Tero Aittokallio received his PhD in Applied Mathematics from the University of Turku in 2001, under the supervision of Prof. Mats Gyllenberg. He then did his post-doctoral training in the Systems Biology Lab at the Institut Pasteur (2006-2007), with Dr. Benno Schwikowski, where he focused on network biology applications using high-throughput experimental assays and network analysis tools such as Cytoscape. In 2007, Dr. Aittokallio launched his independent career as a principal investigator in the Turku Biomathematics Research Group, where he received a five-year appointment as an Academy of Finland Research Fellow (2007-2012). Tero Aittokallio joined FIMM as EMBL Group Leader in the fall of 2011.
email: tero.aittokallio(at)fimm.fi
tel: +358 50 318 2426
Yevhen Akimov received his M.Sc. in Biophysics from the Sevastopol National Technical University. In 2015, he started at Institute for Molecular Medicine Finland as a research assistant in the Sergey Kuznetsov group. Then he got enrolled in FIMM-EMBL Ph.D. program in 2016, joining the Computational Systems Medicine group under Prof. Tero Aittokallio's supervision. Akimov Yevhen's research is focused on the development of next-generation technologies and analysis algorithms for clone tracing experiments tailored to reconstruct clonal heterogeneity of cancer cells. To address this goal, Yevhen Akimov is developing a synthetic biology method for clone isolation based on clone-specific label sequence (DNA-barcode) and statistical methods for the analysis of clonal representation
Franziska Bentz received her M.Sc. in Biology from the Karlsruhe Institute of Technology, Germany. During her Master’s she started to develop computational methods to simplify or improve data analysis compensating for technical and biological errors introduced during the wet-lab procedure. To further enhance both her computational and laboratory skills in a biomedical environment, she got enrolled in the FIMM-EMBL-DSHealth PhD program in 2021, where she did all three of her rotations in the field of cancer research. During her PhD in the Aittokallio group Franziska will apply and develop lineage tracing technologies to unravel and understand tumor heterogeneity.
Yingjia Chen received her BS in Pharmaceutics in June 2018 and graduated from Shanghai Institute of Materia Medica with a MS in Computer-Aided Drug Design. In 2021, She joined Prof. Tero Aittokallio's group at FIMM as a doctoral student. She is interested in leveraging computational tools and approaches to study cancer. Her research focuses on finding effective personalized drug combination therapy and identifying multi-omics biomarker panels for patients with leukemia.
Diogo Dias, M.Sc., earned his Master’s degree in Life Science informatics with a specialisation in Bioinformatics and Systems Medicine at the University of Helsinki in 2022. Within the same year, he was selected to the FIMM-EMBL international PhD programme. His current research is dedicated on improving the success of cancer immunotherapies through computational and experimental work in hematological cancers. His PhD is a collaborative effort between the Satu Mustjoki and Tero Aittokallio groups, with the goal of discovering synergistic effects in high-throughput co-culture drug screenings with immune cells.
Liye He received his MSc degree in computer science from University of Helsinki, Finland. He started his PhD at the Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland since July 2015 under the supervision of Prof. Tero Aittokallio. His PhD projects focuse on building computational tools to identify synergistic and personalised drug combinations for cancer patients using different types of data such as sequencing data. He is interested in applying machine learning methods to tackling real-world challenges.
email: liye.he(at)helsinki.fi
Aleksandr Ianevski received his B.S. in software engineering in July 2015 and M.S. in Bioinformatics at the Aalto University in November 2018. Currently, Aleksandr is a doctoral student in the Computational Systems Medicine research group lead by Tero Aittokallio. He specializes in machine learning, development of computational, biologically relevant methods, statistical data analysis, big data processing, bioinformatics data analysis, bioinformatics tool (including web-tools) development, and interactive visualizations.
Weikaixin Kong received his Bachelor degree (2015-2019) and Master degree (2019-2021) in Pharmaceutical Sciences in Peking University. In 2021, he joined Tero Aittokallio's group at FIMM as a doctoral student. His research focus is to develop and apply machine learning methods to predict effective and safe drug combinations or survival differences among leukemia patients, with the medical aim to explore and better understand the disease mechanisms of leukemias and to develop robust multi-omics signatures for prognostic and treatment prediction.
Anil Kumar received his Ph.D. in Life Science from the Academy of Scientific and Industrial Research 2017 at CSIR-Institute of Genomics and Integrative Biology, New Delhi, under the supervision of Prof. Dwaipayan Bharadwaj. He then joined the Computational Systems Medicine group at FIMM with Prof. Tero Aittokallio as a post-doctoral researcher. His research focuses on the development of methods for the selection of effective and personalized drug combinations for cancer patients using machine learning and molecular data (e.g. exome-sequencing, single-cell RNA sequencing). His research also focuses on identifying the pharmacogenetic variants for various drugs and drug combinations for AML. Currently, he is a joint post-doctoral fellow between Mark Daly and Tero Aittokallio group at FIMM.
email: anil.kumar(at)helsinki.fi
tel: +358442431081
ORCID
Nora has been working as a laboratory technician in Aittokallio group since 2019. She graduated as a biomedical laboratory scientist in 2018, and before joining FIMM, she worked in the Children's and Women's hospital and Anticoagulation laboratories (HUSLAB). Nora did her Bachelor's thesis and practical training in Pirta Hotulainen's lab (Minerva) and is now in Master's Programme in Microbiology and Microbial Biotechnology (MMB). At FIMM, she has learned variety of lab techniques including cell cultures, IF/IHC staining and tissue preparation, organoids, protein work, drug screening and CRISPR-Cas9 editing.
email: nora.linnavirta(at)helsinki.fi
Mitro Miihkinen obtained his PhD from the University of Turku in the fields of molecular cell biology and drug development in 2020. During his PhD Mitro studied cancer-relevant cell adhesion processes using both targeted and de novo approaches under the dual supervision of Johanna Ivaska and Guillaume Jacquemet. Since computational approaches are indispensable for modern life-sciences, he then joined Tero Aittokallio’s lab to achieve full competency in both experimental and computational aspects of biomedicine. In Aittokallio lab, Mitro’s main focus is to uncover illness-defining cellular traits by using powerful experimental-computational approaches with a heavy focus on advanced cancer. His reseach aims at producing new biological insights together with novel and viable treatment options to improve patient well-being.
Kristen Nader received her MSc in Bioinformatics at KU Leuven, Belgium. In 2021, she was accepted as a FIMM-EMBL rotation student and later joined as a PhD student under the supervision of the Aittokallio and Pitkänen groups. She is interested in multi-omics data integration and single-cell technologies to study and target tumor heterogeneity. Her current research is on predicting personalised drug combinations using machine learning and single-cell transcriptomics.
Ziaurrehman Tanoli completed his PhD from the Pakistan Institute of Engineering and Applied Sciences in 2013. During his PhD, he developed several machine learning (ML) based methods to classify G protein-coupled receptors. During his first postdoc at the University of Sannio, Italy, 2014-2015, he developed ML-based pipelines to identify long noncoding RNAs. From 2015 onwards, he has pursued postdoc research at the University of Helsinki. He has expertise in drug repurposing, drug combination prediction, drug-target interaction prediction, side effect predictions, multivariate and survival analysis of clinical data, biomarker identification, comparative genomics, and text mining for identifying drugs, disease genes, and interactions from literature.
Sanna completed her Master’s thesis in Olli Kallioniemi’s group at FIMM and graduated in 2014 from the University of Helsinki with a Master of Science in Biology. After her graduation she worked as a laboratory technician, first at the Curie Institute in France (2014-2015), and then at the High-throughput Biomedicine Unit (2015-2016) as well as Tero Aittokallio’s research group (2015-2018) at FIMM. In 2019 she enrolled in PhD training under the supervision of Prof. Tero Aittokallio and Prof. Satu Mustjoki. Sanna’s research aims to find novel individualized therapies for T-cell prolymphocytic leukemia patients by high-throughput drug screening, CRISPR-Cas9 experiments and meta-analyses.
Aron Schulman completed his B.Sc. (Tech) degree on Bioinformation Technology in 2021 in Aalto University. He continued his studies in Aalto with a Master's programme in Life Science Technologies and started working on his Master's thesis with Dr. Ziaurrehman Tanoli as his advisor in 2023. Aron's thesis work focuses on predicting drug-target interactions across several protein superfamilies using attention-based deep learning models. He is also interested in expanding the applications of Transformer-based natural language processing models to other aspects of drug discovery, such as drug repurposing, toxicity prediction and drug-disease interactions.
Tian received his B.Eng. in pharmaceutical engineering in 2015, and then M.Sc. in pharmacoinformatics in 2018. Tian was enrolled as FIMM/HIIT-EMBL doctoral student in August 2018. He then did rotations in groups at both FIMM and Aalto University. Tian is currently under joint supervision of Prof. Tero Aittokallio, Prof. Juho Rousu, and Prof. Esa Pitkänen. His research focus is to apply machine learning to multi-omics data, to understand mechanisms of complex diseases.
Huiyan Ying received her Bachelor degree in 2016 and Master degree in 2019 majoring in Pharmaceutical Sciences from Jiangnan University. In 2021, she joined Prof. Tero Aittokallio's group at FIMM as a doctoral student focusing on the role of cell-cell communication in breast cancer metastasis. By better understanding of cell-cell communication networks at metastatic sites, her work aims to map how cancer cells integrate different microenvironmental cues to support immune evasion and metastatic growth. Furthermore, using experimental-computational pipelines, the PhD work attempts to increase the susceptibility of breast cancer metastases for approved pharmaceuticals.
Jie received her B.Sc. in Biotechnology in June 2018 and graduated from Peking University with a M.Sc. in Pharmaceutical Sciences in 2021. In 2022, she joined Prof. Tero Aittokallio's research group at FIMM as a doctoral student. Her research focuses on personalized treatment for various types of leukemia patients based on integrated experimental and computational methods, with the aim to identify new disease targets and personalized treatment regimens for leukemia patients.