imputation

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

The paper improves genotype imputation in underrepresented populations by adding population-specific SNPs to existing reference panels, showing improved accuracy in a Tanzanian cohort.

Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients

The paper improves genotype imputation for CF patients using the TOPMed reference panel and a CF-specific imputation panel, enhancing marker coverage and PRS accuracy.

Fluorescence visualization of deep-buried hollow organs

This paper develops bright fluorophores and uses heavy water to improve fluorescence imaging of deep-buried hollow organs, achieving better visualization and diagnosis.

KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population

The paper imputes KIR gene content from SNPs in the Finnish population with high accuracy using a stand-alone model trained on biobank data.

OaAEP1-mediated PNA-protein conjugation enables erasable imaging of membrane protein

This paper introduces a method for site-specific conjugation of proteins to PNA using a strict protein ligase, enabling erasable imaging of membrane proteins.

Simultaneous Optimization of Excitation Wavelength and Emission Window for Semiconducting Polymer Nanoparticles to Improve Imaging Quality

This study optimizes excitation wavelength and emission window for SPNs to improve imaging quality, showing L1057 NPs achieve superior resolution and signal-to-background ratio in the NIR-IIb window.

Increasing calling accuracy, coverage, and read depth in sequence data by the use of haplotype blocks

The paper introduces HBimpute, an imputation pipeline that improves calling accuracy, coverage, and read depth from low-read-depth sequencing data, achieving results comparable to high-density arrays.

Novel design of imputation-enabled SNP arrays for breeding and research applications supporting multi-species hybridisation

The paper introduces a novel SNP array design for multi-species hybridisation in breeding and research, demonstrating its utility in wheat and barley with high-resolution data and imputation capabilities.

Adjustment for SNPs instead of demographic and clinical covariates in GWAS

This study evaluates imputation methods for ancient DNA data using Beagle 4.0 and 1000 Genomes reference data, showing high accuracy at low coverage and benefits of phased references and low-coverage samples.

Deep Learning-powered Bessel-beam Multi-parametric Photoacoustic Microscopy

This paper develops a Bessel-beam multi-parametric photoacoustic microscopy system enhanced by deep learning to improve quantitative imaging of hemoglobin concentration, oxygen saturation, and cerebral blood flow in live mouse brains.

Isotropic Three-Dimensional Dual-Color Super-Resolution Microscopy with Metal-Induced Energy Transfer

The paper combines MIET imaging with dSTORM to achieve isotropic 3D super-resolution and dual-color imaging of sub-cellular structures.

Self-confocal NIR-II fluorescence microscopy for in vivo imaging

This paper introduces self-confocal NIR-II fluorescence microscopy systems for in vivo imaging, improving adjustability and enabling cerebrovascular and hepatic imaging.

Nfeature: A platform for computing features of nucleotide sequences

Nfeature computes a large number of features for DNA and RNA sequences, providing a standalone package and web platform for researchers.

PIPP: Improving peptide identity propagation using neural networks

The paper introduces an embedding-based method for peptide identity propagation that improves missing value reduction and false discovery rate estimation in mass spectrometry data.

Fast volumetric imaging with line-scan confocal microscopy by an electro-tunable lens

This paper introduces an electro-tunable lens in line-scan confocal microscopy to enable fast volumetric imaging with high acquisition rates and depth resolution.

Performance of genetic imputation across commercial crop species

The paper demonstrates accurate genetic imputation in maize, sugar beet, and wheat without pedigrees, outperforming Beagle 5.1 in most scenarios.

Label-free adaptive optics single-molecule localization microscopy for whole animals

This paper develops a label-free adaptive optics method for SMLM, enabling deep-tissue super-resolution imaging in whole animals by correcting tissue aberrations.

A general design of caging-group free photoactivatable fluorophores for live-cell nanoscopy

This paper introduces a method to create caging-group free photoactivatable fluorophores for live-cell nanoscopy, demonstrating their utility in multiple superresolution techniques.

Genome-wide Imputation Using the Practical Haplotype Graph in the Heterozygous Crop Cassava

The paper demonstrates the effectiveness of the Practical Haplotype Graph for genotype imputation in the highly heterozygous crop cassava, achieving higher accuracy than Beagle.

Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation

The paper develops a wheat haplotype graph database for efficient genotype storage and imputation, showing improved accuracy over existing methods.

Enhanced fluorescence from semiconductor quantum dot-labelled cells excited at 280 nm

This study compares 280 nm and 365 nm excitation of semiconductor quantum dots in cells, finding higher fluorescence intensity and no increased photobleaching at 280 nm.

Constructing germline research cohorts from the discarded reads of clinical tumor sequences

The paper demonstrates that discarded tumor sequencing reads can be used to impute germline genotypes, enabling the construction of large germline research cohorts from existing clinical data.

AN ECONOMIC, SQUARE-SHAPED FLAT-FIELD ILLUMINATION MODULE FOR TIRF-BASED SUPER-RESOLUTION MICROSCOPY

The paper introduces a cost-effective flat-field illumination module for TIRF-based super-resolution microscopy to address uneven illumination issues.

Evaluating de novo assembly and binning strategies for time-series drinking water metagenomes.

This study evaluates assembly and binning strategies for time-series drinking water metagenomes to maximize the recovery of high-quality MAGs.

De-noising Spatial Transcriptomics Data Based on Position and Image Information

This paper develops Sprod, a method to denoise spatial transcriptomics data using location and image information, improving downstream analyses.

CpG Transformer for imputation of single-cell methylomes

The paper introduces CpG Transformer, a model for imputing single-cell methylomes, achieving state-of-the-art performance on scBS-seq and scRRBS-seq datasets.

CPExtract, a Software for the Automated Tracer-Based Pathway Specific Screening of Secondary Metabolites in LC-HRMS Data

CPExtract automatically searches LC-HRMS data for user-defined isotopolog patterns from labeled tracers, enabling pathway-specific metabolite detection in fungi.

Expanding the pool of public controls for GWAS via a method for combining genotypes from arrays and sequencing

This paper introduces a method to combine genotypes from genotyping arrays and whole genome sequencing to expand public controls for GWAS, improving power for non-European ancestries.

Sodium sulfite as a switching agent for single molecule based super-resolution optical microscopy

The paper demonstrates that sodium sulfite can act as a switching agent in super-resolution microscopy, simplifying buffer solutions and enabling techniques like dSTORM and SOFI.

Deep-Learning Super-Resolution Microscopy Reveals Nanometer-Scale Intracellular Dynamics at the Millisecond Temporal Resolution

This paper introduces a deep learning method for single-frame super-resolution microscopy, enabling live-cell imaging at nanometer-scale spatial and millisecond temporal resolutions.