09 Postdoctoral Fellowship at University of Helsinki, Finland

Spatial tumor-immune interactions are key determinants of therapy responses in ovarian cancer. Our aim is to identify the spatial transcriptional regulation of tumor cell states that drive chemoresistance in ovarian cancer. In this project, we will integrate multiplexed single-cell spatial proteomics, transcriptomics and chromatin states using unique novel spatial technologies and analytical methods. The two EMBL groups have highly synergistic approaches enabling an unprecedented analysis and exploitation of rich spatial multi-omics datasets generated in a unique prospective clinical trial (NCT06117384). The results will pave the way for the development of more effective treatments for ovarian cancer patients.

This position is based at the newly founded Multimodality Research Group in the Department of Languages and funded by an ERC Consolidator Grant awarded to Associate Professor Tuomo Hiippala. The project develops novel methods and resources for studying multimodality, or how human communication naturally combines multiple ‘modes’ of expression. These methods and resources are used to develop empirically founded theories of multimodal communication in the domain of everyday cultural artefacts. The data studied in the project includes, for example, school textbooks, user-generated explanation videos on social media, news broadcasts, instruction manuals and online newspapers.

The research in this project is focused on structural biology and biophysics of protein interactions in neuronal synapse function and in regulation of synapse loss in Alzheimer’s disease (AD) by the complement system (see e.g Chernyaeva et al. EMBO Reports (2023)). We have long standing interest in complement research (e.g. Kajander et al. PNAS (2011); Bhattacharjee et al. J Biol Chem (2013)), and synaptic adhesion (e.g. Karki et al. Sci Reports (2020), Kim et al. PNAS (2022)). Other projects in the group focus currently e.g. on endoplasmic reticulum stress response regulation, and overall on the HiLIFE protein crystallization core facility operation and related projects.

The successful candidate will work on protein production and molecular interaction studies of complement proteins protective of neuronal synapses in AD, in collaboration with Dr. Karita Haapasalo’s group at the medical faculty. Specifically, protein-protein interactions of complement proteins and ApoE and synaptic proteins will be studied biophysically, biochemically, and by structural biology methods to visualize at the atomic level the protein interactions involved in the complement function at the synapse in disease states.

This position is based at the newly founded Multimodality Research Group in the Department of Languages and funded by an ERC Consolidator Grant awarded to Associate Professor Tuomo Hiippala. The project develops novel methods and resources for studying multimodality, or how human communication naturally combines multiple ‘modes’ of expression. These methods and resources are used to develop empirically founded theories of multimodal communication in the domain of everyday cultural artefacts. The data studied in the project includes, for example, school textbooks, user-generated explanation videos on social media, news broadcasts, instruction manuals and online newspapers.

Human tumors are characterized by recurrent mutations in the well-defined cancer driver genes, but also non-mutational epigenetic reprogramming and phenotypic plasticity controlled by transcription factors (TF) are important contributors to tumorigenesis. Extensive consortium efforts have mapped the mutational and epigenetic landscapes of human cancers. However, the commonly used epigenomics methods such as ChIP-seq are correlative in nature and report a lot of spurious sites that might not be linked to gene expression, highlighting the need for novel innovative approaches to understand cancer genome and epigenome. Here, we will utilize cutting-edge long-read nanopore sequencing combined with deep machine learning approaches to model the epigenetic changes and mutational mechanisms in cancers originating from endodermal tissues. The goal is to reveal novel mechanistic details about the development of human cancer.

Pyramidal neurons in the mammalian cortex use complex dendrites to integrate input from diverse brain regions in a parallel manner. To enable parallel processing, local intracellular organelles involved in synaptic metabolism such as the endoplasmic reticulum (ER) and mitochondria are fine-tuned to local synaptic function. So far, we do not have a complete landscape of ER and mitochondria distribution in individual neurons. This project will 1) mine existing electron microscopy (EM) connectomics databases to reconstruct the ER and mitochondria landscape for individual cortical pyramidal neurons and investigate this organelle landscape in relation to known electrophysiological features of individual neurons.

Researcher will have an opportunity to join the already established project or initiate their own project within the main research areas of the group (comorbidity between sleep disorders and pain, circadian regulation of pain and pain chronopharmacology). We are looking for an ambitious early career researcher with advanced analytical and problem-solving skills.

The successful applicant has at least two first authorship publications and a doctoral degree in neuroscience, biology, chronobiology, pharmacology, sleep medicine or other related discipline. The degree requirement must be met by the beginning of employment.

Previous experience with pain, sleep and circadian research is considered a strong merit for this position. Excellent communication and writing skills in English and ability to work in the international team setting are expected. The successful applicant will take part in experiments, supervision of students, drafting of the manuscripts and funding applications.

We are seeking an ambitious fellow with a PhD and strong background in one or more of the following fields:
•    Primary stem cell systems
•    Metabolism
•    Spatial Omics methods
•    Transcriptomics /epigenetics.
•    Experience with preclinical cancer models, mouse work are considered a benefit.

 

Candidates are also encouraged to start new projects and research directions. Applicants must be able to perform as part of a team as well as independently, have good social skills and communication skills in English. Basic knowledge and interest in cancer biology or metabolism are expected. Candidates are expected to co-mentor doctoral and master’s students.