imputation

Improved quantitation in data-independent acquisition proteomics via retention time boundary imputation

This paper introduces a method to improve quantitation in DIA proteomics by imputing peptide retention time boundaries, leading to more accurate quantifications and better estimation of radiation exposure.

scHiCSRS: A Self-Representation Smoothing Method with Gaussian Mixture Model for Imputing single-cell Hi-C Data

scHiCSRS improves scHi-C data quality by distinguishing structural zeros from dropouts, leading to more accurate clustering in downstream analysis.

Cross-species and tissue imputation of species-level DNA methylation samples across mammalian species.

The paper develops CMImpute, a method to impute DNA methylation data for unprofiled species-tissue combinations, achieving strong correlation with observed values and imputing 19,786 new combinations.

A Palette of Bridged Bicycle-Strengthened Fluorophores

This paper introduces a new class of fluorophores with enhanced photostability, solubility, and tunable properties for advanced biological imaging applications.

Near-Zero Photon Bioimaging

This paper introduces near-zero photon imaging, a method that captures high-fidelity biological images at ultralow irradiance and high speed using AI.

Contextual High-throughput 3D Volume Electron Microscopy Data Acquisition Using Artificial Intelligence

The paper introduces an AI-driven method to improve 3D volume electron microscopy data acquisition by dynamically adjusting resolution, reducing acquisition time across various organisms and tissues.

A Spectral Image Scanning Microscope for Multi-Color High-Resolution Imaging

This paper introduces a spectral CSD-ISM system for high-resolution, multi-color imaging with improved speed and resolution.

PerfectlyAverage: a classical open-source software method to determine the optimal averaging parameters in laser scanning fluorescence microscopy

PerfectlyAverage determines optimal averaging parameters in laser scanning fluorescence microscopy by analyzing SNR, photobleaching, and PSD to reduce acquisition time.

DNA-PAINT imaging with hydrogel imprinting and clearing

This study shows that polyacrylamide hydrogels support DNA-PAINT imaging by preserving nanoscale docking strand positioning and enhancing diffusion and accessibility.

Model-free machine learning-based 3D single molecule localisation microscopy

This paper introduces a machine learning-based 3D SMLM method called easyZloc that works with standard microscopes and reduces computational demands.

Deep Volumetric Localization Super-Resolution Microscopy

This paper introduces VLM, a super-resolution microscopy method that combines hardware and algorithmic improvements to achieve high-fidelity 3D single-molecule imaging with 10 nm and 25 nm localization precision.

Discovering disease genetic variation impacting gene expression in 103 brain tissues with the Brain Ontology Expression (BRONTE) graph neural network model

The paper imputes gene expression in 103 brain tissues using BRONTE, a graph neural network, and identifies new genes and tissues affected by genetic variants linked to brain-related traits.

Large-Scale Information Retrieval and Correction of Noisy Pharmacogenomic Datasets through Residual Thresholded Deep Matrix Factorization

This paper introduces RT-DMF, a deep learning framework to correct noise and impute missing values in pharmacogenomic datasets, improving downstream analysis.

Nonlinear Singular Value Decomposition Beamforming for Ultrasound Imaging of Gas Vesicles

This paper introduces nonlinear singular value decomposition beamforming for ultrasound imaging of gas vesicles, achieving comparable sensitivity to existing methods with fewer pulse transmissions and improved signal-to-background ratio.

Mesoscopic SCAPE Microscope with a Rescanned, Super-oblique Illumination Plane

This paper introduces a mesoscopic SCAPE microscope with a super-oblique light sheet and rescanning strategy, achieving high-resolution volumetric imaging over large fields of view.

ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

ibaqpy computes iBAQ values for proteomics data using SDRF metadata, improving scalability and reproducibility in large-scale experiments.

Improving MALDI Mass Spectrometry Imaging Performance: Low-Temperature Thermal Evaporation for Controlled Matrix Deposition and Improved Image Quality

This paper introduces low-temperature thermal evaporation (LTE) for matrix deposition in MALDI-MSI, showing improved image quality, purity, and stability compared to traditional methods.

Open-Source 3D Active Sample Stabilization for Fluorescence Microscopy

This paper introduces an open-source 3D active stabilization system for fluorescence microscopy to maintain sample stability during long imaging sessions.

Optimizing Cost-Effective Gene Expression Phenotyping Approaches in Cattle Using 3' mRNA Sequencing

This paper optimizes 3' mRNA sequencing for cost-effective gene expression phenotyping in cattle using whole blood samples, identifying the best library prep kit and sequencing depth.

Wavefront estimation through structured detection in laser scanning microscopy

This paper introduces a convolutional neural network for aberration correction in laser scanning microscopy using detector array data, achieving high-resolution imaging with minimal sample stress.

Optical sectioning for reflection interference microscopy

This paper introduces two optical sectioning methods for RICM to reduce background noise and improve image quality in complex biological samples.

Fluorescent anionic cyanine plasma membrane probes for live cell and in vivo imaging

The paper introduces anionic cyanine-based plasma membrane probes for live cell and in vivo imaging, showing improved staining and visualization of neuronal structures in mice.

Photoactivatable Plasma Membrane Probe Through Self-Triggered Photooxidation Cascade for Live Super-Resolution Microscopy

In-gel refolding allows fluorescence detection of fully denatured GFPs after SDS-PAGE

This paper introduces a method to refold fully denatured GFPs within SDS-PAGE gels using cyclodextrin and methanol, enabling in-gel fluorescence detection.

Accelerated multi-shell diffusion MRI with Gaussian process estimated reconstruction of multi-band imaging

This paper introduces a method to accelerate multi-shell diffusion MRI by using Gaussian process reconstruction, improving image quality and enabling faster scans.

LEOPARD: missing view completion for multi-timepoints omics data via representation disentanglement and temporal knowledge transfer

LEOPARD completes missing views in multi-timepoint omics data by disentangling content and temporal representations, outperforming existing methods on benchmark datasets.

SpatialAgent: An Autonomous AI Agent for Spatial Biology

SpatialAgent integrates large language models with dynamic tool retrieval, multimodal interpretation, and claim verification to automate end-to-end spatial biology workflows from gene-panel design to tissue annotation and hypothesis generation.

Imputing not available values in single-cell DNA methylation data using the median is straightforward and effective

The paper shows that using the median to impute missing values in single-cell DNA methylation data is effective and accurate for downstream analysis.

Ocelli: an open-source tool for the visualization of developmental multimodal single-cell data

Ocelli is a Python tool for visualizing developmental multimodal single-cell data using diffusion-based modeling, improving computational efficiency and low-dimensional representation quality.

Learning interpretable representation for context-specific transcription regulatory networks using a foundation model

ChromBERT, a foundation model pre-trained on ChIP-seq data, generates interpretable representations of context-specific transcription regulatory networks and improves imputation and modeling of regulatory effects in cell types.