10 papers · ranked by Valyu relevance
Peter G. Hawkins, Eli M. Swanson, Megan Feichtel
The size of individual single cell samples continues to grow with advancing technologies, as do the number of samples included in individual experiments and across organizations. This presents challenges for processing this data at scale, both in terms of computational throughput and the required size of the machines…
Shuchen Wang, Yiqi Xu, Yuewei Zhan, Martin Echavarria Galindo + 13 more
Genetic circuits enable precise control over cellular behavior. As circuits become more complex, implementing them within a single cell population becomes difficult. Tasks can instead be distributed in engineered consortia. However, selecting appropriate consortia and harnessing the natural traits of each species for…
Ge Zhang
bcftools is the standard toolkit for handling VCF and BCF variant files, but it processes records on a single core; its --threads option speeds up only compression of the output, not the work done on variant records. Processing large call sets is therefore slow, and users often divide the genome and reassemble the…
Bing Han, Sheng Li
Germinal is a recently described computational pipeline for de novo antibody design that combines AlphaFold-Multimer hallucination with antibody language model guidance to generate epitope- targeted antibodies. Germinal identified binders with nanomolar-to-low-micromolar affinities by testing only 43–101 designs per…
Yiming Cheng, Yan Li
Spatial heterogeneity in drug distribution, particularly within solid tumors, can compromise target engagement and drive therapeutic failure in oncology, yet it is rarely represented in population pharmacokinetic (PopPK) analyses. Standard empirical compartmental or semi-mechanistic models assume “well-stirred”…
Denise Moerel, Tijl Grootswagers, Genevieve L. Quek, Manuel Varlet
Collaboration is a cornerstone of human behaviour, enabling individuals to achieve complex goals that transcend individual capabilities. While previous research has largely focused on the alignment of neural representations across brains during social interactions, real-world cooperation frequently involves…
Christos Papalitsas, Ioannis Mouratidis, Michail Patsakis, Evangelos Stogiannos + 2 more
The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of…
Kayson Fakhar, Danyal Akarca, Andrea I. Luppi, Stuart Oldham + 5 more
Brains are often described as cost-efficient communication networks, optimally balancing the cost of long connections with the benefits of fast communication. Here, inspired by the “use it or lose it” principle, we present a novel game-theoretic model of self-organizing neural units and show that the brain is, in fact…
Carlos Antolín, Joan Falcó-Roget, Luis Serrano-Fernández, Néstor Parga
Decision-making depends on coordinated computations distributed across dorsal and ventral circuits, often described as actor–critic systems. We examined how this division of labor gives rise to value- and decision-related representations by training a bimodular recurrent network on an economic choice task and…
Dhruv D. Jatkar, M. Ali Al-Radhawi, Christopher A. Voigt, Eduardo D. Sontag
Implementing logic functions in living cells is a fundamental area of interest among synthetic biologists. The goal of designing biochemical circuits in synthetic biology is to make modular and tractable systems that perform well with predictable behaviors. Developing formalisms towards the design of such systems has…