Publications

Comprehensive phenotyping of circulating immune cell subsets in people living with HIV
Navas A, van de Wijer L, Jacobs-Cleophas MCP, Schimmel-Naber AM, van Cranenbroek B, van der Heijden WA, van der Lei RJ, Vergara Z, Netea MG, van der Ven AJAM, Kapinsky M, Koenen HJPM, Joosten LAB
J Immunol Methods; 2022 Aug; 507:113307; doi: 10.1016/j.jim.2022,113307

People with HIV have higher percentages of circulating CCR5+ CD8+ T cells and lower percentages CCR5+ regulatory T cells
van Eekeren L, Matzaraki V, Zhang Z, van de Wijer L, Blaauw MJT, de Jonge MI, Vandekerckhove L, Trypsteen W, Joosten LAB, Netea MG, de Mast Q, Koenen HJPM, Li L, van der Ven AJAM
Sci Rep; 2022 Jul 6; 12(1); doi: 10.1038/s41598-022-15646-0

Unbiased metabolomics links fatty acid pathways to psychiatric symptoms in people living with HIV
Meeder E, Matzaraki V, Vadaq N, Van de Wijer L, Van der Ven A, Schellekens A
J Clin Med; 2021 Dec; 10(23); doi: 10.3390/jcm10235466

Plasmatic coagulation capacity correlates with inflammation and Abacavir use during chronic HIV infection
van der Heijden WA, Wan J, van de Wijer L, Jaeger M, Netea MG, van der Ven AJ, de Groot PG, Roest M, de Mast Q.
J Acquir Immune Defic Syndr; 2021 May 1;87(1):711-719. doi: 1097/QAI.0000000000002633

Substance use, unlike dolutegravir, is associated with mood symptoms in people living with HIV
van de Wijer L, van der Heijden WA, van Verseveld M, Netea M, de Mast Q, Schellekens A, van der Ven AJ.
AIDS behav; 2021 April 27. doi: 1007/s10461-021-03272-2

The Architecture of Circulating Immune Cells Is Dysregulated in People Living with Hiv on Long Term Antiretroviral Treatment and Relates with Markers of the Hiv-1 Reservoir, Cytomegalovirus, and Microbial Translocation
Van de Wijer L, van der Heijden WA, Ter Horst R, Jaeger M, Trypsteen W, Rutsaert S, van Cranenbroek, van Rijssen BE, Joosten I, Joosten L, Vandekerckhove L, Schoofs T, van Lunzen J, Netea MG, Koenen HJPM, van der Ven AJAM, de Mast Q.
Front Immunol; 2021 Apr 19;12:661990. doi: 3389/fimmu.2021.661990

Long-term treated HIV infection is associated with platelet mitochondrial dysfunction
van der Heijden WA, Wan J, van de Wijer L, Jaeger M, Grintjes K, Netea MG, Urbanus RT, van Crevel R, van den Heuvel LP, Brink M, Rodenburg RJ, de Groot PG, van der Ven AJ, de Mast Q.
Scientific Reports; 2021 Mar 18;11(1):6246. doi: 1038/s41598-021-85775-5

Chronic HIV infection induces transcriptional and functional reprogramming of innate immune cells
van der Heijden WA, van de Wijer L, Keramati F, Trypsteen W, Rutsaert S, ter Horst R, Jaeger M, Koenen HJPM, Stunnenberg HG, Joosten I, Verweij PE, van Lunzen J, Dinarello CA, Joosten LAB, Vandekerckhove L, Netea MG, van der Ven AJ, de Mast Q.
JCI Insight; 2021 Apr 8;6(7):e145928. doi: 1172/jci.insight.145928

A Genome-Wide Functional Genomics Approach Identifies Susceptibility Pathways to Fungal Bloodstream Infection in Humans.
Jaeger M, Matzaraki V, Aguirre-Gamboa R, Gresnigt MS, Chu X, Johnson MD, Oosting M, Smeekens SP, Withoff S, Jonkers I, Perfect JR, van de Veerdonk FL, Kullberg BJ, Joosten LAB, Li Y, Wijmenga C, Netea MG, Kumar V. J Infect Dis. 2019 Apr 24. pii: jiz206. doi: 10.1093/infdis/jiz206.

A systems genomics approach identifies SIGLEC15 as a susceptibility factor in recurrent vulvovaginal candidiasis.
Jaeger M, Pinelli M, Borghi M, Constantini C, Dindo M, van Emst L, Puccetti M, Pariano M, Ricaño-Ponce I, Büll C, Gresnigt MS, Wang X, Gutierrez Achury J, Jacobs CWM, Xu N, Oosting M, Arts P, Joosten LAB, van de Veerdonk FL, Veltman JA, Ten Oever J, Kullberg BJ, Feng M, Adema GJ, Wijmenga C, Kumar V, Sobel J, Gilissen C, Romani L, Netea MG.Sci Transl Med. 2019 Jun 12;11(496). pii: eaar3558. doi: 10.1126/scitranslmed.aar3558.

The Inter-Relationship of Platelets with Interleukin-1β-Mediated Inflammation in Humans.
Tunjungputri RN, Li Y, de Groot PG, Dinarello CA, Smeekens SP, Jaeger M, Doppenberg-Oosting M, Cruijsen M, Lemmers H, Toenhake-Dijkstra H, Aguirre-Gamboa R, Kumar V, Wijmenga C, Joosten LAB, Netea MG, van der Ven A, de Mast Q.Thromb Haemost. 2018 Dec;118(12):2112-2125. doi: 10.1055/s-0038-1675603. Epub 2018 Nov 19.

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses.
Bakker OB, Aguirre-Gamboa R, Sanna S, Oosting M, Smeekens SP, Jaeger M, Zorro M, Võsa U, Withoff S, Netea-Maier RT, Koenen HJPM, Joosten I, Xavier RJ, Franke L, Joosten LAB, Kumar V, Wijmenga C, Netea MG, Li Y.
Nat Immunol. 2018 Jul ;19(7):776-786.doi: 10.1038/s41590-018-0121-3. Epub 2018 May 21

Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming.
Christ A, Günther P, Lauterbach MAR, Duewell P, Biswas D, Pelka K, Scholz CJ, Oosting M, Haendler K, Baßler K, Klee K, Schulte-Schrepping J, Ulas T, Moorlag SJCFM, Kumar V, Park MH, Joosten LAB, Groh LA, Riksen NP, Espevik T, Schlitzer A, Li Y, Fitzgerald ML, Netea MG, Schultze JL, Latz E.
Cell. 2018 Jan 11;172(1-2):162-175.e14.

BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
Arts RJW, Moorlag SJCFM, Novakovic B, Li Y, Wang SY, Oosting M, Kumar V, Xavier RJ, Wijmenga C, Joosten LAB, Reusken CBEM, Benn CS, Aaby P, Koopmans MP, Stunnenberg HG, van Crevel R, Netea MG.
Cell Host Microbe. 2018 Jan 10;23(1):89-100.e5

The NOD2 receptor is crucial for immune responses towards New World Leishmania species 
Dos Santos JC, Damen MSMA, Oosting M, de Jong DJ, Heinhuis B, Gomes RS, Araújo CS, Netea MG, Ribeiro-Dias F, Joosten LAB.
Sci Rep. 2017 Nov 9;7(1):15219.

An integrative genomic approach identifies novel pathways that influence candidaemia susceptibility
Matzaraki V, Gresnigt MS, Jaeger M, Ricaño-Ponce I, Johnson MD, Oosting M, Franke L, Withoff S, Perfect JR, Joosten LAB, Kullberg BJ, van de Veerdonk FL, Jonkers I, Li Y, Wijmenga C, Netea MG, Kumar V.
PLoS One. 2017 Jul 20.

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits
Aguirre-Gamboa R, Joosten I, Urbano PC, van der Molen RG, van Rijssen E, van Cranenbroek B, Oosting M, Smeekens S, Jaeger M, Zorro M, Withoff S, van Herwaarden AE, Sweep FC, Netea RT, Swertz MA, Franke L, Xavier RJ, Joosten LA, Netea MG, Wijmenga C, Kumar V, Li Y, Koenen HJ.
Cell Rep. 2016 Nov 2. pii: S2211-1247(16)31473-5

Functional and Genomic Architecture of Borrelia burgdorferi-Induced Cytokine Responses in Humans
Oosting M, Kerstholt M, Ter Horst R, Li Y, Deelen P, Smeekens S, Jaeger M, Lachmandas E, Vrijmoeth H, Lupse M, Flonta M, Cramer RA, Kullberg BJ, Kumar V, Xavier R, Wijmenga C, Netea MG, Joosten LA.
Cell Host Microbe. 2016 Nov 1. pii: S1931-3128(16)30432-2

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans
Yang Li, Marije Oosting, Sanne P. Smeekens, Martin Jaeger, Raul Aguirre-Gamboa, Kieu T.T. Le, Patrick Deelen, Isis Ricaño-Ponce, Teske Schoffelen, Anne F.M. Jansen, Morris A. Swertz, Sebo Withoff, Esther van de Vosse, Marcel van Deuren, Frank van de Veerdonk, Alexandra Zhernakova, Jos W.M. van der Meer, Ramnik J. Xavier, Lude Franke, Leo A.B. Joosten, Cisca Wijmenga, Vinod Kumar, Mihai G. Netea
Cell. 2016 Nov; 167(4):p1099–1110.e14

Host and Environmental Factors Influencing Individual Human Cytokine Responses
Rob ter Horst, Martin Jaeger, Sanne P. Smeekens, Marije Oosting, Morris A. Swertz, Yang Li, Vinod Kumar, Dimitri A. Diavatopoulos, Anne F.M. Jansen, Heidi Lemmers, Helga Toenhake-Dijkstra, Antonius E. van Herwaarden, Matthijs Janssen, Renate G. van der Molen, Irma Joosten, Fred C.G.J. Sweep, Johannes W. Smit, Romana T. Netea-Maier, Mieke M.J.F. Koenders, Ramnik J. Xavier, Jos W.M. van der Meer, Charles A. Dinarello, Norman Pavelka, Cisca Wijmenga, Richard A. Notebaart, Leo A.B. Joosten, Mihai G. Netea.
Cell. 2016 Nov; 167(4):p1111–1124.e13

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity
Melanie Schirmer, Sanne P. Smeekens, Hera Vlamakis, Martin Jaeger, Marije Oosting, Eric A. Franzosa, Trees Jansen, Liesbeth Jacobs, Marc Jan Bonder, Alexander Kurilshikov, Jingyuan Fu, Leo A.B. Joosten, Alexandra Zhernakova, Curtis Huttenhower, Cisca Wijmenga, Mihai G. Netea, Ramnik J. Xavier
Cell. 2016 Nov; 167(4):p1125–1136.e8

The effect of host genetics on the gut microbiome
Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A.
Nat Genet. 2016 Nov;48(11):1407-1412

Understanding human immune function using the resources from the Human Functional Genomics Project
Netea MG, Joosten LA, Li Y, Kumar V, Oosting M, Smeekens S, Jaeger M, Ter Horst R, Schirmer M, Vlamakis H, Notebaart R, Pavelka N, Aguirre-Gamboa RR, Swertz MA, Tunjungputri RN, van de Heijden W, Franzosa EA, Ng A, Graham D, Lassen K, Schraa K, Netea-Maier R, Smit J, de Mast Q, van de Veerdonk F, Kullberg BJ, Tack C, van de Munckhof I, Rutten J, van der Graaf J, Franke L, Hofker M, Jonkers I, Platteel M, Maatman A, Fu J, Zhernakova A, van der Meer JW, Dinarello CA, van der Ven A, Huttenhouwer C, Koenen H, Joosten I, Xavier RJ, Wijmenga C.
Nat Med. 2016 Aug 4;22(8):831-3

Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi 
Li Y, Oosting M, Deelen P, Ricaño-Ponce I, Smeekens S, Jaeger M, Matzaraki V, Swertz MA, Xavier RJ, Franke L, Wijmenga C, Joosten LA, Kumar V, Netea MG.
Nat Med. 2016 Aug;22(8):952-60

A novel biomarker panel for irritable bowel syndrome and the application in the general population
Mujagic Z, Tigchelaar EF, Zhernakova A, Ludwig T, Ramiro-Garcia J, Baranska A, Swertz MA, Masclee AA, Wijmenga C, van Schooten FJ, Smolinska A, Jonkers DM.
Sci Rep. 2016 Jun 6;6:26420

Association of a variable number tandem repeat in the NLRP3 gene in women with susceptibility to RVVC
Jaeger M, Carvalho A, Cunha C, Plantinga TS, van de Veerdonk F, Puccetti M, Galosi C, Joosten LA, Dupont B, Kullberg BJ, Sobel JD, Romani L, Netea MG.
Eur J Clin Microbiol Infect Dis. 2016 May;35(5):797-801

Proton pump inhibitors affect the gut microbiome
Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A.
Gut. 2016 May;65(5):740-8

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J.
Science. 2016 Apr 29;352(6285):565-9

Population-level analysis of gut microbiome variation
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D’hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J.
Science. 2016 Apr 29;352(6285):560-4

Gut microbiota composition associated with stool consistency
Tigchelaar EF, Bonder MJ, Jankipersadsing SA, Fu J, Wijmenga C, Zhernakova A.
Gut. 2016 Mar;65(3):540-2

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids
Fu J, Bonder MJ, Cenit MC, Tigchelaar EF, Maatman A, Dekens JA, Brandsma E, Marczynska J, Imhann F, Weersma RK, Franke L, Poon TW, Xavier RJ, Gevers D, Hofker MH, Wijmenga C, Zhernakova A.
Circulation research. 2015 Oct 9;117(9):817-24

An introduction to LifeLines DEEP: study design and baseline characteristics
Ettje F Tigchelaar, Alexandra Zhernakova, Jackie A.M. Dekens, Gerben Hermes, Agnieszka Baranska, Zlatan Mujagic, Morris A Swertz, Angélica M Muñoz, Patrick Deelen, Maria C Cénit, Lude Franke, Salome Scholtens, Ronald P Stolk, Cisca Wijmenga, Edith J.M. Feskens.
BMJ Open. 2015 Aug 28;5(8):e006772

Multivariate inference of pathway activity in host immunity and response to therapeutics
Goel G, Conway KL, Jaeger M, Netea MG, Xavier RJ.
Nucleic Acids Res. 2014 Dec 1;42(16):10288-306

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity
Saeed S, Quintin J, Kerstens HH, Rao NA, Aghajanirefah A, Matarese F, Cheng SC, Ratter J, Berentsen K, van der Ent MA, Sharifi N, Janssen-Megens EM, Ter Huurne M, Mandoli A, van Schaik T, Ng A, Burden F, Downes K, Frontini M, Kumar V, Giamarellos-Bourboulis EJ, Ouwehand WH, van der Meer JW, Joosten LA, Wijmenga C, Martens JH, Xavier RJ, Logie C, Netea MG, Stunnenberg HG.
Science. 2014 Sep 26;345(6204):1251086

mTOR- and HIF-1α-mediated aerobic glycolysis as metabolic basis for trained immunity
Cheng SC, Quintin J, Cramer RA, Shepardson KM, Saeed S, Kumar V, Giamarellos-Bourboulis EJ, Martens JH, Rao NA, Aghajanirefah A, Manjeri GR, Li Y, Ifrim DC, Arts RJ, van der Meer BM, Deen PM, Logie C, O’Neill LA, Willems P, van de Veerdonk FL, van der Meer JW, Ng A, Joosten LA, Wijmenga C, Stunnenberg HG, Xavier RJ, Netea MG.
Science. 2014 Sep 26;345(6204):1250684

Immunochip SNP array identifies novel genetic variants conferring susceptibility to candidaemia
Kumar V, Cheng SC, Johnson MD, Smeekens SP, Wojtowicz A, Giamarellos-Bourboulis E, Karjalainen J, Franke L, Withoff S, Plantinga TS, van de Veerdonk FL, van der Meer JW, Joosten LA, Sokol H, Bauer H, Herrmann BG, Bochud PY, Marchetti O, Perfect JR, Xavier RJ, Kullberg BJ, Wijmenga C, Netea MG.
Nat Commun. 2014 Sep 8;5:4675.

Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses
Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers D.
J Innate Immun. 2014;6(3):253-62

Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans
Smeekens SP, Ng A, Kumar V, Johnson MD, Plantinga TS, van Diemen C, Arts P, Verwiel ET, Gresnigt MS, Fransen K, van Sommeren S, Oosting M, Cheng SC, Joosten LA, Hoischen A, Kullberg BJ, Scott WK, Perfect JR, van der Meer JW, Wijmenga C, Netea MG, Xavier RJ.
Nat Commun. 2013;4:1342

Cytokine gene polymorphisms and the outcome of invasive candidiasis: a prospective cohort study
Johnson MD, Plantinga TS, van de Vosse E, Velez Edwards DR, Smith PB, Alexander BD, Yang JC, Kremer D, Laird GM, Oosting M, Joosten LA, van der Meer JW, van Dissel JT, Walsh TJ, Perfect JR, Kullberg BJ, Scott WK, Netea MG.
Clin Infect Dis. 2012 Feb 15;54(4):502-10

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