imputation

CUE: CpG impUtation Ensemble for DNA Methylation Levels Across the Human Methylation450 (HM450) and EPIC (HM850) BeadChip Platforms

CUE imputes DNA methylation from HM450 to HM850 platforms, achieving lower RMSE and higher accuracy than existing methods across two cohorts.

Highly responsive single-fluorophoreindicator to explore lactate dynamics in high calcium environments

The paper develops a single-fluorophore lactate indicator, CanlonicSF, suitable for high Ca2+ environments, showing improved sensitivity and specificity over existing FRET-based indicators.

Intravital Deep-Tumor Single-Beam 2-, 3- and 4-Photon Microscopy

This paper demonstrates that high-pulse-energy low-duty-cycle infrared excitation enables deeper tissue penetration in tumors and bone compared to conventional 2-photon excitation, allowing simultaneous multi-parameter imaging.

Deep-fUS: functional ultrasound imaging of the brain using deep learning and sparse data

This paper develops a deep learning method to reconstruct functional ultrasound images from sparse data, achieving 95% compression while maintaining sensitivity to task-evoked cortical activation.

A Flexible, Interpretable, and Accurate Approach for Imputing the Expression of Unmeasured Genes

This paper introduces SampleLASSO, a method for imputing unmeasured gene expression in microarray data, showing it outperforms existing methods across multiple tasks.

SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation

SIMPLEs improves scRNA-seq imputation by preserving gene modules and cell clusters, outperforming existing methods and revealing biological insights.

Dual-view oblique plane microscopy (dOPM)

This paper introduces a new dual-view oblique plane microscopy technique that improves resolution and reduces shadow artefacts in multi-cellular spheroid imaging.

Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data

Epiclomal clusters sparse single-cell DNA methylation data and imputes missing values, outperforming non-probabilistic methods and revealing sub-clonal methylation patterns in tumour genomes.

PBLR: an accurate single cell RNA-seq data imputation tool considering cell heterogeneity and prior expression level of dropouts

PBLR imputes dropout events in scRNA-seq data by considering cell heterogeneity and prior expression levels, improving low-dimensional representation and subpopulation detection.

A Modular Approach to Active Focus Stabilization for Fluorescence Microscopy

This paper presents a modular, cost-effective system for detecting and correcting z-drift in fluorescence microscopy, demonstrating its effectiveness through temperature perturbation and simulated stage movement tests.

Correlation imputation in single cell RNA-seq using auxiliary information and ensemble learning

This paper introduces SCENA, a method that imputes gene correlations in scRNA-seq data using ensemble learning and auxiliary information, improving downstream analyses.

Zero-shot imputations across species are enabled through joint modeling of human and mouse epigenomics

The paper extends an imputation method to enable cross-species predictions by jointly modeling human and mouse epigenomic data, improving imputation accuracy for mouse and enabling zero-shot predictions for human assays in mouse.

AlphaImpute2: Fast and accurate pedigree and population based imputation for hundreds of thousands of individuals in livestock populations

AlphaImpute2 improves imputation accuracy and speed for large livestock populations, outperforming existing methods in both metrics.

Live cell PNA labelling enables erasable fluorescence imaging of membrane proteins

The paper introduces a method for live-cell imaging of membrane proteins using PNA tags and demonstrates its application in tracking EGFR internalization.

Label-free and Multimodal Second Harmonic Generation Light Sheet Microscopy

This paper demonstrates a label-free SHG-LSM technique for 3D imaging of collagen and other harmonophores, combining SHG with light sheet microscopy for multimodal imaging.

starmapVR: immersive visualisation of single cell spatial omic data

starmapVR provides an immersive visualization tool for single-cell and spatial omic data using VR, supporting 3D and 2.5D views with multiple interaction methods.

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

The paper constructs a maize pangenome haplotype graph (PHG) to improve genotype imputation accuracy across diverse germplasm using WGS and GBS data.

3D Interferometric Lattice Light-Sheet Imaging

This paper introduces 3D-iLLS, a live-cell imaging technique that improves 4D resolution and signal-to-noise ratio by combining SPIM with 4Pi interferometry.

Single particle-resolution fluorescence microscopy of nanoplastics

This paper develops STED microscopy techniques to image nanoplastics at single-particle resolution, enabling precise localization and quantification in complex environments.

Synthetic observations from deep generative models and binary omics data with limited sample size

The paper evaluates generative models for binary omics data with small sample sizes, finding DBMs and VAEs perform better than GANs for recovering pairwise relationships.

A High-Performance Genetically Encoded Fluorescent Biosensor for Imaging Physiological Peroxynitrite

This paper introduces pnGFP-Ultra, a fluorescent biosensor for detecting peroxynitrite in live cells with high selectivity and sensitivity.

Enhancing SNR and generating contrast for cryo-EM images with convolutional neural networks

This study shows that convolutional neural networks can enhance SNR and generate contrast in cryo-EM images, improving image processing outcomes.

MSImpute: Imputation of label-free mass spectrometry peptides by low-rank approximation

The paper introduces msImpute, a low-rank approximation method for imputing missing values in mass spectrometry data, showing it performs well when data are missing at random.

Non-invasive brain-spine interface: continuous brain control of trans-spinal magnetic stimulation using EEG

This paper presents a non-invasive brain-spine interface that uses EEG to control trans-spinal magnetic stimulation for leg neurorehabilitation, showing efficient artifact removal and user comfort.

Bioorthogonal red and far-red fluorogenic probes for wash-free live-cell and super-resolution microscopy

The paper develops new fluorogenic probes for live-cell and super-resolution microscopy with minimal label size and efficient quenching.

Transient Room Lighting for Ambient Light Multiphoton Microscopy

The paper introduces a lighting system for multiphoton microscopy that enables imaging in a lit room by interleaving capture and illumination, achieving image quality comparable to dark-room conditions.

Deep learning-enhanced light-field imaging with continuous validation

This paper introduces a deep learning framework for light-field microscopy that uses continuous validation during image reconstruction, achieving high-quality video-rate reconstructions of medaka heart dynamics and zebrafish neural activity.

Multicolor structured illumination microscopy and quantitative control of polychromatic coherent light with a digital micromirror device

This paper develops a method to enable multicolor coherent structured illumination microscopy using a digital micromirror device, overcoming the blazed grating effect and demonstrating improved resolution and signal-to-noise.

DreamAI: algorithm for the imputation of proteomics data

An ensemble of six imputation methods, built through the NCI-CPTAC Proteogenomics DREAM Challenge, fills missing values in labeled LC-MS/MS proteomics data, helping most for low-abundance proteins.

HiFi-SIM: reconstructing high-fidelity structured illumination microscope images

HiFi-SIM improves structured illumination microscopy image fidelity by reducing artifacts and enhancing axial resolution without requiring precise PSF calibration or parameter tuning.