Discover, rate, and discuss biology preprints.

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.

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.

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.

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, 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.

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.

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.

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.

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.

GLnexus, a joint variant caller backed by an incrementally growable gVCF database, largely matched GATK on 50,000 exomes while keeping more rare indels and using 3.8–6.6-fold fewer core-hours.

FASTmrMLM swaps mrMLM's numerical gradients and Hessians for analytic ones, cutting runtime by more than 50% while matching or slightly beating its simulated power and accuracy.

MOFA, a sparse Bayesian factor model with mixed likelihoods, separates shared from modality-specific multi-omic variation, recovering IGHV, trisomy 12 and oxidative-stress axes in 200 leukaemia samples.

Encoding imputed genotype probabilities at 8 bits in BGEN gave compact files, ~240 million probabilities parsed per second and association results near-identical to 20-bit data (UK BiLEVE chromosome 22).

ampvis2 unifies 16S amplicon count tables, taxonomy, and sample metadata in one R object, feeding ggplot2 heatmaps at any taxonomic rank and single-call ordination (seven methods).

Aggregating UMI counts from a cell's nearest neighbours, chosen step-wise on variance-stabilised profiles, cuts technical noise enough that PCA and hierarchical clustering resolve cell types and T cell subsets.

Deep learning rivals or beats baselines across imaging, health records, genomics and drug discovery but is not yet transformative; scarce labels, privacy and opacity remain hurdles.

An average-pairwise Tanimoto internal diversity metric shows reinforcement learning and ORGAN generators lose diversity among desired molecules, ending far below reference-set diversity.

NanoPack bundles Python3 tools (command line, GUI, web service) for QC plotting, summary statistics, read filtering and contaminant removal of Oxford Nanopore and PacBio long reads.

Python toolkit Scanpy, built on HDF5-backed AnnData, achieves speedups of 5 to 16 times over Cell Ranger's R kit and clusters 1.3 million cells without subsampling.

Fine-tuned ImageNet ResNets beat Inception models on tissue micro-array and BreaKHis slides, reaching 99.8% across four tumour tissues and 96.4% across four malignant sub-types.