Home| Non-clinical Senior Lecturer |
Contact details:
| Tel: | +44 20 7882 2374 |
| Email: | e.stupka@qmul.ac.uk |
| Address: | Centre for Digestive Diseases, |
Biography
As a biologist by training, I began my career in bioinformatics as part of the initial Ensembl team at the European Bioinformatics Institute, where I contributed to the annotation of the human genome (Nature, 2001), as well as the development of the widely used BioPerl software library and the overall Ensembl platform. Having gained a broad background in the dark art of genome annotation as well as all the more mundane problems of managing complex bioinformatics pipelines utilizing cluster computing I was given the opportunity to lead the bioinformatics team which was responsible for the annotation of the Fugu genome (Science, 2002) in Singapore, lead by Nobel Laureate Sydney Brenner. Working on the Fugu genome I furthered my technical interest in bioinformatics workflows and developed a generic workflow system (BioPipe). Above all, working on the second vertebrate genome to be annotated allowed me to venture in the field of comparative genomics and thus developed an interest in functional elements of the genome which escaped canonical gene annotation. Thus as I moved to the Telethon Institute of Genetics and Medicine, I focused on the discovery and annotation of many such elements, including 20,000 novel vertebrate enhancers (Genome Biology, 2006), 5,000 novel genes (Genome Research, 2007) and a small contribution to the pivotal Fantom3 transcriptome paper (Science, 2005) which for the first time indicated the level of transcriptome complexity which we now know to be part of every gene in the genome. I searched for a closer interaction with the clinical world in order to apply the knowledge gained to real-world clinical problems. Thus, after a move to Trieste, Italy, I decided to return to the UK, where I now hold a joint appointment between the BICMS and the UCL Cancer Institute. Here I am focused entirely on utilising next-generation sequencing data to develop fine-grained, genome-centric, comprehensive models and molecular networks of disease.
Research Activity
Our laboratory is interested in understanding how functional elements in the genome contribute to the molecular networks underlying disease. Having been involved in the annotation of the human genome as well as other chordate genomes we have come to appreciate how large-scale bioinformatics pipelines often recapitulate the current, often biased, understanding of genome function. Thus we shifted our focus to the elucidation of novel functional elements in the genome, contributing to the discovery and characterization of vertebrate enhancers, novel genes and non-coding RNAs. Owing to recent developments in next-generation sequencing technologies, we now have the ability to obtain quantitative signals from a wide variety of functional elements in the genome. The lab is now strongly focused on the analysis of next-generation sequencing data and on devising strategies in collaboration with other laboratories, to build novel systems biology approaches to model “next generation molecular networks”. This approach is being applied to several projects, including two EU funded projects, DOPAMINET and P3AGI. Thus the lab is developing pipelines and tools to analyze and integrate a wide variety of data including genome re-sequencing, RNASeq, small RNA seq, Chip-Seq.
Our lab has also helped to organize a community of bioinformaticians with an interest in next-generation sequencing named the Virtual Bioinformatics Lab, which organizes biweekly tutorials as well as day-long technical hands-on meetings.
Key Publications
• Licastro D, Gennarino VA, Petrera F, Sanges R, Banfi S and Stupka E. Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements. BMC Genomics 2010, 11:151
• Velho S, Oliveira C, Paredes J, Sousa S, Leite M, Matos P, Milanezi F, Ribeiro AS, Mendes N, Licastro D, Karhu A, Oliveira MJ, Ligtenberg M, Hamelin R, Carneiro F, Lindblom A, Peltomaki P, Castedo S, Schwartz S Jr, Jordan P, Aaltonen LA, Hofstra RM, Suriano G, Stupka E, Fialho AM, Seruca R. Mixed lineage kinase 3 gene mutations in mismatch repair deficient gastrointestinal tumours. Hum Mol Genet. 2010 Feb 15;19(4):697-706
• Oliveira C, Senz J, Kaurah P, Pinheiro H, Sanges R, Haegert A, Corso G, Schouten J, Fitzgerald R, Vogelsang H, Keller G, Dwerryhouse S, Grimmer D, Chin SF, Yang HK, Jackson CE, Seruca R, Roviello F, Stupka E, Caldas C, Huntsman D. Germline CDH1 deletions in hereditary diffuse gastric cancer families. Hum Mol Genet. 2009 May 1;18(9):1545-55. Epub 2009 Jan 24.
• Roma G, Cobellis G, Claudiani P, Maione F, Cruz P, Tripoli G, Sardiello M, Peluso I, Stupka E*. A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells. Genome Res. 2007 Jul;17(7):1051-60. Epub 2007 May 31.
• Sanges R, Kalmar E, Claudiani P, D'Amato M, Muller F, Stupka E*. Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage.Genome Biol. 2006;7(7):R56.
• Carninci P and the FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). The transcriptional landscape of the mammalian genome. Science. 2005 Sep 2;309(5740):1559-63.
• Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res. 2003 Jan 1;31(1):38-42.
• Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct;12(10):1611-8.
• Aparicio S, Chapman J, Stupka E*, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002 Aug 23;297(5585):1301-10. Epub 2002 Jul 25.
• Lander ES and the International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921.
