imputation

Single-shot Echo Planar Time-resolved Imaging for multi-echo functional MRI and distortion-free diffusion imaging

This paper introduces single-shot Echo Planar Time-resolved Imaging (ss-EPTI) to improve motion robustness, temporal resolution, and SNR efficiency in dynamic imaging applications.

Self-supervised deep learning of gene-gene interactions for improved gene expression recovery

This paper improves gene expression recovery in scRNA-seq by using self-supervised deep learning to model gene-gene interactions.

A dual-gene reporter-amplifier architecture for enhancing the sensitivity of molecular MRI by water exchange

This paper develops a dual-gene reporter-amplifier system to enhance MRI sensitivity by using Aqp1 to facilitate water exchange, enabling detection of low-abundance Oatp1b3-expressing cells.

Spectrally Resolved Localization Microscopy with Ultrahigh-Throughput

This paper develops an ultrahigh-throughput SMLM methodology using a color glass filter to achieve sub-10 nm localization and sub-5 nm spectral precision for multicolor imaging.

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

SnapFISH-IMPUTE imputes missing values in multiplexed DNA FISH data, improving downstream analysis by preserving pairwise distances and enhancing clustering and enhancer-promoter loop detection.

User-friendly Oblique Plane Microscopy on a fully functional commercially available microscope base

This paper presents an oblique plane microscope compatible with a commercial base, showing minimal impact on resolution and data fidelity despite objective lens displacement.

Engineering paralog-specific PSD-95 synthetic binders as potent and minimally invasive imaging probes

The paper develops synthetic binders specific to PSD-95 for imaging endogenous proteins with minimal impact on function and compatibility with super-resolution techniques.

Genotype imputation in F2 crosses of inbred lines

The paper evaluates genotype imputation in F2 crosses of inbred medaka lines, finding that imputation performance plateaus with increased sequencing coverage and develops a computational pipeline for cost-benefit analysis.

GenomeMUSter mouse genetic variation service enables multi-trait, multi-population data integration and analyses

GenomeMUSter integrates and harmonizes mouse genetic variation data across populations to enable multi-trait, multi-population analyses and improve variant-phenotype association studies.

Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC)

The paper introduces Brick-MIC, an affordable, open-source 3D-printed microscopy platform that enables single-molecule and super-resolution imaging techniques.

SEAD: an augmented reference panel with 22,134 haplotypes boosts the rare variants imputation and GWAS analysis in Asian population

The paper introduces SEAD, an Asian reference panel that improves rare variant imputation and GWAS analysis, identifying a novel association between SNTG1 and hip BMD.

Deep3DSIM: Super-resolution imaging of thick tissue using 3D structured illumination with adaptive optics

This paper introduces Deep3DSIM, an upright 3D-SIM system with adaptive optics for deep tissue imaging, achieving high-quality imaging up to 130 micrometers in Drosophila brain.

Phase diversity-based wavefront sensing for fluorescence microscopy

This paper introduces a phase diversity-based wavefront sensing method for fluorescence microscopy to correct optical aberrations efficiently and accurately.

Selphi: Empowering GWAS Discovery through Enhanced Genotype Imputation

Selphi improves genotype imputation accuracy, especially for rare variants, enhancing GWAS discovery and polygenic risk scores.

SUMMIT-FA: A new resource for improved transcriptome imputation using functional annotations

SUMMIT-FA improves gene expression prediction accuracy using functional annotations and eQTL data, enhancing gene-trait association detection in GWAS.

Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging

This paper imputes single-cell protein abundance in multiplex tissue imaging data from a breast cancer cohort using machine learning, showing improved accuracy and biological relevance.

High-speed Auto-Polarization Synchronization Modulation Three-dimensional Structured Illumination Microscopy

This paper introduces a high-speed 3DSIM system using DMD and electro-optic modulators, achieving improved resolution and imaging speed for various biological specimens.

FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe

FLiPPR improves LiP-MS data analysis by formalizing data imputation, merging data, and correcting multiple hypotheses, enhancing statistical trends and metadata collection.

Whole-genome sequencing of Bantu-speakers from Angola and Mozambique reveals complex dispersal patterns and interactions throughout sub-Saharan Africa

This study uses whole-genome sequencing of Bantu-speakers from Angola and Mozambique to reveal complex dispersal patterns and interactions in sub-Saharan Africa, including admixture and heterogeneous population histories.

Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by synthesis while reducing duplicates

This study compares imputation accuracy between avidity sequencing and sequencing by synthesis, finding comparable performance with lower duplication rates in avidity sequencing.

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data

mb-PHENIX denoises microbiota data by combining diffusion and supervised UMAP, improving differential abundance analysis in sparse and noisy count matrices.

Low-cost 3D printed lenses for brightfield and fluorescence microscopy

The paper presents low-cost 3D printed lenses for brightfield and fluorescence microscopy, demonstrating sub-cellular resolution comparable to commercial optics.

Deep Learning Model Imputes Missing Stains in Multiplex Images

The paper introduces a deep learning model, MAXIM, to impute missing protein markers in multiplex images, improving efficiency in staining and imaging processes.

Deep Learning-based Phenotype Imputation on Population-scale Biobank Data Increases Genetic Discoveries

AutoComplete improves phenotype imputation in biobank data, enhancing GWAS power and genetic discovery.

flowVI: Flow Cytometry Variational Inference

flowVI is a deep generative model for integrating flow cytometry datasets, improving imputation and enabling atlas construction by modeling noise and batch effects.

A novel f-divergence based generative adversarial imputation method for scRNA-seq data analysis

This paper introduces sc-f GAIN, an f-divergence-based generative adversarial imputation method for scRNA-seq data that improves accuracy and robustness compared to traditional methods.

The Soifua Manuia reference panel with 2,570 Samoan haplotypes improve genotype imputation quality among Samoans

The paper constructs a Samoan-specific imputation reference panel, showing improved genotype imputation quality compared to existing panels for Samoan populations.

Extended-depth of field random illumination microscopy, EDF-RIM, provides super-resolved projective imaging

EDF-RIM improves imaging speed and light dose while maintaining resolution for thick biological samples.

Cell segmentation and gene imputation for imaging-based spatial transcriptomics

RedeFISH improves imaging-based spatial transcriptomics by simultaneously segmenting cells and imputing gene expression using single-cell RNA sequencing data.

Foundation Models Meet Imbalanced Single-Cell Data When Learning Cell Type Annotations

This study evaluates how single-cell foundation models handle imbalanced cell-type data and finds that scGPT and scBERT outperform Geneformer, with random oversampling improving performance.