Genomics & Functional Genomics
Targeted variant detection using unaligned RNA-Seq readsThis study introduces km, an approach leveraging k-mer decomposition to identify targeted mutations. It can detect single-base mutations, insertions and deletions, as well as fusions. An analysis of over 10,000 RNA-seq samples shows fast mutation detection via km.
Kinesin-8B controls basal body function and flagellum formation and is key to malaria transmissionThis comprehensive study describes the key role and real-time dynamics of Plasmodium kinesin-8B in microtubule-based basal body and axoneme assembly during flagellum (male gamete) formation and parasite transmission.
TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assayThe authors present a novel method for obtaining chromatin profiles from low cell numbers without prior nuclei isolation. The method is successfully implemented in generating epigenetic profile from 100 cells with high signal-to-noise ratio.
CRISPR-induced double-strand breaks trigger recombination between homologous chromosome armsCRISPR–Cas9 enables recombination between homologous chromosome arms at predefined sites and also underscores the need for caution when applying CRISPR technologies in translational medicine.
Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer’s diseaseThis study describes a gauge for brain aging predictive of cognitive decline and Alzheimer's disease synergistic with the APOE ε4 allele.
A network of human functional gene interactions from knockout fitness screens in cancer cellsThe function of human genes can be strongly inferred from their knockout fitness profiles across hundreds of CRISPR screens, illuminating the modular organization of the cell.
Intra-individual methylomics detects the impact of early-life adversityThis study shows that methylation profile changes across time in the same individual distinguish a stressful experience from typical infancy, providing a potential predictive marker of vulnerability to disease.
Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elementsThis study shows that addition of a single transcription factor binding site can be sufficient to convert a gene into a glucocorticoid receptor target.
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogsComparison of observed exon–exon junction counts to those predicted from estimated transcript abundances can identify genes with misannotated or misquantified transcripts.
Evolution of gene expression levels in the male reproductive organs of Anopheles mosquitoesExpression patterns of transcripts in reproductive tissues reveal the phylogeny of the An. gambiae complex and are indicative of molecular function, transcription regulatory networks, and protein–protein interaction networks.