 |  |  |  |  | Table of ContentsArticles Reports News & Views Reports Articles |  Volume 12, Number 12 |
Articles  | Analysis of human phosphoproteomic data from 399 perturbations shows that substrate‐based kinase activity inference can inform on the global cellular signaling state and the properties of the decision‐making process. David Ochoa, Mindaugas Jonikas, Robert T Lawrence, Bachir El Debs, Joel Selkrig, Athanasios Typas, Judit Villén, Silvia DM Santos, and Pedro Beltrao |
 | Genome‐wide analyses using two divergent mouse strains and their F1 hybrids demonstrate the predominant contribution of cis‐regulatory changes in the evolution of mouse alternative polyadenylation (APA). Mei‐Sheng Xiao, Bin Zhang, Yi‐Sheng Li, Qingsong Gao, Wei Sun, and Wei Chen |
Reports  | i3C captures chromatin folding in intact nuclei without a need for cross‐linking and reveals that native interactions resemble cross‐linked ones, yet they display improved signal‐to‐noise ratios and highlight how cis‐elements and TADs contribute to 3D genomic organization. Lilija Brant, Theodore Georgomanolis, Milos Nikolic, Chris A Brackley, Petros Kolovos, Wilfred van Ijcken, Frank G Grosveld, Davide Marenduzzo, and Argyris Papantonis |
News & Views  | Chemical crosslinking in 3C‐based methods may introduce biases in detectable chromatin interactions. In their recent study, Papantonis and colleagues (Brant et al, 2016) developed alternate new methods for detecting chromatin contacts without chemical crosslinking. M Jordan Rowley and Victor G Corces |
Reports  | A novel theoretical–experimental framework is used to show that even in the case of ultrafast adaptation to an environmental stressor, there is no need to invoke epigenetic mechanisms as explanatory variables. Arne B Gjuvsland, Enikö Zörgö, Jeevan KA Samy, Simon Stenberg, Ibrahim H Demirsoy, Francisco Roque, Ewa Maciaszczyk‐Dziubinska, Magdalena Migocka, Elisa Alonso‐Perez, Martin Zackrisson, Robert Wysocki, Markus J Tamás, Inge Jonassen, Stig W Omholt, and Jonas Warringer |
Articles  | Single‐cell measurements of calcium responses to ATP, in combination with analyses of the full distribution of kinetic parameters, reveal the existence of three major distinct cellular states within the population. Jason Yao, Anna Pilko, and Roy Wollman |
 | Pairwise genetic interaction mapping between Legionella pneumophila effectors, followed by functional and structural analyses, reveals diverse mechanisms of effector–effector modulation. Malene L Urbanus, Andrew T Quaile, Peter J Stogios, Mariya Morar, Chitong Rao, Rosa Di Leo, Elena Evdokimova, Mandy Lam, Christina Oatway, Marianne E Cuff, Jerzy Osipiuk, Karolina Michalska, Boguslaw P Nocek, Mikko Taipale, Alexei Savchenko, and Alexander W Ensminger |
 | A bacterial “race” in a microfluidic device revealed non‐genetic diversity in behavior and performance of clonal E. coli cells. The “shape” of behavioral diversity affected population performance as much as the mean behavior, supporting the hypothesis that this shape is evolvable. Adam James Waite, Nicholas W Frankel, Yann S Dufour, Jessica F Johnston, Junjiajia Long, and Thierry Emonet |
 | A combination of single‐cell imaging and mathematical modeling shows how the cyanobacterial circadian clock can double its frequency from one peak to two peaks every 24 h using an oscillatory incoherent feedforward loop circuit. Bruno MC Martins, Arijit K Das, Liliana Antunes, and James CW Locke |
 | Longitudinal plasma proteome profiling of 52 obese individuals during weight loss and maintenance reveals 93 significantly altered proteins, including panels correlating with inflammation and insulin resistance. Philipp E Geyer, Nicolai J Wewer Albrechtsen, Stefka Tyanova, Niklas Grassl, Eva W Iepsen, Julie Lundgren, Sten Madsbad, Jens J Holst, Signe S Torekov, and Matthias Mann |
 | A workflow for designing optimized gene circuits without extensive prior knowledge is presented. A mechanistic model guides the generation of a combinatorial circuit library, whose mechanistic characterization is in turn used to validate the model. Joerg Schreiber, Meret Arter, Nicolas Lapique, Benjamin Haefliger, and Yaakov Benenson |
 | Receptor abundance varies both from cell to cell and over time. Mathematical modeling and experimentation show that a yeast GPCR pathway compensates for these variations by responding to the fraction, and not to the number, of occupied receptors. Alan Bush, Gustavo Vasen, Andreas Constantinou, Paula Dunayevich, Inés Lucía Patop, Matías Blaustein, and Alejandro Colman‐Lerner |
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