Angela Teresa Ciuffi

Publications | Mémoires et thèses

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66 publications

2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2001 | 1998 |
 
Entry of Polarized Effector Cells into Quiescence Forces HIV Latency.
Dobrowolski C., Valadkhan S., Graham A.C., Shukla M., Ciuffi A., Telenti A., Karn J., 2019/03/26. mBio, 10 (2). Peer-reviewed.
Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection.
Golumbeanu M., Desfarges S., Hernandez C., Quadroni M., Rato S., Mohammadi P., Telenti A., Beerenwinkel N., Ciuffi A., 2019/01/18. Scientific reports, 9 (1) p. 213. Peer-reviewed.
 
Nouveautés dans le dépistage, la prévention et la prise en charge du VIH en 2018 [Diagnosis, prevention and treatment of HIV : what's new in 2018 ?]
D'Incau S., Viala B., Ciuffi A., Cavassini M., Calmy A., 2019/01/09. Revue medicale suisse, 15 (N° 632-633) pp. 107-112. Peer-reviewed.
Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.
Golumbeanu M., Cristinelli S., Rato S., Munoz M., Cavassini M., Beerenwinkel N., Ciuffi A., 2018/04/24. Cell reports, 23 (4) pp. 942-950. Peer-reviewed.
The use of single-cell RNA-Seq to understand virus-host interactions.
Cristinelli S., Ciuffi A., 2018/04. Current opinion in virology, 29 pp. 39-50. Peer-reviewed.
 
Trends in HCV treatment uptake, efficacy and impact on liver fibrosis in the Swiss HIV Cohort Study.
Béguelin C., Suter A., Bernasconi E., Fehr J., Kovari H., Bucher H.C., Stoeckle M., Cavassini M., Rougemont M., Schmid P. et al., 2018/03. Liver international, 38 (3) pp. 424-431. Peer-reviewed.
 
Time to Switch to Second-line Antiretroviral Therapy in Children With Human Immunodeficiency Virus in Europe and Thailand.
European Pregnancy and Paediatric HIV Cohort Collaboration (EPPICC) Study Group in EuroCoord, 2018/02/01. Clinical infectious diseases, 66 (4) pp. 594-603. Peer-reviewed.
 
Unravelling HIV-1 Latency, One Cell at a Time.
Kok Y.L., Ciuffi A., Metzner K.J., 2017/11. Trends in microbiology, 25 (11) pp. 932-941. Peer-reviewed.
Single-cell analysis identifies cellular markers of the HIV permissive cell.
Rato S., Rausell A., Muñoz M., Telenti A., Ciuffi A., 2017/10. PLoS pathogens, 13 (10) pp. e1006678. Peer-reviewed.
Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis.
Turk T., Bachmann N., Kadelka C., Böni J., Yerly S., Aubert V., Klimkait T., Battegay M., Bernasconi E., Calmy A. et al., 2017/09/12. eLife, 6 p. 1. Peer-reviewed.
 
Ethnicity predicts viral rebound after travel to the tropics in HIV-infected travelers to the tropics in the Swiss HIV Cohort Study.
Gebreselassie H.M., Kraus D., Fux C.A., Haubitz S., Scherrer A., Hatz C., Veit O., Stoeckle M., Fehr J., de Lucia S. et al., 2017/09. HIV medicine, 18 (8) pp. 564-572. Peer-reviewed.
Exploring viral infection using single-cell sequencing.
Rato S., Golumbeanu M., Telenti A., Ciuffi A., 2017/07/15. Virus research, 239 pp. 55-68. Peer-reviewed.
 
Single-virus tracking uncovers the missing link between HIV integration site location and viral gene expression.
Ciuffi A., Cristinelli S., Rato S., 2017/01/05. Nature structural & molecular biology, 24 (1) pp. 8-11. Peer-reviewed.
Associations Between Antiretroviral Treatment and Avascular Bone Necrosis: The Swiss HIV Cohort Study.
Bayard C., Ledergerber B., Flepp M., Lecompte T., Moulin E., Hoffmann M., Weber R., Staehelin C., Di Benedetto C., Fux C.A. et al., 2017. Open forum infectious diseases, 4 (4) pp. ofx177. Peer-reviewed.
HIV-1 latent reservoir: size matters.
Hodel F., Patxot M., Snäkä T., Ciuffi A., 2016/12. Future virology, 11 (12) pp. 785-794. Peer-reviewed.
 
Determinants of HIV-1 broadly neutralizing antibody induction.
Rusert P., Kouyos R.D., Kadelka C., Ebner H., Schanz M., Huber M., Braun D.L., Hozé N., Scherrer A., Magnus C. et al., 2016/11. Nature medicine, 22 (11) pp. 1260-1267. Peer-reviewed.
Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.
Trypsteen W., Mohammadi P., Van Hecke C., Mestdagh P., Lefever S., Saeys Y., De Bleser P., Vandesompele J., Ciuffi A., Vandekerckhove L. et al., 2016/10/26. Scientific reports, 6 p. 36111. Peer-reviewed.
Innate immune defects in HIV permissive cell lines.
Rausell A., Muñoz M., Martinez R., Roger T., Telenti A., Ciuffi A., 2016/06/27. Retrovirology, 13 (1) p. 43. Peer-reviewed.
Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation
White Cory H, Moesker Bastiaan, Ciuffi Angela, Beliakova-Bethell Nadejda, 2016/05/25. World Journal of Clinical Infectious Diseases, 6 (2) pp. 6-21. Peer-reviewed.
The benefits of integration.
Ciuffi A., 2016/04. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 22 (4) pp. 324-332. Peer-reviewed.
 
Guanylate Binding Protein (GBP) 5 Is an Interferon-Inducible Inhibitor of HIV-1 Infectivity.
Krapp C., Hotter D., Gawanbacht A., McLaren P.J., Kluge S.F., Stürzel C.M., Mack K., Reith E., Engelhart S., Ciuffi A. et al., 2016. Cell Host and Microbe, 19 (4) pp. 504-514. Peer-reviewed.
Single-Cell Genomics for Virology.
Ciuffi A., Rato S., Telenti A., 2016. Viruses, 8 (5) pp. 1711-1717. Peer-reviewed.
 
Viral cell biology: HIV RNA gets methylated.
Ciuffi A., 2016. Nature Microbiology, 1 p. 16037. Peer-reviewed.
Bioinformatics and HIV Latency.
Ciuffi A., Mohammadi P., Golumbeanu M., di Iulio J., Telenti A., 2015. Current Hiv/aids Reports, 12 (1) pp. 97-106. Peer-reviewed.
Dual and Opposite Effects of hRAD51 Chemical Modulation on HIV-1 Integration.
Thierry S., Benleulmi M.S., Sinzelle L., Thierry E., Calmels C., Chaignepain S., Waffo-Teguo P., Merillon J.M., Budke B., Pasquet J.M. et al., 2015. Chemistry and Biology, 22 (6) pp. 712-723. Peer-reviewed.
Dynamic models of viral replication and latency.
Mohammadi P., Ciuffi A., Beerenwinkel N., 2015. Current Opinion in Hiv and Aids, 10 (2) pp. 90-95.
HIV-1 immune activation induces Siglec-1 expression and enhances viral trans-infection in blood and tissue myeloid cells.
Pino M., Erkizia I., Benet S., Erikson E., Fernández-Figueras M.T., Guerrero D., Dalmau J., Ouchi D., Rausell A., Ciuffi A. et al., 2015. Retrovirology, 12 p. 37. Peer-reviewed.
Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses.
McLaren P.J., Gawanbacht A., Pyndiah N., Krapp C., Hotter D., Kluge S.F., Götz N., Heilmann J., Mack K., Sauter D. et al., 2015. Retrovirology, 12 (1) p. 41. Peer-reviewed.
Dynamics of HIV latency and reactivation in a primary CD4+ T cell model.
Mohammadi P., di Iulio J., Muñoz M., Martinez R., Bartha I., Cavassini M., Thorball C., Fellay J., Beerenwinkel N., Ciuffi A. et al., 2014. Plos Pathogens, 10 (5) pp. e1004156.
GuavaH: a compendium of host genomic data in HIV biology and disease.
Bartha I., McLaren P.J., Ciuffi A., Fellay J., Telenti A., 2014. Retrovirology, 11 p. 6. Peer-reviewed.
24 Hours in the Life of HIV-1 in a T Cell Line.
Mohammadi P., Desfarges S., Bartha I., Joos B., Zangger N., Muñoz M., Günthard H.F., Beerenwinkel N., Telenti A., Ciuffi A., 2013. Plos Pathogens, 9 (1) pp. e1003161.
State of genomics and epigenomics research in the perspective of HIV cure.
Ciuffi A., Telenti A., 2013. Current Opinion in HIV and AIDS, 8 (3) pp. 176-181.
Susceptibility and adaptation to human TRIM5α alleles at positive selected sites in HIV-1 capsid.
Rahm N., Gfeller D., Snoeck J., Martinez R., McLaren P.J., Ortiz M., Ciuffi A., Telenti A., 2013. Virology, 441 (2) pp. 162-170.
Viral integration and consequences on host gene expression
Desfarges S., Ciuffi A., 2012. pp. 147-155 dans Witzany G. (eds.) Viruses: Essential Agents of Life chap. 7, Springer.
A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing.
Meylan S., Groner A.C., Ambrosini G., Malani N., Quenneville S., Zangger N., Kapopoulou A., Kauzlaric A., Rougemont J., Ciuffi A. et al., 2011/07. Bmc Genomics, 12 p. 378. Peer-reviewed.
Estimating the net contribution of interleukin-28B variation to spontaneous hepatitis C virus clearance.
di Iulio J., Ciuffi A., Fitzmaurice K., Kelleher D., Rotger M., Fellay J., Martinez R., Pulit S., Furrer H., Günthard H.F. et al., 2011/05. Hepatology, 53 (5) pp. 1446-1454. Peer-reviewed.
Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell.
Lefebvre G., Desfarges S., Uyttebroeck F., Muñoz M., Beerenwinkel N., Rougemont J., Telenti A., Ciuffi A., 2011. Journal of Virology, 85 (13) pp. 6205-6211.
Identification of HIV integration sites in infected host genomic DNA.
Ciuffi A., Barr S.D., 2011. Methods, 53 (1) pp. 39-46. Peer-reviewed.
LEDGF/p75 TATA-less promoter is driven by the transcription factor Sp1.
Desfarges S., Abderrahmani A., Hernàndez-Novoa B., Munoz M., Ciuffi A., 2011. Journal of Molecular Biology, 414 (2) pp. 177-193. Peer-reviewed.
 
Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses.
Rahm N., Yap M., Snoeck J., Zoete V., Muñoz M., Radespiel U., Zimmermann E., Michielin O., Stoye J.P., Ciuffi A. et al., 2011. Journal of Virology, 85 (9) pp. 4173-4183.
KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading.
Groner A.C., Meylan S., Ciuffi A., Zangger N., Ambrosini G., Dénervaud N., Bucher P., Trono D., 2010/03. Plos Genetics, 6 (3) pp. e1000869. Peer-reviewed.
Retroviral Integration Site Selection
Desfarges S., Ciuffi A., 2010. Viruses-Basel, 2 (1) pp. 111-130. Peer-reviewed.
ZNRD1 (zinc ribbon domain-containing 1) is a host cellular factor that influences HIV-1 replication and disease progression.
Ballana Ester, Senserrich Jordi, Pauls Eduardo, Faner Rosa, Maria Mercader Josep, Uyttebroeck Frederic, Palou Eduard, Pau Mena Maria, Grau Eulalia, Clotet Bonaventura et al., 2010. Clinical Infectious Diseases, 50 (7) pp. 1022-1032.
 
Methods for integration site distribution analyses in animal cell genomes.
Ciuffi A., Ronen K., Brady T., Malani N., Wang G., Berry C.C., Bushman F.D., 2009/04. Methods, 47 (4) pp. 261-268. Peer-reviewed.
 
Activity of ancestral restriction factors against ancient retroviruses
Rahm Nadia, Snoeck Joke, Ortiz Millan, Ciuffi Angela, Telenti Amalio, 2009. pp. - dans Frontiers of Retrovirology: Complex retroviruses, retroelements and their hosts, Retrovirology. Peer-reviewed.
 
Analysis of LEDGF/p75 expression regulation
Desfarges S., Roulin P., Moraz M.-L., Hernandez-Novoa B., Munoz M., Ciuffi A., 2009. pp. - dans Frontiers of Retrovirology : Complex retroviruses, retroelements and their hosts, Retrovirology. Peer-reviewed.
 
Evolutionary trajectories of primate genes involved in HIV pathogenesis.
Ortiz Millan, Ciuffi Angela, Xenarios Ioannis, Martin Olivier, Patin Etienne, Guex Nicolas, Quintana-Murci Luis, Telenti Amalio, 2009. Molecular Biology and Evolution, 26 (12) pp. 2865-2875.
 
Mechanisms governing lentivirus integration site selection.
Ciuffi A., 2008/12. Current Gene Therapy, 8 (6) pp. 419-429. Peer-reviewed.
 
DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer.
Wang G.P., Garrigue A., Ciuffi A., Ronen K., Leipzig J., Berry C., Lagresle-Peyrou C., Benjelloun F., Hacein-Bey-Abina S., Fischer A. et al., 2008/05. Nucleic Acids Research, 36 (9) pp. e49. Peer-reviewed.
 
Antiretroviral activity of ancestral TRIM5alpha.
Goldschmidt V., Ciuffi A., Ortiz M., Brawand D., Muñoz M., Kaessmann H., Telenti A., 2008. Journal of Virology, 82 (5) pp. 2089-2096. Peer-reviewed.
Genomic determinants of the efficiency of internal ribosomal entry sites of viral and cellular origin
Kazadi K., Loeuillet C., Deutsch S., Ciuffi A., Muñoz M., Beckmann J.S., Moradpour D., Antonarakis S.E., Telenti A., 2008. Nucleic Acids Research, 36 (21) pp. 6918-25. Peer-reviewed.
In vitro whole-genome analysis identifies a susceptibility locus for HIV-1.
Loeuillet C., Deutsch S., Ciuffi A., Robyr D., Taffé P., Muñoz M., Beckmann J.S., Antonarakis S.E., Telenti A., 2008. PLoS Biology, 6 (2) pp. e32. Peer-reviewed.
 
HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
Wang G. P., Ciuffi A., Leipzig J., Berry C. C., Bushman F. D., 2007/08. Genome Research, 17 (8) pp. 1186-94. Peer-reviewed.
 
Modulating target site selection during human immunodeficiency virus DNA integration in vitro with an engineered tethering factor
Ciuffi A., Diamond T. L., Hwang Y., Marshall H. M., Bushman F. D., 2006/09. Human Gene Therapy, 17 (9) pp. 960-7. Peer-reviewed.
 
HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry
Barr S. D., Ciuffi A., Leipzig J., Shinn P., Ecker J. R., Bushman F. D., 2006/08. Molecular Therapy, 14 (2) pp. 218-25. Peer-reviewed.
 
Retroviral DNA integration: HIV and the role of LEDGF/p75
Ciuffi A., Bushman F. D., 2006/07. Trends in Genetics, 22 (7) pp. 388-95. Peer-reviewed.
 
Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts
Ciuffi A., Mitchell R. S., Hoffmann C., Leipzig J., Shinn P., Ecker J. R., Bushman F. D., 2006/02. Molecular Therapy, 13 (2) pp. 366-73. Peer-reviewed.
Retroviral DNA integration: viral and cellular determinants of target-site selection.
Lewinski M.K., Yamashita M., Emerman M., Ciuffi A., Marshall H., Crawford G., Collins F., Shinn P., Leipzig J., Hannenhalli S. et al., 2006. PLoS Pathogens, 2 (6) pp. e60. Peer-reviewed.
 
A role for LEDGF/p75 in targeting HIV DNA integration
Ciuffi A., Llano M., Poeschla E., Hoffmann C., Leipzig J., Shinn P., Ecker J. R., Bushman F., 2005/12. Nature Medicine, 11 (12) pp. 1287-9. Peer-reviewed.
 
Genome-wide analysis of retroviral DNA integration
Bushman F., Lewinski M., Ciuffi A., Barr S., Leipzig J., Hannenhalli S., Hoffmann C., 2005/11. Nature Reviews Microbiology, 3 (11) pp. 848-58. Peer-reviewed.
 
Interactions of processed Nef (58-206) with virion proteins of HIV type 1
Ciuffi A., Munoz M., Bleiber G., Favre M., Stutz F., Telenti A., Meylan P. R., 2004/04. AIDS Research and Human Retroviruses, 20 (4) pp. 399-407.
 
Entry and transcription as key determinants of differences in CD4 T-cell permissiveness to human immunodeficiency virus type 1 infection.
Ciuffi A., Bleiber G., Muñoz M., Martinez R., Loeuillet C., Rehr M., Fischer M., Günthard H.F., Oxenius A., Meylan P. et al., 2004. Journal of virology, 78 (19) pp. 10747-54. Peer-reviewed.
 
Génétique humaine et VIH
Ciuffi A., Bleiber G., Telenti A., 2003. Médecine et Hygiène, 61 (2453) pp. 1926-1928.
 
Protection from HIV-1 infection of primary CD4 T cells by CCR5 silencing is effective for the full spectrum of CCR5 expression.
Butticaz C., Ciuffi A., Muñoz M., Thomas J., Bridge A., Pebernard S., Iggo R., Meylan P., Telenti A., 2003. Antiviral therapy, 8 (5) pp. 373-7. Peer-reviewed.
 
Individual contributions of mutant protease and reverse transcriptase to viral infectivity, replication, and protein maturation of antiretroviral drug-resistant human immunodeficiency virus type 1.
Bleiber G., Munoz M., Ciuffi A., Meylan P., Telenti A., 2001. Journal of virology, 75 (7) pp. 3291-300. Peer-reviewed.
 
The nef gene controls syncytium formation in primary human lymphocytes and macrophages infected by HIV type 1
Meylan P. R., Baumgartner M., Ciuffi A., Munoz M., Sahli R., 1998/11. AIDS Research and Human Retroviruses, 14 (17) pp. 1531-42.
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