Benjamin Berkhout

Research output

Research output per year 1980 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2015 2016 2017 2018 2024

• 494 Article
• 49 Review article
• 28 Editorial
• 22 Chapter
• 26 More
  • 22 Comment/Letter to the editor
  • 2 Book editing
  • 2 Erratum/Corrigendum

Research output per year

Research output per year

Search results

• 2015

  Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis: A Combined Mathematical Model and Phylogenetic Analysis

  AUTHOR GROUP & ATHENA observational cohort, 1 Nov 2015, In: PLoS medicine. 12, 11, p. e1001898; discussion e1001898 e1001898.

  Research output: Contribution to journal › Article › Academic › peer-review
  53 Citations (Scopus)

• Gene Therapy Strategies to Block HIV-1 Replication by RNA Interference

  Herrera-Carrillo, E. & Berkhout, B., 2015, In: Advances in experimental medicine and biology. 848, p. 71-95

  Research output: Contribution to journal › Article › Academic › peer-review
  11 Citations (Scopus)

• High current CD4+ T cell count predicts suboptimal adherence to antiretroviral therapy

  Pasternak, A. O., de Bruin, M., Bakker, M., Berkhout, B. & Prins, J. M., 2015, In: PLOS ONE. 10, 10, p. e0140791 11 p., e0140791.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  13 Citations (Scopus)

• HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5' splice site

  Mueller, N., Berkhout, B. & Das, A. T., 2015, In: Journal of general virology. 96, Part 7, p. 1906-1917

  Research output: Contribution to journal › Article › Academic › peer-review
  16 Citations (Scopus)

• Hiv-1-transcriptie: recente verrassingen

  Harwig, A. & Berkhout, B., 2015, In: HIV Bulletin. 3, p. 7-9

  Research output: Contribution to journal › Article › Professional

• HIV-1 transcriptional silencing caused by TRIM22 inhibition of Sp1 binding to the viral promoter

  Turrini, F., Marelli, S., Kajaste-Rudnitski, A., Lusic, M., van Lint, C., Das, A. T., Harwig, A., Berkhout, B. & Vicenzi, E., 2015, In: Retrovirology. 12, 1, p. 104

  Research output: Contribution to journal › Article › Academic › peer-review
  62 Citations (Scopus)

• Human immunodeficiency virus type 1 splicing at the major splice donor site is controlled by highly conserved RNA sequence and structural elements

  Mueller, N., Klaver, B., Berkhout, B. & Das, A. T., 2015, In: Journal of general virology. 96, 11, p. 3389-3395

  Research output: Contribution to journal › Article › Academic › peer-review
  7 Citations (Scopus)

• Immunogenicity of Stabilized HIV-1 Envelope Trimers with Reduced Exposure of Non-neutralizing Epitopes

  de Taeye, S. W., Ozorowski, G., Torrents de la Peña, A., Guttman, M., Julien, J-P., van den Kerkhof, T. L. G. M., Burger, J. A., Pritchard, L. K., Pugach, P., Yasmeen, A., Crampton, J., Hu, J., Bontjer, I., Torres, J. L., Arendt, H., DeStefano, J., Koff, W. C., Schuitemaker, H., Eggink, D., Berkhout, B., & 11 othersDean, H., Labranche, C., Crotty, S., Crispin, M., Montefiori, D. C., Klasse, P. J., Lee, K. K., Moore, J. P., Wilson, I. A., Ward, A. B. & Sanders, R. W., 2015, In: Cell. 163, 7, p. 1702-1715

  Research output: Contribution to journal › Article › Academic › peer-review
  265 Citations (Scopus)

• In silico prediction of ebolavirus RNA polymerase inhibition by specific combinations of approved nucleotide analogues

  van Hemert, F. J., Zaaijer, H. L. & Berkhout, B., 2015, In: Journal of clinical virology. 73, p. 89-94

  Research output: Contribution to journal › Article › Academic › peer-review
  4 Citations (Scopus)

• Jan van der Noordaa (1934-2015); A Virologist Pur Sang

  Berkhout, B. & Bukrinsky, M., 2015, In: Viruses. 7, 9, p. 5016-5017

  Research output: Contribution to journal › Article › Academic › peer-review

• Mechanistic insights on the Dicer-independent AGO2-mediated processing of AgoshRNAs

  Liu, Y. P., Karg, M., Harwig, A., Herrera-Carrillo, E., Jongejan, A., van Kampen, A. & Berkhout, B., 2015, In: RNA biology. 12, 1, p. 92-100

  Research output: Contribution to journal › Article › Academic › peer-review
  19 Citations (Scopus)

• On the biased nucleotide composition of the human coronavirus RNA genome

  Berkhout, B. & van Hemert, F., 2015, In: Virus Research. 202, p. 41-47

  Research output: Contribution to journal › Article › Academic › peer-review
  41 Citations (Scopus)

• On the primer binding site mutation that appears and disappears during HIV and SIV replication

  Berkhout, B. & Das, A. T., 2015, In: Retrovirology. 12, p. 75

  Research output: Contribution to journal › Article › Academic › peer-review
  3 Citations (Scopus)

• Reactivation of Neutralized HIV-1 by Dendritic Cells Is Dependent on the Epitope Bound by the Antibody

  van Montfort, T., Thomas, A. A. M., Krawczyk, P. M., Berkhout, B., Sanders, R. W. & Paxton, W. A., 2015, In: Journal of immunology (Baltimore, Md.. 195, 8, p. 3759-3768

  Research output: Contribution to journal › Article › Academic › peer-review
  4 Citations (Scopus)

• Specific mutations in the C-terminus domain of HBV surface antigen significantly correlate with low level of serum HBV-DNA in patients with chronic HBV infection

  Mirabelli, C., Surdo, M., van Hemert, F., Lian, Z., Salpini, R., Cento, V., Cortese, M. F., Aragri, M., Pollicita, M., Alteri, C., Bertoli, A., Berkhout, B., Micheli, V., Gubertini, G., Santoro, M. M., Romano, S., Visca, M., Bernassola, M., Longo, R., de Sanctis, G. M., & 13 othersTrimoulet, P., Fleury, H., Marino, N., Mazzotta, F., Cappiello, G., Spanò, A., Sarrecchia, C., Zhang, J. M., Andreoni, M., Angelico, M., Verheyen, J., Perno, C. F. & Svicher, V., 2015, In: Journal of Infection. 70, 3, p. 288-298

  Research output: Contribution to journal › Article › Academic › peer-review
  14 Citations (Scopus)

• The HIV-1 leader RNA is exquisitely sensitive to structural changes

  van Bel, N., Ghabri, A., Das, A. T. & Berkhout, B., 2015, In: Virology. 483, p. 236-252

  Research output: Contribution to journal › Article › Academic › peer-review
  14 Citations (Scopus)

• The impact of HIV-1 genetic diversity on the efficacy of a combinatorial RNAi-based gene therapy

  Herrera-Carrillo, E. & Berkhout, B., 2015, In: Gene therapy. 22, 6, p. 485-495

  Research output: Contribution to journal › Article › Academic › peer-review
  22 Citations (Scopus)

• Toward optimization of AgoshRNA molecules that use a non-canonical RNAi pathway: variations in the top and bottom base pairs

  Herrera-Carrillo, E., Harwig, A. & Berkhout, B., 2015, In: RNA biology. 12, 4, p. 447-456

  Research output: Contribution to journal › Article › Academic › peer-review
  14 Citations (Scopus)

• Towards Antiviral shRNAs Based on the AgoshRNA Design

  Liu, Y. P., Karg, M., Herrera-Carrillo, E. & Berkhout, B., 2015, In: PLOS ONE. 10, 6, p. e0128618

  Research output: Contribution to journal › Article › Academic › peer-review
  9 Citations (Scopus)

• With a Little Help from my Enteric Microbial Friends

  Berkhout, B., 2015, In: Frontiers in Medicine. 2, p. 30

  Research output: Contribution to journal › Article › Academic › peer-review
  1 Citation (Scopus)
• 2014

  A short sequence motif in the 5' leader of the HIV-1 genome modulates extended RNA dimer formation and virus replication

  van Bel, N., Das, A. T., Cornelissen, M., Abbink, T. E. M., Berkhout, B. & Abbink, G. E. M., 2014, In: Journal of Biological Chemistry. 289, 51, p. 35061-35074

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  17 Citations (Scopus)

• Comparison of droplet digital PCR and seminested real-time PCR for quantification of cell-associated HIV-1 RNA

  Kiselinova, M., Pasternak, A. O., de Spiegelaere, W., Vogelaers, D., Berkhout, B. & Vandekerckhove, L., 2014, In: PLOS ONE. 9, 1, p. e85999

  Research output: Contribution to journal › Article › Academic › peer-review
  132 Citations (Scopus)

• Differential binding of tenofovir and adefovir to reverse transcriptase of hepatitis B virus

  van Hemert, F. J., Berkhout, B. & Zaaijer, H. L., 2014, In: PLOS ONE. 9, 9, p. e106324

  Research output: Contribution to journal › Article › Academic › peer-review
  18 Citations (Scopus)

• HIV-1-based lentiviral vectors

  Liu, Y. P. & Berkhout, B., 2014, In: Methods in molecular biology (Clifton, N.J.). 1087, p. 273-284

  Research output: Contribution to journal › Article › Academic › peer-review
  14 Citations (Scopus)

• HIV-1 splicing at the major splice donor site is restricted by RNA structure

  Mueller, N., van Bel, N., Berkhout, B. & Das, A. T., 2014, In: Virology. 468-470, p. 609-620

  Research output: Contribution to journal › Article › Academic › peer-review
  25 Citations (Scopus)

• Interplay between viral Tat protein and c-Jun transcription factor in controlling LTR promoter activity in different human immunodeficiency virus type I subtypes

  van der Sluis, R. M., Derking, R., Breidel, S., Speijer, D., Berkhout, B. & Jeeninga, R. E., 2014, In: Journal of general virology. 95, PART 4, p. 968-979 12 p.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  13 Citations (Scopus)

• In Vivo SELEX of Single-Stranded Domains in the HIV-1 Leader RNA

  van Bel, N., Das, A. T. & Berkhout, B., 2014, In: Journal of Virology. 88, 4, p. 1870-1880

  Research output: Contribution to journal › Article › Academic › peer-review
  17 Citations (Scopus)

• Obituary: Axel Rethwilm (1959-2014)

  Berkhout, B., Bodem, J., Erlwein, O., Herchenröder, O., Khan, A. S., Lever, A. M., Lindemann, D., Linial, M. L., Löchelt, M., McClure, M. O., Scheller, C. & Weiss, R. A., 2014, In: Retrovirology. 11, 1, p. 85

  Research output: Contribution to journal › Article › Academic › peer-review

• On the nucleotide composition and structure of retroviral RNA genomes

  van Hemert, F., van der Kuyl, A. C. & Berkhout, B., 2014, In: Virus Research. 193, p. 16-23

  Research output: Contribution to journal › Article › Academic › peer-review
  19 Citations (Scopus)

• Probing the shRNA characteristics that hinder Dicer recognition and consequently allow Ago-mediated processing and AgoshRNA activity

  Herrera-Carrillo, E., Harwig, A., Liu, Y. P. & Berkhout, B., 2014, In: RNA (New York, N.Y.). 20, 9, p. 1410-1418

  Research output: Contribution to journal › Article › Academic › peer-review
  30 Citations (Scopus)

• Retroviral microRNAs

  Harwig, A., Das, A. T. & Berkhout, B., 2014, In: Current opinion in virology. 7, p. 47-54

  Research output: Contribution to journal › Article › Academic › peer-review
  38 Citations (Scopus)

• Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

  de Vree, P. J. P., de Wit, E., Yilmaz, M., van de Heijning, M., Klous, P., Verstegen, M. J. A. M., Wan, Y., Teunissen, H., Krijger, P. H. L., Geeven, G., Eijk, P. P., Sie, D., Ylstra, B., Hulsman, L. O. M., van Dooren, M. F., van Zutven, L. J. C. M., van den Ouweland, A., Verbeek, S., van Dijk, K. W., Cornelissen, M., & 20 othersDas, A. T., Berkhout, B., Sikkema-Raddatz, B., van den Berg, E., van der Vlies, P., Weening, D., den Dunnen, J. T., Matusiak, M., Lamkanfi, M., Ligtenberg, M. J. L., ter Brugge, P., Jonkers, J., Foekens, J. A., Martens, J. W., van der Luijt, R., van Amstel, H. K. P., van Min, M., Splinter, E., de Laat, W. & Ben, B., 2014, In: Nature biotechnology. 32, 10, p. 1019-1025

  Research output: Contribution to journal › Article › Academic › peer-review
  191 Citations (Scopus)

• The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome

  van Bel, N., van der Velden, Y., Bonnard, D., Le Rouzic, E., Das, A. T., Benarous, R. & Berkhout, B., 2014, In: PLOS ONE. 9, 7, p. e103552

  Research output: Contribution to journal › Article › Academic › peer-review
  20 Citations (Scopus)

• The impact of unprotected T cells in RNAi-based gene therapy for HIV-AIDS

  Herrera-Carrillo, E., Liu, Y. P. & Berkhout, B., 2014, In: Molecular therapy. 22, 3, p. 596-606

  Research output: Contribution to journal › Article › Academic › peer-review
  17 Citations (Scopus)

• The search for a T cell line for testing novel antiviral strategies against HIV-1 isolates of diverse receptor tropism and subtype origin

  Herrera-Carrillo, E., Paxton, W. A. & Berkhout, B., 2014, In: Journal of virological methods. 203, p. 88-96

  Research output: Contribution to journal › Article › Academic › peer-review
  8 Citations (Scopus)
• 2013

  An AP-1 binding site in the enhancer/core element of the HIV-1 promoter controls the ability of HIV-1 to establish latent infection

  Duverger, A., Wolschendorf, F., Zhang, M., Wagner, F., Hatcher, B., Jones, J., Cron, R. Q., van der Sluis, R. M., Jeeninga, R. E., Berkhout, B. & Kutsch, O., 2013, In: Journal of Virology. 87, 4, p. 2264-2277

  Research output: Contribution to journal › Article › Academic › peer-review
  73 Citations (Scopus)

• An AUG codon upstream of rev and env open reading frames ensures optimal translation of the simian immunodeficiency virus Env protein

  van der Velden, G. J., Vink, M. A., Klaver, B., Das, A. T. & Berkhout, B., 2013, In: Virology. 436, 1, p. 191-200

  Research output: Contribution to journal › Article › Academic › peer-review
  3 Citations (Scopus)

• Anti-HBV treatment induces novel reverse transcriptase mutations with reflective effect on HBV S antigen

  Cento, V., van Hemert, F., Neumann-Fraune, M., Mirabelli, C., Di Maio, V-C., Salpini, R., Bertoli, A., Micheli, V., Gubertini, G., Romano, S., Visca, M., de Sanctis, G-M., Berkhout, B., Marino, N., Mazzotta, F., Cappiello, G., Spanò, A., Sarrecchia, C., Ceccherini-Silberstein, F., Andreoni, M., & 4 othersAngelico, M., Verheyen, J., Perno, C. F. & Svicher, V., 2013, In: Journal of Infection. 67, 4, p. 303-312

  Research output: Contribution to journal › Article › Academic › peer-review
  26 Citations (Scopus)

• Antiviral strategies combining antiretroviral drugs with RNAi-mediated attack on HIV-1 and cellular co-factors

  Boutimah, F., Eekels, J. J. M., Liu, Y. P. & Berkhout, B., 2013, In: Antiviral Research. 98, 1, p. 121-129

  Research output: Contribution to journal › Article › Academic › peer-review
  24 Citations (Scopus)

• Autologous antibody capture to enrich immunogenic viruses for viral discovery

  Oude Munnink, B. B., Jazaeri Farsani, S. M., Deijs, M., Jonkers, J., Verhoeven, J. T. P., Ieven, M., Goossens, H., de Jong, M. D., Berkhout, B., Loens, K., Kellam, P., Bakker, M., Canuti, M., Cotten, M. & van der Hoek, L., 2013, In: PLOS ONE. 8, 11, p. e78454

  Research output: Contribution to journal › Article › Academic › peer-review
  15 Citations (Scopus)

• Comparative Immunogenicity of Evolved V1V2-Deleted HIV-1 Envelope Glycoprotein Trimers

  Bontjer, I., Melchers, M., Tong, T., van Montfort, T., Eggink, D., Montefiori, D., Olson, W. C., Moore, J. P., Binley, J. M., Berkhout, B. & Sanders, R. W., 2013, In: PLOS ONE. 8, 6, p. e67484

  Research output: Contribution to journal › Article › Academic › peer-review
  7 Citations (Scopus)

• Conditionally-live attenuated SIV upregulates global T effector memory cell frequency under replication permissive conditions

  Manoussaka, M. S., Berry, N., Ferguson, D., Stebbings, R., Robinson, M., Ham, C., Page, M., Li, B., Das, A. T., Berkhout, B., Almond, N. & Cranage, M. P., 2013, In: Retrovirology. 10, 1, p. 59

  Research output: Contribution to journal › Article › Academic › peer-review
  14 Citations (Scopus)

• Dendritic Cell-induced Activation of Latent HIV-1 Provirus in Actively Proliferating Primary T Lymphocytes

  van der Sluis, R. M., van Montfort, T., Pollakis, G., Sanders, R. W., Speijer, D., Berkhout, B. & Jeeninga, R. E., 2013, In: PLoS pathogens. 9, 3, p. e1003259-(15 p.) e1003259.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  38 Citations (Scopus)

• Design of lentivirally expressed siRNAs

  Liu, Y. P. & Berkhout, B., 2013, In: Methods in molecular biology (Clifton, N.J.). 942, p. 233-257

  Research output: Contribution to journal › Article › Academic › peer-review
  7 Citations (Scopus)

• Dicer-independent processing of short hairpin RNAs

  Liu, Y. P., Schopman, N. C. T. & Berkhout, B., 2013, In: Nucleic Acids Research. 41, 6, p. 3723-3733

  Research output: Contribution to journal › Article › Academic › peer-review
  70 Citations (Scopus)

• Establishment and molecular mechanisms of HIV-1 latency in T cells

  van der Sluis, R. M., Jeeninga, R. E. & Berkhout, B., 2013, In: Current opinion in virology. 3, 6, p. 700-706

  Research output: Contribution to journal › Article › Academic › peer-review
  21 Citations (Scopus)

• Has the rate of CD4 cell count decline before initiation of antiretroviral therapy changed over the course of the Dutch HIV epidemic among MSM?

  AUTHOR GROUP, van Dissel, J. T., Arend, S. M., van Nieuwkoop, C., de Boer, M. G. J., Jolink, H., den Hollander, J. G., Pogany, K., Bronsveld, W., Kortmann, W., van Twillert, G., van Houte, D. P. F., Polée, M. B., van Vonderen, M. G. A., ten Napel, C. H. H., Kootstra, G. J., Brinkman, K., Blok, W. L., Frissen, P. H. J., Schouten, W. E. M., & 29 othersvan den Berk, G. E. L., Juttmann, J. R., van Kasteren, M. E. E., Brouwer, A. E., Mulder, J. W., van Gorp, E. C. M., Smit, P. M., Weijer, S., van Eeden, A., Verhagen, D. W. M., Sprenger, H. G., Doedens, R., Scholvinck, E. H., van Assen, S., Stek, C. J., Hoepelman, I. M., Mudrikova, T., Schneider, M. M. E., Jaspers, C. A. J. J., Ellerbroek, P. M., Peters, E. J. G., Maarschalk-Ellerbroek, L. J., Oosterheert, J. J., Arends, J. E., Wassenberg, M. W. M., van der Hilst, J. C. H., Richter, C., van der Berg, J. P. & Gisolf, E. H., 27 May 2013, In: PLOS ONE. 8, 5, p. e64437 e64437.

  Research output: Contribution to journal › Article › Academic › peer-review

  Open Access
  12 Citations (Scopus)

• High prevalence of hepatitis B virus dual infection with genotypes A and G in HIV-1 infected men in Amsterdam, the Netherlands, during 2000-2011

  van der Kuyl, A. C., Zorgdrager, F., Hogema, B., Bakker, M., Jurriaans, S., Back, N. K. T., Berkhout, B., Zaaijer, H. L. & Cornelissen, M., 2013, In: BMC Infectious Diseases. 13, 1, p. 540

  Research output: Contribution to journal › Article › Academic › peer-review
  17 Citations (Scopus)

• Human immunodeficiency virus type 1 gp120 envelope characteristics associated with disease progression differ in family members infected with genetically similar viruses

  Baan, E., van der Sluis, R. M., Bakker, M. E., Bekker, V., Pajkrt, D., Jurriaans, S., Kuijpers, T. W., Berkhout, B., Wolthers, K. C., Paxton, W. A. & Pollakis, G., 2013, In: Journal of general virology. 94, 1, p. 20-29

  Research output: Contribution to journal › Article › Academic › peer-review
  2 Citations (Scopus)

• In memoriam Kuan-Teh Jeang (1958-2013): retrovirologist par excellence and founding editor of Retrovirology

  Beemon, K. & Berkhout, B., 2013, In: Journal of Virology. 87, 12, p. 6539-6540

  Research output: Contribution to journal › Article › Academic › peer-review