Using a mathematical model, Jan et al. evaluate the relative circadian and sleep-wake contributions in time course transcriptome data and find that genes and tissues have distinct sensitivities, explaining the divergent molecular responses to sleep perturbations. Université de Lausanne

Preview by Yun Min Song & Jae Kyoung Kim cell.com/cell-systems/f…

Duan et al. present SEMPER, a method that uses leaky scanning to control protein ratios for precise, user-defined multi-protein expression from a single transcript, applied to fluorescent protein, gas vesicle, and antibody expression Mikhail Shapiro 🇺🇦 cell.com/cell-systems/f…

Vilar & Saiz develop a theory to analyze strong perturbations in quasi-equilibrium systems and use it to quantify the effects of DNA replication in gene regulation, showing that TFs can coordinate their effects to suppress non-equilibrium effects cell.com/cell-systems/a…

Moore et al. show how the E. coli chemotaxis signaling pathway can integrate multiple ambient signals to modulate sensory diversity in an isogenic population enabling the population to modulate the no. of cells committing to tracking each signal Emonet Lab cell.com/cell-systems/f…

Using #MathematicalModeling & experimental approaches in a study funded by #NCICSBC & #PSON, Maximilian Strobl, Cancer Ecology and Evolution Lab: CEEL, Sandy Anderson, et al. revealed an effective dose-escalating #PARPinhibitor strategy for #OvarianCancer Cell Systems sciencedirect.com/science/articl…. #AdaptiveTherapy

I am happy to share our recently published paper on Cell Systems. In this study, we developed an integrated experimental and computational approach to profile PanINs and examine the surrounding microenvironment. sciencedirect.com/science/articl…

Exciting to see our paper, with Vahid Shahrezaei and Philipp Thomas, now published in Cell Systems! We use stochastic modelling and time-resolved scRNA-seq data to identify global patterns of transcription regulation: sciencedirect.com/science/articl…

Using #MathematicalModeling, and experimental approaches in a study funded by #PSON & #NCICSBC, Maximilian Strobl, Cancer Ecology and Evolution Lab: CEEL, Sandy Anderson, et al. revealed an effective dose-escalating #PARPi strategy in #OvarianCancer using #AdaptiveTherapy Cell Systems sciencedirect.com/science/articl….

The Cell Systems editors invited me to share my first-round review comments as a standalone article, so you can see more of my thoughts about the contributions of this work at doi.org/10.1016/j.cels…

Lian et al. use a variational autoencoder based generative model to design synthetic SH3 domains that experimentally recapitulate the function of natural SH3 domains in the yeast osmotic shock response pathway in vivo Pritzker School of Molecular Engineering Andrew Ferguson cell.com/cell-systems/f…

.Dimitris Volteras Vahid Shahrezaei & Philipp Thomas present a method for quantifying transcription dynamics from time-resolved single-cell RNA-sequencing data to identify patterns of transcription regulation and its coupling to the cell cycle on a genome-wide scale cell.com/cell-systems/f…

A semi-supervised imaging, spatial transcriptomics, and single-cell workflow uncovers transitions of PanIN progression and the surrounding microenvironment. Luciane T Kagohara 🇧🇷🧬👩🏻‍🔬👩🏻‍💻 Dr. Elana J Fertig cell.com/cell-systems/a…

Tan and Meyer argue that data representation should mirror experiment structure and propose that many biological datasets can be better analyzed as tensors. They provide guidance on applying tensor-based analyses and review how this approach can yield deeper insights into