Methods & Resources
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.
Human organotypic brain slice culture: a novel framework for environmental research in neuro-oncologyTherapeutically resected, adult brain segments were maintained and characterized for an extended period to study glioblastoma progression and treatment in its almost natural environment.
Gene editing enables T-cell engineering to redirect antigen specificity for potent tumor rejectionTargeted integration of a tumor-reactive T-cell receptor into the TRAC locus using CRISPR-Cas9 and AAV6 redirects primary human T cells against tumor cells in vitro and in vivo.
Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humansThis article presents a comprehensive study of the IGHV and TRBV gene families in a globally diverse sample of humans and shows that the two gene families exhibit starkly different patterns of variation.
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.
Optimized ChIP-seq method facilitates transcription factor profiling in human tumorsThis study presents an optimized ChIP-seq protocol to enhance transcription factor profiling in human tumours, enabling the analysis of highly challenging samples, including core needle biopsies.
Re-annotation of eight Drosophila genomesUsing a well-annotated genome to inform the annotation of genomes in a phylogeny.
Ribosomal stalling landscapes revealed by high-throughput inverse toeprinting of mRNA librariesHigh-throughput inverse toeprinting identifies peptide-encoding transcripts that induce ribosome stalling and allows the systematic analysis of sequence-dependent translational events.
Distinctive features of lincRNA gene expression suggest widespread RNA-independent functionsCombining single-cell RNA-seq of mouse ESCs and NPCs, lincRNA gene deletions, conditional RNA depletion, and nuclear exosome profiling distinguishes RNA-dependent and RNA-independent lincRNA gene activities.
Silica-based solid-phase extraction of cross-linked nucleic acid–bound proteinsThe 2C method allows the rapid and straightforward isolation of nucleic acid–protein complexes, greatly simplifying downstream applications for the study of DNA– and RNA–protein interactions.