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List of works by Sacha van Hijum

A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children ⬇️

scientific article

Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis

scientific article

Advances and perspectives in computational prediction of microbial gene essentiality

scientific article published on 08 February 2016

Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice.

scientific article published on 29 August 2015

An In vitro Model for Bacterial Growth on Human Stratum Corneum.

scientific article

Application of state-of-art sequencing technologies to indigenous food fermentations ⬇️

scientific article published on 06 September 2012

BAGEL: a web-based bacteriocin genome mining tool.

scientific article

Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress

scientific article published on 20 January 2014

Characterization of the global impact of low temperature gas plasma on vegetative microorganisms

article

CiVi: circular genome visualization with unique features to analyze sequence elements.

scientific article published on 24 April 2015

Complete Resequencing and Reannotation of the Lactobacillus plantarum WCFS1 Genome ⬇️

scientific article published on January 1, 2012

Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.

scientific article published on 26 March 2010

Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? ⬇️

scientific article published on July 10, 2012

Degenerate target sites mediate rapid primed CRISPR adaptation.

scientific article

Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress

scientific article published on 8 November 2013

Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU

scientific article published on 8 May 2015

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5.

scientific article published on 6 October 2016

Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine.

scientific article published on 12 March 2015

Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland.

scientific article published on 25 November 2015

Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.

scientific article published on 16 March 2017

Draft Genome Sequences of 24 Lactococcus lactis Strains

scientific article published on 30 March 2017

ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.

scientific article

Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains

scientific article published on 10 February 2014

FACIL: Fast and Accurate Genetic Code Inference and Logo

scientific article

Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness

scientific article published on 4 November 2014

Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media.

scientific article

From microbial gene essentiality to novel antimicrobial drug targets

scientific article

Genome Analysis of Moraxella catarrhalis Strain RH4, a Human Respiratory Tract Pathogen

scientific article published in 2012

Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman.

scientific article

Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730).

scientific article published on May 2012

Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1 ⬇️

scientific article published on September 20, 2012

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.

scientific article published on 21 February 2011

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine.

scientific article published on 11 September 2017

Genotype-phenotype matching analysis of 38 Lactococcus lactisstrains using random forest methods ⬇️

scientific article published on March 26, 2013

Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin

scientific article published on 08 October 2016

Gut microbiome in ADHD and its relation to neural reward anticipation

scientific article published on September 2017

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses.

scientific article published on 11 January 2018

MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context.

scientific article

Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.

scientific article published on September 2009

MicroPreP: a cDNA microarray data pre-processing framework.

scientific article

Microbial bioinformatics for food safety and production

scientific article

Microbiome dynamics of human epidermis following skin barrier disruption.

scientific article

Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus

scientific article

Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis.

scientific article published on 29 November 2010

Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877

scientific article published on 25 November 2015

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats

scientific article published on 16 July 2016

PreP: gene expression data pre-processing

scientific article

Primary cilia-regulated transcriptome in the renal collecting duct

scientific article published on 8 February 2018

Projector: automatic contig mapping for gap closure purposes.

scientific article published on November 2003

Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction

scientific article

Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae.

scientific article published on 20 June 2006

Reply to Meisel et al

scientific article published on 22 November 2016

Resequencing of the Lactobacillus plantarum Strain WJL Genome.

scientific article published on 25 November 2015

SIMAGE: simulation of DNA-microarray gene expression data

scientific article

Saturation and quantization reduction in microarray experiments using two scans at different sensitivities

scientific article published on 8 June 2004

Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer.

scientific article published on February 2013

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.

scientific article published on 21 September 2010

Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis

scientific article

Structure-function relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria

scientific article

The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element.

scientific article

The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition

scientific article

The relative value of operon predictions.

scientific article published on 17 April 2008

Transcriptome Analysis of a Spray Drying-Resistant Subpopulation Reveals a Zinc-Dependent Mechanism for Robustness in SK11

scientific article published on 15 October 2018

Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance

scientific article published on May 2006

Transcriptomic signatures of peroxisome proliferator-activated receptor α (PPARα) in different mouse liver models identify novel aspects of its biology

scientific article

Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes.

scientific article published on 20 December 2016

UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons.

scientific article published in August 2003

Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening

scientific article published on 25 March 2016

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