Helena Kilpinen, PhD
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.
Francesco Iacoviello, BSc
I am currently enrolled in the Genetics and Molecular Biosciences (GMB) MSc Programme at the Faculty of Biological and Environmental Sciences, University of Helsinki. Before coming to Finland, I obtained a B.Sc in Biotechnology at the University of Milan-Bicocca in 2018 with a major focus on Molecular Genetics and Epigenetics, and to further my knowledge in these two topics I enrolled in the Genetics and Genomics study track of the GMB Programme. My previous work strived to find new ways to treat neurodevelopmental disorders (NDD) through changes in the epigenetic machinery, however in order to achieve this goal it is pivotal to be able to address the cellular basis of developmental disorders. Induced pluripotent stem cells (iPSCs) models have been shown to be incredible tools for modelling NDDs and complex human traits, therefore for my master thesis project I am interested in using iPSC models to define cell-level phenotypical differences between healthy individuals and patients affected by NDDs.
Dimitri Meistermann, PhD
I took my first steps in the academic world at the University of Nantes (France) and graduated with a master’s degree in Bioinformatics in 2016. Next, I pursued a Ph.D. supervised by Dr. Laurent David and Pr. Jérémie Bourdon at the Center for Research in Transplantation and Immunology in Nantes. This work focused on human preimplantation development, first with the characterization of naive (preimplantation like) pluripotency. The second part of my Ph.D was the study of the cell fate events during preimplantation development using single-cell RNA-Seq. At the beginning of my research, RNA-Seq and especially single-cell transcriptomics were emerging technologies: the analysis of data produced by these techniques was, and remains, a computational and statistical challenge that led me to specialize in these tasks. I am also particularly interested in understanding the mechanisms underlying cell fate. I joined the Kilpinen group in January 2021 as a postdoctoral fellow where I am investing how neurodevelopmental disorders affect cell trajectories during neurogenesis.
Pau Puigdevall-Costa, PhD
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.
I 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.
Rosa Woldegebriel, PhD
Rosa completed her PhD in human/medical genetics at the Medical Neurogenetics group at the University of Helsinki in 2021 with focus on characterization and modeling of a rare neurological syndrome. During her doctoral training, she was also a visiting researcher at King’s College London, completing a project on gene editing of human induced pluripotent stem cells. Prior to her doctoral studies, she completed a master’s degree in neuroscience from the University of Helsinki focusing on axon degeneration diseases using stem cell based neuronal model systems. Rosa has also undertaken research in the ERASMUS Medical Center in the Netherlands and RIKEN Brain Science Institute in Japan in the field of neuroscience, and completed a bachelor’s degree in psychology and cognitive neuroscience from the University of Nottingham, UK. In her postdoctoral research, Rosa is studying cellular phenotypes in neurodevelopmental disorders by stem cell based neuronal model systems. She uses next generation sequencing technologies including single cell RNA sequencing, and complementary high-content imaging to identify disease phenotypes in patient and gene edited neurons. She is also interested in compound screening to reverse disease phenotypes that could be used in development of therapies for rare diseases.
Nicola Maestro, M.Sc. – Research Assistant
Prijesh Mulji, B.Sc. – MRes project student
Dara Vakili, B.Sc. – BSc project student, undergraduate researcher
Christmas lunch Dec-2019 in London with the Castellano group.