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CherryML is a method to scale up maximum likelihood estimation for general phylogenetic models of molecular evolution, providing several orders of magnitude speedup over traditional methods.
The PanGenome Research Tool Kit (PGR-TK) achieves flexible and scalable representation, visualization and analysis of genomic variation using pangenome graphs.
CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis) learns representations of molecular pixel profiles from multiplexed images that can be clustered to quantify subcellular landmarks and capture interpretable cellular phenotypes.
SIMBA learns a co-embedding space of single cells and multiple features such as genes, chromatin-accessible regions and transcription-factor-binding sequences, boosting the performances of various analyses of cellular diversity and regulation.
MISAR-seq combines spatial-ATAC-seq and RNA-seq for spatial profiling of both chromatin accessibility and gene expression, as demonstrated in the developing mouse brain.
The miniature RNA-guided endonuclease IscB and its ωRNA were engineered for efficient gene editing in mammalian cells. Fusions of ‘enIscB’ to T5 exonuclease and cytosine or adenosine deaminase yield versatile tools for genome engineering.
TomoTwin is a deep metric learning-based particle picking method for cryo-electron tomograms. TomoTwin obviates the need for annotating training data and retraining a picking model for each protein.
The light-sensitive LOV domain was engineered into the TurboID enzyme, creating ‘LOV-Turbo’. LOV-Turbo enables optogenetic control over proximity labeling, increasing the spatiotemporal precision of this technique.
XTC is a supervised deep-learning-based image-restoration approach that is trained with images from different modalities and applied to an in vivo modality with no ground truth. XTC’s capabilities are demonstrated in synapse tracking in the mouse brain.
3D Flexible Refinement (3DFlex) is a generative neural network model for continuous molecular heterogeneity for cryo-EM data that can be used to determine the structure and motion of flexible biomolecules. It enables visualization of nonrigid motion and improves 3D structure resolution by aggregating information from particle images spanning the conformational landscape of the target molecule.
iGluSnFR variants with improved signal-to-noise ratios and targeting to postsynaptic sites have been developed, enabling the analysis of glutamatergic neurotransmission in vivo as illustrated in the mouse visual and somatosensory cortex.
Photoselective sequencing combines targeted illumination and photocaged fragment libraries to enable the spatial analysis of genomic sequence and chromatin accessibility profiles with subcellular resolution in the context of complex tissues.
Editor summary: A native-mass-spectrometry-based approach analyzes integral membrane protein–lipid complexes directly from near-physiological membrane conditions, providing information about protein oligomeric states, lipid identities, and membrane properties.
Nano-DMS-MaP combines the power of DMS mutational profiling and long-read nanopore sequencing to resolve structural differences among RNA isoforms, revealing the structural landscape of HIV-1 transcripts in cells.
The NEMO series of genetically encoded calcium indicators report calcium activity in neuronal and non-neuronal cells with high signal-to-baseline ratio, which is shown in neuronal culture, slice preparations, in vivo and in planta.