Articles in 2017

Proteome thermal stability is probed using limited proteolysis and mass spectrometry.

Two complementary approaches for directing human hematopoietic stem cells along the T cell lineage will have applications in both fundamental and translational research.

An iterative clustering approach finds the few genes that mark discrete cell states and their transitions during early mouse development.

The appetite for political engagement among scientists across the United States has increased since the 2016 election. If well channeled and sustained, this would be a positive development that could last beyond the current administration's tenure.

A “simple but a bit crazy idea” to tag ubiquitin and practice multilingual, multidisciplinary proteomics.

In vitro culture of mouse embryonic and extra-embryonic stem cells recapitulates embryogenesis.

PCR duplicates—sequencing reads from the same original genomic fragment—can cause headaches. But there are remedies.

HipSTR accurately genotypes and phases short tandem repeats, enabling robust genome-wide analyses of short tandem repeat variations.

SCnorm normalizes single-cell RNA-seq data for improved downstream analyses such as differential expression and cell-state discrimination.

A gain-of-function mutation in a sodium/potassium pump renders cells resistant to a small-molecule drug and provides an efficient coselection strategy to enrich for CRISPR-induced mutations at an independent locus.

CREST-seq allows functional screening of cis-regulatory elements through the use of sgRNA pairs to introduce tiled deletions in regions of interest. The analysis of a 2-megabase target region shows that promoters can act as distal enhancers for unrelated genes.

Iterative expansion microscopy (iExM) is a strategy that achieves high resolution expansion microscopy by expanding samples multiple times. Expanding a sample twice enables ∼4.5 × 4.5 ∼20× physical expansion and ∼25 nm resolution.

An ultrafast, fragment-ion indexing–based database search tool, MSFragger, makes open searching practical and enables comprehensive identification of modified peptides in mass spectrometry–based proteomics data sets.

This paper describes a fully defined, nonxenogeneic in vitro niche for the differentiation of haematopoietic stem and progenitor cells to progenitor T cells in mouse and human.

DeActs are genetically encoded tools that perturb the actin cytoskeleton. In contrast to drugs such as latrunculin, they can be targeted to specific cell types, which is demonstrated in the developing mouse brain and in Caenorhabditis elegans.