Research Briefing

Filter By:

Article Type
Year
  • PROBER is a fast and sensitive episome-based method to identify sequence-specific DNA-binding proteins from living cells using proximity proteomics. This method quantifies steady-state and inducible association of transcription factors and corresponding chromatin regulators to specific DNA sequences as well as binding quantitative trait loci present as a result of single nucleotide variants.

    Research Briefing
  • The Integrative Genome Modeling (IGM) platform incorporates information from multiple, complementary experimental data sources to accurately simulate whole diploid genome structures. We show that such structures have high predictive power and give access to a large variety of structural observables for the characterization of the gene microenvironment.

    Research Briefing
  • Bioluminescent phasor is a new technology for multiplexed, excitation-free imaging at the microscale using luciferase–luciferin pairs. This platform can readily unmix the broad, overlapping emission spectra of bioluminescent reporters, making possible the dynamic tracking of cellular and molecular features over prolonged time periods.

    Research Briefing
  • Adenosine-to-inosine RNA editing is a common post-transcriptional modification, but can be challenging to identify correctly from Illumina data. We show that Oxford Nanopore RNA sequencing, combined with deep learning models, can be used to accurately detect inosine-containing sites in native transcriptomes and to estimate the modification rate of each site.

    Research Briefing
  • Determining the functional properties of a protein from its structure is challenging. This study presents an interpretable deep learning model that directly learns function-bearing structural motifs from raw data, allowing accurate mapping of protein binding sites and antibody epitopes onto a protein structure.

    Research Briefing
  • Repository-scale analysis of hundreds of millions to billions of mass spectra is a challenging endeavor due to the complexity and volume of associated data. A deep neural network embedding method is presented that enables large-scale investigation of repeatedly observed yet consistently unidentified mass spectra.

    Research Briefing
  • Tangram, gimVI and SpaGE outperformed other integration methods for predicting the spatial distributions of RNA transcripts, while Cell2location, SpatialDWLS and RCTD were the top-performing methods for the cell type deconvolution of spots in histological sections.

    Research Briefing
  • Neuromechanical simulations enable the study of how interactions between organisms and their physical surroundings give rise to behavior. NeuroMechFly is an open-source neuromechanical model of adult Drosophila, with data-driven morphological biorealism that enables a synergistic cross-talk between computational and experimental neuroscience.

    Research Briefing
  • Counting of RNA molecules using unique molecular identifiers (UMIs) is ubiquitous in single-cell sequencing. Here, we introduce molecular spikes, a new type of RNA spike-ins with in-built UMIs. These versatile molecular spikes have many uses in experimental and computational method development and routine biological applications.

    Research Briefing
  • By providing challenges to the metagenomics community based on complex and realistic metagenome benchmark datasets, CAMI — the community-driven initiative for the Critical Assessment of Metagenome Interpretation — has created a comprehensive assessment of the performance of metagenomics software for common analyses. As part of its second contest, CAMI II, it evaluates ~5,000 submissions from 76 software programs and their different versions.

    Research Briefing
  • A simple and affordable technique passively clears and images whole mammalian bodies or large tissues. This technique is compatible with the use of endogeneous fluoresent proteins, without the loss of signal associated with other existing methods for whole-animal clearing.

    Research Briefing