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2018

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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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

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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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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Zondervan, Niels A; van Dam, Jesse C J; Schaap, Peter J; dos Santos, Vitor Martins 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, ARTICLE NUMBER = 347), pp. 29, 2018, ISSN: 1422-0067.

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van der Ark, Kees C H; Aalvink, Steven; Suarez-Diez, Maria; Schaap, 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, 2018, ISSN: 17517915.

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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.

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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; 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.

BibTeX

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.

BibTeX

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.

Links | BibTeX

126 entries « 1 of 3 »