Discover, rate, and verify biology preprints.

Cytoscape stringApp: Network analysis and visualization of proteomics data

stringApp, a Cytoscape app, imports STRING and STITCH networks with disease, tissue, localization and drug-target annotations, enabling GUI-based enrichment, clustering and visualization of proteomics data.

The multi-speed genome of Fusarium oxysporum reveals association of histone modifications with sequence divergence and footprints of past horizontal chromosome transfer events

Fusarium oxysporum chromosomes fall into four classes by divergence and dispensability; H3K27me3-marked regions diverge faster, and tomato pathogenicity regions show footprints of horizontal transfer.

Moana: A robust and scalable cell type classification framework for single-cell RNA-Seq data

Chained linear SVMs on kNN-smoothed, PCA-transformed scRNA-seq classify closely related PBMC subtypes across 10x chemistries, plus a 'mirror validation' check that estimates accuracy without ground truth.

SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology

Split k-mer matching lets SKA cluster and align related bacterial genomes from raw reads, matching a mapping pipeline's MRSA outbreak tree topology with nearly 17 times less CPU time.

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

apeglm replaces DESeq2's Normal prior on log fold changes with an adaptive Cauchy prior, reducing variance for low-count genes while preserving true large effect sizes.

Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation

SCoPE-MS combines acoustic cell lysis with isobaric tandem-mass-tag carrier channels to quantify over a thousand proteins in single mammalian cells, resolving cancer cell types and stem cell differentiation.

NetWheels: A web application to create high quality peptide helical wheel and net projections.

NetWheels, an R/shiny web application, draws customizable peptide helical wheel and net projections, accommodates non-α helix geometries, and exports publication-quality images plus reloadable parameter sets.

Meta-analysis of genome-wide association studies for body fat distribution in 694,649 individuals of European ancestry

Meta-analysis of waist-to-hip ratio adjusted for BMI in 694,649 European-ancestry individuals identifies 463 signals in 346 loci, roughly one-third sexually dimorphic and mostly stronger in women.

CORnet: Modeling the Neural Mechanisms of Core Object Recognition

CORnet-S, a four-area recurrent network with areas pre-mapped to V1, V2, V4 and inferior temporal cortex, ranks among top Brain-Score models while having a shorter longest convolutional path than competitors.

Overcoming systematic errors caused by log-transformation of normalized single-cell RNA sequencing data

Log-transforming normalized scRNA-seq counts with a pseudo-count of 1 creates spurious expression differences and artificial clusters or trajectories when size factors vary; a derived larger pseudo-count bounds this error.

HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps

HiGlass, a web-based, containerized viewer, enables continuous multiscale navigation of Hi-C contact maps alongside genomic tracks using composable views linked by location and zoom.

Zero-preserving imputation of scRNA-seq data using low-rank approximation

Truncated SVD plus a per-gene threshold at the most negative value fills dropouts while leaving biological zeros alone, and runs on 50,000 cells in about 40 minutes.

Neural Correlates of Motor Imagery, Action Observation, and Movement Execution: A Comparison Across Quantitative Meta-Analyses

Coordinate-based meta-analyses reveal a premotor, rostral parietal, and somatosensory core shared by motor imagery, action observation, and execution; only imagery and execution share putamen and cerebellum.

Generative adversarial networks simulate gene expression and predict perturbations in single cells

A Wasserstein GAN trained on three batch-uncorrected mouse epidermal scRNA-seq datasets simulates realistic cells, predicts differentiation via latent arithmetic, and infers gene networks recovering Gata6 targets.

Scaling accurate genetic variant discovery to tens of thousands of samples

Per-sample assembly with gVCF output, followed by joint genotyping, lets GATK HaplotypeCaller scale linearly with cohort size while calling indels more accurately than SAMtools, UnifiedGenotyper or Platypus.

fastp: an ultra-fast all-in-one FASTQ preprocessor

fastp unifies FASTQ quality control, adapter trimming, filtering, and base correction in one scan; single-threaded, it ran 2–5 times faster than FASTQC, Cutadapt, or Trimmomatic.

The DOE Systems Biology Knowledgebase (KBase)

Open-source KBase platform unites reference genomes and biochemistry, over 70 apps, Jupyter-based Narratives with provenance, and a Docker SDK for reproducible plant and microbial systems biology.

Cheating on cheaters dramatically affects social interactions in Pseudomonas aeruginosa

When pyoverdine and elastase are both needed, a pvdS mutant outcompetes the lasR cheater in P. aeruginosa and averts population collapse; a cost-ratio model with quorum sensing explains this.

Analysis of shared heritability in common disorders of the brain

Genetic correlations across 25 brain disorders (215,683 cases) reveal broad psychiatric common-variant sharing, largely distinct neurological disorders, and migraine as the only significant cross-category link.

Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics

Slingshot builds a cluster-level minimum spanning tree to find branching lineages without fixing their number, then fits simultaneous principal curves for stable per-lineage pseudotimes.