Dr Ian Sudbery

School of Biosciences

Senior Lecturer

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

Featured 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) A mechanism for oxidative damage repair at gene regulatory elements. Nature, 609(7929), 1038-1047. View this article in WRRO
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) Chromatin-based, in cis and in trans regulatory rewiring underpins distinct oncogenic transcriptomes in multiple myeloma. Nature Communications, 12.
Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D & Wilson SA (2019) Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome. Molecular Cell. View this article in WRRO
Srivastava A, Malik L, Smith T, Sudbery I & Patro R (2019) Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Genome Biology, 20. View this article in WRRO
Lesbirel S, Viphakone N, Parker M, Parker J, Heath C, Sudbery I & Wilson SA (2018) The m6A-methylase complex recruits TREX and regulates mRNA export. Scientific Reports, 8(1). View this article in WRRO
Smith TS, Heger A & Sudbery I (2017) UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Research, 27, 491-499. View this article in WRRO
Greig JA, Sudbery IM, Richardson JP, Naglik JR, Wang Y & Sudbery PE (2015) Cell Cycle-Independent Phospho-Regulation of Fkh2 during Hyphal Growth Regulates Candida albicans Pathogenesis. PLOS Pathogens, 11(1), e1004630-e1004630. View this article in WRRO
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) Next-generation Sequencing of Advanced Prostate Cancer Treated with Androgen-deprivation Therapy. European Urology, 66(1), 32-39.
Sims D, Sudbery I, Ilott NE, Heger A & Ponting CP (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics, 15(2), 121-132.

Preprints

Tabakhi S, Vandermeulen C, Sudbery I & Lu H (2024) Heterogeneous graph attention network improves cancer multiomics integration, arXiv.
Riley JJ, Alexandru-Crivac CN, Bryce-Smith S, Wilson SA & Sudbery IM (2024) Widespread 3’ UTR splicing regulates expression of oncogene transcripts in sequence-dependent and independent manners, Cold Spring Harbor Laboratory.

All publications

Journal articles

Watson S, Porter H, Sudbery I & Thompson R (2024) Modification of Seurat v4 for the development of a phase assignment tool able to distinguish between G2 and mitotic cells. International Journal of Molecular Sciences, 25(9). View this article in WRRO
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) Aging-related defects in macrophage function are driven by MYC and USF1 transcriptional programs. Cell Reports, 43(4). View this article in WRRO
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) A mechanism for oxidative damage repair at gene regulatory elements. Nature, 609(7929), 1038-1047. View this article in WRRO
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) Chromatin-based, in cis and in trans regulatory rewiring underpins distinct oncogenic transcriptomes in multiple myeloma. Nature Communications, 12.
Baidžajevas K, Hadadi É, Lee B, Lum J, Shihui F, Sudbery I, Kiss-Tóth E, Wong SC & Wilson HL (2020) Macrophage polarisation associated with atherosclerosis differentially affects their capacity to handle lipid. Atherosclerosis. View this article in WRRO
Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D & Wilson SA (2019) Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome. Molecular Cell. View this article in WRRO
Kaneva IN, Sudbery IM, Dickman MJ & Sudbery PE (2019) Proteins that physically interact with the phosphatase Cdc14 in Candida albicans have diverse roles in the cell cycle. Scientific Reports, 9. View this article in WRRO
Srivastava A, Malik L, Smith T, Sudbery I & Patro R (2019) Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Genome Biology, 20. View this article in WRRO
Lesbirel S, Viphakone N, Parker M, Parker J, Heath C, Sudbery I & Wilson SA (2018) The m6A-methylase complex recruits TREX and regulates mRNA export. Scientific Reports, 8(1). View this article in WRRO
Liao C, Beveridge R, Hudson JJR, Parker JD, Chiang S-C, Ray S, Ashour ME, Sudbery I, Dickman MJ & El-Khamisy SF (2018) UCHL3 Regulates Topoisomerase-Induced Chromosomal Break Repair by Controlling TDP1 Proteostasis. Cell Reports, 23(11), 3352-3365. View this article in WRRO
Smith TS, Heger A & Sudbery I (2017) UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Research, 27, 491-499. View this article in WRRO
Greig JA, Sudbery IM, Richardson JP, Naglik JR, Wang Y & Sudbery PE (2015) Cell Cycle-Independent Phospho-Regulation of Fkh2 during Hyphal Growth Regulates Candida albicans Pathogenesis. PLOS Pathogens, 11(1), e1004630-e1004630. View this article in WRRO
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) Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer. BMC Cancer, 14(1). View this article in WRRO
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) Next-generation Sequencing of Advanced Prostate Cancer Treated with Androgen-deprivation Therapy. European Urology, 66(1), 32-39.
Sims D, Ilott NE, Sansom SN, Sudbery IM, Johnson JS, Fawcett KA, Berlanga-Taylor AJ, Luna-Valero S, Ponting CP & Heger A (2014) CGAT: computational genomics analysis toolkit. Bioinformatics, 30(9), 1290-1291.
Sims D, Sudbery I, Ilott NE, Heger A & Ponting CP (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics, 15(2), 121-132.
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) High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC Genetics, 11(1), 25-25.
Sudbery I, Enright AJ, Fraser AG & Dunham I (2010) Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis. BMC Genomics, 11(1), 175-175.
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) Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biology, 10. View this article in WRRO
Turner DJ, Keane TM, Sudbery I & Adams DJ (2009) Next-generation sequencing of vertebrate experimental organisms. Mammalian Genome, 20(6), 327-338.
Phillips AJ, Sudbery I & Ramsdale M (2003) Apoptosis induced by environmental stresses and amphotericin B in Candida albicans. Proceedings of the National Academy of Sciences, 100(24), 14327-14332.
Tamblin-Hopper P, Kiss-Toth E, Sudbery I, Young D & Wilkinson JM () The potential therapeutic applications of long non-coding RNAs. Journal of Translational Genetics and Genomics, 8(2), 225-43.
Baquero-Pérez B, Yonchev ID, Delgado-Tejedor A, Medina R, Puig-Torrents M, Sudbery I, Begik O, Wilson SA, Novoa EM & Díez J () N6-methyladenosine modification is not a general trait of viral RNA genomes. 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 () MAF functions as a pioneer transcription factor that initiates and sustains myelomagenesis. Blood Advances.
Niespolo C, Johnston JM, Deshmukh SR, Satam S, Shologu Z, Villacanas O, Sudbery IM, Wilson HL & Kiss-Toth E () Tribbles-1 Expression and Its Function to Control Inflammatory Cytokines, Including Interleukin-8 Levels are Regulated by miRNAs in Macrophages and Prostate Cancer Cells. Frontiers in Immunology, 11.
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 () CGAT-core: a python framework for building scalable, reproducible computational biology workflows. F1000Research, 8, 377-377.
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 () CGAT-core: a python framework for building scalable, reproducible computational biology workflows. F1000Research, 8, 377-377. View this article in WRRO
Huang Z-X, Zhao P, Zeng G-S, Wang Y-M, Sudbery I & Wang Y () Phosphoregulation of Nap1 Plays a Role in Septin Ring Dynamics and Morphogenesis in Candida albicans. mBio, 5(1).
Farcas AM, Blackledge NP, Sudbery I, Long HK, McGouran JF, Rose NR, Lee S, Sims D, Cerase A, Sheahan TW , Koseki H et al () KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. eLife, 1.

Conference proceedings papers

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) Oncogenic MAF in Co-Operation with IRF4 Confers Extensive Chromatin Re-Arrangement in Plasma Cells and Generates 'Neo-Enhancers' That Regulate Genes Critical for Myeloma Biology. 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) Distinct Chromatin Accessibility Changes, Aberrant Transcription Factor Networks Combined with Novel Oncogenic Enhancers Characterise Myeloma-Initiating Genetic Events. 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) BS25 Investigating the MIR-101-3P/TRIB1 axis in macrophage immunometabolism. Basic Science
Baidzajevas K, Hadadi E, Lee B, Lum J, Sudbery I, Lai S, Wong SC, Kiss-Toth E & Wilson H (2017) 201 Human oxidised phospholipid macrophages have high lipoprotein handling capabilities without readily forming unwanted foam cells. 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)

Theses / Dissertations

Sudbery I (2010) 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) Heterogeneous graph attention network improves cancer multiomics integration, arXiv.
Riley JJ, Alexandru-Crivac CN, Bryce-Smith S, Wilson SA & Sudbery IM (2024) Widespread 3’ UTR splicing regulates expression of oncogene transcripts in sequence-dependent and independent manners, 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) N⁶-methyladenosine modification is not a general trait of viral RNA genomes, 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) Ageing-related defects in macrophage function are driven byMYCandUSF1transcriptional programmes, Cold Spring Harbor Laboratory.
Watson S, Porter H, Sudbery I & Thompson R (2022) Modification of Seurat v4 for the development of a phase assignment tool able to distinguish between G2 and Mitotic cells, Cold Spring Harbor Laboratory.
Alvarez-Benayas J, Katsarou A, Trasanidis N, Chaidos A, May PC, Ponnusamy K, Xiao X, Bua M, Atta M, Roberts IAG , Auner HW et al () Over-accessible chromatin links myeloma initiating genetic events to oncogenic transcriptomes and aberrant transcription factor regulatory networks.
Viphakone N, Sudbery IM, Heath CG, Sims D & Wilson SA () Co-transcriptional loading of RNA export factors shapes the human transcriptome.
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 () CGAT-core: a python framework for building scalable, reproducible computational biology workflows, Cold Spring Harbor Laboratory.
Srivastava A, Malik L, Smith T, Sudbery I & Patro R () Alevin efficiently estimates accurate gene abundances from dscRNA-seq data.
Kaneva I, Sudbery I, Dickman MJ & Sudbery PE () A proteome-wide screen reveals widespread roles for the phosphatase Cdc14 in theCandida albicanscell cycle.
Smith T, Heger A & Sudbery I () UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy, Cold Spring Harbor Laboratory.

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