Our publications

Over the years, researchers at the Hanze Sequency Facility have gained extensive insights and developed advanced sequencing solutions. This has resulted in a numerous amount of publications. A selection of these publications is presented below.

2025

• Impact of expression systems on the transcriptome of Bacillus subtilis: insights for enhanced production of glutaminase PrgA. (Biwen Wang) 
• Ribosome pausing in amylase producing Bacillus subtilis during long fermentation. (Biwen Wang)

2024

• Inactivation of the conserved protease LonA increases production of xylanase and amylase in Bacillus subtilis. (Biwen Wang) 
• Engineering a cleaved, prefusion-stabilized influenza B virus hemagglutinin by identification and locking of all six pH switches. (Fin Milder)
• Membrane depolarization kills dormant Bacillus subtilis cells by generating a lethal dose of ROS. (Biwen Wang)
• Development of a split-luciferase assay to establish optimal protein secretion conditions for protein production by Bacillus subtilis. (Biwen Wang)
• Improving gene set enrichment analysis (GSEA) by using regulation directionality. (Biwen Wang) 

2023

• A proteomics approach to identify COPD-related changes in lung fibroblasts. (Wynand Alkema)
• Enhancing breadth and durability of humoral immune responses in non-human primates with an adjuvanted group 1 influenza hemagglutinin stem antigen. (Fin Milder) 
• Induction of the CtsR regulon improves Xylanase production in Bacillus subtilis. (Biwen Wang) 
• Metabolic and chromosomal changes in a Bacillus subtilis whiA mutant. (Biwen Wang) 
• Dual Action of Eeyarestatin 24 on Sec-Dependent Protein Secretion and Bacterial DNA. (Biwen Wang)

2022

• A proteomics approach to identify COPD-related changes in lung fibroblasts. (Wynand Alkema)
• Enhancing breadth and durability of humoral immune responses in non-human primates with an adjuvanted group 1 influenza hemagglutinin stem antigen. (Fin Milder) 
• Induction of the CtsR regulon improves Xylanase production in Bacillus subtilis. (Biwen Wang) 
• Metabolic and chromosomal changes in a Bacillus subtilis whiA mutant. (Biwen Wang) 
• Dual Action of Eeyarestatin 24 on Sec-Dependent Protein Secretion and Bacterial DNA. (Biwen Wang)

2021

• Charting host-microbe co-metabolism in skin aging and application to metagenomics data. (Wynand Alkema)
• A circadian clock in a nonphotosynthetic prokaryote. (Jasper Bosman / Hanze DataLab)
• Different Resource Allocation in a Bacillus subtilis Population Displaying Bimodal Motility. (Biwen Wang)
• A flat embedding method for transmission electron microscopy reveals an unknown mechanism of tetracycline. (Biwen Wang)
• Maternal pre-pregnancy overweight and neonatal gut bacterial colonization are associated with cognitive development and gut microbiota composition in pre-school-age offspring. (Wynand Alkema)
• Blood-Based Immune Profiling Combined with Machine Learning Discriminates Psoriatic Arthritis from Psoriasis Patients. (Wynand Alkema)
• High throughput screening of technological and biopreservation traits of a large set of wild lactic acid bacteria from Brazilian artisanal cheeses. (Wynand Alkema)

2020

• Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data. (Ronald Wedema / Hanze DataLab)
• Live Biotherapeutic Products, A Road Map for Safety Assessment. (Wynand Alkema)
• Magnesium prevents vascular calcification in Klotho deficiency. (Wynand Alkema)

2019

• Biosynthetic homeostasis and resilience of the complement system in health and infectious disease. (Wynand Alkema)
• Multiple Interactions Between Cancer Cells and the Tumor Microenvironment Modulate TRAIL Signaling: Implications for TRAIL Receptor Targeted Therapy. (Margot de Looff)
• Are There Circadian Clocks in Non-Photosynthetic Bacteria? (Jasper Bosman / Hanze DataLab)

2018

• An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae. (Ronald Wedema / Hanze DataLab)
• Magnesium deficiency prevents high-fat-diet-induced obesity in mice. (Wynand Alkema)
• Primary cilia-regulated transcriptome in the renal collecting duct. (Wynand Alkema)
• Evidence for multiple modes of neutrophil serine protease recognition by the EAP family of Staphylococcal innate immune evasion proteins. (Fin Milder)

2016

• Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis. (Wynand Alkema)
• Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5. (Wynand Alkema)
• High-throughput screening of a large collection of non-conventional yeasts reveals their potential for aroma formation in food fermentation. (Wynand Alkema)
• Economic Evaluations of Pharmacogenetic and Pharmacogenomic Screening Tests: A Systematic Review. Second Update of the Literature. (Margot de Looff)