Mr Peter Stenson

2024

• Kars, M. E., Wu, Y., Stenson, P. D., Cooper, D. N., Burisch, J., Peter, I. and Itan, Y. 2024. The landscape of rare genetic variation associated with inflammatory bowel disease and Parkinson’s disease comorbidity. Genome Medicine 16(1), article number: 66. (10.1186/s13073-024-01335-2)

2023

• Stein, D. et al. 2023. Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set. Genome Medicine 15(1), article number: 103. (10.1186/s13073-023-01261-9)
• Zhang, P. et al. 2023. Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites. Proceedings of the National Academy of Sciences of the United States of America 120(46), article number: e2314225120. (10.1073/pnas.2314225120)
• Shao, Y. et al. 2023. Phylogenomic analyses provide insights into primate evolution. Science 380(6648), pp. 913-924. (10.1126/science.abn6919)
• Wu, Y. et al. 2023. Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients. Nature Communications 14(1), article number: 2256. (10.1038/s41467-023-37849-3)
• Wu, Y. et al. 2023. Identifying shared genetic factors underlying epilepsy and congenital heart disease in Europeans. Human Genetics 142, pp. 275-288. (10.1007/s00439-022-02502-4)
• 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)

2022

• Zhang, P. et al. 2022. Genome-wide detection of human variants that disrupt intronic branchpoints. Proceedings of the National Academy of Sciences 119(44), article number: e2211194119. (10.1073/pnas.2211194119)
• Rastogi, R., Stenson, P. D., Cooper, D. N. and Bejerano, G. 2022. X-CAP improves pathogenicity prediction of stopgain variants. Genome Medicine 14(1), article number: 81. (10.1186/s13073-022-01078-y)
• Qi, M. et al. 2022. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Human Mutation 43(3), pp. 328-346. (10.1002/humu.24314)
• Quinodoz, M. et al. 2022. Analysis of missense variants in the human genome reveals widespread gene-specific clustering and improves prediction of pathogenicity. American Journal of Human Genetics 109(3), pp. 457-470. (10.1016/j.ajhg.2022.01.006)

2021

• Serrano, C. et al. 2021. Compensatory epistasis explored by molecular dynamics simulations. Human Genetics 140(9), pp. 1329-1342. (10.1007/s00439-021-02307-x)
• Kars, M. E. et al. 2021. The genetic structure of the Turkish population reveals high levels of variation and admixture. Proceedings of the National Academy of Sciences 118(36), article number: e2026076118. (10.1073/pnas.2026076118)

2020

• 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)
• Rausell, A. et al. 2020. Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes. Proceedings of the National Academy of Sciences 117(24), pp. 13626-13636. (10.1073/pnas.1917993117)
• Birgmeier, J. et al. 2020. AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature. Science Translational Medicine 12(544), article number: eaau9113. (10.1126/scitranslmed.aau9113)

2019

• 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)
• Zhang, P., Boisson, B., Stenson, P. D., Cooper, D. N., Casanova, J., Abel, L. and Itan, Y. 2019. SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data. Nucleic Acids Research 47(W1), pp. W623-W631. (10.1093/nar/gkz326)
• Jagadeesh, K. A., Paggi, J. M., Ye, J. S., Stenson, P. D., Cooper, D. N., Bernstein, J. A. and Bejerano, G. 2019. S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing. Nature Genetics 51(4), pp. 755-763. (10.1038/s41588-019-0348-4)
• Maffucci, P. et al. 2019. Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis. Proceedings of the National Academy of Sciences 116, pp. 950-959. (10.1073/pnas.1808403116)

2018

• Requena, D. et al. 2018. CDG: an online server proposing biologically closest disease-causing genes and pathologies and its application to primary immunodeficiency. Frontiers in Immunology 9, article number: 1340. (10.3389/fimmu.2018.01340)

2017

• 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)
• 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)

2016

• Lek, M. et al. 2016. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, pp. 285-291. (10.1038/nature19057)
• 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)
• Itan, Y. et al. 2016. The mutation significance cutoff: gene-level thresholds for variant predictions [Letter]. Nature Methods 13(2), pp. 109-110. (10.1038/nmeth.3739)

2015

• Turner, T. N., Douville, C., Kim, D., Stenson, P. D., Cooper, D. N., Chakravarti, A. and Karchin, R. 2015. Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns. Human Molecular Genetics 24(21), pp. 5995-6002. (10.1093/hmg/ddv309)
• Douville, C. et al. 2015. Assessing the pathogenicity of insertion and deletion variants with the Variant Effect Scoring Tool (VEST-Indel). Human Mutation 37(1), pp. 28-35. (10.1002/humu.22911)
• The 1000 Genomes Project Consortium, ., Auton, A., Abecasis, G. R., Cooper, D. N., Ball, E. V. and Stenson, P. D. 2015. A global reference for human genetic variation. Nature 526, pp. 68-74. (10.1038/nature15393)
• Karageorgos, I. et al. 2015. Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach. Human Genomics 9, article number: 12. (10.1186/s40246-015-0034-2)
• Johnston, J. et al. 2015. Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations. American Journal of Human Genetics 96(6), pp. 913-925. (10.1016/j.ajhg.2015.04.013)
• Rivas, M. A. et al. 2015. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348(6235), pp. 666-669. (10.1126/science.1261877)
• Grimm, D. G. et al. 2015. The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity. Human Mutation 36(5), pp. 513-523. (10.1002/humu.22768)

2014

• Chen, Y. et al. 2014. A probabilistic model to predict clinical phenotypic traits from genome sequencing. PLoS Computational Biology 10(9), article number: e1003825. (10.1371/journal.pcbi.1003825)
• 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)
• 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

• Niknafs, N. et al. 2013. MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Human Genetics 132(11), pp. 1235-1243. (10.1007/s00439-013-1325-0)
• Gonsalves, S. et al. 2013. Using exome data to identify malignant hyperthermia susceptibility mutations. Anesthesiology 119(5), pp. 1043-1053. (10.1097/ALN.0b013e3182a8a8e7)
• Douville, C. et al. 2013. CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics 29(5), pp. 647-648. (10.1093/bioinformatics/btt017)
• Shihab, H. A. et al. 2013. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Human Mutation 34(1), pp. 57-65. (10.1002/humu.22225)

2012

• 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)
• Scally, A. et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483(7388), pp. 169-175. (10.1038/nature10842)
• McVean, G. A. et al. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422), pp. 56-65. (10.1038/nature11632)

2011

• Yan, G. et al. 2011. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques [Letter]. Nature Biotechnology 29(11), pp. 1019-1023. (10.1038/nbt.1992)
• Ivanov, D., Hamby, S. E., Stenson, P. D., Phillips, A. D., Kehrer-Sawatzki, H., Cooper, D. N. and Chuzhanova, N. 2011. Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes. Human Mutation 32(6), pp. 620-632. (10.1002/humu.21483)
• Necsulea, A., Popa, A., Cooper, D. N., Stenson, P. D., Mouchiroud, D., Gautier, C. and Duret, L. 2011. Meiotic recombination favors the spreading of deleterious mutations in human populations. Human Mutation 32(2), pp. 198-206. (10.1002/humu.21407)
• 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)
• Fechtel, K., Osterbur, M. L., Kehrer-Sawatzki, H., Stenson, P. D. and Cooper, D. N. 2011. Delineating the Hemostaseome as an aid to individualize the analysis of the hereditary basis of thrombotic and bleeding disorders. Human Genetics 130(1), pp. 149-166. (10.1007/s00439-011-0984-y)

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.
• Stenson, P. D. and Cooper, D. N. 2010. Prospects for the automated extraction of mutation data from the scientific literature [Editorial]. Human Genomics 5(1), pp. 1-4.
• Quemener, S. et al. 2010. Complete ascertainment of intragenic copy number mutations (CNMs) in theCFTRgene and its implications for CNM formation at other autosomal loci. Human Mutation 31(4), pp. 421-428. (10.1002/humu.21196)
• 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)
• Pagon, R. A. et al. 2010. Databases in human and medical genetics. In: Speicher, M. R., Antonarakis, S. E. and Motulsky, A. G. eds. Vogel and Motulsky's Human Genetics: Problems and Approaches. 4th ed.. London: Springer, pp. 941-961.

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)

2008

• Bacolla, A. et al. 2008. Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. Genome Research 18(10), pp. 1545-1553. (10.1101/gr.078303.108)

2007

• Gibbs, R. A., Rogers, J., Katz, M. G., Ball, E. V., Cooper, D. N., Stenson, P. D. and Zweig, A. S. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316(5822), pp. 222-34. (10.1126/science.1139247)
• 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

• Cooper, D. N., Stenson, P. D. and Chuzhanova, N. A. 2006. The Human Gene Mutation Database (HGMD) and its exploitation in the study of mutational mechanisms. Current Protocols in Bioinformatics 1(1.13) (10.1002/0471250953.bi0113s12)

2005

• Chen, J. M., Chuzhanova, N., Stenson, P. D., Ferec, C. and Cooper, D. N. 2005. Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions. Human Mutation 26(4), pp. 363-373. (10.1002/humu.20230)
• Chen, J. M., Stenson, P. D., Cooper, D. N. and Ferec, C. 2005. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease [review]. Human Genetics -Berlin- 117(5), pp. 411-427. (10.1007/s00439-005-1321-0)
• Ball, E. V., Stenson, P. D., Abeysinghe, S. S., Krawczak, M., Cooper, D. N. and Chuzanhova, N. A. 2005. Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Human Mutation 26(3), pp. 205-213. (10.1002/humu.20212)
• Chen, J. M., Chuzhanova, N., Stenson, P. D., Ferec, C. and Cooper, D. N. 2005. Complex gene rearrangements caused by serial replication slippage. Human Mutation 26(2), pp. 125-134. (10.1002/humu.20202)

2004

• Abeysinghe, S. S., Stenson, P. D., Krawczak, M. and Cooper, D. N. 2004. Gross Rearrangement Breakpoint Database (GRaBD)[review]. Human Mutation 23(3), pp. 219-221. (10.1002/humu.20006)
• Gibbs, R. A. et al. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982), pp. 493-521. (10.1038/nature02426)
• Huang, H. et al. 2004. Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome Biology(5), pp. R47-R47. (10.1186/gb-2004-5-7-r47)

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)

2000

• Krawczak, M., Chuzhanova, N. A., Stenson, P. D., Johansen, B. N., Ball, E. V. and Cooper, D. N. 2000. Changes in primary DNA sequence complexity influence the phenotypic consequences of mutations in human gene regulatory regions. Human Genetics -Berlin- 107(4), pp. 362-365. (10.1007/s004390000393)
• Krawczak, M., Ball, E. V., Fenton, I., Stenson, P. D., Abeysinghe, S., Thomas, N. and Cooper, D. N. 2000. Human gene mutation database-a biomedical information and research resource. Human Mutation 15(1), pp. 45-51. (10.1002/(sici)1098-1004(200001)15:1%3C45::aid-humu10%3E3.0.co;2-t)

1999

• Krawczak, M., Ball, E. V., Stenson, P. D. and Cooper, D. N. 1999. HGMD: the human gene mutation database. In: Letovsky., S. I. ed. Bioinformatics; databases and systems. Boston: Kluwer Academic Publishers, pp. 99-104.