dimensionality reduction

Eigenmode decomposition of asymmetries in whole-brain effective connectivity reveals multiscale hierarchical dynamics

This paper decomposes whole-brain effective connectivity to reveal multiscale hierarchical dynamics and their relation to temporal irreversibility and individual-specific signatures.

STRIDE: A Sequencing Depth-Insensitive Metric for Robust Comparison between Sparse Chromosome Conformation Capture Data

This paper introduces STRIDE, a sequencing depth-insensitive metric for comparing sparse single-cell Hi-C data, enabling robust analysis of 3D genome organization.

The sex determination gene fruitless is essential for male Aedes aegypti mosquito swarming and attraction to female flight sounds

This study shows that the fruitless gene in male Aedes aegypti mosquitoes is essential for swarming and attraction to female flight sounds, with its disruption causing loss of these behaviors.

Universal principles of protein resource allocation among cellular organelles revealed by yeast large-scale absolute quantitative proteomics

This study uses yeast large-scale absolute quantitative proteomics to reveal universal principles of protein resource allocation among cellular organelles and its relationship to physiological parameters and species divergence.

Pareto optimization of masked superstrings improves compression of pan-genome k-mer sets

This paper introduces a Pareto optimization method for masked superstrings to improve the compression of pan-genome k-mer sets, achieving 12-19% better compressibility.

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity

STARIT converts spatial transcriptomics data into image tensors for deep learning analysis, enabling subcellular heterogeneity-based cell state identification.

LGTM: Gaussian Process Modulated Neural Topic Modeling for Longitudinal Microbiome

LGTM couples a neural topic model with additive basis-function Gaussian processes, learning microbial co-abundance topics and how covariates relate to their trajectories in longitudinal gut microbiome data.

The impact of behavioural activity on the EEG power spectrum, its source localisation, and global functional connectivity in rats

This study examines how behavioural activity affects EEG power spectrum, source localization, and global functional connectivity in freely moving rats, identifying specific frequency band changes.

A dataset of differentiable biologically-derived single neuron models

The paper presents a database of over 1,000 differentiable single-neuron models fitted to mouse and human patch-clamp recordings, with PyTorch code for integration into machine learning.

Automated inference of respiratory and syringeal biomechanical trajectories from birdsong acoustics

This paper introduces VIBE, a tool that automatically infers biomechanical control parameters from birdsong acoustics, validated against empirical measurements and neural data.

Interpretable models for scRNA-seq data embedding with multi-scale structure preservation

This paper introduces two tools for improving the trustworthiness of single-cell dimensionality reduction by enhancing quality metrics and multi-scale structure preservation.

Intrinsic timescale develops hierarchically from sensorimotor to association cortex in youth and stabilizes in adulthood

Resting-state fMRI intrinsic timescale lengthens with age in association, not sensorimotor, cortex during ages 8-22, following the sensorimotor-association axis in two cohorts; it is largely age-stable in young adults.

RNabel-A Standalone Software Tool for Annotating Tandem Mass Spectra of Modified Ribonucleic Acids

RNabel is a software tool for annotating tandem mass spectra of modified RNAs, supporting various modifications and formats, and providing quality metrics for spectral analysis.

Autoencoders for unsupervised analysis of rat myeloarchitecture

This study uses unsupervised deep learning to analyze rat brain histology, revealing tissue organization and detecting pathological changes without manual annotations.

Self-supervised Internal Learning Enhances Isotropic Resolution for Three-dimensional Fluorescence Microscopy

This paper introduces DeepIso, a self-supervised framework that enhances isotropic resolution in 3D fluorescence microscopy by restoring axial frequency content without requiring explicit PSF models or system calibration.

msaGUI: Multispectral Analysis Graphical User Interface for Ratiometric Analysis and Background Correction

msaGUI is a no-code tool for analyzing and visualizing multispectral images through customizable workflows and exportable outputs.

Code-Multiplexed Multi-Frequency Impedance Cytometry with a Unified Deep-Unfolding Network

This paper develops a deep-unfolding network for code-multiplexed, multi-frequency impedance cytometry to resolve signal overlaps and enable label-free single-cell analysis.

Broadband backscattering confocal microscopy enables label-free 3D live cell nanoscale sensitive imaging

This paper introduces broadband backscattering confocal microscopy (BBCM) for label-free 3D live cell imaging with improved contrast and size sensitivity.

Microglia modulate concussion biomarkers and cognitive recovery in male mice

This study shows microglia influence concussion recovery and identifies EV miRNA biomarkers affected by microglial presence.

Towards foundation models that learn across biological scales

The paper introduces Xpressor, a framework for cross-scale learning in biology, improving cell-type prediction and embedding quality.

White-matter-microstructure-informed whole-brain models reveal localized excitation-inhibition imbalance in schizophrenia

The paper develops white-matter-microstructure-informed whole-brain models to identify excitation-inhibition imbalance in schizophrenia, improving model performance and diagnostic prediction.

Reproducibility of Diffusion, Shape, and Connectivity Metrics Across Scanners: Implications for Multi-Site Tractography

The paper evaluates the reproducibility of diffusion, shape, and connectivity metrics across scanners in multi-site tractography studies and finds shape metrics show the highest reproducibility.

Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention

This paper introduces SHARP, a method to enhance Hi-C data resolution while avoiding artificial structures by decomposing signals and using multi-scale attention.

Anatomy-aware, label-informed approach improves image registration for challenging datasets

This paper introduces a label-informed image registration method that improves registration accuracy for challenging datasets, particularly in developmental studies.

CORSICA: Reproducible Suppression of Cochlear Implant Artifacts in EEG evoked by Continuous Speech

CORSICA suppresses cochlear implant artifacts in speech-evoked EEG data using cross-correlation with speech stimuli, outperforming alternative methods with minimal manual intervention.

A framework for analyzing C. elegans neural activity using multi-dimensional hyperbolic embedding

The paper analyzes C. elegans neural activity in response to bacterial stimuli, showing that hyperbolic embedding better describes neural dynamics than Euclidean space.

Multi-Stage Singular Value Decomposition for Ultrafast Ultrasound Imaging of Microbubbles

This paper introduces MS-SVD, a multi-stage SVD framework for ultrafast CEUS imaging that improves microbubble detection and vascular contrast by separating nonlinear signals from tissue clutter.

Weighted sliced inverse regression for scalable supervised dimensionality reduction of spatial transcriptomics data

This paper introduces wSIR, a scalable supervised dimensionality reduction method for spatial transcriptomics data, which retains predictive power of spatial coordinates and is demonstrated on breast cancer and embryonic development datasets.

NUCGEN3D: A synthetic framework for large-scale 3D nuclear segmentation with open-source training data and models

The paper introduces NucGen3D, a synthetic framework for generating 3D nuclear segmentation datasets, and trains models that outperform existing methods on real-world data.

Architecture of the Serotonergic Projectome in the Mouse Brain

Whole-brain axon tracing in 110 mouse brains divides raphe serotonin neurons into five projectomic groups, tied to transcriptome plus position and to dissociable behavioral effects of depletion.