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Cell Systems 19Nov2021 Diagram 1

Wayne Stallaert, Ph.D., Katarzyna M. Kedziora, et al., published in Cell Systems: The structure of the human cell cycle.









Graphic Cell 2021 Sept 26

Bei Liu, Orrin J. Stone, Michael Pablo, Cody Herron, Ana T. Nogueira, Onur Dagliyan, Jonathan B. Grimm, Luke D. Lavis, Timothy C. Elston, Klaus M. Hahn, publication in Cell “Biosensors based on peptide exposure show single molecule conformations in live cells” Link to paper HERE







Stanley and YiHaidong Yi, Natalie Stanley, publication in bioRxiv “CytoSet: Predicting clinical outcomes via set-modeling

of cytometry data” Link to paper HERE







Khem Ghusinga PNAS PublicationKhem Raj Ghusinga publication in PNAS “Molecular switch architecture determines response

properties of signaling pathways”  Link to paper HERE











Amy PomeroyAmy Pomeroy publication in Science Signaling “A predictive model of gene expression reveals the role of network motifs in the mating response of yeast” Link to paper HERE







Christoph RauRau Lab publication in PLOS Genetics “Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for “polygenic epistasis” Link to paper HERE





Adam Palmer



Adam Palmer’s publication in Cancer Research “A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts” Link to paper HERE




Pub - Boyce Feb 2021 Mathematics Department’s publication in Elsevier “Bioprosthetic aortic valve diameter and thickness are directly related to leaflet fluttering: Results from a combined experimental and computational modeling study” Link to paper HERE






Dittmer Lab Jan 2021 PublicationLabs: Dittmer, Damania, Baric, Heise and U. Wisconsin’s Gabriele Neumann, Peter Halfmann, Yoshihiro Kawaoka  publication of novel modulators of p53-signaling encoded by unknown genes of emerging viruses Link to paper HERE







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