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Consolidation alters motor sequence-specific distributed representations

In human fMRI, consolidated finger sequences are more discriminable than new ones in sensorimotor putamen, premotor and prefrontal cortices, but less so in hippocampus and caudate.

Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank

Exomes of 49,960 UK Biobank participants reveal 231,631 predicted loss-of-function variants (>10-fold more than imputed data); burden tests implicate PIEZO1, MEPE, and COL6A1 in disease traits.

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

scRNA-seq of 21465 mouse neural tube cells (e9.5-e13.5) maps spinal progenitor and neuron types, validates new subtype markers, and reveals temporally staged transcription-factor modules.

Uncovering hypergraphs of cell-cell interaction from single cell RNA-sequencing data

scTensor stacks ligand-receptor coexpression across cell-type pairs into a tensor and applies non-negative Tucker decomposition, recovering many-to-many cell-cell interactions that a label-permutation test missed in simulation.

Determinants of Minimum Acceptable Diet among 6-23 Months Age Children in Ethiopia: A Multilevel Analysis of The Ethiopian Demographic Health Survey

Only 6.1% of Ethiopian 6-23-month-olds received a minimum acceptable diet (EDHS 2016); child age, paternal education, maternal employment, water access, media exposure and region were associated with it.

fastq-pair: efficient synchronization of paired-end fastq files

fastq-pair, a C tool, re-pairs paired-end fastq files by hashing read identifiers and file offsets, writing matched pairs plus singleton files with linear time and memory scaling.

METASPACE: A community-populated knowledge base of spatial metabolomes in health and disease

An open-source cloud engine annotates imaging mass spectrometry data at controlled false discovery rate; publicly shared results reached over 3200 datasets and 6 million metabolite images by January 2019.

Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions.

A meta-analysis of 807,553 people from 23andMe, UK Biobank and PGC finds 102 depression variants. 87 of them replicate in 1,306,354 individuals, and heritability is enriched in prefrontal brain regions.

Single cell RNA-Seq reveals distinct stem cell populations that drive sensory hair cell regeneration in response to loss of Fgf and Notch signaling

Single-cell profiling of zebrafish lateral line neuromasts resolves support cell subtypes and lineages, and fgf3 mutant data show Fgf and Notch restrain Wnt-driven proliferation in parallel.

Pathway enrichment analysis of -omics data

Step-by-step protocol for interpreting omics gene lists via g:Profiler or GSEA enrichment testing, then grouping redundant enriched pathways into themes with Cytoscape Enrichment Map.

CaImAn: An open source tool for scalable Calcium Imaging data Analysis

CaImAn, an open-source library, automates motion correction, source extraction, deconvolution and cross-session registration for calcium imaging, detecting neurons near human level (F1 0.75 batch, 0.76 online).

dmrff: identifying differentially methylated regions efficiently with power and control

Combining nearby CpG summary statistics by inverse-variance weighted meta-analysis holds false positives at the nominal level where comb-p and DMRcate inflate, and supports multi-cohort meta-analysis.

Improved peak-calling with MACS2

Running MACS2 in default single-end mode on paired-end ATAC-seq miscalculates fragment coverage and calls low-coverage peaks; a modified MACS2 adds peak-length and gap parameters and fixes calculation bugs.

A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content

Nanopore chromosome assembly of high-CBDA cultivar CBDRx places cannabinoid synthase genes in three linked chromosome 9 regions; CBDA synthase and the THC/CBD QTL sit in hemp-derived sequence.

A rapid and robust method for single cell chromatin accessibility profiling

Upfront bulk Tn5 tagging then single-nucleus sorting into plates gives scATAC-seq libraries with higher complexity than Fluidigm C1, resolving 12 clusters among 3,385 mouse splenocytes.

FMRIPrep: a robust preprocessing pipeline for functional MRI

fMRIPrep, a BIDS-driven, self-adapting fMRI preprocessing pipeline, earned above-acceptable expert quality ratings on 50 of 54 OpenfMRI datasets and introduced less smoothing than FSL feat.

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

decontam, an R package, classifies contaminant sequences in marker-gene and metagenomic data by their inverse frequency-DNA concentration relationship and higher prevalence in negative controls.

High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries

FastANI accurately estimates average nucleotide identity (ANI) up to 782-fold faster than BLAST; across 90K prokaryotic genomes, an 83-95% ANI gap supports a 95% species boundary.

Discovery Of The First Genome-Wide Significant Risk Loci For ADHD

Genome-wide association meta-analysis of 20,183 ADHD cases and 35,191 controls finds 12 significant loci; signal concentrates in conserved regions, constrained genes, and CNS regulatory elements.

GimmeMotifs: an analysis framework for transcription factor motif analysis

GimmeMotifs bundles motif discovery, scanning, clustering and benchmarking; across 495 ENCODE ChIP-seq peak sets, the best motif from 14 finders out-scored BioProspector, the top single finder, on ROC AUC.