dimensionality reduction

The C. elegans Connectome Toolbox: an open, extensible framework for multimodal connectomic data integration and analysis

The paper introduces the C. elegans Connectome Toolbox, a framework for integrating and analyzing multimodal connectomic data, enabling comparison across datasets and modalities.

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Deep Recovery of Effective Migration Surfaces

This paper introduces dreems, a graph neural network that efficiently estimates effective migration surfaces from genetic data, achieving lower error and faster computation than existing methods.

PHATE-Derived Ancestry Coordinates Capture Continuous Population Structure in Human Genomic Data

This paper shows PHATE can better capture continuous population structure in genomic data than PCA or UMAP by tuning scale and balancing populations.

PhenoMe: An interactive AI framework for interpretable, microscopy-driven phenotyping

PhenoMe provides an open-source framework for analyzing microscopy images using foundation model-derived embeddings and experimental metadata to enable phenotyping and data exploration.

NeuralFieldManifold: Uncovering the Manifold Geometry of Local Field Potentials

This paper introduces a geometric framework for analyzing local field potentials (LFPs) by modeling their dynamics as low-dimensional K-tori and validates it across neural datasets.

RNA assignment and segmentation geometry in Visium HD profiles of fibrostenotic Crohn's disease

The paper evaluates segmentation methods for reconstructing cell-like profiles from spatial transcriptomics data but finds no reliable method under the given constraints.

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 2: Morphological criteria for small and medium-sized species

This paper develops a morphological identification framework for small and medium-sized ruminant postcranial bones using statistical classifiers to improve taxonomic accuracy in Southeast Asia.

Ground-truth evaluation of sparse autoencoder features on spatial, single-cell and language-model embeddings

The paper evaluates sparse autoencoder features on various embeddings, finding that reproducibility does not guarantee meaningfulness, and proposes reporting features with concept coverage and purity.

Auditory tracking magnitude, temporal alignment, and anatomical distribution during wakefulness and propofol-based anesthesia

The paper examines how auditory tracking changes during wakefulness and propofol anesthesia by analyzing response magnitude, temporal alignment, and anatomical distribution using sEEG data.

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.

Rapid changes in wing size and shape during the transition to laboratory conditions in a Neotropical drosophilid

This study tracks rapid wing size and shape changes in Drosophila sturtevanti across generations in lab conditions, showing genetic and environmental influences on morphology.

Streamline CNV - A Handy Nextflow Pipeline for Chromosomal Copy Number Variation Analysis

Streamline CNV is a Nextflow pipeline for CNV analysis that simplifies processing, visualization, and interpretation of copy number data across various sequencing types and species.

Aberrant cortical reorganization and astrogliosis underlie memory deficit post-traumatic brain injury: a longitudinal multiscale multimodal study

This study uses multiscale multimodal data integration in a mouse model of traumatic brain injury to identify biomarkers of memory deficits and network dedifferentiation.

Vascularized Organoids Emerge from a Heart-Foregut-like Intermediate Recapitulating Early Human Development

This study shows that heart/foregut-like structures form from human pluripotent stem cells, developing into vascularized cardiac organoids with multiple cell types.

CnidoSite: A Multi-Omics Database for Cnidarians

CnidoSite provides a centralized multi-omics database for cnidarians, integrating genomic, transcriptomic, proteomic, and phenotypic data to study thermal tolerance and environmental adaptation.

A community benchmark enables high-resolution, cross-lab quantification of mouse social behavior

The paper introduces a benchmark dataset and tool for cross-lab quantification of mouse social behavior, achieving high-resolution and reproducible classification.

scOmnom: scalable end-to-end single-cell RNA-seq analysis with auditable resolution selection

scOmnom provides a scalable, semi-automated workflow for single-cell RNA-seq analysis, enabling auditable clustering-resolution selection and annotation refinement across large datasets.

Enhanced stroke volume and divergence of the human left ventricle

The paper compares left ventricular phenotypes across humans, chimpanzees, and macaques to identify structural and functional traits associated with higher stroke volume in humans.

The trade-off between fractal morphology and function of Drosophila neurons

The paper analyzes the fractal morphology of Drosophila neurons and finds that fractal dimensions correlate with functional classes, showing specialization in morphology for distinct functions.

Movie Watching for Individual Functional Brain Network Estimation in Adolescents

This study compares functional brain network estimation using resting state crosshair fixation and movie watching in adolescents, finding similar network topography with minor border shifts.

LightSuite: scalable atlas registration and cell detection across the central nervous system

LightSuite enables scalable, multimodal registration and cell detection across the central nervous system, improving precision and reproducibility in large animal studies.

Attentional modulation of persistent visual representations after stimulus offset is coordinated across primary visual and anterior cingulate cortices

The paper shows that visual and auditory context representations are maintained in V1 and ACC after stimulus offset, supporting cross-modal attentional control.

HERO: A hierarchy-aware analysis pipeline for reducing and refining whole-brain atlas-mapped cellular datasets

HERO reduces and refines whole-brain atlas-mapped cellular datasets by performing hierarchy-aware selection, refinement, and visualization, improving interpretability and reproducibility.

tRNAZAP: Deep learning toolkit for nanopore tRNA signal analysis

tRNAZAP is a deep learning toolkit for analyzing nanopore tRNA sequencing data, achieving high accuracy in segmentation and classification tasks.

How aging reshapes implicit learning: behavioral and oscillatory evidence from an EEG-adapted Fast Mapping paradigm.

This study examines age-related changes in implicit learning using EEG and behavioral measures, finding that older adults show reorganized neural mechanisms for implicit encoding.

AnnZarro: scalable, interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data

AnnZarro enables interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data through a browser-based viewer linked to AnnData objects.

Linear NeuroPaint: An Efficient Baseline for Cross-Session Neural Alignment and Inpainting

Linear NeuroPaint evaluates a linear model for cross-session neural alignment and inpainting, finding it less accurate than nonlinear models but computationally efficient.

Unraveling phenotypic variation in multiscale behavioral dynamics

Comparing coarse-grained dynamics across resolutions, weighted by sampling uncertainty, yields phenotypic spaces linking E. coli run speed to CheB and showing paramecia experience narrows zebrafish variability.

Functional tradeoffs promote morphological disparity in the bat nasal cavity

The paper examines how functional tradeoffs in bat nasal cavity morphology, specifically turbinal structures, are influenced by echolocation mode and diet, revealing patterns of morphological diversity.