clustering

Development of py-mea-span for comprehensive analysis of multi-electrode array data and its application to LGI2-deficient neurons

Open-source Python package parses Axion spk files directly and matches NeuralMetric Tool outputs, then reveals burst and network burst hyperexcitability, without synchrony change, in LGI2-knockdown human iPSC neurons.

A clinically annotated proteomic and histological resource of 1,000 colorectal cancers

Deep proteomics of 997 treatment-naïve colorectal cancers defines six subgroups, splitting chromosomally unstable tumors into three and revealing a rare adverse subgroup, with H&E slide benchmarks.

Panagram reveals pangenome architectures underlying trait variation in plants and animals

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

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.

A surviving beta cell subpopulation enriched in patients with T1D

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.

Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

In 174 sedentary adults, resistance exercise changed more muscle molecular features than endurance exercise across omes and time points; network analysis nominates MEF2A and NFIC as regulatory hubs.

Multi-Trajectory Pseudotime Inference via Permutation Factorizations

Factorizing multiple monotone pseudotimes into one shared donor permutation plus cluster-specific warps (HiP-BIND) yields Alzheimer's donor orderings agreeing better with Braak, ADNC and CERAD staging than single-trajectory B-BIND.

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.

replicateFest: An R Package and Shiny App for Analysis of T Cell Receptor Repertoire Data from the Functional Expansion

replicateFest uses negative binomial models for replicated and Fisher's exact tests for unreplicated FEST TCR-seq to call antigen-expanded clonotypes, recovering all nine published HIV-1 responders.

Reliable Evaluation of Transductive Population Graph Neural Networks for Multisite Autism fMRI

Site-aware population GNN on ABIDE-I: cohort AUC about 0.94 (kept with site-only edges) was not reproduced by a site-prior classifier (0.506); a directed-edge support gain (+0.252) vanished when symmetrised (−0.003).

Transcriptionally distinct atypical B cell populations contribute to insulin autoreactivity and show differential activation, isotype switching, and somatic hypermutation in early-stage type 1 diabetes individuals

B cells from 24 early-stage type 1 diabetes individuals include four atypical clusters differing in switching and mutation; Cluster 10 had the highest insulin-binding antibody rate (5/16).

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

Tfh dysfunction is associated with poor responses to HBV vaccination

HBV vaccine-draining lymph node biopsies tie low antibody titers to reduced, interferon-skewed GNG4+ germinal center T follicular helper cells; public B cell clonotypes did not track response.

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.

HiMaLAYAS: enrichment-based annotation and visualization of hierarchically clustered matrices

HiMaLAYAS, a Python package, cuts dendrograms, tests clusters for categorical annotation enrichment (hypergeometric, Benjamini-Hochberg FDR), and renders significant annotations beside clustered heatmaps in one workflow.

Late lactation represents the main window for sow-to-piglet transmission of persistent gut strains

Long-read 16S-ITS-23S tracking in 17 sow-piglet families shows maternal putative-strain sharing peaks in late lactation, which supplies most maternally derived strains persisting post-weaning.

Somatic genetic variation shapes clonal selection of memory NK cells

Whole-exome sequencing of memory NK cells from 81 CMV-seropositive donors reveals dominant somatic clones, early-life origin, and positive selection, with Kmt2d loss shifting mouse NK fitness.

Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning

Rsearch runs VSEARCH from R with quality plots, trimming optimizers and phyloseq conversion; on a 16S mock community it matched DADA2's abundance accuracy with fewer, more prevalent OTUs.

Chemotherapy-Induced Oral Mucosal Injury Is Defined by p53 Activation, Cell Cycle Arrest and Diverse Epithelial Progenitor Dynamics

In 5-FU-treated mice, oral and intestinal epithelial atrophy stems from p53-linked cell cycle arrest, not apoptosis, while a chemoresistant AP-1/p53 basal cluster expands in tongue.

Revisiting bacterial division control with likelihood inference: limited identifiability of simple models

Likelihood comparison on six E. coli mother-machine datasets finds sizer, adder, and log-foldchange division rules only weakly separable, while a neural conditional cycle-duration model fits best.

A high-resolution blood immune cell doublet atlas via imaging spectral cytometry

Image-based gating on an imaging spectral cytometer resolves 12 high-purity immune doublet types in human blood; in tuberculosis, doublet frequencies are unchanged but tightly contacting T cell-monocyte doublets increase.

Systematic Comparison of 10X Genomics and Parse Single Cell RNA Technologies across PBMC and CD8+ TEMRA Cells

Side-by-side PBMC and CD8+ TEMRA profiling shows Parse favors longer transcripts but underdetects cytotoxic genes (GNLY, PRF1, GZMB), so 10X Chromium better resolves TEMRA subsets.

The Cerebellar Engine: Multiscale Digital Brain Co-simulations Reveal How Cerebellar Spiking Architecture Shapes Cortical Coherence

In a mouse whole-brain co-simulation with a spiking olivocerebellar network, cutting mossy-fiber input to cerebellar nuclei lowers M1-S1 gamma coherence, while removing Purkinje inhibition raises it.

Cellquant: a vibecoder's guide to image analysis

One Python script, configured through LLM-assisted command-line calls, segments and quantifies 2D/3D multi-channel fluorescence images with provenance records; in a yeast temperature series it exposed a non-responding subpopulation.

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.

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

Genome-scale CRISPRi perturb-seq in 22 million primary human CD4+ T cells maps stimulation-specific regulators and links perturbation signatures to T cell states and autoimmune genetics.

KSTITCH links cellular morphology and gene expression in spatial transcriptomics

STITCH pairs size-independent tangent-PCA contour shape modes with expression factors by canonical correlation, recovering keratinocyte, fibroblast and melanoma shape-expression links in Xenium and CosMx data.

The diverse functions of viral microproteins

A >50,000-element viral smORF library screened by growth, MHC-I, ER stress, Perturb-seq and mass spectrometry yields >2,000 active microproteins and shows EBV BNLF2b inhibits PKA by mimicry.

Minimally invasive monitoring of clonal evolution through integrated single cell and ctDNA analysis

cfClone, a Bayesian model, deconvolves cfDNA whole-genome sequencing using scWGS-derived haplotype-specific clone copy-number profiles to estimate tumour fraction, clonal prevalence, and flag missed clones.

FlyPredictome: A structural atlas of predicted protein-protein interactions in Drosophila

FlyPredictome scores 1.5 million AlphaFold-Multimer predictions of Drosophila protein pairs with a contact-aware integrated Local Interaction Score (iLIS), yielding residue-level interfaces enriched for phenotype-associated missense alleles.