René L. Warren

ntSynt-viz: Visualizing synteny patterns across multiple genomes

ntSynt-viz sorts genomes and chromosomes by synteny, normalizes strands, and draws chromosome-painting ribbon plots easier to interpret than NGenomeSyn output for human and hoverfly genomes.

Pathogen-specific antimicrobial activity prediction with biological large language model-based methods

The paper introduces triAMPh, a framework for predicting pathogen-specific antimicrobial peptide activity using biological large language models, showing it matches or outperforms existing methods.

aaKomp: Alignment-free amino acid k-mer matching for genome completeness assessment at scale

aaKomp provides a fast, memory-efficient, alignment-free method for genome completeness assessment, outperforming existing tools in speed and scalability.

Concordance and dissonance: A genome-wide analysis of self-declared versus inferred ancestry in 10,250 participants from the HostSeq cohort

The paper compares self-declared and genome-inferred ancestry in 10,250 HostSeq participants, finding high concordance for some groups and lower for others, highlighting the complexity of admixture and the need for complementary approaches.

Multi-genome synteny detection using minimizer graph mappings

The paper introduces ntSynt, a tool for detecting multi-genome synteny blocks using minimizer graphs, showing high coverage and efficiency across diverse genomes.

Efficacy and safety evaluation of artificial intelligence-identified antimicrobial peptides for use against avian pathogenic Escherichia coli in the poultry industry

This study evaluates three AI-identified antimicrobial peptides for efficacy and safety against avian pathogenic Escherichia coli in poultry, showing improved survival and immune modulation without adverse effects.

Mining the UniProtKB/Swiss-Prot database forantimicrobial peptides

The paper identifies novel antimicrobial peptides from the UniProtKB/Swiss-Prot database using AMPlify, prioritizing 40 for chicken applications and testing 38 for antimicrobial activity.

GoldPolish-Target: Targeted long-read genome assembly polishing

GoldPolish-Target polishes targeted regions of genome assemblies, reducing errors and improving accuracy with lower computational demands.

ntRoot: Computational Inference of Human Ancestry at Scale from Genomic Data

ntRoot infers human super-population ancestry from genomic data with high accuracy and efficiency, outperforming traditional methods on large datasets.

GoldRush: A de novo long read genome assembler with linear time complexity

GoldRush is a de novo long read genome assembler with linear time complexity, achieving efficient assembly of large genomes with high contiguity and low memory usage.

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

RNA-Bloom2 is a reference-free transcriptome assembler for long-read data, showing competitive performance with reference-based methods and lower resource usage.

aaHash: recursive amino acid sequence hashing

aaHash is a recursive amino acid sequence hashing algorithm that improves speed and sensitivity for protein sequence analysis.

Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

Meta-NanoSim simulates and characterizes nanopore metagenomic data to improve microbial abundance estimation and guide algorithm development.

AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens

AMPlify is a deep learning model that predicts antimicrobial peptides from bullfrog genomes, identifying novel peptides effective against WHO priority pathogens including drug-resistant bacteria.

LongStitch: High-quality genome assembly correction and scaffolding using long reads

LongStitch improves draft genome assemblies using long reads, significantly increasing contiguity and accuracy compared to existing methods.

Retrospective in silico HLA predictions from COVID-19 patients reveal alleles associated with disease prognosis

The paper uses in silico HLA predictions from COVID-19 patients to identify alleles associated with disease prognosis, finding significant associations with A*11:01, C*04:01, and DQA1*01:02.

ntHits: de novo repeat identification of genomics data using a streaming approach

ntHits identifies repeat elements in genomics data using a streaming algorithm, efficiently detecting repetitive k-mers with high accuracy and low resource usage.

RNA-Bloom provides lightweight reference-free transcriptome assembly for single cells

RNA-Bloom is a de novo RNA-seq assembler for scRNA-seq data that reconstructs cell-specific isoforms and detects gene fusions, outperforming bulk RNA-seq methods.

Trans-NanoSim characterizes and simulates nanopore RNA-seq data

Trans-NanoSim simulates nanopore RNA-seq reads using features learned from real data, enabling cost-effective development of analytical tools.

Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

The paper sequences and assembles the largest complete mitochondrial genome of a gymnosperm, Sitka spruce, revealing a complex multipartite structure.

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs

ntJoin improves genome assemblies using reference sequences through a lightweight graph-based method, achieving faster and more memory-efficient results than existing tools.

Establishment of an eHAP1 Human Haploid Cell Line Hybrid Reference Genome Assembled from Short and Long Reads

The paper generates a high-quality hybrid reference genome for the eHAP1 haploid cell line using long and short reads, identifies structural variants, and highlights their potential regulatory impact.

ntEdit: scalable genome sequence polishing

ntEdit is a genome polishing tool that efficiently corrects base errors in genomic sequences across various species and coverage levels.

Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

Tigmint corrects genome assembly errors using linked reads from long molecules, improving assembly contiguity and reducing misassemblies.

Pan-cancer analysis reveals complex tumor-specific alternative polyadenylation

The paper analyzes APA patterns in 114 cancer-related genes across 33 cancer types to show complex 3 UTR cleavage changes in tumors.

ARKS: chromosome-scale scaffolding of human genomedrafts with linked read kmers

ARKS improves human genome assemblies using linked read kmers, achieving five-fold better contiguity than baseline methods.

Visualizing genome synteny with xmatchview

The paper introduces xmatchview and xmatchview-conifer, two Python tools for visualizing genome synteny and comparing genomes.

It’s okay to be green: Draft genome of the North American bullfrog (Rana [Lithobates] catesbeiana)

The paper reports the first draft genome of the North American bullfrog, providing genomic resources for amphibian research and supporting taxonomic classification.

ARCS: Assembly Roundup by Chromium Scaffolding

ARCS uses Chromium linked read barcoding information to improve draft genome contiguity, increasing contiguity six-fold with moderate coverage.

Overlapping long sequence reads: Current innovations and challenges in developing sensitive, specific and scalable algorithms

The paper reviews and benchmarks overlap detection tools for error-prone long reads, evaluating their performance, efficiency, and scalability.