Helena Kilpinen, PhD

Leena Kilpinen-Barrett V07 06-09-19

Helena is a HiLIFE assistant professor in genome biology at the Faculty of Biological and Environmental Sciences and a research group leader at FIMM.

Helena received her PhD from the University of Helsinki in 2011 where she studied the genetic mechanisms underlying autism spectrum disorders with Prof. Leena Peltonen-Palotie and Dr. Iiris Hovatta. For her postdoctoral training, she transitioned to functional genomics, studying how DNA sequence variation influences different levels of gene regulation in human cells, first at the University of Geneva, Switzerland, with Prof. Emmanouil Dermitzakis, and then at the European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK, with Dr. Oliver Stegle. Helena joined the Human Induced Pluripotent Stem Cell Initiative (HipSci) in 2014 and has since focused on characterising non-coding genetic variation in induced pluripotent stem cells (iPSC), most recently in the context of rare human diseases.

Helena started her research group in 2016, jointly at the UCL Great Ormond Street Institute of Child Health in London and the Wellcome Sanger Institute in Cambridge, UK, where she held a MRC eMedLab Career Development Fellowship in Medical Bioinformatics.

Pau Puigdevall Costa, PhD

Pau Puidgevall

I graduated in Biotechnology at the University of Girona, Catalonia, in 2013, and specialized in biochemical engineering after a short internship at the Molecular Cell Physiology Department from the Vrije Universiteit, Amsterdam. I shifted to computational work during an MSc in Bioinformatics for Health Science at Pompeu Fabra University. In 2015, I started my PhD in the Functional Genomics group lead by Dr. Robert Castelo. I searched for genetic modifiers of penetrance in human inherited disease, mainly focusing on a particular family disease case study of pulmonary arterial hypertension. I also participated in the development of the R/Bioconductor package GenomicScores, which enables a fast and seamless way to retrieve genome-wide position specific scores of conservation, allele frequency, constraint, fitness and deleteriousness. I received my PhD in early 2019 and joined Helena’s group as a postdoctoral researcher in Feb 2019. I was captivated by the ongoing projects on computational genomics of cellular variation. In line of my previous research, I am very interested in understanding how the genetic background may impact the penetrance and the variable expressivity of pathogenic mutations in rare disease. I will address this question by using iPSC-based disease models directly obtained from patients and profiled by different omics tools, including scRNA-seq and ATAC-seq data. My post-doc is a collaborative project with Dr. Sergi Castellano (ICH).

Charlotte Roth, M.Sc.


During my medical training in France, I acquired substantial knowledge on human physiopathology and therapeutic strategies. The emergence of human iPS cells and CRISPR-Cas9 technology drastically changed the scope of genetic engineering and disease modelling experiments and played an important role in my decision to focus purely on a research career path since. I completed a Brain and Mind MSc at UCL in 2018, where I quickly acquired a significant interest in CRISPR-Cas9 and iPSC technologies. After graduating from UCL, I first joined Prof. Jorge Ferrer’s research group at Imperial College London. This position helped me broaden my skill set in genomics. I then joined Dr Kilpinen’s lab at UCL as a Research Assistant in October 2019. My project focuses on investigating genetic background effects in iPSC-based disease models. I am using state-of-the-art experimental technologies such as single-cell ATAC-sequencing and genome engineering to profile iPSC-derived neuronal cells. I am also in the process of learning computational skills.

Anna Saukkonen, B.Sc.

Anna Saukkonen V06 06-09-19I graduated from the University of Aberdeen with a BSc in Biochemistry. I am currently in my first year of the LIDo PhD programme doing a project with Helena’s group and Dr. Alan Hodgkinson’s group (KCL). Having a wet research laboratory background, I am excited to now move into the computational biology field. In my project I am looking at allele-specific expression from data generated by the HipSci project. Differential levels of gene expression associated with distinct genotypes are most often studied on a population level and with common genetic variants. This approach, although informative, often misses the important rare variants. In my project I am tackling these issues by looking at allele-specific expression within single individuals, using the full information of their genomes.

Ziba Shadman, M.Sc.


I completed my BSc in Medical Genetics at Queen Mary University of London and my MSc in Reproductive & Developmental Biology at Imperial College London. I am primarily interested in human iPSC research and have been working in this field over the past year. I joined Dr Kilpinen’s lab in November 2019 as an Advanced Research Assistant. I am based at the Wellcome Sanger Institute where I work on an Open Targets collaboration. In my current project, I am differentiating human iPSC lines from the HipSci project into cortical neurons to study effects of genetic variation on phenotypic variability in neurodevelopmental disorders. Combined with CRISPR gene editing and scRNA-seq analysis, this project opens windows in understanding specific mutations and their effects in rare genetic diseases and this is why I am passionate about my role in the project.

Dara Vakili, B.Sc.

Dara Vakili V05 06-09-19

I first joined the group in the summer of 2016 as an undergraduate student in my final year of UCL Applied Medical Sciences BSc. I am currently studying medicine at Imperial College London. Having done placements in microbiology and tissue engineering labs, I now aspire to be a part of the big data revolution in healthcare and science. I am deeply fascinated by the discoveries around the human genome, especially findings in cancer genomics, and the translation of these to medicine. Currently, I am studying iPSC cell lines from the HipSci project and comparing profiles of gene expression and alternative splicing in patient-derived cells to improve our understanding of these as disease models.


Nicola Maestro, M.Sc. – Research Assistant
Prijesh Mulji, B.Sc. – MRes project student


Christmas lunch Dec-2019 with the Castellano group.