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Items: 1 to 50 of 516

1.

"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
2.

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 Jan 29. pii: jbc.RA119.007360. doi: 10.1074/jbc.RA119.007360. [Epub ahead of print]

3.

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
4.

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. 2018 Nov 1;14:32-40. doi: 10.1016/j.omtn.2018.10.016. [Epub ahead of print]

5.

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.

6.

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.

7.

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.

8.

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. 2018 Sep 27. doi: 10.1111/liv.13978. [Epub ahead of print]

PMID:
30260075
9.

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.

10.

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
11.

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.

12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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
20.

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
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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
38.

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.

39.

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.

40.

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.

41.

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.

42.

A Combinatorial CRISPR-Cas9 Attack on HIV-1 DNA Extinguishes All Infectious Provirus in Infected T Cell Cultures.

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

Cell Rep. 2016 Dec 13;17(11):2819-2826. doi: 10.1016/j.celrep.2016.11.057.

43.

The influence of the 5΄-terminal nucleotide on AgoshRNA activity and biogenesis: importance of the polymerase III transcription initiation site.

Herrera-Carrillo E, Gao ZL, Harwig A, Heemskerk MT, Berkhout B.

Nucleic Acids Res. 2017 Apr 20;45(7):4036-4050. doi: 10.1093/nar/gkw1203.

44.

Attacking HIV-1 RNA versus DNA by sequence-specific approaches: RNAi versus CRISPR-Cas.

Herrera-Carrillo E, Berkhout B.

Biochem Soc Trans. 2016 Oct 15;44(5):1355-1365. Review.

PMID:
27911718
45.

HIV-1 Escape from a Peptidic Anchor Inhibitor through Stabilization of the Envelope Glycoprotein Spike.

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

J Virol. 2016 Nov 14;90(23):10587-10599. doi: 10.1128/JVI.01616-16. Print 2016 Dec 1.

46.

HIV Reservoir: Finding the Right Needles in a Needlestack.

Pasternak AO, Berkhout B.

Cell Host Microbe. 2016 Sep 14;20(3):280-282. doi: 10.1016/j.chom.2016.08.011.

47.

Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage.

van Hemert F, van der Kuyl AC, Berkhout B.

J Gen Virol. 2016 Oct;97(10):2608-2619. doi: 10.1099/jgv.0.000579. Epub 2016 Aug 11.

PMID:
27519195
48.

From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.

Cornelissen M, Gall A, Vink M, Zorgdrager F, Binter Š, Edwards S, Jurriaans S, Bakker M, Ong SH, Gras L, van Sighem A, Bezemer D, de Wolf F, Reiss P, Kellam P, Berkhout B, Fraser C, van der Kuyl AC; BEEHIVE Consortium.

Virus Res. 2017 Jul 15;239:10-16. doi: 10.1016/j.virusres.2016.08.004. Epub 2016 Aug 4.

49.

A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal.

Mueller N, Das AT, Berkhout B.

Viruses. 2016 Jul 21;8(7). pii: E200. doi: 10.3390/v8070200.

50.

Widespread hepatitis B virus genotype G (HBV-G) infection during the early years of the HIV epidemic in the Netherlands among men who have sex with men.

Cornelissen M, Zorgdrager F, Bruisten SM, Bakker M, Berkhout B, van der Kuyl AC.

BMC Infect Dis. 2016 Jun 10;16:268. doi: 10.1186/s12879-016-1599-7.

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