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Faculty of Biology and Medicine

Department of Fundamental Microbiology

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Publications | Masters and Phd thesis

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Publications

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2023 | ...

Chromosome organization shapes replisome dynamics in<i>Caulobacter crescentus</i>

Zhang Chen, Joseph Asha Mary, Casini Laurent, Collier Justine, Badrinarayanan Anjana, Manley Suliana.

[DOI][serval:BIB_95BB8A544E4B]

2023

Structural Basis of the Allosteric Inhibition of Human ABCG2 by Nanobodies.

Irobalieva R.N., Manolaridis I., Jackson S.M., Ni D., Pardon E., Stahlberg H., Steyaert J., Locher K.P., 2023/10/01. Journal of molecular biology, 435 (19) p. 168234. Peer-reviewed.

[DOI][Pmid][serval:BIB_6BB4EE9A8301]

A spatially structured mathematical model of the gut microbiome reveals factors that increase community stability.

Shibasaki S., Mitri S., 2023/09/15. iScience, 26 (9) p. 107499. Peer-reviewed.

[DOI][Pmid][serval:BIB_1DE0C547D7D9]

Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens.

Garrido-Sanz D., Vesga P., Heiman C.M., Altenried A., Keel C., Vacheron J., 2023/09. The ISME journal, 17 (9) pp. 1369-1381. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_7AA32FDA31E2]

preview resource BIB_6D567F950048.P001

SMC-based immunity against extrachromosomal DNA elements.

Liu H.W., Roisné-Hamelin F., Gruber S., 2023/08/31. Biochemical Society transactions, 51 (4) pp. 1571-1583. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_6D567F950048]

Activation mechanism of a short argonaute-TIR prokaryotic immune system.

Ni D., Lu X., Stahlberg H., Ekundayo B., 2023/07/21. Science advances, 9 (29) pp. eadh9002. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_58AA34EEF11C]

Microbial interactions in theory and practice: when are measurements compatible with models?

Picot A., Shibasaki S., Meacock O.J., Mitri S., 2023/07/06. Current opinion in microbiology, 75 p. 102354. Peer-reviewed.

[DOI][Pmid][serval:BIB_89918B5E96B2]

Fully co-factor-free ClearTau platform produces seeding-competent Tau fibrils for reconstructing pathological Tau aggregates.

Limorenko G., Tatli M., Kolla R., Nazarov S., Weil M.T., Schöndorf D.C., Geist D., Reinhardt P., Ehrnhoefer D.E., Stahlberg H. et al., 2023/07/04. Nature communications, 14 (1) p. 3939. Peer-reviewed.

[DOI][Pmid][serval:BIB_9BD5065EE4F5]

Prevalence and associated risk factors of intestinal parasitic infections among children in pastoralist and agro-pastoralist communities in the Adadle woreda of the Somali Regional State of Ethiopia

Lanker Kayla C., Muhummed Abdifatah M., Cissé Guéladio, Zinsstag Jakob, Hattendorf Jan, Yusuf Ramadan Budul, Hassen Shamil Barsenga, Tschopp Rea, Vonaesch Pascale, 2023/07/03. PLOS Neglected Tropical Diseases, 17 (7) pp. e0011448. Peer-reviewed.

[DOI][Pmid][serval:BIB_301D1EFA3E37]

Structure-function analysis of the cyclic β-1,2-glucan synthase

Sedzicki Jaroslaw, Ni Dongchun, Lehmann Frank, Stahlberg Henning, Dehio Christoph, 2023/05/05..

[DOI][serval:BIB_8B068C070C58]

De novo design of protein interactions with learned surface fingerprints.

Gainza P., Wehrle S., Van Hall-Beauvais A., Marchand A., Scheck A., Harteveld Z., Buckley S., Ni D., Tan S., Sverrisson F. et al., 2023/05. Nature, 617 (7959) pp. 176-184. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_E5B235F60B9D]

preview resource BIB_B07E342B8378.P001

Breaking down microbial hierarchies.

Sulheim S., Mitri S., 2023/05. Trends in microbiology, 31 (5) pp. 426-427. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_B07E342B8378]

preview resource BIB_5D0D254CCA47.P001

Robustness and innovation in synthetic genotype networks.

Santos-Moreno J., Tasiudi E., Kusumawardhani H., Stelling J., Schaerli Y., 2023/04/28. Nature communications, 14 (1) p. 2454. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_5D0D254CCA47]

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.

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

preview resource BIB_DE830FAC2E3E.P001

Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range.

Ni D., Turelli P., Beckert B., Nazarov S., Uchikawa E., Myasnikov A., Pojer F., Trono D., Stahlberg H., Lau K., 2023/04. PLoS pathogens, 19 (4) pp. e1011206. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_DE830FAC2E3E]

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]

preview resource BIB_6391CD6FACE0.P001

Going with the membrane flow: the impact of polarized secretion on bulk plasma membrane flows.

Gerganova V., Martin S.G., 2023/02. The FEBS journal, 290 (3) pp. 669-676. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_6391CD6FACE0]

preview resource BIB_5438E395CE11.P001

A focus on yeast mating: From pheromone signaling to cell-cell fusion.

Sieber B., Coronas-Serna J.M., Martin S.G., 2023/01/15. Seminars in cell & developmental biology, 133 pp. 83-95. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_5438E395CE11]

preview resource BIB_E6A07B0FAF00.P001

Gaps in the wall: understanding cell wall biology to tackle amoxicillin resistance in Streptococcus pneumoniae.

Gibson P.S., Veening J.W., 2023/01/11. Current opinion in microbiology, 72 p. 102261. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_E6A07B0FAF00]

preview resource BIB_4DECE69353E7.P001

Competence remodels the pneumococcal cell wall exposing key surface virulence factors that mediate increased host adherence.

Minhas V., Domenech A., Synefiaridou D., Straume D., Brendel M., Cebrero G., Liu X., Costa C., Baldry M., Sirard J.C. et al., 2023/01. PLoS biology, 21 (1) pp. e3001990. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_4DECE69353E7]

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Masters thesis

Publications (3)

preview resource BIB_5EE7C27A1A6C.P001

Phages anti-Pseudomonas aeruginosa pour le traitement des plaies brûlées infectées. Evaluation in vitro et résultats préliminaires de la mise au point d'un modèle ex vivo.

AL-DOUROBI K., 2015. 29, Université de Lausanne, Faculté de biologie et médecine, QUE Y.-A. (dir.).

[URN][serval:BIB_5EE7C27A1A6C]

preview resource BIB_976FDB34002D.P001

Caractéristiques épidémiologiques, cliniques et diagnostiques de cas d'encéphalites à tique chez des patients précédemment vaccinés en Suisse

CRISINEL M., 2014. 22, Université de Lausanne, Faculté de biologie et médecine, MEYLAN P. (dir.).

[URN][serval:BIB_976FDB34002D]

preview resource BIB_2DB67075AB75.P001

Cloning of bacteriophage lysins and evaluation of their antibacterial activity against Enterococcus faecalis

STRITT K., 2014. 28, Université de Lausanne, Faculté de biologie et médecine, MOREILLON P. (dir.).

[URN][serval:BIB_2DB67075AB75]

Phd thesis

Publications (48)

Taxonomic and functional diversity of Swiss cheese starter cultures

Somerville Vincent, 2023/01/10., Université de Lausanne, Faculté de biologie et médecine, Engel Philipp (dir.).

[serval:BIB_014DCD5701D2]

Impact of methylated adenines in the genome of the Caulobacter Alphaproteobacterium

CASINI Laurent, 2023., Université de Lausanne, Faculté de biologie et médecine, Collier Justine (dir.).

[serval:BIB_CAFDEC5CE0CB]

Multi-Partite Metabolic Interactions in The Honey Bee Gut Microbiota Between The Symbionts Snodgrassella and Gilliamella and Their Host

El Chazli Yassine, 2023., Université de Lausanne, Faculté de biologie et médecine, Engel Philipp (dir.).

[serval:BIB_3F59D129E8A7]

preview resource BIB_BBAE9A5D70E9.P002

Two design frameworks for optimizing microbial community functions

Shibasaki Shota, 2022/07/26., Université de Lausanne, Faculté de biologie et médecine, Mitri Sara (dir.).

[URN][serval:BIB_BBAE9A5D70E9]

preview resource BIB_DCA360AEEEF8.P002

Regulation of actin assembly for the formation of the fusion focus in fission yeast

Billault-Chaumartin Ingrid, 2022/03/04., Université de Lausanne, Faculté de biologie et médecine, Martin Sophie (dir.).

[URN][serval:BIB_DCA360AEEEF8]

Synthetic gene regulatory networks for pattern formation

Barbier Içvara, 2022., Université de Lausanne, Faculté de biologie et médecine, Schaerli Yolanda (dir.).

[URN][serval:BIB_38BCCE1D6958]

preview resource BIB_104C862F01EA.P001

Ecological dynamics of a synthetic bacterial community growing in a gradient of nutrients and toxicity

DI MARTINO Rita, 2022., Université de Lausanne, Faculté de biologie et médecine, Mitri Sara (dir.).

[URN][serval:BIB_104C862F01EA]

Drivers and consequences of amoxicillin resistance in the opportunistic human pathogen Streptococcus pneumoniae

Gibson Paddy Susanne, 2022., Université de Lausanne, Faculté de biologie et médecine, Veening Jan-Willem (dir.).

[URN][serval:BIB_D428B0D38196]

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]

preview resource BIB_B23C3169CE8F.P002

Harnessing CRISPR-Cas9 for use in the opportunistic human pathogen Streptococcus pneumoniae

Synefiaridou Dimitra, 2021/03/19., Université de Lausanne, Faculté de biologie et médecine, Veening Jan-Willem (dir.).

[URN][serval:BIB_B23C3169CE8F]

Genetic determinants underlying the colonization of Frischella perrara in the honey bee gut

Schmidt Konstantin, 2021/01/17., Université de Lausanne, Faculté de biologie et médecine, Engel Philipp (dir.).

[serval:BIB_158FE1740064]

preview resource BIB_BE570D550B30.P002

SMC and SMC-like proteins in genome folding and maintenance in Bacillus subtilis

Anchimiuk Anna, 2021., Université de Lausanne, Faculté de biologie et médecine, Gruber Stephan (dir.).

[URN][serval:BIB_BE570D550B30]

Chromosome organization by Smc and ParABS in Bacillus subtilis

Bock Florian Patrick, 2021., Université de Lausanne, Faculté de biologie et médecine, Gruber Stephan (dir.).

[URN][serval:BIB_11EAA5A91B09]

preview resource BIB_629178A23ED0.P001

Mechanisms underlying the evolution and coexistence of closely related gut bacteria in the honey bee, Apis mellifera

BROCHET Silvia, 2021., Université de Lausanne, Faculté de biologie et médecine, Engel Philipp (dir.).

[URN][serval:BIB_629178A23ED0]

SociaI interactions within a synthetic microbial community

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

[serval:BIB_C847D8E9D758]

DNA MISMATCH AND VERY SMALL PATCH REPAIR IN CAULOBACTER CRESCENTUS

CHAI Tiancong, 2020., Université de Lausanne, Faculté de biologie et médecine, Collier Justine (dir.).

[serval:BIB_8D9058AF0C4E]

Characterization of the epitranscriptomic landscape of HIV-infected cells

CRISTINELLI Sara, 2020., Université de Lausanne, Faculté de biologie et médecine, CIUFFI Angela (dir.).

[serval:BIB_407BFDD102D4]

Study of Cdc42 positive feedback regulation and polarized growth in S. pombe by optogenetics

Lamas Herrera Iker, 2020., Université de Lausanne, Faculté de biologie et médecine, Martin Sophie G. (dir.).

[serval:BIB_ED5F5DC1DFD2]

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]

DNA binding and dynamic architecture of bacterial condensin

VAZQUEZ NUNEZ Roberto Jareth, 2020., Université de Lausanne, Faculté de biologie et médecine, Gruber Stephan (dir.).

[serval:BIB_6AEB02B45199]

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]

preview resource BIB_06E4E8E84D5E.P002

Interactions between the gut symbiont Frischella perrara and its host the honey bee (Apis mellifera)

Emery Olivier, 2019/07/16., Université de Lausanne, Faculté de biologie et médecine, Engel Philipp (dir.).

[URN][serval:BIB_06E4E8E84D5E]

preview resource BIB_20FC452BD829.P002

Study of DNA repair and recombination mechanisms in Chinese hamster ovary cells

Bosshard Sandra, 2019/05., Université de Lausanne, Faculté de biologie et médecine, Mermod Nicolas (dir.).

[URN][serval:BIB_20FC452BD829]

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]

TOWARDS FUNCTIONAL UNDERSTANDING OF THE HONEY BEE GUT MICROBIOTA

KESNEROVA Lucie, 2019., Université de Lausanne, Faculté de biologie et médecine, Engel Philipp (dir.).

[URN][serval:BIB_04EA9E96A809]

preview resource BIB_9CA10CB4F6E4.P003

Single-cell analysis of osmostress genes transcription

Wosika-Witz Victoria, 2019., Université de Lausanne, Faculté de biologie et médecine, Pelet Serge (dir.).

[URN][serval:BIB_9CA10CB4F6E4]

preview resource BIB_722D3D16077B.P002

Regulation of transcription dynamics in single cells

Aymoz Delphine, 2018/01/18. 236, Université de Lausanne, Faculté de biologie et médecine, Pelet Serge (dir.).

[URN][serval:BIB_722D3D16077B]

preview resource BIB_BD5011C1A48E.P003

DYNAMIC SINGLE CELL MEASUREMENTS OF SIGNALLING CASCADE ACTIVITY

Durandau Eric, 2017/10/06., Université de Lausanne, Faculté de biologie et médecine, Pelet Serge (dir.).

[URN][serval:BIB_BD5011C1A48E]

preview resource BIB_FB118BB07158.P001

Molecular basis and regulation of insect pathogenicity in plant-beneficial pseudomonads

Kupferschmied P., 2015/09., Université de Lausanne, Faculté de biologie et médecine, Keel C. (dir.).

[URN][serval:BIB_FB118BB07158]

preview resource BIB_533BFE2E0864.P001

The role of MAR elements in DNA recombination

Kostyrko K., 2015/08. 210, Université de Lausanne, Faculté de biologie et médecine, Mermod N. (dir.).

[URN][serval:BIB_533BFE2E0864]

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]

preview resource BIB_CEA71D5DBA04.P001

Analyse des modifications de la chromatine impliquées dans l'effet barrière de CTF1 aux télomères humains

Esnault Germain, 2008. 106, Université de Lausanne, Faculté de biologie et médecine, Mermod Nicolas (dir.).

[URN][serval:BIB_CEA71D5DBA04]

Architectural features of bacterial genomes and their applications

Guy L., 2007. 235, Université de Lausanne, Faculté de biologie et médecine, Moreillon P. (dir.).

[serval:BIB_E8102DC60CAF]

Identification and quantification techniques in mass spectrometry-based proteomics

Panchaud A., 2007. 258, Université de Lausanne, Faculté de biologie et médecine, Moreillon P. (dir.).

[serval:BIB_865BBBFC97E0]

preview resource BIB_A9F833DEAECB.P001

Prospective determination of imipenem concentration of the plasma of critically-ill children

Giannoni E., 2006. 21, Université de Lausanne, Faculté de biologie et médecine, Moreillon P. (dir.).

[URN][serval:BIB_A9F833DEAECB]

Role of penicillin-binding proteins in Streptococcus gordonii

Haenni M., 2006. 153, Université de Lausanne, Faculté de biologie et médecine, Moreillon P. (dir.).

[serval:BIB_1079323162EF]

Role of Staphylococcus aureus surface proteins in experimental endocarditis

Widmer E., 2006. 133, Université de Lausanne, Faculté de biologie et médecine, Moreillon P. (dir.).

[serval:BIB_D16B6BF9E390]

Use of fluorescent proteins to monitor the regulation of antifungal activity in root-associated Pseudomonas fluorescens CHA0

Baehler E., 2005. 189, Université de Lausanne, Faculté de biologie et médecine, Keel C. (dir.).

[serval:BIB_43346]

Cell-cell communication in the biocontrol strain Pseudomonas fluorescens CHA0

Dubuis C., 2005. 99, Université de Lausanne, Faculté de biologie et médecine, Haas D. (dir.).

[serval:BIB_43347]

Methicillin-resistant Staphylococcus aureus resensitization by protein synthesis inhibitors : proposal for a mechanism

Guignard B., 2005. 164, Université de Lausanne, Faculté de biologie et médecine, Moreillon P. (dir.).

[serval:BIB_43348]

Pyochelin-mediated signalling in Pseudomonas aeruginosa

Michel L., 2005. 119, Université de Lausanne, Faculté de biologie et médecine, Haas D. (dir.).

[serval:BIB_43349]

Role of the Bacillus subtilis W23 stress response extracytoplasmic function sigma factor σM in two essential processes - teichoic acid biosynthesis and cell division

Minnig K., 2004. 143, Université de Lausanne, Faculté de biologie et médecine, Mauël C. (dir.).

[serval:BIB_43343]

Regulation of 2,4-diacetylphloroglucinol biosynthetic gene expression in Pseudomonas fluorescens CHA0.

Gigot-Bonnefoy C., 2003., Université de Lausanne, Faculté de biologie et médecine.

[serval:BIB_43339]

New regulatory elements in the quorum sensing network of Pseudomonas aeruginosa PAO1.

Heurlier K., 2003., Université de Lausanne, Faculté de biologie et médecine.

[serval:BIB_43340]

Antibiotic-dependent correlation between drug-induced killing and loss of luminescence in Streptococcus gordinii expressing luciferase

Loeliger Barbara, 2003. 11, Université de Lausanne, Faculté de médecine, Caldelari Isabelle, Bizzini Alain, Stutzmann Meier P, Majcherczyk Paul, Moreillon Philippe (dir.).

[URN][serval:BIB_3BC330D73EF3]

Post-transcriptional regulation of the hydrogen cyanide biosynthetic genes hcnABC in Pseudomonas fluorescens CHA0.

Starke K., 2003., Université de Lausanne, Faculté de biologie et médecine.

[serval:BIB_43342]

Salicylate biosynthesis in Pseudomonas aeruginosa PAO1.

Gaille C, 2002., Université de Lausanne, Faculté de biologie et médecine.

[serval:BIB_43338]

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