MEET THE TEAM!
DENIS SCHAPIRO
Group Leader
Dr. Denis Schapiro is a Research Group Leader at the Heidelberg University Hospital focusing on spatial omics technologies and analysis.
Before moving to Heidelberg, he was an Independent Fellow at the Laboratory of Systems Pharmacology at Harvard Medical School and the Klarman Cell Observatory at the Broad Institute where he was a a Damon Runyon Quantitative Biology Fellow mentored by Prof. Peter Sorger and Prof. Aviv Regev.
Previously, he was supported by the SNFS Mobility Fellowship.
Denis obtained his PhD from the University of Zurich and ETH Zurich in the laboratory of Prof. Bernd Bodenmiller where he worked on Imaging Mass Cytometry and corresponding analysis tools focusing on highly multiplexed image analysis. Denis is the lead developer of the histology topography cytometry analysis toolbox (histoCAT) and the multiple choice microscopy pipeline (MCMICRO).
Prior to this, he received his diploma (Dipl. Biol. (t.o)) at the University of Stuttgart and Harvard Medical School working with Prof. Peter Sorger and Prof. Alfred Goldberg. He was also an intern at the Complex Systems Modeling Group at Bayer AG in Leverkusen focusing on PBPK modeling.
TEAM MEMBERS
LYDIA ROEDER
Administrative Team
After finishing my studies at the Heidelberg Institute of Foreign Languages, I worked as a freelancer for many years. In 2000 I started as a secretary at the University Hospital (Dental Clinic, Institute of Human Genetics, Institute of Medical Informatics) and in February 2023 I joined the Saez Rodríguez-Group and Schapiro-Group as administrative assistant.
FLORIAN WÜNNEMANN
Postdoc
Florian joined the lab as a Postdoc in January 2022 to work on spatial omics technologies in the context of cardiovascular diseases. He acquired his PhD from the University of Muenster working with the group of Dr. Gregor Aldenfinger at the CHU Ste Justine research center in Montreal, Canada, with a focus on the genetics of congenital heart diseases. He recently finished a Postdoc with Guillaume Lettre at the Montreal heart institute, where he studied the genetics of complex cardiovascular diseases. Florian has extensive experience in working with single-cell omics technologies, rare and complex human genetic diseases and bioinformatics data analysis.
VICTOR PEREZ
Postdoc
Victor received his BSc in Physics at UNAM, Mexico and an MSc in biophysics at TU Dresden. He did his PhD research in the group of Prof. Dr. Ernst H.K. Stelzer in Frankfurt working on the topics of super-resolution fluorescence microscopy and image reconstruction. He joined our lab after acquiring experience in industry at BASF where he developed several image analysis and image acquisition workflows to accelerate and standardize data extraction routines. His aim in the group is to establish standard analysis pipelines to classify spatial landmarks in highly-multiplexed images of stained tumors. Classification of these landmarks, which include cell-cell interactions and location/composition of cell niches, should lead to tumor profiling and the exploration of more efficient therapeutic approaches adapted to the spatial-omics profile of the tumor.
MIGUEL IBARRA
PhD Candidate
Miguel received a BSc in Genomics at UNAM, Mexico, and an MSc in Life Science Informatics at University Bonn, Germany. He has worked at the Center for Genomic Sciences (UNAM), Southeast Center for Integrative Metabolomics at (University of Florida), Fraunhofer Institute for Algorithms and Scientific Computing SCAI, and at the Institute for Genomics Statistics and Bioinformatics (University of Bonn). Miguel specialises in the development and optimisation of pipelines with clean computer code for data and image analysis. He is a curious person by nature, and passionate about technology and he believes modern biology requires a multitude of backgrounds and comprehensive cooperation among them to solve - the not so easy questions - that come our way. This is what motivated him to join the Schapiro lab for his Ph.D..
KREŠIMIR BEŠTAK
PhD Candidate
Krešo finished his BSc in Molecular Biology in Zagreb, Croatia, and completed his MSc in Systems Biology at Heidelberg University. His Master thesis was done in the Schapiro group working on Highly multiplexed imaging analysis of mouse models of acute myocardial infarction. The project included antibody panel optimisation and creating a dataset of full mouse heart cross sections that was then processed and analysed. His main interests are pipeline and tool development with a focus on image processing steps such as segmentation. The experience of working in a novel field in a cooperative environment has motivated him to pursue a PhD in the Schapiro group. Personal interests include playing and listening to music, table tennis and solving the occasional Rubik's cube.
MARGOT CHAZOTTE
Master Student
Margot is currently a Molecular Biosciences masters student at the Heidelberg University with a focus on Systems Biology. She has a bachelor's degree in Biosciences from Heidelberg University which provides her with a strong background in biology as well as computational sciences.
CHIARA SCHILLER
PhD Candidate
Chiara completed her BSc in Molecular Biomedicine at the University of Bonn and pursued her MSc in Molecular Biosciences at the University of Heidelberg. During her Master's program, she specialized in Bioinformatics and worked at the DKFZ and NCT Heidelberg, as well as at ETH Zurich. In her master thesis with the Schapiro lab, she compared different spatial neighborhood analysis tools using in silico generated tissue data and is excited to continue working on downstream spatial analysis. Leveraging her expertise in both Molecular Biomedicine and Bioinformatics, she is dedicated to developing statistical and machine learning methods for spatial tissue analysis with the goal of clinical applicability. The interdisciplinary, collaborative and social environment at the Schapirolab made her decision very easy to stay as a PhD. Chiara is additionally affiliated with the lab of Julio Saez-Rodriguez as an associated member. Outside of the lab, she is always up for bouldering or cooking sessions.
Lukas Hatscher
PhD Candidate
Lukas graduated from med school in early 2022. In his MD and MSc theses, he focused on the inflammatory responses of human dendritic cells. Being exposed to big RNAseq datasets during his wet lab research sparked his interest in computational biology. After a short clinical residency in rheumatology, Lukas joined the group in February 2024. Lukas aims to combine his medical background and interest in pathology with computational skills to tackle current challenges in tumor(-immunology) by leveraging spatial omics technologies. Outside of work, Lukas enjoys playing squash and going on bike tours.
AROJ HADA
Staff Scientist
Aroj received a BSc in Biotechnology at Kathmandu University, Nepal, and an Erasmus Mundus Joint Master’s Degree in MedicAl Imaging and Applications (MAIA). He has joined the Schapiro lab as a Staff Scientist under the AI-Health Innovation Cluster. Aroj has experience in working with Microscopy Image analysis using Computer Vision, Machine Learning, and Deep Learning. Because of his background in Biotech and Medical Imaging, he aspires to work in between AI and Biology, especially along the lines of Spatial omics and Imaging Genetics.
ALUMNI
MATHIAS NORDBECK
Internship
CHARLOTTE WESTHOVEN
Internship
SIMON KAYSER
Internship
MORITZ NEESEN
Internship
NIKLAS STOTZEM
Visiting Researcher
TOBIAS FAEHLING
Internship