Bill Lyons Informatics Centre
A new hub of bioinformatics expertise for cancer genomics.
The Bill Lyons Informatics Centre (BLIC) is a sixth floor extension to the existing UCL Cancer Institute. Named following a lead gift from the Lyons Charitable Trust, it was completed in November 2013. The new Centre provides a base for up to 12 bioinformaticians and computational biologists. The centre focuses on genomics studies.
Facilities
To ensure the efficient handling of large data sets, the Bill Lyons Informatics Centre has a dedicated network access to the central UCL IT facilities, including the Myriad and the Computer Science HPC clusters as well as the UCL Research Data Storage services.
Bill Lyons Informatics Centre Team
Dr Javier Herrero
Centre Lead
Dr Herrero joined from the European Bioinformatics Institute, where he coordinated the Ensembl project and led its Comparative Genomics team. He participated in the functional interpretation of results in the ENCODE and 1000 Genomes projects alongside the analysis of many of the mammalian genomes sequenced recently. Dr Herrero completed his PhD at the CNIO in 2004. His work focused on the analysis of gene expression patterns. He also developed the Gene Expression Pattern Analysis Suite server.
Dhruva Biswas
MBPhD student
Translational Cancer Therapeutics Laboratory
Dhruva became a PhD student in Charles Swanton's laboratory in 2016. Alongside his pre-clinical medical studies at the University of Cambridge, Dhruva took computational projects in cellular electrophysiology, translational neuromodeling, and neuronal networks. As an MBPhD student at UCL, Dhruva is interested in translating principles and approaches from theoretical neuroscience to cancer bioinformatics, specifically contributing to the understanding of tumour evolution.
Senior Research Fellow
Lucia joined the centre in 2015. She is interested in studying the genetic basis of complex diseases and the interaction between genetic, environmental and epigenetic factors, and translating these findings into personalised medicine. Lucia completed her PhD in 2007 at UAM (Madrid, Spain), working on the development of bioinformatics tools for the analysis of genetic polymorphisms, followed by a joint postdoctoral role at the International Computer Science Institute and University of California.
Chuling Ding
PhD student
Chuling is interested in new methodologies to study cancer evolution using single cell data and epigenomic data. She will be mainly focusing on the dataset from the CRUK Glioma Cellular Genetics Resource (GCGR) and the Small Intestinal Neuro-Endocrine Tumours (SI-NETs) project. Before starting at the BLIC, she completed her MSc Cancer project in Tariq Enver's lab at UCL Cancer Institute, working on alternative transcript usage in childhood Acute Lymphoblastic Leukaemia.
Senior Research Fellow
Stephen works in Viral Oncology, including Kaposi Sarcoma and HPV tumours like Cervical and Head and Neck, though he has worked with many others on a variety of papers and projects. His broad interest is in mining the public tumour databases for hidden patterns, particularly mutational signatures related to innate immune responses (e.g. AID,APOBECs) and disregulated DNA repair (e.g. FHIT,XRCC1). My specific skills are in programming R and Python, and sporadic unix proficiency.
Garima Khandelwal
Research Associate
Garima joined Dr Herrero's group in 2018. She focuses on the analysis of whole-exome data from the national NCRI Multiple Myeloma clinical trial with Prof. Kwee Yong, and how to identify how transcription factors, chromatin modifiers and non-coding RNAs act to regulate cell differentiation with Prof. Richard Jenner. Garima completed her PhD in Computational Chemistry from IIT Delhi where she developed energy-based signatures for deciphering prokaryotic genome organization.
Mark Tran
PhD student
Prior to joining the UCL Cancer Institute, Mark worked on retinal stem cells in Rachael Pearson’s lab at the UCL Institute of Ophthalmology and completed a MRes in Stem Cells and Development Biology. As a PhD student in the UCL Cancer Institute, he is mainly interested in finding novel ways of mapping subclonal copy-number, gene expression and methylation events onto tumour evolutionary trees.
Krupa Thakkar
MSc student: May-Sep 2019
Rachel Rosenthal
PhD student, Personalised Medicine Group: Oct 2014 - Nov 2019
Watcharaporn Tanchotsrinon
Research Associate: July 2018 - Sep 2019
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José Afonso Guerra-Assunção
Research Associate: Feb 2016 - Sep 2019
Cecilia Wieder
Undergrad student: Sep 2018 - Apr 2019
Mariana Buongermino Pereira
Research Associate, Attard lab: Jan 2018 - Mar 2019
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Philippe Pinel
Intern: July - Dec 2018
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Helena Vincentelli
Research Fellow, Urological Cancer Biology Group: June 2017 - Aug 2018
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Po Liu
Visiting MD student, Personalised Medicine Group: Dec 2017 - Mar 2018
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Chela James
Research Associate, Stem Cell Laboratory: May 2016 - Jan 2018
John Ambrose
Research Associate: Jun 2014 - Oct 2017
Now at Genomics England
Annabel Tran
MSc student: May-Aug 2016
Visiting scientist: Sep-Nov 2016
Gerald Goh
Research Associate, Personalised Medicine Group: Oct 2014 - Oct 2016
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James Barrett
Research Associate, Medical Genomics Group: Jun 2014 - Aug 2016
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Arnulf Hertweck
Research Associate, Regulatory Genomics: Jul 2014 - Apr 2016
Waqasuddin Khan
Visiting Researcher: Mar-May 2016
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Da-Peng Wang
Research Associate, Stem Cell Laboratory: Mar 2014 - Jan 2016
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Duke (Thanabodee) Yeh
MSc Cancer student: May-Sep 2015
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Yaseen Ladak
Research Associate: Mar-Jul 2015
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This addition to the UCL Cancer Institute is instrumental for many genomics projects currently being developed, from cancer classification to personal genomics and patient stratification.
News
Friday 2 March 2018
All the best, Po Liu!
We have been lucky to have Po at the BLIC for 3 months. In that time, he has been looking at cancer neo-antigens using neural networks. Nice piece of work in such a short time!
January 2018
Mariana Pereira (Gert Attard's group) joins the BLIC
Mariana is a new bioinformatician in Gert Attard's group and she is joining the BLIC. Her project focuses on estimating tumour content from plasma DNA. Welcome on-board!
Po Liu, visitor at the BLIC
Monday 11 Dec 2017. An MD student from University of Sidney, visiting Charlie Swanton's group is joining the BLIC today to delve in cancer neo-antigens. Welcome Po!
Farewell John Ambrose!
Friday 20 Oct 2017. After 3 years of hard work, John has decided to join Genomics England and we wish him all the best in his new enterprise. Luckily, he will be close by and we hope to see him from time to time.
Helena Vincentelli (Mark Linch's group) joins the BLIC
Tue 27 June 2017. Helena is joining the BLIC to work on a prostate cancer heterogeneity in Dr Mark Linch’s Urological Cancer Biology Group. We hope the BLIC is a great environment for the success of your research!
Waqasuddin's last day
Tuesday 10 May 2016. After 2 months at the BLIC, it is time to say farewell to Waqas! Coffee, tea, cake and a group picture to remember the day.
Chela James and Annabel Tran start at the BLIC
Tuesday 3 May 2016. Just after the early May bank holiday, we have two newcomers at the BLIC. Chela James from joins Tariq Enver's group and will be hosted at the BLIC. Annabel Tran is our 2016 MSc Cancer student who will be studying cancer driver genes until early September.
Waqasuddin Khan is visiting the BLIC
Monday 14 March 2016. Waqasuddin (Waqas for short) Khan has arrived today at the BLIC where he will spend 2 months studying variants that affect Transcription Factor Binding Sites in enhancers. He comes from the Jamil-ur-Rahman Center for Genome Research, ICCBS, University of Karachi (Pakistan) with a Charles Wallace Visiting Fellowship from the British Council Pakistan.
deconstructSigs package on CRAN
Friday 15 January 2016. Rachel Rosenthal has just published her first R package on CRAN: deconstructSigs. The package is inspired by the work of Alexandrov et al, 2013 on mutational signatures. This tools identifies the weighted combination of the aforementioned signatures that, when summed, most closely reconstructs the mutational profile for a given sample.
Single cell RNA-seq symposium
Wednesday 9 December. Today we have had John Marioni from EMBL-EBI and CRUK Cambridge Institute) as our special guest for the Single Cell RNA-seq symposium. The event started his presentation entitled "Using single-cell transcriptomics to study early development" and continued with an in-depth discussion on different aspects of single cell analysis, including technical approached, data analysis and biological interpretation of the results.
Patrick Lombard joins the BLIC
Monday 2 November 2015. Patrick Lombard has joined UCL today. Working in the Genetics & Cell Biology of Sarcoma group headed by Adrienne Flanagan, Patrick will initially be based at the BLIC where he will be focusing on the analysis whole-exome sequencing data.
ChIP-seq symposium
Wednesday 16 September 2015. Many thanks to Anna Poetsch (The Francis Crick Institute) and Steven Wilder (EMBL-EBI) for their participation on the ChIP-seq symposium today. Following their presentation on "What determines Pol2 positioning at transcriptional start sites" and "Dwelling on ChIP-seq QC problems: enrichment, reproducibility and peak-caller issues" respectively at the Bill Lyons Informatics Centre, the discussion continued in the afternoon. Richard Jenner, Chris Barrington and Jason Wray introduced different topics around the quantification, reproducibility and comparison of ChIP-seq data.
Lucia Conde joins the group
Monday 1 June 2015. Lucia Conde has just joined the bioinformatics team. She worked as a postdoctoral researcher in Dr. Christine Skibola's lab at UC Berkeley (CA, USA) and UAB (AL, USA) conducting statistical and bioinformatic data analyses on population studies, with a major focus on Non Hodgkin's lymphoma and other haematological malignancies.
BLIC Seminar: Andrea Sottoriva
Wednesday 22 April 2015. Today Andrea Sottoriva presented his latest work on "Neutral evolution and star-like phylogenies in next-generation sequencing data". He introduced the so-called 'Big Bang' model of tumour growth. Read the original paper.
Yaseen Ladak joins the group
Monday 2 March 2015. Welcome to Yaseen, new member of the bioinformatics team. Yaseen has built his bioinformatics in several places, including the Wellcome Trust Sanger Institute and Kings College London. Apart from his experience with NGS data, he also brings new expertise the design of CRISPR guide sequences and in the analysis of mass spectrometry data.
BLIC Seminar: Robert Sugar
Wednesday 19 November 2014. Robert Sugar from the EMBL-EBI (now at Intel) presented his research work on the analysis of Hi-C data and the lessons learned on how the promoters and the enhancers interact with one another and with the genes they regulate.
Single Cell Genomics facilities
Thursday 23 October 2014. The Medical Research Council has awarded £3.6M to the UCL Cancer Institute for establishing a new facility for the study of individual Circulating Tumour Cells (CTCs). The Bill Lyons Informatics Center will be instrumental in the analysis of these data. Read more.
First bioinformatics seminar
Thursday 11 September 2014. Together with other bioinformaticians and computational biologists from other teams at the UCL Cancer Institute, we have had our first bioinformatics seminar today. While the topic was very technical on this occasion, we have talked about how to make the best of the compute resources available at UCL, it was a nice way to exchange knowledge, ideas and tips on our every day life.
John Ambrose joins the team
Monday 9 June 2014. We welcome John to the Bill Lyons Informatics Centre. John, the third full-time recruit for the BLIC, has just completed his PhD in HIV molecular epidemiology at the University of Liverpool. His expertise in phylogeny and genome analysis is a great addition to the group.
Stephen Henderson moves to the BLIC
Monday 14 april 2014. Stephen has moved today to the Bill Lyons Informatics Centre, after spending a few years in Chris Boshoff's group. His wide range of bioinformatics skills, especially his expertise on gene expression analysis, will greatly benefit the team.
Opening event
Thursday 4 April 2014. Frank Dobson, MP for Holborn and St. Pancras and a former Secretary of State for Health open the new Centre. The event was attended by representatives of the Bill Lyons Charitable Trust and other funders. View full information, UCL News.
It all started on...
Monday 3 May 2014. First day at the Bill Lyons Informatics Centre. For the time being, it is only Javier Herrero on the 6th floor of the Paul O'Gorman building.
