Research Output

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

An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida

Batianis, C., Kozaeva, E., Damalas, S., Martin Pascual, M., Volke, D., Nikel, P. I. & Martins dos Santos, V. A. P., Mar 2020, In : Microbial Biotechnology. 13, 2, p. 368-385

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models.

Saccenti, E., Hendriks, M. H. W. B. & Smilde, A. K., 16 Jan 2020, In : Scientific Reports. 10, 1, 438.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Ganguly, J., Martin-Pascual, M. & van Kranenburg, R., Mar 2020, In : Microbial Biotechnology. 13, 2, p. 339-349

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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., Feb 2020, In : Trends in Biotechnology. 38, 2, p. 191-201

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Differential Network Analysis Reveals Metabolic Determinants Associated with Mortality in Acute Myocardial Infarction Patients and Suggests Potential Mechanisms Underlying Different Clinical Scores Used To Predict Death

Vignoli, A., Tenori, L., Giusti, B., Valente, S., Carrabba, N., Balzi, D., Barchielli, A., Marchionni, N., Gensini, G. F., Marcucci, R., Gori, A. M., Luchinat, C. & Saccenti, E., 7 Feb 2020, In : Journal of Proteome Research. 19, 2, p. 949-961 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Genetic Safeguards for Safety-by-design: So Close Yet So Far

Asín García, E., Kallergi, A., Landeweerd, L. & Martins dos Santos, V. A. P., 10 May 2020, In : Trends in Biotechnology. 1016.

Research output: Contribution to journalArticleAcademicpeer-review

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

Strepis, N., Naranjo, H. D., Meier-Kolthoff, J., Göker, M., Shapiro, N., Kyrpides, N., Klenk, H. P., Schaap, P. J., Stams, A. J. M. & Sousa, D. Z., 8 Jan 2020, In : BMC Genomics. 21, 1, 24.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Integrated Univariate, Multivariate, and Correlation-Based Network Analyses Reveal Metabolite-Specific Effects on Bacterial Growth and Biofilm Formation in Necrotizing Soft Tissue Infections

Afzal, M., Saccenti, E., Madsen, M. B., Hansen, M. B., Hyldegaard, O., Skrede, S., Martins Dos Santos, V. A. P., Norrby-Teglund, A. & Svensson, M., 7 Feb 2020, In : Journal of Proteome Research. 19, 2, p. 688-698

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Intestinimonas-like bacteria are important butyrate producers that utilize Nε-fructosyllysine and lysine in formula-fed infants and adults

Bui, T. P. N., Troise, A. D., Nijsse, B., Roviello, G. N., Fogliano, V. & de Vos, W. M., Jul 2020, In : Journal of Functional Foods. 70, 103974.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

MEMOTE for standardized genome-scale metabolic model testing

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B. E., Edirisinghe, J. N., Faria, J. P., Feist, A. M., Fengos, G., Fleming, R. M. T., García-Jiménez, B., Hatzimanikatis, V. & 49 others, van Helvoirt, W., Henry, C. S., Hermjakob, H., Herrgård, M. J., Kaafarani, A., Kim, H. U., King, Z., Klamt, S., Klipp, E., Koehorst, J. J., König, M., Lakshmanan, M., Lee, D. Y., Lee, S. Y., Lee, S., Lewis, N. E., Liu, F., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G. L., Monk, J. M., Nielsen, J., Nielsen, L. K., Nogales, J., Nookaew, I., Palsson, B. O., Papin, J. A., Patil, K. R., Poolman, M., Price, N. D., Resendis-Antonio, O., Richelle, A., Rocha, I., Sánchez, B. J., Schaap, P. J., Malik Sheriff, R. S., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaça, P., Vik, J. O., Wodke, J. A. H., Xavier, J. C., Yuan, Q., Zakhartsev, M. & Zhang, C., 1 Mar 2020, In : Nature Biotechnology. 38, 3, p. 272-276 5 p.

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access
1 Citation (Scopus)

Metagenomic-and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes

Peng, P., Lu, Y., Bosma, T. N. P., Nijenhuis, I., Nijsse, B., Shetty, S. A., Ruecker, A., Umanets, A., Ramiro-Garcia, J., Kappler, A., Sipkema, D., Smidt, H. & Atashgahi, S., May 2020, In : Microorganisms. 8, 5, 665.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis

Poncheewin, W., Hermes, G. D. A., Van Dam, J. C. J., Koehorst, J. J., Smidt, H. & Schaap, P. J., 23 Jan 2020, In : Frontiers in Genetics. 10, 1366.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

On the Use of Correlation and MI as a Measure of Metabolite—Metabolite Association for Network Differential Connectivity Analysis

Jahagirdar, S. & Saccenti, E., 24 Apr 2020, In : Metabolites. 10, 4, 26 p., 10040171.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Organohalide-respiring Desulfoluna species isolated from marine environments

Peng, P., Goris, T., Lu, Y., Nijsse, B., Burrichter, A., Schleheck, D., Koehorst, J. J., Liu, J., Sipkema, D., Sinninghe Damste, J. S., Stams, A. J. M., Häggblom, M. M., Smidt, H. & Atashgahi, S., Mar 2020, In : ISME Journal. 14, p. 815–827

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Relationship between energy balance and metabolic profiles in plasma and milk of dairy cows in early lactation

Xu, W., Vervoort, J., Saccenti, E., Kemp, B., van Hoeij, R. J. & van Knegsel, A. T. M., 26 Feb 2020, In : Journal of Dairy Science. 103, p. 4795–4805

Research output: Contribution to journalArticleAcademicpeer-review

The association between breastmilk oligosaccharides and faecal microbiota in healthy breastfed infants at two, six, and twelve weeks of age

Borewicz, K., Gu, F., Saccenti, E., Hechler, C., Beijers, R., de Weerth, C., van Leeuwen, S. S., Schols, H. A. & Smidt, H., 1 Dec 2020, In : Scientific Reports. 10, 1, 4270.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Open Access

Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets

Suarez-Diez, M., Porras, S., Laguna-Teno, F., Schaap, P. J. & Tamayo-Ramos, J. A., 24 Feb 2020, In : Scientific Reports. 10, 1, 3232.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2019

A FAIR approach to genomics

Koehorst, J. J., 2019, Wageningen: Wageningen University. 245 p.

Research output: Thesisinternal PhD, WU

Open Access

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
2 Citations (Scopus)

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

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
9 Citations (Scopus)

Bioprospecting of Trichococcus species

Strepis, N., 2019, Wageningen: Wageningen University. 228 p.

Research output: Thesisinternal PhD, WU

Open Access

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
2 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
4 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
8 Citations (Scopus)

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
5 Citations (Scopus)

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

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

Open Access
3 Citations (Scopus)
Open Access

Insight into the molecular mechanisms of organic acid pathways in Aspergillus niger

Laothanachareon, T., 2019, Wageningen: Wageningen University. 252 p.

Research output: Thesisinternal PhD, WU

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

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
6 Citations (Scopus)

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
Open Access
1 Citation (Scopus)

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

3 Citations (Scopus)
Open Access
2 Citations (Scopus)

Modeling metabolism of Mycobacterium tuberculosis

Rienksma, R. A., 2019, Wageningen: Wageningen University. 167 p.

Research output: Thesisinternal PhD, WU

Open Access

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
25 Citations (Scopus)

PathwayLevelDataIntegration

Benis, N., Sep 2019

Research output: Non-textual formSoftwareOther research output

Open Access

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

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

5 Citations (Scopus)

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

1 Citation (Scopus)

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

Pseudomonas putida KT2440 is HV1 certified, not GRAS

Kampers, L. F. C., Volkers, R. J. M. & Martins dos Santos, V. A. P., Sep 2019, In : Microbial Biotechnology. 12, 5, p. 845-848

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access
1 Citation (Scopus)

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

Semantic systems biology of prokaryotes: heterogeneous data integration to understand bacterial metabolism

van Dam, J. C. J., 2019, Wageningen: Wageningen University. 255 p.

Research output: Thesisinternal PhD, WU

Open Access

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

3 Citations (Scopus)

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

2 Citations (Scopus)