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Bill Lyons Informatics Centre team

Centre Lead: Dr Javier Herrero

Javier Herrero

Email: javier.herrero@ucl.ac.uk
UCL profile: Dr Javier Herrero

Prior to joining the UCL Cancer Institute, Dr Herrero was based at the European Bioinformatics Institute as coordinator of the Ensembl project and leading the Ensembl Comparative Genomics team. He has participated in the functional interpretation of the results in the ENCODE and 1000 Genomes projects as well as in the analysis of many of the mammalian genomes sequenced in the last few years.

Dr Herrero completed his PhD at the CNIO in 2004. His work focused on the analysis of gene expression patterns. In addition, Javier developed the GEPAS (Gene Expression Pattern Analysis Suite) server.


Dhruva Biswas
Dhruva Biswas - MB PhD student, Translational Cancer Therapeutics Laboratory (Sep 2016 - )
Email: dhruva.biswas.15@ucl.ac.uk

Dhruva is as a PhD student in Charles Swanton’s laboratory, starting in September 2016. Alongside his pre-clinical medical studies at the University of Cambridge Dhruva undertook computational projects in cellular electrophysiology, translational neuromodeling, and neuronal networks. As an MB PhD student at University College London Dhruva is interested in translating principles and approaches from theoretical neuroscience to cancer bioinformatics, specifically contributing to the understanding of tumour evolution.


Lucia Conde
Lucia Conde - Research Associate (Jun 2015 - )
Email: l.conde@ucl.ac.uk

Lucia completed her PhD in 2007 at UAM (Madrid, Spain), working on the development of bioinformatics tools for the analysis of genetic polymorphisms. In 2008 she started a joint postdoctoral position at the International Computer Science Institute (Berkeley, CA, USA) and the University of California, Berkeley (CA, USA) under the supervision of Drs. Eran Halperin and Christine Skibola. Since 2009, she has continued her work at Dr. Skibola's group at UC Berkeley, conducting statistical and bioinformatic data analyses on population studies with a major focus on Non Hodgkin's lymphoma and other haematological malignancies.

Lucia joined Dr. Herrero's group at the Bill Lyons Informatics Centre at the UCL Cancer Institute in June 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 personalized medicine.


José Afonso Guerra-Assunção
José Afonso Guerra-Assunção - Research Associate (Feb 2016 - )
Email: a.guerra@ucl.ac.uk

José Afonso has joined the BLIC after working at the London School of Hygiene & Tropical Medicine (Jan 2013 - Feb 2014) and at the Barts Cancer Institute (Mar 2014 - Jan 2016).

He trained in Microbiology and Genetics at the Universidade de Lisboa and then completed his PhD on the evolutionary analysis of microRNAs at the European Bioinformatics Institute (EBI) in the group of Anton Enright.


Stephen Henderson
Stephen Henderson - Research Associate (Apr 2014 - )
Email: s.henderson@ucl.ac.uk

Stephen’s recent work has been in Viral Oncology, including Kaposi Sarcoma and HPV tumours like Cervical and Head and Neck, though he has also worked with many others within UCL and beyond on a variety of papers and projects. Stephen’s 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 (OK) and Python (less OK), enough statistical know-how to avoid the Dunning-Kruger effect, sporadic unix proficiency, plus a broad but shallow understanding of machine learning and other bioinformatics tools.


Garima Khandelwal
Garima Khandelwal - Research Associate (May 2018 - )
Email: g.khandelwal@ucl.ac.uk

Garima completed her PhD in Computational Chemistry from IIT Delhi where she developed energy-based signatures for deciphering prokaryotic genome organization. She did her postdoc in Dr. Crispin Miller’s group at Cancer Research UK, Manchester Institute. Her main project was to develop a method to identify long non-coding RNAs folding into similar structures. During hertime at CRUK-MI, she has also worked on NGS data from melanoma and lung cancer.

She joined Prof. Herrero's group at the the UCL Cancer Institute in May 2018. She will be majorly focusing on the analysis of whole-exome data from the national NCRI Multiple Myeloma clinical trial with Prof. Kwee Yong and to identify how transcription factors, chromatin modifiers and non-coding RNAs act to regulate cell differentiation with Prof. Richard Jenner.


Mariana Pereira
Mariana Buongermino Pereira - Research Associate, Attard lab (Jan 2018 - )
Email: mariana.pereira@ucl.ac.uk

Mariana works with prostate cancer, estimating tumour content from plasma samples. Before joining the UCL Cancer Institute, Mariana completed her PhD in mathematical statitsics/ bioinformatics at Chalmers University of Technology, Sweden. During her PhD she studied statistical modelling of DNA sequence data. More specifically she applied hidden Markov models to the prediction of mobile elements in bacterial genomes, and studied normalisation methods of shotgun metagenomic data.


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Philippe Pinel
Philippe Pinel - Intern (since July 2018)

Email: p.pinel@ucl.ac.uk

Philippe is an intern for six months, starting July 2018, who completed his first year master at Mines ParisTech, a french engineering school. His knowlegde in computer science, mathematics, statistical analysis and biology from his previous studies are used in his project to study non-coding mutations in cancer


Rachel Rosenthal
Rachel Rosenthal  - PhD student, Personalised Medicine Group (Oct 2014 - )
Email: rachel.rosenthal.14@ucl.ac.uk

Rachel is a PhD student in Charles Swanton's lab. My work for BLIC will be to use computational methods to identify potential neo-antigens in a lung cancer cohort as part of the TRACERx project. Before coming to UCL, Rachel worked in Barry Taylor's lab at UCSF and completed a MSc in systems biology at ETH Zurich, where she studied how to model allosteric interactions in bacteria undergoing a fast shift in carbon substrate.


Watcharaporn (Pink) Tanchotsrinon
Watcharaporn Tanchotsrinon - Research Associate (July 2018 - )

Email: p.tanchotsrinon@ucl.ac.uk

Watcharaporn is currently a lecturer of HRH Princess Chulabhorn College of Medical Science, Thailand. She completed her Ph.D. of Computer Science and Information Technology from Chulalongkorn University of Thailand in 2016. Her research concerned with building prediction algorithm based on artificial neural networks for HPV genotyping. She is interested in pattern recognition based on AI for enhancing medical diagnosis, treatment, and prevention. 

For her background, She completed her M.Sc. in Computer Science and Information, and her B.SC. in Biochemistry from Chulalongkorn University of Thailand.


Helena Vincentelli
Helena Vincentelli - Research Fellow, Urological Cancer Biology Group (June 2017 - )

Email: h.vincentelli@ucl.ac.uk

Helena is a Research Fellow in Dr Mark Linch’s Urological Cancer Biology Group. Her recent work has been in translational prostate cancer studies in collaboration with UCLH and the Francis Crick. The studies look into prostate cancer heterogeneity and signaling pathways at the genomic and proteomic level.

Helena is also involved in the development of novel informatics platforms for improved data collection for metastatic prostate cancer at UCLH.

Previously, Helena completed her BSc and MSc in biomedical engineering, with her masters thesis project at the Luscombe lab in the Francis Crick investigating RNA metabolism in sympathetic neurons through RNAseq data.


Former members

Po Liu
Visiting MD student, Personalised Medicine Group: Dec 2017 - Mar 2018
LinkedIn

Chela James
Research Associate, Stem Cell Laboratory: May 2016 - Jan 2018
Chela is still at the UCL Cancer Institute, but has moved down to the 5th floor

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
LinkedIn

James Barrett
Research Associate, Medical Genomics Group: Jun 2014 - Aug 2016
Web page

Arnulf Hertweck
Research Associate, Regulatory Genomics: Jul 2014 - Apr 2016
Arnulf is still at the UCL Cancer Institute, but has moved down to the 5th floor

Waqasuddin Khan
Visiting Researcher: Mar - May 2016
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Da-Peng Wang
Research Associate, Stem Cell Laboratory: Mar 2014 - Jan 2016
LinkedIn

Duke (Thanabodee) Yeh
MSc Cancer student: May - Sep 2015
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Yaseen Ladak
Research Associate: Mar - Jul 2015
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