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Liens UNIL

Faculty of Biology and Medicine

Department of Fundamental Microbiology

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Publications

Publications | Masters and Phd thesis

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Publications

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In Press | 2024 | 2023 | 2022 | ...

In Press

PneumoBrowse 2: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae.

Janssen A.B., Gibson P.S., Bravo A.M., de Bakker V., Slager J., Veening J.W. Nucleic acids research. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_8FB8F0A27BF6]

2024

Triggering Toll-Like Receptor 5 Signaling During Pneumococcal Superinfection Prevents the Selection of Antibiotic Resistance.

Costa C., Sirard J.C., Gibson P.S., Veening J.W., Gjini E., Baldry M., 2024/11/15. The Journal of infectious diseases, 230 (5) pp. e1126-e1135. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_DBC6497572C4]

Uncovering the arsenal of class II bacteriocins in salivarius streptococci.

Damoczi J., Knoops A., Martou M.S., Jaumaux F., Gabant P., Mahillon J., Veening J.W., Mignolet J., Hols P., 2024/11/14. Communications biology, 7 (1) p. 1511. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_403C07B3C6ED]

CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria.

Jana B., Liu X., Dénéréaz J., Park H., Leshchiner D., Liu B., Gallay C., Zhu J., Veening J.W., van Opijnen T., 2024/09. Nature microbiology, 9 (9) pp. 2395-2409. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_A51A94333B3E]

An efficient in vivo-inducible CRISPR interference system for group A Streptococcus genetic analysis and pathogenesis studies.

Bjånes E., Stream A., Janssen A.B., Gibson P.S., Bravo A.M., Dahesh S., Baker J.L., Varble A., Nizet V., Veening J-W, 2024/08/14. mBio, 15 (8) pp. e0084024. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_181A2B7D79BE]

preview resource BIB_992AD6896096.P001

Genome-wide CRISPRi screens for high-throughput fitness quantification and identification of determinants for dalbavancin susceptibility in Staphylococcus aureus.

Liu X., de Bakker V., Heggenhougen M.V., Mårli M.T., Frøynes A.H., Salehian Z., Porcellato D., Morales Angeles D., Veening J-W, Kjos M., 2024/07/23. mSystems, 9 (7) pp. e0128923. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_992AD6896096]

preview resource BIB_37194217F7F5.P001

The function of CozE proteins is linked to lipoteichoic acid biosynthesis in Staphylococcus aureus.

Barbuti M.D., Lambert E., Myrbråten I.S., Ducret A., Stamsås G.A., Wilhelm L., Liu X., Salehian Z., Veening J-W, Straume D. et al., 2024/06/12. mBio, 15 (6) pp. e0115724. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_37194217F7F5]

preview resource BIB_D94E11A04C85.P001

AmiA and AliA peptide ligands, found in Klebsiella pneumoniae, are imported into pneumococci and alter the transcriptome.

Lux J., Sánchez García L., Chaparro Fernández P., Laloli L., Licheri M.F., Gallay C., Hermans PWM, Croucher N.J., Veening J.W., Dijkman R. et al., 2024/05/30. Scientific reports, 14 (1) p. 12416. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_D94E11A04C85]

preview resource BIB_0D45EBD017A6.P001

Klebsiella pneumoniae peptide hijacks a Streptococcus pneumoniae permease to subvert pneumococcal growth and colonization.

Lux J., Portmann H., Sánchez García L., Erhardt M., Holivololona L., Laloli L., Licheri M.F., Gallay C., Hoepner R., Croucher N.J. et al., 2024/04/08. Communications biology, 7 (1) p. 425. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_0D45EBD017A6]

A conserved antigen induces respiratory Th17-mediated broad serotype protection against pneumococcal superinfection.

Liu X., Van Maele L., Matarazzo L., Soulard D., Alves Duarte da Silva V., de Bakker V., Dénéréaz J., Bock F.P., Taschner M., Ou J. et al., 2024/03/13. Cell host & microbe, 32 (3) pp. 304-314.e8. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_8FC71E910A82]

preview resource BIB_003C384BFE4A.P001

Klebsiella pneumoniae OmpR facilitates lung infection through transcriptional regulation of key virulence factors.

Janssen A.B., de Bakker V., Aprianto R., Trebosc V., Kemmer C., Pieren M., Veening J-W, 2024/01/11. Microbiology spectrum, 12 (1) pp. e0396623. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_003C384BFE4A]

preview resource BIB_1CBBE39ACD1F.P001

The ClpX chaperone and a hypermorphic FtsA variant with impaired self-interaction are mutually compensatory for coordinating Staphylococcus aureus cell division.

Henriksen C., Baek K.T., Wacnik K., Gallay C., Veening J.W., Foster S.J., Frees D., 2024/01. Molecular microbiology, 121 (1) pp. 98-115. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_1CBBE39ACD1F]

Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions.

Sollier J., Basler M., Broz P., Dittrich P.S., Drescher K., Egli A., Harms A., Hierlemann A., Hiller S., King C.G. et al., 2024/01. Nature microbiology, 9 (1) pp. 1-3. Peer-reviewed.

[DOI][WoS][Pmid][serval:BIB_EB304466645B]

preview resource BIB_8C35F63DFBAE.P001

BactEXTRACT: an R Shiny app to quickly extract, plot and analyse bacterial growth and gene expression data.

Dénéréaz J., Veening J.W., 2024. Access microbiology, 6 (1). Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_8C35F63DFBAE]

2023

Liver macrophages and sinusoidal endothelial cells execute vaccine-elicited capture of invasive bacteria.

Wang J., An H., Ding M., Liu Y., Wang S., Jin Q., Wu Q., Dong H., Guo Q., Tian X. et al., 2023/12/20. Science translational medicine, 15 (727) pp. eade0054. Peer-reviewed.

[DOI][Pmid][serval:BIB_838C6AA2F99F]

preview resource BIB_335B2F934BB3.P001

Synthetic genetic oscillators demonstrate the functional importance of phenotypic variation in pneumococcal-host interactions.

Rueff A.S., van Raaphorst R., Aggarwal S.D., Santos-Moreno J., Laloux G., Schaerli Y., Weiser J.N., Veening J.W., 2023/11/17. Nature communications, 14 (1) p. 7454. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_335B2F934BB3]

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]

2022

preview resource BIB_36598FCE0CFF.P001

Pneumolysin promotes host cell necroptosis and bacterial competence during pneumococcal meningitis as shown by whole-animal dual RNA-seq.

Jim K.K., Aprianto R., Koning R., Domenech A., Kurushima J., van de Beek D., Vandenbroucke-Grauls CMJE, Bitter W., Veening J.W., 2022/12/20. Cell reports, 41 (12) p. 111851. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_36598FCE0CFF]

preview resource BIB_30D01D9D0A5B.P001

A Genome-Wide CRISPR Interference Screen Reveals an StkP-Mediated Connection between Cell Wall Integrity and Competence in Streptococcus salivarius.

Knoops A., Waegemans A., Lamontagne M., Decat B., Mignolet J., Veening J.W., Hols P., 2022/12/20. mSystems, 7 (6) pp. e0073522. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_30D01D9D0A5B]

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Phd thesis

Publications (7)

Inference through interference: bacterial fitness landscapes by CRISPRi-seq

de Bakker Vincent, 2023/12/11., Université de Lausanne, Faculté de biologie et médecine, Veening Jan-Willem (dir.).

[URN][serval:BIB_7EDC3C2C9029]

preview resource BIB_5547E108E640.P002

A systems biology approach to bacterial gene essentiality

Martins Bravo Afonso, 2023/10/06., Université de Lausanne, Faculté de biologie et médecine, Veening Jan-Willem (dir.).

[URN][serval:BIB_5547E108E640]

Genome-wide genetic interaction networks: from methods to insights into the pneumococcal cell cycle

DÉNÉRÉAZ Julien, 2023., Université de Lausanne, Faculté de biologie et médecine, Veening Jan-Willem (dir.).

[URN][serval:BIB_3603AC5DD4C7]

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]

preview resource BIB_D428B0D38196.P001

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]

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]

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