Post-Doc Students
Dr Chris Steele
Post-Doc
Bio
Summer Internship Students
Emily Warburton
Summer Internship, Summer 2022
I am currently a second year medical student at UCL, and last year I was awarded the Rani Rawji Studentship (2022), which allowed me to complete a research project in the Pillay lab over the summer. During my placement, I explored the possibilities of digital pathology using the software QuPath. Specifically, I looked into quantifying beta-2-microglobulin (B2M) expression in head and neck cancers, and quantifying tumour-infiltrating lymphocytes (TILs) in undifferentiated pleomorphic sarcomas. Both of these created possible methods/pipelines to be able to use in a variety of pathological slide images.
Aliza Butt
Summer Internship, Summer 2019
'During the summer of my first year of undergraduate study, I carried out a four-week internship in Dr Pillay's lab which focuses on Sarcoma Biology and Genomics. Throughout the internship, I experienced the daily life of a research technician within a lab and a researcher working within a team. I gained a lot from all the lab techniques that I observed, from histology procedures, such as sectioning and embedding, to molecular techniques, such as DNA/RNA extraction, quality control, and PCR. I was given the opportunity to shadow an MSc student and attend lab meetings which gave me greater insight into the different types of research being performed concerning sarcoma biology and genomics. I also attended seminars presented by world leading researchers which gave me insight into the various research topics currently being investigated concerning cancer medicine and motivated me further to pursue a career in cancer research. Overall, working in Dr Pillay's lab made me interested in the field of bioinformatics and computational biology and how important it is for future research, and this has been the reason why I am now gaining skills in cancer informatics as I pursue a career in cancer research.
Masters Students
Daniel Silva
MSc Cancer Student, Class of 2020
As part of my MSc Cancer research project at UCL, I had the opportunity to investigate the tumour mutational burden (TMB) of undifferentiated pleomorphic sarcomas (UPS). Here I was involved in identifying patient sample subsets of hypermutational state and any potential cancer driver genes responsible for hypermutation across Vortex and GeDDiS datasets in patient samples diagnosed with UPS. Under the supervision of Dr Nischalan Pillay and the guidance of members of the Sarcoma Biology and Genomics research group, I acquired invaluable knowledge in cancer genomics and the principles of next generation sequencing (NGS), topics novel to me in a research environment. Additionally, I gained significant experience using Programming Language Software R packages, learning to edit, and run existing scripts and develop my own workflows for somatic mutational calling (SMC), skills which will prove vital when it comes to the future analysis of large quantities of data. These coding scripts were readily applied to patient genomic datasets in combination with statistical testing, and manual curation using the Integrative Genomics Viewer software to gain a true understanding of the TMB in UPS, recognising the pitfalls of mutation calling using NGS technologies. I am currently a PhD Student at the UCL Division of Surgery and Interventional Science, tackling the mechanisms of therapeutic ultrasound on biomimetic models of cancer, under the supervision of Dr Pierre Gélat and Dr Umber Cheema. My exhilarating time at the Sarcoma Biology and Genomics research group made me an increasingly confident and organised individual, which has not only provided me with aptitudes required to perform at the level of a postgraduate research student, but have also set a strong foundation for me to develop on throughout my research career.
Deb Keya
I am a Molecular Biologist working at a research organisation called Child Health Research Foundation in Bangladesh. My work mainly focusses on whole genome sequencing of pathogens to understand infectious diseases in paediatric patients as well as establishing a scRNA seq platform to investigate the oropharyngeal microenvironment in health and disease. I completed my MSc research project on deciphering immune landscape in the tumour microenvironment of advanced soft tissue sarcoma under the supervision of Dr Nischalan Pillay in 2019. I had a wonderful time working in Nisch's lab as I got to have hands on experience in important wet lab techniques alongside learning about advanced bioinformatics. The team is built of incredible scientists who can go above and beyond to help others and my time at the Pillay lab would not have been the same without them. This goes without saying that the transferable skills and interdisciplinary research experience from Nisch's lab paved the path for my career in biomedical research.
Masters Student, 2019-2020
Andreas Loesch
Masters Student, 2021-2022
I joined the Pillay lab for 9 months in 2021-2022 to conduct my Master's thesis. I had studied Biology with a focus on Cell Biology and entry-level Bioinformatics and had developed a superficial interest in Cancer Genomics. As I had briefly worked on cancer copy number data analysis before, Nischalan assigned me to a postdoc's subproject on copy number signatures in cancer cell lines. The postdoc, Christopher Steele, would be my day-to-day mentor whereas Nischalan would occasionally adjust the project's overall direction after mutual, constructive discussions.
Foremost, the Pillay lab showed me how science can be done in a small, highly interactive group of motivated colleagues and made me feel part of it. In the weekly group meetings, all members showed genuine interest in both my project as well as in comments and questions I had about theirs. My impression was that although the environment was generally ambitious, it did not come at the expense of breeding competition between colleagues. The group meetings also regularly allocated time to get everyone on the same page in an educational way.
Practically, through the stay I acquired a much improved grasp on all areas of the scientific process, from experiment planning over intricacies of statistical analyses to communication of results. Learning how to handle cancer copy number data, including raw data processing and state-of-the-art analyses, has given me a niche in the broader field of Cancer Genomics which remains valuable at my current position.
Over the course of the project I had been given ample opportunities to start connecting to the wider research community. This was not only confined to colleagues I got to know in London through various meetings and talks. The Pillay lab supported me to present my research at the RECOMB 2022 conference in San Diego, USA, which was a seminal experience for me.
I'm currently a PhD student, still focusing on Cancer Genomics. Looking back, the stay at the Pillay lab crucially developed my motivation, skills and confidence needed to pursue such a position.
