Topic: gene expression

Analyze gene expression within tissue using imaging-based and sequencing-based spatial transcriptomics. Guided R/Bioconductor labs cover cell segmentation, quality control, interactive exploration and integration with single-cell datasets. Downstream analyses characterize cellular niches, neighbourhoods and cell–cell communication. The course concludes with project design and a team hackathon using participant or public data, connecting computational outputs to biological interpretation. 2026-12-14–2026-12-18, 14:00–18:00 daily, Europe/Berlin (CET, UTC+01:00). Online course; fee €530. Designe

Jennifer Brophy presents two methods for programming when and where genes are expressed in plants and their associated microbes. One creates a chemical signal using the noncanonical amino acid O-methyl-L-tyrosine. Engineered Arabidopsis, tomato and poplar produce the signal, while engineered Bacillus subtilis and soil bacteria respond by activating gene expression. Restricting signal production to selected plant tissues allows local control of microbial activity. The second approach builds a genetic circuit that counts successive branching events in roots. It produces different expression pat

The development of the iPS cell technology has revolutionized our ability to study development and diseases in defined in vitro cell culture systems. The talk will focus on Rett Syndrome and discuss two topics: (i) the use of gene editing as an approach to therapy and (ii) the role of MECP2 in gene expression (i) The mutation of the X-linked MECP2 gene is causative for the disease. In a female patient, every cell has a wt copy that is, however, in 50% of the cells located on the inactive X chromosome. We have used epigenetic gene editing tools to activate the wt MECP2 allele on the inactive X

Embryos issue instructions to their cells in the form of patterns of signaling activity. Within these patterns, the distribution of signaling in time and space directs the fate of embryonic cells. Tools to perturb developmental signaling with high resolution in space and time can help reveal how these patterns are decoded to make appropriate fate decisions. In this talk, I will present new optogenetic reagents and an experimental pipeline for creating designer Nodal signaling patterns in live zebrafish embryos. Our improved optoNodal reagents eliminate dark activity and improve response kineti

The basis of the mind, of mental states, and complex behaviors is the flow of energy through microscopic and macroscopic brain structures. Energy flow through brain circuits is powered by thousands of mitochondria populating the inside of every neuron, glial, and other nucleated cell across the brain-body unit. This seminar will cover emerging approaches to study the mind-mitochondria connection and present early attempts to map the distribution and diversity of mitochondria across brain tissue. In rodents, I will present convergent multimodal evidence anchored in enzyme activities, gene expr

The epileptogenesis process is associated with large-scale changes in gene expression, which contribute to the remodelling of brain networks permanently altering excitability. About 80% of the protein coding genes are under the influence of the circadian rhythms. These are 24-hour endogenous rhythms that determine a large number of daily changes in physiology and behavior in our bodies. In the brain, the master clock regulates a large number of pathways that are important during epileptogenesis and established-epilepsy, such as neurotransmission, synaptic homeostasis, inflammation, blood-brain

The advent of next generation sequencing ushered in a ten-year period of exuberant technology development, enabling the quantification of gene expression and epigenetic features within individual cells, and within intact tissue sections. In this seminar, I will outline our technological contributions, beginning with the development of Drop-seq, a method for high-throughput single cell analysis, followed by the development of Slide-seq, a technique for measuring genome-wide expression at 10 micron spatial resolution. Using a combination of these techniques, we recently constructed a compreh

Gonadal steroid hormones are the principal drivers of sex-variable biology in vertebrates. In the brain, estrogen (17β-estradiol) establishes neural sex differences in many species and modulates mood, behavior, and energy balance in adulthood. To understand the diverse effects of estradiol on the brain, we profiled the genomic binding of estrogen receptor alpha (ERα), providing the first picture of the neural actions of any gonadal hormone receptor. To relate ERα target genes to brain sex differences we assessed gene expression and chromatin accessibility in the posterior bed nucleus of the st

The hippocampus is a brain region with key roles in memory formation, cognitive flexibility and emotional control. Yet hippocampal function is impaired severely during aging and in neurodegenerative diseases, and impairments in hippocampal function underlie age-related cognitive decline. Accumulating evidence suggests that the deterioration of the neuron-specific epigenetic landscape during aging contributes to their progressive, age-related dysfunction. For instance, we have recently shown that aging is associated with pronounced alterations of neuronal DNA methylation patterns in the hippoca

Genome-wide association studies (GWAS) have identified multiple disease-associated genetic variations across different psychiatric disorders raising the question of how these genetic variants relate to the corresponding pharmacological treatments. In this talk, I will outline our work investigating whether functional information from a range of open bioinformatics datasets such as protein interaction network (PPI), brain eQTL, and gene expression pattern across the brain can uncover the relationship between GWAS-identified genetic variation and the genes targeted by current drugs for psychiatr

Proper development of the nervous system depends not only on the inherited DNA sequence, but also on proper regulation of gene expression, as controlled in part by epigenetic mechanisms present in the parental gametes. In this presentation an internationally recognized research advocate explains why researchers concerned about the origins of increasingly prevalent neurodevelopmental disorders such as autism and attention deficit hyperactivity disorder should look beyond genetics in probing the origins of dysregulated transcription of brain-related genes. The culprit for a subset of cases, she

Brains do not fossilise, but as they grow and expand during fetal and infant development, they leave an imprint in the bony braincase. Such imprints of fossilised braincases provide direct evidence of brain evolution, but the underlying biological changes have remained elusive. Combining data from fossil skulls, ancient genomes, brain imaging and gene expression helps shed light on the evolutionary changes shaping the human brain. I will highlight two examples separated by more than 3 million years: the evolution of brain growth in Lucy and her kind, and differences between modern humans and N

MicroRNAs are small noncoding RNAs that provide a critical layer of gene expression control. Individual microRNAs variably exert effects across networks of genes via sequence-specific binding to mRNAs, fine-tuning protein levels. This helps coordinate the timing and specification of cell fate transitions during brain development and maintains neural circuit function and plasticity by activity-dependent (re)shaping of synapses and the levels of neurotransmitter components. MicroRNA levels have been found to be altered in tissue from the epileptogenic zone resected from adults with drug-resistan

Three intimately related dimensions of the mammalian genome—linear DNA sequence, gene transcription, and 3D genome architecture—are crucial for the development of nervous systems. Changes in the linear genome (e.g., de novo mutations), transcriptome, and 3D genome structure lead to debilitating neurodevelopmental disorders, such as autism and schizophrenia. However, current technologies and data are severely limited: (1) 3D genome structures of single brain cells have not been solved; (2) little is known about the dynamics of single-cell transcriptome and 3D genome after birth; (3) true de nov

In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. A theoretical model for chromatin (the minimal chromatin model) explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data is presented. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. This model was generalized by u

Over the past years, genetic studies have uncovered hundreds of genetic variants to be associated with complex brain disorders. While this really represents a big step forward in understanding the genetic etiology of brain disorders, the functional interpretation of these variants remains challenging. We aim to help with the functional characterization of variants through transcriptomic data analysis. For instance, we rely on brain transcriptome atlases, such as Allen Brain Atlases, to infer functional relations between genes. One example of this is the identification of signaling mechanisms o

The precise spatial localization of molecular signals within tissues richly informs the mechanisms of tissue formation and function. Here, we’ll introduce Slide-seq, a technology which enables transcriptome-wide measurements with near-single cell spatial resolution. We’ll describe recent experimental and computational advances to enable Slide-seq in biological contexts in biological contexts where high detection sensitivity is important. More broadly, we’ll discuss the promise and challenges of spatial transcriptomics for tissue genomics. Lastly, we’ll touch upon novel molecular recording tech

It is sometimes said that there are two reasons why physics is so successful as a science. One is that it deals with very simple problems. The other is that it attempts to account only for universal aspects of systems at a desired level of description, with lower level phenomena subsumed into a small number of adjustable parameters. It is a widespread belief that this approach seems unlikely to be useful in biology, which is intimidatingly complex, where “everything has an exception”, and where there are a huge number of undetermined parameters. I will try to argue, nonetheless, that there are

In the last decades, the post-transcriptional control of gene expression has become an area of intense investigation, delineating a complex scenario where several factors (e.g. RNA-binding proteins, coding and non-coding RNAs) orchestrate the fate of a given transcript. An intriguing hypothesis suggests that loss of RNA homeostasis is a central feature of many pathological states, including eye diseases. Since the elav (embryonic lethal, abnormal visual system) gene discovery in the Drosophila melanogaster, the mammalian ELAV-like family has confirmed its leading role in controlling the RNA me

I will introduce a web portal for the retinal neuroscience community to explore the catalog of mouse retinal ganglion cell (RGC) types, including data on light responses, correspondences with morphological types in EyeWire, and gene expression data from single-cell transcriptomics. Our current classification includes 43 types, accounting for 90% of the cells in EyeWire. Many of these cell types have new stories to tell, and I will cover two of them that represent opposite ends of the spectrum of levels of analysis in my lab. First, I will introduce the “Bursty Suppressed-by-Contrast” RGC and s

Our research team runs several related projects studying the cellular and molecular mechanisms involved in the development of axonal connections in the brain. In particular, our aim is to uncover the principles underlying thalamocortical axonal wiring, maintenance and ultimately the rewiring of connections, through an integrated and innovative experimental programme. The development of the thalamocortical wiring requires a precise topographical sorting of its connections. Each thalamic nucleus receives specific sensory information from the environment and projects topographically to its corres

Joint exploration of behavior, genes and brain structure holds the promise to provide a better understanding of neural circuits than unimodal data analyses. Several consortia provide extensive data resources of different modalities. However, analyses of heteromodal data require the expertise of computer scientists for fusing the different resources into a common space. To tackle this limitation, we extended BrainTrawler, our web-based visual analytics frame work for exploration of neurobiological data of human and mice, with a selection of publicly available gene expression and connectivity da

OBJECTIVE: Alzheimer's disease (AD) stands as the prevalent neurodegenerative condition globally, characterized by symptoms such as memory loss, language difficulties, disorientation, diminished motivation, self-neglect, mood fluctuations, and behavioral challenges. Despite its widespread impact, the precise cellular mechanisms underlying the onset of AD remain elusive. This study aims to uncover potential pathophysiological contributors to AD by analyzing gene expression levels through bioinformatics approaches. METHODS: GSE129296 dataset downloaded from Gene Expression Omnibus (GEO) database