Stable developmental patterns of gene expression without morphogen gradients. by Maciej Majka, Nils B Becker, Pieter Rein Ten Wolde, Marcin Zagorski, Thomas R Sokolowski

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Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model. by Elias Vera-Siguenza, Cristina Escribano-Gonzalez, Irene Serrano-Gonzalo, Kattri-Liis Eskla, Fabian Spill, Daniel Tennant

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Stimulus uncertainty and relative reward rates determine adaptive responding in perceptual decision-making. by Luis de la Cuesta-Ferrer, Christina Koß, Sarah Starosta, Nils Kasties, Daniel Lengersdorf, Frank Jäkel, Maik C Stüttgen

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Predicting potential recovery of the endangered bromeliad Tillandsia utriculata: An agent-based modeling approach. by Alexandra M Campbell, Anna C Kula, Rachel S Jabaily, Brad Oberle, Brian Sidoti, Alex Capaldi, Erin N Bodine

“…Some rare species may persist through rapid evolution to tolerate or escape new threats, but representing the underlying ecological and evolutionary processes at the appropriate scale is analytically and computationally challenging. …”
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Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. by Rebecca B Hoyle, Daniele Avitabile, Andrzej M Kierzek

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Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction. by Boyu Jiang, Nick Quinn-Bohmann, Christian Diener, Vignesh Bose Nathan, Yu Han-Hallett, Lavanya Reddivari, Sean M Gibbons, Priyanka Baloni

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Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills. by Russell Dinnage, Marian Kleineberg

“…Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phenotypes at unprecedented scales. …”
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A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. by Linnea Österberg, Iván Domenzain, Julia Münch, Jens Nielsen, Stefan Hohmann, Marija Cvijovic

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How does a small molecule bind at a cryptic binding site? by Yibing Shan, Venkatesh P Mysore, Abba E Leffler, Eric T Kim, Shiori Sagawa, David E Shaw

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Stochastic shielding and edge importance for Markov chains with timescale separation. by Deena R Schmidt, Roberto F Galán, Peter J Thomas

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Community detection in empirical kinase networks identifies new potential members of signalling pathways. by Celia De Los Angeles Colomina Basanta, Marya Bazzi, Maruan Hijazi, Conrad Bessant, Pedro R Cutillas

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Machine-learning-accelerated mechanistic exploration of interface modification in lithium metal anode by Genming Lai, Ruiqi Zhang, Chi Fang, Juntao Zhao, Taowen Chen, Yunxing Zuo, Bo Xu, Jiaxin Zheng

“…HAML offers a promising approach for addressing the challenge of designing stable interfaces while reducing computational costs. This work provides valuable insights for advancing the understanding and optimization of interface behaviors in Li metal batteries.…”
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Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis. by Jörn Diedrichsen, Nikolaus Kriegeskorte

“…Representational models specify how activity patterns in populations of neurons (or, more generally, in multivariate brain-activity measurements) relate to sensory stimuli, motor responses, or cognitive processes. In an experimental context, representational models can be defined as hypotheses about the distribution of activity profiles across experimental conditions. …”
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Scoring epidemiological forecasts on transformed scales. by Nikos I Bosse, Sam Abbott, Anne Cori, Edwin van Leeuwen, Johannes Bracher, Sebastian Funk

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Patient-specific data fusion defines prognostic cancer subtypes. by Yinyin Yuan, Richard S Savage, Florian Markowetz

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Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression. by Berta Verd, Anton Crombach, Johannes Jaeger

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Modeling historic incidence trends implies early field cancerization in esophageal squamous cell carcinoma. by Georg E Luebeck, Thomas L Vaughan, Kit Curtius, William D Hazelton

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Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission. by Israel Ukawuba, Jeffrey Shaman

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Experimental studies and dynamics modeling analysis of the swimming and diving of whirligig beetles (Coleoptera: Gyrinidae). by Zhonghua Xu, Scott C Lenaghan, Benjamin E Reese, Xinghua Jia, Mingjun Zhang

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Segment-specific adhesion as a driver of convergent extension. by Renske M A Vroomans, Paulien Hogeweg, Kirsten H W J ten Tusscher

“…Computational modelling studies play an important role in unravelling the multiscale feedbacks underlying convergent extension. …”
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