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Faculty of Biology and Medicine

Department of Fundamental Microbiology

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van der Meer Jan Roelof

Publications

Publications | Masters and Phd thesis

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Publications

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2024 | 2023 | 2022 | 2021 | ...

2024

preview resource BIB_E3381CFCB35A.P001

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions.

Čaušević S., Dubey M., Morales M., Salazar G., Sentchilo V., Carraro N., Ruscheweyh H.J., Sunagawa S., van der Meer J.R., 2024/03/22. Nature communications, 15 (1) p. 2557. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_E3381CFCB35A]

2023

preview resource BIB_C8BBFFC92257.P001

Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.

Benigno V., Carraro N., Sarton-Lohéac G., Romano-Bertrand S., Blanc D.S., van der Meer J.R., 2023/12/20. mSphere, 8 (6) pp. e0051723. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_C8BBFFC92257]

From microbiome composition to functional engineering, one step at a time.

Burz S.D., Causevic S., Dal Co A., Dmitrijeva M., Engel P., Garrido-Sanz D., Greub G., Hapfelmeier S., Hardt W-D, Hatzimanikatis V. et al., 2023/12/20. Microbiology and molecular biology reviews, 87 (4) pp. e0006323. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_422DE1C48246]

preview resource BIB_46EF5F18A042.P001

Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere.

Garrido-Sanz D., Čaušević S., Vacheron J., Heiman C.M., Sentchilo V., van der Meer J.R., Keel C., 2023/09/29. Microbiome, 11 (1) p. 214. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_46EF5F18A042]

Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding.

Guex I., Mazza C., Dubey M., Batsch M., Li R., van der Meer J.R., 2023/08. PLoS computational biology, 19 (8) pp. e1011402. Peer-reviewed.

[DOI][Pmid][serval:BIB_1DE186CB16FB]

preview resource BIB_E45105A859F9.P001

Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2.

Morales M., Sentchilo V., Carraro N., Causevic S., Vuarambon D., van der Meer J.R., 2023/04/27. mSystems, 8 (2) pp. e0117422. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_E45105A859F9]

STrack: A Tool to Simply Track Bacterial Cells in Microscopy Time-Lapse Images.

Todorov H., Miguel Trabajo T., van der Meer J.R., 2023/04/20. mSphere, 8 (2) pp. e0065822. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_CC63374B0997]

preview resource BIB_B2A6E41DC556.P001

Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida.

Daveri A., Benigno V., van der Meer J.R., 2023/03/21. Nucleic acids research, 51 (5) pp. 2345-2362. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_B2A6E41DC556]

2022

preview resource BIB_4D561966E16C.P001

A bistable prokaryotic differentiation system underlying development of conjugative transfer competence.

Sulser S., Vucicevic A., Bellini V., Moritz R., Delavat F., Sentchilo V., Carraro N., van der Meer J.R., 2022/06. PLoS genetics, 18 (6) pp. e1010286. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_4D561966E16C]

preview resource BIB_A9FCFB45172D.P001

Recent advances in microbial community analysis from machine learning of multiparametric flow cytometry data.

Özel Duygan B.D., van der Meer J.R., 2022/06. Current opinion in biotechnology, 75 p. 102688. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_A9FCFB45172D]

preview resource BIB_7CFDBD42F375.P001

Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation.

Čaušević S., Tackmann J., Sentchilo V., von Mering C., van der Meer J.R., 2022/04/26. mSystems, 7 (2) pp. e0016022. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_7CFDBD42F375]

Subcellular Localization Defects Characterize Ribose-Binding Mutant Proteins with New Ligand Properties in Escherichia coli.

Tavares D., van der Meer J.R., 2022/01/25. Applied and environmental microbiology, 88 (2) pp. e0211721. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_B146B2AFB72E]

2021

Assessing Antibiotics Biodegradation and Effects at Sub-inhibitory Concentrations by Quantitative Microbial Community Deconvolution

Özel Duygan Birge D., Gaille Caroline, Fenner Kathrin, van der Meer Jan R., 2021/09/16. Frontiers in Environmental Science, 9 p. 737247.

[DOI][WoS][serval:BIB_4D5A579D7A32]

preview resource BIB_595C7D7FADB0.P001

Predicting spatial patterns of soil bacteria under current and future environmental conditions.

Mod H.K., Buri A., Yashiro E., Guex N., Malard L., Pinto-Figueroa E., Pagni M., Niculita-Hirzel H., van der Meer J.R., Guisan A., 2021/09. The ISME journal, 15 (9) pp. 2547-2560. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_595C7D7FADB0]

A Miniaturized Microbe-Silicon-Chip Based on Bioluminescent Engineered Escherichia coli for the Evaluation of Water Quality and Safety.

Sciuto E.L., Corso D., Libertino S., van der Meer J.R., Faro G., Coniglio M.A., 2021/07/16. International journal of environmental research and public health, 18 (14) p. 7580. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_DC12ED645274]

preview resource BIB_48CD2F7B7CBA.P001

Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils.

Morales M., Sentchilo V., Hadadi N., van der Meer J.R., 2021/04/29. Environmental microbiome, 16 (1) p. 8. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_48CD2F7B7CBA]

preview resource BIB_D2457E5CE56F.P001

Environmental connectivity controls diversity in soil microbial communities.

Dubey M., Hadadi N., Pelet S., Carraro N., Johnson D.R., van der Meer J.R., 2021/04/22. Communications biology, 4 (1) p. 492. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_D2457E5CE56F]

Miniaturized electrochemical biosensor based on whole-cell for heavy metal ions detection in water.

Sciuto E.L., Petralia S., van der Meer J.R., Conoci S., 2021/04. Biotechnology and bioengineering, 118 (4) pp. 1456-1465. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_99F692FA2472]

preview resource BIB_E4E8C7ED5B31.P001

Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry.

Özel Duygan B.D., Rey S., Leocata S., Baroux L., Seyfried M., van der Meer J.R., 2021/02/09. mSystems, 6 (1) pp. e01143-20. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_E4E8C7ED5B31]

preview resource BIB_7CA24711D1A5.P001

Ribose-Binding Protein Mutants With Improved Interaction Towards the Non-natural Ligand 1,3-Cyclohexanediol.

Tavares D., van der Meer J.R., 2021. Frontiers in bioengineering and biotechnology, 9 p. 705534. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_7CA24711D1A5]

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Phd thesis

Publications (17)

Experimental evolution of a duplicated dual-color-emitting fluorescent protein

Mihajlović Ljiljana, 2022., Université de Lausanne, Faculté de biologie et médecine, Schaerli Yolanda (dir.).

[serval:BIB_A1E27CF77561]

preview resource BIB_4151C844762F.P002

Environmental activity of the inoculant Pseudomonas veronii 1YdBTEX2 during bioaugmentation in natural and polluted soils

Morales-Otero Marian, 2021/08/04., Université de Lausanne, Faculté de biologie et médecine, van der Meer Jan (dir.).

[URN][serval:BIB_4151C844762F]

SociaI interactions within a synthetic microbial community

PICCARDI Philippe, 2021., Université de Lausanne, Faculté de biologie et médecine, Mitri Sara (dir.).

[serval:BIB_C847D8E9D758]

preview resource BIB_F6204BD64773.P001

Changing the ligand-binding specificity of E. coli periplasmic binding protein RbsB by rational design and screening

TAVARES Diogo, 2020., Université de Lausanne, Faculté de biologie et médecine, VAN DER MEER Jan Roelof (dir.).

[URN][serval:BIB_F6204BD64773]

Assessing chemical biodegradability through rapid detection of microbial community changes

Özel Duygan Birge Didem, 2020., Université de Lausanne, Faculté de biologie et médecine, Van der Meer Jan Roelof (dir.).

[serval:BIB_6FF1A761CE63]

PROBING THE SOIL MICROBIAL INTERACTOME

DUBEY Manupriyam, 2019., Université de Lausanne, Faculté de biologie et médecine, van der Meer Jan Roelof (dir.).

[serval:BIB_2EE65D2A5A87]

FUNGAL BIOGEOGRAPHY IN THE WESTERN SWISS ALPS: Linking high-throughput sequencing and spatial ecology to characterise the diversity, distribution patterns and environmental niche of soil fungi along environmental gradients

PINTO-FIGUEROA Eric Alejandro, 2017., Université de Lausanne, Faculté de biologie et médecine, Guisan Antoine (dir.).

[serval:BIB_7D11EC9E2088]

Development of synthetic signalling pathways based on periplasmatic binding proteins and hybrid chemoreceptors

Reimer Artur, 2017., Université de Lausanne, Faculté de biologie et médecine, van der Meer Jan Roelof (dir.).

[serval:BIB_3663E57164DE]

preview resource BIB_7C8C3CFFF826.P001

DEVELOPMENT OF SYNTHETIC CHEMOTAXIS BASED BACTERIAL BIOREPORTERS

Roggo Clémence, 2017., Université de Lausanne, Faculté de biologie et médecine, Roelof van der Meer Jan (dir.).

[URN][serval:BIB_7C8C3CFFF826]

preview resource BIB_A58E1EDC611D.P001

Environmental activity of bacteria degrading pollutants

Moreno Forero S. C., 2015/10. 232, Université de Lausanne, Faculté de biologie et médecine, van der Meer R. J. (dir.).

[URN][serval:BIB_A58E1EDC611D]

Regulation of bistable ICEclc transfer in pseudomonas knackmussii B13

Sulser S., 2015. 164, Université de Lausanne, Faculté de biologie et médecine, van der Meer J. R. (dir.).

[serval:BIB_93DE57406195]

Development of an integrated whole cell biosensor for arsenic

Merulla D., 2014. 136, Université de Lausanne, Faculté de biologie et médecine, van der Meer J. R. (dir.).

[serval:BIB_A2A4B804440E]

preview resource BIB_15BF456327FB.P001

A single cell approach to studying ICEclc behaviour in pseudomonas

Reinhard F. F., 2014. 307, Université de Lausanne, Faculté de biologie et médecine, van der Meer J. R. (dir.).

[URN][serval:BIB_15BF456327FB]

preview resource BIB_17A1A45CC8EE.P001

Dibenzofuran degradation by Sphingomonas wittichii RW1 under environmental stresses

Coronado E., 2013/02., Université de Lausanne, Faculté de biologie et médecine, van der Meer J. R. (dir.).

[URN][serval:BIB_17A1A45CC8EE]

preview resource BIB_2388C5EDEED4.P001

Regulation of horizontal gene transfer of the catabolic island ICEclc

Pradervand N., 2013. 209, Université de Lausanne, Faculté de biologie et médecine, van der Meer J. R. (dir.).

[URN][serval:BIB_2388C5EDEED4]

Pollution stress on aquatic microbial communities

Czechowska-Kusio K. R., 2011. 209, Université de Lausanne, Faculté de biologie et médecine, van der Meer J. R. (dir.).

[serval:BIB_8D08C81B0596]

preview resource BIB_144C279A288C.P001

On the use of reporter bacteria for measuring availability of organic contaminants

Tecon R., 2009/04. 179, Université de Lausanne, Faculté de biologie et médecine, van der Meer J. R. (dir.).

[URN][serval:BIB_144C279A288C]

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