Genomics & Functional Genomics
A comprehensive resource for retrieving, visualizing, and integrating functional genomics dataThis study presents qcGenomics, a user-friendly online resource for ultrafast retrieval, visualization, and comparative analysis of tens of thousands of genomics datasets to gain new functional insight from global or focused multi-dimensional data integration.
Reference-free transcriptome exploration reveals novel RNAs for prostate cancer diagnosisA reference-free computational workflow for the discovery of unannotated RNA biomarkers retrieves novel noncoding RNAs with high potential for prostate cancer diagnosis.
Defining the expression of piRNA and transposable elements in Drosophila ovarian germline stem cells and somatic support cellsComprehensive transcriptional characterization of mRNA and small RNA in early Drosophila germline stem cells reveals novel piRNA clusters, transposon dynamics, and alternative splicing events.
Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotionThis work explores quantitative chromatin accessibility, transcriptional and cis-acting gene regulatory variations underlying mouse strain–specific differences in drug-induced liver tumor promotion sensitivity.
Sufficiency analysis of estrogen responsive enhancers using synthetic activatorsEnhancers bound by synthetic activators can recreate a transcriptional response to estrogen, drive different levels of gene expression, and work independently to regulate transcription.
Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptomeA genome-wide comparative analysis of “cryptic” aslncRNAs decay in RNAi-capable and RNAi-deficient budding yeasts suggests an evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeSBRAPeS is a software for B-cell receptor reconstruction in single cells from very short (25–30 bp) read lengths, which achieves similar success rates and accuracy as applying other methods on long reads.
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.