dimensionality reduction

Evaluation of fluorescent proteins for compatibility with STED microscopy systems using two-color spectroscopies

The paper evaluates fluorescent proteins for STED microscopy compatibility using two-color spectroscopy, showing improved 3D resolution in compatible proteins.

Cross-individual translation of spontaneous zebrafish brain activity through a shared latent representation

The paper introduces LaRBMs to uncover a shared latent representation of spontaneous brain activity across individuals, showing functional cell assemblies are conserved in larval zebrafish.

Layer-specific cortical processing dissociates sensory and cognitive influences on pain

The paper uses high-resolution fMRI to show that sensory and cognitive influences on pain are processed in distinct cortical layers, linking circuit organization to behavioral outcomes.

Disagreement between demultiplexing methods reveals structured cell quality gradients in multiplexed single-cell data

This paper introduces Split-flow, a pipeline that uses concordance between demultiplexing methods to classify cell quality in multiplexed single-cell data, revealing structured quality gradients.

TiDHy: Timescale Demixing via Hypernetworks to learn simultaneous dynamics from mixed observations

TiDHy demixes simultaneous latent dynamical systems from mixed observations, capturing multiple timescales of variation in synthetic and real-world data.

Quantifying Cross-Modal Association Confidence for Single-Cell RNA-ATAC Integration

The paper introduces CLIC scores to quantify confidence in gene-peak associations for single-cell RNA-ATAC integration, improving integration accuracy and biological interpretability.

MSK-Morph: An automated framework to systematically morph landmark-defined musculoskeletal models into subject-specific bone geometries

MSK-Morph automates the transformation of template musculoskeletal models into subject-specific bone geometries using medical imaging data.

Tract-explainable and underexplained synchrony play complementary roles in the functional organization of the brain

The paper dissects brain functional synchrony into tract-explainable and tract-underexplained components, revealing their distinct roles in brain organization across species.

Lense: Optimizing data preprocessing in single-cell omics using LLMs

Lense optimizes single-cell omics preprocessing by using language models to select the best pipeline based on visual comparisons of low-dimensional representations.

Deep Computational Anatomy via Latent-Aligned Multiview Normalizing Flows

The paper introduces LAMNr flows for multimodal data analysis, enabling shared latent subspaces and cross-view imputation, with applications in biological imaging.

3DBrainOne: an integrated end-to-end platform for 3D histological analysis of whole mouse brains

3DBrainOne provides an end-to-end platform for 3D histological analysis of mouse brains, enabling automated cell counting and region-wise quantification.

From lab to ocean: bridging swimming energetics and wild movements to understand red drum (Sciaenops ocellatus) behavior in a tidal estuary

Red drum lowered oxygen consumption behind mangrove- and oyster-mimicking bluff bodies at flows to 100 cm/s, yet telemetered fish were detected mostly in low-velocity nearshore habitat.

FiberLM: A Transformer-Based Model for Mouse Brain Diffusion MRI Tractography Guided by Viral Tracer Data

FiberLM improves mouse brain tractography by reducing false connections and aligning with viral tracer data using a Transformer model trained on Allen Mouse Brain Connectivity Atlas data.

A Pleiotropic Map of Brain Imaging Genetics Reveals Biologically Distinct Latent Endophenotypes

The paper introduces DIMPLE-GWAS, a dimensionality reduction framework for GWAS of brain scans, identifying 25 latent phenotypes with higher heritability and discovering 104 new significant loci.

SPIFEE - A pipeline for analyzing traces of live-cell fluorescence microscopy data

SPIFEE is a pipeline that improves the analysis of live-cell fluorescence microscopy data by reducing noise and extracting features more accurately and objectively.

Test-retest reliable and site-robust Hidden Markov Model framework for discovering whole-brain beta activity

This paper introduces a Hidden Markov Model (HMM) framework to automatically segment beta activity from MEG data, showing good test-retest reliability and multisite transferability.

A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-Seq data

Comparing local point neighborhoods before and after dimensionality reduction reveals that standard scRNA-seq pipelines, t-SNE, and UMAP often distort local neighborhoods by more than 95%, altering downstream clustering.

A Fractal-Dimension Framework for Quantifying Self-Similarity in Chromatin Folding

This paper introduces a fractal-dimension framework to quantify self-similarity in chromatin folding using Hi-C data, revealing fractal-like organization and scale-dependent patterns in chromatin structure.

Individual differences reveal distinct age and pubertal contributions to the refinement of the functional cortical hierarchy during adolescence

The paper examines how age and pubertal stage independently influence the refinement of the functional cortical hierarchy during adolescence using longitudinal data.

ORBIT: Orthogonal Rotation for Biological Inter-species Transfer

ORBIT aligns cross-species coexpression network embeddings using orthogonal Procrustes rotation, achieving higher cross-species retrieval quality than autoencoders.

Fast and interpretable quantification of biological shape heterogeneity via stratified Wasserstein kernel

The paper introduces a method to quantify biological shape heterogeneity using a stratified Wasserstein kernel, demonstrating its application to 2D and 3D biological datasets.

Fully Automated EEG Source Imaging Using Structured Sparsity for Single and Multiple Synchronous Epileptic Activities

This paper introduces an automated EEG source imaging method using structured sparsity to improve localization of epileptic activity in single and multiple synchronous cases.

BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution

BandHiC reduces memory usage for Hi-C matrices by 99% using a banded storage strategy while enabling efficient analysis of ultra-high-resolution data.

Where is ADHD in the brain? Evidence for a neurodevelopmental continuum of brain dynamics

The paper investigates neural dynamics and cortical excitability in ADHD and typically developing individuals, finding a developmental continuum rather than distinct diagnostic differences.

Protracted functional and structural reorganization of human prefrontal cortex supports lateralized category geometries

This paper shows that human ventrolateral prefrontal cortex (VLPFC) develops distinct category-selective representations that undergo prolonged, hemisphere-specific refinement, unlike ventral temporal cortex which shows early, stable organization.

Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation

The paper evaluates five single-cell RNA sequencing pipelines using Omnibenchmark, highlighting differences in parameter implementation across tools.

cellNexus: Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data

cellNexus enhances Human Cell Atlas data by adding quality control, metadata, normalization, and analysis layers to enable multi-study analyses and large-scale biological discovery.

A Python Dash App and cPanel workflow to automate metabolomics data analyses and visualisation

The paper presents a Python Dash App and cPanel workflow to automate metabolomics data analysis and visualization, enabling interactive statistical analysis and result sharing.

Cell Type Weighted Dimensionality Reduction

This paper introduces CWDR, a dimensionality reduction method that improves visualization of cell types by incorporating lineage information, reducing overlap between clusters in high-dimensional data.

DiffuST: a latent diffusion model for spatial transcriptomics denoising

DiffuST denoises spatial transcriptomics data by integrating spatial features and pathology images, improving downstream analysis and biological insights.