Dr Ian Sudbery

School of Biosciences

Senior Lecturer

Profile photo of Ian Sudbery
Profile picture of Profile photo of Ian Sudbery
i.sudbery@sheffield.ac.uk
+44 114 222 2738
Profile
  • 2022 - present: Senior Lecturer in Bioinformatics, School of Biosciences, the University of Sheffield
  • 2014 - 2022: Lecturer in Bioinformatics, School of Biosciences, the University of Sheffield
  • 2011 - 2014: CGAT Fellow, MRC Functional Genomics Unit at the University of Oxford
  • 2009 - 2011: Postdoctoral Research Fellow, Department of Systems Biology, Harvard Medical School
  • 2007 - 2008: Postdoctoral Research Assistant, Wellcome Trust Sanger Institute
  • 2003 - 2007: PhD in Functional Genomics, The Wellcome Trust Sanger Institute/University of Cambridge
Research interests

How do cells integrate information to make decisions about what genes should be expressed at a given time and in a given place? How do these processes malfunction to produce disease states? The correct regulation of gene expression is essential for the proper functioning of the cell, and incorrect regulation of genes is central to the mechanisms of many diseases.

My interests rest in understanding how the many levels of eukaryotic gene regulation work together to perform these functions, using computational and functional genomics tools.

The role of microRNAs in regulatory networks

MicroRNAs (miRNAs) are short, single stranded RNAs that act to down regulate the expression of their targets by transcript destabilisation and translational inhibition. What roles to these molecules play in the information processing systems of the cell?

How might these roles differ from that provided by transcriptional inhibitors? We know that miRNAs are found enriched in different topologies of network motifs than transcription factors. What might explain this?

Mathematical modelling suggests that miRNAs might threshold the expression of their target genes, only allowing protein production once transcription exceeds a particular rate. However, thus far experimental tests of this model are lacking in realistic in vivo settings.

We are studying evidence that might speak to the applicability of this model in real biology, and studying the consequences of this behaviour on regulatory networks and the identification of miRNA targets.

Misregulation of chromatin structure in disease

A cell’s DNA does not exist as a single extended string of nucleic acids in the way often imagined, but rather is packed and folded in a myriad of ways to form a complex three dimensional structure. At least some of this structure is thought to be important for the regulation of gene expression.

Transcription of metazoan genes is regulated by sequences known as enhancers which integrate diverse signals to make decisions about expression, and then communicate these decisions through their interactions with promoters. This communication is thought to take place via physical interactions between promoters and enhancers.

Together with collaborators from the Imperial University we are investigating how this three dimensional structure might contribute to the mis-regulation of gene expression in both monogenic disease and cancer using high-throughput, next-generation sequencing based assays of chromatin conformation.

Publications

Show: Featured publications All publications

Journal articles

  • Ray S, Abugable AA, Parker J, Liversidge K, Palminha NM, Liao C, Acosta-Martin AE, Souza CDS, Jurga M, Sudbery I & El-Khamisy SF (2022) . Nature, 609(7929), 1038-1047.
  • Alvarez-Benayas J, Trasanidis N, Katsarou A, Ponnusamy K, Chaidos A, May PC, Xiao X, Bua M, Atta M, Roberts IAG , Auner HW et al (2021) . Nature Communications, 12.
  • Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D & Wilson SA (2019) . Molecular Cell, 75(2), 310-323.e8.
  • Srivastava A, Malik L, Smith T, Sudbery I & Patro R (2019) . Genome Biology, 20.
  • Lesbirel S, Viphakone N, Parker M, Parker J, Heath C, Sudbery I & Wilson SA (2018) . Scientific Reports, 8(1).
  • Smith TS, Heger A & Sudbery I (2017) . Genome Research, 27, 491-499.
  • Greig JA, Sudbery IM, Richardson JP, Naglik JR, Wang Y & Sudbery PE (2015) . PLoS Pathogens, 11(1).
  • Rajan P, Sudbery IM, Villasevil MEM, Mui E, Fleming J, Davis M, Ahmad I, Edwards J, Sansom OJ, Sims D , Ponting CP et al (2014) . European Urology, 66(1), 32-39.
  • Sims D, Sudbery I, Ilott NE, Heger A & Ponting CP (2014) . Nature Reviews Genetics, 15(2), 121-132.

Preprints

  • Tabakhi S, Vandermeulen C, Sudbery I & Lu H (2024) , arXiv.
  • Riley JJ, Alexandru-Crivac CN, Bryce-Smith S, Wilson SA & Sudbery IM (2024) , Cold Spring Harbor Laboratory.

All publications

Journal articles

  • Riley JJ, Alexandru-Crivac CN, Bryce-Smith S, Wilson SA & Sudbery IM (2025) . Nucleic Acids Research, 53(14), gkaf700.
  • Watson S, Porter H, Sudbery I & Thompson R (2024) . International Journal of Molecular Sciences, 25(9).
  • Moss CE, Johnston SA, Kimble JV, Clements M, Codd V, Hamby S, Goodall AH, Deshmukh S, Sudbery I, Coca D , Wilson HL et al (2024) . Cell Reports, 43(4).
  • Baquero-Pérez B, Yonchev ID, Delgado-Tejedor A, Medina R, Puig-Torrents M, Sudbery I, Begik O, Wilson SA, Novoa EM & Díez J (2024) . Nature Communications, 15(1).
  • Katsarou A, Trasanidis N, Ponnusamy K, Kostopoulos IV, Alvarez-Benayas J, Papaleonidopoulou F, Keren K, Sabbattini PMR, Feldhahn N, Papaioannou M , Hatjiharissi E et al (2023) . Blood Advances, 7(21), 6395-6410.
  • Ray S, Abugable AA, Parker J, Liversidge K, Palminha NM, Liao C, Acosta-Martin AE, Souza CDS, Jurga M, Sudbery I & El-Khamisy SF (2022) . Nature, 609(7929), 1038-1047.
  • Alvarez-Benayas J, Trasanidis N, Katsarou A, Ponnusamy K, Chaidos A, May PC, Xiao X, Bua M, Atta M, Roberts IAG , Auner HW et al (2021) . Nature Communications, 12.
  • Niespolo C, Johnston JM, Deshmukh SR, Satam S, Shologu Z, Villacanas O, Sudbery IM, Wilson HL & Kiss-Toth E (2020) . Frontiers in Immunology, 11.
  • Baidžajevas K, Hadadi É, Lee B, Lum J, Shihui F, Sudbery I, Kiss-Tóth E, Wong SC & Wilson HL (2020) . Atherosclerosis, 305, 10-18.
  • Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D & Wilson SA (2019) . Molecular Cell, 75(2), 310-323.e8.
  • Kaneva IN, Sudbery IM, Dickman MJ & Sudbery PE (2019) . Scientific Reports, 9.
  • Srivastava A, Malik L, Smith T, Sudbery I & Patro R (2019) . Genome Biology, 20.
  • Lesbirel S, Viphakone N, Parker M, Parker J, Heath C, Sudbery I & Wilson SA (2018) . Scientific Reports, 8(1).
  • Liao C, Beveridge R, Hudson JJR, Parker JD, Chiang S-C, Ray S, Ashour ME, Sudbery I, Dickman MJ & El-Khamisy SF (2018) . Cell Reports, 23(11), 3352-3365.
  • Smith TS, Heger A & Sudbery I (2017) . Genome Research, 27, 491-499.
  • Greig JA, Sudbery IM, Richardson JP, Naglik JR, Wang Y & Sudbery PE (2015) . PLoS Pathogens, 11(1).
  • Rajan P, Stockley J, Sudbery IM, Fleming JT, Hedley A, Kalna G, Sims D, Ponting CP, Heger A, Robson CN , McMenemin RM et al (2014) . BMC Cancer, 14.
  • Rajan P, Sudbery IM, Villasevil MEM, Mui E, Fleming J, Davis M, Ahmad I, Edwards J, Sansom OJ, Sims D , Ponting CP et al (2014) . European Urology, 66(1), 32-39.
  • Huang Z-X, Zhao P, Zeng G-S, Wang Y-M, Sudbery I & Wang Y (2014) . mBio, 5(1).
  • Sims D, Sudbery I, Ilott NE, Heger A & Ponting CP (2014) . Nature Reviews Genetics, 15(2), 121-132.
  • Sims D, Ilott NE, Sansom SN, Sudbery IM, Johnson JS, Fawcett KA, Berlanga-Taylor AJ, Luna-Valero S, Ponting CP & Heger A (2014) . Bioinformatics, 30(9), 1290-1291.
  • Daelemans C, Ritchie ME, Smits G, Abu-Amero S, Sudbery IM, Forrest MS, Campino S, Clark TG, Stanier P, Kwiatkowski D , Deloukas P et al (2010) . BMC Genetics, 11(1).
  • Sudbery I, Enright AJ, Fraser AG & Dunham I (2010) . BMC Genomics, 11(1).
  • Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD , Li H et al (2009) . Genome Biology, 10.
  • Turner DJ, Keane TM, Sudbery I & Adams DJ (2009) . Mammalian Genome, 20(6), 327-338.
  • Phillips AJ, Sudbery I & Ramsdale M (2003) . Proceedings of the National Academy of Sciences, 100(24), 14327-14332.
  • Tamblin-Hopper P, Kiss-Toth E, Sudbery I, Young D & Wilkinson JM () . Journal of Translational Genetics and Genomics, 8(2), 225-43.
  • Cribbs AP, Luna-Valero S, George C, Sudbery IM, Berlanga-Taylor AJ, Sansom SN, Smith T, Ilott NE, Johnson J, Scaber J , Brown K et al () . F1000Research, 8, 377-377.
  • Farcas AM, Blackledge NP, Sudbery I, Long HK, McGouran JF, Rose NR, Lee S, Sims D, Cerase A, Sheahan TW , Koseki H et al () . eLife, 1.

Conference proceedings

  • Katsarou A, Trasanidis N, Alvarez-Benayas J, Papaleonidopoulou F, Keren K, Kostopoulos IV, Ponnusamy K, Xiao X, Feldhahn N, Roberts I , Hatjiharissi E et al (2019) . Blood, Vol. 134(Supplement_1) (pp 3783-3783)
  • Trasanidis N, Alvarez-Benayas J, Katsarou A, Chaidos A, May PC, Ponnusamy K, Xiao X, Bua M, Atta M, Roberts I , Auner HW et al (2019) . Blood, Vol. 134(Supplement_1) (pp 1769-1769)
  • Niespolo C, Salamanca Viloria J, Deshmukh S, Villacanas Perez O, Sudbery I, Wilson H & Kiss-Toth E (2019) . Basic Science (pp A156.3-A156)
  • Baidzajevas K, Hadadi E, Lee B, Lum J, Sudbery I, Lai S, Wong SC, Kiss-Toth E & Wilson H (2017) . Heart, Vol. 103(Suppl 5) (pp A136.1-A136)
  • Rajan P, Sudbery IM, Stockley J, Fleming J, Sims D, Ponting CP, Heger A, Robson CN, McMenemin RM, Pedley ID & Leung HY (2014) Next generation sequencing of advanced non-castrate prostate cancer treated with docetaxel chemotherapy. BRITISH JOURNAL OF SURGERY, Vol. 101 (pp 63-63)
  • Daelemans C, Ritchie ME, Abu-Amero S, Sudbery IM, Stanier P, Forrest MS, Deloukas P, Tavare S, Moore GE & Dunham I (2009) Assessment of candidate imprinted genes in the human term placenta. JOURNAL OF MEDICAL GENETICS, Vol. 46 (pp S88-S88)

Software, code or databases

  • Sudbery I CGAT-core.
  • Sudbery I UMI-Tools.
  • Sudbery I CGAT: Computational Genomics Analysis Toolkit.

Theses

  • Sudbery I (2007) Methods for genome-scale gene perturbation studies of the TRAILinduced apoptosis pathway in mammalian cell culture..

Preprints

  • Tabakhi S, Vandermeulen C, Sudbery I & Lu H (2024) , arXiv.
  • Riley JJ, Alexandru-Crivac CN, Bryce-Smith S, Wilson SA & Sudbery IM (2024) , Cold Spring Harbor Laboratory.
  • Baquero-Perez B, Yonchev ID, Delgado-Tejedor A, Medina R, Puig-Torrents M, Sudbery I, Begik O, Wilson SA, Maria Novoa E & Díez J (2023) , Cold Spring Harbor Laboratory.
  • Moss CE, Johnston S, Clements M, Codd V, Hamby S, Goodall AH, Deshmukh S, Sudbery I, Coca D, Wilson HL & Kiss-Toth E (2023) , Cold Spring Harbor Laboratory.
  • Watson S, Porter H, Sudbery I & Thompson R (2022) , Cold Spring Harbor Laboratory.
  • Cribbs A, Luna-Valero S, George C, Sudbery IM, Berlanga-Taylor AJ, Sansom SN, Smith T, Ilott NE, Johnson J, Scaber J , Brown K et al (2019) , Cold Spring Harbor Laboratory.
  • Viphakone N, Sudbery IM, Heath CG, Sims D & Wilson SA (2018) , Cold Spring Harbor Laboratory.
  • Srivastava A, Malik L, Smith T, Sudbery I & Patro R (2018) , Cold Spring Harbor Laboratory.
  • Kaneva I, Sudbery I, Dickman MJ & Sudbery PE (2018) , Cold Spring Harbor Laboratory.
  • Smith T, Heger A & Sudbery I (2016) , Cold Spring Harbor Laboratory.
Teaching activities

I teach on MBB165, MBB265, MBB(6)329, MBB(6)344, MBB380, MBB363.