imputation

A resampling-based approach to share reference panels

The paper introduces RESHAPE, a method to anonymize reference panels by simulating descendant genomes, enabling genotype imputation while protecting privacy.

Coumarin as a general switching auxiliary to prepare photochromic and spontaneously blinking fluorophores

This paper introduces a method to create photochromic and blinking fluorophores by combining rhodamine and coumarin dyes, enhancing SMLM labeling options.

Flat-field superresolution structured illumination microscopy with joint temporal-spatial light modulation

This paper introduces a flat-field structured illumination microscopy method to improve field uniformity and enable large-scale imaging of whole cells and pathological samples.

ATP-Independent Water-Soluble Luciferins Enable Non-Invasive High-Speed Video-Rate Bioluminescence Imaging of Mice

The paper develops new luciferin substrates that enhance bioluminescence brightness and stability, enabling high-speed video-rate imaging of mice with improved sensitivity and non-invasive monitoring of calcium activity.

Accurate cross-platform GWAS analysis via two-stage imputation

This paper introduces TSIM, a two-stage imputation method for GWAS that harmonizes heterogeneous genotyping data, controlling errors and replicating known associations without false positives.

Multiplexed in vivo imaging with fluorescence lifetime modulating tags

This paper introduces FAST tags that modulate fluorescence lifetime to enable multiplexed imaging of up to six targets in live cells and zebrafish embryos.

BiGCN: Leveraging Cell and Gene Similarities for Single-cell Transcriptome Imputation with Bi-Graph Convolutional Networks

BiGCN improves single-cell RNA-seq imputation by integrating cell similarities and gene co-expression using dual graph convolutional networks, outperforming existing methods in imputation and clustering.

omicsMIC: a Comprehensive Benchmarking Platform for Robust Comparison of Imputation Methods in Mass Spectrometry-based Omics Data

omicsMIC benchmarks 28 imputation methods for mass spectrometry-based omics data, enabling researchers to evaluate and select methods based on real-time visualizations.

MIM-CyCIF: Masked Imaging Modeling for Enhancing Cyclic Immunofluorescence (CyCIF) with Panel Reduction and Imputation

The paper introduces a computational method to reduce CyCIF panel size while preserving information content through masked imaging modeling and imputation.

Blended Genome Exome (BGE) as a Cost Efficient Alternative to Deep Whole Genomes or Arrays

The paper introduces a cost-efficient sequencing method called Blended Genome Exome (BGE) that combines low-coverage whole genome and high-coverage exome data, achieving >99% concordance with 30x WGS for variant imputation and rare coding variant calling.

The covariance environment defines cellular niches for spatial inference

This paper introduces COVET and ENVI to model spatial niches and improve gene expression imputation and spatial context inference from single-cell data.

Three-dimensional multi-target super-resolution microscopy of cells using Metal-Induced Energy Transfer and DNA-PAINT

This paper introduces MIET-PAINT, a method combining DNA-PAINT and Metal-Induced Energy Transfer to achieve nanometer-scale 3D imaging with high multiplexing capability.

Completion of the DrugMatrix Toxicogenomics Database using ToxCompl

The paper predicts missing toxicogenomics data in the DrugMatrix database using ToxiCompl, a hybrid method combining matrix factorization and Bayesian optimization, showing alignment with biological expectations.

Fast volumetric fluorescence lifetime imaging of multicellular systems using single-objective light-sheet microscopy

This paper accelerates fluorescence lifetime imaging (FLIM) using single-objective light-sheet microscopy, achieving faster and less phototoxic imaging of live multicellular systems.

Adaptive Optics in an Oblique Plane Microscope

This paper demonstrates adaptive optics in an oblique plane microscope, improving resolution and signal strength in zebrafish embryos.

scDTL: single-cell RNA-seq imputation based on deep transfer learning using bulk cell information

scDTL improves scRNA-seq imputation by integrating bulk RNA-seq data through deep transfer learning and domain adaptation.

Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA

This study evaluates how post-mortem damage and contamination affect imputation performance in ancient DNA, finding that ATLAS improves results for highly damaged genomes and contamination above 5% reduces accuracy.

Fast and accurate imputation of genotypes from noisy low-coverage sequencing data in bi-parental populations

NOISYmputer improves genotype and recombination breakpoint imputation from noisy low-coverage sequencing data, outperforming existing tools in accuracy and efficiency.

Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping

This paper uses a generative AI model to improve 3D tissue imaging by interpolating and restoring images, enhancing resolution and reducing artifacts across multiple modalities and species.

Multi-condition and multi-modal temporal profile inference during mouse embryonic development

This paper introduces Sunbear, a framework for integrating multi-condition and multi-modal single-cell profiles across time to infer temporal profiles and predict dynamic relationships in mouse embryonic development.

Last-century vegetation dynamics in a highland Pyrenean national park and implications for conservation

This paper reconstructs sub-decadal vegetation dynamics in a Pyrenean national park, showing that forest composition remained stable despite park establishment and restrictions, but declined later due to climate factors and human activities.

Synthesis of arbitrary interference patterns using a single galvanometric mirror, and its application to Structured Illumination Microscopy

The paper introduces SWIFT, a new interferometer that projects arbitrary interference patterns using a single galvanometric mirror, and applies it to 2D and 3D Structured Illumination Microscopy.

Designed fluorescent protein cages as fiducial markers for targeted cell imaging

The paper introduces designed fluorescent protein cages that target specific subcellular locations in mammalian cells for imaging, demonstrating their ability to penetrate cells and be detected with confocal microscopy.

MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments

MAPFX improves analysis of massively-parallel cytometry data by preprocessing, background correction, and imputing missing markers to enhance biological signal preservation and reduce technical variation.

A series of spontaneously blinking dyes for super-resolution microscopy

This paper introduces a series of spontaneously blinking dyes with adjustable duty cycles for improved single-molecule localization microscopy in cells and dense structures.

Photo-Uncaging Triggers on Self-Blinking to Control Single-Molecule Fluorescence Kinetics for Super-Resolution Imaging

The paper develops a new fluorophore, NOSR, that enables controlled single-molecule blinking for improved super-resolution imaging of microtubules and mitochondrial outer membranes.

Far-red chemigenetic biosensors for multi-dimensional and super-resolved kinase activity imaging

The paper introduces far-red chemigenetic kinase activity biosensors enabling five-color multiplexing, 4D imaging, and super-resolution via STED microscopy.

Gentle rhodamines for live-cell fluorescence microscopy

This paper introduces Gentle Rhodamines with reduced phototoxicity for live-cell imaging, enabling time-lapse and voltage imaging with less cellular damage.

Super-resolved protein imaging using bifunctional light-up aptamers

This paper introduces bifunctional light-up aptamers for super-resolved protein imaging, demonstrating their effectiveness in SMLM with high localization precision and advantages over antibody-based methods.

scMeFormer: a transformer-based deep learning model for imputing DNA methylation states in single cells enhances the detection of epigenetic alterations in schizophrenia