Personal reflections on a legendary scientist, leader, builder, and mentor

Organized by Julia Zeitlinger, Ph.D., Neşet Özel, Ph.D., and Tatjana Sauka-Spengler, Ph.D.

Abstract. Aspergillus fumigatus is a notorious pathogenic fungus responsible for various harmful, sometimes lethal, diseases known as aspergilloses. Unders

Aspergillus fumigatus is a notorious pathogenic fungus responsible for various harmful, sometimes lethal, diseases known as aspergilloses. Understanding the gene regulatory networks that specify the expression programs underlying this fungus’ diverse phenotypes can shed mechanistic insight into its growth, development, and determinants of pathogenicity. We used eighteen publicly available RNA-seq datasets of Aspergillus fumigatus to construct a comprehensive gene regulatory network resource. Our resource, named GRAsp (Gene Regulation of Aspergillus fumigatus), was able to recapitulate known regulatory pathways such as response to hypoxia, iron and zinc homeostasis, and secondary metabolite synthesis. Further, GRAsp was experimentally validated in two cases: one in which GRAsp accurately identified an uncharacterized transcription factor negatively regulating the production of the virulence factor gliotoxin and another where GRAsp revealed the bZip protein, AtfA, as required for fungal responses to microbial signals known as lipo-chitooligosaccharides. Our work showcases the strength of using network-based approaches to generate new hypotheses about regulatory relationships in Aspergillus fumigatus. We also unveil an online, user-friendly version of GRAsp available to the Aspergillus research community.

UW–Madison researchers have discovered a mechanism that could one day help people at risk of developing the metabolic disease.

Modulating the unfolded protein response (UPR) can induce protective dedifferentiation of β-cells in non-obese diabetic mice. Here, the authors show that β-cell deletion of UPR transcription factor XB...

Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence conservation.

Abstract. Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regul

Understanding why a model makes a certain prediction can be as crucial as the prediction's accuracy in many applications. However, the highest accuracy for large modern datasets is often achieved by c...

Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

Latent representations for generative models.

Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of natural language processing is to ...

WABI Conference on Algorithms in Bioinformatics

This Perspective explores causal machine learning in single-cell genomics, addressing challenges such as generalization, interpretability and cell dynamics, while highlighting advances and the potenti...

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Learn how MSK researchers are deploying mRNA vaccines against pancreatic cancer.

We created the MPRA Dataset Collection (MDC), a curated resource of MPRA data from 12 studies comprising over 150 million labeled DNA subsequences. These datasets include both random and natural genom...

Accurately predicting high-resolution chromatin accessibility signals is crucial for precisely identifying regulatory elements and understanding their role in gene expression regulation. In the absenc...

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