11 papers · ranked by Valyu relevance
Julius F. Witte, Artur Lissin, Isabel Schober, Christian Ebeling + 16 more
The vast amount of existing data on microbial strains holds immense potential to revolutionize bioindustry through the application of Artificial Intelligence (AI). However, the training of robust predictive AI models requires large-scale, unified, and non-redundant microbial datasets, which is currently severely…
Huihai Wu, Ashleigh Lister, Iain Macaulay, Katie Long + 10 more
Single-cell and spatial transcriptomics are transforming our understanding of cellular heterogeneity and tissue organization, yet their analytical complexity remains a major bottleneck. Here, we present EISCA and EISTA, two standardized, end-to-end pipelines for single-cell RNA- seq and imaging-based spatial…
Zichao Jin, Jiaoru Wang, Wenjiang Huang, Jingcheng Zhang + 2 more
Accurate, reliable, large-scale disease predictions are essential to ensure rice production. Existing disease prediction models often face a trade-off between interpretability and predictive capability, necessitating the integration of mechanistic knowledge and data-driven learning within a modelling framework.…
Jackie Rao, Muntadher Jihad, Giulia Biffi, Paul D.W. Kirk
Identifying cell types from single-cell RNA sequencing (scRNA-seq) data typically requires several separate and often uninterpretable steps: dimensionality reduction, batch-correction, clustering, marker-gene identification and the discovery of finer-grained structure. Here we introduce scFLAME (single-cell Factor…
Matheus da Silveira Costa, Henrique Izaias Marcelo, Gabriel Albanese Kafouri, Vinicius de Camargo
Colorectal cancer (CRC) is a major cause of cancer-related mortality, with distant metastasis strongly associated with poor clinical outcomes. Integrating transcriptomic and epigenomic data through machine learning may improve the molecular characterization of metastatic CRC. We analyzed 518 primary tumors from the…
Pedro C Carvalho, Tori Millsteed, Robert J Henry
Spatial transcriptomics (ST) has emerged as a transformative approach for visualizing tissue landscapes, yet it faces significant challenges regarding data standardization, sparsity, and the analysis of complex genomes, particularly polyploid plants. To address these limitations, we introduce Poly Pipeline, a robust…
Eliezer Masliah
How transient neural representations become integrated and stable enough to function as internal neural models remains incompletely understood. Grounded in efficient coding, Bayesian and predictive frameworks, recurrent and attractor dynamics, neural state-space models, and systems neuroscience, the Principle of…
Viktor Studenyak, Jürgen Jost, Christian F. Doeller, Andrej Bicanski
The Dentate Gyrus (DG) is a key part of the hippocampus, and damage to the DG produces a wide range of pathologies, including overgeneralization of contexts, affective dysregulation (4), and epileptogenic effects (60). The canonical model of the DG focuses on pattern separation for subsequent memory storage in the…
Wagner Fischer, Raquel de Faria Godoi Silva, Antonio Conceição Paranhos Filho
Biological invasions by feral swine are among the most important drivers of ecological change worldwide, yet invasion dynamics remain poorly documented in tropical South America. In Brazil, the recent spread of wild boar and wild boar–domestic pig hybrids (javaporcos) overlaps with long-established populations of…
Maria Juliana Rodriguez-Cubillos, Tomasz Zieliński, Jason R. Swedlow, T. Ian Simpson + 1 more
Ensuring the availability and accessibility of research data is fundamental to advancing knowledge, as codified in the FAIR principles (Findable, Accessible, Interoperable, and Reusable). Accurate metadata documentation is indispensable for meeting these principles; however, entries in deposition databases often…
Alexander Adrian-Hamazaki, Paul Pavlidis
It is widely accepted in genomics that coexpression of RNA transcripts suggests a commonality of function. This intuition is explicitly leveraged in machine learning methods that predict gene function, where it is often combined with other features such as protein interactions and sequence similarity. For example…