Matthias
Nees
Adjunct Professor, Department of Biology
Senior Research Fellow, Institute of Biomedicine
PhD, Dr. rer. nat.

Contact

+358 45 606 6406
Itäinen Pitkäkatu 4
20520
Turku

Areas of expertise

Translational Oncology
Cell Culture Model Systems
Personalised Medicine
Organoids
Tumor Models

Biography

01/2015 – now:  Adjunct Professor, University of Turku, Dept. Biomedicine and Anatomy; Coordinator of the High Content Screening Laboratory (HCSLab) 

Physiologically relevant models for translational oncology and personalized medicine, advanced 3D cell & tissue-culture models for early stage drug discovery, functional drug target validation (siRNA, shRNA). Phenotypic & high content screening, automated image analyses, elucidation of MOA and functional validation of diagnostic biomarkers

09/2016 – 10/2018 Docent at SRH Fernhochschule „The Mobile University“: Bachelor Degree Program Pharmaceutical Management & Technologies

Preparation of teaching materials for eLearning platforms, text books, podcasts and ePubs, lectures, workshops, coaching of students – online and on-site 

03/2005 – 12/2014 Group Leader and Principal Investigator, VTT Technical Research Centre of Finland OY, Turku (Teams “Systems Biology” and “Cell Culture Model Systems”)

Cell- and tissue-based model systems (3D organoid and tissue cultures) for phenotypic high content screening, automated image analysis & machine learning. Team Leader, management of interdisciplinary research groups (incl. Programmers, Biologists, Medical Students, Technicians, PostDocs, Masters’ and PhD students). Public/private partnerships PPP with industry partners, mainly funded by European Community (IMI, FP7, EuroTransBio, Marie Curie Training Networks, etc.), or Business Finland (formerly Tekes). 

04/2002 – 02/2005: Staff Scientist - Molecular Medicine Partnership Unit – European Molecular Biology Laboratory EMBL & University Hospital Heidelberg

Laboratory operations and management: gene expression analyses (microarrays), personalized medicine (childhood leukaemia and sarcomas), biobanking, genetic analyses (DNA sequencing); Diagnostics

06/2000 – 03/2002 – Staff Scientist – Clinical Cooperation Unit German Cancer Research Center (DKFZ) and University Hospital Heidelberg, Germany 

Translational oncology and personalized medicine: characterization of patient virus load and virus typing (HPV); primary cell- and tissue cultures, in vitro models for organotypic assays; microarray studies. Diagnostics: functional and diagnostic evaluation of biomarkers, DNA cloning and sequencing 

06/1997 –05/2000: Postdoctoral Fellow – National Cancer Institute NCI, National Institutes of Health NIH – Bethesda, Maryland, USA

Personalized medicine: in vitro model systems for disease progression, based on primary patient tissues and cell cultures, immortalization of primary cells by viral vectors & oncogenes

11/1993-04/1997: PhD thesis at German Cancer Research Center (DKFZ) Heidelberg, Germany – Dept. Applied Tumour Virology/Prof. Harald zur Hausen

Translational oncology: primary cell culture models for cancer initiation and progression

08/1992 - 10/1993: Master’s Thesis at the University Hospital Heidelberg, Germany – Molecular Biology Laboratory of the Ear, Neck & Throat Clinics HNO 

Translational oncology: analysis of mutations in primary patient materials, DNA sequencing

08/1990 – 07/1992 Scientific Research Assistant University Hospital Heidelberg/Germany


Teaching

Professor, SRH Fernhochschule – “The Mobile University” 09/(2016 – 09 / 2018: Bachelor degree program in Pharma-Management & Technology

  • Pre-clinical and clinical drug development
  • Drug formulation and pharmaceutical drug development
  • Quality control/quality management and instrumental analytics, GMP
  • Industrial biotechnology, biologicals/biosimilars, and fermentation technologies (Upstream- and Downstream Processing)
  • Organic chemistry and biochemistry; Biochemistry of Nutrition
  • Molecular and cell biology
  • Drug market registration (EMA and FDA)
  • Drug safety and pharmacovigilance

Adjunct Professor and Docent, University of Turku/Finland; Master’s degree programme in Biomedical imaging (BIMA), Turku Bioimaging:

  • “Fluorescence in Bioanalytical Research” (ANAT5105, lecturer) 2015
  • “Bioimaging and microscopy”, ÅA_0432, lecturer) 2013, 2014, 2015 

Masters’ Degree Program, University of Turku:

  • “Bioinformatics in Drug Discovery” (DRUG0007, lecturer) 2015
  • “Genetics and drug discovery in cancer research”, (FYGE3209, organizer and lecturer, 2013 -2014)
  •  “Drug development in the pharmaceutical industry” (FYGE3208, organizer & lecturer, 2012 -2013);
  • “Cancer Functional Genetics: From Mechanisms to Drug Discovery” (organizer & lecturer, 2008-11)
  •  “Cancer Genetics & Genomics” (organizer & lecturer, 2005 - 2007
  • FinPharma Doctoral Program Drug Discovery (FPDP-DD):
  • “Epigenetic Processes as Drug Targets in Prostate Cancer”, FinPharma Graduate School

Turku Centre for Biotechnology CBT - Turku Centre for Computer Science (TUCS):

  •  Systems Biology at University of Turku (2012 – 2015)
  •  Computational Biology C, for students of Bioinformatics; March 2012 - 2015
  •  “TERBIO Functional Genomics, Proteomics & Bioinformatics Course”, 2006-2015
Karolinska Institutet, Stockholm/Sweden
  • Nanotoxicology MiniSymposium, Institute for Toxicology, August 16, 2012
  • Advanced Cell Culture Training Course, Institute for Toxicology, Sept. 10- 12, 2010

Research

Drug Discovery:  Coordination of contract research projects with the pharmaceutical industry, custom research organizations (CROs), small- and medium-size enterprises SMEs, and non-profit research institutes/universities. Early stage, preclinical drug discovery and lead development studies. 

Model Systems for Cancer: Evaluation of in vitro & in vivo models (e.g. Xenografts, patient-derived PDX, genetically engineered mouse models GEMMs; tissue slices and explant cultures)

Cell- and tissue-based model systems: Complex organotypic or 3D model systems (organoids) to recapitulate the architecture of solid cancer tissues. Methods for microscopic imaging, automated image analysis (“machine vision”), phenotypic- or imaging-based high content screening (HCS).

Cancer Biomarker Research: Protein/biomarker expression in cancers using tissue microarrays TMA, RNA- and antibody-based protein immune-fluorescence and immune histochemistry methods on fresh & FFPE-tissues (IHC, ISH).

Clinical cooperation units with Department of Pathology and Dept. of Urology at Turku University Hospital TYKS): Biobanking of primary, patient-derived materials (“Turku Prostate Cancer Consortium, TPCC”). Novel methods to isolate and successfully propagate primary cell cultures for personalized medicine and drug sensitivity-testing.

Bioinformatics & systems biology: Genome-wide mRNA studies (DNA Microarrays, Next Generation Sequencing,NGS, quantitative and realtime PCR, qRT-PCR).  Investigating alternative splicing, DNA copy-number alterations and mutations (CGH & SNP arrays; Sanger & NG Sequencing) in cancer and cancer progression.

Publications

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