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Items: 1 to 50 of 525

1.

Elimination of infectious HIV DNA by CRISPR-Cas9.

Das AT, Binda CS, Berkhout B.

Curr Opin Virol. 2019 Aug 23;38:81-88. doi: 10.1016/j.coviro.2019.07.001. [Epub ahead of print] Review.

2.

A trip down memory lane with Retrovirology.

Benkirane M, Berkhout B, Borrow P, Fassati A, Fujii M, Garcia-Martinez JV, Margolis D, Nijhuis M, Parent L, Strebel K, Venter F, Kirchhoff F, Lever A, Ross S, Mak J.

Retrovirology. 2019 Aug 21;16(1):22. doi: 10.1186/s12977-019-0485-y. No abstract available.

3.

On the generation of the MSD-Ѱ class of defective HIV proviruses.

Das AT, Pasternak AO, Berkhout B.

Retrovirology. 2019 Jul 11;16(1):19. doi: 10.1186/s12977-019-0481-2.

4.

IFI16 Targets the Transcription Factor Sp1 to Suppress HIV-1 Transcription and Latency Reactivation.

Hotter D, Bosso M, Jønsson KL, Krapp C, Stürzel CM, Das A, Littwitz-Salomon E, Berkhout B, Russ A, Wittmann S, Gramberg T, Zheng Y, Martins LJ, Planelles V, Jakobsen MR, Hahn BH, Dittmer U, Sauter D, Kirchhoff F.

Cell Host Microbe. 2019 Jun 12;25(6):858-872.e13. doi: 10.1016/j.chom.2019.05.002. Epub 2019 Jun 4.

PMID:
31175045
5.

Interferon-inducible TRIM22 contributes to maintenance of HIV-1 proviral latency in T cell lines.

Turrini F, Saliu F, Forlani G, Das AT, Van Lint C, Accolla RS, Berkhout B, Poli G, Vicenzi E.

Virus Res. 2019 Aug;269:197631. doi: 10.1016/j.virusres.2019.05.009. Epub 2019 May 25.

PMID:
31136823
6.

Influence of a 3' Terminal Ribozyme on AgoshRNA Biogenesis and Activity.

Herrera-Carrillo E, Gao Z, Berkhout B.

Mol Ther Nucleic Acids. 2019 Jun 7;16:452-462. doi: 10.1016/j.omtn.2019.04.001. Epub 2019 Apr 8.

7.

Boosting AgoshRNA activity by optimized 5'-terminal nucleotide selection.

Gao Z, Berkhout B, Herrera-Carrillo E.

RNA Biol. 2019 Jul;16(7):890-898. doi: 10.1080/15476286.2019.1599259. Epub 2019 Apr 16.

8.

The Impact of HIV-1 Genetic Diversity on CRISPR-Cas9 Antiviral Activity and Viral Escape.

Darcis G, Binda CS, Klaver B, Herrera-Carrillo E, Berkhout B, Das AT.

Viruses. 2019 Mar 13;11(3). pii: E255. doi: 10.3390/v11030255.

9.

Dendritic cells potently purge latent HIV-1 beyond TCR-stimulation, activating the PI3K-Akt-mTOR pathway.

van Montfort T, van der Sluis R, Darcis G, Beaty D, Groen K, Pasternak AO, Pollakis G, Vink M, Westerhout EM, Hamdi M, Bakker M, van der Putten B, Jurriaans S, Prins JH, Jeeninga R, Thomas AAM, Speijer D, Berkhout B.

EBioMedicine. 2019 Apr;42:97-108. doi: 10.1016/j.ebiom.2019.02.014. Epub 2019 Feb 26.

10.

"Integration of viral sequences into eukaryotic host genomes: legacy of ancient infections".

Tomonaga K, Suzuki N, Berkhout B.

Virus Res. 2019 Mar;262:1. doi: 10.1016/j.virusres.2018.12.012. No abstract available.

PMID:
30732705
11.

HIV-1 anchor inhibitors and membrane fusion inhibitors target distinct but overlapping steps in virus entry.

Eggink D, Bontjer I, de Taeye SW, Langedijk JPM, Berkhout B, Sanders RW.

J Biol Chem. 2019 Apr 12;294(15):5736-5746. doi: 10.1074/jbc.RA119.007360. Epub 2019 Jan 29.

12.

Citizen science for better management: Lessons learned from three Norwegian beach litter data sets.

Falk-Andersson J, Berkhout BW, Abate TG.

Mar Pollut Bull. 2019 Jan;138:364-375. doi: 10.1016/j.marpolbul.2018.11.021. Epub 2018 Nov 29.

PMID:
30660285
13.

A Single H1 Promoter Can Drive Both Guide RNA and Endonuclease Expression in the CRISPR-Cas9 System.

Gao Z, Herrera-Carrillo E, Berkhout B.

Mol Ther Nucleic Acids. 2019 Mar 1;14:32-40. doi: 10.1016/j.omtn.2018.10.016. Epub 2018 Nov 1.

14.

Euclidean Distance Analysis Enables Nucleotide Skew Analysis in Viral Genomes.

van Hemert F, Jebbink M, van der Ark A, Scholer F, Berkhout B.

Comput Math Methods Med. 2018 Oct 30;2018:6490647. doi: 10.1155/2018/6490647. eCollection 2018.

15.

Improvement of the CRISPR-Cpf1 system with ribozyme-processed crRNA.

Gao Z, Herrera-Carrillo E, Berkhout B.

RNA Biol. 2018;15(12):1458-1467. doi: 10.1080/15476286.2018.1551703. Epub 2018 Nov 29.

16.

Posttranscriptional Regulation of HIV-1 Gene Expression during Replication and Reactivation from Latency by Nuclear Matrix Protein MATR3.

Sarracino A, Gharu L, Kula A, Pasternak AO, Avettand-Fenoel V, Rouzioux C, Bardina M, De Wit S, Benkirane M, Berkhout B, Van Lint C, Marcello A.

MBio. 2018 Nov 13;9(6). pii: e02158-18. doi: 10.1128/mBio.02158-18.

17.

SNP rs688 within the low-density lipoprotein receptor (LDL-R) gene associates with HCV susceptibility.

Steba GS, Koekkoek SM, Tanck MWT, Vanhommerig JW, van der Meer JTM, Kwa D, Brinkman K, Prins M, Berkhout B, Pollakis G, Molenkamp R, Schinkel J, Paxton WA; MOSAIC (MSM observational Study of Acute infection with Hepatitis C) Study Group and the ACS (Amsterdam Cohort Studies).

Liver Int. 2019 Mar;39(3):463-469. doi: 10.1111/liv.13978. Epub 2018 Oct 17.

18.

RNA Polymerase II Activity of Type 3 Pol III Promoters.

Gao Z, Herrera-Carrillo E, Berkhout B.

Mol Ther Nucleic Acids. 2018 Sep 7;12:135-145. doi: 10.1016/j.omtn.2018.05.001. Epub 2018 May 8.

19.

Human Immunodeficiency Virus Resistance to Dolutegravir: Are We Looking in the Wrong Place?

Darcis G, Berkhout B.

J Infect Dis. 2018 Nov 5;218(12):2020. doi: 10.1093/infdis/jiy474. No abstract available.

PMID:
30085190
20.

RNAi-mediated antiviral immunity in mammals.

Berkhout B.

Curr Opin Virol. 2018 Oct;32:9-14. doi: 10.1016/j.coviro.2018.07.008. Epub 2018 Jul 14. Review.

21.

Short Communication: Protective Efficacy of Broadly Neutralizing Antibody PGDM1400 Against HIV-1 Challenge in Humanized Mice.

van der Velden YU, Villaudy J, Siteur-van Rijnstra E, van der Linden CA, Frankin E, Weijer K, Schermer E, Vink MA, Berkhout B, Sanders RW, van Gils MJ.

AIDS Res Hum Retroviruses. 2018 Sep;34(9):790-793. doi: 10.1089/AID.2018.0114. Epub 2018 Aug 22.

PMID:
30003812
22.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C; BEEHIVE Collaboration.

Virus Evol. 2018 May 18;4(1):vey007. doi: 10.1093/ve/vey007. eCollection 2018 Jan.

23.

The HIV-1 Tat Protein Enhances Splicing at the Major Splice Donor Site.

Mueller N, Pasternak AO, Klaver B, Cornelissen M, Berkhout B, Das AT.

J Virol. 2018 Jun 29;92(14). pii: e01855-17. doi: 10.1128/JVI.01855-17. Print 2018 Jul 15.

24.

The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012.

van der Kuyl AC, Vink M, Zorgdrager F, Bakker M, Wymant C, Hall M, Gall A, Blanquart F, Berkhout B, Fraser C, Cornelissen M; BEEHIVE Collaboration.

Virus Res. 2018 May 2;250:51-64. doi: 10.1016/j.virusres.2018.04.008. Epub 2018 Apr 11.

25.

How Polypurine Tract Changes in the HIV-1 RNA Genome Can Cause Resistance against the Integrase Inhibitor Dolutegravir.

Das AT, Berkhout B.

MBio. 2018 Apr 10;9(2). pii: e00006-18. doi: 10.1128/mBio.00006-18. No abstract available.

26.

Tackling HIV Persistence: Pharmacological versus CRISPR-Based Shock Strategies.

Darcis G, Das AT, Berkhout B.

Viruses. 2018 Mar 29;10(4). pii: E157. doi: 10.3390/v10040157. Review.

27.

Delineation of the Exact Transcription Termination Signal for Type 3 Polymerase III.

Gao Z, Herrera-Carrillo E, Berkhout B.

Mol Ther Nucleic Acids. 2018 Mar 2;10:36-44. doi: 10.1016/j.omtn.2017.11.006. Epub 2017 Nov 21.

28.

Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes.

Cornelissen M, Gall A, van der Kuyl A, Wymant C, Blanquart F, Fraser C, Berkhout B.

Methods Mol Biol. 2018;1746:55-61. doi: 10.1007/978-1-4939-7683-6_5.

PMID:
29492886
29.

CRISPR-Cas Antiviral Strategies.

Jin DY, Berkhout B.

Virus Res. 2018 Jan 15;244:285. doi: 10.1016/j.virusres.2017.12.010. No abstract available.

PMID:
29406152
30.

What do we measure when we measure cell-associated HIV RNA.

Pasternak AO, Berkhout B.

Retrovirology. 2018 Jan 29;15(1):13. doi: 10.1186/s12977-018-0397-2. Review.

31.

DC-SIGN Polymorphisms Associate with Risk of Hepatitis C Virus Infection Among Men who Have Sex with Men but not Among Injecting Drug Users.

Steba GS, Koekkoek SM, Vanhommerig JW, Brinkman K, Kwa D, Van Der Meer JTM, Prins M, Berkhout B, Tanck M, Paxton WA, Molenkamp R, Schinkel J; MSM Observational Study of Acute Infection with Hepatitis C (MOSAIC) Study Group and Amsterdam Cohort Studies (ACS).

J Infect Dis. 2018 Jan 17;217(3):353-357. doi: 10.1093/infdis/jix587.

32.

The HIV-1 integrase-LEDGF allosteric inhibitor MUT-A: resistance profile, impairment of virus maturation and infectivity but without influence on RNA packaging or virus immunoreactivity.

Amadori C, van der Velden YU, Bonnard D, Orlov I, van Bel N, Le Rouzic E, Miralles L, Brias J, Chevreuil F, Spehner D, Chasset S, Ledoussal B, Mayr L, Moreau F, García F, Gatell J, Zamborlini A, Emiliani S, Ruff M, Klaholz BP, Moog C, Berkhout B, Plana M, Benarous R.

Retrovirology. 2017 Nov 9;14(1):50. doi: 10.1186/s12977-017-0373-2.

33.

The Battle of RNA Synthesis: Virus versus Host.

Harwig A, Landick R, Berkhout B.

Viruses. 2017 Oct 21;9(10). pii: E309. doi: 10.3390/v9100309. Review.

34.

Dicer-independent processing of small RNA duplexes: mechanistic insights and applications.

Herrera-Carrillo E, Berkhout B.

Nucleic Acids Res. 2017 Oct 13;45(18):10369-10379. doi: 10.1093/nar/gkx779. Review.

35.

Dendritic cells as natural latency reversing agent: A wake-up call for HIV-1.

van Montfort T, Speijer D, Berkhout B.

Virulence. 2017 Nov 17;8(8):1494-1497. doi: 10.1080/21505594.2017.1371898. Epub 2017 Sep 28. No abstract available.

36.

Combinatorial CRISPR-Cas9 and RNA Interference Attack on HIV-1 DNA and RNA Can Lead to Cross-Resistance.

Zhao N, Wang G, Das AT, Berkhout B.

Antimicrob Agents Chemother. 2017 Nov 22;61(12). pii: e01486-17. doi: 10.1128/AAC.01486-17. Print 2017 Dec.

37.

HIV-1 tolerates changes in A-count in a small segment of the pol gene.

Klaver B, van der Velden Y, van Hemert F, van der Kuyl AC, Berkhout B.

Retrovirology. 2017 Sep 5;14(1):43. doi: 10.1186/s12977-017-0367-0.

38.

Analysis of AgoshRNA maturation and loading into Ago2.

Harwig A, Kruize Z, Yang Z, Restle T, Berkhout B.

PLoS One. 2017 Aug 15;12(8):e0183269. doi: 10.1371/journal.pone.0183269. eCollection 2017.

39.

A Fourth Generation Lentiviral Vector: Simplifying Genomic Gymnastics.

Berkhout B.

Mol Ther. 2017 Aug 2;25(8):1741-1743. doi: 10.1016/j.ymthe.2017.06.005. No abstract available.

40.

CRISPR-Cas based antiviral strategies against HIV-1.

Wang G, Zhao N, Berkhout B, Das AT.

Virus Res. 2018 Jan 15;244:321-332. doi: 10.1016/j.virusres.2017.07.020. Epub 2017 Jul 29. Review.

41.

Improving miRNA Delivery by Optimizing miRNA Expression Cassettes in Diverse Virus Vectors.

Herrera-Carrillo E, Liu YP, Berkhout B.

Hum Gene Ther Methods. 2017 Aug;28(4):177-190. doi: 10.1089/hgtb.2017.036. Review.

42.

Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.

Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C; BEEHIVE collaboration.

PLoS Biol. 2017 Jul 13;15(7):e1002608. doi: 10.1371/journal.pbio.1002608. eCollection 2017 Jul.

43.

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.

Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C; BEEHIVE collaboration.

PLoS Biol. 2017 Jun 12;15(6):e2001855. doi: 10.1371/journal.pbio.2001855. eCollection 2017 Jun. Erratum in: PLoS Biol. 2017 Jul 13;15(7):e1002608.

44.

Mutation of nucleotides around the +1 position of type 3 polymerase III promoters: The effect on transcriptional activity and start site usage.

Gao Z, Harwig A, Berkhout B, Herrera-Carrillo E.

Transcription. 2017;8(5):275-287. doi: 10.1080/21541264.2017.1322170. Epub 2017 Jun 9.

45.

Influence of the loop size and nucleotide composition on AgoshRNA biogenesis and activity.

Herrera-Carrillo E, Harwig A, Berkhout B.

RNA Biol. 2017 Nov 2;14(11):1559-1569. doi: 10.1080/15476286.2017.1328349. Epub 2017 Nov 3.

46.

Silencing of HIV-1 by AgoshRNA molecules.

Herrera-Carrillo E, Harwig A, Berkhout B.

Gene Ther. 2017 Aug;24(8):453-461. doi: 10.1038/gt.2017.44. Epub 2017 May 29.

PMID:
28553929
47.

Novel AgoshRNA molecules for silencing of the CCR5 co-receptor for HIV-1 infection.

Herrera-Carrillo E, Berkhout B.

PLoS One. 2017 May 24;12(5):e0177935. doi: 10.1371/journal.pone.0177935. eCollection 2017.

48.

Professor Mark Wainberg.

Benkirane M, Berkhout B, Borrow P, Fassati A, Fujii M, Garcia JV, Gorry P, Lever A, Mak J, Nijhuis M, Strebel K, Venter F, Weiss R.

Retrovirology. 2017 May 5;14(1):30. doi: 10.1186/s12977-017-0353-6. No abstract available.

49.

Biological or pharmacological activation of protein kinase C alpha constrains hepatitis E virus replication.

Wang W, Wang Y, Debing Y, Zhou X, Yin Y, Xu L, Herrera Carrillo E, Brandsma JH, Poot RA, Berkhout B, Neyts J, Peppelenbosch MP, Pan Q.

Antiviral Res. 2017 Apr;140:1-12. doi: 10.1016/j.antiviral.2017.01.005. Epub 2017 Jan 8.

50.

Role of Occult and Post-acute Phase Replication in Protective Immunity Induced with a Novel Live Attenuated SIV Vaccine.

Berry N, Manoussaka M, Ham C, Ferguson D, Tudor H, Mattiuzzo G, Klaver B, Page M, Stebbings R, Das AT, Berkhout B, Almond N, Cranage MP.

PLoS Pathog. 2016 Dec 21;12(12):e1006083. doi: 10.1371/journal.ppat.1006083. eCollection 2016 Dec.

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