Publications

158 entries « 3 of 4 »

2015

Saccenti, Edoardo; Camacho, José

Determining the number of components in principal components analysis: A comparison of statistical, crossvalidation and approximated methods Journal Article

Chemometrics and Intelligent Laboratory Systems, 149 , pp. 99 - 116, 2015, ISSN: 0169-7439.

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Atashgahi, Siavash; Aydin, Rozelin; Dimitrov, Mauricio R; Sipkema, Detmer; Hamonts, Kelly; Lahti, Leo; Maphosa, Farai; Kruse, Thomas; Saccenti, Edoardo; Springael, Dirk; Dejonghe, Winnie; Smidt, Hauke

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river Journal Article

Scientific Reports, 5 , pp. 17284, 2015, (Article).

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Cacciatore, Stefano; Saccenti, Edoardo; Piccioli, Mario

Hypothesis: The Sound of the Individual Metabolic Phenotype? Acoustic Detection of NMR Experiments Journal Article

OMICS: A Journal of Integrative Biology, 19 (3), pp. 147-156, 2015, ISSN: 1536-2310.

BibTeX

Ghini, Veronica; Saccenti, Edoardo; Tenori, Leonardo; Assfalg, Michael; Luchinat, Claudio

Allostasis and Resilience of the Human Individual Metabolic Phenotype Journal Article

Journal of Proteome Research, 14 (7), pp. 2951-2962, 2015, ISSN: 1535-3893, (doi: 10.1021/acs.jproteome.5b00275).

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Saccenti, Edoardo; Camacho, José

On the use of the observation-wise k-fold operation in PCA cross-validation Journal Article

Journal of Chemometrics, 29 , pp. 467 - 478, 2015, ISSN: 1099-128X.

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Saccenti, Edoardo; van Duynhoven, John; Jacobs, Doris M; Smilde, Age K; Hoefsloot, Huub C J

Strategies for Individual Phenotyping of Linoleic and Arachidonic Acid Metabolism Using an Oral Glucose Tolerance Test Journal Article

PLoS ONE, 10 (3), pp. e0119856, 2015, (doi:10.1371/journal.pone.0119856).

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Smilde, Age K; Timmerman, Marieke E; Saccenti, Edoardo; Jansen, Jeroen J; Hoefsloot, Huub C J

Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances Journal Article

Journal of Chemometrics, 29 (5), pp. 277-288, 2015, ISSN: 1099-128X.

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Sutton, Nora B; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H M

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation Journal Article

PLoS ONE, 10 (8), pp. e0134615, 2015, (doi:10.1371/journal.pone.0134615).

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2014

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

Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets Journal Article

Seminars in Immunology, 26 (6), pp. 610–622, 2014, ISSN: 1044-5323.

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Reijnders, Maarten J M F; van Heck, Ruben G A; Lam, Carolyn M C; Scaife, Mark A; dos Santos, Vitor Martins A P; Smith, Alison G; Schaap, Peter J

Green genes: Bioinformatics and systems-biology innovations drive algal biotechnology Journal Article

Trends in Biotechnology, 32 (12), pp. 617–626, 2014, ISSN: 18793096.

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Worm, Petra; Koehorst, Jasper J; Visser, Michael; ñ, Vicente Sedano-N{ú} T; Schaap, Peter J; Plugge, Caroline M; Sousa, Diana Z; Stams, Alfons J M

A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities Miscellaneous

2014, ISSN: 18792650.

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Staals, Raymond H J; Zhu, Yifan; Taylor, David W; Kornfeld, Jack E; Sharma, Kundan; Barendregt, Arjan; Koehorst, Jasper J; Vlot, Marnix; Neupane, Nirajan; Varossieau, Koen; Sakamoto, Keiko; Suzuki, Takehiro; Dohmae, Naoshi; Yokoyama, Shigeyuki; Schaap, Peter J; Urlaub, Henning; Heck, Albert J R; Nogales, Eva; Doudna, Jennifer A; Shinkai, Akeo; VanderOost, John

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus Journal Article

Molecular Cell, 56 (4), pp. 518–530, 2014, ISSN: 10974164.

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Bert De Rybel* Milad Adibi*, Alice Breda Jos Wendrich Margot Smit Ond?ej Novák Nobutoshi Yamaguchi Saiko Yoshida Gert Van Isterdael Joakim Palovaara Bart Nijsse Mark Boekschoten Guido Hooiveld Tom Beeckman Doris Wagner Karin Ljung Christian Fleck S R E V; Weijers, Dolf

Integration of growth and patterning during vascular tissue formation in Arabidopsis Journal Article

Science, 345 (6197), pp. 1255215, 2014.

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Kuever, Jan; Visser, Michael; Loeffler, Claudia; Boll, Matthias; Worm, Petra; Sousa, Diana Z; Plugge, Caroline M; Schaap, Peter J; Muyzer, Gerard; Pereira, Ines A C; Parshina, Sofiya N; Goodwin, Lynne A; Kyrpides, Nikos C; Detter, Janine; Woyke, Tanja; Chain, Patrick; Davenport, Karen W; Rohde, Manfred; Spring, Stefan; Klenk, Hans-Peter; Stams, Alfons J M

Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium Journal Article

Standards in Genomic Sciences, 9 (3), pp. 821–839, 2014, ISSN: 1944-3277.

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Visser, M; Parshina, S N; Alves, J I; Sousa, D Z; Pereira, A C; Muyzer, G; Kuever, J

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans Journal Article

Standards in Genomic Sciences, 9 (3), pp. 655–675, 2014, ISSN: 1944-3277.

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Barbier, Mariette; Damron, Heath F; Bielecki, Piotr; Suárez-Diez, María; Pucha?ka, Jacek; Albertí, Sebastian; dos Santos, Vitor Martins; Goldberg, Joanna B

From the Environment to the Host: Re-Wiring of the Transcriptome of Pseudomonas aeruginosa from 22°C to 37°C Journal Article

PLoS ONE, 9 (2), pp. e89941, 2014.

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Méndez-García, Celia; Mesa, Victoria; Sprenger, Richard R; Richter, Michael; Diez, María Suárez; Solano, Jennifer; Bargiela, Rafael; Golyshina, Olga V; Manteca, Ángel; Ramos, Juan Luis; Gallego, José R; Llorente, Irene; dos Santos, Vitor AP Martins; Jensen, Ole N; Peláez, Ana I; Sánchez, Jesús; Ferrer, Manuel

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage Journal Article

The ISME Journal, 2014, ISSN: 1751-7370.

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Kubacka, Anna; Diez, María Suárez; Rojo, David; Bargiela, Rafael; Ciordia, Sergio; Zapico, Inés; Albar, Juan P; Barbas, Coral; dos Santos, Vitor Martins A P; Fernández-García, Marcos; Ferrer, Manuel

Understanding the antimicrobial mechanism of TiO2-based nanocomposite films in a pathogenic bacterium Journal Article

Scientific Reports, 4 , 2014.

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Fineran, Peter C; Gerritzen, Matthias J H; Suárez-Diez, María; Künne, Tim; Boekhorst, Jos; van Hijum, Sacha A F T; Staals, Raymond H J; Brouns, Stan J J

Degenerate target sites mediate rapid primed CRISPR adaptation Journal Article

Proceedings of the National Academy of Sciences, 111 (16), pp. E1629–E1638, 2014, ISSN: 0027-8424, 1091-6490.

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van Dam, Jesse CJ; Schaap, Peter J; dos Santos, Vitor AP Martins; Suárez-Diez, María

Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis Journal Article

BMC Systems Biology, 8 (1), pp. 111, 2014, ISSN: 1752-0509.

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Saccenti, Edoardo; Suarez-Diez, Maria; Luchinat, Claudio; Santucci, Claudio; Tenori, Leonardo

Probabilistic networks of blood metabolites in healthy subjects as indicators of latent cardiovascular risk Journal Article

Journal of Proteome Research, 2014, ISSN: 1535-3893.

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Akudibillah, Grodon; Boas, Sonja E M; Carreres, Benoit; Dallinga, Marchien G; van Dijk, Aalt-Jan; Gupta Shishir, K; Hunt, Alexander; Jakobsen, Annika; Kasbawati, ; Merks, Roeland M H; Molenaar, Jaap; Overal, Gosse; Palm, Margriet M; Perenboom, Thijs; Prasad, Mridula; Rejnders, Maarten; Rens, Elisabeth G; Ryback, Brendan; Scheider, Linda; Srivastava, Mugdha; Willemsen, Marcel; Xunxun, Wu; Zagaris, Antonios

Scientific Report: Training Workshop Interdisciplinary Life Sciences Journal Article

PeerJ, 2:e654v1 , 2014.

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Sloothaak, Jasper; Schilders, Mike; Schaap, Peter J; de Graaff, Leo H

Overexpression of the Aspergillus niger GatA transporter leads to preferential use of D-galacturonic acid over D-xylose Journal Article

AMB Express, 4 (1), pp. 66, 2014, ISSN: 2191-0855.

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Calabrò, Antonio; Gralka, Ewa; Luchinat, Claudio; Saccenti, Edoardo; Tenori, Leonardo

A Metabolomic Perspective on Coeliac Disease Journal Article

Autoimmune diseases, 2014 , 2014, ISSN: 2090-0422.

BibTeX

Saccenti, Edoardo; Hoefsloot, Huub CJ; Smilde, Age K; Westerhuis, Johan A; Hendriks, Margriet MWB

Reflections on univariate and multivariate analysis of metabolomics data Journal Article

Metabolomics, 10 (3), pp. 361-374, 2014, ISSN: 1573-3882.

BibTeX

Saccenti, Edoardo; Tenori, Leonardo

Multivariate Modeling of the collaboration between Luigi Illica and Giuseppe Giacosa for the librettos of three operas by Giacomo Puccini Journal Article

Literary and Linguistic Computing, pp. fqu006, 2014, ISSN: 0268-1145.

BibTeX

Saccenti, Edoardo; Tenori, Leonardo; Verbruggen, Paul; Timmerman, Marieke E; Bouwman, Jildau; van der Greef, Jan; Luchinat, Claudio; Smilde, Age K

Of Monkeys and Men: A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species Journal Article

PloS one, 9 (9), pp. e106077, 2014, (doi:10.1371/journal.pone.0106077).

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2013

Reeve, Wayne; De Meyer, Sofie ; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Rui, Tian; Tiwari, Ravi; Howieson, John; Yates, Ron; O'Hara, Graham; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Peters, Lin; Pitluck, Sam; Woyke, Tanja; Kyrpides, Nikos

Genome sequence of the Lebeckia ambigua-nodulating "Burkholderia sprentiae" strain WSM5005(T.). Journal Article

Standards in genomic sciences, 9 (2), pp. 385–94, 2013, ISSN: 1944-3277.

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Flahaut, Nicolas A L; Wiersma, Anne; Van De Bunt, Bert ; Martens, Dirk E; Schaap, Peter J; Sijtsma, Lolke; Dos Santos, Vitor A.Martins ; De Vos, Willem M

Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation Journal Article

Applied Microbiology and Biotechnology, 97 (19), pp. 8729–8739, 2013, ISSN: 01757598.

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Staals, Raymond H J; Agari, Yoshihiro; Maki-Yonekura, Saori; Zhu, Yifan; Taylor, David W; VanDuijn, Esther; Barendregt, Arjan; Vlot, Marnix; Koehorst, Jasper J; Sakamoto, Keiko; Masuda, Akiko; Dohmae, Naoshi; Schaap, PeterJ; Doudna, Jennifer A; Heck, Albert J R; Yonekura, Koji; Van der Oost, John ; Shinkai, Akeo

Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus Journal Article

Molecular Cell, 52 (1), pp. 135–145, 2013, ISSN: 10972765.

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

Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation Journal Article

Proteomics, 13 (18-19), pp. 2886–2894, 2013, ISSN: 16159853.

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van der Meide, Nathalie M A; Roders, Nathalie; Sloet van Oldruitenborgh-Oosterbaan, Marianne M; Schaap, Peter J; van Oers, Monique M; Leibold, Wolfgang; Savelkoul, Huub F J; Tijhaar, Edwin

Cloning and expression of candidate allergens from Culicoides obsoletus for diagnosis of insect bite hypersensitivity in horses Journal Article

Veterinary Immunology and Immunopathology, 153 (3-4), pp. 227–239, 2013, ISSN: 01652427.

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Liebensteiner, M G; Pinkse, M W H; Schaap, P J; Stams, A J M; Lomans, B P

Archaeal (Per)Chlorate Reduction at High Temperature: An Interplay of Biotic and Abiotic Reactions Journal Article

Science, 340 (6128), pp. 85–87, 2013, ISSN: 0036-8075.

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Visser, Michael; Worm, Petra; Muyzer, Gerard; ê, In; Schaap, Peter J; Plugge, Caroline M; Kuever, Jan; Parshina, Sofiya N; Nazina, Tamara N; Ivanova, Anna E; Bernier-Latmani, Rizlan; a Goodwin, Lynne; Kyrpides, Nikos C; Woyke, Tanja; Chain, Patrick; Davenport, Karen W; Spring, Stefan; Klenk, Hans-Peter; Stams, Alfons J M

Genome analysis of Desulfotomaculum kuznetsovii strain 17T reveals a physiological similarity with Pelotomaculum thermopropionicum strain SIT. Journal Article

Standards in Genomic Sciences, 8 (1), pp. 69–87, 2013, ISSN: 1944-3277.

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Leimena, Milkha M; Ramiro-Garcia, Javier; Davids, Mark; van den Bogert, Bartholomeus; Smidt, Hauke; Smid, Eddy J; Boekhorst, Jos; Zoetendal, Erwin G; Schaap, Peter J; Kleerebezem, Michiel

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets Journal Article

BMC Genomics, 14 (1), pp. 530, 2013, ISSN: 1471-2164.

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Oosterkamp, Margreet J; Veuskens, Teun; Talarico Saia, Flávia ; Weelink, Sander A B; Goodwin, Lynne A; Daligault, Hajnalka E; Bruce, David C; Detter, John C; Tapia, Roxanne; Han, Cliff S; Land, Miriam L; Hauser, Loren J; Langenhoff, Alette A M; Gerritse, Jan; van Berkel, Willem J H; Pieper, Dietmar H; Junca, Howard; Smidt, Hauke; Schraa, Gosse; Davids, Mark; Schaap, Peter J; Plugge, Caroline M; Stams, Alfons J M

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T Journal Article

PLoS ONE, 8 (6), pp. e66971, 2013, ISSN: 19326203.

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Quax, Tessa E F; Wolf, Yuri I; Koehorst, Jasper J; Wurtzel, Omri; VanderOost, Richard; Ran, Wenqi; Blombach, Fabian; Makarova, Kira S; Brouns, Stan J J; Forster, Anthony C; Wagner, Gerhart E H; Sorek, Rotem; Koonin, Eugene V; VanderOost, John

Differential translation tunes uneven production of operon-encoded proteins Journal Article

Cell Reports, 4 (5), pp. 938–944, 2013, ISSN: 22111247.

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van der Meide, Nathalie M A; è, Beno{î}t Carr; Hagelaar, Rico; Savelkoul, Huub F J; Tijhaar, Edwin; Schaap, Peter J

De novo assembly and transcriptome characterization of Obsoletus complex Culicoides insects: vector for arboviruses and causative agent of a skin allergy in horses Journal Article

PhD Dissertation, Wageningen University and Research center, pp. 93, 2013.

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2012

Hesselman, Matthijn C; Koehorst, Jasper J; Slijkhuis, Thijs; Odoni, Dorett I; Hugenholtz, Floor; van Passel, Mark W J

The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts. Journal Article

Journal of biological engineering, 6 (1), pp. 14, 2012, ISSN: 1754-1611.

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Spring, Stefan; Visser, Michael; Lu, Megan; Copeland, Alex; Lapidus, Alla; Lucas, Susan; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Ivanova, Natalia; Land, Miriam; Hauser, Loren; Larimer, Frank; Rohde, Manfred; Göker, Markus; Detter, John C; Kyrpides, Nikos C; Woyke, Tanja; Schaap, Peter J; Plugge, Caroline M; Muyzer, Gerard; Kuever, Jan; ê, In; Parshina, Sofiya N; Bernier-Latmani, Rizlan; Stams, Alfons J M; Klenk, Hans-Peter

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT) Journal Article

Standards in Genomic Sciences, 7 (2), pp. 294–309, 2012, ISSN: 1944-3277.

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Saccenti, E; Tenori, L

Stylometric Investigation of Dante’s Divina Commedia by Means of Multivariate Data Analysis Techniques Journal Article

International Journal of Computational Linguistics Research, 3 (2), pp. 35:48, 2012.

BibTeX

Szyma?ska, Ewa; Saccenti, Edoardo; Smilde, Age K; Westerhuis, Johan A

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies Journal Article

Metabolomics, 8 (1), pp. 3-16, 2012, ISSN: 1573-3882.

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2011

Rooijers, Koos; Kolmeder, Carolin; Juste, Catherine; ë, Jo; de Been, Mark; Boeren, Sjef; Galan, Pilar; Beauvallet, Christian; de Vos, Willem M; Schaap, Peter J

An iterative workflow for mining the human intestinal metaproteome Journal Article

BMC Genomics, 12 (1), pp. 6, 2011, ISSN: 1471-2164.

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Andersen, Mikael R; Salazar, Margarita P; Schaap, Peter J; Van De Vondervoort, Peter J I; Culley, David; Thykaer, Jette; Frisvad, Jens C; Nielsen, Kristian F; Albang, Richard; Albermann, Kaj; Berka, Randy M; Braus, Gerhard H; Braus-Stromeyer, Susanna A; Corrochano, Luis M; Dai, Ziyu; Van Dijck, Piet W M; Hofmann, Gerald; Lasure, Linda L; Magnuson, Jon K; Menke, Hildegard; Meijer, Martin; Meijer, Susan L; Nielsen, Jakob B; Nielsen, Michael L; Van Ooyen, Albert J J; Pel, Herman J; Poulsen, Lars; Samson, Rob A; Stam, Hein; Tsang, Adrian; Van Den Brink, Johannes M; Atkins, Alex; Aerts, Andrea; Shapiro, Harris; Pangilinan, Jasmyn; Salamov, Asaf; Lou, Yigong; Lindquist, Erika; Lucas, Susan; Grimwood, Jane; Grigoriev, Igor V; Kubicek, Christian P; Martinez, Diego; Van Peij, No{ë}l N M E; Roubos, Johannes A; Nielsen, Jens; Baker, Scott E

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 Journal Article

Genome Research, 21 (6), pp. 885–897, 2011, ISSN: 10889051.

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Ferreira de Oliveira, Jos?? Miguel P; van Passel, Mark W J; Schaap, Peter J; de Graaff, Leo H

Proteomic analysis of the secretory response of aspergillus niger to D-maltose and D-xylose Journal Article

PLoS ONE, 6 (6), pp. e20865, 2011, ISSN: 19326203.

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Oakman, C; Tenori, L; Claudino, WM; Cappadona, S; Nepi, S; Battaglia, A; Bernini, P; Zafarana, E; Saccenti, E; Fornier, M

Identification of a serum-detectable metabolomic fingerprint potentially correlated with the presence of micrometastatic disease in early breast cancer patients at varying risks of disease relapse by traditional prognostic methods Journal Article

Annals of oncology, 22 (6), pp. 1295-1301, 2011, ISSN: 0923-7534.

BibTeX

Saccenti, Edoardo; Smilde, Age K; Saris, Wim HM

Beethoven’s deafness and his three styles Journal Article

BMJ, 343 , pp. d7589, 2011, ISSN: 1756-1833.

BibTeX

Saccenti, Edoardo; Smilde, Age K; Westerhuis, Johan A; Hendriks, Margriet M W B

Tracy–Widom statistic for the largest eigenvalue of autoscaled real matrices Journal Article

Journal of Chemometrics, 25 (12), pp. 644-652, 2011, ISSN: 1099-128X.

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Saccenti, E; Westerhuis, J A; Smilde, A K; van der Werf, M J; Hageman, J A; Hendriks, M M W B

Simplivariate models: uncovering the underlying biology in functional genomics data Journal Article

PloS one, 6 (6), pp. e20747, 2011, ISSN: 1932-6203.

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2010

Braaksma, Machtelt; Martens-Uzunova, Elena S; Punt, Peter J; Schaap, Peter J

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data Journal Article

BMC Genomics, 11 (1), pp. 584, 2010, ISSN: 1471-2164.

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158 entries « 3 of 4 »