Publications

158 entries « 2 of 4 »

2017

Claassens, Nico J; Siliakus, Melvin F; Spaans, Sebastiaan K; Creutzburg, Sjoerd C A; Nijsse, Bart; Schaap, Peter J; Quax, Tessa E F; Van Der Oost, John

Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms Journal Article

PLoS ONE, 12 (9), pp. e0184355, 2017, ISSN: 19326203.

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Gerritsen, Jacoline; Hornung, Bastian; Renckens, Bernadette; van Hijum, Sacha A F T; Martins dos Santos, Vitor A P; Rijkers, Ger T; Schaap, Peter J; de Vos, Willem M; Smidt, Hauke

Genomic and functional analysis of textlessitextgreaterRomboutsia ilealistextless/itextgreater CRIB textlesssuptextgreaterTtextless/suptextgreater reveals adaptation to the small intestine Journal Article

PeerJ, 5 , pp. e3698, 2017, ISSN: 2167-8359.

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Odoni, Dorett I; van Gaal, Merlijn P; Schonewille, Tom; Tamayo-Ramos, Juan A; Martins dos Santos, Vitor A P; Suarez-Diez, Maria; Schaap, Peter J

Aspergillus niger secretes citrate to increase iron bioavailability Journal Article

Frontiers in Microbiology, 8 (AUG), pp. 1424, 2017, ISSN: 1664302X.

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Ouwerkerk, Janneke P; Koehorst, Jasper J; Schaap, Peter J; Ritari, Jarmo; Paulin, Lars; Belzer, Clara; de Vos, Willem M

Complete Genome Sequence of Akkermansia glycaniphila Strain Pyt T , a Mucin-Degrading Specialist of the Reticulated Python Gut Journal Article

Genome Announcements, 5 (1), pp. e01098–16, 2017, ISSN: 2169-8287.

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Smith, R W; Fleck, C

Pollen Tip Growth Incollection

Obermeyer, G; Feijó, J (Ed.): (13), Springer International Publishing AG, 2017, ISBN: 978-3-319-56644-3.

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Timmers, Peer H A; Welte, Cornelia U; Koehorst, Jasper J; Plugge, Caroline M; Jetten, Mike S M; Stams, Alfons J M

Reverse Methanogenesis and Respiration in Methanotrophic Archaea Journal Article

Archaea, 2017 , pp. 1–22, 2017, ISSN: 14723646.

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Van Den Bergh, Tom ; Tamo, Giorgio; Nobili, Alberto; Tao, Yifeng; Tan, Tianwei; Bornscheuer, Uwe T; Kuipers, Remko K P; Vroling, Bas; De Jong, Rene M; Subramanian, Kalyanasundaram; Schaap, Peter J; Desmet, Tom; Nidetzky, Bernd; Vriend, Gert; Joosten, Henk Jan

CorNet: Assigning function to networks of co-evolving residues by automated literature mining Journal Article

PLoS ONE, 12 (5), pp. e0176427, 2017, ISSN: 19326203.

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van Dam, Jesse C J; Koehorst, Jasper J; Vik, Jon Olav; Schaap, Peter J; Suarez-Diez, Maria

Interoperable genome annotation with GBOL, an extendable infrastructure for functional data mining Journal Article

bioRxiv, 2017.

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Bergey, F; Saccenti, E; Jonkers, D; van den Heuvel, T; Jeuring, S; Pierik, M; dos Santos, Martins V

P316 New approaches for IBD management based on text mining of digitalised medical reports and latent class modelling Journal Article

Journal of Crohn's and Colitis, 11 (suppl_1), pp. S237-S238, 2017, ISSN: 1873-9946, (10.1093/ecco-jcc/jjx002.441 doi: 10.1093/ecco-jcc/jjx002.441).

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Lingen, Henk Van J; Edwards, Joan E; Vaidya, Jueeli D; van Gastelen, Sanne; Saccenti, Edoardo; van den Bogert, Bartholomeus; Bannink, André; Smidt, Hauke; Plugge, Caroline M; Dijkstra, Jan

Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen Journal Article

Frontiers in Microbiology, 8 , 2017.

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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, 2017, ISSN: 1535-3893.

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Benis, Nirupama Benis; Kar, Soumya; dos Santos, Vitor Martins; Smits, Mari; Schokker, Dirkjan; Diez, Maria Suarez

Multi-level integration of environmentally perturbed internal phenotypes reveals key points of connectivity between them Journal Article

Frontiers in Physiology, 8 , 2017, ISSN: 1664-042X.

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Odoni, Dorett I; Tamayo-Ramos, Juan A; Sloothaak, Jasper; van Heck, Ruben G A; Santos, Vitor Martins Dos A P; de Graaff, Leo H; Suarez-Diez, Maria; Schaap, Peter J

Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation Journal Article

PeerJ, 5 , pp. e3133, 2017, ISSN: 2167-8359.

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Atashgahi, Siavash; Lu, Yue; Zheng, Ying; Saccenti, Edoardo; Suarez-Diez, Maria; Ramiro-Garcia, Javier; Eisenmann, Heinrich; Elsner, Martin; Stams, Alfons J M; Springael, Dirk; Dejonghe, Winnie; Smidt, Hauke

Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol Journal Article

Environmental Microbiology, 19 (3), pp. 968–981, 2017, ISSN: 1462-2920.

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Suarez-Diez, Maria; Adam, Jonathan; Adamski, Jerzy; Chasapi, Styliani A; Luchinat, Claudio; Peters, Annette; Prehn, Cornelia; Santucci, Claudio; Spyridonidis, Alexandros; Spyroulias, Georgios A; Tenori, Leonardo; Wang-Sattler, Rui; Saccenti, Edoardo

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling Journal Article

Journal of Proteome Research, 2017, ISSN: 1535-3907.

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Venkatasubramanian, Prashanna Balaji; Toydemir, Gamze; de Wit, Nicole; Saccenti, Edoardo; dos Santos, Vitor Martins A P; van Baarlen, Peter; Wells, Jerry M; Suarez-Diez, Maria; Mes, Jurriaan J

Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity Journal Article

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

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2016

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

Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data Journal Article

Scientific Reports, 6 , pp. 38699, 2016, ISSN: 2045-2322.

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Sloothaak, Jasper; Odoni, Dorett I; Martins dos Santos, Vitor A P; Schaap, Peter J; Tamayo-Ramos, Juan Antonio

Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger Journal Article

PLoS Genetics, 12 (12), pp. e1006468, 2016, ISSN: 15537404.

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Smith, Robert W; Helwig, Britta; Westphal, Adrie H; Pel, Eran; Hörner, Maximilian; Beyer, Hannes M; Samodelov, Sophia L; Weber, Wilfried; Zurbriggen, Matias D; Borst, Jan Willem; Fleck, Christian

Unearthing the transition rates between photoreceptor conformers Journal Article

BMC Systems Biology, 10 (1), pp. 110, 2016, ISSN: 1752-0509.

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Mehboob, Farrakh; Oosterkamp, Margreet J; Koehorst, Jasper J; Farrakh, Sumaira; Veuskens, Teun; Plugge, Caroline M; Boeren, Sjef; de Vos, Willem M; Schraa, Gosse; Stams, Alfons J M; Schaap, Peter J

Genome and proteome analysis of Pseudomonas chloritidismutans AW-1Tthat grows on n-decane with chlorate or oxygen as electron acceptor Journal Article

Environmental Microbiology, 18 (10), pp. 3247–3257, 2016, ISSN: 14622920.

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Künne, Tim; Kieper, Sebastian N; Bannenberg, Jasper W; Vogel, Anne I M; Miellet, Willem R; Klein, Misha; Depken, Martin; Suarez-Diez, Maria; Brouns, Stan J J

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation Journal Article

Molecular Cell, 63 (5), pp. 852–864, 2016, ISSN: 1097-4164.

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Visser, Michael; Pieterse, Mervin M; Pinkse, Martijn W H; Nijsse, Bart; Verhaert, Peter D E M; de Vos, Willem M; Schaap, Peter J; Stams, Alfons J M

Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by genome and proteome analysis Journal Article

Environmental microbiology, 18 (9), pp. 2843–2855, 2016, ISSN: 14622920.

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Nobrega, Franklin L; Ferreira, Débora; Martins, Ivone M; Suarez-Diez, Maria; Azeredo, Joana; Kluskens, Leon D; Rodrigues, Lígia R

Screening and characterization of novel specific peptides targeting MDA-MB-231 claudin-low breast carcinoma by computer-aided phage display methodologies Journal Article

BMC Cancer, 16 , pp. 881, 2016, ISSN: 1471-2407.

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Bosma, Elleke F; Koehorst, Jasper J; van Hijum, Sacha A F T; Renckens, Bernadet; Vriesendorp, Bastienne; van de Weijer, Antonius H P; Schaap, Peter J; de Vos, Willem M; van der Oost, John; van Kranenburg, Richard

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T Journal Article

Standards in Genomic Sciences, 11 (1), pp. 52, 2016, ISSN: 1944-3277.

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Davids, Mark; Hugenholtz, Floor; Dos Santos, Vitor Martins ; Smidt, Hauke; Kleerebezem, Michiel; Schaap, Peter J

Functional profiling of unfamiliar microbial communities using a validated de novo assembly metatranscriptome pipeline Journal Article

PLoS ONE, 11 (1), pp. e0146423, 2016, ISSN: 19326203.

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Mehboob, Farrakh; Oosterkamp, Margreet J; Koehorst, Jasper J; Farrakh, Sumaira; Veuskens, Teun; Plugge, Caroline M; Boeren, Sjef; de Vos, Willem M; Schraa, Gosse; Stams, Alfons J M; Schaap, Peter J

Genome and proteome analysis of P seudomonas chloritidismutans AW-1 T that grows on n -decane with chlorate or oxygen as electron acceptor Journal Article

Environmental Microbiology, 18 (10), pp. 3247–3257, 2016, ISSN: 14622912.

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Sloothaak, Jasper; Tamayo-Ramos, Juan Antonio; Odoni, Dorett I; Laothanachareon, Thanaporn; Derntl, Christian; Mach-Aigner, Astrid R; Martins dos Santos, Vitor A P; Schaap, Peter J

Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus niger and Trichoderma reesei Journal Article

Biotechnology for Biofuels, 9 (1), pp. 148, 2016, ISSN: 1754-6834.

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Benis, N; Schokker, D; Kramer, F; Smits, MA; Suarez-Diez, M

Building pathway graphs from BioPAX data in R [version 2; referees: 3 approved, 1 approved with reservations] Journal Article

F1000Research, 5 (2414), 2016.

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Strepis, Nikolaos; Sánchez-Andrea, Irene; van Gelder, Antonie H; van Kruistum, Henri; Shapiro, Nicole; Kyrpides, Nikos; Göker, Markus; Klenk, Hans Peter; Schaap, Peter; Stams, Alfons J M; Sousa, Diana Z

Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses Journal Article

International Journal of Systematic and Evolutionary Microbiology, 66 (10), pp. 3957–3963, 2016, ISSN: 14665026.

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Atashgahi, Siavash; Lu, Yue; Zheng, Ying; Saccenti, Edoardo; Suarez-Diez, Maria; Ramiro-Garcia, Javier; Eisenmann, Heinrich; Elsner, Martin; Stams, Alfons J M; Springael, Dirk; Dejonghe, Winnie; Smidt, Hauke

Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol Journal Article

Environmental Microbiology, pp. n/a-n/a, 2016, ISSN: 1462-2920.

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Camacho, J; Saccenti, E

Group-wise PCA for exploratory data analysis Journal Article

Journal of computational and graphical statistics, In press , 2016.

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Karlsson-Vinkhuyzen, Sylvia I; Friberg, Lars; Saccenti, Edoardo

Read all about it!? Public accountability, fragmented global climate governance and the media Journal Article

Climate Policy, pp. 1-12, 2016, ISSN: 1469-3062.

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Koehorst, Jasper J; Saccenti, Edoardo; Schaap, Peter J; dos Santos, Vitor AP Martins; Suarez-Diez, Maria

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics Journal Article

F1000Research, 5 , 2016.

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Saccenti, Edoardo

Correlation Patterns in Experimental Data Are Affected by Normalization Procedures: Consequences for Data Analysis and Network Inference Journal Article

Journal of Proteome Research, 2016, ISSN: 1535-3893, (doi: 10.1021/acs.jproteome.6b00704).

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Saccenti, Edoardo; Menichetti, Giulia; Ghini, Veronica; Remondini, Daniel; Tenori, Leonardo; Luchinat, Claudio

Entropy-Based Network Representation of the Individual Metabolic Phenotype Journal Article

Journal of Proteome Research, 15 (9), pp. 3298-3307, 2016, ISSN: 1535-3893, (doi: 10.1021/acs.jproteome.6b00454).

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Saccenti, Edoardo; Timmerman, Marieke E

Approaches to Sample Size Determination for Multivariate Data: Applications to PCA and PLS-DA of Omics Data Journal Article

Journal of Proteome Research, 15 (8), pp. 2379-2393, 2016, ISSN: 1535-3893, (doi: 10.1021/acs.jproteome.5b01029).

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Saccenti, Edoardo; Timmerman, Marieke E

Considering Horn’s Parallel Analysis from a Random Matrix Theory Point of View Journal Article

Psychometrika, pp. 1-24, 2016, ISSN: 1860-0980.

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Stroeve, Johanna H M; Saccenti, Edoardo; Bouwman, Jildau; Dane, Adrie; Strassburg, Katrin; Vervoort, Jacques; Hankemeier, Thomas; Astrup, Arne; Smilde, Age K; van Ommen, Ben; Saris, Wim H M

Weight loss predictability by plasma metabolic signatures in adults with obesity and morbid obesity of the DiOGenes study Journal Article

Obesity, 24 (2), pp. 379-388, 2016, ISSN: 1930-739X.

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2015

Martin G Liebensteiner Martijn W H Pinkse, Bart Nijsse Peter Verhaert Nicolas Tsesmetzis Alfons Stams D E M J M; Lomans, Bart P

Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes Journal Article

Environmental Microbiology Reports, 7 (6), pp. 936-945, 2015.

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Fiebig, Anne; Loof, Torsten G; Babbar, Anshu; Itzek, Andreas; Koehorst, Jasper J; Schaap, Peter J; Nitsche-Schmitz, Patric D

Comparative Genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice Journal Article

International Journal of Medical Microbiology, 305 (6), pp. 532–543, 2015, ISSN: 16180607.

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Saccenti, Edoardo; Nieuwenhuijse, David; Koehorst, Jasper J; Dos Santos, Vitor A.P.Martins ; Schaap, Peter J

Assessing the metabolic diversity of streptococcus from a protein domain point of view Journal Article

PLoS ONE, 10 (9), pp. e0137908, 2015, ISSN: 19326203.

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Oosterkamp, Margreet J; Boeren, Sjef; Atashgahi, Siavash; Plugge, Caroline M; Schaap, Peter J; Stams, Alfons J M

Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC Journal Article

FEMS Microbiology Letters, 362 (11), 2015, ISSN: 15746968.

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Swarts, Daan C; Koehorst, Jasper J; Westra, Edze R; Schaap, Peter J; Van Der Oost, John

Effects of argonaute on gene expression in Thermus thermophilus Journal Article

PLoS ONE, 10 (4), pp. e0124880, 2015, ISSN: 19326203.

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Rienksma, Rienk A; Suarez-Diez, Maria; Mollenkopf, Hans-Joachim; Dolganov, Gregory M; Dorhoi, Anca; Schoolnik, Gary K; dos Santos, Vitor AP Martins; Kaufmann, Stefan HE; Schaap, Peter J; Gengenbacher, Martin

Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing Journal Article

BMC Genomics, 16 (1), pp. 34, 2015, ISSN: 1471-2164.

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Benis, Nirupama; Schokker, Dirkjan; Suarez-Diez, Maria; dos Santos, Vitor AP Martins; Smidt, Hauke; Smits, Mari A

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets Journal Article

BMC Genomics, 16 (1), pp. 556, 2015, ISSN: 1471-2164.

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Suarez-Diez, Maria; Saccenti, Edoardo

Effects of Sample Size and Dimensionality on the Performance of Four Algorithms for Inference of Association Networks in Metabonomics Journal Article

Journal of Proteome Research, 14 (12), pp. 5119–5130, 2015, ISSN: 1535-3893.

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Goris, Tobias; Hornung, Bastian; Kruse, Thomas; Reinhold, Anika; Westermann, Martin; Schaap, Peter J; Smidt, Hauke; Diekert, Gabriele

Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S Journal Article

Standards in Genomic Sciences, 10 (1), pp. 15, 2015, ISSN: 1944-3277.

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Reijnders, Maarten J M F; Carreres, Benoit M; Schaap, Peter J

Algal Omics: The Functional Annotation Challenge Journal Article

Current Biotechnology, 4 (4), pp. 457–463, 2015, ISSN: 22115501.

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Sloothaak, J; Odoni, D I; de Graaff, L H; Martins dos Santos, V A P; Schaap, P J; Tamayo-Ramos, J A

Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters Journal Article

Biotechnology for Biofuels, 8 (1), pp. 150, 2015, ISSN: 1754-6834.

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van Dam, Jesse CJ; Koehorst, Jasper J; Schaap, Peter J; Martins dos Santos, Vitor AP ; Suarez-Diez, Maria

RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource Journal Article

Journal of Biomedical Semantics, 6 (1), pp. 39, 2015, ISSN: 2041-1480.

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158 entries « 2 of 4 »