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Ben Berkhout

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TOP 3
Fatima Boutimah; Julia J M Eekels; Ying-Poi Liu; Ben Berkhout
Antiviral strategies combining antiretroviral drugs with RNAi-mediated attack on HIV-1 and cellular co-factors.
Ying-Poi Liu; Nick C T Schopman; Ben Berkhout
Dicer-independent processing of short hairpin RNAs.
Renée M van der Sluis; Thijs van Montfort; Ben Berkhout; Georgios Pollakis; Rogier W Sanders; Dave Speijer; Rienk E Jeeninga
Dendritic cell-induced activation of latent HIV-1 provirus in actively proliferating primary T lymphocytes.

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All Publications

2013: Fatima Boutimah; Julia J M Eekels; Ying-Poi Liu; Ben Berkhout
Antiviral strategies combining antiretroviral drugs with RNAi-mediated attack on HIV-1 and cellular co-factors.
Antiviral research 2013;98(1):121-9.
2013: Ying-Poi Liu; Nick C T Schopman; Ben Berkhout
Dicer-independent processing of short hairpin RNAs.
Nucleic acids research 2013;41(6):3723-33.
2013: Renée M van der Sluis; Thijs van Montfort; Ben Berkhout; Georgios Pollakis; Rogier W Sanders; Dave Speijer; Rienk E Jeeninga
Dendritic cell-induced activation of latent HIV-1 provirus in actively proliferating primary T lymphocytes.
PLoS pathogens 2013;9(3):e1003259.
2013: Gisela J van der Velden; Monique A Vink; Atze T Das; Bep Klaver; Ben Berkhout
An AUG codon upstream of rev and env open reading frames ensures optimal translation of the simian immunodeficiency virus Env protein.
Virology 2013;436(1):191-200.
2013: Alexander O Pasternak; Vladimir V Lukashov; Ben Berkhout
Cell-associated HIV RNA: a dynamic biomarker of viral persistence.
Retrovirology 2013;10():41.
2013: Ben Berkhout; Persephone Borrow; Ariberto Fassati; Andrew Lever; Mark Wainberg; Masahiro Fujii
Monsef Benkirane awarded 2013 Ming K. Jeang Foundation Retrovirology Prize: Landmark HIV-1 research honoured.
Retrovirology 2013;10():38.
2013: Ben Berkhout; Persephone Borrow; Monsef Benkirane; Ariberto Fassati; Masahiro Fujii; Andrew Lever; Srimathy Sriskantharajah; Mark Wainberg; Matthew Cockerill
Obituary: Kuan-Teh Jeang.
Retrovirology 2013;10():28.
2013: Ben Berkhout; Kevin M Coombs
Quantitative omics and its application to study virus-host interactions-a new frontier.
Frontiers in microbiology 2013;4():31.
2013: Renée M van der Sluis; Thijs van Montfort; Rogier W Sanders; Nick C T Schopman; Ben Berkhout; Mireille Centlivre; Marion Cornelissen; Rienk E Jeeninga; William A Paxton; Georgios Pollakis
Quantitation of HIV-1 DNA with a sensitive TaqMan assay that has broad subtype specificity.
Journal of virological methods 2013;187(1):94-102.
2013: Ying-Poi Liu; Ben Berkhout
Design of lentivirally expressed siRNAs.
Methods in molecular biology (Clifton, N.J.) 2013;942():233-57.
2012: Gisela J van der Velden; Atze T Das; Bep Klaver; Ben Berkhout
Upstream AUG codons in the simian immunodeficiency virus SIVmac239 genome regulate Rev and Env protein translation.
Journal of virology 2012;86(22):12362-71.
2012: Nick C T Schopman; Antoine van Kampen; Thijs van Montfort; Marcel Willemsen; Jaap G Haasnoot; Stefanie A Knoepfel; Georgios Pollakis; Rogier W Sanders; Ben Berkhout
Selective packaging of cellular miRNAs in HIV-1 particles.
Virus research 2012;169(2):438-47.
2012: J J M Eekels; D Geerts; Rienk E Jeeninga; A O Pasternak; A M Schut; Ben Berkhout
A competitive cell growth assay for the detection of subtle effects of gene transduction on cell proliferation.
Gene therapy 2012;19(11):1058-64.
2012: Gisela J van der Velden; Monique A Vink; Ben Berkhout; Atze T Das
Tat has a dual role in simian immunodeficiency virus transcription.
The Journal of general virology 2012;93(Pt 10):2279-89.
2012: Nicolas Legrand; Christel H Uittenbogaart; Gisela J van der Velden; Kees Weijer; Ben Berkhout; Bianca Blom; Atze T Das; Marc Douaisi; Raphaël Ho Tsong Fang; Mireille Centlivre
A doxycycline-dependent human immunodeficiency virus type 1 replicates in vivo without inducing CD4+ T-cell depletion.
The Journal of general virology 2012;93(Pt 9):2017-27.
2012: Stefanie A Knoepfel; Puri Fortes; Amaya Abad; Xabi Abad; Ben Berkhout
Design of modified U1i molecules against HIV-1 RNA.
Antiviral research 2012;94(3):208-16.
2012: Mark Melchers; David C Montefiori; John P Moore; William C Olson; Tommy Tong; Ben Berkhout; James M Binley; Ilja Bontjer; Andrea Cerutti; Nancy P-Y Chung; Dirk Eggink; Maurizio Gentile; Per Johan Klasse; Rogier W Sanders
Targeting HIV-1 envelope glycoprotein trimers to B cells by using APRIL improves antibody responses.
Journal of virology 2012;86(5):2488-500.
2012: Geert J Schenk; Mireille Centlivre; Albertus G de Boer; P C Joost Haasnoot; Nicolas Legrand; Jaap Rip; Ben Berkhout
Efficient CRM197-mediated drug targeting to monocytes.
Journal of controlled release : official journal of the Controlled Release Society 2012;158(1):139-47.
2012: Ben Berkhout; Dirk Eggink; Rogier W Sanders
Is there a future for antiviral fusion inhibitors?
Current opinion in virology 2012;2(1):50-9.
2012: Ben Berkhout; Atze T Das
HIV-1 Escape From RNAi Antivirals: Yet Another Houdini Action?
Molecular therapy. Nucleic acids 2012;1():e26.
2012: Antoinette C van der Kuyl; Ben Berkhout
The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus.
Retrovirology 2012;9():92.
2012: Atze T Das; Alex Harwig; Martine M Vrolijk; Ben Berkhout
Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging.
Retrovirology 2012;9():59.
2012: Julia Jm Eekels; Dirk Geerts; Rienk E Jeeninga; Sophie Sagnier; Martine Biard-Piechaczyk; Ben Berkhout
Inhibition of HIV-1 replication with stable RNAi-mediated knockdown of autophagy factors.
Virology journal 2012;9():69.
2011: Thijs van Montfort; Michael Tuen; Ben Berkhout; Maikel Boot; Dirk Eggink; Catarina E Hioe; Rogier W Sanders
HIV-1 N-glycan composition governs a balance between dendritic cell-mediated viral transmission and antigen presentation.
Journal of immunology (Baltimore, Md. : 1950) 2011;187(9):4676-85.
2011: Dirk Eggink; Johannes P M Langedijk; Ben Berkhout; Ilja Bontjer; Rogier W Sanders
Resistance of human immunodeficiency virus type 1 to a third-generation fusion inhibitor requires multiple mutations in gp41 and is accompanied by a dramatic loss of gp41 function.
Journal of virology 2011;85(20):10785-97.
2011: Ben Berkhout; Rogier W Sanders
Molecular strategies to design an escape-proof antiviral therapy.
Antiviral research 2011;92(1):7-14.
2011: Ingrid M M Schellens; Hanneke Schuitemaker; Debbie Van Baarle; Hanneke W M van Deutekom; Can Keşmir; Neeltje Kootstra; Frank Miedema; Marjon Navis; Ben Berkhout; Brigitte Boeser-Nunnink; José A M Borghans
Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic.
AIDS (London, England) 2011;25(14):1691-700.
2011: Atze T Das; Alex Harwig; Ben Berkhout
The HIV-1 Tat protein has a versatile role in activating viral transcription.
Journal of virology 2011;85(18):9506-16.
2011: Ben Berkhout; Kelly Arts; Truus E M Abbink
Ribosomal scanning on the 5'-untranslated region of the human immunodeficiency virus RNA genome.
Nucleic acids research 2011;39(12):5232-44.
2011: Antoinette C van der Kuyl; Ben Berkhout
XMRV: not a mousy virus.
Journal of the Formosan Medical Association = Taiwan yi zhi 2011;110(5):273-4.
2011: Mireille Centlivre; Nicolas Legrand; Radjin Steingrover; Renee van der Sluis; Marlous L Grijsen; Margreet Bakker; Suzanne Jurriaans; Ben Berkhout; William A Paxton; Jan M Prins; Georgios Pollakis
Altered dynamics and differential infection profiles of lymphoid and myeloid cell subsets during acute and chronic HIV-1 infection.
Journal of leukocyte biology 2011;89(5):785-95.
2011: Ben Berkhout
HIV-1 as RNA evolution machine.
RNA biology 2011;8(2):225-9.
2011: Ben Berkhout; Dirk Eggink
New pathogenic viruses and novel antiviral drugs.
Expert review of anti-infective therapy 2011;9(2):161-3.
2011: Renée M van der Sluis; Marja L van Gerven; Ben Berkhout; Georgios Pollakis; Rienk E Jeeninga
Latency profiles of full length HIV-1 molecular clone variants with a subtype specific promoter.
Retrovirology 2011;8():73.
2011: Formijn J van Hemert; Ben Berkhout; Neeltje A Kootstra; Vladimir V Lukashov; Maarten A A van de Klundert; Hans L Zaaijer
Protein X of hepatitis B virus: origin and structure similarity with the central domain of DNA glycosylase.
PloS one 2011;6(8):e23392.
2011: Mark Melchers; John P Moore; Carolien van de Sandt; Thijs van Montfort; Ben Berkhout; Ilja Bontjer; Kathryn David; Robert P de Vries; Dirk Eggink; Katie Matthews; Rogier W Sanders
A stabilized HIV-1 envelope glycoprotein trimer fused to CD40 ligand targets and activates dendritic cells.
Retrovirology 2011;8():48.
2011: Ying-Poi Liu; Jan-Tinus Westerink; Karin von Eije; Ben Berkhout
RNAi-inducing lentiviral vectors for anti-HIV-1 gene therapy.
Methods in molecular biology (Clifton, N.J.) 2011;721():293-311.
2011: Jaap G Haasnoot; Ben Berkhout
RNAi and cellular miRNAs in infections by mammalian viruses.
Methods in molecular biology (Clifton, N.J.) 2011;721():23-41.
2011: Julia J M Eekels; Dirk Geerts; Rienk E Jeeninga; Ben Berkhout
Long-term inhibition of HIV-1 replication with RNA interference against cellular co-factors.
Antiviral research 2011;89(1):43-53.
2010: Ilja Bontjer; Mark Melchers; Dirk Eggink; Kathryn David; John P Moore; Ben Berkhout; Rogier W Sanders
Stabilized HIV-1 envelope glycoprotein trimers lacking the V1V2 domain, obtained by virus evolution.
The Journal of biological chemistry 2010;285(47):36456-70.
2010: Nick C T Schopman; Stephan Heynen; Joost Haasnoot; Ben Berkhout
A miRNA-tRNA mix-up: tRNA origin of proposed miRNA.
RNA biology 2010;7(5):573-6.
2010: Alexander O. Pasternak; Suzanne Jurriaans; Margreet Bakker; Ben Berkhout; Vladimir V Lukashov
Steady increase in cellular HIV-1 load during the asymptomatic phase of untreated infection despite stable plasma viremia.
AIDS (London, England) 2010;24(11):1641-9.
2010: Workenesh Ayele; Yared Mekonnen; Tsehaynesh Messele; Yohannes Menigstu; Aster Tsegaye; Margreet Bakker; Ben Berkhout; Wendelien Dorigo-Zetsma; Dawit Wolday; Jaap Goudsmit; Roel Coutinho; Michel P De Baar; William A Paxton; Georgios Pollakis
Differences in HIV type 1 RNA plasma load profile of closely related cocirculating Ethiopian subtype C strains: C and C'.
AIDS research and human retroviruses 2010;26(7):805-13.
2010: Ying-Poi Liu; Monique A Vink; Jan-Tinus Westerink; Eva Ramirez de Arellano; Pavlina Konstantinova; Olivier ter Brake; Ben Berkhout
Titers of lentiviral vectors encoding shRNAs and miRNAs are reduced by different mechanisms that require distinct repair strategies.
RNA (New York, N.Y.) 2010;16(7):1328-39.
2010: Atze T Das; Ben Berkhout
HIV-1 evolution: frustrating therapies, but disclosing molecular mechanisms.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2010;365(1548):1965-73.
2010: Dirk Eggink; Mark Melchers; Manfred Wuhrer; Thijs van Montfort; Antu K Dey; Benno A Naaijkens; Kathryn B David; Valentin Le Douce; André M Deelder; Kenneth Kang; William C Olson; Ben Berkhout; Cornelis H Hokke; John P Moore; Rogier W Sanders
Lack of complex N-glycans on HIV-1 envelope glycoproteins preserves protein conformation and entry function.
Virology 2010;401(2):236-47.
2010: Lia van der Hoek; Gabriele Ihorst; Klaus Sure; Astrid Vabret; Ronald Dijkman; Michel de Vries; Johannes Forster; Ben Berkhout; Klaus Uberla
Burden of disease due to human coronavirus NL63 infections and periodicity of infection.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2010;48(2):104-8.
2010: Nick C T Schopman; Ying-Poi Liu; Pavlina Konstantinova; Karin von Eije; Ben Berkhout
Optimization of shRNA inhibitors by variation of the terminal loop sequence.
Antiviral research 2010;86(2):204-11.
2010: Ben Berkhout
Hepatitis C virus therapy: blocking the little microRNA helper of the virus.
Journal of the Formosan Medical Association = Taiwan yi zhi 2010;109(3):173-6.
2010: Antoinette C van der Kuyl; Marion Cornelissen; Ben Berkhout
Of Mice and Men: On the Origin of XMRV.
Frontiers in microbiology 2010;1():147.
2010: Dirk Eggink; Ben Berkhout; Rogier W Sanders
Inhibition of HIV-1 by fusion inhibitors.
Current pharmaceutical design 2010;16(33):3716-28.
2010: Rogier W Sanders; Ben Berkhout
Sealing the envelope - the HIV-1 envelope glycoproteins as targets for therapeutics and vaccines.
Current pharmaceutical design 2010;16(33):3699-700.
2010: Marion Cornelissen; Fokla Zorgdrager; Petra Blom; Suzanne Jurriaans; Sjoerd Repping; Elisabeth van Leeuwen; Margreet Bakker; Ben Berkhout; Antoinette C van der Kuyl
Lack of detection of XMRV in seminal plasma from HIV-1 infected men in The Netherlands.
PloS one 2010;5(8):e12040.
2010: Antoinette C van der Kuyl; Karolina Kozaczynska; Kevin K Ariën; Youssef Gali; Victoria R Balázs; Stefan J Dekker; Fokla Zorgdrager; Guido Vanham; Ben Berkhout; Marion Cornelissen
Analysis of infectious virus clones from two HIV-1 superinfection cases suggests that the primary strains have lower fitness.
Retrovirology 2010;7():60.
2010: Nick C T Schopman; Karin von Eije; Ben Berkhout
Anticipating and blocking HIV-1 escape by second generation antiviral shRNAs.
Retrovirology 2010;7():52.
2010: Karin von Eije; Jan-Tinus Westerink; Ben Berkhout
Lentiviral vector engineering for anti-HIV RNAi gene therapy.
Methods in molecular biology (Clifton, N.J.) 2010;614():201-13.
2010: Karin von Eije; Xue Zhou; S M Pouw; K Weijer; W Kleibeuker; Atze T Das; Bianca Blom; J Seppen; Ben Berkhout; Nicolas Legrand
Autoregulatory lentiviral vectors allow multiple cycles of doxycycline-inducible gene expression in human hematopoietic cells in vivo.
Gene therapy 2010;17(1):14-25.
2009: Ying-Poi Liu; Karin von Eije; Nick C T Schopman; Jan-Tinus Westerink; Olivier ter Brake; Joost Haasnoot; Ben Berkhout
Combinatorial RNAi against HIV-1 using extended short hairpin RNAs.
Molecular therapy : the journal of the American Society of Gene Therapy 2009;17(10):1712-23.
2009: Ying-Poi Liu; Jens Gruber; Jaap G Haasnoot; Pavlina Konstantinova; Ben Berkhout
RNAi-mediated inhibition of HIV-1 by targeting partially complementary viral sequences.
Nucleic acids research 2009;37(18):6194-204.
2009: Dirk Eggink; Johannes P M Langedijk; Alexandre Bonvin; Yiqun Deng; Min Lu; Ben Berkhout; Rogier W Sanders
Detailed mechanistic insights into HIV-1 sensitivity to three generations of fusion inhibitors.
The Journal of biological chemistry 2009;284(39):26941-50.
2009: Ben Berkhout
Toward a durable anti-HIV gene therapy based on RNA interference.
Annals of the New York Academy of Sciences 2009;1175():3-14.
2009: Walter de Vries; Jaap G Haasnoot; Ron Fouchier; Peter de Haan; Ben Berkhout
Differential RNA silencing suppression activity of NS1 proteins from different influenza A virus strains.
The Journal of general virology 2009;90(Pt 8):1916-22.
2009: Rienk E Jeeninga; Menno D De Jong; Ben Berkhout
The new influenza A (H1N1) pandemic.
Journal of the Formosan Medical Association = Taiwan yi zhi 2009;108(7):523-5.
2009: Karin J von Eije; Olivier ter Brake; Ben Berkhout
Stringent testing identifies highly potent and escape-proof anti-HIV short hairpin RNAs.
The journal of gene medicine 2009;11(6):459-67.
2009: Guylaine Haché; Truus E M Abbink; Ben Berkhout; Reuben S Harris
Optimal translation initiation enables Vif-deficient human immunodeficiency virus type 1 to escape restriction by APOBEC3G.
Journal of virology 2009;83(11):5956-60.
2009: Wendy Kleibeuker; Xue Zhou; Mireille Centlivre; Nicolas Legrand; Mark Page; Neil Almond; Ben Berkhout; Atze T Das
A sensitive cell-based assay to measure the doxycycline concentration in biological samples.
Human gene therapy 2009;20(5):524-30.
2009: Ben Berkhout
A new Houdini act: multiple routes for HIV-1 escape from RNAi-mediated inhibition.
Future microbiology 2009;4(2):151-4.
2009: Esther Schnettler; Walter de Vries; Hans Hemmes; Joost Haasnoot; Richard Kormelink; Rob Goldbach; Ben Berkhout
The NS3 protein of rice hoja blanca virus complements the RNAi suppressor function of HIV-1 Tat.
EMBO reports 2009;10(3):258-63.
2009: Ben Berkhout; Olivier ter Brake
Towards a durable RNAi gene therapy for HIV-AIDS.
Expert opinion on biological therapy 2009;9(2):161-70.
2009: Alexander O. Pasternak; Suzanne Jurriaans; Margreet Bakker; Jan M Prins; Ben Berkhout; Vladimir V Lukashov
Cellular levels of HIV unspliced RNA from patients on combination antiretroviral therapy with undetectable plasma viremia predict the therapy outcome.
PloS one 2009;4(12):e8490.
2009: Ying-Poi Liu; Ben Berkhout
Lentiviral delivery of RNAi effectors against HIV-1.
Current topics in medicinal chemistry 2009;9(12):1130-43.
2009: Antonia V Bordería; Ben Berkhout
Towards a genetic AIDS vaccine.
Retrovirology 2009;6():93.
2009: Ben Berkhout; William A Paxton
HIV vaccine: it may take two to tango, but no party time yet.
Retrovirology 2009;6():88.
2009: Luuk Gras; Suzanne Jurriaans; Margreet Bakker; Ard van Sighem; Daniela Bezemer; Christophe Fraser; Joep Lange; Jan M Prins; Ben Berkhout; Frank de Wolf
Viral load levels measured at set-point have risen over the last decade of the HIV epidemic in the Netherlands.
PloS one 2009;4(10):e7365.
2009: Karin von Eije; Ben Berkhout
RNA-interference-based gene therapy approaches to HIV type-1 treatment: tackling the hurdles from bench to bedside.
Antiviral chemistry & chemotherapy 2009;19(6):221-33.
2009: Workenesh Ayele; Tsehai Assefa; Sileshi Lulseged; Belete Tegbaru; Hiwot Berhanu; Wegene Tamene; Zenit Ahmedin; Birzaf W Tensai; Mengistu Tafesse; Jaap Goudsmit; Ben Berkhout; William A Paxton; Michel P Debaar; Tsehaynesh Messele; Georgios Pollakis
RNA detection and subtype C assessment of HIV-1 in infants with diarrhea in Ethiopia.
The open AIDS journal 2009;3():19-23.
2009: Martine M Vrolijk; Alex Harwig; Ben Berkhout; Atze T Das
Destabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation.
Retrovirology 2009;6():13.
2009: Jaap G Haasnoot; Ben Berkhout
Nucleic acids-based therapeutics in the battle against pathogenic viruses.
Handbook of experimental pharmacology 2009;(189):243-63.
2009: Ben Berkhout; Atze T Das
Virus evolution as a tool to study HIV-1 biology.
Methods in molecular biology (Clifton, N.J.) 2009;485():436-51.
2009: Ilja Bontjer; Aafke Land; Dirk Eggink; Erwin Verkade; Kiki Tuin; Chris Baldwin; Georgios Pollakis; William A Paxton; Ineke Braakman; Ben Berkhout; Rogier W Sanders
Optimization of human immunodeficiency virus type 1 envelope glycoproteins with V1/V2 deleted, using virus evolution.
Journal of virology 2009;83(1):368-83.
2009: O ter Brake; Nicolas Legrand; K J von Eije; Karin von Eije; H Spits; K Weijer; B Blom; Ben Berkhout
Evaluation of safety and efficacy of RNAi against HIV-1 in the human immune system (Rag-2(-/-)gammac(-/-)) mouse model.
Gene therapy 2009;16(1):148-53.
2008: Ben Berkhout
Infectious diseases of the nervous system: pathogenesis and worldwide impact.
IDrugs : the investigational drugs journal 2008;11(11):791-5.
2008: Alison C Mathewson; Alexandra Bishop; Yongxiu Yao; Fred Kemp; Junyuan Ren; Hongying Chen; Xiaodong Xu; Ben Berkhout; Lia van der Hoek; Ian M Jones
Interaction of severe acute respiratory syndrome-coronavirus and NL63 coronavirus spike proteins with angiotensin converting enzyme-2.
The Journal of general virology 2008;89(Pt 11):2741-5.
2008: Rogier W Sanders; Shang-Te Danny Hsu; Eelco van Anken; I Marije Liscaljet; Martijn Dankers; Ilja Bontjer; Aafke Land; Ineke Braakman; Alexandre Bonvin; Ben Berkhout
Evolution rescues folding of human immunodeficiency virus-1 envelope glycoprotein GP120 lacking a conserved disulfide bond.
Molecular biology of the cell 2008;19(11):4707-16.
2008: Ben Berkhout
An eye-opener for RNAi therapeutics.
Journal of the Formosan Medical Association = Taiwan yi zhi 2008;107(10):749-50.
2008: Eelco van Anken; Rogier W Sanders; I Marije Liscaljet; Aafke Land; Ilja Bontjer; Sonja Tillemans; Alexey A Nabatov; William A Paxton; Ben Berkhout; Ineke Braakman
Only five of 10 strictly conserved disulfide bonds are essential for folding and eight for function of the HIV-1 envelope glycoprotein.
Molecular biology of the cell 2008;19(10):4298-309.
2008: Olivier ter Brake; Karin von Eije; Ben Berkhout
Probing the sequence space available for HIV-1 evolution.
AIDS (London, England) 2008;22(14):1875-7.
2008: Mireille Centlivre; Bep Klaver; Ben Berkhout; Atze T Das
Functional analysis of the complex trans-activating response element RNA structure in simian immunodeficiency virus.
Journal of virology 2008;82(18):9171-8.
2008: Wayne C Koff; C L Parks; Ben Berkhout; J Ackland; S Noble; I D Gust
Replicating viral vectors as HIV vaccines Summary Report from IAVI Sponsored Satellite Symposium, International AIDS Society Conference, July 22, 2007.
Biologicals : journal of the International Association of Biological Standardization 2008;36(5):277-86.
2008: Martine M Vrolijk; Marcel Ooms; Alex Harwig; Atze T Das; Ben Berkhout
Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA.
Nucleic acids research 2008;36(13):4352-63.
2008: Chris Baldwin; Ben Berkhout
Mechanistic studies of a T20-dependent human immunodeficiency virus type 1 variant.
Journal of virology 2008;82(15):7735-40.
2008: Alexander O. Pasternak; Karen W Adema; Margreet Bakker; Suzanne Jurriaans; Ben Berkhout; Marion Cornelissen; Vladimir V Lukashov
Highly sensitive methods based on seminested real-time reverse transcription-PCR for quantitation of human immunodeficiency virus type 1 unspliced and multiply spliced RNA and proviral DNA.
Journal of clinical microbiology 2008;46(7):2206-11.
2008: Dirk Eggink; Chris E Baldwin; Yiqun Deng; Johannes P M Langedijk; Min Lu; Rogier W Sanders; Ben Berkhout
Selection of T1249-resistant human immunodeficiency virus type 1 variants.
Journal of virology 2008;82(13):6678-88.
2008: Luis Menéndez-Arias; Ben Berkhout
Retroviral reverse transcription.
Virus research 2008;134(1-2):1-3.
2008: Truus E M Abbink; Ben Berkhout
HIV-1 reverse transcription initiation: a potential target for novel antivirals?
Virus research 2008;134(1-2):4-18.
2008: Ying-Poi Liu; Jaap G Haasnoot; Olivier ter Brake; Ben Berkhout; Pavlina Konstantinova
Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron.
Nucleic acids research 2008;36(9):2811-24.
2008: Jeffrey H Ringrose; Rienk E Jeeninga; Ben Berkhout; Dave Speijer
Proteomic studies reveal coordinated changes in T-cell expression patterns upon infection with human immunodeficiency virus type 1.
Journal of virology 2008;82(9):4320-30.
2008: W de Vries; Jaap G Haasnoot; J van der Velden; T van Montfort; Fokla Zorgdrager; William A Paxton; Marion Cornelissen; F van Kuppeveld; Peter de Haan; Ben Berkhout
Increased virus replication in mammalian cells by blocking intracellular innate defense responses.
Gene therapy 2008;15(7):545-52.
2008: Kyle R Bonneau; Sharon Ng; Hillary Foster; Kelly B Choi; Ben Berkhout; Arnold Rabson; Carl E Mackewicz; Jay A Levy
Derivation of infectious HIV-1 molecular clones with LTR mutations: sensitivity to the CD8+ cell noncytotoxic anti-HIV response.
Virology 2008;373(1):30-8.
2008: Olivier ter Brake; Karen 't Hooft; Ying-Poi Liu; Karin von Eije; Karin Jasmijn von Eije; Ben Berkhout
Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition.
Molecular therapy : the journal of the American Society of Gene Therapy 2008;16(3):557-64.
2008: Truus E M Abbink; Ben Berkhout
RNA structure modulates splicing efficiency at the human immunodeficiency virus type 1 major splice donor.
Journal of virology 2008;82(6):3090-8.
2008: Karin Jasmijn von Eije; Karin von Eije; Ben Berkhout
Human immunodeficiency virus type 1 escape is restricted when conserved genome sequences are targeted by RNA interference.
Journal of virology 2008;82(6):2895-903.
2008: Colette Smit; charlotte van den berg; Ronald B Geskus; Ben Berkhout; Roel Coutinho; Maria Prins
Risk of hepatitis-related mortality increased among hepatitis C virus/HIV-coinfected drug users compared with drug users infected only with hepatitis C virus: a 20-year prospective study.
Journal of acquired immune deficiency syndromes (1999) 2008;47(2):221-5.
2008: Michel de Vries; Krzysztof Pyrc; Ron Berkhout; Wilma Vermeulen-Oost; Ronald Dijkman; Maarten F Jebbink; Sylvia Bruisten; Ben Berkhout; Lia van der Hoek
Human parechovirus type 1, 3, 4, 5, and 6 detection in picornavirus cultures.
Journal of clinical microbiology 2008;46(2):759-62.
2008: Formijn J van Hemert; Hans L Zaaijer; Ben Berkhout; Vladimir V Lukashov
Mosaic amino acid conservation in 3D-structures of surface protein and polymerase of hepatitis B virus.
Virology 2008;370(2):362-72.
2008: Formijn J van Hemert; Hans L Zaaijer; Ben Berkhout; Vladimir V Lukashov
Occult hepatitis B infection: an evolutionary scenario.
Virology journal 2008;5():146.
2008: Krzysztof Pyrc; Maarten F Jebbink; Ben Berkhout; Lia van der Hoek
Detection of new viruses by VIDISCA. Virus discovery based on cDNA-amplified fragment length polymorphism.
Methods in molecular biology (Clifton, N.J.) 2008;454():73-89.
2008: Andrew M L Lever; Ben Berkhout
2008 Nobel prize in medicine for discoverers of HIV.
Retrovirology 2008;5():91.
2008: Olivier ter Brake; Joost Haasnoot; Jens Kurreck; Ben Berkhout
ESF-EMBO symposium: antiviral applications of RNA interference.
Retrovirology 2008;5():81.
2008: Walter de Vries; Ben Berkhout
RNAi suppressors encoded by pathogenic human viruses.
The international journal of biochemistry & cell biology 2008;40(10):2007-12.
2008: Atze T Das; Bep Klaver; Mireille Centlivre; Alex Harwig; Marcel Ooms; Mark Page; Neil Almond; Fang Yuan; Mike Piatak; Jeffrey D Lifson; Ben Berkhout
Optimization of the doxycycline-dependent simian immunodeficiency virus through in vitro evolution.
Retrovirology 2008;5():44.
2008: Rienk E Jeeninga; Ellen M Westerhout; Marja L van Gerven; Ben Berkhout
HIV-1 latency in actively dividing human T cell lines.
Retrovirology 2008;5():37.
2008: Ben Berkhout; Robert Gorelick; Michael F Summers; Yves Mély; Jean-Luc Darlix
6th international symposium on retroviral nucleocapsid.
Retrovirology 2008;5():21.
2008: Rogier W Sanders; Eelco van Anken; Alexei A Nabatov; I Marije Liscaljet; Ilja Bontjer; Dirk Eggink; Mark Melchers; Els Busser; Martijn M Dankers; Fedde Groot; Ineke Braakman; Ben Berkhout; William A Paxton
The carbohydrate at asparagine 386 on HIV-1 gp120 is not essential for protein folding and function but is involved in immune evasion.
Retrovirology 2008;5():10.
2008: Ben Berkhout
A balancing act: viruses and miRNAs.
Journal of the Formosan Medical Association = Taiwan yi zhi 2008;107(1):1-3.
2008: Ping-sheng Wu; Luan-Yin Chang; Ben Berkhout; L van der Hoek; Chun-Yi Lu; Chuan-Liang Kao; Ping-Ing Lee; Pei-Lan Shao; Chin-Yun Lee; Fu-Yuan Huang; Li-Min Huang
Clinical manifestations of human coronavirus NL63 infection in children in Taiwan.
European journal of pediatrics 2008;167(1):75-80.
2007: Jaap G Haasnoot; Ellen M Westerhout; Ben Berkhout
RNA interference against viruses: strike and counterstrike.
Nature biotechnology 2007;25(12):1435-43.
2007: Ben Berkhout
Third European Congress of Virology. 1-5 September 2007, Nuremberg, Germany.
IDrugs : the investigational drugs journal 2007;10(11):772-4.
2007: Atze T Das; Bep Klaver; Alex Harwig; Monique Vink; Marcel Ooms; Mireille Centlivre; Ben Berkhout
Construction of a doxycycline-dependent simian immunodeficiency virus reveals a nontranscriptional function of tat in viral replication.
Journal of virology 2007;81(20):11159-69.
2007: Ben Berkhout; Kuan-Teh Jeang
RISCy business: MicroRNAs, pathogenesis, and viruses.
The Journal of biological chemistry 2007;282(37):26641-5.
2007: Olivier ter Brake; Ben Berkhout
Lentiviral vectors that carry anti-HIV shRNAs: problems and solutions.
The journal of gene medicine 2007;9(9):743-50.
2007: Youssef Gali; Ben Berkhout; Guido Vanham; Margreet Bakker; Nicole Back; Kevin Ariën
Survey of the temporal changes in HIV-1 replicative fitness in the Amsterdam Cohort.
Virology 2007;364(1):140-6.
2007: Atze T Das; Alex Harwig; Martine M Vrolijk; Ben Berkhout
The TAR hairpin of human immunodeficiency virus type 1 can be deleted when not required for Tat-mediated activation of transcription.
Journal of virology 2007;81(14):7742-8.
2007: Jaap G Haasnoot; Walter de Vries; Ernst-Jan Geutjes; Marcel Prins; Peter de Haan; Ben Berkhout
The Ebola virus VP35 protein is a suppressor of RNA silencing.
PLoS pathogens 2007;3(6):e86.
2007: Formijn J van Hemert; Ben Berkhout; Vladimir V Lukashov
Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae.
Virology 2007;361(2):447-54.
2007: Krzysztof Pyrc; Ben Berkhout; Lia van der Hoek
Identification of new human coronaviruses.
Expert review of anti-infective therapy 2007;5(2):245-53.
2007: Krzysztof Pyrc; Ben Berkhout; Lia van der Hoek
The novel human coronaviruses NL63 and HKU1.
Journal of virology 2007;81(7):3051-7.
2007: Lia van der Hoek; Georgios Pollakis; Vladimir V Lukashov; Maarten F Jebbink; Rienk E Jeeninga; Margreet Bakker; Nicole Dukers; Suzanne Jurriaans; William A Paxton; Nicole Back; Ben Berkhout
Characterization of an HIV-1 group M variant that is distinct from the known subtypes.
AIDS research and human retroviruses 2007;23(3):466-70.
2007: Krzysztof Pyrc; Ben Berkhout; Lia van der Hoek
Antiviral strategies against human coronaviruses.
Infectious disorders drug targets 2007;7(1):59-66.
2007: Mireille Centlivre; Monica Sala; Simon Wain-Hobson; Ben Berkhout
In HIV-1 pathogenesis the die is cast during primary infection.
AIDS (London, England) 2007;21(1):1-11.
2007: Andrea Crotti; Giulia D Chiara; Silvia Ghezzi; Rossella Lupo; Rienk E Jeeninga; Elio Liboi; Patricia M-J Lievens; Elisa Vicenzi; Chiara Bovolenta; Ben Berkhout; Guido Poli
Heterogeneity of signal transducer and activator of transcription binding sites in the long-terminal repeats of distinct HIV-1 subtypes.
The open virology journal 2007;1():26-32.
2007: Chris Baldwin; Ben Berkhout
HIV-1 drug-resistance and drug-dependence.
Retrovirology 2007;4():78.
2007: Colette Smit; Christiaan Pfrommer; Adrian Mindel; Janette Taylor; Joke Spaargaren; Ben Berkhout; Roel Coutinho; Nicole Dukers
Rise in seroprevalence of herpes simplex virus type 1 among highly sexual active homosexual men and an increasing association between herpes simplex virus type 2 and HIV over time (1984-2003).
European journal of epidemiology 2007;22(12):937-44.
2007: Ronald B Geskus; Maria Prins; Jean-Baptiste Hubert; Frank Miedema; Ben Berkhout; Christine Rouzioux; Jean-Francois Delfraissy; Laurence Meyer
The HIV RNA setpoint theory revisited.
Retrovirology 2007;4():65.
2007: Ying-Poi Liu; Jaap G Haasnoot; Ben Berkhout
Design of extended short hairpin RNAs for HIV-1 inhibition.
Nucleic acids research 2007;35(17):5683-93.
2007: Marcel Ooms; Truus E M Abbink; Chi Pham; Ben Berkhout
Circularization of the HIV-1 RNA genome.
Nucleic acids research 2007;35(15):5253-61.
2007: Truus E M Abbink; Ben Berkhout
HIV-1 reverse transcription: close encounters between the viral genome and a cellular tRNA.
Advances in pharmacology (San Diego, Calif.) 2007;55():99-135.
2007: Ellen M Westerhout; Ben Berkhout
A systematic analysis of the effect of target RNA structure on RNA interference.
Nucleic acids research 2007;35(13):4322-30.
2007: Martin R Jakobsen; Martin Roelsgaard Jakobsen; Jesper Wengel; Ben Berkhout; Jørgen Kjems
Efficient inhibition of HIV-1 expression by LNA modified antisense oligonucleotides and DNAzymes targeted to functionally selected binding sites.
Retrovirology 2007;4():29.
2007: Formijn J van Hemert; Vladimir V Lukashov; Ben Berkhout
Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function.
Virology journal 2007;4():25.
2007: Tim Van Opijnen; Anthony de Ronde; Maarten C Boerlijst; Ben Berkhout
Adaptation of HIV-1 depends on the host-cell environment.
PloS one 2007;2(3):e271.
2007: charlotte van den berg; Colette Smit; Margreet Bakker; Ronald B Geskus; Ben Berkhout; Suzanne Jurriaans; Roel A Coutinho; Katja C Wolthers; Maria Prins
Major decline of hepatitis C virus incidence rate over two decades in a cohort of drug users.
European journal of epidemiology 2007;22(3):183-93.
2007: Pavlina Konstantinova; Olivier ter Brake; Jaap G Haasnoot; Peter de Haan; Ben Berkhout
Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome.
Retrovirology 2007;4():15.
2007: Antoinette C van der Kuyl; Remco van den Burg; Fokla Zorgdrager; Fedde Groot; Ben Berkhout; Marion Cornelissen
Sialoadhesin (CD169) expression in CD14+ cells is upregulated early after HIV-1 infection and increases during disease progression.
PloS one 2007;2(2):e257.
2007: Marcel Ooms; Daniel Cupac; Truus E M Abbink; Hendrik Huthoff; Ben Berkhout
The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation.
Nucleic acids research 2007;35(5):1649-59.
2007: Xue Zhou; Jori Symons; Rieuwert Hoppes; Christel Krueger; Christian Berens; Wolfgang Hillen; Ben Berkhout; Atze T Das
Improved single-chain transactivators of the Tet-On gene expression system.
BMC biotechnology 2007;7():6.
2006: Qi Zheng; Yiqun Deng; Jie Liu; Lia van der Hoek; Ben Berkhout; Min Lu
Core structure of S2 from the human coronavirus NL63 spike glycoprotein.
Biochemistry 2006;45(51):15205-15.
2006: Krzysztof Pyrc; Ronald Dijkman; Lea Deng; Maarten F Jebbink; Howard A Ross; Ben Berkhout; Lia van der Hoek
Mosaic structure of human coronavirus NL63, one thousand years of evolution.
Journal of molecular biology 2006;364(5):964-73.
2006: Olivier ter Brake; Pavlina Konstantinova; Mustafa Ceylan; Ben Berkhout
Silencing of HIV-1 with RNA interference: a multiple shRNA approach.
Molecular therapy : the journal of the American Society of Gene Therapy 2006;14(6):883-92.
2006: Sunil Ahuja; Fernando Aiuti; Ben Berkhout; Peter Biberfeld; Dennis R Burton; Vittorio Colizzi; Steven G Deeks; Ronald C Desrosiers; Manfred P Dierich; Robert W Doms; Michael Emerman; Robert C Gallo; Marc Girard; Warner Greene; James A Hoxie; Eric Hunter; George Klein; Bette Korber; Daniel R Kuritzkes; Michael M Lederman; Michael H Malim; Preston A Marx; Joseph M McCune; Andrew McMichael; Christopher J Miller; Veronica Miller; Luc Montagnier; David C Montefiori; John P Moore; Douglas F Nixon; Julie Overbaugh; C. David Pauza; Douglas D Richman; Michael S Saag; Quentin Sattentau; Robert T Schooley; Robin Shattock; George M Shaw; Mario Stevenson; Alexandra Trkola; Mark A Wainberg; Robin A Weiss; Steven Wolinsky; Jerome A Zack
A plea for justice for jailed medical workers.
Science (New York, N.Y.) 2006;314(5801):924-5.
2006: Angelique A C Lemckert; Jos M Grimbergen; Shirley Smits; Eric Hartkoorn; Lennart Holterman; Ben Berkhout; Dan H Barouch; Ronald Vogels; Paul H A Quax; Jaap Goudsmit; Menzo J E Havenga
Generation of a novel replication-incompetent adenoviral vector derived from human adenovirus type 49: manufacture on PER.C6 cells, tropism and immunogenicity.
The Journal of general virology 2006;87(Pt 10):2891-9.
2006: Xue Zhou; Monique Vink; Bep Klaver; Ben Berkhout; Atze T Das
Optimization of the Tet-On system for regulated gene expression through viral evolution.
Gene therapy 2006;13(19):1382-90.
2006: Pavlina Konstantinova; W de Vries; Jaap G Haasnoot; Olivier ter Brake; Peter de Haan; Ben Berkhout
Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA.
Gene therapy 2006;13(19):1403-13.
2006: Fedde Groot; Toni M M van Capel; Martien L Kapsenberg; Ben Berkhout; Esther C de Jong
Opposing roles of blood myeloid and plasmacytoid dendritic cells in HIV-1 infection of T cells: transmission facilitation versus replication inhibition.
Blood 2006;108(6):1957-64.
2006: Fedde Groot; Rogier W Sanders; Olivier ter Brake; Kamran Nazmi; Enno C I Veerman; Jan G M Bolscher; Ben Berkhout
Histatin 5-derived peptide with improved fungicidal properties enhances human immunodeficiency virus type 1 replication by promoting viral entry.
Journal of virology 2006;80(18):9236-43.
2006: Lia van der Hoek; Krzysztof Pyrc; Ben Berkhout
Human coronavirus NL63, a new respiratory virus.
FEMS microbiology reviews 2006;30(5):760-73.
2006: Ellen M Westerhout; Monique Vink; P C Joost Haasnoot; Atze T Das; Ben Berkhout
A conditionally replicating HIV-based vector that stably expresses an antiviral shRNA against HIV-1 replication.
Molecular therapy : the journal of the American Society of Gene Therapy 2006;14(2):268-75.
2006: Ben Berkhout; Nicole Back; Anthony de Ronde; Suzanne Jurriaans; Margreet Bakker; Neil T Parkin; Lia van der Hoek
Identification of alternative amino acid substitutions in drug-resistant variants of the HIV-1 reverse transcriptase.
AIDS (London, England) 2006;20(11):1515-20.
2006: Martin Lützelberger; Line S Reinert; Atze T Das; Ben Berkhout; Jørgen Kjems
A novel splice donor site in the gag-pol gene is required for HIV-1 RNA stability.
The Journal of biological chemistry 2006;281(27):18644-51.
2006: Tim Van Opijnen; Maarten C Boerlijst; Ben Berkhout
Effects of random mutations in the human immunodeficiency virus type 1 transcriptional promoter on viral fitness in different host cell environments.
Journal of virology 2006;80(13):6678-85.
2006: Xue Zhou; Monique Vink; Bep Klaver; Koen Verhoef; Giuseppe Marzio; Atze T Das; Ben Berkhout
The genetic stability of a conditional live HIV-1 variant can be improved by mutations in the Tet-On regulatory system that restrain evolution.
The Journal of biological chemistry 2006;281(25):17084-91.
2006: Krzysztof Pyrc; Berend Jan Bosch; Ben Berkhout; Maarten F Jebbink; Ronald Dijkman; Peter J M Rottier; Lia van der Hoek
Inhibition of human coronavirus NL63 infection at early stages of the replication cycle.
Antimicrobial agents and chemotherapy 2006;50(6):2000-8.
2006: Ben Berkhout; Jaap G Haasnoot
The interplay between virus infection and the cellular RNA interference machinery.
FEBS letters 2006;580(12):2896-902.
2006: Scott R Eberhardy; Joao Goncalves; Sofia Coelho; David J Segal; Ben Berkhout; Carlos F Barbas
Inhibition of human immunodeficiency virus type 1 replication with artificial transcription factors targeting the highly conserved primer-binding site.
Journal of virology 2006;80(6):2873-83.
2006: Chiara Rizzi; Massimo P Crippa; Rienk E Jeeninga; Ben Berkhout; Francesco Blasi; Guido Poli; Massimo Alfano
Pertussis toxin B-oligomer suppresses IL-6 induced HIV-1 and chemokine expression in chronically infected U1 cells via inhibition of activator protein 1.
Journal of immunology (Baltimore, Md. : 1950) 2006;176(2):999-1006.
2006: Luan-Yin Chang; Bor-Luen Chiang; Chuan-Liang Kao; Mei-Hwan Wu; Pei-Jer Chen; Ben Berkhout; Hui-Ching Yang; Li-Min Huang
Lack of association between infection with a novel human coronavirus (HCoV), HCoV-NH, and Kawasaki disease in Taiwan.
The Journal of infectious diseases 2006;193(2):283-6.
2006: Kimberley Benschop; Janke Schinkel; R P Minnaar; Dasja Pajkrt; L Spanjerberg; H C Kraakman; Ben Berkhout; Hans L Zaaijer; Marcel G H M Beld; Katja C Wolthers
Human parechovirus infections in Dutch children and the association between serotype and disease severity.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2006;42(2):204-10.
2006: Ronald Dijkman; Maarten F Jebbink; berry wilbrink; Krzysztof Pyrc; Hans L Zaaijer; Philip D Minor; Sally Franklin; Ben Berkhout; Volker Thiel; Lia van der Hoek
Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes.
Virology journal 2006;3():106.
2006: Chris E Baldwin; Ben Berkhout
Second site escape of a T20-dependent HIV-1 variant by a single amino acid change in the CD4 binding region of the envelope glycoprotein.
Retrovirology 2006;3():84.
2006: Xue Zhou; Monique Vink; Ben Berkhout; Atze T Das
Modification of the Tet-On regulatory system prevents the conditional-live HIV-1 variant from losing doxycycline-control.
Retrovirology 2006;3():82.
2006: Fedde Groot; Taco W Kuijpers; Ben Berkhout; Esther C de Jong
Dendritic cell-mediated HIV-1 transmission to T cells of LAD-1 patients is impaired due to the defect in LFA-1.
Retrovirology 2006;3():75.
2006: Lia van der Hoek; Klaus Sure; Gabriele Ihorst; Alexander Stang; Krzysztof Pyrc; Maarten F Jebbink; Gudula Petersen; Johannes Forster; Ben Berkhout; Klaus Uberla
Human coronavirus NL63 infection is associated with croup.
Advances in experimental medicine and biology 2006;581():485-91.
2006: M K Smith; Sonia M Tusell; Emily A Travanty; Ben Berkhout; Lia van der Hoek; Kathryn V Holmes
Human angiotensin-converting enzyme 2 (ACE2) is a receptor for human respiratory coronavirus NL63.
Advances in experimental medicine and biology 2006;581():285-8.
2006: Stefan Pöhlmann; Thomas Gramberg; Anja Wegele; Krzysztof Pyrc; Lia van der Hoek; Ben Berkhout; Heike Hofmann
Interaction between the spike protein of human coronavirus NL63 and its cellular receptor ACE2.
Advances in experimental medicine and biology 2006;581():281-4.
2006: Heike Hofmann; Andrea Marzi; Thomas Gramberg; Martina Geier; Krzysztof Pyrc; Lia van der Hoek; Ben Berkhout; Stefan Pöhlmann
Attachment factor and receptor engagement of SARS coronavirus and human coronavirus NL63.
Advances in experimental medicine and biology 2006;581():219-27.
2006: Yvonne Piotrowski; Lia van der Hoek; Krzysztof Pyrc; Ben Berkhout; Ralf Moll; Rolf Hilgenfeld
Nonstructural proteins of human coronavirus NL63.
Advances in experimental medicine and biology 2006;581():97-100.
2006: Rienk E Jeeninga; Barbara Jan; Henk van den Berg; Ben Berkhout
Construction of doxycyline-dependent mini-HIV-1 variants for the development of a virotherapy against leukemias.
Retrovirology 2006;3():64.
2006: Ellen M Westerhout; Olivier ter Brake; Ben Berkhout
The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference.
Retrovirology 2006;3():57.
2006: Fedde Groot; Toni M M van Capel; Joost Schuitemaker; Ben Berkhout; Esther C de Jong
Differential susceptibility of naïve, central memory and effector memory T cells to dendritic cell-mediated HIV-1 transmission.
Retrovirology 2006;3():52.
2006: Pavlina Konstantinova; Peter de Haan; Atze T Das; Ben Berkhout
Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1.
Nucleic acids research 2006;34(8):2206-18.
2006: Jaap G Haasnoot; Ben Berkhout
RNA interference: its use as antiviral therapy.
Handbook of experimental pharmacology 2006;(173):117-50.
2006: Jan M Ruijter; Helene H Thygesen; Onard J L M Schoneveld; Atze T Das; Ben Berkhout; Wouter H Lamers
Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology.
Retrovirology 2006;3():2.
2006: Olga J A E Ophorst; K Radosević; Menzo J E Havenga; Maria G Pau; Lennart Holterman; Ben Berkhout; Jaap Goudsmit; Moriya Tsuji
Immunogenicity and protection of a recombinant human adenovirus serotype 35-based malaria vaccine against Plasmodium yoelii in mice.
Infection and immunity 2006;74(1):313-20.
2005: Ben Berkhout
RNAi Europe 2005.
IDrugs : the investigational drugs journal 2005;8(12):978-81.
2005: Marloes A Naarding; Irene S Ludwig; Fedde Groot; Ben Berkhout; Teunis B H Geijtenbeek; Georgios Pollakis; William A Paxton
Lewis X component in human milk binds DC-SIGN and inhibits HIV-1 transfer to CD4+ T lymphocytes.
The Journal of clinical investigation 2005;115(11):3256-64.
2005: Lia van der Hoek; Klaus Sure; Gabriele Ihorst; Alexander Stang; Krzysztof Pyrc; Maarten F Jebbink; Gudula Petersen; Johannes Forster; Ben Berkhout; Klaus Uberla
Croup is associated with the novel coronavirus NL63.
PLoS medicine 2005;2(8):e240.
2005: M Gunnar Andersson; P C Joost Haasnoot; Ning Xu; Saideh Berenjian; Ben Berkhout; Göran Akusjärvi
Suppression of RNA interference by adenovirus virus-associated RNA.
Journal of virology 2005;79(15):9556-65.
2005: Lia van der Hoek; Ben Berkhout
Questions concerning the New Haven coronavirus.
The Journal of infectious diseases 2005;192(2):350-1; author reply 353-4.
2005: Melaku Adal; Workenesh Ayele; Dawit Wolday; Kifle Dagne; Tsehaynesh Messele; Tesfaye Tilahun; Ben Berkhout; Shlomo Mayaan; Georgios Pollakis; Wendelien Dorigo-Zetsma
Evidence of genetic variability of human immunodeficiency virus type 1 in plasma and cervicovaginal lavage in ethiopian women seeking care for sexually transmitted infections.
AIDS research and human retroviruses 2005;21(7):649-53.
2005: Ronald B Geskus; Laurence Meyer; Jean-Baptiste Hubert; Hanneke Schuitemaker; Ben Berkhout; Christine Rouzioux; Ioannis Theodorou; Jean-François Delfraissy; Maria Prins; Roel A Coutinho
Causal pathways of the effects of age and the CCR5-Delta32, CCR2-64I, and SDF-1 3'A alleles on AIDS development.
Journal of acquired immune deficiency syndromes (1999) 2005;39(3):321-6.
2005: Tim Van Opijnen; Ben Berkhout
The host environment drives HIV-1 fitness.
Reviews in medical virology 2005;15(4):219-33.
2005: Truus E M Abbink; Marcel Ooms; P C Joost Haasnoot; Ben Berkhout
The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation.
Biochemistry 2005;44(25):9058-66.
2005: Antoinette C van der Kuyl; Karolina Kozaczynska; Remco van den Burg; Fokla Zorgdrager; Nicole Back; Suzanne Jurriaans; Ben Berkhout; Peter Reiss; Marion Cornelissen
Triple HIV-1 infection.
The New England journal of medicine 2005;352(24):2557-9.
2005: Ariel Fernández; Dan S Tawfik; Ben Berkhout; Rogier Sanders; Andrzej Kloczkowski; Taner Sen; Bob Jernigan
Protein promiscuity: drug resistance and native functions--HIV-1 case.
Journal of biomolecular structure & dynamics 2005;22(6):615-24.
2005: Heike Hofmann; Krzysztof Pyrc; Lia van der Hoek; Martina Geier; Ben Berkhout; Stefan Pöhlmann
Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(22):7988-93.
2005: Rienk E Jeeninga; Barbara Jan; Birgit van der Linden; Henk van den Berg; Ben Berkhout
Construction of a minimal HIV-1 variant that selectively replicates in leukemic derived T-cell lines: towards a new virotherapy approach.
Cancer research 2005;65(8):3347-55.
2005: Atze T Das; Chris E Baldwin; Monique Vink; Ben Berkhout
Improving the safety of a conditional-live human immunodeficiency virus type 1 vaccine by controlling both gene expression and cell entry.
Journal of virology 2005;79(6):3855-8.
2005: Lia van der Hoek; Nicole Back; Maarten F Jebbink; Anthony de Ronde; Margreet Bakker; Suzanne Jurriaans; Peter Reiss; Neil Parkin; Ben Berkhout
Increased multinucleoside drug resistance and decreased replicative capacity of a human immunodeficiency virus type 1 variant with an 8-amino-Acid insert in the reverse transcriptase.
Journal of virology 2005;79(6):3536-43.
2005: Atze T Das; Monique Vink; Ben Berkhout
Alternative tRNA priming of human immunodeficiency virus type 1 reverse transcription explains sequence variation in the primer-binding site that has been attributed to APOBEC3G activity.
Journal of virology 2005;79(5):3179-81.
2005: Fedde Groot; Teunis B H Geijtenbeek; Rogier W Sanders; Chris E Baldwin; Marta Sanchez-Hernandez; René Floris; Yvette van Kooyk; Esther C de Jong; Ben Berkhout
Lactoferrin prevents dendritic cell-mediated human immunodeficiency virus type 1 transmission by blocking the DC-SIGN--gp120 interaction.
Journal of virology 2005;79(5):3009-15.
2005: Elien Moës; Leen Vijgen; Els Keyaerts; Kalina T Zlateva; Sandra Li; Piet Maes; Krzysztof Pyrc; Ben Berkhout; Lia van der Hoek; Marc Van Ranst
A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium.
BMC infectious diseases 2005;5():6.
2005: Olivier ter Brake; Ben Berkhout
A novel approach for inhibition of HIV-1 by RNA interference: counteracting viral escape with a second generation of siRNAs.
Journal of RNAi and gene silencing : an international journal of RNA and gene targeting research 2005;1(2):56-65.
2005: Ben Berkhout
It's the virus, stupid--part 2.
Retrovirology 2005;2():78.
2005: Micha Nethe; Ben Berkhout; Antoinette C van der Kuyl
Retroviral superinfection resistance.
Retrovirology 2005;2():52.
2005: Pia S Kivelä; Anneke Krol; Mika Salminen; Ronald B Geskus; Jukka Suni; Veli-Jukka Anttila; Kirsi Liitsola; Veera Zetterberg; Frank Miedema; Ben Berkhout; Roel A Coutinho; Matti Ristola
High plasma HIV load in the CRF01-AE outbreak among injecting drug users in Finland.
Scandinavian journal of infectious diseases 2005;37(4):276-83.
2005: David M Markusic; Ronald P J Oude Elferink; Atze T Das; Ben Berkhout; Jurgen Seppen
Comparison of single regulated lentiviral vectors with rtTA expression driven by an autoregulatory loop or a constitutive promoter.
Nucleic acids research 2005;33(6):e63.
2005: Ben Berkhout; Anthony de Ronde; Lia van der Hoek
Aggressive HIV-1?
Retrovirology 2005;2():13.
2005: Ellen M Westerhout; Marcel Ooms; Monique Vink; Atze T Das; Ben Berkhout
HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome.
Nucleic acids research 2005;33(2):796-804.
2004: Anne-Marie Lemieux; Marie-Eve Paré; Brigitte Audet; Eric Legault; Sylvain Lefort; Nancy Boucher; Sébastien Landry; Tim Van Opijnen; Ben Berkhout; Mojgan H Naghavi; Michel J Tremblay; Benoit Barbeau
T-cell activation leads to poor activation of the HIV-1 clade E long terminal repeat and weak association of nuclear factor-kappaB and NFAT with its enhancer region.
The Journal of biological chemistry 2004;279(51):52949-60.
2004: Lennart Holterman; Ronald Vogels; Remko van der Vlugt; Martijn Sieuwerts; Jos M Grimbergen; Jorn Kaspers; Eric Geelen; Esmeralda van der Helm; Angelique A C Lemckert; Gert Gillissen; Sandra Verhaagh; Jerome H H V Custers; David Zuijdgeest; Ben Berkhout; Margreet Bakker; Paul H A Quax; Jaap Goudsmit; Menzo J E Havenga
Novel replication-incompetent vector derived from adenovirus type 11 (Ad11) for vaccination and gene therapy: low seroprevalence and non-cross-reactivity with Ad5.
Journal of virology 2004;78(23):13207-15.
2004: Chris E Baldwin; Rogier W Sanders; Yiqun Deng; Suzanne Jurriaans; Joep M A Lange; Min Lu; Ben Berkhout
Emergence of a drug-dependent human immunodeficiency virus type 1 variant during therapy with the T20 fusion inhibitor.
Journal of virology 2004;78(22):12428-37.
2004: Yana Kiselyeva; Yoshinori Ito; Rosangela G Lima; Jean-Charles Grivel; Atze T Das; Ben Berkhout; Leonid Margolis
Depletion of CD4 T lymphocytes in human lymphoid tissue infected ex vivo with doxycycline-dependent HIV-1.
Virology 2004;328(1):1-6.
2004: Marcel Ooms; Hendrik Huthoff; Rodney Russell; Chen Liang; Ben Berkhout
A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions.
Journal of virology 2004;78(19):10814-9.
2004: Truus E M Abbink; Nancy Beerens; Ben Berkhout
Forced selection of a human immunodeficiency virus type 1 variant that uses a non-self tRNA primer for reverse transcription: involvement of viral RNA sequences and the reverse transcriptase enzyme.
Journal of virology 2004;78(19):10706-14.
2004: Ben Berkhout; Anthony de Ronde
APOBEC3G versus reverse transcriptase in the generation of HIV-1 drug-resistance mutations.
AIDS (London, England) 2004;18(13):1861-3.
2004: Daniela Bezemer; Suzanne Jurriaans; Maria Prins; Lia van der Hoek; Jan M Prins; Frank de Wolf; Ben Berkhout; Roel A Coutinho; Nicole Back
Declining trend in transmission of drug-resistant HIV-1 in Amsterdam.
AIDS (London, England) 2004;18(11):1571-7.
2004: Rogier W Sanders; Els Busser; John P Moore; Min Lu; Ben Berkhout
Evolutionary repair of HIV type 1 gp41 with a kink in the N-terminal helix leads to restoration of the six-helix bundle structure.
AIDS research and human retroviruses 2004;20(7):742-9.
2004: Tim Van Opijnen; Joost Kamoschinski; Rienk E Jeeninga; Ben Berkhout
The human immunodeficiency virus type 1 promoter contains a CATA box instead of a TATA box for optimal transcription and replication.
Journal of virology 2004;78(13):6883-90.
2004: Ben Berkhout; René Floris; Isidra Recio; Servaas Visser
The antiviral activity of the milk protein lactoferrin against the human immunodeficiency virus type 1.
Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 2004;17(3):291-4.
2004: Stefan Kostense; Wouter Koudstaal; Mieke Sprangers; Gerrit Jan Weverling; Germaine Penders; Niels Helmus; Ronald Vogels; Margreet Bakker; Ben Berkhout; Menzo J E Havenga; Jaap Goudsmit
Adenovirus types 5 and 35 seroprevalence in AIDS risk groups supports type 35 as a vaccine vector.
AIDS (London, England) 2004;18(8):1213-6.
2004: Hendrik Huthoff; Atze T Das; Monique Vink; Bep Klaver; Fokla Zorgdrager; Marion Cornelissen; Ben Berkhout
A human immunodeficiency virus type 1-infected individual with low viral load harbors a virus variant that exhibits an in vitro RNA dimerization defect.
Journal of virology 2004;78(9):4907-13.
2004: Atze T Das; Xue Zhou; Monique Vink; Bep Klaver; Koen Verhoef; Giuseppe Marzio; Ben Berkhout
Viral evolution as a tool to improve the tetracycline-regulated gene expression system.
The Journal of biological chemistry 2004;279(18):18776-82.
2004: Ben Berkhout
RNA interference as an antiviral approach: targeting HIV-1.
Current opinion in molecular therapeutics 2004;6(2):141-5.
2004: Lia van der Hoek; Krzysztof Pyrc; Maarten F Jebbink; Wilma Vermeulen-Oost; Ron J M Berkhout; Katja C Wolthers; Pauline M E Wertheim-van Dillen; Jos Kaandorp; Joke Spaargaren; Ben Berkhout
Identification of a new human coronavirus.
Nature medicine 2004;10(4):368-73.
2004: Tim Van Opijnen; Rienk E Jeeninga; Maarten C Boerlijst; Georgios Pollakis; Veera Zetterberg; Mika Salminen; Ben Berkhout
Human immunodeficiency virus type 1 subtypes have a distinct long terminal repeat that determines the replication rate in a host-cell-specific manner.
Journal of virology 2004;78(7):3675-83.
2004: Hendrik Huthoff; Frederic Girard; Sybren S Wijmenga; Ben Berkhout
Evidence for a base triple in the free HIV-1 TAR RNA.
RNA (New York, N.Y.) 2004;10(3):412-23.
2004: Atze T Das; Thijn R Brummelkamp; Ellen M Westerhout; Monique Vink; Mandy Madiredjo; René Bernards; Ben Berkhout
Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition.
Journal of virology 2004;78(5):2601-5.
2004: Krzysztof Pyrc; Maarten F Jebbink; Ben Berkhout; Lia van der Hoek
Genome structure and transcriptional regulation of human coronavirus NL63.
Virology journal 2004;1():7.
2004: Antoinette C van der Kuyl; Remco van den Burg; Mark J Hoyer; Rob A Gruters; Albert D M E Osterhaus; Ben Berkhout
SIVdrl detection in captive mandrills: are mandrills infected with a third strain of simian immunodeficiency virus?
Retrovirology 2004;1():36.
2004: Atze T Das; Koen Verhoef; Ben Berkhout
A conditionally replicating virus as a novel approach toward an HIV vaccine.
Methods in enzymology 2004;388():359-79.
2004: Rogier W Sanders; Martijn M Dankers; Els Busser; Michael Caffrey; John P Moore; Ben Berkhout
Evolution of the HIV-1 envelope glycoproteins with a disulfide bond between gp120 and gp41.
Retrovirology 2004;1():3.
2004: Marcel Ooms; Koen Verhoef; Edwin Southern; Hendrik Huthoff; Ben Berkhout
Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays.
Nucleic acids research 2004;32(2):819-27.
2003: Tadeusz Kulinski; Mikolaj Olejniczak; Hendrik Huthoff; Lukasz Bielecki; Katarzyna Pachulska-Wieczorek; Atze T Das; Ben Berkhout; Ryszard W Adamiak
The apical loop of the HIV-1 TAR RNA hairpin is stabilized by a cross-loop base pair.
The Journal of biological chemistry 2003;278(40):38892-901.
2003: Hendrik Huthoff; Katarzyna Bugala; Jan Barciszewski; Ben Berkhout
On the importance of the primer activation signal for initiation of tRNA(lys3)-primed reverse transcription of the HIV-1 RNA genome.
Nucleic acids research 2003;31(17):5186-94.
2003: Chris E Baldwin; Rogier W Sanders; Ben Berkhout
Inhibiting HIV-1 entry with fusion inhibitors.
Current medicinal chemistry 2003;10(17):1633-42.
2003: Cândida F Pereira; Judith T M L Paridaen; Karla Rutten; Marleen C D G Huigen; Marja van de Bovenkamp; Jeena Middel; Nancy Beerens; Ben Berkhout; Rob Schuurman; Lawrence J Marnett; Jan Verhoef; Hans S L M Nottet
Aspirin-like molecules that inhibit human immunodeficiency virus 1 replication.
Antiviral research 2003;58(3):253-63.
2003: Ann Brasey; Marcelo Lopez-Lastra; Théophile Ohlmann; Nancy Beerens; Ben Berkhout; Jean-Luc Darlix; Nahum Sonenberg
The leader of human immunodeficiency virus type 1 genomic RNA harbors an internal ribosome entry segment that is active during the G2/M phase of the cell cycle.
Journal of virology 2003;77(7):3939-49.
2003: Truus E M Abbink; Ben Berkhout
A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon.
The Journal of biological chemistry 2003;278(13):11601-11.
2003: Ebbe Sloth Andersen; Rienk E Jeeninga; Christian K Damgaard; Ben Berkhout; Jørgen Kjems
Dimerization and template switching in the 5' untranslated region between various subtypes of human immunodeficiency virus type 1.
Journal of virology 2003;77(5):3020-30.
2003: P C Joost Haasnoot; Daniel Cupac; Ben Berkhout
Inhibition of virus replication by RNA interference.
Journal of biomedical science 2003;10(6 Pt 1):607-16.
2003: René Florisa; Isidra Recio; Ben Berkhout; Servaas Visser
Antibacterial and antiviral effects of milk proteins and derivatives thereof.
Current pharmaceutical design 2003;9(16):1257-75.
2002: Ben Berkhout; Koen Verhoef; Giuseppe Marzio; Bep Klaver; Monique Vink; Xue Zhou; Atze T Das
Conditional virus replication as an approach to a safe live attenuated human immunodeficiency virus vaccine.
Journal of neurovirology 2002;8 Suppl 2():134-7.
2002: Vincent Quivy; Emmanuelle Adam; Yves Collette; Dominique Demonte; Alain Chariot; Caroline Vanhulle; Ben Berkhout; Rémy Castellano; Yvan de Launoit; Arsène Burny; Jacques Piette; Vincent Bours; Carine Van Lint
Synergistic activation of human immunodeficiency virus type 1 promoter activity by NF-kappaB and inhibitors of deacetylases: potential perspectives for the development of therapeutic strategies.
Journal of virology 2002;76(21):11091-103.
2002: Atze T Das; Xue Zhou; Monique Vink; Bep Klaver; Ben Berkhout
Conditional live virus as a novel approach towards a safe live attenuated HIV vaccine.
Expert review of vaccines 2002;1(3):293-301.
2002: Annette M G Dirac; Hendrik Huthoff; Jørgen Kjems; Ben Berkhout
Requirements for RNA heterodimerization of the human immunodeficiency virus type 1 (HIV-1) and HIV-2 genomes.
The Journal of general virology 2002;83(Pt 10):2533-42.
2002: Rogier W Sanders; Mika S Vesanen; Norbert Schuelke; Aditi Master; Linnea Schiffner; Roopa Kalyanaraman; Maciej Paluch; Ben Berkhout; Paul J Maddon; William C Olson; Min Lu; John P Moore
Stabilization of the soluble, cleaved, trimeric form of the envelope glycoprotein complex of human immunodeficiency virus type 1.
Journal of virology 2002;76(17):8875-89.
2002: Hendrik Huthoff; Ben Berkhout
Multiple secondary structure rearrangements during HIV-1 RNA dimerization.
Biochemistry 2002;41(33):10439-45.
2002: Ben Berkhout; Jeroen L B van Wamel; Leonie Beljaars; Dirk K F Meijer; Servaas Visser; René Floris
Characterization of the anti-HIV effects of native lactoferrin and other milk proteins and protein-derived peptides.
Antiviral research 2002;55(2):341-55.
2002: Rogier W Sanders; Esther C de Jong; Chris E Baldwin; Joost Schuitemaker; Martien L Kapsenberg; Ben Berkhout
Differential transmission of human immunodeficiency virus type 1 by distinct subsets of effector dendritic cells.
Journal of virology 2002;76(15):7812-21.
2002: Annette M G Dirac; Hendrik Huthoff; Jørgen Kjems; Ben Berkhout
Regulated HIV-2 RNA dimerization by means of alternative RNA conformations.
Nucleic acids research 2002;30(12):2647-55.
2002: Ben Berkhout; Marcel Ooms; Nancy Beerens; Hendrik Huthoff; Edwin Southern; Koen Verhoef
In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes.
The Journal of biological chemistry 2002;277(22):19967-75.
2002: Leonie Beljaars; René Floris; Ben Berkhout; Catharina Smit; Dirk K F Meijer; Grietje Molema
The influence of charge clustering on the anti-HIV-1 activity and in vivo distribution of negatively charged albumins.
Biochemical pharmacology 2002;63(9):1663-73.
2002: Nancy Beerens; Ben Berkhout
Switching the in vitro tRNA usage of HIV-1 by simultaneous adaptation of the PBS and PAS.
RNA (New York, N.Y.) 2002;8(3):357-69.
2002: Giuseppe Marzio; Monique Vink; Koen Verhoef; Anthony de Ronde; Ben Berkhout
Efficient human immunodeficiency virus replication requires a fine-tuned level of transcription.
Journal of virology 2002;76(6):3084-8.
2002: Nancy Beerens; Ben Berkhout
The tRNA primer activation signal in the human immunodeficiency virus type 1 genome is important for initiation and processive elongation of reverse transcription.
Journal of virology 2002;76(5):2329-39.
2002: Ben Berkhout; Giuseppe Marzio; Koen Verhoef
Control over HIV-1 replication by an antibiotic; a novel vaccination strategy with a drug-dependent virus.
Virus research 2002;82(1-2):103-8.
2002: Ben Berkhout; Andrei Grigoriev; Margreet Bakker; Vladimir V Lukashov
Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure.
AIDS research and human retroviruses 2002;18(2):133-41.
2001: Ben Berkhout
Retroviral nucleocapsid--third international symposium.
IDrugs : the investigational drugs journal 2001;4(11):1250-1.
2001: Marta Gómez-Gonzalo; Marta Carretero; Joaquín Rullas; Enrique Lara-Pezzi; José Aramburu; Ben Berkhout; José Alcamí; Manuel López-Cabrera
The hepatitis B virus X protein induces HIV-1 replication and transcription in synergy with T-cell activation signals: functional roles of NF-kappaB/NF-AT and SP1-binding sites in the HIV-1 long terminal repeat promoter.
The Journal of biological chemistry 2001;276(38):35435-43.
2001: Annette M G Dirac; Hendrik Huthoff; Jørgen Kjems; Ben Berkhout
The dimer initiation site hairpin mediates dimerization of the human immunodeficiency virus, type 2 RNA genome.
The Journal of biological chemistry 2001;276(34):32345-52.
2001: Nancy Beerens; Fedde Groot; Ben Berkhout
Initiation of HIV-1 reverse transcription is regulated by a primer activation signal.
The Journal of biological chemistry 2001;276(33):31247-56.
2001: Ben Berkhout; N L Vastenhouw; BI Klasens; Hendrik Huthoff
Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription.
RNA (New York, N.Y.) 2001;7(8):1097-114.
2001: Hendrik Huthoff; Ben Berkhout
Mutations in the TAR hairpin affect the equilibrium between alternative conformations of the HIV-1 leader RNA.
Nucleic acids research 2001;29(12):2594-600.
2001: Giuseppe Marzio; Koen Verhoef; Monique Vink; Ben Berkhout
In vitro evolution of a highly replicating, doxycycline-dependent HIV for applications in vaccine studies.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(11):6342-7.
2001: Rienk E Jeeninga; Wilco Keulen; C Boucher; Rogier W Sanders; Ben Berkhout
Evolution of AZT resistance in HIV-1: the 41-70 intermediate that is not observed in vivo has a replication defect.
Virology 2001;283(2):294-305.
2001: Ben Berkhout; Atze T Das; Nancy Beerens
HIV-1 RNA editing, hypermutation, and error-prone reverse transcription.
Science (New York, N.Y.) 2001;292(5514):7.
2001: Koen Verhoef; Patricia S Bilodeau; Jeroen L B van Wamel; J Kjems; C Martin Stoltzfus; Ben Berkhout
Repair of a Rev-minus human immunodeficiency virus type 1 mutant by activation of a cryptic splice site.
Journal of virology 2001;75(7):3495-500.
2001: Ben Berkhout; Koen Verhoef
Evolution of live-attenuated virus vaccines.
Developments in biologicals 2001;106():217-21; discussion 253-63.
2001: Hendrik Huthoff; Ben Berkhout
Two alternating structures of the HIV-1 leader RNA.
RNA (New York, N.Y.) 2001;7(1):143-57.
2001: Koen Verhoef; Giuseppe Marzio; W Hillen; H Bujard; Ben Berkhout
Strict control of human immunodeficiency virus type 1 replication by a genetic switch: Tet for Tat.
Journal of virology 2001;75(2):979-87.
2000: Nancy Beerens; Fedde Groot; Ben Berkhout
Stabilization of the U5-leader stem in the HIV-1 RNA genome affects initiation and elongation of reverse transcription.
Nucleic acids research 2000;28(21):4130-7.
2000: Nancy Beerens; Ben Berkhout
In vitro studies on tRNA annealing and reverse transcription with mutant HIV-1 RNA templates.
The Journal of biological chemistry 2000;275(20):15474-81.
2000: Rienk E Jeeninga; Maarten Hoogenkamp; M Armand-Ugon; Michel P De Baar; Koen Verhoef; Ben Berkhout
Functional differences between the long terminal repeat transcriptional promoters of human immunodeficiency virus type 1 subtypes A through G.
Journal of virology 2000;74(8):3740-51.
2000: Michel P De Baar; Anthony de Ronde; Ben Berkhout; Marion Cornelissen; KH van der Horn; AM van der Schoot; Frank de Wolf; Vladimir V Lukashov; Jaap Goudsmit
Subtype-specific sequence variation of the HIV type 1 long terminal repeat and primer-binding site.
AIDS research and human retroviruses 2000;16(5):499-504.
2000: Nancy Beerens; Bep Klaver; Ben Berkhout
A structured RNA motif is involved in correct placement of the tRNA(3)(Lys) primer onto the human immunodeficiency virus genome.
Journal of virology 2000;74(5):2227-38.
2000: Ben Berkhout; Jeroen L B van Wamel
The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure.
RNA (New York, N.Y.) 2000;6(2):282-95.
2000: Ben Berkhout
Multiple biological roles associated with the repeat (R) region of the HIV-1 RNA genome.
Advances in pharmacology (San Diego, Calif.) 2000;48():29-73.
2000: stefania mitola; R Soldi; I Zanon; L Barra; M I Gutierrez; Ben Berkhout; M Giacca; Federico Bussolino
Identification of specific molecular structures of human immunodeficiency virus type 1 Tat relevant for its biological effects on vascular endothelial cells.
Journal of virology 2000;74(1):344-53.
1999: Atze T Das; Aafke Land; Ineke Braakman; Bep Klaver; Ben Berkhout
HIV-1 evolves into a nonsyncytium-inducing virus upon prolonged culture in vitro.
Virology 1999;263(1):55-69.
1999: Ben Berkhout
HIV-1 evolution under pressure of protease inhibitors: climbing the stairs of viral fitness.
Journal of biomedical science 1999;6(5):298-305.
1999: Wilco Keulen; Albert van Wijk; Rob Schuurman; Ben Berkhout; Charles A B Boucher
Increased polymerase fidelity of lamivudine-resistant HIV-1 variants does not limit their evolutionary potential.
AIDS (London, England) 1999;13(11):1343-9.
1999: Koen Verhoef; Ben Berkhout
A second-site mutation that restores replication of a Tat-defective human immunodeficiency virus.
Journal of virology 1999;73(4):2781-9.
1999: BI Klasens; Hendrik Huthoff; Atze T Das; Rienk E Jeeninga; Ben Berkhout
The effect of template RNA structure on elongation by HIV-1 reverse transcriptase.
Biochimica et biophysica acta 1999;1444(3):355-70.
1999: B B Oude Essink; Ben Berkhout
The fidelity of reverse transcription differs in reactions primed with RNA versus DNA primers.
Journal of biomedical science 1999;6(2):121-32.
1999: Ben Berkhout; Maarten F Jebbink; J Zsíros
Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus.
Journal of virology 1999;73(3):2365-75.
1999: Koen Verhoef; Rogier W Sanders; V Fontaine; S Kitajima; Ben Berkhout
Evolution of the human immunodeficiency virus type 1 long terminal repeat promoter by conversion of an NF-kappaB enhancer element into a GABP binding site.
Journal of virology 1999;73(2):1331-40.
1999: Ben Berkhout; Koen Verhoef; Jeroen L B van Wamel; Nicole Back
Genetic instability of live, attenuated human immunodeficiency virus type 1 vaccine strains.
Journal of virology 1999;73(2):1138-45.
1999: BI Klasens; M Thiesen; A Virtanen; Ben Berkhout
The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure.
Nucleic acids research 1999;27(2):446-54.
1999: J Zsíros; Maarten F Jebbink; Vladimir V Lukashov; PA Voûte; Ben Berkhout
Biased nucleotide composition of the genome of HERV-K related endogenous retroviruses and its evolutionary implications.
Journal of molecular evolution 1999;48(1):102-11.
1999: Atze T Das; Bep Klaver; Ben Berkhout
A hairpin structure in the R region of the human immunodeficiency virus type 1 RNA genome is instrumental in polyadenylation site selection.
Journal of virology 1999;73(1):81-91.
1998: Rienk E Jeeninga; Hendrik Huthoff; A P Gultyaev; Ben Berkhout
The mechanism of actinomycin D-mediated inhibition of HIV-1 reverse transcription.
Nucleic acids research 1998;26(23):5472-9.
1998: Koen Verhoef; M Bauer; Andreas Meyerhans; Ben Berkhout
On the role of the second coding exon of the HIV-1 Tat protein in virus replication and MHC class I downregulation.
AIDS research and human retroviruses 1998;14(17):1553-9.
1998: Atze T Das; Bep Klaver; Ben Berkhout
The 5' and 3' TAR elements of human immunodeficiency virus exert effects at several points in the virus life cycle.
Journal of virology 1998;72(11):9217-23.
1998: Ben Berkhout; Atze T Das; Jeroen L B van Wamel
The native structure of the human immunodeficiency virus type 1 RNA genome is required for the first strand transfer of reverse transcription.
Virology 1998;249(2):211-8.
1998: J Zsíros; Maarten F Jebbink; PA Voûte; Ben Berkhout
Identification of novel human endogenous retroviral sequences belonging to the HERV-K family.
AIDS research and human retroviruses 1998;14(12):1093-8.
1998: Atze T Das; A P van Dam; Bep Klaver; Ben Berkhout
Improved envelope function selected by long-term cultivation of a translation-impaired HIV-1 mutant.
Virology 1998;244(2):552-62.
1998: Jeroen L B van Wamel; Ben Berkhout
The first strand transfer during HIV-1 reverse transcription can occur either intramolecularly or intermolecularly.
Virology 1998;244(2):245-51.
1998: BI Klasens; Atze T Das; Ben Berkhout
Inhibition of polyadenylation by stable RNA secondary structure.
Nucleic acids research 1998;26(8):1870-6.
1998: Ben Berkhout; Atze T Das
Similarity of chemokines charge and the V3 domain of HIV-1 env protein.
Emerging infectious diseases 1998;4(2):335-6.
1998: J Zsíros; Maarten F Jebbink; Vladimir V Lukashov; PA Voûte; Ben Berkhout
Evolutionary relationships within a subgroup of HERV-K-related human endogenous retroviruses.
The Journal of general virology 1998;79 ( Pt 1)():61-70.
1997: Nicole Back; Ben Berkhout
Limiting deoxynucleoside triphosphate concentrations emphasize the processivity defect of lamivudine-resistant variants of human immunodeficiency virus type 1 reverse transcriptase.
Antimicrobial agents and chemotherapy 1997;41(11):2484-91.
1997: Koen Verhoef; M Koper; Ben Berkhout
Determination of the minimal amount of Tat activity required for human immunodeficiency virus type 1 replication.
Virology 1997;237(2):228-36.
1997: Ben Berkhout
The primer binding site on the RNA genome of human and simian immunodeficiency viruses is flanked by an upstream hairpin structure.
Nucleic acids research 1997;25(20):4013-7.
1997: Ben Berkhout; G C Derksen; Nicole Back; Bep Klaver; C G de Kruif; Servaas Visser
Structural and functional analysis of negatively charged milk proteins with anti-HIV activity.
AIDS research and human retroviruses 1997;13(13):1101-7.
1997: B B Oude Essink; Nicole Back; Ben Berkhout
Increased polymerase fidelity of the 3TC-resistant variants of HIV-1 reverse transcriptase.
Nucleic acids research 1997;25(16):3212-7.
1997: Atze T Das; Bep Klaver; Ben Berkhout
Sequence variation of the human immunodeficiency virus primer-binding site suggests the use of an alternative tRNA(Lys) molecule in reverse transcription.
The Journal of general virology 1997;78 ( Pt 4)():837-40.
1997: Wilco Keulen; Nicole Back; Albert van Wijk; Charles A B Boucher; Ben Berkhout
Initial appearance of the 184Ile variant in lamivudine-treated patients is caused by the mutational bias of human immunodeficiency virus type 1 reverse transcriptase.
Journal of virology 1997;71(4):3346-50.
1997: Atze T Das; Bep Klaver; BI Klasens; Jeroen L B van Wamel; Ben Berkhout
A conserved hairpin motif in the R-U5 region of the human immunodeficiency virus type 1 RNA genome is essential for replication.
Journal of virology 1997;71(3):2346-56.
1997: Ben Berkhout; Bep Klaver; Atze T Das
Forced evolution of a regulatory RNA helix in the HIV-1 genome.
Nucleic acids research 1997;25(5):940-7.
1997: Koen Verhoef; M Tijms; Ben Berkhout
Optimal Tat-mediated activation of the HIV-1 LTR promoter requires a full-length TAR RNA hairpin.
Nucleic acids research 1997;25(3):496-502.
1997: Wilco Keulen; Monique Nijhuis; Rob Schuurman; Ben Berkhout; C Boucher
Reverse transcriptase fidelity and HIV-1 variation.
Science (New York, N.Y.) 1997;275(5297):229; author reply 230-1.
1996: B B Oude Essink; Atze T Das; Ben Berkhout
HIV-1 reverse transcriptase discriminates against non-self tRNA primers.
Journal of molecular biology 1996;264(2):243-54.
1996: Koen Verhoef; A Klein; Ben Berkhout
Paracrine activation of the HIV-1 LTR promoter by the viral Tat protein is mechanistically similar to trans-activation within a cell.
Virology 1996;225(2):316-27.
1996: Ben Berkhout; Jeroen L B van Wamel
Role of the DIS hairpin in replication of human immunodeficiency virus type 1.
Journal of virology 1996;70(10):6723-32.
1996: Nicole Back; Monique Nijhuis; Wilco Keulen; Charles A B Boucher; B O Oude Essink; A B van Kuilenburg; A H van Gennip; Ben Berkhout
Reduced replication of 3TC-resistant HIV-1 variants in primary cells due to a processivity defect of the reverse transcriptase enzyme.
The EMBO journal 1996;15(15):4040-9.
1996: Wilco Keulen; Charles A B Boucher; Ben Berkhout
Nucleotide substitution patterns can predict the requirements for drug-resistance of HIV-1 proteins.
Antiviral research 1996;31(1-2):45-57.
1996: Ben Berkhout; Jeroen L B van Wamel
Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site.
The Journal of biological chemistry 1996;271(4):1837-40.
1996: Ben Berkhout
Structure and function of the human immunodeficiency virus leader RNA.
Progress in nucleic acid research and molecular biology 1996;54():1-34.
1996: Ben Berkhout; Jeroen L B van Wamel
Identification of a novel splice acceptor in the HIV-1 genome: independent expression of the cytoplasmic tail of the envelope protein.
Archives of virology 1996;141(5):839-55.
1995: B B Oude Essink; Atze T Das; Ben Berkhout
Structural requirements for the binding of tRNA Lys3 to reverse transcriptase of the human immunodeficiency virus type 1.
The Journal of biological chemistry 1995;270(40):23867-74.
1995: Ben Berkhout; Jeroen L B van Wamel; Bep Klaver
Requirements for DNA strand transfer during reverse transcription in mutant HIV-1 virions.
Journal of molecular biology 1995;252(1):59-69.
1995: Formijn J van Hemert; Ben Berkhout
The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability.
Journal of molecular evolution 1995;41(2):132-40.
1995: Arie van der Ende; C T Hopman; Sebastian A J Zaat; B B Essink; Ben Berkhout; Jacob Dankert
Variable expression of class 1 outer membrane protein in Neisseria meningitidis is caused by variation in the spacing between the -10 and -35 regions of the promoter.
Journal of bacteriology 1995;177(9):2475-80.
1995: Atze T Das; Bep Klaver; Ben Berkhout
Reduced replication of human immunodeficiency virus type 1 mutants that use reverse transcription primers other than the natural tRNA(3Lys).
Journal of virology 1995;69(5):3090-7.
1995: Atze T Das; Ben Berkhout
Efficient extension of a misaligned tRNA-primer during replication of the HIV-1 retrovirus.
Nucleic acids research 1995;23(8):1319-26.
1995: Ben Berkhout; Bep Klaver
Revertants and pseudo-revertants of human immunodeficiency virus type 1 viruses mutated in the long terminal repeat promoter region.
The Journal of general virology 1995;76 ( Pt 4)():845-53.
1995: Ben Berkhout; Jeroen L B van Wamel
Inhibition of human immunodeficiency virus expression by sense transcripts encoding the retroviral leader RNA.
Antiviral research 1995;26(2):101-15.
1995: Ben Berkhout; Bep Klaver; Atze T Das
A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses.
Virology 1995;207(1):276-81.
1994: S E Koken; Jeroen L B van Wamel; Ben Berkhout
A sensitive promoter assay based on the transcriptional activator Tat of the HIV-1 virus.
Gene 1994;144(2):243-7.
1994: Bep Klaver; Ben Berkhout
Comparison of 5' and 3' long terminal repeat promoter function in human immunodeficiency virus.
Journal of virology 1994;68(6):3830-40.
1994: Bep Klaver; Ben Berkhout
Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus.
The EMBO journal 1994;13(11):2650-9.
1994: Ben Berkhout; Formijn J van Hemert
The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins.
Nucleic acids research 1994;22(9):1705-11.
1994: S E Koken; A E Greijer; Koen Verhoef; Jeroen L B van Wamel; A G Bukrinskaya; Ben Berkhout
Intracellular analysis of in vitro modified HIV Tat protein.
The Journal of biological chemistry 1994;269(11):8366-75.
1994: Atze T Das; S E Koken; B B Essink; Jeroen L B van Wamel; Ben Berkhout
Human immunodeficiency virus uses tRNA(Lys,3) as primer for reverse transcription in HeLa-CD4+ cells.
FEBS letters 1994;341(1):49-53.
1994: Bep Klaver; Ben Berkhout
Premature strand transfer by the HIV-1 reverse transcriptase during strong-stop DNA synthesis.
Nucleic acids research 1994;22(2):137-44.
1994: B B Oude Essink; Ben Berkhout
The restriction enzyme BanI is inhibited by dcm-methylation of the GGCGCm5C site.
Nucleic acids research 1994;22(1):108.
1993: Kuan-Teh Jeang; Ben Berkhout; B Dropulic
Effects of integration and replication on transcription of the HIV-1 long terminal repeat.
The Journal of biological chemistry 1993;268(33):24940-9.
1993: Ben Berkhout; Bep Klaver
In vivo selection of randomly mutated retroviral genomes.
Nucleic acids research 1993;21(22):5020-4.
1993: Koen Verhoef; S E Koken; Ben Berkhout
Electroporation of the HIV Tat trans-activator protein into cells.
Analytical biochemistry 1993;210(1):210-4.
1993: Ben Berkhout; I Schoneveld
Secondary structure of the HIV-2 leader RNA comprising the tRNA-primer binding site.
Nucleic acids research 1993;21(5):1171-8.
1993: Ben Berkhout; B B Essink; I Schoneveld
In vitro dimerization of HIV-2 leader RNA in the absence of PuGGAPuA motifs.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1993;7(1):181-7.
1992: S E Koken; Jeroen L B van Wamel; Jaap Goudsmit; Ben Berkhout; J L Geelen
Natural variants of the HIV-1 long terminal repeat: analysis of promoters with duplicated DNA regulatory motifs.
Virology 1992;191(2):968-72.
1992: Kuan-Teh Jeang; Ben Berkhout
Kinetics of HIV-1 long terminal repeat trans-activation. Use of intragenic ribozyme to assess rate-limiting steps.
The Journal of biological chemistry 1992;267(25):17891-9.
1992: Ben Berkhout
Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis.
Nucleic acids research 1992;20(1):27-31.
1992: Ben Berkhout; Kuan-Teh Jeang
Functional roles for the TATA promoter and enhancers in basal and Tat-induced expression of the human immunodeficiency virus type 1 long terminal repeat.
Journal of virology 1992;66(1):139-49.
1991: Ben Berkhout; Kuan-Teh Jeang
Detailed mutational analysis of TAR RNA: critical spacing between the bulge and loop recognition domains.
Nucleic acids research 1991;19(22):6169-76.
1991: C Hall; Ben Berkhout; B Alarcon; Jaime Sancho; T Wileman; Cox Terhorst
Requirements for cell surface expression of the human TCR/CD3 complex in non-T cells.
International immunology 1991;3(4):359-68.
1991: A Gatignol; Alicia Buckler-White; Ben Berkhout; Kuan-Teh Jeang
Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR.
Science (New York, N.Y.) 1991;251(5001):1597-600.
1991: Kuan-Teh Jeang; Y Chang; Ben Berkhout; Marie-Louise Hammarskjöld; D Rekosh
Regulation of HIV expression: mechanisms of action of Tat and Rev.
AIDS (London, England) 1991;5 Suppl 2():S3-14.
1990: Ben Berkhout; Kuan-Teh Jeang
Down modulation of HIV-1 gene expression using a procaryotic RNA-binding protein.
Nucleic acids research 1990;18(23):6903-7.
1990: D N SenGupta; Ben Berkhout; A Gatignol; A M Zhou; R H Silverman
Direct evidence for translational regulation by leader RNA and Tat protein of human immunodeficiency virus type 1.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(19):7492-6.
1990: Ben Berkhout; A Gatignol; A B Rabson; Kuan-Teh Jeang
TAR-independent activation of the HIV-1 LTR: evidence that tat requires specific regions of the promoter.
Cell 1990;62(4):757-67.
1990: Ben Berkhout; A Gatignol; Jonathan Silver; Kuan-Teh Jeang
Efficient trans-activation by the HIV-2 Tat protein requires a duplicated TAR RNA structure.
Nucleic acids research 1990;18(7):1839-46.
1989: Ben Berkhout; Kuan-Teh Jeang
trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: a quantitative analysis.
Journal of virology 1989;63(12):5501-4.
1989: Ben Berkhout; R H Silverman; Kuan-Teh Jeang
Tat trans-activates the human immunodeficiency virus through a nascent RNA target.
Cell 1989;59(2):273-82.
1988: Ben Berkhout; B Alarcon; Cox Terhorst
Transfection of genes encoding the T cell receptor-associated CD3 complex into COS cells results in assembly of the macromolecular structure.
The Journal of biological chemistry 1988;263(17):8528-36.
1988: Ben Berkhout; C Hall; Cox Terhorst
Complete cDNA sequence coding for the human T cell receptor alpha chain HPB-ALL.
Nucleic acids research 1988;16(11):5209.
1988: B Alarcon; Ben Berkhout; J Breitmeyer; Cox Terhorst
Assembly of the human T cell receptor-CD3 complex takes place in the endoplasmic reticulum and involves intermediary complexes between the CD3-gamma.delta.epsilon core and single T cell receptor alpha or beta chains.
The Journal of biological chemistry 1988;263(6):2953-61.
1987: Ben Berkhout; B F Schmidt; A van Strien; Jacques H van Boom; J van Westrenen; Jan van Duin
Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene.
Journal of molecular biology 1987;195(3):517-24.
1987: B F Schmidt; Ben Berkhout; G P Overbeek; A van Strien; Jan van Duin
Determination of the RNA secondary structure that regulates lysis gene expression in bacteriophage MS2.
Journal of molecular biology 1987;195(3):505-16.
1986: Ben Berkhout; C J van der Laken; P H van Knippenberg
Formylmethionyl-tRNA binding to 30 S ribosomes programmed with homopolynucleotides and the effect of translational initiation factor 3.
Biochimica et biophysica acta 1986;866(2-3):144-53.
1985: Ben Berkhout; M H de Smit; Remco Spanjaard; T Blom; Jan van Duin
The amino terminal half of the MS2-coded lysis protein is dispensable for function: implications for our understanding of coding region overlaps.
The EMBO journal 1985;4(12):3315-20.
1985: Ben Berkhout; J van Duin
Mechanism of translational coupling between coat protein and replicase genes of RNA bacteriophage MS2.
Nucleic acids research 1985;13(19):6955-67.
1985: Ben Berkhout; J D Macfarlane; A Cats
Symptomatic osteoarthrosis of the knee: a follow-up study.
British journal of rheumatology 1985;24(1):40-5.
1985: Ben Berkhout; R A Kastelein; Jan van Duin
Translational interference at overlapping reading frames in prokaryotic messenger RNA.
Gene 1985;37(1-3):171-9.
1983: R A Kastelein; Ben Berkhout; Jan van Duin
Opening the closed ribosome-binding site of the lysis cistron of bacteriophage MS2.
Nature 1983;305(5936):741-3.
1983: R A Kastelein; Ben Berkhout; G P Overbeek; Jan van Duin
Effect of the sequences upstream from the ribosome-binding site on the yield of protein from the cloned gene for phage MS2 coat protein.
Gene 1983;23(3):245-54.
1980: K van der Laken; H Bakker-Steeneveld; Ben Berkhout; P H van Knippenberg
The role of the codon and the initiation factor IF-2 in the selection of N-blocked aminoacyl-tRNA for initiation.
European journal of biochemistry / FEBS 1980;104(1):19-33.