AIMC Journal:
bioRxiv

Showing 1941 to 1950 of 4956 articles

Stimulus-Driven Leakage in Naturalistic Neuroimaging

bioRxiv Mar 25, 2026
This article elucidates a methodological pitfall of cross-validation for evaluating predictive models applied to naturalistic neuroimaging data---namely, "stimulus-driven leakage." While this problem has been well known as "leakage in training exampl...
View on bioRxiv DOI

Brieflow: An Integrated Computational Pipeline for High-Throughput Analysis of Optical Pooled Screening Data

bioRxiv Mar 25, 2026
Optical pooled screening (OPS) has emerged as a powerful technique for functional genomics, enabling researchers to link genetic perturbations with complex cellular morphological phenotypes at unprecedented scale. However, OPS data analysis presents ...
View on bioRxiv DOI

Deconvolution of omics data in Python with Deconomix -- cellular compositions, cell-type specific gene regulation, and background contributions

bioRxiv Mar 24, 2026
Background: Gene expression profiles derived from heterogeneous bulk samples contain signals from various cell populations. Cell-type deconvolution approaches are computational tools to reverse engineer the composition of bulks in term of cell popula...
View on bioRxiv DOI

Optimizing Biophysical Large-Scale Brain Circuit Models With Deep Neural Networks

bioRxiv Mar 24, 2026
Biophysical modeling provides mechanistic insights into brain function, spanning single-neuron dynamics to large-scale circuit models. These models are governed by biologically meaningful parameters, many of which can be experimentally measured. Some...
View on bioRxiv DOI

Evolution as Active Geometry: The Geometric State Equation of the Tree of Life

bioRxiv Mar 21, 2026
Any process that generates information at a constant rate into a branching hierarchy faces a geometric packing problem: the number of distinguishable lineages grows exponentially, but Euclidean space grows only polynomially. We show that this tension...
View on bioRxiv DOI

miRBind2 enables sequence-only prediction of miRNA binding and transcript repression

bioRxiv Mar 21, 2026
Motivation: MicroRNAs (miRNAs) regulate gene expression by guiding Argonaute proteins to partially complementary sites on target RNAs. While classical prediction methods rely on engineered features such as seed match categories, evolutionary conserva...
View on bioRxiv DOI

BAF complexes maintain accessibility at stimulus-responsive chromatin and are required for transcriptional stimulus responses

bioRxiv Mar 21, 2026
Background Gene expression changes in response to developmental and environmental cues rely on cis-regulatory sequence elements (cREs). BRG1/BRM-Associated Factors (BAF) chromatin remodeling complexes maintain chromatin accessibility at many cREs, en...
View on bioRxiv DOI

Hidden Diversity in Yeast tRNAs: Comparative Genomics and Modification Mapping in a Eukaryotic Subphylum

bioRxiv Mar 21, 2026
tRNA are adapter molecules with an integral role in translation and further roles in stress adaptation. Processing of tRNA is tightly regulated and includes the enzymatic addition of several post-transcriptional modifications that are required for tr...
View on bioRxiv DOI

Ancestral state reconstruction with discrete characters using deep learning

bioRxiv Mar 21, 2026
Ancestral state reconstruction is a classical problem of broad relevance in phylogenetics. Likelihood-based methods for reconstructing ancestral states under discrete character models, such as Markov models, have proven extremely useful, but only wor...
View on bioRxiv DOI

Novel 4D tensor decomposition-based approach integrating tri-omics profiling data can identify functionally relevant gene clusters

bioRxiv Mar 21, 2026
Integrating transcriptome, translatome, and proteome data remains challenging because changes in mRNA, ribosome occupancy, and protein abundance do not always occur simultaneously. To address this, we applied tensor-decomposition-based unsupervised f...
View on bioRxiv DOI
Popular Topics
Popular Journals