Publications

158 entries « 1 of 4 »

2018

Thanaporn Laothanachareon Juan Antonio Tamayo-Ramos, Bart Nijsse ; Schaap, Peter J

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

Frontiers in Microbiology, 9 , pp. 2269, 2018, ISSN: 1664-302X.

Abstract | Links | BibTeX

dos Rienk A. Rienksma Peter J. Schaap, Vitor Martins Santos A P; Suarez-Diez, Maria

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection Journal Article

Frontiers in Cellular and Infection Microbiology, 8 , pp. 264, 2018, ISSN: 2235-2988.

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Daas, Martinus J A; Nijsse, Bart; van de Weijer, Antonius H P; Groenendaal, Bart W A J; Janssen, Fons; van der Oost, John; van Kranenburg, Richard

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

BMC Biotechnology, 18 (1), pp. 42, 2018, ISSN: 1472-6750.

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Smith, Robert W; van Rosmalen, Rik P; Martins dos Santos, Vitor A P; Fleck, Christian

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

BMC Systems Biology, 12 (1), pp. 72, 2018, ISSN: 1752-0509.

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Hornung, Bastian; van den Bogert, Bartholomeus; Davids, Mark; dos Santos, Vitor Martins A P; Plugge, Caroline M; Schaap, Peter J; Smidt, Hauke

The Rumen Metatranscriptome Landscape Reflects Dietary Adaptation and Methanogenesis in Lactating Dairy Cows Journal Article

bioRxiv, 2018.

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Atashgahi, Siavash; Hornung, Bastian; Waals, Marcelle J; Rocha, Ulisses Nunes; Hugenholtz, Floor; Nijsse, Bart; Molenaar, Douwe; Spanning, Rob; Stams, Alfons JM; Gerritse, Jan; others,

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

Scientific reports, 8 (1), pp. 4490, 2018.

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Lieven, Christian; Beber, Moritz Emanuel; Olivier, Brett G; Bergmann, Frank T; Babaei, Parizad; Bartell, Jennifer A; Blank, Lars M; Chauhan, Siddharth; Correia, Kevin; Diener, Christian; others,

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite Journal Article

bioRxiv, pp. 350991, 2018.

BibTeX

Vitale, Raffaele; Saccenti, Edoardo

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

Chemometrics and Intelligent Laboratory Systems, 181 , pp. 79–94, 2018, ISSN: 0169-7439.

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Gaspari, Erika; Franke, Annika; Robles-Diaz, Diana; Zweigerdt, Robert; Roeder, Ingo; Zerjatke, Thomas; Kempf, Henning

Paracrine mechanisms in early differentiation of human pluripotent stem cells: Insights from a mathematical model Journal Article

Stem Cell Research, 32 , pp. 1–7, 2018, ISSN: 1873-5061.

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Laothanachareon, Thanaporn; Tamayo Ramos, J A; Nijsse, Bart; Peter J,

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

Frontiers in Microbiology, 9 , 2018, ISSN: 1664-302X.

Abstract | Links | BibTeX

'e, Ros A; Arnell, P; Madsen, M B; o, Nedreb B G; Norrby-Teglund, A; Hyldegaard, O; dos Santos, V M; Bergey, F; Saccenti, E; Skrede, S

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

Acta Anaesthesiologica Scandinavica, 62 (8), pp. 1171–1177, 2018, ISSN: 0001-5172.

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Vazquez-Vilar, Marta; Orzaez, Diego; Patron, Nicola

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

Plant Science, 273 , pp. 33–41, 2018, ISSN: 0168-9452.

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Martinus J A, ; Nijsse, Bart; van de Weijer, {Antonius H P }; Bart W A J, ; Janssen, Fons; van der Oost, John ; van Kranenburg, Richard

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

BMC Biotechnology, 18 (1), 2018, ISSN: 1472-6750.

Abstract | Links | BibTeX

Robert W, ; van Rosmalen, {Rik P }; Martins dos Santos, {Vitor A P }; Fleck, Christian

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

BMC Systems Biology, 12 , 2018, ISSN: 1752-0509.

Abstract | Links | BibTeX

van Sluijs, L; Sterken, M G; Wang, Yiru; Ritmahan, Wannisa; Gultom, Mitra; Pankok, Frederik; Blokhina, T; Riksen, J A G; Volkers, J M; Snoek, L B; Pijlman, G P; Kammenga, J E

Predicting individual differences in viral susceptibility caused by natural genetic variation within species Conference

2018, (EMBO Workshop: C. elegans Development, Cell Biology, and Gene Expression ; Conference date: 13-06-2018 Through 17-06-2018).

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Sinha, Neeraj; Suarez-Diez, Maria; Guido J E J, ; Keijer, Jaap; dos Santos, {Vitor Martin} ; van Schothorst, {Evert M }

A constraint-based model analysis of enterocyte mitochondrial adaptation to dietary interventions of lipid type and lipid load Journal Article

Frontiers in Physiology, 9 , 2018, ISSN: 1664-042X.

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Gutierrez-Urrutia, Izabook; Matthieu J, ; Sandro L, ; Meneses, Claudio; Martins dos Santos, {Vitor A P }; Castro-Nallar, Eduardo; Poblete-Castro, Ignacio

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

Journal of Biotechnology, 275 , pp. 13–16, 2018, ISSN: 0168-1656.

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Saccenti, Edoardo; Age K, ; 'e, Jos

Group-wise ANOVA simultaneous component analysis for designed omics experiments Journal Article

Metabolomics, 14 (6), 2018, ISSN: 1573-3882.

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Loo Wee, ; Bastian V H, ; Aalvink, Steven; Peter J, ; de Vos, {Willem M }; Knol, Jan; Belzer, Clara

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach Journal Article

Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygi"ene, microbiologie en serologie, 111 (6), pp. 859–873, 2018, ISSN: 0003-6072.

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van Sluijs, L; Sterken, M G; Wang, Yiru; Ritmahan, Wannisa; Gultom, Mitra; Pankok, Frederik; Blokhina, T; Riksen, J A G; Volkers, J M; Snoek, L B; Pijlman, G P; Kammenga, J E

Genetic variation causes differential viral susceptibilities in the model organism Caenorhabditis elegans Conference

2018, (FEBS Workshop 2018: The molecular basis of diseases: Can we infer phenotypes from protein variant analysis? ; Conference date: 23-05-2018 Through 25-05-2018).

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Grima, Ramon; Sonntag, Sebastian; Venezia, Filippo; Kircher, Stefan; Robert W, ; Fleck, Christian

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

Physical Biology, 15 (5), 2018, ISSN: 1478-3967.

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Sterken, M G; Snoek, L B; Bevers, R P J; Volkers, J M; Riksen, J A G; Kammenga, J E

Population complexity trumps model complexity in understanding trait variation Conference

2018, (Population, Evolutionary and Quantative Genetics Conference ; Conference date: 13-05-2018 Through 16-05-2018).

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van der Ark, {Kees C H }; Aalvink, Steven; Suarez-Diez, Maria; Peter J, ; de Vos, {Willem M }; Belzer, Clara

Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation Journal Article

Microbial Biotechnology, 11 (3), pp. 476–485, 2018, ISSN: 1751-7907.

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Jasper J, ; van Dam, {Jesse C J }; Saccenti, Edoardo; Martins Dos Santos, {Vitor A P }; Suarez-Diez, Maria; Peter J,

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles Journal Article

Bioinformatics, 34 (8), pp. 1401–1403, 2018, ISSN: 1367-4803.

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Rosato, Antonio; Tenori, Leonardo; Cascante, Marta; De Atauri Carulla, {Pedro Ramon} ; Martins dos Santos, {Vitor A P }; Saccenti, Edoardo

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

Metabolomics, 14 (4), 2018, ISSN: 1573-3882.

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Hugenholtz, Floor; Davids, Mark; Schwarz, Jessica; "u, Michael M; 'e, Daniel Tom; Schaap, Peter; Guido J E J, ; Smidt, Hauke; Kleerebezem, Michiel

Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut Journal Article

PLoS One, 13 (4), 2018, ISSN: 1932-6203.

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de Jaeger, Lenny ; Benoit M, ; Springer, Jan; Peter J, ; Eggink, Gerrit; Martins dos Santos, {Vitor A P }; Rene H, ; Dirk E,

Neochloris oleoabundans is worth its salt: Transcriptomic analysis under salt and nitrogen stress Journal Article

PLoS One, 13 (4), 2018, ISSN: 1932-6203.

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Embregts, C W E; Rigaudeau, D; Tacchi, L; Pijlman, G P; Kampers, L; 'y, Vesel T; 'a, Pokorov D; Boudinot, P; Wiegertjes, G F; Forlenza, M

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

Fish and Shellfish Immunology, 2018, ISSN: 1050-4648.

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Alistair M, ; Dal Bosco, Cristina ; Chlap, Phillip; Bensch, Robert; Harz, Hartmann; Ren, Fugang; Bergmann, Stefan; Wend, Sabrina; Weber, Wilfried; Ken Ichiro, ; Matias D, ; Uhl, Rainer; Ronneberger, Olaf; Palme, Klaus; Fleck, Christian; Dovzhenko, Alexander

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

Cell Reports, 22 (11), pp. 3044–3057, 2018, ISSN: 2211-1247.

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Hornung, Bastian; Martins dos Santos, {Vitor A P }; Smidt, Hauke; Peter J,

Studying microbial functionality within the gut ecosystem by systems biology Journal Article

Genes & Nutrition, 13 (1), 2018, ISSN: 1555-8932.

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Abdul Hamid, ; Saccenti, Edoardo; Gao, Xin; Ryan T, ; Martins dos Santos, {Vitor A P }; Roy, Raja; David S,

Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine Journal Article

Metabolomics, 14 (3), 2018, ISSN: 1573-3882.

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'e, Jos; Saccenti, Edoardo

Group-wise partial least square regression Journal Article

Journal of Chemometrics, 32 (3), 2018, ISSN: 0886-9383.

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Xu, Wei; Saccenti, E; Vervoort, J J M; Kemp, B; van Knegsel, A T M

Prediction of Metabolic Status of Dairy Cows in Early Lactation Using On-farm Cow Data with Machine Learning Algorithms Book Chapter

Abstract of the WIAS Science Day 2018, pp. 22–22, 2018.

BibTeX

Niels A, ; Van Dam, {Jesse C J }; Peter J, ; Martins dos Santos, {Vitor A P }; Suarez-Diez, Maria

Regulation of three virulence strategies of Mycobacterium tuberculosis: A success story Journal Article

International Journal of Molecular Sciences, 19 (2), 2018, ISSN: 1661-6596.

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Madsen, M B; Skrede, S; Bruun, T; Arnell, P; 'e, Ros A; Nekludov, M; Karlsson, Y; Bergey, F; Saccenti, E; Martins dos Santos, V A P; Perner, A; Norrby-Teglund, A; Hyldegaard, O

Necrotizing soft tissue infections - a multicentre, prospective observational study (INFECT): Protocol and statistical analysis plan Journal Article

Acta Anaesthesiologica Scandinavica, 62 (2), pp. 272–279, 2018, ISSN: 0001-5172.

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Jueeli D, ; van den Bogert, Bartholomeus ; Boekhorst, Jos; Saccenti, Edoardo; Caroline M, ; Smidt, Hauke

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows Journal Article

Frontiers in Microbiology, 9 (JAN), 2018, ISSN: 1664-302X.

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Vignoli, Alessia; Tenori, Leonardo; Luchinat, Claudio; Saccenti, Edoardo

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

Journal of Proteome Research, 17 (1), pp. 97–107, 2018, ISSN: 1535-3893.

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Versluis, Dennis; Nijsse, Bart; Naim, Mohd Azrul; Koehorst, Jasper J; Wiese, Jutta; Imhoff, Johannes F; Schaap, Peter J; van Passel, Mark W J; Smidt, Hauke; Sipkema, Detmer

Comparative genomics highlights symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio Journal Article

Genome Biology and Evolution, pp. evx271, 2018.

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2017

Sinha, Neeraj; Suarez-Diez, Maria; van Schothorst, Evert M; Keijer, Jaap; dos Santos, Vitor Martins A P; Hooiveld, Guido J E J

Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition Journal Article

Scientific Reports, 7 (1), 2017, ISSN: 2045-2322.

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Smith, Robert W; van Sluijs, Bob; Fleck, Christian

Designing synthetic networks in silico: a generalised evolutionary algorithm approach Journal Article

BMC Systems Biology, 11 (1), pp. 118, 2017, ISSN: 1752-0509.

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Koehorst, Jasper J; van Dam, Jesse C J; Saccenti, Edoardo; Martins dos Santos, Vitor A P; Suarez-Diez, Maria; Schaap, Peter J

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles Journal Article

Bioinformatics, 2017, ISSN: 1367-4803.

Abstract | Links | BibTeX

Smith, Robert W; Helwig, Britta; Westphal, Adrie H; Pel, Eran; Borst, Jan Willem; Fleck, Christian

Interactions Between phyB and PIF Proteins Alter Thermal Reversion Reactions in vitro Journal Article

Photochemistry and Photobiology, 93 (6), pp. 1525–1531, 2017, ISSN: 00318655.

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Kamminga, Tjerko; Slagman, Simen Jan; Bijlsma, Jetta J E; Martins dos Santos, Vitor A P; Suarez-Diez, Maria; Schaap, Peter J

Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate Journal Article

Biotechnology and Bioengineering, 114 (10), pp. 2339–2347, 2017, ISSN: 10970290.

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Ottman, Noora; Davids, Mark; Suarez-Diez, Maria; Boeren, Sjef; Schaap, Peter J; dos Santos, Vitor A.P.Martins; Smidt, Hauke; Belzer, Clara; de Vos, Willem M

Genomescale model and omics analysis of metabolic capacities of Akkermansia muciniphila reveal a preferential mucin-degrading lifestyle Journal Article

Applied and Environmental Microbiology, 83 (18), 2017, ISSN: 10985336.

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Schulze, Stefan; Urzica, Eugen; Reijnders, Maarten J M F; van de Geest, Henri; Warris, Sven; Bakker, Linda V; Fufezan, Christian; Martins dos Santos, Vitor A P; Schaap, Peter J; Peters, Sander A; Hippler, Michael

Identification of methylated GnTI-dependent N-glycans in Botryococcus brauni Journal Article

New Phytologist, 215 (4), pp. 1361–1369, 2017, ISSN: 14698137.

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Weusthuis, Ruud A; Mars, Astrid E; Springer, Jan; Wolbert, Emil JH; van der Wal, Hetty; de Vrije, Truus G; Levisson, Mark; Leprince, Audrey; Houweling-Tan, Bwee G; PHA Moers, Antoine ; Hendriks, Sjon NA; Mendes, Odette; Griekspoor, Yvonne; Werten, Marc WT; Schaap, Peter J; van der Oost, John; Eggink, Gerrit

Monascus ruber as cell factory for lactic acid production at low pH Journal Article

Metabolic Engineering, 42 , pp. 66–73, 2017, ISSN: 10967184.

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Peng, Peng; Zheng, Ying; Koehorst, Jasper J; Schaap, Peter J; Alfons, Alfons J; Smidt, Hauke; Atashgahi, Siavash

Concurrent haloalkanoate degradation and chlorate reduction by Pseudomonas chloritidismutans AW-1T Journal Article

Applied and Environmental Microbiology, 83 (12), pp. e00325–17, 2017, ISSN: 10985336.

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Kamminga, Tjerko; Koehorst, Jasper J; Vermeij, Paul; Slagman, Simen-Jan; Martins dos Santos, Vitor A P; Bijlsma, Jetta J E; Schaap, Peter J

Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life Journal Article

Frontiers in Cellular and Infection Microbiology, 7 (February), pp. 31, 2017, ISSN: 2235-2988.

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Palakawong Na Ayudthaya, Susakul ; Strepis, Nikolaos; Pristaš, Peter; Plugge, Caroline M

Draft Genome Sequence of Actinomyces glycerinitolerans Strain G10T, Isolated from Sheep Rumen Fluid. Journal Article

Genome announcements, 5 (7), pp. e01589–16, 2017, ISSN: 2169-8287.

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Carreres, B M; de Jaeger, L; Springer, J; Barbosa, M J; Breuer, G; van den End, E J; Kleinegris, D M M; Schäffers, I; Wolbert, E J H; Zhang, H; Lamers, P P; Draaisma, R B; Martins dos Santos, V A P; Wijffels, R H; Eggink, G; Schaap, P J; Martens, D E

Draft Genome Sequence of the Oleaginous Green Alga textlessitextgreaterTetradesmus obliquustextless/itextgreater UTEX 393 Journal Article

Genome Announcements, 5 (3), pp. e01449–16, 2017, ISSN: 2169-8287.

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158 entries « 1 of 4 »