Research Output 2009 2020

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2020

All sparse PCA models are wrong, but some are useful. Part I: Computation of scores, residuals and explained variance

Camacho, J., Smilde, A. K., Saccenti, E. & Westerhuis, J. A., 15 Jan 2020, In : Chemometrics and Intelligent Laboratory Systems. 196, 103907.

Research output: Contribution to journalArticleAcademicpeer-review

Principal component analysis
Factorization
2019
4 Citations (Scopus)

A Medicago truncatula SWEET transporter implicated in arbuscule maintenance during arbuscular mycorrhizal symbiosis

An, J., Zeng, T., Ji, C., de Graaf, S., Zheng, Z., Xiao, T. T., Deng, X., Xiao, S., Bisseling, T., Limpens, E. & Pan, Z., Oct 2019, In : New Phytologist. 224, 1, p. 396-408

Research output: Contribution to journalArticleAcademicpeer-review

Medicago truncatula
Symbiosis
symbiosis
transporters
Maintenance
1 Citation (Scopus)

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions

Odoni, D. I., Vazquez-Vilar, M., van Gaal, M. P., Schonewille, T., Martins Dos Santos, V. A. P., Tamayo-Ramos, J. A., Suarez-Diez, M. & Schaap, P. J., 1 Apr 2019, In : FEMS Microbiology Letters. 366, 7, fnz071.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Aspergillus niger
Citric Acid
Computational Biology
Saccharomyces cerevisiae
Arginine

Assessment of the Accuracy of High-Throughput Sequencing of the ITS1 Region of Neocallimastigomycota for Community Composition Analysis

Edwards, J. E., Hermes, G. D. A., Kittelmann, S., Nijsse, B. & Smidt, H., 18 Oct 2019, In : Frontiers in Microbiology. 10, 2370.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Neocallimastigomycota
Fungi
Clone Cells
Herbivory
Biomass
2 Citations (Scopus)

Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women

Hechler, C., Borewicz, K., Beijers, R., Saccenti, E., Riksen-Walraven, M., Smidt, H. & de Weerth, C., 14 Mar 2019, In : Scientific Reports. 9, 1, 4463.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbiota
Pregnant Women
Mothers
Pregnancy
Anxiety
1 Citation (Scopus)

Cofactors revisited – Predicting the impact of flavoprotein-related diseases on a genome scale

Wegrzyn, A. B., Stolle, S., Rienksma, R. A., Martins dos Santos, V. A. P., Bakker, B. M. & Suarez-Diez, M., 1 Feb 2019, In : Biochimica et Biophysica Acta - Molecular Basis of Disease. 1865, 2, p. 360-370

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Flavoproteins
Biomarkers
Genome
Multiple Acyl Coenzyme A Dehydrogenase Deficiency
Flavins
3 Citations (Scopus)

Consistency, inconsistency, and ambiguity of metabolite names in biochemical databases used for genome-scale metabolic modelling

Pham, N., van Heck, R. G. A., van Dam, J. C. J., Schaap, P. J., Saccenti, E. & Suarez-Diez, M., 6 Feb 2019, In : Metabolites. 9, 2, 28.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolites
Names
Genes
Genome
Databases
3 Citations (Scopus)

Correlating Infant Fecal Microbiota Composition and Human Milk Oligosaccharide Consumption by Microbiota of 1-Month-Old Breastfed Infants

Borewicz, K., Gu, F., Saccenti, E., Arts, I. C. W., Penders, J., Thijs, C., van Leeuwen, S. S., Lindner, C., Nauta, A., van Leusen, E., Schols, H. A. & Smidt, H., 24 Apr 2019, In : Molecular Nutrition and Food Research. 1801214.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbiota
Human Milk
breast milk
Oligosaccharides
oligosaccharides

CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313

Ganguly, J., Martin-Pascual, M. & van Kranenburg, R., 5 Dec 2019, In : Microbial Biotechnology.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Genes
Phosphate Acetyltransferase
L-Lactate Dehydrogenase
Genetic Promoter Regions

Designing Eukaryotic Gene Expression Regulation Using Machine Learning

de Jongh, R. P. H., van Dijk, A. D. J., Julsing, M. K., Schaap, P. J. & de Ridder, D., 17 Aug 2019, In : Trends in Biotechnology.

Research output: Contribution to journalArticleAcademicpeer-review

Gene expression regulation
Gene Expression Regulation
Gene expression
Learning systems
Gene Expression

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcusfuriosus Phosphoglucose Isomerase

Subramanian, K., Mitusińska, K., Raedts, J., Almourfi, F., Joosten, H. J., Hendriks, S., Sedelnikova, S. E., Kengen, S. W. M., Hagen, W. R., Góra, A., Martins Dos Santos, V. A. P., Baker, P. J., van der Oost, J. & Schaap, P. J., 31 May 2019, In : Biomolecules. 9, 6, 212.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Glucose-6-Phosphate Isomerase
Protein Engineering
Metals
Glucose-6-Phosphate
Mutation

Diversity of tryptophan halogenases in sponges of the genus Aplysina

Gutleben, J., Koehorst, J. J., McPherson, K., Pomponi, S., Wijffels, R. H., Smidt, H. & Sipkema, D., 1 Aug 2019, In : FEMS microbiology ecology. 95, 8, fiz108.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Porifera
Chloroflexi
sponge
Actinobacteria
Psychrobacter
2 Citations (Scopus)

Genetic and molecular analysis of trichome development in Arabis alpina

Chopra, D., Mapar, M., Stephan, L., Albani, M. C., Deneer, A., Coupland, G., Willing, E. M., Schellmann, S., Schneeberger, K., Fleck, C., Schrader, A. & Hülskamp, M., 11 Jun 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 24, p. 12078-12083 6 p.

Research output: Contribution to journalArticleAcademicpeer-review

Arabis
Trichomes
Molecular Biology
Arabidopsis
Genes

High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis

Benis, N., Wells, J. M., Smits, M. A., Kar, S. K., Van Der Hee, B., Martins Dos Santos, V. A. P., Suarez-Diez, M. & Schokker, D., 30 Dec 2019, In : BMC Genomics. 20, 1, 1028.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Homeostasis
Intestinal Mucosa
Organoids
Intestines
Maintenance

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

Kampers, L. F. C., van Heck, R. G. A., Donati, S., Saccenti, E., Volkers, R. J. M., Schaap, P. J., Suarez-Diez, M., Nikel, P. I. & Martins Dos Santos, V. A. P., 22 Oct 2019, In : Microbial Cell Factories. 18, 1, 1 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Pseudomonas putida
Adenosinetriphosphate
Computer Simulation
Adenosine Triphosphate
Metabolites
3 Citations (Scopus)

Live cell imaging of meiosis in Arabidopsis thaliana

Prusicki, M. A., Keizer, E. M., van Rosmalen, R. P., Komaki, S., Seifert, F., Müller, K., Wijnker, E., Fleck, C. & Schnittger, A., 20 May 2019, In : eLife. 8, e42834.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Cyclin A
Meiosis
Chromosomes
Arabidopsis
Microtubules

Macrophage-Specific NF-κB Activation Dynamics Can Segregate Inflammatory Bowel Disease Patients

Papoutsopoulou, S., Burkitt, M. D., Bergey, F., England, H., Hough, R., Schmidt, L., Spiller, D. G., White, M. H. R., Paszek, P., Jackson, D. A., Martins Dos Santos, V. A. P., Sellge, G., Pritchard, D. M., Campbell, B. J., Müller, W. & Probert, C. S., 11 Sep 2019, In : Frontiers in Immunology. 10, 11 p., 2168.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Inflammatory Bowel Diseases
Macrophages
Crohn Disease
Luciferases
Cytokines
Open Access
Clostridium kluyveri
Carbon Monoxide
Ethanol
Coculture Techniques
Thermodynamics

Metabolomics in systems medicine: an overview of methods and applications

Karakitsou, E., Foguet, C., de Atauri, P., Kultima, K., Khoonsari, P. E., Martins dos Santos, V. A. P., Saccenti, E., Rosato, A. & Cascante, M., 1 Jun 2019, In : Current Opinion in Systems Biology. 15, p. 91-99 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Metabolomics
Systems Analysis
Medicine
Precision Medicine
Bioelectric potentials
Open Access
Host-Pathogen Interactions
Mycobacterium tuberculosis
Pharmaceutical Preparations
Metabolome
arginine glutamate
8 Citations (Scopus)

Nmr spectroscopy for metabolomics research

Emwas, A. H., Roy, R., McKay, R. T., Tenori, L., Saccenti, E., Nagana Gowda, G. A., Raftery, D., Alahmari, F., Jaremko, L., Jaremko, M. & Wishart, D. S., 27 Jun 2019, In : Metabolites. 9, 7, 123.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolomics
Spectrum Analysis
Magnetic Resonance Spectroscopy
Spectroscopy
Nuclear magnetic resonance
1 Citation (Scopus)

Patient’s characteristics and outcomes in necrotising soft-tissue infections: results from a Scandinavian, multicentre, prospective cohort study

Madsen, M. B., Skrede, S., Perner, A., Arnell, P., Nekludov, M., Bruun, T., Karlsson, Y., Hansen, M. B., Polzik, P., Hedetoft, M., Rosén, A., Saccenti, E., Bergey, F., Martins Dos Santos, V. A. P., Norrby-teglund, A. & Hyldegaard, O., Sep 2019, In : Intensive Care Medicine. 45, 9, p. 1241-1251

Research output: Contribution to journalArticleAcademicpeer-review

Soft Tissue Infections
Cohort Studies
Prospective Studies
Mortality
Streptococcus
3 Citations (Scopus)

Phytochrome B dynamics departs from photoequilibrium in the field

Sellaro, R., Smith, R. W., Legris, M., Fleck, C. & Casal, J. J., Feb 2019, In : Plant Cell and Environment. 42, 2, p. 606-617

Research output: Contribution to journalArticleAcademicpeer-review

Phytochrome B
phytochrome
Light
shade
Phytochrome

Prediction of metabolic status of dairy cows in early lactation with on-farm cow data and machine learning algorithms

Xu, W., van Knegsel, A. T. M., Vervoort, J. J. M., Bruckmaier, R. M., van Hoeij, R. J., Kemp, B. & Saccenti, E., Nov 2019, In : Journal of Dairy Science. 102, 11, p. 10186-10201

Research output: Contribution to journalArticleAcademicpeer-review

artificial intelligence
early lactation
Lactation
dairy cows
cows

Propionibacterium ruminifibrarum sp. nov., isolated from cow rumen fibrous content

Vaidya, J. D., Hornung, B. V. H., Smidt, H., Edwards, J. E. & Plugge, C. M., 2019, In : International Journal of Systematic and Evolutionary Microbiology. 69, 8, p. 2584-2590

Research output: Contribution to journalArticleAcademicpeer-review

Propionibacterium
Rumen
alcohol
rumen
cows

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

Kamminga, T., Slagman, S. J., Martins dos Santos, V. A. P., Bijlsma, J. J. E. & Schaap, P. J., Aug 2019, In : Trends in Biotechnology. 37, 8, p. 805-816

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bacterial Vaccines
Bioengineering
Vaccines
Antigens
Screening
1 Citation (Scopus)

Semi-supervised multivariate statistical network monitoring for learning security threats

Camacho, J., Macia-Fernandez, G., Fuentes-Garcia, N. M. & Saccenti, E., 1 Aug 2019, In : IEEE Transactions on Information Forensics and Security. 14, 8, p. 2179-2189 8628992.

Research output: Contribution to journalArticleAcademicpeer-review

Supervised learning
Intrusion detection
Principal component analysis
Monitoring

Simulation and reconstruction of metabolite-metabolite association networks using a metabolic dynamic model and correlation based-algorithms

Jahagirdar, S., Suarez-diez, M. & Saccenti, E., 21 Jan 2019, In : Journal of Proteome Research. 18, 3, p. 1099-1113

Research output: Contribution to journalArticleAcademicpeer-review

Metabolites
Dynamic models
Metabolomics
Biological Phenomena
Metabolome

The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

Carreres, B. M., Mitsue León-Saiki, G., Schaap, P. J., Remmers, I. M., van der Veen, D., Martins dos Santos, V. A. P., Wijffels, R. H., Martens, D. E. & Suarez-Diez, M., 1 Jun 2019, In : Algal Research. 40, 101477.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Tetradesmus
starch
photoperiod
process energy
scotophase
5 Citations (Scopus)

The effect of prebiotic fortified infant formulas on microbiota composition and dynamics in early life

Borewicz, K., Suarez-Diez, M., Hechler, C., Beijers, R., de Weerth, C., Arts, I., Penders, J., Thijs, C., Nauta, A., Lindner, C., Van Leusen, E., Vaughan, E. E. & Smidt, H., 21 Feb 2019, In : Scientific Reports. 9, 1, 2434.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Prebiotics
Infant Formula
Microbiota
Bifidobacterium
Human Milk

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

van Dam, J. C. J., Koehorst, J. J., Vik, J. O., Martins dos Santos, V. A. P., Schaap, P. J. & Suarez-Diez, M., 4 Nov 2019, In : Scientific Data. 6, 1, 1 p., 254.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
ontology
Biology
Ontology
Annotation
biology
9 Citations (Scopus)

Vaccination of carp against SVCV with an oral DNA vaccine or an insect cells-based subunit vaccine

Embregts, C. W. E., Rigaudeau, D., Tacchi, L., Pijlman, G. P., Kampers, L., Veselý, T., Pokorová, D., Boudinot, P., Wiegertjes, G. F. & Forlenza, M., Feb 2019, In : Fish and Shellfish Immunology. 85, p. 66-77

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Subunit Vaccines
DNA Vaccines
vaccination
subunit vaccines
vaccine
2018
9 Citations (Scopus)

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

Atashgahi, S., Hornung, B., van der Waals, M. J., Da Rocha, U. N., Hugenholtz, F., Nijsse, B., Molenaar, D., van Spanning, R., Stams, A. J. M., Gerritse, J. & Smidt, H., 1 Dec 2018, In : Scientific Reports. 8, 1, 4490.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Microbial Consortia
Benzene
Nitrates
Oxygen
Genes
1 Citation (Scopus)
Open Access
Enterocytes
Fatty Acids
Lipids
Dietary Carbohydrates
Mitochondrial Proteins
13 Citations (Scopus)

Age and Sex Effects on Plasma Metabolite Association Networks in Healthy Subjects

Vignoli, A., Tenori, L., Luchinat, C. & Saccenti, E., 5 Jan 2018, In : Journal of Proteome Research. 17, 1, p. 97-107

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolites
Healthy Volunteers
Plasmas
Association reactions
Electric network analysis
7 Citations (Scopus)

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

Versluis, D., Nijsse, B., Naim, M. A., Koehorst, J. J., Wiese, J., Imhoff, J. F., Schaap, P. J., van Passel, M. W. J., Smidt, H. & Sipkema, D., 8 Jan 2018, In : Genome Biology and Evolution. 10, 1, p. 125-142

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Porifera
Genomics
genomics
sponge
Genome
1 Citation (Scopus)

Comparison of dimensionality assessment methods in Principal Component Analysis based on permutation tests

Vitale, R. & Saccenti, E., 15 Oct 2018, In : Chemometrics and Intelligent Laboratory Systems. 181, p. 79-94

Research output: Contribution to journalArticleAcademicpeer-review

Principal component analysis
Proteomics
Sensory analysis
Metabolomics
6 Citations (Scopus)

Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake

Middleton, A. M., Dal Bosco, C., Chlap, P., Bensch, R., Harz, H., Ren, F., Bergmann, S., Wend, S., Weber, W., Hayashi, K. I., Zurbriggen, M. D., Uhl, R., Ronneberger, O., Palme, K., Fleck, C. & Dovzhenko, A., 13 Mar 2018, In : Cell Reports. 22, 11, p. 3044-3057

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Indoleacetic Acids
Data structures
Fluxes
Plant Cells
Plant Growth Regulators
10 Citations (Scopus)
Open Access
Mucins
Expectorants
Acetyl Coenzyme A
Butyrates
Operon

Diabetes and necrotizing soft tissue infections—A prospective observational cohort study: Statistical analysis plan

Rosén, A., Arnell, P., Madsen, M. B., Nedrebø, B. G., Norrby-Teglund, A., Hyldegaard, O., dos Santos, V. M., Bergey, F., Saccenti, E. & Skrede, S., 1 Sep 2018, In : Acta Anaesthesiologica Scandinavica. 62, 8, p. 1171-1177

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Soft Tissue Infections
Observational Studies
Cohort Studies
Mortality
Renal Replacement Therapy
1 Citation (Scopus)

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Smith, R. W., van Rosmalen, R. P., Martins dos Santos, V. A. P. & Fleck, C., 19 Jun 2018, In : BMC Systems Biology. 12, 72.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Boidae
Python
Metabolic Networks and Pathways
Theoretical Models
Mathematical Model
8 Citations (Scopus)

DNA assembly standards: Setting the low-level programming code for plant biotechnology

Vazquez-Vilar, M., Orzaez, D. & Patron, N., Aug 2018, In : Plant Science. 273, p. 33-41

Research output: Contribution to journalArticleAcademicpeer-review

Biotechnology
Synthetic Biology
biotechnology
synthetic biology
DNA
1 Citation (Scopus)

Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes

Daas, M. J. A., Nijsse, B., van de Weijer, A. H. P., Groenendaal, B. W. A. J., Janssen, F., van der Oost, J. & van Kranenburg, R., 27 Jun 2018, In : BMC Biotechnology. 18, 1, 42.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Geobacillus
Cellulase
Genes
Glucosides
Hydrolases
2 Citations (Scopus)

Expression of the alternative oxidase influences jun n-terminal kinase signaling and cell migration

Andjelković, A., Mordas, A., Bruinsma, L., Ketola, A., Cannino, G., Giordano, L., Dhandapani, P. K., Szibor, M., Dufour, E. & Jacobs, H. T., Dec 2018, In : Molecular and Cellular Biology. 38, 24, e00110-18. .

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Cell Movement
Phosphotransferases
Wound Healing
Thorax
Thermogenesis

Forward Genetics by Genome Sequencing Uncovers the Central Role of the Aspergillus niger goxB Locus in Hydrogen Peroxide Induced Glucose Oxidase Expression

Laothanachareon, T., Tamayo Ramos, J. A., Nijsse, B. & Schaap, P. J., 24 Sep 2018, In : Frontiers in Microbiology. 9, SEP, 14 p., 02269.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Glucose Oxidase
Aspergillus niger
Hydrogen Peroxide
Genome
Glucose
17 Citations (Scopus)

From correlation to causation: analysis of metabolomics data using systems biology approaches

Rosato, A., Tenori, L., Cascante, M., De Atauri Carulla, P. R., Martins dos Santos, V. A. P. & Saccenti, E., 1 Apr 2018, In : Metabolomics. 14, 4, 37.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolomics
Systems Biology
Information Systems
Causality
Metabolome

Genome sequence of two members of the chloroaromatic-degrading MT community: Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3

Gutierrez-Urrutia, I., Miossec, M. J., Valenzuela, S. L., Meneses, C., Martins dos Santos, V. A. P., Castro-Nallar, E. & Poblete-Castro, I., 10 Jun 2018, In : Journal of Biotechnology. 275, p. 13-16

Research output: Contribution to journalArticleAcademicpeer-review

Achromobacter denitrificans
Pseudomonas
Genes
Genome
Open Reading Frames
2 Citations (Scopus)

Group-wise ANOVA simultaneous component analysis for designed omics experiments

Saccenti, E., Smilde, A. K. & Camacho, J., 1 Jun 2018, In : Metabolomics. 14, 6, 73.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Analysis of variance (ANOVA)
Analysis of Variance
Experiments
Principal Component Analysis
Principal component analysis
2 Citations (Scopus)

Group-wise partial least square regression

Camacho, J. & Saccenti, E., Mar 2018, In : Journal of Chemometrics. 32, 3, e2964.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Partial Least Squares Regression
Partial Least Squares
Principal component analysis
Data structures
Visualization
1 Citation (Scopus)

Insight into nuclear body formation of phytochromes through stochastic modelling and experiment

Grima, R., Sonntag, S., Venezia, F., Kircher, S., Smith, R. W. & Fleck, C., 18 May 2018, In : Physical Biology. 15, 5, 056003.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Phytochrome B
Phytochrome
Plant Photoreceptors
Plant Proteins
Light