I am a postdoctoral researcher with a strong interest towards cancer genetics. I try to identify genetic defects that would explain cancer susceptibility in family materials. I do this mainly by analyzing high throughput sequencing and genotype data. I also work towards uncovering and characterizing the biological mechanisms by which the genetic defects predispose to tumors. Lately my work has been mostly concentrating on genetic susceptibility to small bowel neuroendocrine tumors, as well as colorectal and small bowel adenocarcinoma.

Mervi Aavikko contact information

 

I'm a postdoctoral research with a background in molecular genetics, and gene therapy development. My current interest is to study the genetics of microsatellite unstable colorectal cancer using several different research techniques, including whole genome, RNA and Nanopore sequencing and subsequent data analysis.  I'm very interested in combining basic research with translational and therapy targeted genetics.

Saija Ahonen contact info

I am a postdoctoral researcher in cancer biology and genetics. My main project aims to characterize the different genetic subclasses of uterine leiomyoma (UL). In particular, the study aims to uncover distinct features of ULs by investigating chromatin accessibility, genome architecture and transcriptional activity in the 4 main genetic subclasses of the tumor, analyzing both flash-frozen and fresh samples. The techniques I am currently employing are ATAC-seq, ChIP-seq and Hi-C. Beyond this, I exploit CRISPR/Cas9 technique to generate UL cell line derived from myometrium immortalized cells.

Davide Berta contact info

I am a postdoctoral researcher with a background in molecular biology and cancer gene therapy. I have a strong interest in translational research and precision medicine. My current work focuses on the development of patient-derived 2D and 3D models of uterine leiomyoma, as predictive preclinical models for drug discovery and drug design. I mainly perform cell culture experiments, genotypic and phenotypic characterization of in vitro-generated models and high-throughput drug sensitivity assays.

Simona Bramante contact info

My main interest is to further understand the role of retrotransposon insertions in cancer by utilizing whole genome and Nanopore sequencing. My current research focus is the characterization of somatic and germline retrotransposon insertions in 202 whole genome colorectal tumors.

Tatiana Cajuso contact info

I am a geneticist working on my PhD. My thesis project deals with hereditary cancer susceptibility, and my aim has been to identify novel predisposing mutations for various cancer phenotypes. In most of my studies I have utilized the data in the Finnish Cancer Registry and the Population Information System databases to identify cancer patients with a potential genetic predisposition.

Iikki Donner contact info

My research is focused on the molecular genetic changes in small bowel and colorectal cancers. My current projects include the characterization of both synchronous colorectal cancers and small bowel adenocarcinomas by utilizing exome sequencing.

Ulrika Hänninen contact info

I am a second year molecular biosciences student.  I work as a research assistant. Mainly my work consists of cell culturing and using techniques such as chromatin immunoprecipitation for characterization of different leiomyoma subclasses.

Maija Jäntti contact info

My research is focused on identification and understanding molecular changes, genetic and epigenetic, that are critical for tumor development and progression. Identification of new genotype/phenotype correlations also in other clinical conditions are among my research interests. The work involves analysis and interpretation of next-generation sequencing data, transcriptome and methylation profiling and various cellular works.

Auli Karhu contact info

My duties consist mainly of the next-generation sequencing data analysis in various cancer projects, the development/maintenance of the BasePlayer software (https://baseplayer.fi), general bioinformatics assistance, and the finalization of my PhD studies. I am particularly useful, when the data analysis concerns DNA alterations in coding or noncoding genome.

Riku Katainen contact info

I work as a lab technician. My duties include purchasing procedures of goods and services in our laboratory (tendering process). I am also involved in performing all types of experiments carried out in the lab, e.g. DNA\RNA extraction and purification, PCR, qPCR, immunohistochemistry, western blot and others.

Justyna Kolakowska contact info

 

 

My main interest is to identify genetic variants that contribute to the initiation and progression of microsatellite unstable colorectal cancer through large scale sequencing. My current research focuses on utilizing different algorithms to identify the most likely cancer causing genes. I am also interested in the distribution of mutations in the repetitive regions of the genome in microsatellite unstable colorectal cancer.

Johanna Kondelin contact info

I am a PhD student in bioinformatics. My work focuses on the genetics of uterine leiomyomas (ULs). During the thesis project, I use e.g. whole-genome sequencing, RNA-seq and whole-genome bisulfite sequencing data to further characterize ULs. Long non-coding RNAs, single-cell transcriptomics and population-level predisposition are among my research interests.

Heli Kuisma contact info

Postdoctoral researcher. I received my PhD in computer science in January 2018, and I joined Aaltonen lab in August 2018. My work mainly focuses on methods for RNA-seq data analysis.

Anna Kuosmanen contact info

I recently joined the group as a PhD student and I will be working with microsatellite unstable colorectal cancer.

Samantha Martin contact info

I have worked as a research nurse in Aaltonen lab since Dec 2000. My responsibilities are genealogy work and sample management. I maintain and develop our database and combine cancer data with our sample database. As extra curriculum I am also the groups worry person, I co-arrange our recreational activities and I’m in charge of the safety issues.

Sini Marttinen contact info

I am part of our bioinformatics team. My main responsibilities are all data integrated actions and I try to create an illusion of easiness for our researchers, so that they wouldn't need to worry about their samples. Our data collection is ever increasing and the fluid use of it is a complex puzzle that we are trying solve on a daily basis.

Heikki Metsola contact info

Academy of Finland Postdoctoral Researcher

My research focuses on both benign and malignant uterine smooth muscle tumors. What are the different molecular and genetic mechanisms underlying their growth and development?

I’m currently working at the Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.

Netta Mäkinen contact info

I’m a second year medical student, and am interested in both clinical work and research. I work as a research assistant, and help out in the CRC project, mainly cutting samples, making and staining slides, as well as extracting DNA.

Petra Nygren contact info

I am a senior laboratory technician. My duties principally include experimental planning and research. I troubleshoot and develop better working practices and design protocols for complex samples to facilitate and improve the quality and the quantity of data. I maintain our sample collection, manage the use of DNA stocks and the preparation of samples, including library preps for various downstream applications. I undertake the comparison of data and analysis, including interpretation and evaluation of results. On a general basis I perform various molecular genetic techniques such as DNA isolations, quantification analysis, PCR, fragment analysis, western blots, isolation of RNA and sequencing.

Alison Ollikainen contact info

I am a senior staff scientist working both in Aaltonen and Taipale groups. My research is Bioinformatics and Computational Biology from genetics and functional regulatory genomics perspective. I'm involved especially with genetic epidemiology and biobank research related projects and have special interest in functional genomics, gene regulation and functional understanding of non-coding genetic variation.

Kimmo Palin contact info

I am a third year MD-PhD student. I recently joined the group to work on the leiomyoma Project.

Joonatan Patomo contact info

I work as a research assistant in bioinformatics. My main focus is on annotating and analysing genomic variants.

Roosa-Maria Plaketti contact info

I am a research nurse.  While my work includes some genealogy and databasing tasks, I also support the lab by being responsible for ordering and compiling patient records as well as collecting and providing patient samples to the researchers such as fresh frozen tissue and FFPE blocks and slides.

Marjo Rajalaakso contact info

I joined the Aaltonen lab as a postdoctoral researcher in 2018. I have a strong background in innate immune signaling and working with primary human blood cells and tissues in translational studies involving complex and familial inflammatory diseases. At the Aaltonen lab, my work will focus on studying the genetics and cellular mechanisms of cancer types strongly associated with inflammation, including colitis-associated colorectal cancer. 

Kristiina Rajamäki contact info

I work as a senior scientist / bioinformatican. My duties include basic research and related IT-support and -development. For my research I develop computational methods for processing and analyzing genomic information related to group's interests. In IT-support, I work with others to implement new methods and processes to improve our existing analysis pipelines. I also test new methods and instruct others in the selection and use of bioinformatics tools.

Janne Ravantti contact info

I am an M.Sc. student in genetics and I work on my Master’s thesis project in the lab. My project aims to characterize different subclasses of uterine leiomyoma by analyzing chromatin organization of myomas and myometrium with techniques such as ChIP-seq, ATAC-seq and Hi-C.

Maritta Räisänen contact info

 

 

I’m a PhD student in the early phases of my project. My main focus is on studying environmental causes of tumorigenesis by trying to detect patterns of genetic damage in the tumors of patients who have had substantial exposure to carcinogenic agents due to their work environment or lifestyle choices. Finding such patients for study involves utilizing data sets gathered by Finnish national institutes over the past decades. Another branch of my project concerns using the same data to recognize familial cancer clustering that cannot be readily explained by previously known cancer syndromes, the reason behind which we will then study at the genomic level.

Lauri Sipilä contact info

My main duties involve genealogy work and databasing. I also have a variety of secretarial and administrative duties which include updating group's webpage, processing an assortment of paperwork, checking invoices, control of supplies, domestic and international travel arrangements as well as submitting travel expenses etc.

Sirpa Soisalo contact info

I am an MSc student in bioinformatics. My research is focused on retrotransposons in the human genome. I detect somatic and germline transposons from whole-genome sequencing data and study the relationship between cancer and retrotransposition.

Päivi Sulo contact info

I’m a PhD student having my Master’s degree major in genetics and specialty in bioinformatics. My own project is about methylation in colorectal cancer. As a bioinformatican I’m balancing between genetics and computers. My job is to formulate the biological research questions in such a way that computers can understand them. Even though R and shell scripts are pedantic and sometimes frustrating tools they are researcher's best colleagues in this task.

Aurora Taira contact info

My research projects focus on characterizing the genetic background of uterine leiomyomas. The work involves analyzing whole genome, exome, and SNP array data.

Jaana Tolvanen contact info

I am a third-year student at Aalto University, my major is bioinformationtechnology. I work in Aaltonen lab as a research assistant. Among other things, I have looked somatic and germline structural variants in colorectal cancer.

Emilia Vartiainen contact info

I am junior laboratory manager. My duties include taking care of reagent and supply orders. I also maintain our patient lymphoblastoid cell line collection.

Generally I perform various techniques such as exome library prepping, DNA/RNA isolations, PCR/qPCR, immunohistochemistry, fragment analysis and cell culture.

Iina Vuoristo contact info

Postdoctoral researcher. I received my PhD in computer science from the University of Helsinki in 2012. Since then I have continued at Aaltonen lab as a postdoc. My work involves bioinformatics and computational data analysis of the various high-throughput data. My current interests are in statistical inference and data science.

Niko Välimäki contact info

I am the laboratory manager handling most of the techniques and equipment used in the lab. I am responsible for the chemicals and their safety handling, maintenance and service of the equipment and guiding of new members of the lab. In general I do various molecular genetic techniques, for example DNA, RNA and protein extractions, PCR, qPCR, Western blots, immunohistochemistry, cell culture, exome sequencing and bacterial methods, and I maintain the sample collection.

Inga-Lill Åberg contact info