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Ben Berkhout

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Publications

TOP 3
Liu Ying Poi; von Eije Karin Jasmijn; Schopman Nick C T; Westerink Jan-Tinus; Brake Olivier ter; Haasnoot Joost; Berkhout Ben
Combinatorial RNAi against HIV-1 using extended short hairpin RNAs.
Liu Ying Poi; Gruber Jens; Haasnoot Joost; Konstantinova Pavlina; Berkhout Ben
RNAi-mediated inhibition of HIV-1 by targeting partially complementary viral sequences.
Berkhout Ben
Toward a durable anti-HIV gene therapy based on RNA interference.

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All Publications

2009: Liu Ying Poi; von Eije Karin Jasmijn; Schopman Nick C T; Westerink Jan-Tinus; Brake Olivier ter; Haasnoot Joost; Berkhout Ben
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: Liu Ying Poi; Gruber Jens; Haasnoot Joost; Konstantinova Pavlina; Berkhout Ben
RNAi-mediated inhibition of HIV-1 by targeting partially complementary viral sequences.
Nucleic acids research 2009;37(18):6194-204.
2009: Berkhout Ben
Toward a durable anti-HIV gene therapy based on RNA interference.
Annals of the New York Academy of Sciences 2009;1175():3-14.
2009: de Vries Walter; Haasnoot Joost; Fouchier Ron; de Haan Peter; Berkhout Ben
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: Jeeninga Rienk E; de Jong Menno D; Berkhout Ben
The new influenza A (H1N1) pandemic.
Journal of the Formosan Medical Association = Taiwan yi zhi 2009;108(7):523-5.
2009: von Eije Karin J; ter Brake Olivier; Berkhout Ben
Stringent testing identifies highly potent and escape-proof anti-HIV short hairpin RNAs.
The journal of gene medicine 2009;11(6):459-67.
2009: Haché Guylaine; Abbink Truus E M; Berkhout Ben; Harris Reuben S
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: Kleibeuker Wendy; Zhou Xue; Centlivre Mireille; Legrand Nicolas; Page Mark; Almond Neil; Berkhout Ben; Das Atze T
A sensitive cell-based assay to measure the doxycycline concentration in biological samples.
Human gene therapy 2009;20(5):524-30.
2009: Berkhout Ben
A new Houdini act: multiple routes for HIV-1 escape from RNAi-mediated inhibition.
Future microbiology 2009;4(2):151-4.
2009: Berkhout Ben; ter Brake Olivier
Towards a durable RNAi gene therapy for HIV-AIDS.
Expert opinion on biological therapy 2009;9(2):161-70.
2009: ter Brake O; Legrand N; von Eije K J; Centlivre M; Spits H; Weijer K; Blom B; Berkhout B
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.
2009: Liu Ying Poi; Berkhout Ben
Lentiviral delivery of RNAi effectors against HIV-1.
Current topics in medicinal chemistry 2009;9(12):1130-43.
2009: Bordería Antonia V; Berkhout Ben
Towards a genetic AIDS vaccine.
Retrovirology 2009;6():93.
2009: Berkhout Ben; Paxton William A
HIV vaccine: it may take two to tango, but no party time yet.
Retrovirology 2009;6():88.
2009: von Eije Karin J; Berkhout Ben
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: Ayele Workenesh; Assefa Tsehai; Lulseged Sileshi; Tegbaru Belete; Berhanu Hiwot; Tamene Wegene; Ahmedin Zenit; Tensai Birzaf W; Tafesse Mengistu; Goudsmit Jaap; Berkhout Ben; Paxton William A; Debaar Michel P; Messele Tsehaynesh; Pollakis Georgios
RNA Detection and Subtype C Assessment of HIV-1 in Infants with Diarrhea in Ethiopia.
The open AIDS journal 2009;3():19-23.
2009: Vrolijk Martine M; Harwig Alex; Berkhout Ben; Das Atze T
Destabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation.
Retrovirology 2009;6():13.
2009: Haasnoot Joost; Berkhout Ben
Nucleic acids-based therapeutics in the battle against pathogenic viruses.
Handbook of experimental pharmacology 2009;(189):243-63.
2009: Berkhout Ben; Das Atze T
Virus evolution as a tool to study HIV-1 biology.
Methods in molecular biology (Clifton, N.J.) 2009;485():436-51.
2008: Berkhout Ben
Infectious diseases of the nervous system: pathogenesis and worldwide impact.
IDrugs : the investigational drugs journal 2008;11(11):791-5.
2008: Mathewson Alison C; Bishop Alexandra; Yao Yongxiu; Kemp Fred; Ren Junyuan; Chen Hongying; Xu Xiaodong; Berkhout Ben; van der Hoek Lia; Jones Ian M
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: Sanders Rogier W; Hsu Shang-Te D; van Anken Eelco; Liscaljet I Marije; Dankers Martijn; Bontjer Ilja; Land Aafke; Braakman Ineke; Bonvin Alexandre M J J; Berkhout Ben
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: Berkhout Ben
An eye-opener for RNAi therapeutics.
Journal of the Formosan Medical Association = Taiwan yi zhi 2008;107(10):749-50.
2008: van Anken Eelco; Sanders Rogier W; Liscaljet I Marije; Land Aafke; Bontjer Ilja; Tillemans Sonja; Nabatov Alexey A; Paxton William A; Berkhout Ben; Braakman Ineke
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: ter Brake Olivier; von Eije Karin J; Berkhout Ben
Probing the sequence space available for HIV-1 evolution.
AIDS (London, England) 2008;22(14):1875-7.
2008: Centlivre Mireille; Klaver Bep; Berkhout Ben; Das Atze T
Functional analysis of the complex trans-activating response element RNA structure in simian immunodeficiency virus.
Journal of virology 2008;82(18):9171-8.
2008: Vrolijk Martine M; Ooms Marcel; Harwig Alex; Das Atze T; Berkhout Ben
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: Baldwin Chris; Berkhout Ben
Mechanistic studies of a T20-dependent human immunodeficiency virus type 1 variant.
Journal of virology 2008;82(15):7735-40.
2008: Pasternak Alexander O; Adema Karen W; Bakker Margreet; Jurriaans Suzanne; Berkhout Ben; Cornelissen Marion; Lukashov Vladimir V
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: Eggink Dirk; Baldwin Christopher E; Deng Yiqun; Langedijk Johannes P M; Lu Min; Sanders Rogier W; Berkhout Ben
Selection of T1249-resistant human immunodeficiency virus type 1 variants.
Journal of virology 2008;82(13):6678-88.
2008: Menéndez-Arias Luis; Berkhout Ben
Retroviral reverse transcription.
Virus research 2008;134(1-2):1-3.
2008: Abbink Truus E M; Berkhout Ben
HIV-1 reverse transcription initiation: a potential target for novel antivirals?
Virus research 2008;134(1-2):4-18.
2008: Liu Ying Poi; Haasnoot Joost; ter Brake Olivier; Berkhout Ben; Konstantinova Pavlina
Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron.
Nucleic acids research 2008;36(9):2811-24.
2008: Ringrose Jeffrey H; Jeeninga Rienk E; Berkhout Ben; Speijer Dave
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: de Vries W; Haasnoot J; van der Velden J; van Montfort T; Zorgdrager F; Paxton W; Cornelissen M; van Kuppeveld F; de Haan P; Berkhout B
Increased virus replication in mammalian cells by blocking intracellular innate defense responses.
Gene therapy 2008;15(7):545-52.
2008: ter Brake Olivier; 't Hooft Karen; Liu Ying Poi; Centlivre Mireille; von Eije Karin Jasmijn; Berkhout Ben
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: Abbink Truus E M; Berkhout Ben
RNA structure modulates splicing efficiency at the human immunodeficiency virus type 1 major splice donor.
Journal of virology 2008;82(6):3090-8.
2008: Bonneau Kyle R; Ng Sharon; Foster Hillary; Choi Kelly B; Berkhout Ben; Rabson Arnold; Mackewicz Carl E; Levy Jay A
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: von Eije Karin Jasmijn; ter Brake Olivier; Berkhout Ben
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: Smit Colette; van den Berg Charlotte; Geskus Ronald; Berkhout Ben; Coutinho Roel; Prins Maria
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: de Vries Michel; Pyrc Krzysztof; Berkhout Ron; Vermeulen-Oost Wilma; Dijkman Ronald; Jebbink Maarten F; Bruisten Sylvia; Berkhout Ben; van der Hoek Lia
Human parechovirus type 1, 3, 4, 5, and 6 detection in picornavirus cultures.
Journal of clinical microbiology 2008;46(2):759-62.
2008: Berkhout Ben
A balancing act: viruses and miRNAs.
Journal of the Formosan Medical Association = Taiwan yi zhi 2008;107(1):1-3.
2008: van Hemert Formijn J; Zaaijer Hans L; Berkhout Ben; Lukashov Vladimir V
Mosaic amino acid conservation in 3D-structures of surface protein and polymerase of hepatitis B virus.
Virology 2008;370(2):362-72.
2008: van Hemert Formijn J; Zaaijer Hans L; Berkhout Ben; Lukashov Vladimir V
Occult hepatitis B infection: an evolutionary scenario.
Virology journal 2008;5():146.
2008: Pyrc Krzysztof; Jebbink Maarten F; Berkhout Ben; van der Hoek Lia
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: Lever Andrew M L; Berkhout Ben
2008 Nobel prize in medicine for discoverers of HIV.
Retrovirology 2008;5():91.
2008: ter Brake Olivier; Haasnoot Joost; Kurreck Jens; Berkhout Ben
ESF-EMBO symposium: antiviral applications of RNA interference.
Retrovirology 2008;5():81.
2008: de Vries Walter; Berkhout Ben
RNAi suppressors encoded by pathogenic human viruses.
The international journal of biochemistry & cell biology 2008;40(10):2007-12.
2008: Das Atze T; Klaver Bep; Centlivre Mireille; Harwig Alex; Ooms Marcel; Page Mark; Almond Neil; Yuan Fang; Piatak Mike; Lifson Jeffrey D; Berkhout Ben
Optimization of the doxycycline-dependent simian immunodeficiency virus through in vitro evolution.
Retrovirology 2008;5():44.
2008: Jeeninga Rienk E; Westerhout Ellen M; van Gerven Marja L; Berkhout Ben
HIV-1 latency in actively dividing human T cell lines.
Retrovirology 2008;5():37.
2008: Berkhout Ben; Gorelick Robert; Summers Michael F; Mély Yves; Darlix Jean-Luc
6th international symposium on retroviral nucleocapsid.
Retrovirology 2008;5():21.
2008: Sanders Rogier W; van Anken Eelco; Nabatov Alexei A; Liscaljet I Marije; Bontjer Ilja; Eggink Dirk; Melchers Mark; Busser Els; Dankers Martijn M; Groot Fedde; Braakman Ineke; Berkhout Ben; Paxton William A
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.
2007: Haasnoot Joost; Westerhout Ellen M; Berkhout Ben
RNA interference against viruses: strike and counterstrike.
Nature biotechnology 2007;25(12):1435-43.
2007: Berkhout Ben
Third European Congress of Virology. 1-5 September 2007, Nuremberg, Germany.
IDrugs : the investigational drugs journal 2007;10(11):772-4.
2007: Das Atze T; Klaver Bep; Harwig Alex; Vink Monique; Ooms Marcel; Centlivre Mireille; Berkhout Ben
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: ter Brake Olivier; Berkhout Ben
Lentiviral vectors that carry anti-HIV shRNAs: problems and solutions.
The journal of gene medicine 2007;9(9):743-50.
2007: Berkhout Ben; Jeang Kuan-Teh
RISCy business: MicroRNAs, pathogenesis, and viruses.
The Journal of biological chemistry 2007;282(37):26641-5.
2007: Das Atze T; Harwig Alex; Vrolijk Martine M; Berkhout Ben
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: Gali Youssef; Berkhout Ben; Vanham Guido; Bakker Margreet; Back Nicole K T; Ariën Kevin K
Survey of the temporal changes in HIV-1 replicative fitness in the Amsterdam Cohort.
Virology 2007;364(1):140-6.
2007: Haasnoot Joost; de Vries Walter; Geutjes Ernst-Jan; Prins Marcel; de Haan Peter; Berkhout Ben
The Ebola virus VP35 protein is a suppressor of RNA silencing.
PLoS pathogens 2007;3(6):e86.
2007: van Hemert Formijn J; Berkhout Ben; Lukashov Vladimir V
Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae.
Virology 2007;361(2):447-54.
2007: Pyrc Krzysztof; Berkhout Ben; van der Hoek Lia
Identification of new human coronaviruses.
Expert review of anti-infective therapy 2007;5(2):245-53.
2007: Pyrc Krzysztof; Berkhout Ben; van der Hoek Lia
The novel human coronaviruses NL63 and HKU1.
Journal of virology 2007;81(7):3051-7.
2007: van der Hoek Lia; Pollakis Georgios; Lukashov Vladimir V; Jebbink Maarten F; Jeeninga Rienk E; Bakker Margreet; Dukers Nicole; Jurriaans Suzanne; Paxton William A; Back Nicole K T; Berkhout Ben
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: Pyrc K; Berkhout B; van der Hoek L
Antiviral strategies against human coronaviruses.
Infectious disorders drug targets 2007;7(1):59-66.
2007: Centlivre Mireille; Sala Monica; Wain-Hobson Simon; Berkhout Ben
In HIV-1 pathogenesis the die is cast during primary infection.
AIDS (London, England) 2007;21(1):1-11.
2007: Crotti Andrea; Chiara Giulia D; Ghezzi Silvia; Lupo Rossella; Jeeninga Rienk E; Liboi Elio; Lievens Patricia M-J; Vicenzi Elisa; Bovolenta Chiara; Berkhout Ben; Poli Guido
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: Baldwin Chris; Berkhout Ben
HIV-1 drug-resistance and drug-dependence.
Retrovirology 2007;4():78.
2007: Smit Colette; Pfrommer Christiaan; Mindel Adrian; Taylor Janette; Spaargaren Joke; Berkhout Ben; Coutinho Roel; Dukers Nicole H T M
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: Geskus Ronald B; Prins Maria; Hubert Jean-Baptiste; Miedema Frank; Berkhout Ben; Rouzioux Christine; Delfraissy Jean-Francois; Meyer Laurence
The HIV RNA setpoint theory revisited.
Retrovirology 2007;4():65.
2007: Liu Ying Poi; Haasnoot Joost; Berkhout Ben
Design of extended short hairpin RNAs for HIV-1 inhibition.
Nucleic acids research 2007;35(17):5683-93.
2007: Ooms Marcel; Abbink Truus E M; Pham Chi; Berkhout Ben
Circularization of the HIV-1 RNA genome.
Nucleic acids research 2007;35(15):5253-61.
2007: Abbink Truus E M; Berkhout Ben
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: Westerhout Ellen M; Berkhout Ben
A systematic analysis of the effect of target RNA structure on RNA interference.
Nucleic acids research 2007;35(13):4322-30.
2007: Jakobsen Martin R; Haasnoot Joost; Wengel Jesper; Berkhout Ben; Kjems Jørgen
Efficient inhibition of HIV-1 expression by LNA modified antisense oligonucleotides and DNAzymes targeted to functionally selected binding sites.
Retrovirology 2007;4():29.
2007: van Hemert Formijn J; Lukashov Vladimir V; Berkhout Ben
Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function.
Virology journal 2007;4():25.
2007: van Opijnen Tim; de Ronde Anthony; Boerlijst Maarten C; Berkhout Ben
Adaptation of HIV-1 depends on the host-cell environment.
PloS one 2007;2(3):e271.
2007: van den Berg Charlotte H S B; Smit Colette; Bakker Margreet; Geskus Ronald B; Berkhout Ben; Jurriaans Suzanne; Coutinho Roel A; Wolthers Katja C; Prins Maria
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: Konstantinova Pavlina; ter Brake Olivier; Haasnoot Joost; de Haan Peter; Berkhout Ben
Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome.
Retrovirology 2007;4():15.
2007: van der Kuyl Antoinette C; van den Burg Remco; Zorgdrager Fokla; Groot Fedde; Berkhout Ben; Cornelissen Marion
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: Ooms Marcel; Cupac Daniel; Abbink Truus E M; Huthoff Hendrik; Berkhout Ben
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: Zhou Xue; Symons Jori; Hoppes Rieuwert; Krueger Christel; Berens Christian; Hillen Wolfgang; Berkhout Ben; Das Atze T
Improved single-chain transactivators of the Tet-On gene expression system.
BMC biotechnology 2007;7():6.
2006: Zheng Qi; Deng Yiqun; Liu Jie; van der Hoek Lia; Berkhout Ben; Lu Min
Core structure of S2 from the human coronavirus NL63 spike glycoprotein.
Biochemistry 2006;45(51):15205-15.
2006: Pyrc Krzysztof; Dijkman Ronald; Deng Lea; Jebbink Maarten F; Ross Howard A; Berkhout Ben; van der Hoek Lia
Mosaic structure of human coronavirus NL63, one thousand years of evolution.
Journal of molecular biology 2006;364(5):964-73.
2006: ter Brake Olivier; Konstantinova Pavlina; Ceylan Mustafa; Berkhout Ben
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: Lemckert Angelique A C; Grimbergen Jos; Smits Shirley; Hartkoorn Eric; Holterman Lennart; Berkhout Ben; Barouch Dan H; Vogels Ronald; Quax Paul; Goudsmit Jaap; Havenga Menzo J E
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: Zhou X; Vink M; Klaver B; Berkhout B; Das A T
Optimization of the Tet-On system for regulated gene expression through viral evolution.
Gene therapy 2006;13(19):1382-90.
2006: Konstantinova P; de Vries W; Haasnoot J; ter Brake O; de Haan P; Berkhout B
Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA.
Gene therapy 2006;13(19):1403-13.
2006: Groot Fedde; Sanders Rogier W; ter Brake Olivier; Nazmi Kamran; Veerman Enno C I; Bolscher Jan G M; Berkhout Ben
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: van der Hoek Lia; Pyrc Krzysztof; Berkhout Ben
Human coronavirus NL63, a new respiratory virus.
FEMS microbiology reviews 2006;30(5):760-73.
2006: Groot Fedde; van Capel Toni M M; Kapsenberg Martien L; Berkhout Ben; de Jong Esther C
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: Westerhout Ellen M; Vink Monique; Haasnoot P C Joost; Das Atze T; Berkhout Ben
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: Berkhout Ben; Back Nicole Kt; de Ronde Anthony; Jurriaans Suzanne; Bakker Margreet; Parkin Neil T; van der Hoek Lia
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: van Opijnen Tim; Boerlijst Maarten C; Berkhout Ben
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: Lützelberger Martin; Reinert Line S; Das Atze T; Berkhout Ben; Kjems Jørgen
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: Pyrc Krzysztof; Bosch Berend Jan; Berkhout Ben; Jebbink Maarten F; Dijkman Ronald; Rottier Peter; van der Hoek Lia
Inhibition of human coronavirus NL63 infection at early stages of the replication cycle.
Antimicrobial agents and chemotherapy 2006;50(6):2000-8.
2006: Zhou Xue; Vink Monique; Klaver Bep; Verhoef Koen; Marzio Giuseppe; Das Atze T; Berkhout Ben
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: Berkhout Ben; Haasnoot Joost
The interplay between virus infection and the cellular RNA interference machinery.
FEBS letters 2006;580(12):2896-902.
2006: Eberhardy Scott R; Goncalves Joao; Coelho Sofia; Segal David J; Berkhout Ben; Barbas Carlos F
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: Rizzi Chiara; Crippa Massimo P; Jeeninga Rienk E; Berkhout Ben; Blasi Francesco; Poli Guido; Alfano Massimo
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: Ophorst O J A E; Radosevic K; Havenga M J E; Pau M G; Holterman L; Berkhout B; Goudsmit J; Tsuji M
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.
2006: Chang Luan-Yin; Chiang Bor-Luen; Kao Chuan-Liang; Wu Mei-Hwan; Chen Pei-Jer; Berkhout Ben; Yang Hui-Ching; Huang Li-Min;
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: Benschop K S M; Schinkel J; Minnaar R P; Pajkrt D; Spanjerberg L; Kraakman H C; Berkhout B; Zaaijer H L; Beld M G H M; Wolthers K C
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: Dijkman Ronald; Jebbink Maarten F; Wilbrink Berry; Pyrc Krzysztof; Zaaijer Hans L; Minor Philip D; Franklin Sally; Berkhout Ben; Thiel Volker; van der Hoek Lia
Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes.
Virology journal 2006;3():106.
2006: Baldwin Chris E; Berkhout Ben
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: Zhou Xue; Vink Monique; Berkhout Ben; Das Atze T
Modification of the Tet-On regulatory system prevents the conditional-live HIV-1 variant from losing doxycycline-control.
Retrovirology 2006;3():82.
2006: Groot Fedde; Kuijpers Taco W; Berkhout Ben; de Jong Esther C
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: van der Hoek Lia; Sure Klaus; Ihorst Gabriele; Stang Alexander; Pyrc Krzysztof; Jebbink Maarten F; Petersen Gudula; Forster Johannes; Berkhout Ben; Uberla Klaus
Human coronavirus NL63 infection is associated with croup.
Advances in experimental medicine and biology 2006;581():485-91.
2006: Smith M K; Tusell Sonia; Travanty Emily A; Berkhout Ben; van der Hoek Lia; Holmes Kathryn V
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: Pöhlmann Stefan; Gramberg Thomas; Wegele Anja; Pyrc Krzysztof; van der Hoek Lia; Berkhout Ben; Hofmann Heike
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: Hofmann Heike; Marzi Andrea; Gramberg Thomas; Geier Martina; Pyrc Krzysztof; van der Hoek Lia; Berkhout Ben; Pöhlmann Stefan
Attachment factor and receptor engagement of SARS coronavirus and human coronavirus NL63.
Advances in experimental medicine and biology 2006;581():219-27.
2006: Piotrowski Yvonne; van der Hoek Lia; Pyrc Krzysztof; Berkhout Ben; Moll Ralf; Hilgenfeld Rolf
Nonstructural proteins of human coronavirus NL63.
Advances in experimental medicine and biology 2006;581():97-100.
2006: Jeeninga Rienk E; Jan Barbara; van den Berg Henk; Berkhout Ben
Construction of doxycyline-dependent mini-HIV-1 variants for the development of a virotherapy against leukemias.
Retrovirology 2006;3():64.
2006: Westerhout Ellen M; ter Brake Olivier; Berkhout Ben
The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference.
Retrovirology 2006;3():57.
2006: Groot Fedde; van Capel Toni M M; Schuitemaker Joost; Berkhout Ben; de Jong Esther C
Differential susceptibility of naïve, central memory and effector memory T cells to dendritic cell-mediated HIV-1 transmission.
Retrovirology 2006;3():52.
2006: Konstantinova Pavlina; de Haan Peter; Das Atze T; Berkhout Ben
Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1.
Nucleic acids research 2006;34(8):2206-18.
2006: Ruijter Jan M; Thygesen Helene H; Schoneveld Onard J L M; Das Atze T; Berkhout Ben; Lamers Wouter H
Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology.
Retrovirology 2006;3():2.
2005: Berkhout Ben
RNAi Europe 2005.
IDrugs : the investigational drugs journal 2005;8(12):978-81.
2005: Naarding Marloes A; Ludwig Irene S; Groot Fedde; Berkhout Ben; Geijtenbeek Teunis B H; Pollakis Georgios; Paxton William A
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: van der Hoek Lia; Sure Klaus; Ihorst Gabriele; Stang Alexander; Pyrc Krzysztof; Jebbink Maarten F; Petersen Gudula; Forster Johannes; Berkhout Ben; Uberla Klaus
Croup is associated with the novel coronavirus NL63.
PLoS medicine 2005;2(8):e240.
2005: Andersson M Gunnar; Haasnoot P C Joost; Xu Ning; Berenjian Saideh; Berkhout Ben; Akusjärvi Göran
Suppression of RNA interference by adenovirus virus-associated RNA.
Journal of virology 2005;79(15):9556-65.
2005: Adal Melaku; Ayele Workenesh; Wolday Dawit; Dagne Kifle; Messele Tsehaynesh; Tilahun Tesfaye; Berkhout Ben; Mayaan Shlomo; Pollakis Georgios; Dorigo-Zetsma Wendelien
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: Geskus Ronald B; Meyer Laurence; Hubert Jean-Baptiste; Schuitemaker Hanneke; Berkhout Ben; Rouzioux Christine; Theodorou Ioannis D; Delfraissy Jean-François; Prins Maria; Coutinho Roel A
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: van der Hoek Lia; Berkhout Ben
Questions concerning the New Haven coronavirus.
The Journal of infectious diseases 2005;192(2):350-1; author reply 353-4.
2005: van Opijnen Tim; Berkhout Ben
The host environment drives HIV-1 fitness.
Reviews in medical virology 2005;15(4):219-33.
2005: Abbink Truus E M; Ooms Marcel; Haasnoot P C Joost; Berkhout Ben
The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation.
Biochemistry 2005;44(25):9058-66.
2005: van der Kuyl Antoinette C; Kozaczynska Karolina; van den Burg Remco; Zorgdrager Fokla; Back Nicole; Jurriaans Suzanne; Berkhout Ben; Reiss Peter; Cornelissen Marion
Triple HIV-1 infection.
The New England journal of medicine 2005;352(24):2557-9.
2005: Fernández Ariel; Tawfik Dan S; Berkhout Ben; Sanders Rogier; Kloczkowski Andrzej; Sen Taner; Jernigan Bob
Protein promiscuity: drug resistance and native functions--HIV-1 case.
Journal of biomolecular structure & dynamics 2005;22(6):615-24.
2005: Hofmann Heike; Pyrc Krzysztof; van der Hoek Lia; Geier Martina; Berkhout Ben; Pöhlmann Stefan
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: Jeeninga Rienk E; Jan Barbara; van der Linden Birgit; van den Berg Henk; Berkhout Ben
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: Das Atze T; Baldwin Chris E; Vink Monique; Berkhout Ben
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: van der Hoek Lia; Back Nicole; Jebbink Maarten F; de Ronde Anthony; Bakker Margreet; Jurriaans Suzanne; Reiss Peter; Parkin Neil; Berkhout Ben
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: Das Atze T; Vink Monique; Berkhout Ben
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: Groot Fedde; Geijtenbeek Teunis B H; Sanders Rogier W; Baldwin Christopher E; Sanchez-Hernandez Marta; Floris René; van Kooyk Yvette; de Jong Esther C; Berkhout Ben
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: Moës Elien; Vijgen Leen; Keyaerts Els; Zlateva Kalina; Li Sandra; Maes Piet; Pyrc Krzysztof; Berkhout Ben; van der Hoek Lia; Van Ranst Marc
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(1):6.
2005: Ter Brake Olivier; Berkhout Ben
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: Berkhout Ben
It's the virus, stupid--part 2.
Retrovirology 2005;2():78.
2005: Nethe Micha; Berkhout Ben; van der Kuyl Antoinette C
Retroviral superinfection resistance.
Retrovirology 2005;2():52.
2005: Kivelä Pia S; Krol Anneke; Salminen Mika O; Geskus Ronald B; Suni Jukka I; Anttila Veli-Jukka; Liitsola Kirsi; Zetterberg Veera; Miedema Frank; Berkhout Ben; Coutinho Roel A; Ristola Matti A
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: Markusic David; Oude-Elferink Ronald; Das Atze T; Berkhout Ben; Seppen Jurgen
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: Berkhout Ben; de Ronde Anthony; van der Hoek Lia
Aggressive HIV-1?
Retrovirology 2005;2():13.
2005: Westerhout Ellen M; Ooms Marcel; Vink Monique; Das Atze T; Berkhout Ben
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: Holterman Lennart; Vogels Ronald; van der Vlugt Remko; Sieuwerts Martijn; Grimbergen Jos; Kaspers Jorn; Geelen Eric; van der Helm Esmeralda; Lemckert Angelique; Gillissen Gert; Verhaagh Sandra; Custers Jerome; Zuijdgeest David; Berkhout Ben; Bakker Margreet; Quax Paul; Goudsmit Jaap; Havenga Menzo
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: Lemieux Anne-Marie; Paré Marie-Eve; Audet Brigitte; Legault Eric; Lefort Sylvain; Boucher Nancy; Landry Sébastien; van Opijnen Tim; Berkhout Ben; Naghavi Mojgan H; Tremblay Michel J; Barbeau Benoit
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: Baldwin Chris E; Sanders Rogier W; Deng Yiqun; Jurriaans Suzanne; Lange Joep M; Lu Min; Berkhout Ben
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: Kiselyeva Yana; Ito Yoshinori; Lima Rosangela G; Grivel Jean-Charles; Das Atze T; Berkhout Ben; Margolis Leonid B
Depletion of CD4 T lymphocytes in human lymphoid tissue infected ex vivo with doxycycline-dependent HIV-1.
Virology 2004;328(1):1-6.
2004: Ooms Marcel; Huthoff Hendrik; Russell Rodney; Liang Chen; Berkhout Ben
A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions.
Journal of virology 2004;78(19):10814-9.
2004: Abbink Truus E M; Beerens Nancy; Berkhout Ben
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: Berkhout Ben; de Ronde Anthony
APOBEC3G versus reverse transcriptase in the generation of HIV-1 drug-resistance mutations.
AIDS (London, England) 2004;18(13):1861-3.
2004: Sanders Rogier W; Busser Els; Moore John P; Lu Min; Berkhout Ben
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: Bezemer Daniela; Jurriaans Suzanne; Prins Maria; van der Hoek Lia; Prins Jan M; de Wolf Frank; Berkhout Ben; Coutinho Roel; Back Nicole K T
Declining trend in transmission of drug-resistant HIV-1 in Amsterdam.
AIDS (London, England) 2004;18(11):1571-7.
2004: van Opijnen Tim; Kamoschinski Joost; Jeeninga Rienk E; Berkhout Ben
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: Berkhout Ben; Floris René; Recio Isidra; Visser Servaas
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: Kostense Stefan; Koudstaal Wouter; Sprangers Mieke; Weverling Gerrit Jan; Penders Germaine; Helmus Niels; Vogels Ronald; Bakker Margreet; Berkhout Ben; Havenga Menzo; Goudsmit Jaap
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: Huthoff Hendrik; Das Atze T; Vink Monique; Klaver Bep; Zorgdrager Fokla; Cornelissen Marion; Berkhout Ben
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: Berkhout Ben
RNA interference as an antiviral approach: targeting HIV-1.
Current opinion in molecular therapeutics 2004;6(2):141-5.
2004: van der Hoek Lia; Pyrc Krzysztof; Jebbink Maarten F; Vermeulen-Oost Wilma; Berkhout Ron J M; Wolthers Katja C; Wertheim-van Dillen Pauline M E; Kaandorp Jos; Spaargaren Joke; Berkhout Ben
Identification of a new human coronavirus.
Nature medicine 2004;10(4):368-73.
2004: van Opijnen Tim; Jeeninga Rienk E; Boerlijst Maarten C; Pollakis Georgios P; Zetterberg Veera; Salminen Mika; Berkhout Ben
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: Das Atze T; Zhou Xue; Vink Monique; Klaver Bep; Verhoef Koen; Marzio Giuseppe; Berkhout Ben
Viral evolution as a tool to improve the tetracycline-regulated gene expression system.
The Journal of biological chemistry 2004;279(18):18776-82.
2004: Huthoff Hendrik; Girard Frederic; Wijmenga Sybren S; Berkhout Ben
Evidence for a base triple in the free HIV-1 TAR RNA.
RNA (New York, N.Y.) 2004;10(3):412-23.
2004: Das Atze T; Brummelkamp Thijn R; Westerhout Ellen M; Vink Monique; Madiredjo Mandy; Bernards René; Berkhout Ben
Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition.
Journal of virology 2004;78(5):2601-5.
2004: Pyrc Krzysztof; Jebbink Maarten F; Berkhout Ben; van der Hoek Lia
Genome structure and transcriptional regulation of human coronavirus NL63.
Virology journal 2004;1():7.
2004: van der Kuyl Antoinette C; van den Burg Remco; Hoyer Mark J; Gruters Rob A; Osterhaus Albert D M E; Berkhout Ben
SIVdrl detection in captive mandrills: are mandrills infected with a third strain of simian immunodeficiency virus?
Retrovirology 2004;1():36.
2004: Das Atze T; Verhoef Koen; Berkhout Ben
A conditionally replicating virus as a novel approach toward an HIV vaccine.
Methods in enzymology 2004;388():359-79.
2004: Sanders Rogier W; Dankers Martijn M; Busser Els; Caffrey Michael; Moore John P; Berkhout Ben
Evolution of the HIV-1 envelope glycoproteins with a disulfide bond between gp120 and gp41.
Retrovirology 2004;1():3.
2004: Ooms Marcel; Verhoef Koen; Southern Edwin; Huthoff Hendrik; Berkhout Ben
Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays.
Nucleic acids research 2004;32(2):819-27.
2003: Kulinski Tadeusz; Olejniczak Mikolaj; Huthoff Hendrik; Bielecki Lukasz; Pachulska-Wieczorek Katarzyna; Das Atze T; Berkhout Ben; Adamiak Ryszard W
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: Huthoff Hendrik; Bugala Katarzyna; Barciszewski Jan; Berkhout Ben
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: Baldwin C E; Sanders R W; Berkhout B
Inhibiting HIV-1 entry with fusion inhibitors.
Current medicinal chemistry 2003;10(17):1633-42.
2003: Pereira Cândida F; Paridaen Judith T M L; Rutten Karla; Huigen Marleen C D G; van de Bovenkamp Marja; Middel Jeena; Beerens Nancy; Berkhout Ben; Schuurman Rob; Marnett Lawrence J; Verhoef Jan; Nottet Hans S L M
Aspirin-like molecules that inhibit human immunodeficiency virus 1 replication.
Antiviral research 2003;58(3):253-63.
2003: Brasey Ann; Lopez-Lastra Marcelo; Ohlmann Theophile; Beerens Nancy; Berkhout Ben; Darlix Jean-Luc; Sonenberg Nahum
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: Andersen Ebbe Sloth; Jeeninga Rienk E; Damgaard Christian Kroun; Berkhout Ben; Kjems Jørgen
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: Abbink Truus E M; Berkhout Ben
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: Haasnoot P C Joost; Cupac Daniel; Berkhout Ben
Inhibition of virus replication by RNA interference.
Journal of biomedical science 2003;10(6 Pt 1):607-16.
2003: Florisa René; Recio Isidra; Berkhout Ben; Visser Servaas
Antibacterial and antiviral effects of milk proteins and derivatives thereof.
Current pharmaceutical design 2003;9(16):1257-75.
2002: Berkhout Ben; Verhoef Koen; Marzio Giuseppe; Klaver Bep; Vink Monique; Zhou Xue; Das Atze T
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: Quivy Vincent; Adam Emmanuelle; Collette Yves; Demonte Dominique; Chariot Alain; Vanhulle Caroline; Berkhout Ben; Castellano Rémy; de Launoit Yvan; Burny Arsène; Piette Jacques; Bours Vincent; Van Lint Carine
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: Das Atze T; Zhou Xue; Vink Monique; Klaver Bep; Berkhout Ben
Conditional live virus as a novel approach towards a safe live attenuated HIV vaccine.
Expert review of vaccines 2002;1(3):293-301.
2002: Dirac Annette M G; Huthoff Hendrik; Kjems Jørgen; Berkhout Ben
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: Sanders Rogier W; Vesanen Mika; Schuelke Norbert; Master Aditi; Schiffner Linnea; Kalyanaraman Roopa; Paluch Maciej; Berkhout Ben; Maddon Paul J; Olson William C; Lu Min; Moore John P
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: Huthoff Hendrik; Berkhout Ben
Multiple secondary structure rearrangements during HIV-1 RNA dimerization.
Biochemistry 2002;41(33):10439-45.
2002: Berkhout Ben; van Wamel Jeroen L B; Beljaars Leonie; Meijer Dirk K F; Visser Servaas; Floris René
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: Sanders Rogier W; de Jong Esther C; Baldwin Christopher E; Schuitemaker Joost H N; Kapsenberg Martien L; Berkhout Ben
Differential transmission of human immunodeficiency virus type 1 by distinct subsets of effector dendritic cells.
Journal of virology 2002;76(15):7812-21.
2002: Dirac Annette M G; Huthoff Hendrik; Kjems Jørgen; Berkhout Ben
Regulated HIV-2 RNA dimerization by means of alternative RNA conformations.
Nucleic acids research 2002;30(12):2647-55.
2002: Beljaars Leonie; Floris René; Berkhout Ben; Smit Catharina; Meijer Dirk K F; Molema Grietje
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: Berkhout Ben; Ooms Marcel; Beerens Nancy; Huthoff Hendrik; Southern Edwin; Verhoef Koen
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: Beerens Nancy; Berkhout Ben
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: Marzio Giuseppe; Vink Monique; Verhoef Koen; de Ronde Anthony; Berkhout Ben
Efficient human immunodeficiency virus replication requires a fine-tuned level of transcription.
Journal of virology 2002;76(6):3084-8.
2002: Beerens Nancy; Berkhout Ben
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: Berkhout Ben; Marzio Giuseppe; Verhoef Koen
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: Berkhout Ben; Grigoriev Andrei; Bakker Margreet; Lukashov Vladimir V
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: Berkhout B
Retroviral nucleocapsid--third international symposium.
IDrugs : the investigational drugs journal 2001;4(11):1250-1.
2001: Berkhout B; Vastenhouw N L; Klasens B I; Huthoff H
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: Dirac A M; Huthoff H; Kjems J; Berkhout B
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: Beerens N; Groot F; Berkhout B
Initiation of HIV-1 reverse transcription is regulated by a primer activation signal.
The Journal of biological chemistry 2001;276(33):31247-56.
2001: Huthoff H; Berkhout B
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: Marzio G; Verhoef K; Vink M; Berkhout B
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: Jeeninga R E; Keulen W; Boucher C; Sanders R W; Berkhout B
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: Berkhout B; Das A T; Beerens N
HIV-1 RNA editing, hypermutation, and error-prone reverse transcription.
Science (New York, N.Y.) 2001;292(5514):7.
2001: Verhoef K; Bilodeau P S; van Wamel J L; Kjems J; Stoltzfus C M; Berkhout B
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: Huthoff H; Berkhout B
Two alternating structures of the HIV-1 leader RNA.
RNA (New York, N.Y.) 2001;7(1):143-57.
2001: Verhoef K; Marzio G; Hillen W; Bujard H; Berkhout B
Strict control of human immunodeficiency virus type 1 replication by a genetic switch: Tet for Tat.
Journal of virology 2001;75(2):979-87.
2001: Berkhout B; Verhoef K
Evolution of live-attenuated virus vaccines.
Developments in biologicals 2001;106():217-21; discussion 253-63.
2000: Beerens N; Groot F; Berkhout B
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: Beerens N; Berkhout B
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: Jeeninga R E; Hoogenkamp M; Armand-Ugon M; de Baar M; Verhoef K; Berkhout B
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: De Baar M P; De Ronde A; Berkhout B; Cornelissen M; Van Der Horn K H; Van Der Schoot A M; De Wolf F; Lukashov V V; Goudsmit J
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: Beerens N; Klaver B; Berkhout B
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: Berkhout B; van Wamel J L
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: Berkhout B
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.
1999: Das A T; Land A; Braakman I; Klaver B; Berkhout B
HIV-1 evolves into a nonsyncytium-inducing virus upon prolonged culture in vitro.
Virology 1999;263(1):55-69.
1999: Berkhout B
HIV-1 evolution under pressure of protease inhibitors: climbing the stairs of viral fitness.
Journal of biomedical science 1999;6(5):298-305.
1999: Keulen W; van Wijk A; Schuurman R; Berkhout B; Boucher C A
Increased polymerase fidelity of lamivudine-resistant HIV-1 variants does not limit their evolutionary potential.
AIDS (London, England) 1999;13(11):1343-9.
1999: Verhoef K; Berkhout B
A second-site mutation that restores replication of a Tat-defective human immunodeficiency virus.
Journal of virology 1999;73(4):2781-9.
1999: Klasens B I; Huthoff H T; Das A T; Jeeninga R E; Berkhout B
The effect of template RNA structure on elongation by HIV-1 reverse transcriptase.
Biochimica et biophysica acta 1999;1444(3):355-70.
1999: Oude Essink B B; Berkhout B
The fidelity of reverse transcription differs in reactions primed with RNA versus DNA primers.
Journal of biomedical science 1999;6(2):121-32.
1999: Berkhout B; Jebbink M; Zsíros J
Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus.
Journal of virology 1999;73(3):2365-75.
1999: Verhoef K; Sanders R W; Fontaine V; Kitajima S; Berkhout B
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: Berkhout B; Verhoef K; van Wamel J L; Back N K
Genetic instability of live, attenuated human immunodeficiency virus type 1 vaccine strains.
Journal of virology 1999;73(2):1138-45.
1999: Zsíros J; Jebbink M F; Lukashov V V; Voûte P A; Berkhout B
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: Klasens B I; Thiesen M; Virtanen A; Berkhout B
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: Das A T; Klaver B; Berkhout B
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: Jeeninga R E; Huthoff H T; Gultyaev A P; Berkhout B
The mechanism of actinomycin D-mediated inhibition of HIV-1 reverse transcription.
Nucleic acids research 1998;26(23):5472-9.
1998: Verhoef K; Bauer M; Meyerhans A; Berkhout B
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: Das A T; Klaver B; Berkhout B
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: Berkhout B; Das A T; van Wamel J L
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: Zsíros J; Jebbink M F; Voûte P A; Berkhout B
Identification of novel human endogenous retroviral sequences belonging to the HERV-K family.
AIDS research and human retroviruses 1998;14(12):1093-8.
1998: Das A T; van Dam A P; Klaver B; Berkhout B
Improved envelope function selected by long-term cultivation of a translation-impaired HIV-1 mutant.
Virology 1998;244(2):552-62.
1998: van Wamel J L; Berkhout B
The first strand transfer during HIV-1 reverse transcription can occur either intramolecularly or intermolecularly.
Virology 1998;244(2):245-51.
1998: Klasens B I; Das A T; Berkhout B
Inhibition of polyadenylation by stable RNA secondary structure.
Nucleic acids research 1998;26(8):1870-6.
1998: Zsíros J; Jebbink M F; Lukashov V V; Voûte P A; Berkhout B
Evolutionary relationships within a subgroup of HERV-K-related human endogenous retroviruses.
The Journal of general virology 1998;79 ( Pt 1)():61-70.
1997: Back N K; Berkhout B
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: Verhoef K; Koper M; Berkhout B
Determination of the minimal amount of Tat activity required for human immunodeficiency virus type 1 replication.
Virology 1997;237(2):228-36.
1997: Berkhout B
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: Berkhout B; Derksen G C; Back N K; Klaver B; de Kruif C G; Visser S
Structural and functional analysis of negatively charged milk proteins with anti-HIV activity.
AIDS research and human retroviruses 1997;13(13):1101-7.
1997: Oude Essink B B; Back N K; Berkhout B
Increased polymerase fidelity of the 3TC-resistant variants of HIV-1 reverse transcriptase.
Nucleic acids research 1997;25(16):3212-7.
1997: Das A T; Klaver B; Berkhout B
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: Keulen W; Back N K; van Wijk A; Boucher C A; Berkhout B
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: Das A T; Klaver B; Klasens B I; van Wamel J L; Berkhout B
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: Berkhout B; Klaver B; Das A T
Forced evolution of a regulatory RNA helix in the HIV-1 genome.
Nucleic acids research 1997;25(5):940-7.
1997: Verhoef K; Tijms M; Berkhout B
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: Keulen W; Nijhuis M; Schuurman R; Berkhout B; Boucher C
Reverse transcriptase fidelity and HIV-1 variation.
Science (New York, N.Y.) 1997;275(5297):229; author reply 230-1.
1996: Oude Essink B B; Das A T; Berkhout B
HIV-1 reverse transcriptase discriminates against non-self tRNA primers.
Journal of molecular biology 1996;264(2):243-54.
1996: Verhoef K; Klein A; Berkhout B
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: Berkhout B; van Wamel J L
Role of the DIS hairpin in replication of human immunodeficiency virus type 1.
Journal of virology 1996;70(10):6723-32.
1996: Back N K; Nijhuis M; Keulen W; Boucher C A; Oude Essink B O; van Kuilenburg A B; van Gennip A H; Berkhout B
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: Keulen W; Boucher C; Berkhout B
Nucleotide substitution patterns can predict the requirements for drug-resistance of HIV-1 proteins.
Antiviral research 1996;31(1-2):45-57.
1996: Berkhout B; van Wamel J
Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site.
The Journal of biological chemistry 1996;271(4):1837-40.
1996: Berkhout B
Structure and function of the human immunodeficiency virus leader RNA.
Progress in nucleic acid research and molecular biology 1996;54():1-34.
1996: Berkhout B; van Wamel J L
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: Oude Essink B B; Das A T; Berkhout B
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: Berkhout B; van Wamel J; Klaver B
Requirements for DNA strand transfer during reverse transcription in mutant HIV-1 virions.
Journal of molecular biology 1995;252(1):59-69.
1995: van Hemert F J; Berkhout B
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: van der Ende A; Hopman C T; Zaat S; Essink B B; Berkhout B; Dankert J
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: Das A T; Klaver B; Berkhout B
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: Berkhout B; Klaver B
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: Das A T; Berkhout B
Efficient extension of a misaligned tRNA-primer during replication of the HIV-1 retrovirus.
Nucleic acids research 1995;23(8):1319-26.
1995: Berkhout B; van Wamel J L
Inhibition of human immunodeficiency virus expression by sense transcripts encoding the retroviral leader RNA.
Antiviral research 1995;26(2):101-15.
1995: Berkhout B; Klaver B; Das A T
A conserved hairpin structure predicted for the poly(A) signal of human and simian immunodeficiency viruses.
Virology 1995;207(1):276-81.
1994: Koken S E; van Wamel J; Berkhout B
A sensitive promoter assay based on the transcriptional activator Tat of the HIV-1 virus.
Gene 1994;144(2):243-7.
1994: Klaver B; Berkhout B
Comparison of 5' and 3' long terminal repeat promoter function in human immunodeficiency virus.
Journal of virology 1994;68(6):3830-40.
1994: Klaver B; Berkhout B
Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus.
The EMBO journal 1994;13(11):2650-9.
1994: Berkhout B; van Hemert F J
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: Koken S E; Greijer A E; Verhoef K; van Wamel J; Bukrinskaya A G; Berkhout B
Intracellular analysis of in vitro modified HIV Tat protein.
The Journal of biological chemistry 1994;269(11):8366-75.
1994: Das A T; Koken S E; Essink B B; van Wamel J L; Berkhout B
Human immunodeficiency virus uses tRNA(Lys,3) as primer for reverse transcription in HeLa-CD4+ cells.
FEBS letters 1994;341(1):49-53.
1994: Oude Essink B B; Berkhout B
The restriction enzyme BanI is inhibited by dcm-methylation of the GGCGCm5C site.
Nucleic acids research 1994;22(1):108.
1994: Klaver B; Berkhout B
Premature strand transfer by the HIV-1 reverse transcriptase during strong-stop DNA synthesis.
Nucleic acids research 1994;22(2):137-44.
1993: Berkhout B; Klaver B
In vivo selection of randomly mutated retroviral genomes.
Nucleic acids research 1993;21(22):5020-4.
1993: Verhoef K; Koken S E; Berkhout B
Electroporation of the HIV Tat trans-activator protein into cells.
Analytical biochemistry 1993;210(1):210-4.
1993: Berkhout B; Schoneveld I
Secondary structure of the HIV-2 leader RNA comprising the tRNA-primer binding site.
Nucleic acids research 1993;21(5):1171-8.
1993: Berkhout B; Essink B B; Schoneveld I
In vitro dimerization of HIV-2 leader RNA in the absence of PuGGAPuA motifs.
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1993;7(1):181-7.
1992: Koken S E; van Wamel J L; Goudsmit J; Berkhout B; Geelen J L
Natural variants of the HIV-1 long terminal repeat: analysis of promoters with duplicated DNA regulatory motifs.
Virology 1992;191(2):968-72.
1992: Berkhout B
Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis.
Nucleic acids research 1992;20(1):27-31.

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