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Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling
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- Journal Article
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Competitive interactions facilitate resistance development against antimicrobials
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- Journal Article
- A1
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Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance
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- Miscellaneous
- open access
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (vol 52, pg 331, 2020)
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- Journal Article
- A1
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Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii
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- Journal Article
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Whole slide imaging-based prediction of TP53 mutations identifies an aggressive disease phenotype in prostate cancer
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- Journal Article
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Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices
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- Journal Article
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Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data
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- Journal Article
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Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium
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- Journal Article
- A2
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Extracting functional insights from loss-of-function screens using deep link prediction
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- Journal Article
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Antibiotic cycling affects resistance evolution independently of collateral sensitivity
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- Journal Article
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Metagenomics to detect and characterize viruses in food samples at genome level? Lessons learnt from a norovirus study
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- Journal Article
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Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence
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- Journal Article
- A1
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BLSSpeller to discover novel regulatory motifs in maize
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- Miscellaneous
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Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data
(2022) -
OMEN : network-based driver gene identification using mutual exclusivity
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Comparative transcriptome analysis of two maize genotypes with different tolerance to salt stress
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- Journal Article
- A1
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Halvade somatic : somatic variant calling with Apache Spark
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- A2
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A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products
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- Journal Article
- A1
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Phylogenomic investigation of increasing fluoroquinolone resistance among Belgian cases of shigellosis between 2013 and 2018 indicates both travel-related imports and domestic circulation
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- Journal Article
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Whole-genome sequencing-based antimicrobial resistance characterization and phylogenomic investigation of 19 multidrug-resistant and extended-spectrum beta-lactamase-positive escherichia coli strains collected from hospital patients in Benin in 2019
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- Journal Article
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Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations
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Whole genome sequencing provides an added value to the investigation of staphylococcal food poisoning outbreaks
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- Journal Article
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Towards real-time and affordable strain-level metagenomics-based foodborne outbreak investigations using Oxford nanopore sequencing technologies
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- Journal Article
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Network-based analysis to identify drivers of metastatic prostate cancer using GoNetic
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- Conference Paper
- C3
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Multifocality in prostate cancer : implications for PAM50 subtyping using an index lesion-only approach
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- Journal Article
- A1
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Dynamic partitioning of search patterns for approximate pattern matching using search schemes
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- Journal Article
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Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes
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DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil
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- Journal Article
- A1
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A bioinformatics whole-genome sequencing workflow for clinical Mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively characterized with conventional methods and in silico approaches
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- Journal Article
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Application of a strain- level shotgun metagenomics approach on food samples : resolution of the source of a Salmonella food-borne outbreak
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- Journal Article
- A1
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Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods
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- Journal Article
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Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals
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- Journal Article
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First detection of a plasmid-encoded New-Delhi metallo-beta-lactamase-1 (NDM-1) producing Acinetobacter baumannii using whole genome sequencing, isolated in a clinical setting in Benin
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- Miscellaneous
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (vol 11, 4748, 2020)
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- Journal Article
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
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- Journal Article
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Sex differences in oncogenic mutational processes
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- Journal Article
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Pan-cancer analysis of whole genomes
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- Journal Article
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Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates
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- Journal Article
- A1
- open access
Development of an NGS-based workflow for improved monitoring of circulating plasmids in support of risk assessment of antimicrobial resistance gene dissemination
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- Journal Article
- A1
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Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus
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- Journal Article
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A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium
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Culture-independent analysis of linuron-mineralizing microbiota and functions in on-farm biopurification systems via DNA-stable isotope probing : comparison with enrichment culture
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- Journal Article
- A1
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The benefits of whole genome sequencing for foodborne outbreak investigation from the perspective of a national reference laboratory in a smaller country
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- Journal Article
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A practical method to implement strain-level metagenomics-based foodborne outbreak investigation and source tracking in routine
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- Journal Article
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Strain-level metagenomic data analysis of enriched in vitro and in silico spiked food samples : paving the way towards a culture-free foodborne outbreak investigation using STEC as a case study
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- Journal Article
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Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples
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- Journal Article
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First detection of a plasmid located carbapenem resistant bla(VIM-1) gene in E. coli isolated from meat products at retail in Belgium in 2015
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- Journal Article
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Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants
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- Journal Article
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Image-based dynamic phenotyping reveals genetic determinants of filamentation-mediated beta-lactam tolerance
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- Journal Article
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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
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- Journal Article
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Combined burden and functional impact tests for cancer driver discovery using DriverPower
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- Journal Article
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Integrative pathway enrichment analysis of multivariate omics data
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- Journal Article
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
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- Journal Article
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Pathway and network analysis of more than 2500 whole cancer genomes
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A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay
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- Journal Article
- A1
- open access
Managing evidence in food safety and nutrition
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- Journal Article
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Detailed evaluation of data analysis tools for subtyping of bacterial isolates based on whole genome sequencing : Neisseria meningitidis as a proof of concept
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- Journal Article
- A1
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IAMBEE : a web-service for the identification of adaptive pathways from parallel evolved clonal populations
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- Journal Article
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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
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Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java
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- Journal Article
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Associating expression and genomic data using co-occurrence measures
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- Journal Article
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Organellar carbon metabolism is co-ordinated with distinct developmental phases of secondary xylem
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Identification of novel genes involved in acetic acid tolerance of Saccharomyces cerevisiae using pooled-segregant RNA sequencing
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- Journal Article
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The Crabtree effect shapes the Saccharomyces cerevisiae lag phase during the switch between different carbon sources
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- Journal Article
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Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5], 12:i:-
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- Journal Article
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1-((2,4-Dichlorophenethyl)amino)3-phenoxypropan-2-ol kills Pseudomonas aeruginosa through extensive membrane damage
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Modeling multi-valued biological interaction networks using fuzzy answer set programming
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- Journal Article
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Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics
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Catabolic task division between two near-isogenic subpopulations co-existing in a herbicide-degrading bacterial consortium : consequences for the interspecies consortium metabolic model
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Molecular subtyping of Salmonella Typhimurium with multiplex oligonucleotide ligation-PCR (MOL-PCR)
(2017) Diagnostic bacteriology : methods and protocols. In Methods in Molecular Biology 1616. p.39-69 -
- Journal Article
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- open access
Network-based identification of adaptive pathways in evolved ethanol-tolerant bacterial populations
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- Journal Article
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The evolutionary significance of polyploidy
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- Journal Article
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Effect of genomic distance on coexpression of coregulated genes in E. coli
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Principles of systems biology, no. 14 : [...] Network analysis of woody biomass
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Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing
(2017) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 114(5). p.1195-1200 -
Early differences in islets from prediabetic NOD mice : combined microarray and proteomic analysis
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Fermentation assays reveal differences in sugar and (off-) flavor metabolism across different Brettanomyces bruxellensis strains
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- Journal Article
- A1
- open access
Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment
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Simultaneous discovery of cancer subtypes and subtype features by molecular data integration
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- Journal Article
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SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis
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- Journal Article
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Elucidation of the mode of action of a new antibacterial compound active against Staphylococcus aureus and Pseudomonas aeruginosa
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- Journal Article
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EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis
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- Journal Article
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FabR regulates Salmonella biofilm formation via its direct target FabB
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- Journal Article
- A1
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Network-based analysis of eQTL data to prioritize driver mutations
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Optimized MOL-PCR for characterization of microbial pathogens
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Adaptive self-organizing organisms using a bio-inspired gene regulatory network controller: for the aggregation of evolutionary robots under a changing environment
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Studying the relationship between drug resistance and genomic variations in Leishmania donovani using a network-based method
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Adaptation to high ethanol reveals complex evolutionary pathways
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Identifying prokaryotic consortia that live in close interactions with algae
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- Conference Paper
- C3
- open access
User‐friendly WGS analysis of Salmonella Enteritidis PT4 outbreaks
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The usefulness of whole genome sequencing for outbreak investigation of food pathogens, Salmonella Enteritidis as a case study
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- Journal Article
- A1
- open access
PheNetic : network-based interpretation of molecular profiling data
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- Journal Article
- A1
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Adaptation to high ethanol reveals complex evolutionary pathways
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Obg and membrane depolarization are part of a microbial bet-hedging strategy that leads to antibiotic tolerance
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- Journal Article
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Pathway relevance ranking for tumor samples through network-based data integration
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- Journal Article
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Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations
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- Conference Paper
- C3
- open access
Pathway relevance ranking for tumor samples through network-based data integration (award for Outstanding Oral Poster Presentation )
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Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains
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- Journal Article
- A1
- open access
SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering