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Using a dependency-aware deep generative framework, spaVAE efficiently models spatially resolved transcriptomics data and advances diverse analysis tasks. Following similar strategies, spaPeakVAE and spaMultiVAE enable spatial ATAC-seq data and spatial multi-omics data modeling and analysis, respectively.
Spatial transcriptomics and mRNA splicing measurements encode rich spatiotemporal information for cell states and their transitions. We present a multiscale dynamical system method for reconstructing cell-state-specific dynamics and spatial state transitions. This theory-based approach reconciles short-timescale local tensor streamlines between cells with long-timescale transition paths that connect cell attractors.
Pebblescout navigates vast, rapidly growing nucleotide content in resources by providing indexing and search capabilities. We used Pebblescout to index a metagenomic subset of Sequence Read Archive and seven other resources into databases spanning over 3.7 petabases and searchable interactively at a pilot website using queries as short as 42 bases.
The Consortium for Top-Down Proteomics conducted a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories. They report the summary of the outcomes and their recommendations in this Analysis.
OpenFold is a trainable open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license.
By effective and efficient integration of PacBio HiFi, Oxford Nanopore Technologies ultra-long and other sequencing data types, hifiasm (UL) enables telomere-to-telomere diploid and polyploid genome assembly at a population scale.
We developed a two-pronged strategy to functionally probe the enormous repertoire of noncoding DNA within genomes. Our approach markedly improved signal-to-noise ratio and successfully intersected single-cell genomics with reporter assays. The result delivers a multiplex and highly quantitative readout of regulatory sequences’ activity in dynamic and multicellular systems.
By learning to embed DNA k-mers and cells into a joint space, CellSpace improves single-cell ATAC-seq analysis in multiple tasks such as latent structure discovery, transcription factor activity inference and batch effect mitigation.
Single-cell quantitative expression reporters enable high-sensitivity quantitative characterization of cis-regulatory elements at the single-cell level in multicellular systems.
Molecular Pixelation is an optics-free method that uses DNA-tagged antibodies to enable identification of the relative location of proteins on single cells.