V. et al. 2020. Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nature Communications 11(1), article number: 5918. (10.1038/s41467-020-19669-x)
- Stenson, P. D. et al. 2020. The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting. Human Genetics 139, pp. 1197-1207. (10.1007/s00439-020-02199-3)
- Cardoso-Moreira, M., Sarropoulos, I., Velten, B., Mort, M., Cooper, D. N., Huber, W. and Kaessmann, H. 2020. Developmental gene expression differences between humans and mammalian models. Cell Reports 33(4), article number: 108308. (10.1016/j.celrep.2020.108308)
- Short, E. et al. 2020. APC transcription studies and molecular diagnosis of familial adenomatous polyposis. European Journal of Human Genetics 28(1), pp. 118-121. (10.1038/s41431-019-0486-2)
2019
- Lin, H. et al. 2019. RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants. Genome Biology 20(1), article number: 254. (10.1186/s13059-019-1847-4)
- Lin, J. et al. 2019. First estimate of the scale of canonical 5' splice site GT>GC variants capable of generating wild-type transcripts. Human Mutation 40(10), pp. 1856-1873. (10.1002/humu.23821)
- Fragoza, R. et al. 2019. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nature Communications 10(1), article number: 4141. (10.1038/s41467-019-11959-3)
- Cardoso-Moreira, M. et al. 2019. Gene expression across mammalian organ development. Nature 571, pp. 505 - 509. (10.1038/s41586-019-1338-5)
- Pagel, K. A. et al. 2019. Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Computational Biology 15(6), article number: e1007112. (10.1371/journal.pcbi.1007112)
2018
- Robinson-Rechavi, M. et al. 2018. The sequencing and interpretation of the genome obtained from a Serbian individual. PLoS ONE 13(12), article number: e0208901. (10.1371/journal.pone.0208901)
- Caciotti, A. et al. 2018. Mis-splicing of the GALNS gene resulting from deep intronic mutations as a cause of Morquio a disease. BMC Medical Genetics 19(1), article number: 183. (10.1186/s12881-018-0694-6)
- Hurley, J. J. et al. 2018. The impact of chromoendoscopy for surveillance of the duodenum in patients with MUTYH-associated polyposis and familial adenomatous polyposis. Gastrointestinal Endoscopy 88(4), pp. 665-673. (10.1016/j.gie.2018.04.2347)
- Rogers, M. F., Shihab, H. A., Mort, M., Cooper, D., Gaunt, T. R. and Campbell, C. 2018. FATHMM-XF: accurate prediction of pathogenic point mutations via extended features. Bioinformatics 34(3), pp. 511-513. (10.1093/bioinformatics/btx536)
- Zhao, H., Yang, Y., Lu, Y., Mort, M., Cooper, D. N., Zuo, Z. and Zhou, Y. 2018. Quantitative mapping of genetic similarity in human heritable diseases by shared mutations. Human Mutation 39(2), pp. 292-301. (10.1002/humu.23358)
2017
- Thomas, L. E. et al. 2017. Burden and profile of somatic mutation in duodenal adenomas from patients with familial adenomatous- and MUTYH-associated polyposis. Clinical Cancer Research 23(21), pp. 6721-6732. (10.1158/1078-0432.CCR-17-1269)
- Ferlaino, M., Rogers, M. F., Shihab, H. A., Mort, M., Cooper, D., Gaunt, T. R. and Campbell, C. 2017. An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome. BMC bioinformatics 18(1), article number: 442. (10.1186/s12859-017-1862-y)
- Lu, T. et al. 2017. Biological and functional relevance of CASP predictions.. Proteins (10.1002/prot.25396)
- Livingstone, M. et al. 2017. Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants. Human Mutation 38(10), pp. 1336-1347. (10.1002/humu.23283)
- Zhang, X. et al. 2017. regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution. Human Genetics 136(9), pp. 1279-1289. (10.1007/s00439-017-1783-x)
- Pagel, K. A. et al. 2017. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinformatics 33(14), pp. i389-i398. (10.1093/bioinformatics/btx272)
- Stenson, P. D. et al. 2017. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Human Genetics 136(6), pp. 665-677. (10.1007/s00439-017-1779-6)
- Andreoletti, G. et al. 2017. Exome analysis of rare and common variants within the NOD signaling pathway. Scientific Reports 7, article number: 46454. (10.1038/srep46454)
- Knecht, C., Mort, M., Junge, O., Cooper, D. N., Krawczak, M. and Caliebe, A. 2017. IMHOTEP A composite score integrating popular tools for predicting the functional consequences of non-synonymous sequence variants. Nucleic Acids Research 45(3), pp. e13. (10.1093/nar/gkw886)
- Liang, S., Tippens, N. D., Zhou, Y., Mort, M., Stenson, P. D., Cooper, D. N. and Yu, H. 2017. iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations. Genome Biology 18(1), article number: 10. (10.1186/s13059-016-1138-2)
- Li, M. et al. 2017. ExonImpact: prioritizing pathogenic alternative splicing events. Human Mutation 38(1), pp. 16-24. (10.1002/humu.23111)
2016
- Azevedo, L., Mort, M., Costa, A. C., Silva, R. M., Quelhas, D., Amorim, A. and Cooper, D. N. 2016. Improving the in silico assessment of pathogenicity for compensated variants. European Journal of Human Genetics 25(1), pp. 2-7. (10.1038/ejhg.2016.129)
- Wang, Q. et al. 2016. Overview of the interactive task in BioCreative V. Database 2016(baw119) (10.1093/database/baw119)
- Peterson, T. A., Mort, M., Cooper, D. N., Radivojac, P., Kann, M. G. and Mooney, S. D. 2016. Regulatory single-nucleotide variant predictor increases predictive performance of functional regulatory variants. Human Mutation 37(11), pp. 1137-1143. (10.1002/humu.23049)
- Lugo-Martinez, J. et al. 2016. The loss and gain of functional amino acid residues is a common mechanism causing human inherited disease. PLoS Computational Biology 12(8), article number: e1005091. (10.1371/journal.pcbi.1005091)
- Matos, S., Campos, D., Pinho, R., Silva, R. M., Mort, M., Cooper, D. N. and Oliveira, J. L. 2016. Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database 2016, article number: baw096. (10.1093/database/baw096)
- Meyer, M. J. et al. 2016. mutation3D: cancer gene prediction through atomic clustering of coding variants in the structural proteome. Human Mutation 37(5), pp. 447-456. (10.1002/humu.22963)
2015
- Upadhyaya, M. et al. 2015. Correlation of copy number changes and gene expression in neurofibromatosis1-associated malignant peripheral nerve sheath tumours [Abstract]. Pediatric Blood and Cancer 62(S4), pp. S152-S152. (10.1002/pbc.25715)
- Mort, M. E., Carlisle, F., Waite, A., Elliston, L., Allen, N. D., Jones, L. and Hughes, A. 2015. Huntingtin exists as multiple splice forms in human brain. Journal of Huntington's Disease 4(2), pp. 161-171. (10.3233/JHD-150151)
- Folkman, L. et al. 2015. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. Bioinformatics 31(10), pp. 1599-1606. (10.1093/bioinformatics/btu862)
- Shihab, H. A. et al. 2015. An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics 31(10), pp. 1536-1543. (10.1093/bioinformatics/btv009)
- Thomas, L. E. et al. 2015. Evaluation of copy number variation and gene expression in neurofibromatosis type-1-associated malignant peripheral nerve sheath tumours. Human Genomics 9(1), article number: 3. (10.1186/s40246-015-0025-3)
- Winston, J., Duerden, L., Mort, M., Frayling, I., Rogers, M. and Upadhyaya, M. 2015. Identification of two novel SMCHD1 sequence variants in families with FSHD-like muscular dystrophy. European Journal of Human Genetics 23(1), pp. 67-71. (10.1038/ejhg.2014.58)
- Rogers, M. F., Campbell, C., Shihab, H. A., Gaunt, T. R., Mort, M. and Cooper, D. N. 2015. Sequential data selection for predicting the pathogenic effects of sequence variation. Presented at: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington DC, USA, 9-12 November 2015Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on. IEEE pp. 639-644., (10.1109/BIBM.2015.7359759)
2014
- Wei, X. et al. 2014. A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. PLoS Genetics 10(12), article number: e1004819. (10.1371/journal.pgen.1004819)
- Shihab, H. A., Gough, J., Mort, M. E., Cooper, D. N., Day, I. N. M. and Gaunt, T. R. 2014. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Human Genomics 8, article number: 11. (10.1186/1479-7364-8-11)
- Zhang, X. et al. 2014. Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation. Human Molecular Genetics 23(11), pp. 3024-3034. (10.1093/hmg/ddu019)
- Das, J. et al. 2014. Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks. Human Mutation 35(5), pp. 585-593. (10.1002/humu.22534)
- Hughes, A., Mort, M. E., Elliston, L. A., Thomas, R. M., Brooks, S. P., Dunnett, S. B. and Jones, L. 2014. Identification of novel alternative splicing events in the Huntingtin gene and assessment of the functional consequences using structural protein homology modelling. Journal of Molecular Biology 426(7), pp. 1428-1438. (10.1016/j.jmb.2013.12.028)
- Mort, M. et al. 2014. MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing. Genome Biology 15(1), article number: R19. (10.1186/gb-2014-15-1-r19)
- Stenson, P., Mort, M., Ball, E., Shaw, K., Phillips, A. and Cooper, D. 2014. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genetics 133(1), pp. 1-9. (10.1007/s00439-013-1358-4)
2013
- Bagchi, A. et al. 2013. Analysis of features from protein-protein hetero-complex structures to predict protein interaction interfaces using machine learning. Procedia Technology 10, pp. 62-66. (10.1016/j.protcy.2013.12.337)
- Ku, C. S. et al. 2013. A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease. Molecular Psychiatry 18(2), pp. 141-153. (10.1038/mp.2012.58)
- Zhao, H. et al. 2013. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biology 14(3), pp. R23. (10.1186/gb-2013-14-3-r23.)
2012
- Thomas, L., Richards, M., Mort, M. E., Dunlop, E. A., Cooper, D. N. and Upadhyaya, M. 2012. Assessment of the potential pathogenicity of missense mutations identified in the GTPase-activating protein (GAP)-related domain of the neurofibromatosis type-1 (NF1) gene. Human Mutation 33(12), pp. 1687-1696. (10.1002/humu.22162)
- Xue, Y. et al. 2012. Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. American Journal of Human Genetics 91(6), pp. 1022-1032. (10.1016/j.ajhg.2012.10.015)
- Stenson, P. D., Ball, E. V., Mort, M. E., Phillips, A. D., Shaw, K. and Cooper, D. N. 2012. The human gene mutation database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Current Protocols in Bioinformatics 39, pp. 1.13.1-1.13.20. (10.1002/0471250953.bi0113s39)
- Teng, M. et al. 2012. regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions. Bioinformatics 28(14), pp. 1879-1886. (10.1093/bioinformatics/bts275)
- Scally, A. et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483(7388), pp. 169-175. (10.1038/nature10842)
- Thomas, L. et al. 2012. Exploring the somatic NF1 mutational spectrum associated with NF1 cutaneous neurofibromas. European Journal of Human Genetics 20(4), pp. 411-419. (10.1038/ejhg.2011.207)
2011
- Zhang, G., Pei, Z., Ball, E. V., Mort, M. E., Cooper, D. N. and Kehrer-Sawatzki, H. 2011. Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations. Human Genomics 5(5), pp. 453-484.
- Bertola, F. et al. 2011. IDUA mutational profiling of a cohort of 102 European patients with mucopolysaccharidosis type I: identification and characterization of 35 novel α-L-iduronidase (IDUA) alleles. Human Mutation 32(6), pp. E2189-E2210. (10.1002/humu.21479)
- Wolf, A. et al. 2011. Single base-pair substitutions at the translation initiation sites of human genes as a cause of inherited disease. Human Mutation 32(10), pp. 1137-1143. (10.1002/humu.21547)
- Zhao, Y., Clark, W. T., Mort, M. E., Cooper, D. N., Radivojac, P. and Mooney, S. D. 2011. Prediction of functional regulatory SNPs in monogenic and complex disease. Human Mutation 32(10), pp. 1183-1190. (10.1002/humu.21559)
- Sterne-Weiler, T., Howard, J., Mort, M., Cooper, D. N. and Sanford, J. R. 2011. Loss of exon identity is a common mechanism of human inherited disease. Genome Research 21(10), pp. 1563-1571. (10.1101/gr.118638.110)
- Grossi, S. et al. 2011. Molecular genetic analysis of the PLP1 gene in 38 families with PLP1-related disorders: identification and functional characterization of 11 novel PLP1 mutations. Orphanet Journal of Rare Diseases 6, article number: 40. (10.1186/1750-1172-6-40)
2010
- Durbin, R. M. et al. 2010. A map of human genome variation from population-scale sequencing. Nature 467(7319), pp. 1061-1073. (10.1038/nature09534)
- Cooper, D. N., Mort, M. E., Stenson, P. D., Ball, E. V. and Chuzhanova, N. A. 2010. Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides. Human Genomics 4(6), pp. 406-410.
- Mort, M. E. et al. 2010. In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Human Mutation 31(3), pp. 335-346. (10.1002/humu.21192)
- Cooper, D. N. et al. 2010. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Human Mutation 31(6), pp. 631-655. (10.1002/humu.21260)
- Tappino, B. et al. 2010. Identification and characterization of 15 novel GALC gene mutations causing Krabbe disease. Human Mutation 31(12), pp. E1894-E1914. (10.1002/humu.21367)
- Zhang, G., Pei, Z., Krawczak, M., Ball, E. V., Mort, M. E., Kehrer-Sawatzki, H. and Cooper, D. N. 2010. Triangulation of the human, chimpanzee, and Neanderthal genome sequences identifies potentially compensated mutations. Human Mutation 31(12), pp. 1286-1293. (10.1002/humu.21389)
- Cooper, D. N. and Mort, M. 2010. Do inherited disease genes have distinguishing functional characteristics?. Genetic Testing and Molecular Biomarkers 14(3), pp. 289-291. (10.1089/gtmb.2010.0033)
- Cooper, D. N., Ball, E. V. and Mort, M. E. 2010. Chromosomal distribution of disease genes in the human genome. Genetic Testing and Molecular Biomarkers 14(4), pp. 441-446. (10.1089/gtmb.2010.0081)
2009
- Stenson, P. D., Ball, E. V., Howells, K., Phillips, A. D., Mort, M. E. and Cooper, D. N. 2009. The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics [Editorial]. Human Genomics 4(2), pp. 69-72.
- Stenson, P. D., Mort, M., Ball, E., Howells, K., Phillips, A. D., Thomas, N. and Cooper, D. N. 2009. The Human Gene Mutation Database: 2008 update. Genome Medicine 1(1), article number: 13. (10.1186/gm13)
- Li, B. et al. 2009. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25(21), pp. 2744-2750. (10.1093/bioinformatics/btp528)
- Sanford, J. R. et al. 2009. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Research 19(3), pp. 381-394. (10.1101/gr.082503.108)
2008
- Mort, M. E., Ivanov, D., Cooper, D. N. and Chuzhanova, N. 2008. A meta-analysis of nonsense mutations causing human genetic disease. Human Mutation 29(8), pp. 1037-1047. (10.1002/humu.20763)
- Radivojac, P., Baenziger, P. H., Kann, M. G., Mort, M., Hahn, M. W. and Mooney, S. D. 2008. Gain and loss of phosphorylation sites in human cancer. Bioinformatics 24(16), pp. i241-i247. (10.1093/bioinformatics/btn267)
2007
- Krawczak, M., Thomas, N. S., Hundrieser, B., Mort, M., Wittig, M., Hampe, J. and Cooper, D. N. 2007. Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing. Human Mutation 28(2), pp. 150-158. (10.1002/humu.20400)
- Stenson, P. D., Ball, E., Howells, K., Phillips, A., Mort, M. E. and Cooper, D. N. 2007. Human Gene Mutation Database: towards a comprehensive central mutation database [Letter]. Journal of Medical Genetics 45(2), pp. 124-126. (10.1136/jmg.2007.055210)
2006
- Khan, I. A., Mort, M., Buckland, P. R., O'Donovan, M. C., Cooper, D. N. and Chuzhanova, N. A. 2006. In silico discrimination of single nucleotide polymorphisms and pathological mutations in human gene promoter regions by means of local DNA sequence context and regularity.. In silico Biology 6(1-2), pp. 23-34.
2003
- Stenson, P. D. et al. 2003. Human Gene Mutation Database (HGMD): 2003 update. Human Mutation 21(6), pp. 577-581. (10.1002/humu.10212)
Articles
- Lopes-Marques, M., Mort, M., Carneiro, J., Azevedo, A., Amaro, A. P., Cooper, D. N. and Azevedo, L. 2024. Meta-analysis of 46,000 germline de novo mutations linked to human inherited disease. Human Genomics 18(1), article number: 20. (10.1186/s40246-024-00587-8)
- Duffy, ?. et al. 2024. Development of a human genetics-guided priority score for 19,365 genes and 399 drug indications. Nature Genetics 56(1), pp. 51-59. (10.1038/s41588-023-01609-2)
- Fan, C. et al. 2023. Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Human Genetics 142, pp. 245-274. (10.1007/s00439-022-02500-6)
- Neville, M. D. et al. 2021. A platform for curated products from novel Open Reading Frames (nORFs) prompts reinterpretation of disease variants. Genome Research 31(2), pp. 327-336. (10.1101/gr.263202.120)
- Thomas, L. E. et al. 2021. Duodenal adenomas and cancer in MUTYH-associated polyposis: an international cohort study. Gastroenterology 160(3), pp. 952-954. (10.1053/j.gastro.2020.10.038)
- Bacolla, A. et al. 2021. Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin. Nucleic Acids Research 49(1), pp. 221-243. (10.1093/nar/gkaa1120)
- Pejaver, V. et al. 2020. Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nature Communications 11(1), article number: 5918. (10.1038/s41467-020-19669-x)
- Stenson, P. D. et al. 2020. The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting. Human Genetics 139, pp. 1197-1207. (10.1007/s00439-020-02199-3)
- Cardoso-Moreira, M., Sarropoulos, I., Velten, B., Mort, M., Cooper, D. N., Huber, W. and Kaessmann, H. 2020. Developmental gene expression differences between humans and mammalian models. Cell Reports 33(4), article number: 108308. (10.1016/j.celrep.2020.108308)
- Short, E. et al. 2020. APC transcription studies and molecular diagnosis of familial adenomatous polyposis. European Journal of Human Genetics 28(1), pp. 118-121. (10.1038/s41431-019-0486-2)
- Lin, H. et al. 2019. RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants. Genome Biology 20(1), article number: 254. (10.1186/s13059-019-1847-4)
- Lin, J. et al. 2019. First estimate of the scale of canonical 5' splice site GT>GC variants capable of generating wild-type transcripts. Human Mutation 40(10), pp. 1856-1873. (10.1002/humu.23821)
- Fragoza, R. et al. 2019. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nature Communications 10(1), article number: 4141. (10.1038/s41467-019-11959-3)
- Cardoso-Moreira, M. et al. 2019. Gene expression across mammalian organ development. Nature 571, pp. 505 - 509. (10.1038/s41586-019-1338-5)
- Pagel, K. A. et al. 2019. Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Computational Biology 15(6), article number: e1007112. (10.1371/journal.pcbi.1007112)
- Robinson-Rechavi, M. et al. 2018. The sequencing and interpretation of the genome obtained from a Serbian individual. PLoS ONE 13(12), article number: e0208901. (10.1371/journal.pone.0208901)
- Caciotti, A. et al. 2018. Mis-splicing of the GALNS gene resulting from deep intronic mutations as a cause of Morquio a disease. BMC Medical Genetics 19(1), article number: 183. (10.1186/s12881-018-0694-6)
- Hurley, J. J. et al. 2018. The impact of chromoendoscopy for surveillance of the duodenum in patients with MUTYH-associated polyposis and familial adenomatous polyposis. Gastrointestinal Endoscopy 88(4), pp. 665-673. (10.1016/j.gie.2018.04.2347)
- Rogers, M. F., Shihab, H. A., Mort, M., Cooper, D., Gaunt, T. R. and Campbell, C. 2018. FATHMM-XF: accurate prediction of pathogenic point mutations via extended features. Bioinformatics 34(3), pp. 511-513. (10.1093/bioinformatics/btx536)
- Zhao, H., Yang, Y., Lu, Y., Mort, M., Cooper, D. N., Zuo, Z. and Zhou, Y. 2018. Quantitative mapping of genetic similarity in human heritable diseases by shared mutations. Human Mutation 39(2), pp. 292-301. (10.1002/humu.23358)
- Thomas, L. E. et al. 2017. Burden and profile of somatic mutation in duodenal adenomas from patients with familial adenomatous- and MUTYH-associated polyposis. Clinical Cancer Research 23(21), pp. 6721-6732. (10.1158/1078-0432.CCR-17-1269)
- Ferlaino, M., Rogers, M. F., Shihab, H. A., Mort, M., Cooper, D., Gaunt, T. R. and Campbell, C. 2017. An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome. BMC bioinformatics 18(1), article number: 442. (10.1186/s12859-017-1862-y)
- Lu, T. et al. 2017. Biological and functional relevance of CASP predictions.. Proteins (10.1002/prot.25396)
- Livingstone, M. et al. 2017. Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants. Human Mutation 38(10), pp. 1336-1347. (10.1002/humu.23283)
- Zhang, X. et al. 2017. regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution. Human Genetics 136(9), pp. 1279-1289. (10.1007/s00439-017-1783-x)
- Pagel, K. A. et al. 2017. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinformatics 33(14), pp. i389-i398. (10.1093/bioinformatics/btx272)
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- Andreoletti, G. et al. 2017. Exome analysis of rare and common variants within the NOD signaling pathway. Scientific Reports 7, article number: 46454. (10.1038/srep46454)
- Knecht, C., Mort, M., Junge, O., Cooper, D. N., Krawczak, M. and Caliebe, A. 2017. IMHOTEP A composite score integrating popular tools for predicting the functional consequences of non-synonymous sequence variants. Nucleic Acids Research 45(3), pp. e13. (10.1093/nar/gkw886)
- Liang, S., Tippens, N. D., Zhou, Y., Mort, M., Stenson, P. D., Cooper, D. N. and Yu, H. 2017. iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations. Genome Biology 18(1), article number: 10. (10.1186/s13059-016-1138-2)
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- Azevedo, L., Mort, M., Costa, A. C., Silva, R. M., Quelhas, D., Amorim, A. and Cooper, D. N. 2016. Improving the in silico assessment of pathogenicity for compensated variants. European Journal of Human Genetics 25(1), pp. 2-7. (10.1038/ejhg.2016.129)
- Wang, Q. et al. 2016. Overview of the interactive task in BioCreative V. Database 2016(baw119) (10.1093/database/baw119)
- Peterson, T. A., Mort, M., Cooper, D. N., Radivojac, P., Kann, M. G. and Mooney, S. D. 2016. Regulatory single-nucleotide variant predictor increases predictive performance of functional regulatory variants. Human Mutation 37(11), pp. 1137-1143. (10.1002/humu.23049)
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- Meyer, M. J. et al. 2016. mutation3D: cancer gene prediction through atomic clustering of coding variants in the structural proteome. Human Mutation 37(5), pp. 447-456. (10.1002/humu.22963)
- Upadhyaya, M. et al. 2015. Correlation of copy number changes and gene expression in neurofibromatosis1-associated malignant peripheral nerve sheath tumours [Abstract]. Pediatric Blood and Cancer 62(S4), pp. S152-S152. (10.1002/pbc.25715)
- Mort, M. E., Carlisle, F., Waite, A., Elliston, L., Allen, N. D., Jones, L. and Hughes, A. 2015. Huntingtin exists as multiple splice forms in human brain. Journal of Huntington's Disease 4(2), pp. 161-171. (10.3233/JHD-150151)
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- Winston, J., Duerden, L., Mort, M., Frayling, I., Rogers, M. and Upadhyaya, M. 2015. Identification of two novel SMCHD1 sequence variants in families with FSHD-like muscular dystrophy. European Journal of Human Genetics 23(1), pp. 67-71. (10.1038/ejhg.2014.58)
- Wei, X. et al. 2014. A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. PLoS Genetics 10(12), article number: e1004819. (10.1371/journal.pgen.1004819)
- Shihab, H. A., Gough, J., Mort, M. E., Cooper, D. N., Day, I. N. M. and Gaunt, T. R. 2014. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Human Genomics 8, article number: 11. (10.1186/1479-7364-8-11)
- Zhang, X. et al. 2014. Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation. Human Molecular Genetics 23(11), pp. 3024-3034. (10.1093/hmg/ddu019)
- Das, J. et al. 2014. Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks. Human Mutation 35(5), pp. 585-593. (10.1002/humu.22534)
- Hughes, A., Mort, M. E., Elliston, L. A., Thomas, R. M., Brooks, S. P., Dunnett, S. B. and Jones, L. 2014. Identification of novel alternative splicing events in the Huntingtin gene and assessment of the functional consequences using structural protein homology modelling. Journal of Molecular Biology 426(7), pp. 1428-1438. (10.1016/j.jmb.2013.12.028)
- Mort, M. et al. 2014. MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing. Genome Biology 15(1), article number: R19. (10.1186/gb-2014-15-1-r19)
- Stenson, P., Mort, M., Ball, E., Shaw, K., Phillips, A. and Cooper, D. 2014. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genetics 133(1), pp. 1-9. (10.1007/s00439-013-1358-4)
- Bagchi, A. et al. 2013. Analysis of features from protein-protein hetero-complex structures to predict protein interaction interfaces using machine learning. Procedia Technology 10, pp. 62-66. (10.1016/j.protcy.2013.12.337)
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- Zhao, H. et al. 2013. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biology 14(3), pp. R23. (10.1186/gb-2013-14-3-r23.)
- Thomas, L., Richards, M., Mort, M. E., Dunlop, E. A., Cooper, D. N. and Upadhyaya, M. 2012. Assessment of the potential pathogenicity of missense mutations identified in the GTPase-activating protein (GAP)-related domain of the neurofibromatosis type-1 (NF1) gene. Human Mutation 33(12), pp. 1687-1696. (10.1002/humu.22162)
- Xue, Y. et al. 2012. Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. American Journal of Human Genetics 91(6), pp. 1022-1032. (10.1016/j.ajhg.2012.10.015)
- Stenson, P. D., Ball, E. V., Mort, M. E., Phillips, A. D., Shaw, K. and Cooper, D. N. 2012. The human gene mutation database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Current Protocols in Bioinformatics 39, pp. 1.13.1-1.13.20. (10.1002/0471250953.bi0113s39)
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- Scally, A. et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483(7388), pp. 169-175. (10.1038/nature10842)
- Thomas, L. et al. 2012. Exploring the somatic NF1 mutational spectrum associated with NF1 cutaneous neurofibromas. European Journal of Human Genetics 20(4), pp. 411-419. (10.1038/ejhg.2011.207)
- Zhang, G., Pei, Z., Ball, E. V., Mort, M. E., Cooper, D. N. and Kehrer-Sawatzki, H. 2011. Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations. Human Genomics 5(5), pp. 453-484.
- Bertola, F. et al. 2011. IDUA mutational profiling of a cohort of 102 European patients with mucopolysaccharidosis type I: identification and characterization of 35 novel α-L-iduronidase (IDUA) alleles. Human Mutation 32(6), pp. E2189-E2210. (10.1002/humu.21479)
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- Zhao, Y., Clark, W. T., Mort, M. E., Cooper, D. N., Radivojac, P. and Mooney, S. D. 2011. Prediction of functional regulatory SNPs in monogenic and complex disease. Human Mutation 32(10), pp. 1183-1190. (10.1002/humu.21559)
- Sterne-Weiler, T., Howard, J., Mort, M., Cooper, D. N. and Sanford, J. R. 2011. Loss of exon identity is a common mechanism of human inherited disease. Genome Research 21(10), pp. 1563-1571. (10.1101/gr.118638.110)
- Grossi, S. et al. 2011. Molecular genetic analysis of the PLP1 gene in 38 families with PLP1-related disorders: identification and functional characterization of 11 novel PLP1 mutations. Orphanet Journal of Rare Diseases 6, article number: 40. (10.1186/1750-1172-6-40)
- Durbin, R. M. et al. 2010. A map of human genome variation from population-scale sequencing. Nature 467(7319), pp. 1061-1073. (10.1038/nature09534)
- Cooper, D. N., Mort, M. E., Stenson, P. D., Ball, E. V. and Chuzhanova, N. A. 2010. Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides. Human Genomics 4(6), pp. 406-410.
- Mort, M. E. et al. 2010. In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Human Mutation 31(3), pp. 335-346. (10.1002/humu.21192)
- Cooper, D. N. et al. 2010. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Human Mutation 31(6), pp. 631-655. (10.1002/humu.21260)
- Tappino, B. et al. 2010. Identification and characterization of 15 novel GALC gene mutations causing Krabbe disease. Human Mutation 31(12), pp. E1894-E1914. (10.1002/humu.21367)
- Zhang, G., Pei, Z., Krawczak, M., Ball, E. V., Mort, M. E., Kehrer-Sawatzki, H. and Cooper, D. N. 2010. Triangulation of the human, chimpanzee, and Neanderthal genome sequences identifies potentially compensated mutations. Human Mutation 31(12), pp. 1286-1293. (10.1002/humu.21389)
- Cooper, D. N. and Mort, M. 2010. Do inherited disease genes have distinguishing functional characteristics?. Genetic Testing and Molecular Biomarkers 14(3), pp. 289-291. (10.1089/gtmb.2010.0033)
- Cooper, D. N., Ball, E. V. and Mort, M. E. 2010. Chromosomal distribution of disease genes in the human genome. Genetic Testing and Molecular Biomarkers 14(4), pp. 441-446. (10.1089/gtmb.2010.0081)
- Stenson, P. D., Ball, E. V., Howells, K., Phillips, A. D., Mort, M. E. and Cooper, D. N. 2009. The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics [Editorial]. Human Genomics 4(2), pp. 69-72.
- Stenson, P. D., Mort, M., Ball, E., Howells, K., Phillips, A. D., Thomas, N. and Cooper, D. N. 2009. The Human Gene Mutation Database: 2008 update. Genome Medicine 1(1), article number: 13. (10.1186/gm13)
- Li, B. et al. 2009. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25(21), pp. 2744-2750. (10.1093/bioinformatics/btp528)
- Sanford, J. R. et al. 2009. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Research 19(3), pp. 381-394. (10.1101/gr.082503.108)
- Mort, M. E., Ivanov, D., Cooper, D. N. and Chuzhanova, N. 2008. A meta-analysis of nonsense mutations causing human genetic disease. Human Mutation 29(8), pp. 1037-1047. (10.1002/humu.20763)
- Radivojac, P., Baenziger, P. H., Kann, M. G., Mort, M., Hahn, M. W. and Mooney, S. D. 2008. Gain and loss of phosphorylation sites in human cancer. Bioinformatics 24(16), pp. i241-i247. (10.1093/bioinformatics/btn267)
- Krawczak, M., Thomas, N. S., Hundrieser, B., Mort, M., Wittig, M., Hampe, J. and Cooper, D. N. 2007. Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing. Human Mutation 28(2), pp. 150-158. (10.1002/humu.20400)
- Stenson, P. D., Ball, E., Howells, K., Phillips, A., Mort, M. E. and Cooper, D. N. 2007. Human Gene Mutation Database: towards a comprehensive central mutation database [Letter]. Journal of Medical Genetics 45(2), pp. 124-126. (10.1136/jmg.2007.055210)
- Khan, I. A., Mort, M., Buckland, P. R., O'Donovan, M. C., Cooper, D. N. and Chuzhanova, N. A. 2006. In silico discrimination of single nucleotide polymorphisms and pathological mutations in human gene promoter regions by means of local DNA sequence context and regularity.. In silico Biology 6(1-2), pp. 23-34.
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Conferences
- Rogers, M. F., Campbell, C., Shihab, H. A., Gaunt, T. R., Mort, M. and Cooper, D. N. 2015. Sequential data selection for predicting the pathogenic effects of sequence variation. Presented at: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Washington DC, USA, 9-12 November 2015Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on. IEEE pp. 639-644., (10.1109/BIBM.2015.7359759)
- Neville, M. D. et al. 2021. A platform for curated products from novel Open Reading Frames (nORFs) prompts reinterpretation of disease variants. Genome Research 31(2), pp. 327-336. (10.1101/gr.263202.120)
- Thomas, L. E. et al. 2021. Duodenal adenomas and cancer in MUTYH-associated polyposis: an international cohort study. Gastroenterology 160(3), pp. 952-954. (10.1053/j.gastro.2020.10.038)
- Stenson, P. D. et al. 2020. The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting. Human Genetics 139, pp. 1197-1207. (10.1007/s00439-020-02199-3)
- Short, E. et al. 2020. APC transcription studies and molecular diagnosis of familial adenomatous polyposis. European Journal of Human Genetics 28(1), pp. 118-121. (10.1038/s41431-019-0486-2)
- Lin, H. et al. 2019. RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants. Genome Biology 20(1), article number: 254. (10.1186/s13059-019-1847-4)
- Lin, J. et al. 2019. First estimate of the scale of canonical 5' splice site GT>GC variants capable of generating wild-type transcripts. Human Mutation 40(10), pp. 1856-1873. (10.1002/humu.23821)
- Fragoza, R. et al. 2019. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nature Communications 10(1), article number: 4141. (10.1038/s41467-019-11959-3)
- Cardoso-Moreira, M. et al. 2019. Gene expression across mammalian organ development. Nature 571, pp. 505 - 509. (10.1038/s41586-019-1338-5)