Molecular genetics and biology of complex diseases - Juha Kere
Our group’s research focuses on the discovery of gene effects in complex human phenotypes, functional annotation of genes and characterization of gene networks in selected diseases. Three major projects involve the epigenetics and genetics of asthma and allergies (EpiGene project; Reinius & al. 2012, see selected publications), gene networks in dyslexia (Massinen & al. 2011, Tammimies & al. 2012), and human embryonal development from oocyte to implantation (unpublished). In addition, we have been characterizing the population structure of Sweden and Finland (Salmela & al. 2011).
Our group is interdisciplinary and includes members with solid background in genetics, biochemistry, molecular and cellular biology, biostatistics, bioinformatics, and model systems (mouse and zebrafish). We work in tight collaboration with clinical specialists and epidemiologists as well as leading experts on special methodologies, such as single-cell transcriptomics and brain imaging, and are involved in international consortia. We use modern genomics tools such as high-throughput sequencing for discovering gene variants and for gene expression profiling (RNAseq). We have tight collaboration with University of Helsinki where Prof. Kere visits part-time based on a specific contract. This group structure provides an excellent training environment for both post- and predoctoral scientists.
Differences in DNA methylation between different white blood cell types are large and have implications for whole-blood methylation analyses. Methylation profiles (as assayed by the Illumina 450K methylation arrays) from six donors cluster in principal component analysis by cell type rather than individual variation.
I obtained my M.D. and M.Sc. degrees at the University of Cartagena (Colombia). In 2010, I joined Juha Kere’s group as a shared PhD student with Annika Scheynius group. My research is focused on genetic and epigenetic factors conferring susceptibility to atopic eczema, asthma and IgE sensitization. I am also interested in studying the immune response to nematodes.
I joined the Juha Kere group as a PhD student in 2012. My main research interest is studying the molecular mechanisms of the dyslexia candidate genes DYX1C1, DCDC2 and KIAA0319 and their involvement in cilia biology. Genetic studies have led to the identification of a number of dyslexia candidate genes. By performing functional studies we are aiming at understanding the molecular mechanisms of these genes and looking for common molecular pathways behind dyslexia. My favourite methods are immunohistochemistry and subsequent confocal imaging, quantitative PCR and protein biochemistry.
After graduating from Karolinska Institutet in 2011 with a PhD in Cell and Molecular Biology I joined Prof. Juha Kere’s group for my post doctoral studies. The major aim of my research is to understand and dissect the neurodevelopmental causes of complex neurological disorders such as dyslexia using zebrafish as the vertebrate model organism. I have a strong background in developmental biology and chemistry. My current research interests include functional genomics and chemical biology.
I have a Ph.D. in medical genetics and the title Associate professor (docent) since 2012. I am interested in the genetics underlying a variety of human diseases, and I find most phenotypes hard to resist. My speciality is mapping disease genes in large families.
A current list of my publications can be found at: http://scholar.google.com/citations?user=R9FXcHgAAAAJ
I got my Ph.D. in medical genetics in Karolinska Institutet. My long time interest is genetic dissection of human complex diseases. My current focuses are high throughput sequencing-based novel disease gene discovery and development of bioinformatics pipelines. In collaborations with clinical doctors we are currently hunting genes causing genetic disorders including obesity, hyperlipidemia, and scoliosis using whole genome sequencing and exome sequencing. The aim of our studies is to understand underlying mechanisms of disease developments, improve diagnoses, and ultimately for individualizing therapy based on sequence variation profiles.
I joined the Juha Kere’s group as a posdoc in 2013. My current work addresses the validation and functional characterization of novel genes discovered from our single cell RNA-sequencing data on early human pre-implantation development. I am also working on transcriptomics of skin and skin derived cultured keratinocytes. I got my PhD in cell and molecular biology of Neurofibromatosis 1 in 2012 from University of Turku, Finland.
I have interests in transcriptional regulation in human diseases and developments. In collaboration with biologists, geneticists, biochemists and other researchers in the team, I develop new analysis methods to interpret the genome-wide data appropriately on demand. We are using single-cell transcriptome sequencing methods, in parallel I am considering decomposition of the data from tissues/biopsies consist of heterogeneous cells.
Google Scholar : http://scholar.google.com/citations?user=KMXNmQoAAAAJ
Juha Kere (born 1958) is professor of molecular genetics at KI since 2001. He graduated with MD (1984), PhD in molecular genetics (1989) and specialist physician degree in clinical genetics (1994) from University of Helsinki. He was postdoctoral associate at Washington University in St.Louis, Missouri 1990-93 and became acting professor and chief physician of medical genetics at University of Helsinki and Helsinki University Central Hospital 1994. He was then founding director of the Finnish Genome Center 1998-2001, after which he moved to KI. He has published over 400 scientific original and review articles and supervised 35 completed doctoral thesis in Finland and Sweden.
Kaarel Krjutskov is a postdoc and a Marie Curie fellow. He has more than ten years of experience with method development in DNA genotyping to modern RNA sequencing. His research interests are related to female reproductive biology in medical- and basic research level for studying molecular mechanisms behind diseases and identifying novel diagnostic biomarkers.
Ever since I learned what science is, I have wanted to become a scientist. On my way of making the dream come true, I am trying to find key genes in the human preimplantation development. Using human global expression data from embryos, we have identified candidate gene's list. Ongoing functional characterization in vivo and in vitro will hopefully explain what these genes are doing during the first 5 days of human development.
The research in molecular biology has evolved during the recent years with the rapid development of next generation sequencing (NGS). I have special interests in candidate gene identification in human inherited diseases or traits using NGS. In addition, I specialize in sensitive detection and visualization of protein-protein interaction in situ as well as study design and methods design & development.
I am a human geneticist with a background from the pre-sequenced genome era in cloning new genes responsible for meningioma (a type of brain tumor), and from the post-sequenced genome era, in looking for the genes associated with complex phenotypes, such as dyslexia, specific language impairment, and cleft lip and/or palate as well as its syndromic form called Van der Woude syndrome, and trying to elucidate their biological role in those phenotypes.
Some recent relevant publications:
A locus on 2p12 containing the co-regulated MRPL19 and C2ORF3 genes is associated to dyslexia.
Hum. Mol. Genet. 2007 Mar;16(6):667-77
Family history interview of a broad phenotype in specific language impairment and matched controls.
Genes Brain Behav. 2012 Nov;11(8):921-7
Dominant mutations in GRHL3 cause Van der Woude Syndrome and disrupt oral periderm development.
Am. J. Hum. Genet. 2014 Jan;94(1):23-32
I am a molecular biologists with skills both on global analysis level and candidate gene level. I combine knowledge in genetics, epigenetics and transcriptomics to study complex diseases such as asthma and allergy.
Tiina is a molecular biologists with a PhD in medical sciences from Karolinska Institutet. After her PhD she has primarily worked with functional studies studying key genes involved in atherosclerosis and skin diseases. Currently she is also lab manager and coordinator of external NGS collaborations in prof. Kere's research group. Her main interests are candidate gene studies within psoriasis and dyslipidemia.
My main research interest is genetics and epigenetics in complex diseases, with focus on asthma and atopic diseases. However, I am also involved in genetic studies of diseases showing monogenic inheritance and also malformations. I perform studies both in larger birth cohorts and smaller selected clinical materials. Analyses are performed on a global level as well as on a candidate gene level. Currently, the aim of my main project is identification of susceptibility genes in a newly recruited material of infants and small children with acute asthma.
Isabel Tapia Paez
I am a molecular biologist with a PhD in molecular genetics from the Karolinska Institutet in 2003. I have a background in mapping chromosomal aberrations such as translocations and deletions. After receiving my PhD I became interested in performing functional studies using dyslexia as a model. I am currently studying the molecular mechanisms behind the dyslexia candidate genes and their role in ciliopathies.
My main research interest is developmental biology with a specific interest in early genome activation and the characterization of genes important for this process. In addition I am interested in the connection between development and disease, and how we could use our studies of development to gain more knowledge and understanding about disease.
Debora is a shared PhD student between Juha Kere and Peter Swoboda research groups. Her research project is on the RFX transcription factors' regulation on their target genes through the X-box promoter motif binding, with interest in their impact on neurons and in the human brain, and using human cell lines and worm C. elegans as model organisms. Prior to her PhD registration, she did her Honours/Master-level project in Peter Swoboda's group in Karolinska Institutet, Sweden to analyse the RFX transcription factor DAF-19 target genes in different developmental stages of C. elegans and her Bachelor research project in Carolyn Behm's group at The Australian National University to analyse GFP expression in three C. elegans genes of which the homologues serve as potential drug targets for the parasitic worm Haemonchus contortus.