Anne-Ruxandra Carvunis (ETH Zurich, Institute of Molecular Systems Biology, CH)

Anne-Ruxandra Carvunis is Professor of Genome Evolution at the ETH Zurich Department of Biology, and a faculty member at the Institute of Molecular Systems Biology (IMSB), Switzerland. She joins ETH Zurich after a tenure at the University of Pittsburgh, USA. 

Her research is centered on how new genes emerge and integrate into biological networks — a process often referred to as de novo gene birth. She uses a combination of computational modelling and experimental biology to explore the transition from non-coding sequences to functional genes (“proto-genes”), especially in yeast systems. 

Prof. Carvunis studied life sciences and bioinformatics in France, completing her Ph.D. in 2011. She then pursued post-doctoral work and later established her independent research programme, focusing on systems biology of genome innovation.

Her appointment at ETH Zurich (announced July 2025) strengthens the institution’s efforts in evolutionary systems biology and genomics.

 

Title of the talk: The Dark Proteome: a new frontier for systems biology and proteomics

Abstract: For decades, proteomics has focused on the canonical core proteome—proteins encoded by well-annotated genes with recognizable domains and established biological functions. These proteins form the backbone of our molecular knowledge and underpin most current databases and analytical pipelines for basic and medical research. Yet accumulating evidence suggests that this familiar landscape represents only a portion of the protein universe.

Beyond it lies the so-called dark proteome: a vast collection of novel translation products that were missed by traditional approaches and remain unannotated, uncharacterized, and missing from virtually all our biological and biomedical models. This space includes thousands of translated small open reading frames that are evolutionarily young, often species-specific and cell type-specific, and may play important roles in regulation, adaptation, and disease.

The dark proteome poses a major challenge to the assumptions of standard proteomics workflows. Its components are typically very short, low-abundance, rapidly degraded, integrated in membranes and missing from reference databases, making them difficult to detect. Illuminating this hidden layer of biology will require new experimental and computational proteomics approaches. In this talk, I will outline the emerging landscape of the dark proteome, and discuss why uncovering it represents an important frontier—and opportunity—for the proteomics community.

Jesper Olsen (University of Copenhagen, Novo Nordisk Foundation Center for Protein Research, DK)

Jesper Velgaard Olsen is a Professor of Proteomics and Deputy Head of the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen, Denmark. 

He studied analytical chemistry at the University of Southern Denmark, completing an MSc under Prof. Roman Zubarev. He then undertook a PhD in molecular biology/biochemistry in the group of Prof. Matthias Mann, where he helped develop high-resolution mass spectrometry-based proteomics. 

Following a post-doctoral fellowship at the Max Planck Institute for Biochemistry in Munich, where he developed quantitative phosphoproteomics for signalling pathway analysis, he returned to Denmark in 2009 to lead his own group at CPR. 

At CPR, his research focuses on cutting‐edge mass spectrometry methods to dissect protein composition, post-translational modifications, signalling networks and single-cell proteomics. For example, his group recently developed innovative workflows enabling high-throughput deep proteome and phosphoproteome profiling and new approaches to study protein dynamics in single cells.

Prof. Olsen has been recognised with major awards, including the KFJ Pre-clinical Prize for his contributions to mass-spectrometry-based proteomics.

In his role as Deputy Head of CPR, he also leads training and education efforts, supporting the next generation of protein researchers and the development of proteomics technologies.

 

Title of the talk: Single-cell proteomics of protein turnover and abundance

Abstract: Recent advancements in single cell proteomics (SCP) sample preparation workflows, LC-MS equipment and data-independent acquisition (DIA) strategies have enabled unprecedented insights into proteome dynamics at the single-cell level. Protein turnover – the balance between synthesis and degradation – is fundamental to cellular homeostasis and adaptation. However, studying turnover at the single-cell level is challenging due to the inherent heterogeneity of biological systems and technological limitations. To address this, we employed a pulsed stable isotope labeling by amino acids in cell culture (pSILAC) approach to simultaneously analyze protein abundance and turnover in single cells (SC-pSILAC) when analyzed using our Chip-Tip workflow (Ye et al., Nat. Meth. 2025). Analyzing more >1,000 individual pSILAC-labeled cells by narrow-window DIA, we found that two SILAC labels (heavy and light) are detectable from >4,000 proteins in single HeLa cells, human fibroblasts and in human induced pluripotent stem cells (iPSCs). Analysis of iPSCs undergoing undirected differentiation revealed previously undetected subpopulations of cell type states with distinct pSILAC and proteome profiles, offering new insights into the molecular underpinnings of disease progression and therapeutic resistance (Sabatier et al., Cell 2025). We have now extended the pSILAC strategy to study protein turnover and abundance in single cells derived from mouse pre-implantation embryos from oocytes to the 8-cell stage (Schmidt et al., in prep). Protein turnover measurements represent a significant advance in the field of single-cell proteomics, providing a versatile platform for investigating protein dynamics with unprecedented depth and underscores the transformative potential of DIA-based workflows in decoding the complexity of cellular systems, paving the way for new discoveries in biology and medicine.