Michael Love Lab posted in F1000 Research  ” ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R [version 1; peer review: 1 approved with reservations]” Link to paper




Maddox Cell Photo Amy Shaub Maddox Lab posted a publication in bioRxiv, “Novel cytokinetic ring components limit RhoA activity and contractility” Link to paper



 Qian Lab’s recent publication in Nature, “Single-cell transcriptomic reconstructs fate conversion from fibroblast to cardiomyocyte” Link to paper





The recently publication using genomic and computational approaches to identify and annotate non-coding RNAs transcribed at enhancer regions known as enhancer RNAs in breast cancer cells. Enhancer transcription revealed subtype-specific gene expression programs controlling breast cancer pathogenesis. Link to paper




Zylka lab, studies genetic and environmental risks for autism.  In addition, Zylka lab study molecular and brain mechanisms that underlie pain sensation.  Their long-term goal is to uncover new treatments for chronic pain and neurodevelopmental disorders, like autism, Rett syndrome and Angelman syndrome. Link to papers





Many studies employ shape descriptors globally to probe mechanisms of cell morphogenesis. Here, we examined cell behavior very locally along the cell edge. The Hilbert-Huang transform (HHT) was used to extract spectra of instantaneous edge motion frequency and magnitude along the entire cell edge, and these were then used to classify subcellular edge sectors with distinct dynamics. When optogenetics was used to acutely inhibit specific signaling pathways, we found changes in the frequency spectra, but not in the magnitude spectra. After clustering cell edge sectors with distinct morphodynamics we observed that sectors with different frequency spectra are associated with specific signaling dynamics and motility behavior. Together these observations let us conclude that the frequency spectrum encodes the wiring of the molecular circuitry that regulates edge movements, whereas the magnitude captures the activation level of circuitry. Link to paper


Calabrese Lab developed a new method to quantify sequence similarity between evolutionarily unrelated lncRNAs. The method allows us to take sequence information from a well-studied lncRNA, and use it to discover lncRNAs that may be functioning through a related mechanism. Link to paper






MicroRNA profiling in the colon from Crohn’s disease (CD) patients revealed two distinct molecular subtypes, with miR-31 the most significantly differentially expressed between the two. Low colonic miR-31 expression levels at the time of surgery were associated with worse disease outcome in adults and with future development of fibrostenotic ileal CD requiring surgery in children. Link to paper



TNBCvsLuminalRecent work by the Gomez and Johnson labs has led to the discovery of multiple protein kinases and related kinome subnetworks that have distinctive behaviors across breast cancer subtypes as well as in response to drug treatment. Of note was the identification of a number of poorly understood or “dark” kinases that had highly dynamic behavior and thus may represent valuable targets for future drug development. Link to paper