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Testing and Correcting for Weak and Pleiotropic Instruments in Two-Sample Multivariable Mendelian Randomisation

Summary-data conditional F-statistics detect conditionally weak instruments in multivariable Mendelian randomisation, and Q-statistic minimisation gives weak-instrument and balanced-pleiotropy robust estimates plus an exact pleiotropy test.

Single cell transcriptome profiling of the human developing spinal cord reveals a conserved genetic programme with human specific features

Human embryonic spinal cord scRNA-seq (71,219 cells, CS12-CS19) mirrors mouse patterning and neurogenesis but shows floor-plate PAX7, broad ventral NKX6.2 and early OLIG2/NKX2.2 progenitors.

Highly accurate protein structure prediction with AlphaFold

AlphaFold, an attention network over sequence alignments and residue pairs, rivaled experimental accuracy in most CASP14 cases: median backbone r.m.s.d.95 0.96 Å versus 2.8 Å for the runner-up.

Language models enable zero-shot prediction of the effects of mutations on protein function

A single pre-trained protein language model, ESM-1v, scores mutations zero-shot about as well as family-specific DeepSequence across 41 deep mutational scans, with no experimental labels or retraining.

Using Progressive Context Encoders for Anomaly Detection in Digital Pathology Images

A progressive context encoder trained only on normal skin whole slide images flags melanoma regions without manual tumor labels, reaching 89% pixel-level accuracy across 9 test slides.

clusterProfiler: An universal enrichment tool for functional and comparative study

clusterProfiler performs over-representation (Fisher's exact test) and gene set enrichment analyses on Gene Ontology, KEGG, and user-supplied annotations, supporting non-model organisms, multi-condition comparisons, and ggplot2-based visualization.

Spatial single-cell profiling of intracellular metabolomes in situ

SpaceM integrates MALDI-imaging mass spectrometry with pre- and post-MALDI microscopy to measure >100 metabolites in >10000 individual cultured cells alongside fluorescence, morphology and spatial context.

Normative modeling of neuroimaging data using generalized additive models of location scale and shape

Generalized additive models for location, scale and shape (GAMLSS) using SHASH distributions beat Gaussian brain normative models on log score and calibration in most of 150 UK Biobank cortical-thickness regions.

Integrated analysis of multimodal single-cell data

Weighted-nearest neighbor (WNN) analysis in Seurat v4 learns per-cell modality weights to define cell states, enabling a 228-antibody human PBMC CITE-seq reference for RNA-only query mapping.

Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants.

A coronary artery disease GWAS of 181,522 cases among 1,165,690 participants yields 241 associations (54 new); an eight-predictor consensus nominates 185 candidate causal genes, 94 with ≥3 predictors.

Vcflib and tools for processing the VCF variant call format

A C++ library plus 83 command line utilities and 44 scripts (vcflib) for filtering, transforming and computing population-genetic statistics on VCF files, with companion tools bio-vcf, slivar, cyvcf2 and hts-nim.

Genome-wide association study of over 40,000 bipolar disorder cases provides new insights into the underlying biology

Meta-analysis of 41,917 European-ancestry bipolar disorder cases versus 371,549 controls yields 64 risk loci (33 novel), neuronal and synaptic gene enrichment, and 15 eQTL-prioritized genes.

STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data

Genome-aligning STARsolo matches simulated truth (R≈0.99) and CellRanger's counts almost exactly, running up to 4.4 times faster than CellRanger; pseudoaligners call hundreds of false-positive genes per cell.

Accurate de novo identification of biosynthetic gene clusters with GECCO

A linear conditional random field over ordered protein-domain annotations finds biosynthetic gene clusters de novo more precisely than DeepBGC and runs over three times faster on one CPU.

Mendelian randomisation for mediation analysis: current methods and challenges for implementation

Multivariable and two-step Mendelian randomisation recovered direct and indirect effects with little bias in simulations with confounding or measurement error, conditions that biased phenotypic regression mediation.

GPT-2's activations predict the degree of semantic comprehension in the human brain

Across 101 listeners, how well GPT-2 layer-8 activations predict fMRI responses to spoken stories tracks story comprehension, with a correlation of R = 0.50 across subject-story pairs.

Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV

Concurrent multi-omics of SARS-CoV-2 and SARS-CoV in A549 cells, integrated by network diffusion, maps shared and virus-specific host perturbations and nominates antiviral drug hotspots.

cellxgene: a performant, scalable exploration platform for high dimensional sparse matrices

cellxgene couples a Python server to a browser-based JavaScript client, letting researchers cross-filter, re-embed, annotate, and test differential expression in datasets of millions of cells.

Genetic requirements for cell division in a genomically minimal cell

Seven genes, including ftsZ, sepF and five of unknown function, are jointly required to restore near-normal morphology and division in the minimal cell JCVI-syn3.0.

Fast, scalable, and statistically robust cell extraction from large-scale neural calcium imaging datasets

EXTRACT, a GPU-based cell extraction method using one-sided Huber robust regression, processed 199 Allen Brain Observatory sessions (~12 TB) in a day and gave cleaner traces than CAIMAN or CNMF-E.