deconvolution

Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation

This study evaluates how k-mer based tools affect abundance estimation in metagenomic data with closely related references, showing differential performance based on sample-reference distance and reference similarity.

Using Mapping-Profiles to Refine Strain-Level Metagenomic Classification

StrainRefine improves strain-level metagenomic classification by refining read mappings using profile similarity, reducing false positives while maintaining accuracy.

From variability to consensus: rescoring harmonizes peptide identification across diverse search engines and datasets

This study benchmarks rescoring methods across proteomics search engines and datasets, finding that prediction-based approaches improve identification consensus and reduce variability.

Verification of nanopore sequencing technology for clinical carbapenem-resistant Enterobacterales surveillance

This study verifies nanopore sequencing for CRE surveillance by comparing it to routine diagnostics and determining required sequencing depths for various clinical tasks.

Extended t-cores for the de novo identification of transposable elements and other inexact repeats from short read RNAseq data

This paper introduces a de novo method to identify transposable elements and inexact repeats from RNA-seq data without a reference genome, showing effectiveness in both model and non-model species.

Cross-architecture ensembling of DNA foundation models improves the precision and stability of chimera detection in long-read metagenomic bins

The paper evaluates DNA foundation models for chimera detection in long-read metagenomic bins, finding that ensembling improves precision over single models.

BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences

BINSEQ introduces binary formats for sequencing data to enable faster parallel processing, reducing analysis time for genome and transcriptome studies.

Two Novel Genes, Stb23 and Stb24, Conferring Multi-stage Resistance to Zymoseptoria tritici: Rapid Deployment in Marker-Assisted Wheat Breeding

This study identifies two new resistance loci, Stb23 and Stb24, against Zymoseptoria tritici and develops KASP markers for their use in wheat breeding.

A Conditional Random Field approach for de novo reconstruction of bacterial haplotypes from a de Bruijn graph representation

This paper introduces HaploDetox, a method for de novo bacterial haplotype reconstruction using a Conditional Random Field approach on de Bruijn graphs, achieving improved SNP phasing accuracy.

Automated refinement of metagenomic bins and estimation of binning success using itBins

itBins refines metagenomic bins and estimates binning success using %GC content, coverage, and taxonomy, outperforming existing tools in speed and accuracy.

Systematic errors in enzymatic conversion limit cell-free DNA methylation specificity

The paper identifies a systematic over-conversion error in EM-seq that introduces false-positive methylation signals in cfDNA analysis.

NanoSimFormer: An end-to-end Transformer-based simulator for nanopore sequencing signal data

NanoSimFormer generates high-fidelity nanopore sequencing signals optimized for accurate basecalling, outperforming existing simulators across multiple datasets and tasks.

A General Framework for Branch Length Estimation in Ancestral Recombination Graphs

This paper introduces POLEGON, a method for estimating branch lengths in Ancestral Recombination Graphs using uninformative priors, showing improved coalescence time estimates and population size inferences.

Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index

Cleanifier removes human contamination from microbial sequences using a pangenome index and spaced seeds, achieving speed and accuracy comparable to existing tools.

Benchmarking of Human ReadRemoval Strategies for Viral andMicrobial Metagenomics

The paper benchmarks human read removal methods in metagenomics, finding that high-sensitivity Bowtie2 with T2T-CHM13 reference improves removal while preserving microbial data.

Treasure: A Sensitive Pipeline for Species-Level and Functional Microbiome Profiling

The paper introduces a pipeline for functional microbiome profiling using NGS data, showing improved performance over existing methods in analyzing gastric cancer-associated microbiomes.

Population genetic assessment of marine megafauna using seawater environmental DNA: a case study of whale sharks from the Ningaloo Coast World Heritage Area.

This paper develops a genetic toolkit using seawater environmental DNA to study whale shark populations, showing that microhaplotype markers can reliably genotype individuals and capture population-level genetic diversity.

StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples

Development and optimization of the host DNA depletion in blood cultures using a saponin and SAN nucleases-based method

This paper develops and optimizes a method using saponin and SAN nucleases to deplete host DNA from blood cultures, improving bacterial DNA extraction for sepsis diagnosis.

Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools

This study examines differences between Infinium MethylationEPIC v1 and v2, showing high array-level concordance but probe-level variation, and recommends accounting for version differences in analyses.

Genetic deconvolution of embryonic and maternal cell-free DNA in spent culture medium of human preimplantation embryos through deep learning

This paper introduces DECENT, a deep learning method to reconstruct embryonic copy number variations and reduce maternal DNA contamination in cfDNA from SECM, improving the accuracy of noninvasive preimplantation genetic testing.

Integrating Nanopore MinION Sequencing into National Animal Health AMR Surveillance Programs: An Indonesian Pilot Study of Chicken Slaughterhouse Effluent and Rivers

This study evaluates the integration of Nanopore MinION sequencing into a national AMR surveillance program, comparing its cost-benefit and effectiveness with other methods for monitoring antibiotic-resistant E. coli in slaughterhouse effluent and rivers.

Deacon: fast sequence filtering and contaminant depletion

Deacon efficiently filters and depletes contaminant sequences from large genomic datasets using a human pangenome index, achieving high accuracy and speed with minimal computational resources.

Phase-free local ancestry inference mitigates the impact of switch errors on phase-based methods

This study compares phase-free and phase-based local ancestry inference methods, finding phase-free methods provide more accurate results despite lower phase quality.

Single Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting (SNACS): A tool for demultiplexing single-cell DNA sequencing data

The paper introduces SNACS, a method for demultiplexing single-cell DNA sequencing data using SNPs and cell-surface antibodies, achieving higher accuracy than existing methods.

JMod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics

JMod improves sequence identification and quantification in multiplexed DIA proteomics by jointly modeling overlapping mass spectra, enabling higher throughput with maintained accuracy.

Combined genomic and phenotypic classification of inherited and acquired genetic disease with long-read sequencing

This paper uses long-read sequencing to simultaneously detect genetic variation and methylation, enabling phenotypic classification of inherited and acquired genetic diseases.

devider: long-read reconstruction of many diverse haplotypes

divider reconstructs haplotypes from long-read sequencing data, achieving higher accuracy than existing methods on synthetic and real datasets.

Assessing the performance of current strain resolution tools on long-read metagenomes

This study evaluates three strain resolution tools on long-read metagenomes, finding TRACS excels in haplotype completeness and efficiency, while Strainy shows high haplotype accuracy.

Investigating the Role of Management Decisions in Subspecies Hybridization Across the Wild Turkey's Range

This study examines how management decisions affect subspecies hybridization in wild turkeys, finding that introducing more subspecies and unique source states increases admixture, but not the number of relocated counties.