10 papers · ranked by Valyu relevance
John Tower
Biological information is generally thought to be subject to selection for faithful maintenance. However, accurate preservation is often combined with regulated mechanisms that generate state change. Selectively advantageous instability (SAI) is modeled here as instability that is favored because useful alternatives…
Fabio Barteri, Arcadi Navarro, Omar E. Cornejo
Continuous traits evolve unevenly across phylogenies, producing patterns of phenotypic differentiation shaped by both shared ancestry and lineage-specific change. Identifying exceptionally differentiated species pairs may therefore improve genome–phenome comparisons, but existing approaches rarely rank such contrasts…
Fabio Cumbo, Kabir Dhillon, M. Hassan Najafi, Sercan Aygun + 1 more
The exponential growth of genomic databases necessitates alignment-free methods for comparing genomes. While MinHash-based tools have revolutionized this field by efficiently estimating the Average Nucleotide Identity based on k-mer sets, they inherently discard structural genomic information. We introduce HyperSketch…
Peter F. Pelz, Tobias Meck
For nearly a century, the physical origin of metabolic scaling has remained unresolved: metabolism is proportional to body mass in small organisms but follows Kleiber’s three-quarter-power law in larger animals. We derive both regimes from the Metabolic Holon (MH), a locally optimized capillary–tissue oxygen-supply…
Fubo Ma, Kang Li, Yangchao Yu, Lei Zhang + 3 more
Type I interferon (IFN-I) is an important class of cytokines that can inhibit tumuor progression through mechanisms such as immunomodulation of the tumuor microenvironment or targeting cellular components. Although various endogenous and exogenous IFN-I therapeutic strategies have been developed, reports of immune cell…
Gyungwon Yun, Jin Pyo Kang, Ho‐Sung Lee, Ik‐Hyeon Jeon + 5 more
Although probabilistic computing offers a route to quantum-inspired optimization at room temperature, existing probabilistic bits (p-bits) often depend on non-CMOS devices or circuit-intensive randomness. Here, we report a CMOS-compatible p-bit that harnesses intrinsic random telegraph noise (RTN) in a fully depleted…
Yiming Xue, Xiaojian Liu, Weimin Zhu, Shengfan Wang + 2 more
While protein-RNA interactions are fundamental to post-transcriptional processes, achieving a holistic understanding of their regulatory logic remains challenging. Current computational models often treat binding affinity, interface mapping, and RNA design as isolated tasks, thereby failing to provide a unified…
Rui Zhang, Huamin Liu, Shan Jiang, Zhichao Xu + 4 more
The Mongolian Plateau, a typical arid and semi-arid zone in Eurasia, is characterized by highly heterogeneous and fragmented wetland habitats. Phragmites australis, a common wetland species in this region, exhibits remarkable adaptability. Unraveling the coordination between phylogenetic history and local environmental…
Ana Lúcia Leitão, Francisco J Enguita
The evolution of molecular visualization software represents a pivotal yet often underappreciated dimension of computational structural biology and bioinformatics. As the scale and complexity of structural datasets increase, spanning from cryo-electron microscopy reconstructions to proteome-wide AI-predicted models…
Yawako W. Kawaguchi, Masaru Kono, Minako Isoda, Kensuke Kawade + 7 more
Molecular evolutionary rates vary widely among organisms, yet the biological mechanisms underlying this variation and its evolutionary consequences remain poorly understood. In plants, the absence of an early-segregated germline raises the possibility that growth- and environment-dependent physiological processes could…