A5087444401- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- MicroRNA in disease regulation
- Sperm and Testicular Function
- Cancer Genomics and Diagnostics
- Reproductive Biology and Fertility
- Animal Genetics and Reproduction
- Mitochondrial Function and Pathology
- Adipose Tissue and Metabolism
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Neuroscience and Neuropharmacology Research
- Genetics and Neurodevelopmental Disorders
- Stress Responses and Cortisol
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Cell Image Analysis Techniques
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Scientific Computing and Data Management
- Circular RNAs in diseases
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Philosophy and History of Science
University of Zurich
2017-2025
ETH Zurich
2019-2025
SIB Swiss Institute of Bioinformatics
2020-2024
European Institute of Oncology
2013-2024
Istituti di Ricovero e Cura a Carattere Scientifico
2013-2024
Department of Medical Sciences
2023-2024
Neurosciences Institute
2024
Neuroscience Institute
2022-2024
University of California, Los Angeles
2023
Federal Statistical Office
2022
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed detect them. Building on the strengths existing approaches, we developed
Single-cell RNA sequencing (scRNA-seq) has become an empowering technology to profile the transcriptomes of individual cells on a large scale. Early analyses differential expression have aimed at identifying differences between subpopulations identify subpopulation markers. More generally, such methods compare levels across sets cells, thus leading cross-condition analyses. Given emergence replicated multi-condition scRNA-seq datasets, area increasing focus is making sample-level inferences,...
<ns3:p>Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed detect them. Building on the strengths existing</ns3:p><ns3:p> approaches, we developed <ns3:italic>scDblFinder</ns3:italic>, a fast, flexible accurate Bioconductor-based doublet detection method. Here present method, justify its design choices, demonstrate performance both RNA accessibility (ATAC) data, provide some observations formation,...
Protection against deadly pathogens requires the production of high-affinity antibodies by B cells, which are generated in germinal centers (GCs). Alteration GC developmental program is common many cell malignancies. Identification regulators response crucial to develop targeted therapies for dysfunctions, including lymphomas. The histone H3 lysine 27 methyltransferase enhancer zeste homolog 2 (EZH2) highly expressed cells and often constitutively activated GC-derived non-Hodgkin lymphomas...
Abstract Psychiatric diseases have a strong heritable component known to not be restricted DNA sequence-based genetic inheritance alone but also involve epigenetic factors in germ cells. Initial evidence suggested that sperm RNA is causally linked the transmission of symptoms induced by traumatic experiences. Here, we show alterations long contribute specific trauma symptoms. Injection fraction from males exposed postnatal recapitulates effects on food intake, glucose response insulin and...
Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal development malignancy. YY1 acts both as repressor an activator of gene expression. We have identified 23 individuals de novo mutations or deletions phenotypic features that define syndrome cognitive impairment, behavioral alterations, intrauterine growth restriction, feeding problems, various congenital malformations. Our combined clinical molecular data "YY1 syndrome" haploinsufficiency...
ABSTRACT Convergent evidence associates endocrine disrupting chemicals (EDCs) with major, increasingly-prevalent human disorders. Regulation requires elucidation of EDC-triggered molecular events causally linked to adverse health outcomes, but two factors limit their identification. First, experiments frequently use individual chemicals, whereas real life entails simultaneous exposure multiple EDCs. Second, population-based and experimental studies are seldom integrated. This drawback was...
Down syndrome (DS) is mostly caused by a trisomy of the entire Chromosome 21 (Trisomy 21, T21). Here, we use SWATH mass spectrometry to quantify protein abundance and turnover in fibroblasts from monozygotic twin pair discordant for T21, profile expression 11 unrelated DS individuals matched controls. The integration steady-state proteomic data indicates that protein-specific degradation members stoichiometric complexes major determinant T21 gene dosage outcome, both within between...
Abstract We present pipeComp ( https://github.com/plger/pipeComp ), a flexible R framework for pipeline comparison handling interactions between analysis steps and relying on multi-level evaluation metrics. apply it to the benchmark of single-cell RNA-sequencing pipelines using simulated real datasets with known cell identities, covering common methods filtering, doublet detection, normalization, feature selection, denoising, dimensionality reduction, clustering. can easily integrate any...
Highlights•Differences between individuals dominate transcriptional variance•Using multiple clones per individual can be detrimental to differential analysis•We provide resources for the design, analysis, and interpretation of iPSC studiesSummaryBoth promises pitfalls cell reprogramming research platform rest on human genetic variation, making measurement its impact one most urgent issues in field. Harnessing large transcriptomics datasets induced pluripotent stem cells (iPSC), we...
Dissecting the BAZ1B genetic circuitry in neural crest brings out its critical role shaping modern human face.
Abstract The acute stress response mobilizes energy to meet situational demands and re-establish homeostasis. However, the underlying molecular cascades are unclear. Here, we use a brief swim exposure trigger an in mice, which transiently increases anxiety, without leading lasting maladaptive changes. Using multiomic profiling, such as proteomics, phospho-proteomics, bulk mRNA-, single-nuclei small RNA-, TRAP-sequencing, characterize stress-induced events mouse hippocampus over time. Our...
Chronic stress is a risk factor for neuropsychiatric disorders, making the ability to adapt repeated crucial determinant of mental health. On molecular level, it remains unclear whether exposure characterized by habituation - decreased responsiveness same stimulus or emergence new, adaptive responses. Here, we explore how tightly regulated response triggered acute restraint becomes altered after exposure. Transcriptomic sampling mouse hippocampus at multiple time points revealed that leads...
Article16 March 2020Open Access Transparent process Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation Barbora Salovska orcid.org/0000-0002-7093-4576 Yale Cancer Biology Institute, University, West Haven, CT, USA Department of Genome Integrity, Institute Molecular Genetics the Czech Academy Sciences, Prague, Republic Search for more papers by this author Hongwen Zhu Analytical Chemistry CAS Key Laboratory Receptor Research, Shanghai Materia...
Transcription factor (TF)–induced reprogramming of somatic cells into induced pluripotent stem (iPSC) is associated with genome-wide changes in chromatin modifications. Polycomb-mediated histone H3 lysine-27 trimethylation (H3K27me3) has been proposed as a defining mark that distinguishes the from iPSC epigenome. Here, we dissected functional role H3K27me3 TF–induced through inactivation H3K27 methylase EZH2 at onset reprogramming. Our results demonstrate surprisingly establishment proceeds...
RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet no consensus exists as to most appropriate pipeline its with current benchmarks suffering important limitations. Here, we address these challenges through a rich benchmarking resource harnessing (i) two RNAseq datasets including ERCC ExFold spike-ins; (ii) Nanostring measurements panel 150 genes on same samples; (iii) set internal, genetically-determined controls; (iv) reanalysis SEQC dataset; and (v)...
Abstract Single-cell RNA sequencing (scRNA-seq) has quickly become an empowering technology to profile the transcriptomes of individual cells on a large scale. Many early analyses differential expression have aimed at identifying differences between subpopulations, and thus are focused finding subpopulation markers either in single sample or across multiple samples. More generally, such methods can compare levels sets cells, leading cross-condition analyses. However, given emergence...
Article9 October 2020Open Access Transparent process Involvement of circulating factors in the transmission paternal experiences through germline Gretchen van Steenwyk orcid.org/0000-0001-8225-3818 Laboratory Neuroepigenetics, Brain Research Institute, Medical Faculty University Zurich, Switzerland Institute for Neuroscience, Department Health Sciences and Technology, ETH Zurich Neuroscience Center, Search more papers by this author Katharina Gapp Molecular Behavioral Gurdon Cambridge, UK...
The proper development and function of neuronal circuits rely on a tightly regulated balance between excitatory inhibitory (E/I) synaptic transmission, disrupting this can cause neurodevelopmental disorders, for example, schizophrenia. MicroRNA-dependent gene regulation in pyramidal neurons is important cognition, but its role interneurons poorly understood. Here, we identify miR138-5p as regulator short-term memory transmission the mouse hippocampus. Sponge-mediated inactivation...
Abstract Motivation microRNAs are important post-transcriptional regulators of gene expression, but the identification functionally relevant targets is still challenging. Recent research has shown improved prediction microRNA-mediated repression using a biochemical model combined with empirically-derived k-mer affinity predictions; however, these findings not easily applicable. Results We translate this approach into flexible and user-friendly bioconductor package, scanMiR, also available...
Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, methodological framework. Without such framework, oncology will collect piecemeal results, with scant dialogue between the scientific communities studying cancer. We argue one important way forward in...