Multi-color fluorescence live-cell imaging in Dictyostelium discoideum by Hidenori Hashimura, Satoshi Kuwana, Hibiki Nakagawa, Kenichi Abe, Tomoko Adachi, Toyoko Sugita, Shoko Fujishiro, Gen Honda, Satoshi Sawai

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MINN: A metabolic-informed neural network for integrating omics data into genome-scale metabolic modeling by Gabriele Tazza, Francesco Moro, Dario Ruggeri, Bas Teusink, László Vidács

“…On the other hand, mathematical models, such as Genome-Scale Metabolic Models (GEMs), offer a structured framework for analyzing the organization and dynamics of specific cellular mechanisms. …”
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Protein design accelerates the development and application of optogenetic tools by Lingyun Zhu, Yuxuan Wang, Xiaomin Wu, Guohua Wu, Guohao Zhang, Chuanyang Liu, Shaowei Zhang

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Fantastic genes and where to find them expressed in CHO by Markus Riedl, Caterina Ruggeri, Nicolas Marx, Nicole Borth

“…The transcriptome of Chinese hamster ovary (CHO) cells plays a crucial role in determining cellular characteristics that are essential for biopharmaceutical applications. …”
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konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network by Shivam Kumar, Abhinav Agarwal, Dipanka Tanu Sarmah, Samrat Chatterjee

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Wheels turning: CHO cell modeling moves into a digital biomanufacturing era by Sandeep Ranpura, Vishwanathgouda Maralingannavar, Alexandra-Gabriela Gheorghe, Edward Ma, James Morrissey, Michael J. Betenbaugh, Deniz Demirhan

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Role of ferroptosis-related IREB2 in the shared genetic etiology between smoking and facial aging: Insights from large-scale genome-wide cross-trait analysis by Xueyao Cai, Weidong Li, Wenjun Shi, Yuchen Cai, Jianda Zhou

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Open quantum systems theory of ultraweak ultraviolet photon emissions: Revisiting Gurwitsch's onion experiment as a prototype for quantum biology by Nathan S. Babcock

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Directed disruption of IL2 aggregation and receptor binding sites produces designer biologics with enhanced specificity and improved production capacity by Amy Dashwood, Ntombizodwa Makuyana, Rob van der Kant, Arman Ghodsinia, Alvaro R. Hernandez, Stephanie Lienart, Oliver Burton, James Dooley, Magda Ali, Lubna Kouser, Francisco Naranjo, Matthew G. Holt, Frederic Rousseau, Joost Schymkowitz, Adrian Liston

“…Here we use SolubiS and dTANGO, computational algorithm-based methods, to predict mutations within the IL2 structure to improve protein production yield in muteins with altered cellular selectivity, to generate combined muteins with elevated therapeutic potential. …”
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Mapping the 3D genome architecture by Ghazaleh Tavallaee, Elias Orouji

“…These techniques offer unique insights into higher-order chromatin structures by bypassing ligation steps, thus enabling the capture of complex multi-way interactions that are often challenging to resolve with traditional methods. …”
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Mapping Cell Identity from scRNA-seq: A primer on computational methods by Daniele Traversa, Matteo Chiara

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Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes by Md Kamrul Hasan, L. Jeannine Brady

“…Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. …”
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The influence of HIV sense and antisense transcripts on stochastic HIV transcription and reactivation by Kamil Więcek, Janusz Wiśniewski, Heng-Chang Chen

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A novel decoding strategy for ProteinMPNN to design with less visibility to cytotoxic T-lymphocytes by Hans-Christof Gasser, Ajitha Rajan, Javier A. Alfaro

“…We find that our novel decoding strategy can produce structurally similar proteins while incorporating more human like kmers. …”
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pytom-match-pick: A tophat-transform constraint for automated classification in template matching by Marten L. Chaillet, Sander Roet, Remco C. Veltkamp, Friedrich Förster

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Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography by Chia-Chun Hsieh, Zi-Jing Lin, Lee-Jene Lai

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Accurate size-based protein localization from cryo-ET tomograms by Weisheng Jin, Ye Zhou, Alberto Bartesaghi

“…Cryo-electron tomography (cryo-ET) combined with sub-tomogram averaging (STA) allows the determination of protein structures imaged within the native context of the cell at near-atomic resolution. …”
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An ecological and stochastic perspective on persisters resuscitation by Tania Alonso-Vásquez, Michele Giovannini, Gian Luigi Garbini, Mikolaj Dziurzynski, Giovanni Bacci, Ester Coppini, Donatella Fibbi, Marco Fondi

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AttentionEP: Predicting essential proteins via fusion of multiscale features by attention mechanisms by Chuanyan Wu, Bentao Lin, Jialin Zhang, Rui Gao, Rui Song, Zhi-Ping Liu

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Deciphering the proteome of Escherichia coli K-12: Integrating transcriptomics and machine learning to annotate hypothetical proteins by Sagarika Chakraborty, Zachary Ardern, Habibu Aliyu, Anne-Kristin Kaster

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