Kay Nieselt

The PhageExpressionAtlas reveals shared and unique transcriptional patterns across phage-host interactions

The PhageExpressionAtlas provides a unified resource for time-resolved dual RNA-sequencing data from phage infections, enabling analysis of shared and unique transcriptional patterns across phage-host interactions.

PneumoWiki: A pan-genome-based database for the pathogen Streptococcus pneumoniae

PneumoWiki is a pan-genome database for Streptococcus pneumoniae that integrates genomic data and functional annotations across 43 strains to support research and data analysis.

TSSpredator-Web: A web-application for transcription start site prediction and exploration

TSSpredator-Web provides an interactive web tool for predicting and exploring transcription start sites from RNA-seq data in prokaryotes.

Gradient boosting regression and convolution improve deconvolution of bulk transcriptomes

GrooD improves bulk transcriptome deconvolution using gradient boosting and convolution, showing better performance and interpretability on human blood samples from sepsis patients.

The E. coli PeptideAtlas Build: Characterizing the observed Escherichia coli pan-proteome and its post-translational modifications

The paper presents the E. coli PeptideAtlas build, a comprehensive pan-proteome resource covering 4,755 proteins and over 10,000 PTM sites from 40 datasets.

Beyond commensalism: Genomic insights into micrococcin P1-producing Staphylococcus chromogenes

This study identifies MP1-producing S. chromogenes strains with antimicrobial activity and low virulence, suggesting their role as protective commensals in dairy ruminants.

Identification of the negamycin split biosynthetic gene cluster in Kitasatospora purpeofusca ATCC21470

This study identifies and characterizes the negamycin biosynthetic gene cluster in Kitasatospora purpeofusca, enabling scalable production through heterologous expression.

Sequence variability of BamA and FadL candidate vaccinogens suggests divergent evolutionary paths of Treponema pallidum outer membrane proteins

The paper analyzes sequence variability of BamA and FadL outer membrane proteins in 186 Treponema pallidum strains to identify evolutionary patterns and vaccine targets.

A new typing scheme demonstrates high discriminatory power for Treponema pallidum subspecies

This paper introduces a new MLST scheme for Treponema pallidum subspecies with high discriminatory power, validated using global clinical samples and showing distinct genetic clusters.

Genetic modification of intractable staphylococcal clones by heat-shock facilitated phage transduction

This paper introduces a method to genetically modify intractable staphylococcal clones using heat-shock facilitated phage transduction, enabling DNA introduction into bacteria with restriction barriers.

Biotic interactions shape infection outcomes in Arabidopsis

This study identifies key microbial taxa associated with health and disease in Arabidopsis by analyzing microbiome data and using machine learning to distinguish infected from uninfected plants.

TSS-Captur: A User-Friendly Characterization Pipeline for Transcribed but Unclassified RNA transcripts

TSS-Captur characterizes unclassified TSSs by classifying transcripts, predicting termination sites, and analyzing promoter motifs to improve prokaryotic transcriptome understanding.

Multiple regulators control the biosynthesis of brasilicardin in Nocardia terpenica

This study identifies and characterizes transcriptional regulators involved in the biosynthesis of brasilicardin in Nocardia terpenica, revealing their regulatory roles and interactions.

OmicsTIDE: Interactive Exploration of Trends in Multi-Omics Data

OmicsTIDE provides an interactive visualization tool to explore trends in multi-omics data by clustering and comparing regulatory trends across different experimental designs.

Technical report on best practices for hybrid and long read de novo assembly of bacterial genomes utilizing Illumina and Oxford Nanopore Technologies reads

This paper evaluates long read and hybrid assemblers for bacterial genome assembly using Illumina and Oxford Nanopore data, finding that hybrid approaches reduce error rates compared to long reads alone.

DamageProfiler: Fast damage pattern calculation for ancient DNA

DamageProfiler is a Java-based tool for analyzing damage patterns in ancient DNA, providing user-friendly interfaces and output formats for integration into analysis pipelines.

Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production

The paper compares metabolic differences between Streptomyces coelicolor strains M1152 and M145 using omics data and a genome-scale model to identify metabolic changes affecting heterologous compound production.

Efficient Merging of Genome Profile Alignments

The paper introduces GPA, a method that efficiently merges genome profile alignments to produce large-scale whole-genome alignments much faster than conventional methods.

African Nonhuman Primates Are Infected With The Yaws Bacterium Treponema pallidum subsp. pertenue

The paper identifies naturally occurring simian Treponema pallidum subsp. pertenue strains in African nonhuman primates, showing genomic similarity to human TPE strains.

Origin of modern syphilis and emergence of a contemporary pandemic cluster

This study analyzes the genetic patterns of modern syphilis strains and identifies a globally dominant pandemic cluster with azithromycin resistance.