Bunnik Lab

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2017

42.
Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG. Genome organization as a master regulator of transcription in Plasmodium parasites. Genome Research [under review]

41.
Lu XM, Batugedara G, Prudhomme J, Bunnik EM, Le Roch KG. Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acid Research [in press]

40.
Bol S, Caspers J, Buckingham L, Anderson-Shelton GD , Ridgway C, Buffington CAT, Schulz S, Bunnik EM. Responsiveness of cats (Felidae) to silver vine (Actinidia polygama), Tatarian honeysuckle (Lonicera tatarica), valerian (Valeriana officinalis) and catnip (Nepeta cataria). BMC Veterinary Research 13(1):70  PDF  |  PMID: 28302120

39.
Khan S, Oosterhuis K, Wunderlich K, Bunnik EM, Bhaggoe M, Boedhoe S, Karia S, Steenbergen RDM, Bosch L, Serroyen J, Janssen S, Schuitemaker H, Vellinga J, Scheper G, Zahn R, Custers J. Development of a replication-deficient adenoviral vector-based vaccine candidate for the interception of HPV16- and HPV18-induced infections and disease. International Journal of Cancer (2017) 141, 393–404  PDF  |  PMID: 28263390

38.
Batugedara G, Lu XM, Bunnik EM, Le Roch KG. The role of chromatin structure in gene regulation of the human malaria parasite. Trends in Parasitology (2017) 33(5):364-377 [Review]  PDF  |  PMID: 28065669

2016

37.
Bunnik EM, Batugedara G, Saraf A, Prudhomme J, Florens A, Le Roch KG. The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum. Genome Biology (2016) 17:147 >F1000Prime Article Recommendation<  PDF  |  PMID: 27381095

36.
Saraf A, Cervantes S, Bunnik EM, Ponts N, Sardiu ME, Chung DWD, Prudhomme J, Varberg JM, Wen Z, Washburn MP, Florens L, Le Roch KG. Dynamic and combinatorial landscape of histone modifications during the intraerythrocytic developmental cycle of the malaria parasite. Journal of Proteome Research (2016) 15(8):2787-2801  PDF  |  PMID: 27291344

35.
Bunnik EM and Le Roch KG. Epigenetics of malaria parasites. Epigenetics and infectious diseases. (2016) Springer, edited by J Casadesus, W Doerfler, P Boehm and M Noyer-Weidner. [Book Chapter]

2015

34.
Bunnik EM, Lu M, Pokhriyal N, Nasseri S, Lonardi S, Le Roch KG. Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum. BMC Genomics (2015) 16(1):1005  PDF  |  PMID: 26607328

33.
Bol S, Bunnik EM. Lysine supplementation is not effective for the prevention or treatment of feline herpesvirus 1 infection in cats: a systematic review. BMC Veterinary Research (2015) 11:284  PDF  |  PMID: 26573523

32.
Bunnik EM, Le Roch KG. PfAlba1: master regulator of translation in the malaria parasite. Genome Biology (2015) 16(1):221 [Research Highlight]  PDF  |  PMID: 26450574

31.
Bunnik EM, Ay F, Varoquaux N, Vert JP, Noble WS, Le Roch KG. Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum. BioEssays (2015) 37(2):182-194 [Review]  PDF  |  PMID: 25394267

30.
Bunnik EM and Le Roch KG. Mechanisms regulating transcription in Plasmodium falciparum as targets for novel antimalarial drugs. Analysis of parasite biology – from metabolism to drug discovery. (2016) Wiley, edited by S Muller, R Cerdan, E Guca and O Radulescu. [Book Chapter]
2014

29.
Polishko A, Bunnik EM, Le Roch KG, Lonardi S. PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads. BMC Bioinformatics (2014), 15(Suppl 9):S11  PDF  |  PMID: 25252810

28.
Bunnik EM, Polishko A, Prudhomme J, Ponts N, Gill SS, Lonardi S, Le Roch KG. DNA-encoded nucleosome occupancy is associated with transcriptional levels in the human malaria parasite Plasmodium falciparum. BMC Genomics (2014), 15:347  PDF  |  PMID: 24885191

27.
Bunnik EM, Ay F, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG. Three-dimensional modelling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Research (2014), 24:974-988  PDF  |  PMID: 24671853

26.
Cervantes S, Bunnik EM, Saraf A, Connor C, Escalante A, Sardiu M, Ponts N, Prudhomme J, Florens L, Le Roch K. The multifunctional autophagy pathway in the human malaria parasite, Plasmodium falciparum. Autophagy (2014), 10(1):80-92  PDF  |  PMID: 24275162

25.
Bunnik EM and Le Roch KG. Plasmodium »Nucleosome«. Encyclopedia of Malaria. Springer, edited by M Hommel and PG Kremsner. ISBN 978-1-4614-8325-0. Due July 2018. [Book Chapter]
2013

24.
Ponts N, Fu L, Harris EY, Zhang J, Chung DWD, Cervantes MC, Prudhomme J, Atanasova-Penichon V, Zehraoui E, Bunnik EM, Rodrigues EM, Lonardi S, Hicks GR, Wang Y, Le Roch KG. Genome-wide mapping of DNA methylations in the human malaria parasite Plasmodium falciparum. Cell Host & Microbe (2013), 14(6): 696-706 >F1000Prime Article Recommendation<  PDF  |  PMID: 24331467

23.
Bunnik EM, Chung DWD, Hamilton M, Ponts N, Saraf A, Prudhomme J, Florens L, Le Roch KG. Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum. Genome Biology (2013), 14(11):R128  PDF  |  PMID: 24267660

22.
Bunnik EM and Le Roch KG. An introduction to functional genomics and systems biology. Advances in Wound Care (2013), 2(9): 490-498 [Review]  PDF  |  PMID: 24527360
2012

21.
Poon AFY, Swenson LC, Bunnik EM, Edo-Matas D, Schuitemaker H, van ’t Wout AB, Harrigan PR. Reconstructing the Dynamics of HIV Evolution within hosts from serial deep sequence data. PLoS Computational Biology (2012), 8(11): e1002753  PDF  |  PMID: 23133358

20.
Wang Y, Whittall T, Rahman D, Bunnik EM, Vaughan R, Schøller J, Bergmeier LA, Montefiori D, Singh M, Schuitemaker H, Lehner T. The role of innate APOBEC3G and adaptive AID immune responses in HLA-HIV/SIV immunized SHIV infected macaques. PLoS One (2012), 7(4):e34433  PDF  |  PMID: 22514633

19.
Yang GB, Wang Y, Babaahmady K, Schøller J, Rahman D, Bunnik E, Spallek R, Zong CM, Duan JZ, Qin C, Jiang H, Singh M, Vaughan R, Bergmeier L, Schuitemaker H, Shao Y, Lehner T. Immunization with recombinant macaque MHC class I and II, HIVgp140 and SIVp27 complex inhibits SHIV infection in macaques. Journal of General Virolology (2012), 93(7):1506-1518  PDF  |  PMID: 22492918

18.
Bol SM, Booiman T, Van Manen D, Bunnik EM, Van Sighem AI, Sieberer M, Boeser-Nunnink B, De Wolf F, Schuitemaker H, Portegies P, Koostra NA and Van ’t Wout AB. Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia. PLoS ONE (2012), 7(2):e30990  PDF  |  PMID: 22347417
2011

17.
Bol SM, Booiman T, Bunnik EM, Moerland PD, van Dort K, Strauss JF 3rd, Sieberer M, Schuitemaker H, Kootstra NA, van 't Wout AB. Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages. Virology (2011), 420(1):32-42  PDF  |  PMID: 21920574

16.
Bunnik EM, Swenson LC, Edo-Matas D, Huang W, Dong W, Frantzell A, Petropoulos CJ, Coakley E, Schuitemaker H, Harrigan PR, van 't Wout AB. Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing. PLoS Pathogens (2011), 7(6):e1002106  PDF  |  PMID: 21731496

15.
van Gils MJ, Bunnik EM, Boeser-Nunnink BD, Burger JA, Terlouw-Klein M, Verwer N, Schuitemaker H. Longer V1V2 region with increased number of potential N-linked glycosylation sites in the HIV-1 envelope glycoprotein protects against HIV-specific neutralizing antibodies. Journal of Virology (2011), 85(14):6986-95  PDF  |  PMID: 21593147

14.
Bunnik EM, Euler Z, Burger JA, Boeser-Nunnink BD, Grijsen ML, Prins JM, Schuitemaker H. Activity of broadly neutralizing antibodies, including PG9, PG16, and VRC01, against recently transmitted subtype B HIV-1 variants from early and late in the epidemic. Journal of Virology (2011), 85(14):7236-45  PDF  |  PMID: 21561918

13.
Mörner A, Jansson M, Bunnik EM, Schøller J, Vaughan R, Wang Y, Montefiori DC, Otting N, Bontrop R, Bergmeier LA, Singh M, Wyatt RT, Schuitemaker H, Biberfeld G, Thorstensson R, Lehner T. Immunization with recombinant HLA classes I and II, HIV-1 gp140, and SIV p27 elicits protection against heterologous SHIV infection in rhesus macaques. Journal of Virology (2011), 85(13):6442-52 >F1000Prime Article Recommendations: [1] [2] <  PDF  |  PMID: 21490092
2010

12.
Bunnik EM, Euler Z, Welkers MRA, Boeser-Nunnink BDM, Grijsen ML, Prins JM, Schuitemaker H. Adaptation of HIV-1 envelope gp120 to humoral immunity at a population level. Nature Medicine (2010), 16(9):995-997 >F1000Prime Article Recommendations: [1] [2] <  PDF  |  PMID: 20802498

11.
Bunnik EM, van Gils MJ, Lobbrecht MSD, Pisas L, Nanlohy NM, van Baarle D, van Nuenen AC, Hessell AJ, Schuitemaker H. Emergence of b12 neutralization resistant HIV-1 variants during natural infection in the absence of humoral or cellular immune pressure. Journal of General Virology (2010), 91(5): 1354-1364  PDF  |  PMID: 20053822

10.
Euler Z, Bunnik EM, van Gils MJ, Phung P, Schweighardt B, Wrin T, Schuitemaker H. Cross-reactive neutralizing humoral immunity does not protect from HIV-1 disease progression. Journal of Infectious Diseases (2010), 201(7): 1045-1053  PDF  |  PMID: 20170371

9.
van Gils MJ, Bunnik EM, Burger JA, Jacob Y, Schweighardt B, Wrin T, Schuitemaker H. Rapid escape from preserved cross-reactive neutralizing humoral immunity without loss of viral fitness in HIV-1-infected progressors and long-term non-progressors. Journal of Virology (2010), 84(7): 3576-3585  PDF  |  PMID: 20071586

8.
Bunnik EM, Lobbrecht MSD, van Nuenen AC, Schuitemaker H. Escape from autologous humoral immunity of HIV-1 is not associated with a decrease in replicative capacity. Virology (2010), 397(1):224-230  PDF  |  PMID: 19945135
2009

7.
Bunnik EM, van Gils MJ, Lobbrecht MSD, Pisas L, van Nuenen AC, Schuitemaker H. Changing sensitivity to broadly neutralizing antibodies b12, 2G12, 2F5, and 4E10 of primary subtype B HIV-1 variants in the natural course of infection. Virology (2009), 390(2):348-355  PDF  |  PMID: 19539340

6.
Polonis VR, Schuitemaker H, Bunnik EM, Brown BK, Scarlatti G. Impact of host cell variation on the neutralization of HIV-1 in vitro. Current Opinions in HIV and AIDS (2009), 4:400-407 [Review]  PDF  |  PMID: 20048704
2008

5.
Bunnik EM, Pisas L, van Nuenen AC, Schuitemaker H. Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection. Journal of Virology (2008), 82(16):7932-7941 >F1000Prime Article Recommendation<  PDF  |  PMID: 18524815
2007

4.
Vermeulen JN, Prins JM, Bunnik E, Hack EC, Jurriaans S, Miedema F, Lange JMA, Schuitemaker H. Intravenous Immunoglobulin (IVIG) treatment of human immunodeficiency virus type 1 infected therapy-naïve individuals. AIDS Research and Human Retroviruses (2007), 23(11):1348-1353  PDF  |  PMID: 18184076

3.
Bunnik EM, Quakkelaar ED, van Alphen FPJ, Boeser-Nunnink BDM, van Nuenen AC, Schuitemaker H. Escape of human immunodeficiency virus type 1 from broadly neutralizing antibodies is not associated with a reduction of viral replicative capacity in vitro. Virology (2007), 363(2):447-453  PDF  |  PMID: 17355886

2.
Bunnik EM, Quakkelaar ED, van Nuenen AC, Boeser-Nunnink B, Schuitemaker H. Increased neutralization sensitivity of recently emerged CXCR4-using human immunodeficiency virus type 1 strains compared to coexisting CCR5-using variants from the same patient. Journal of Virology (2007), 81(2):525-531  PDF  |  PMID: 17079299
2003

1.
Vader LW, Stepniak DT, Bunnik EM, Kooy YM, de Haan W, Drijfhout JW, Van Veelen PA, Koning F. Characterization of cereal toxicity for celiac disease patients based on protein homology in grains. Gastroenterology (2003), 125(4):1105-1113  PDF  |  PMID: 14517794
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