Dr Benjamin Skinner

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Email
b.skinner@essex.ac.uk -
Telephone
+44 (0) 1206 874868
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Location
3SW.6.18, Colchester Campus
Profile
Biography
I'm a biologist interested in structural and evolutionary genomics - how genomes and the chromosomes they contain change and rearrange over time. Currently I'm looking at the shape and organisation of chromatin in asymmetric cell nuclei - for example sperm - which can give information on mechanisms of chromatin packaging during cellular differentiation. To investigate this, I develop image analysis software to allow high-throughput measurement of shapes from microscopy data. I am also interested in the evolution of sex chromosomes, and computational methods to analyse DNA sequencing data to detect gene amplications and copy number variation between individuals or species.
Qualifications
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PhD in Genetics University of Kent, (2009)
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BSc (Hons) in Biochemistry University of Kent, (2005)
Appointments
University of Essex
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Lecturer, School of Life Sciences, University of Essex (1/7/2019 - present)
Other academic
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Research Associate, Department of Pathology, University of Cambridge (5/8/2009 - 5/7/2019)
Research and professional activities
Research interests
Nuclear morphology
I am interested in the organisation and evolution of genome structure, particularly relating to the shape of nuclei. Cell nuclei can adopt a variety of shapes, depending on species and cell type, and alterations to shape can give information on the cell's genetic constitution. Much of my research has involved developing image analysis tools to allow us to quantify shapes from microscopy images in a rapid, automated, and unbiased manner
Conferences and presentations
Image warping for assessing chromatin organisation in asymmetric nuclei
Invited presentation, International Chromosome Conference / International Colloquium on Animal Cytogenetics and Genomics, Virtual conference, 14/7/2021
Teaching and supervision
Current teaching responsibilities
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Genetics and Evolution (BS102)
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Employability Skills for the Biosciences (BS211)
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Computational Data Analysis: R for Life Sciences (BS231)
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Human Molecular Genetics (BS320)
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Research Project in Biomedical Science (BS831)
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Research Project in Life Sciences (BS832)
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Analysis of Genomic Data (BS939)
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Genomics (BS982)
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Biomedical Science: Practice and Employability (BS214)
Current supervision
Previous supervision

Degree subject: Biological Sciences
Degree type: Doctor of Philosophy
Awarded date: 15/5/2023

Degree subject: Biological Sciences
Degree type: Master of Science (by Dissertation)
Awarded date: 11/2/2022
Publications
Publications (1)
Kopania, EEK., Watson, EM., Rathje, CC., Skinner, BM., Ellis, PJI., Larson, EL. and Good, JM., (2022). The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice
Journal articles (33)
Skinner, BM., (2022). Nuclear Morphology Analysis 2.0.0: Improved image analysis software for measuring nuclear shape. Journal of Open Source Software. 7 (79), 4767-4767
Kopania, EEK., Watson, EM., Rathje, CC., Skinner, BM., Ellis, PJI., Larson, EL. and Good, JM., (2022). The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice.. Genetics. 222 (4), iyac151-
Bergero, R., Ellis, P., Haerty, W., Larcombe, L., Macaulay, I., Mehta, T., Mogensen, M., Murray, D., Nash, W., Neale, MJ., O'Connor, R., Ottolini, C., Peel, N., Ramsey, L., Skinner, B., Suh, A., Summers, M., Sun, Y., Tidy, A., Rahbari, R., Rathje, C. and Immler, S., (2021). Meiosis and beyond – understanding the mechanistic and evolutionary processes shaping the germline genome. Biological Reviews. 96 (3), 822-841
Quilter, CR., Harvey, KM., Bauer, J., Skinner, BM., Gomez, M., Shrivastava, M., Doel, AM., Drammeh, S., Dunger, DB., Moore, SE., Ong, KK., Prentice, AM., Bernstein, RM., Sargent, CA. and Affara, NA., (2021). Identification of methylation changes associated with positive and negative growth deviance in Gambian infants using a targeted methyl sequencing approach of genomic DNA. FASEB BioAdvances. 3 (4), 205-230
Alshaker, H., Mills, R., Hunter, E., Salter, M., Ramadass, A., Skinner, BM., Westra, W., Green, J., Akoulitchev, A., Winkler, M. and Pchejetski, D., (2021). Chromatin conformation changes in peripheral blood can detect prostate cancer and stratify disease risk groups. Journal of Translational Medicine. 19 (1), 46-
Aryee, SND., Owusu-Adjei, D., Osei-Amponsah, R., Skinner, B., Sowatey, E. and Sargent, CA., (2021). Sustainable genomic research for food security in sub-Saharan Africa. Agriculture & Food Security. 10 (1)
Turner, KJ., Watson, EM., Skinner, BM. and Griffin, DK., (2021). Telomere Distribution in Human Sperm Heads and Its Relation to Sperm Nuclear Morphology: A New Marker for Male Factor Infertility?. International Journal of Molecular Sciences. 22 (14), 7599-7599
Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, DM., Billis, K., Chow, W., Eory, L., Finlayson, HA., Flicek, P., Girón, CG., Griffin, DK., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, DA., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, FJ., Nonneman, DJ., O'Connor, RE., Phillippy, AM., Rohrer, GA., Rosen, BD., Rund, LA., Sargent, CA., Schook, LB., Schroeder, SG., Schwartz, AS., Skinner, BM., Talbot, R., Tseng, E., Tuggle, CK., Watson, M., Smith, TPL. and Archibald, AL., (2020). An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience. 9 (6), giaa051-
Skinner, BM., Rathje, CC., Bacon, J., Johnson, EEP., Larson, EL., Kopania, EEK., Good, JM., Yousafzai, G., Affara, NA. and Ellis, PJI., (2019). A high-throughput method for unbiased quantitation and categorization of nuclear morphology. Biology of Reproduction. 100 (5), 1250-1260
Skinner, BM., Bacon, J., Rathje, CC., Larson, EL., Kopania, EEK., Good, JM., Affara, NA. and Ellis, PJI., (2019). Automated Nuclear Cartography Reveals Conserved Sperm Chromosome Territory Localization across 2 Million Years of Mouse Evolution. Genes. 10 (2), 109-109
O’Connor, RE., Kiazim, L., Skinner, B., Fonseka, G., Joseph, S., Jennings, R., Larkin, DM. and Griffin, DK., (2019). Patterns of microchromosome organization remain highly conserved throughout avian evolution. Chromosoma. 128 (1), 21-29
Rathje, CC., Johnson, EEP., Drage, D., Patinioti, C., Silvestri, G., Affara, NA., Ialy-Radio, C., Cocquet, J., Skinner, BM. and Ellis, PJI., (2019). Differential Sperm Motility Mediates the Sex Ratio Drive Shaping Mouse Sex Chromosome Evolution. Current Biology. 29 (21), 3692-3698
Rathje, CC., Randle, SJ., Al Rawi, S., Skinner, BM., Nelson, DE., Majumdar, A., Johnson, EEP., Bacon, J., Vlazaki, M., Affara, NA., Ellis, PJ. and Laman, H., (2019). A Conserved Requirement for Fbxo7 During Male Germ Cell Cytoplasmic Remodeling. Frontiers in Physiology. 10, 1278-
Mandawala, AA., Skinner, BM., Walling, GA., Harvey, KE. and Harvey, SC., (2018). Sperm morphology differences associated with pig fertility
Skinner, BM. and Johnson, EEP., (2017). Nuclear morphologies: their diversity and functional relevance. Chromosoma. 126 (2), 195-212
Osei-Amponsah, R., Skinner, BM., Adjei, DO., Bauer, J., Larson, G., Affara, NA. and Sargent, CA., (2017). Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis.. BMC Genomics. 18 (1), 193-
Skinner, BM., Sargent, CA., Churcher, C., Hunt, T., Herrero, J., Loveland, JE., Dunn, M., Louzada, S., Fu, B., Chow, W., Gilbert, J., Austin-Guest, S., Beal, K., Carvalho-Silva, D., Cheng, W., Gordon, D., Grafham, D., Hardy, M., Harley, J., Hauser, H., Howden, P., Howe, K., Lachani, K., Ellis, PJI., Kelly, D., Kerry, G., Kerwin, J., Ng, BL., Threadgold, G., Wileman, T., Wood, JMD., Yang, F., Harrow, J., Affara, NA. and Tyler-Smith, C., (2016). The pig X and Y Chromosomes: structure, sequence, and evolution. Genome Research. 26 (1), 130-139
Skinner, BM., Lachani, K., Sargent, CA., Yang, F., Ellis, P., Hunt, T., Fu, B., Louzada, S., Churcher, C., Tyler-Smith, C. and Affara, NA., (2015). Expansion of the HSFY gene family in pig lineages. BMC Genomics. 16 (1), 442-
Quilter, CR., Cooper, WN., Cliffe, KM., Skinner, BM., Prentice, PM., Nelson, L., Bauer, J., Ong, KK., Constância, M., Lowe, WL., Affara, NA. and Dunger, DB., (2014). Impact on offspring methylation patterns of maternal gestational diabetes mellitus and intrauterine growth restraint suggest common genes and pathways linked to subsequent type 2 diabetes risk. The FASEB Journal. 28 (11), 4868-4879
Skinner, BM., Al Mutery, A., Smith, D., Völker, M., Hojjat, N., Raja, S., Trim, S., Houde, P., Boecklen, WJ. and Griffin, DK., (2014). Global patterns of apparent copy number variation in birds revealed by cross-species comparative genomic hybridization. Chromosome Research. 22 (1), 59-70
Lithgow, PE., O’Connor, R., Smith, D., Fonseka, G., Al Mutery, A., Rathje, C., Frodsham, R., O’Brien, P., Kasai, F., Ferguson-Smith, MA., Skinner, BM. and Griffin, DK., (2014). Novel tools for characterising inter and intra chromosomal rearrangements in avian microchromosomes. Chromosome Research. 22 (1), 85-97
Romanov, MN., Farré, M., Lithgow, PE., Fowler, KE., Skinner, BM., O’Connor, R., Fonseka, G., Backström, N., Matsuda, Y., Nishida, C., Houde, P., Jarvis, ED., Ellegren, H., Burt, DW., Larkin, DM. and Griffin, DK., (2014). Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics. 15 (1), 1060-
Ellis, PJI., Morris, TJ., Skinner, BM., Sargent, CA., Vickers, MH., Gluckman, PD., Gilmour, S. and Affara, NA., (2014). Thrifty metabolic programming in rats is induced by both maternal undernutrition and postnatal leptin treatment, but masked in the presence of both: implications for models of developmental programming. BMC Genomics. 15 (1), 49-
Skinner, BM., Lachani, K., Sargent, CA. and Affara, NA., (2013). Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region. BMC Genetics. 14 (1), 1-7
Khulan, B., Cooper, WN., Skinner, BM., Bauer, J., Owens, S., Prentice, AM., Belteki, G., Constancia, M., Dunger, D. and Affara, NA., (2012). Periconceptional maternal micronutrient supplementation is associated with widespread gender related changes in the epigenome: a study of a unique resource in the Gambia. Human Molecular Genetics. 21 (9), 2086-2101
Skinner, BM. and Griffin, DK., (2012). Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints. Heredity. 108 (1), 37-41
Völker, M., Backström, N., Skinner, BM., Langley, EJ., Bunzey, SK., Ellegren, H. and Griffin, DK., (2010). Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Research. 20 (4), 503-511
Warren, WC., Clayton, DF., Ellegren, H., Arnold, AP., Hillier, LW., Künstner, A., Searle, S., White, S., Vilella, AJ., Fairley, S., Heger, A., Kong, L., Ponting, CP., Jarvis, ED., Mello, CV., Minx, P., Lovell, P., Velho, TAF., Ferris, M., Balakrishnan, CN., Sinha, S., Blatti, C., London, SE., Li, Y., Lin, Y-C., George, J., Sweedler, J., Southey, B., Gunaratne, P., Watson, M., Nam, K., Backström, N., Smeds, L., Nabholz, B., Itoh, Y., Whitney, O., Pfenning, AR., Howard, J., Völker, M., Skinner, BM., Griffin, DK., Ye, L., McLaren, WM., Flicek, P., Quesada, V., Velasco, G., Lopez-Otin, C., Puente, XS., Olender, T., Lancet, D., Smit, AFA., Hubley, R., Konkel, MK., Walker, JA., Batzer, MA., Gu, W., Pollock, DD., Chen, L., Cheng, Z., Eichler, EE., Stapley, J., Slate, J., Ekblom, R., Birkhead, T., Burke, T., Burt, D., Scharff, C., Adam, I., Richard, H., Sultan, M., Soldatov, A., Lehrach, H., Edwards, SV., Yang, S-P., Li, X., Graves, T., Fulton, L., Nelson, J., Chinwalla, A., Hou, S., Mardis, ER. and Wilson, RK., (2010). The genome of a songbird. Nature. 464 (7289), 757-762
Skinner, BM., Völker, M., Ellis, M. and Griffin, DK., (2009). An Appraisal of Nuclear Organisation in Interphase Embryonic Fibroblasts of Chicken, Turkey and Duck. Cytogenetic and Genome Research. 126 (1-2), 156-164
Skinner, BM., Robertson, LBW., Tempest, HG., Langley, EJ., Ioannou, D., Fowler, KE., Crooijmans, RPMA., Hall, AD., Griffin, DK. and Völker, M., (2009). Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis. BMC Genomics. 10 (1), 357-
Ioannou, D., Tempest, HG., Skinner, BM., Thornhill, AR., Ellis, M. and Griffin, DK., (2009). Quantum dots as new-generation fluorochromes for FISH: an appraisal. Chromosome Research. 17 (4), 519-530
Griffin, DK., Robertson, LBW., Tempest, HG. and Skinner, BM., (2007). The evolution of the avian genome as revealed by comparative molecular cytogenetics. Cytogenetic and Genome Research. 117 (1-4), 64-77
Morris, WB., Stephenson, JE., Robertson, LBW., Turner, K., Brown, H., Ioannou, D., Tempest, HG., Skinner, BM. and Griffin, DK., (2007). Practicable approaches to facilitate rapid and accurate molecular cytogenetic mapping in birds and mammals. Cytogenetic and Genome Research. 117 (1-4), 36-42
Conferences (20)
Johnson, EEP., Skinner, BM., Ellis, PJL. and Affara, NA., (2016). Sex Ratio Distortion in a Y Chromosome Deletion Model
Skinner, BM., Johnson, EEP., Rathje, CC. and Ellis, PJI., (2016). Nuclear Morphology and Fertility in Mouse Sperm
Ellis, PJI., Rathje, CC., Mills, BP., Yousafzai, G., Silvestri, G., Stewart, V., Larson, EL., Good, JM. and Skinner, BM., (2016). Quantitative Morphometric Analysis as a Tool for Investigating the Evolution of Sperm Morphology and Nuclear Organisation in Mouse
Lithgow, PE., O'Connor, RE., Smith, D., Fonseka, G., Al Mutery, A., Rathje, C., Frodsham, R., O'Brien, P., Ferguson-Smith, MA., Skinner, BM. and Griffin, DK., (2015). Inter and intra chromosomal rearrangements in avian microchromosomes
Romanov, MN., Farre, M., Lithgow, PE., O'Connor, R., Fowler, KE., Skinner, BM., Larkin, DM. and Griffin, DK., (2015). Avian ancestral karyotype reconstruction and differential rates of inter-and intra-chromosomal change in different lineages
Skinner, BM., Ellis, PJI., Johnson, EE. and Affara, NA., (2015). Mapping chromosome positions with 'sperm cartography'
Johnson, EEP., Skinner, BM., Ellis, PJI. and Affara, NA., (2015). Investigating physiological and molecular mechanisms of sex ratio distortion
Skinner, BM., Sargent, CA., Yang, F., Lachani, K., Fu, B., Ellis, PJI., Pereira, SLG., Churcher, C., Tyler-Smith, C., Affara, NA. and Grp, PXYS., (2015). A first generation sequence assembly of the pig Y chromosome
Griffin, DK., Voelker, ME., Trim, SA. and Skinner, BM., (2010). Avian "Chromonomics" the bird genome from the chromosome's point of view
Voelker, M., Skinner, BM., Langley, EJ., Bunzey, SK., Gera, C. and Griffin, DK., (2009). How conserved are bird genomes? Insights from the chicken and zebra finch genome projects
Skinner, BM., Robertson, LBW., Tempest, HG., Langley, EJ., Ioannou, D., Fowler, KE., Crooijmans, RPMA., Hall, AD., Griffin, DK. and Voelker, ME., (2009). Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis
Skinner, BM., Voelker, M., Al Mutery, A. and Griffin, DK., (2009). An overview of copy number variation in birds
Ioannou, D., Tempest, HG., Skinner, BM., Thornhill, AR., Ellis, M. and Griffin, DK., (2009). Quantum dots as new-generation fluorochromes for FISH: an appraisal
Skinner, BM., Voelker, M., Ellis, M. and Griffin, DK., (2009). A detailed appraisal of nuclear organization in chicken embryonic fibroblasts and comparative genomics in turkey and duck
Volker, M., Skinner, BM., Tempest, HG. and Griffin, DK., (2008). Evolution of the avian genome as revealed by molecular cytogenetics
Skinner, BM., Volker, M., Fonseka, GL., Ellis, M. and Griffin, DK., (2008). Nuclear (genome) organisation and comparative genomics in birds
Fonseka, GL., Ioannou, D., Skinner, BM., Ellis, M. and Griffin, DK., (2008). Manual vs. automated methods to assess nuclear organisation
Fowler, KE., Skinner, BM., Robertson, LBW., Tempest, HG., Volker, M. and Griffin, DK., (2008). Molecular cytogenetic maps of turkey, duck and zebra finch and their implications for genome evolution
Morris, W., Stephenson, J., Robertson, L., Turner, K., Brown, H., Ioannou, D., Tempest, H., Skinner, B. and Griffin, D., (2007). Computer based learning approaches to facilitate rapid and accurate molecular cytogenetic mapping in birds and mammals
Cheng, R., Finch, K., Skinner, B. and Griffin, D., (2007). Sperm aneuploidy screening in ICSI males: To automate or not to automate
Reports and Papers (1)
Skinner, BM., Bacon, J., Rathje, CC., Larson, EL., Kopania, EEK., Good, JM., Affara, NA. and Ellis, PJI., (2019). Automated nuclear cartography reveals conserved sperm chromosome territory localization across 2 million years of mouse evolution
Grants and funding
2019
Development of an in-vitro model for Parkinson's disease
University of Essex
Contact
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