imputation

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

Creating Artificial Human Genomes Using Generative Models

This study uses generative models to create artificial human genomes that can improve genetic research without compromising privacy.

Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx)

This paper introduces TREx, a modified expansion microscopy method that achieves ten-fold sample expansion without specialized equipment, enabling high-resolution imaging of both thick tissue sections and cultured cells.

Consequences of the Nyquist-Shannon sampling criterion in Mesoscopic Multiphoton Microscopy to avail full-field sub-micron resolution resolvability

This paper addresses the Nyquist-Shannon sampling limitation in mesoscopic multiphoton microscopy, demonstrating a method to achieve high-resolution imaging without compromising speed or photon budget.

Laser-free super-resolution microscopy

This paper demonstrates laser-free super-resolution microscopy using a conventional microscope and deep blue excitation, achieving 90 nm resolution on mouse and amphibian meiotic chromosomes.

metabaR : an R package for the evaluation and improvement of DNA metabarcoding data quality

metabaR is an R package that improves DNA metabarcoding data quality by identifying artefacts, assessing filtering thresholds, and providing visualisation tools for ecological analysis.

Fluorescence-based 3D targeting of FIB-SEM acquisition of small volumes in large samples

The paper presents a method to precisely target FIB-SEM acquisition of fluorescently labeled cells in large samples using fluorescence preservation and confocal imaging.

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

This paper introduces DEWAKSS, a method for denoising single-cell genomics data by optimally tuning kNN- and diffusion-based approaches to preserve biological variance and improve clustering.

Nebulosa recovers single cell gene expression signals by kernel density estimation

Nebulosa recovers gene expression signals in single-cell data using kernel density estimation to address drop-out and low expression issues.

Optimal recovery of missing values for non-negative matrix factorization

This paper develops an algorithm for imputing missing values in non-negative matrix factorization, showing it performs as well as or better than existing methods.

Automated Workflow For Peptide-level Quantitation From DIA/ SWATH-MS Data

The paper describes an open-source workflow for peptide-level quantitation from DIA/SWATH-MS data using Docker-based containerization.

Efficient phasing and imputation of low-coverage sequencing data using large reference panels

This study introduces GLIMPSE, a method for efficient phasing and imputation of low-coverage sequencing data, showing improved accuracy and cost-effectiveness compared to existing methods.

Compressed sensing-based super-resolution ultrasound imaging for faster acquisition and high quality images

This paper introduces an L1H-CS based SRUS imaging technique that improves image quality and reduces acquisition time for visualizing microvasculature in vivo.

Design of a radial multi-offset detection pattern for in vivo phase contrast imaging of the retinal ganglion cells in humans

This paper designs a radial multi-offset detection pattern for in vivo phase contrast imaging of human retinal ganglion cells, achieving improved contrast and robustness compared to previous methods.

SeqRepo: A system for managing local collections biological sequences

SeqRepo is a system for managing local biological sequence collections, offering performance benefits and a new identifier convention for seamless integration of public and private sequences.

Confocal imaging capacity on a widefield microscope using a spatial light modulator

This paper enhances widefield microscopes with a spatial light modulator to achieve confocal-like optical sectioning, improving visualization of dim neuronal fibers in C. elegans.

Flexible multiplane structured illumination microscope with a four-camera detector

The paper introduces a multi-camera structured illumination microscope that captures 3D fluorescent images without axial movement, enabling rapid 3D imaging modes.

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

PTM-Shepherd automates analysis of post-translational modifications from open search proteomics data, improving detection of artifacts and biases across experiments.

Optimized cryo-EM data acquisition workflow by sample thickness determination

This paper optimizes cryo-EM data acquisition by determining sample thickness before collection, improving efficiency and reducing suboptimal image capture.

High-speed, multicolor, structured illumination microscopy using a hexagonal single mode fiber array

This paper introduces a fiber-based structured illumination microscopy technique that achieves high-speed, multicolor imaging with improved spectral efficiency.

High-resolution population-specific recombination rates and their effect on phasing and genotype imputation

The paper maps high-resolution recombination rates in Finns and compares their impact on phasing and imputation to non-Finnish Europeans, finding minimal effect on accuracy.

Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations

The paper introduces a method to phase and impute genotypes of missing parents in bi-parental plant populations, achieving high accuracy for both parents and their descendants.

FITs: Forest of imputation trees for recovering true signals in single-cell open chromatin profiles

FITs recovers true signals from sparse and noisy single-cell open-chromatin profiles by using a forest of imputation trees to avoid bias and preserve cell-type-specific activity.

Investigating the accuracy of imputed genotypes in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

The paper evaluates imputation accuracy in Nellore cattle using two bovine genome assemblies, showing improved accuracy with larger reference and target panels.

Breaking the limit of 3D fluorescence microscopy by dual-stage-processing network

This paper introduces a dual-stage deep-learning network to enhance 3D fluorescence microscopy resolution and throughput, achieving faster imaging with improved contrast and subcellular detail.

Fast retrograde access to projection neuron circuits underlying vocal learning in songbirds

The paper introduces a viral tool for fast retrograde labeling of projection neurons in songbirds and mice, enabling detailed analysis of vocal learning circuits.

I-Impute: a self-consistent method to impute single cell RNA sequencing data

I-Impute is a self-consistent imputation method for scRNA-seq data that outperforms existing tools in correlation and clustering accuracy on both simulated and real datasets.

MINSTED fluorescence localization and nanoscopy

The paper introduces MINSTED, a STED-based super-resolution microscopy method that achieves high localization precision with reduced fluorophore bleaching, and demonstrates its application in imaging Mic60 proteins in human cells.

Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images

This paper develops a deep-learning method to denoise and reconstruct SR-SIM images, improving image quality and robustness across varying noise levels and microscope settings.

A red fluorescent protein with improved monomericity enables ratiometric voltage imaging with ASAP3

The paper develops a ratiometric voltage indicator by fusing an improved red fluorescent protein to ASAP3, enabling motion artifact-free voltage imaging in motile cells.