Misuse of the Michaelis-Menten rate law for protein interaction networks and its remedy von Kim, Jae Kyoung, Tyson, John J

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MiMeNet: Exploring microbiome-metabolome relationships using neural networks von Reiman, Derek, Layden, Brian T, Dai, Yang

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Inferring a spatial code of cell-cell interactions across a whole animal body von Armingol, Erick, Ghaddar, Abbas, Joshi, Chintan J, Baghdassarian, Hratch, Shamie, Isaac, Chan, Jason, Her, Hsuan-Lin, Berhanu, Samuel, Dar, Anushka, Rodriguez-Armstrong, Fabiola, Yang, Olivia, O'Rourke, Eyleen J, Lewis, Nathan E

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MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics von Haiman, Zachary B, Zielinski, Daniel C, Koike, Yuko, Yurkovich, James T, Palsson, Bernhard O

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Calibrating agent-based models to tumor images using representation learning von Cess, Colin G, Finley, Stacey D

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A flexible generative algorithm for growing in silico placentas von de Oliveira, Diana C, Cheikh Sleiman, Hani, Payette, Kelly, Hutter, Jana, Story, Lisa, Hajnal, Joseph V, Alexander, Daniel C, Shipley, Rebecca J, Slator, Paddy J

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Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis von Saxton, Harry, Xu, Xu, Schenkel, Torsten, Clayton, Richard H, Halliday, Ian

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Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments von VanderDoes, Jeremy, Marceaux, Claire, Yokote, Kenta, Asselin-Labat, Marie-Liesse, Rice, Gregory, Hywood, Jack D

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Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics von Rojas Chávez, Roberth Anthony, Fili, Mohammad, Han, Changze, Rahman, Syed A, Bicar, Isaiah G L, Gregory, Sullivan, Helverson, Annika, Hu, Guiping, Darbro, Benjamin W, Das, Jishnu, Brown, Grant D, Haim, Hillel

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Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy von Hallström, Erik, Kandavalli, Vinodh, Ranefall, Petter, Elf, Johan, Wählby, Carolina

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Strain design optimization using reinforcement learning von Sabzevari, Maryam, Szedmak, Sandor, Penttilä, Merja, Jouhten, Paula, Rousu, Juho

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Systems approach for congruence and selection of cancer models towards precision medicine von Zou, Jian, Shah, Osama, Chiu, Yu-Chiao, Ma, Tianzhou, Atkinson, Jennifer M, Oesterreich, Steffi, Lee, Adrian V, Tseng, George C

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Generalized Michaelis-Menten rate law with time-varying molecular concentrations von Lim, Roktaek, Martin, Thomas L P, Chae, Junghun, Kim, WooJoong, Ghim, Cheol-Min, Kim, Pan-Jun

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Robustness and parameter geography in post-translational modification systems von Nam, Kee-Myoung, Gyori, Benjamin M, Amethyst, Silviana V, Bates, Daniel J, Gunawardena, Jeremy

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Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods von Jiang, Richard, Singh, Prashant, Wrede, Fredrik, Hellander, Andreas, Petzold, Linda

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Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria von Norris, Noele, Levine, Naomi M, Fernandez, Vicente I, Stocker, Roman

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Enhanced perfusion following exposure to radiotherapy: A theoretical investigation von Köry, Jakub, Narain, Vedang, Stolz, Bernadette J, Kaeppler, Jakob, Markelc, Bostjan, Muschel, Ruth J, Maini, Philip K, Pitt-Francis, Joe M, Byrne, Helen M

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Discovering adaptation-capable biological network structures using control-theoretic approaches von Bhattacharya, Priyan, Raman, Karthik, Tangirala, Arun K

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Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism von Dougherty, Bonnie V, Moore, Connor J, Rawls, Kristopher D, Jenior, Matthew L, Chun, Bryan, Nagdas, Sarbajeet, Saucerman, Jeffrey J, Kolling, Glynis L, Wallqvist, Anders, Papin, Jason A

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Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding von Guex, Isaline, Mazza, Christian, Dubey, Manupriyam, Batsch, Maxime, Li, Renyi, van der Meer, Jan Roelof

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