Helena Kilpinen, PhD — Principal Investigator
Helena is a HiLIFE assistant professor in genome biology at the Faculty of Biological and Environmental Sciences and a research group leader at FIMM and the Neuroscience Center.
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.
Artur Gynter, BSc — Research Assistant (MSc project)
During the early stages of my studies, I was mostly interested in software engineering and computer science. However during my BSc studies in 2020, I got a unique opportunity to participate in iGEM, international synthetic biology competition, which introduced me to the computational possibilities in the field of biology. This led me to pursue a MSc degree in Life Science Technologies majoring in Bioinformatics and Digital Health at the Aalto University, Finland. Before joining the Kilpinen group in May 2022, I was working as a research assistant in Algorithmic Bioinformatics Group at the University of Helsinki studying the association between protein evolution and sequence alignment. At the Kilpinen group, I am working on cell type deconvolution with computational methods and I look forward to improving my understanding of biology, specifically human genetics, and to extend my skills in bioinformatics.
Nelli Jalkanen, MSc — Doctoral Researcher
I am currently working on my PhD as a joint project between the Kilpinen and Pietiläinen research groups. After a BSc in Psychology at University of Dundee, I completed an MSc in Translational Medicine at University of Helsinki, which sparked my interest in the molecular mechanisms and genetics of neuropsychiatric disorders. During my MSc research training, I had the chance to work on creating and validating CRISPR-Cas9 edited iPSC lines to model patient-specific mutations associated with mitochondrial diseases. I am especially interested in what the genome can reveal about disease risk and pathophysiology, and how it can be interpreted in an accurate and meaningful way to understand complex diseases. In my PhD project, I am using iPSC-derived neuronal disease models and high-throughput genomics and transcriptomics tools to understand functional consequences of dysregulation of gene expression in schizophrenia and intellectual disability.
Kavya Kalpana Ganesh — Doctoral Researcher
Riina Lampela, MSc — Laboratory Coordinator
I am the laboratory coordinator for the Kilpinen group. I obtained my BSc degree in human genetics at UCL (London, UK) after which I continued my studies in Sweden, obtaining my MSc degree in biomedicine from Karolinska Institutet. I had the opportunity to work in the group of Prof. Outi Hovatta, looking into the immunological properties of stem cell transplants in mice given immunosuppressive treatment, and stayed as a research assistant in the group after finishing my studies. Prompted by my interest in stem cells, I continued my studies at the University of Cambridge where I obtained a MSc in Research in Stem Cell Biology. Taking time off academia, I got a chance to live in Malaysia for two years followed by a stint in Switzerland where I worked for a scientific publishing company, Frontiers Media. In 2018 I returned to my native Finland, where I have worked as a laboratory coordinator at the University of Helsinki ever since, joining the Kilpinen group in June 2021. I am currently responsible for the day-to-day activities of the group as well as the stem cell work and other technical aspects for ongoing projects.
Dimitri Meistermann, PhD — Postdoctoral Researcher
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, PhD — Postdoctoral Researcher
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 Prof. Sergi Castellano (UCL).
Charlotte Roth, MSc — Doctoral Researcher
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. I will start a part-time PhD in July 2021.
Adithi Sundaresh, MSc — Doctoral Researcher
I completed my BSc in Biotechnology from Ramaiah Institute of Technology in Bangalore, India, and my MSc in Genetics and Molecular Biosciences in the University of Helsinki. My BSc thesis, conducted at the Indian Institute of Science, was on the topic of regulatory mechanisms in X-chromosome inactivation. Previously, I have worked in human molecular genetics and molecular diagnostics, studying the association of genetic variation with disease phenotypes as well as utilizing known variants in clinical diagnosis. This led me to develop a keen interest in understanding how these combined genotypic effects not only associate with disease but contribute to shaping the disease phenotypes at a molecular and cellular level. Based on this interest, I carried out my MSc thesis project in the Kilpinen group focused on single cell and molecular characterization of neurodevelopment in vitro. Currently, I work both experimentally and computationally to study cellular models of neurodevelopment and pooled iPSC-based approaches for neurodevelopmental disease modeling.
Nicola Maestro, MSc – Research Assistant (UCL)
Prijesh Mulji, BSc – MRes Project Student (UCL)
Dara Vakili, BSc – BSc Project Student, undergraduate researcher (UCL)
Ziba Shadman, MSc – Advanced Research Assistant (WSI)
Sanni Tähtinen, BSc – BSc Project Student (UH)
Francesco Iacoviello, BSc – M.Sc. Project Student (UH)
Rosa Woldegebriel, PhD – Postdoctoral Researcher (UH)
Anna Saukkonen, MSc – Doctoral Researcher (UCL/KCL)
Christmas lunch Dec-2019 in London with the Castellano group.