imputation

Rapid and accurate multi-phenotype imputation for millions of individuals

The paper introduces PIXANT, a multi-phenotype imputation method that improves GWAS power by imputing 425 phenotypes for 277,301 individuals, leading to the discovery of 18.4% more GWAS loci.

Integration and querying of multimodal single-cell data with PoE-VAE

This paper introduces a VAE-based model for integrating multimodal single-cell data, showing it can map queries across modalities and improve data imputation and biological discovery.

Using Beads as a Focus Fiduciary to Aid Software-based Autofocus Accuracy in Microscopy

This paper describes using microbeads to improve autofocus accuracy in brightfield microscopy for long-term live cell imaging.

A Novel Efficient Algorithm for Common Variants Genotyping from Low-Coverage Sequencing Data

The paper introduces Limpute, an efficient algorithm for genotyping common variants from low-coverage sequencing data, achieving high imputation accuracy with faster runtime than GLIMPSE2.

Plasma membrane labelling efficiency, internalization and partitioning of functionalized fluorescent lipids as a function of lipid structure

This study compares lipid-based probes for plasma membrane labeling in live, fixed, and permeabilized cells, identifying a superior probe based on its lipid structure.

Cellularly-Retained Fluorogenic Probes for Sensitive Cell-Resolved Bioactivity Imaging

This paper develops a fluorogenic probe scaffold that retains fluorescent products within cells to improve imaging sensitivity and resolution for quantifying low-turnover biological processes.

An open-sourced 3D printable microscope with a large CNC stage

The paper presents an open-source 3D-printable microscope designed for molecular biology applications, featuring a CNC stage and customizable optical components.

Penalized likelihood optimization for censored missing value imputation in proteomics

The paper introduces Pirat, a method for imputing missing values in proteomics data by modeling instrument limits and peptide correlations, showing improved performance over existing methods.

Three-dimensional single-cell transcriptome imaging of thick tissues

This paper introduces a 3D MERFISH method for imaging thick tissues, demonstrating its application on mouse brain sections with high accuracy.

pyALRA: python implementation of low-rank zero-preserving approximation of single cell RNA-seq

pyALRA provides a Python implementation of ALRA for imputing dropouts in single-cell RNA-seq with improved speed and memory efficiency.

Obtaining super-resolved images at the mesoscale through Super-Resolution Radial Fluctuations

This paper demonstrates a method to achieve high-resolution imaging over a large field of view using SRRF and Mesolens, achieving 446.3 nm resolution with minimal error.

EpiAgent: Foundation model for single-cell epigenomic data

EpiAgent is a foundation model for single-cell epigenomic data that excels in feature extraction, cell annotation, and data imputation.

Evaluation of imputation performance of multiple reference panels in a Pakistani population

This study evaluates imputation performance of reference panels in a Pakistani population, finding that ex1KG outperforms TOPMed despite its smaller size.

A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations

The paper describes a cost-effective, high-throughput genotyping method for heterogeneous stock rats using low-coverage sequencing data, achieving high accuracy comparable to high-coverage sequencing.

Nanobodies against the myelin enzyme CNPase as tools for structural and functional studies

This paper develops nanobodies against CNPase, showing distinct epitopes and functional applications in imaging and as intrabodies.

Local Haplotype Classifiers enable Efficient, Flexible, and Secure Genotype Imputation and Downstream Analyses

The paper introduces a privacy-preserving genotype imputation method using haplotype classifiers, improving accuracy and throughput compared to linear models.

Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning

The paper introduces a deep learning model to augment cancer cell line multi-omic data, increasing the number of profiles and uncovering drug resistance mechanisms.

Whole-Brain Three-Dimensional Imaging of RNAs at Single-Cell Resolution

The paper develops TRIC-DISCO, a pipeline for whole-brain 3D RNA imaging in adult mice, enabling single-cell resolution of transcriptional signatures and markers without strict RNase-free conditions.

Benchmarking for genotyping and imputation using degraded DNA for forensic applications across diverse populations

This paper benchmarks genotyping and imputation methods for degraded DNA in forensic applications across diverse populations, finding that ATLAS outperforms conventional tools and that reference panel diversity improves accuracy.

Harmonic imaging for nonlinear detection of acoustic biomolecules

This study introduces harmonic xAM (HxAM) imaging to improve GV detection sensitivity and imaging depth in vivo.

Improving genome-scale metabolic models of incomplete genomes with deep learning

This paper introduces DNNGIOR, a deep learning method to improve genome-scale metabolic models of incomplete genomes by imputing missing reactions based on reaction frequency and phylogenetic distance.

Long axial-range double-helix point spread functions for 3D volumetric super-resolution imaging

This paper introduces long axial-range double-helix PSFs for 3D super-resolution imaging, enabling stitching-free imaging of whole mammalian cells with improved speed and resolution.

Cytometry Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper

The paper introduces cyMAE, a masked autoencoder for automated immunophenotyping, showing it improves accuracy and interpretability over manual methods in cytometry data analysis.

CpGPT: a Foundation Model for DNA Methylation

CpGPT is a foundation model for DNA methylation analysis that outperforms specialized models in aging-related tasks and can impute methylation profiles across diverse conditions.

Flowtigs: safety in flow decompositions for assembly graphs

This paper introduces flowtigs, a characterization of safe walks for flow decompositions in general graphs, and demonstrates their application to improve metagenomic assembly contiguity.

Low-Rank Full Matrix Factorization for dropout imputation in single cell RNA-seq and benchmarking with imputation algorithms for downstream applications

This paper develops an imputation algorithm for single-cell RNA-seq and benchmarks it against other methods across various downstream analyses.

GrapHiC: An integrative graph based approach for imputing missing Hi-C reads

GrapHiC improves Hi-C read imputation by integrating Hi-C and ChIP-seq data in a graph framework, enhancing performance on sparse and cross-cell-type inputs.

Exploring transient states of PAmKate to enable improved cryogenic single-molecule imaging

This study investigates the photophysical properties of PAmKate to enhance cryogenic single-molecule imaging by improving emitter localization rates through a 2-color bleaching process.

Targeted Photoactivatable Green-Emitting BODIPY Based on Directed Photooxidation Induced Activation and its Application to Live Dynamic Super-Resolution Microscopy

This paper develops a green-emitting photoactivatable BODIPY dye with a new photoactivation mechanism and demonstrates its use in live-cell super-resolution microscopy.

Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research

The paper describes the development of a web platform for Cannabis sativa multi-omics research, integrating datasets and providing APIs for omics analyses.