Recent Publications
- Tamir TY, Chaudhary S, Li AX, Trojan SE, Flower CT, Vo P, Cui Y, Davis JC, Mukkamala RS, Venditti FN, Hillis AL, Toker A, Vander Heiden MG, Spinelli JB, Kennedy NJ, Davis RJ, White FM.
Can Chen, Chen Liao, and Yang-Yu Liu published in Nature April 2023 Paper: Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning 
Can Chen, Xu-Wen Wang, and Yang-Yu Liu published in arXiv online publication 2312.07737v2: Stability of Ecological Systems: A Theoretical Review
Harlin Lee, Aaqib Saeed, Learning from Time Series for Health Workshop at NeurIPS’22 Paper: Automatic Sleep Scoring from Large-scale Multi-channel Pediatric EEG
Harlin Lee, Boyue Li, Shelly DeForte, Mark L. Splaingard, Yungui Huang, Yuejie Chi & Simon L. Linwood, published in Nature:
William H. Weir, Peter J. Mucha, William Y. Kim, published in Cell:听 A bipartite graph-based expected networks approach identifies DDR genes not associated with TMB yet predictive of immune checkpoint blockade response 
Wayne Stallaert, Ph.D., Katarzyna M. Kedziora, et al., published in Cell Systems: The structure of the human cell cycle.
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
Haidong Yi, Natalie Stanley, publication in bioRxiv: CytoSet: Predicting clinical outcomes via set-modeling of cytometry data
Khem Raj Ghusinga publication in PNAS:
Amy Pomeroy publication in Science Signaling: .
Rau Lab publication in PLoS Genetics:
Adam Palmer’s publication in Cancer Research:
Mathematics Department’s publication in Elsevier: .
Labs: Dittmer, Damania, Baric, Heise and U. Wisconsin’s Gabriele Neumann, Peter Halfmann, Yoshihiro Kawaoka’s publication of 听
Michael Love Lab published in F1000 Research
Amy Shaub Maddox Lab posted a publication in bioRxiv:
Qian Lab’s recent publication in听Nature:听.
The recent 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: .
Zylka lab, studies genetic and environmental risks for autism.听 In addition, Zylka lab study molecular and brain mechanisms that underlie pain sensation.听 Their long-term goal is to uncover new treatments for chronic pain and neurodevelopmental disorders, like autism, Rett syndrome and Angelman syndrome.
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. Full results can be found in the publication:
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. Full results can be found in the publication:
MicroRNA profiling in the colon from Crohn鈥檚 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听in adults and with future development of fibrostenotic ileal CD requiring surgery in children. Full results can be found in the publication:
Recent 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 鈥渄ark鈥� kinases that had highly dynamic behavior and thus may represent valuable targets for future drug development. Full results can be found in the publication: