bioRxiv

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Temporal adaptation aids object recognition in deep convolutional neural networks in suboptimal viewing scenario’s

bioRxiv Jan 1, 2025
The primate visual system excels in recognizing objects under challenging viewing scenario’s. A neural mechanism that is thought to play a key role in this ability is rapid temporal adaptation, or the adjustment of neurons’ activity based on recent h...
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Detection of alternative splicing: deep sequencing or deep learning?

bioRxiv Jan 1, 2025
Alternative splicing (AS) is a central mechanism of gene regulation that enables condition- and tissue-specific expression of gene isoforms. Its dysregulation plays a role in diseases such as cancer, neurological disorders, and metabolic conditions. ...
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From manual counting to YOLO: Using computer vision to automate large-scale fecundity assays in C. elegans

bioRxiv Jan 1, 2025
Fecundity measurements play a crucial role in life history research, providing insights into reproductive fitness, population dynamics, and environmental responses. In the model nematode Caenorhabditis elegans, fecundity assays are widely used to stu...
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Toward a model of uORF-mediated translational control: An integrated bioinformatic and experimental approach

bioRxiv Jan 1, 2025
Upstream open reading frames (uORFs) are short translated regions that occur in the 5□ untranslated regions (5□ UTRs) of mRNA transcripts where they primarily serve to repress expression translation of the downstream primary open reading frame (pORF)...
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Deep neurobehavioral phenotyping uncovers neural fingerprints of locomotor deficits in Parkinson’s disease

bioRxiv Jan 1, 2025
Gait deficits present an unresolved therapeutic challenge in Parkinson’s Disease. At the behavioral level, symptoms exhibit heterogeneity, including bradykinesia and hypokinesia during cyclical limb movement, as well as sudden interruptions in the ga...
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Leaping over the blood-brain barrier: DNA methylation as a link between peripheral and central immune systems

bioRxiv Jan 1, 2025
The majority of existing DNA methylation (DNAm) studies have used peripheral surrogate tissues to research molecular mechanisms underlying brain-related traits. Epigenetic processes in the brain have yet to be fully elucidated by DNAm findings from p...
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A transformer-based language model reveals developmental constraint and network complexity during zebrafish embryogenesis

bioRxiv Jan 1, 2025
Understanding how regulatory complexity and constraint shape organismal development remains a central challenge in biology. The developmental hourglass framework posits that mid-embryogenesis –the phylotypic stage– is a period of heightened conservat...
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DeepDiff-SHAP: Interpretable deep learning for subgroup-specific causal inference using conditional SHAP

bioRxiv Jan 1, 2025
Precision medicine aims to tailor healthcare strategies to individual differences in genetic, clinical, and environmental factors. However, identifying subgroup-specific causal relationships in complex biomedical data remains a major challenge, espec...
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ProteomeLM: A proteome-scale language model allowing fast prediction of protein-protein interactions and gene essentiality across taxa

bioRxiv Jan 1, 2025
Language models starting from biological sequence data are advancing many inference problems, both at the scale of single proteins, and at the scale of genomic neighborhoods. In this paper, we introduce ProteomeLM, a transformer-based language model ...
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Fast, flexible, learning-free organoid quantification and tracking with OrganoSeg2

bioRxiv Jan 1, 2025
Organoids are routinely imaged by brightfield microscopy at low magnification, but these images are challenging to analyze quantitatively at scale. Given differences in organoid-culture format and image acquisition among research groups, there is a g...
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