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2018

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

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.

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

Comparative proteomics of textlessitextgreaterRhizopus delemartextless/itextgreater 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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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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Benis, Nirupama; Kar, Soumya K; dos Santos, Vitor Martins A P; Smits, Mari A; Schokker, Dirkjan; Suarez-Diez, Maria

Multi-Level Integration of Environmentally Perturbed Internal Phenotypes Reveals Key Points of Connectivity between Them Journal Article

Frontiers in Physiology, 8 , pp. 388, 2017, ISSN: 1664-042X.

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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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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: 1535-3893, (doi: 10.1021/acs.jproteome.7b00106).

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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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2016

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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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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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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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

6 , pp. 38699, 2016, (Article).

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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

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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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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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.

Abstract | Links | BibTeX

112 entries « 1 of 3 »