Publications
73 results found
Vejnar CE, Zdobnov EM, 2012, miRmap: Comprehensive prediction of microRNA target repression strength, NUCLEIC ACIDS RESEARCH, Vol: 40, Pages: 11673-11683, ISSN: 0305-1048
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- Citations: 246
Ambrosioni J, Junier T, Delhumeau C, et al., 2012, Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections, AIDS, Vol: 26, Pages: 2079-2086, ISSN: 0269-9370
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- Citations: 40
Ambrosioni J, Junier T, Delhumeau C, et al., 2012, Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections., AIDS, Vol: 26, Pages: 2079-2086
OBJECTIVE: To evaluate HIV-1 transmission trends and the impact of highly active antiretroviral therapy (HAART) on newly diagnosed HIV infections in Geneva, Switzerland. DESIGN: Retrospective molecular epidemiology analysis of all newly HIV-diagnosed individuals between 2008 and 2010. METHODS: Phylogenetic analyses were performed using pol sequences of 780 newly HIV-1 diagnosed individuals between 2000 and 2010 (mandatory reporting) and 1058 individuals diagnosed before 2000. All clusters (bootstrap value >98%) including individuals diagnosed in 2008-2010 were analyzed. Recent HIV infections (<1 year) were determined by documented seroconversion and/or fraction of ambiguous nucleotides. Median viral load and HAART coverage during the study period were obtained from patients included in the Swiss HIV Cohort Study (SHCS). RESULTS: Among 142 newly diagnosed individuals during 2008-2010, 49% had a recent infection and 42% were included in transmission clusters. Among the latter, two-thirds were included in new clusters and one-third expanded previously known clusters. MSM carrying resistant strains were more frequently included in clusters. Only 1.8% of individuals diagnosed before 2000 and 10.8% diagnosed during 2000-2008 were included in clusters involving individuals diagnosed between 2008 and 2010. During 2008-2010, the median population viral load of SHCS-enrolled individuals was significantly lower for individuals diagnosed before 2000 than for those diagnosed during 2000-2008 and 2008-2010 and HAART coverage significantly higher. CONCLUSIONS: MSM with recent HIV infection are a significant source of onward transmission. Individuals diagnosed before 2000 were only exceptionally related to newly diagnosed infections between 2008 and 2010. Prevention campaigns need to be focused on improving diagnosis for recently infected individuals.
Cordey S, Petty TJ, Schibler M, et al., 2012, Identification of Site-Specific Adaptations Conferring Increased Neural Cell Tropism during Human Enterovirus 71 Infection, PLOS PATHOGENS, Vol: 8, ISSN: 1553-7366
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- Citations: 73
Li J, Waterhouse RM, Zdobnov EM, 2011, A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits, BMC EVOLUTIONARY BIOLOGY, Vol: 11, ISSN: 1471-2148
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- Citations: 12
Tapparel C, Cordey S, Junier T, et al., 2011, Rhinovirus Genome Variation during Chronic Upper and Lower Respiratory Tract Infections, PLOS ONE, Vol: 6, ISSN: 1932-6203
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- Citations: 48
Dunand-Sauthier I, Santiago-Raber M-L, Capponi L, et al., 2011, Silencing of c-Fos expression by microRNA-155 is critical for dendritic cell maturation and function, BLOOD, Vol: 117, Pages: 4490-4500, ISSN: 0006-4971
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- Citations: 109
Kirkness EF, Haas BJ, Sun W, et al., 2011, Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle (vol 107, pg 12168, 2010), PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 108, Pages: 6335-6336, ISSN: 0027-8424
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- Citations: 4
Papaioannou MD, Lagarrigue M, Vejnar CE, et al., 2011, Loss of Dicer in Sertoli Cells Has a Major Impact on the Testicular Proteome of Mice, MOLECULAR & CELLULAR PROTEOMICS, Vol: 10, ISSN: 1535-9476
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- Citations: 85
Colbourne JK, Pfrender ME, Gilbert D, et al., 2011, The Ecoresponsive Genome of Daphnia pulex, SCIENCE, Vol: 331, Pages: 555-561, ISSN: 0036-8075
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- Citations: 912
Waterhouse RM, Zdobnov EM, Tegenfeldt F, et al., 2011, OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011, NUCLEIC ACIDS RESEARCH, Vol: 39, Pages: D283-D288, ISSN: 0305-1048
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- Citations: 106
Waterhouse RM, Zdobnov EM, Kriventseva EV, 2011, Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi, GENOME BIOLOGY AND EVOLUTION, Vol: 3, Pages: 75-86, ISSN: 1759-6653
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- Citations: 53
Arensburger P, Megy K, Waterhouse RM, et al., 2010, Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics, SCIENCE, Vol: 330, Pages: 86-88, ISSN: 0036-8075
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- Citations: 341
Bartholomay LC, Waterhouse RM, Mayhew GF, et al., 2010, Pathogenomics of Culex quinquefasciatus and Meta-Analysis of Infection Responses to Diverse Pathogens, SCIENCE, Vol: 330, Pages: 88-90, ISSN: 0036-8075
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- Citations: 116
Kirkness EF, Haas BJ, Sun W, et al., 2010, Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 107, Pages: 12168-12173, ISSN: 0027-8424
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- Citations: 366
Junier T, Zdobnov EM, 2010, The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell, BIOINFORMATICS, Vol: 26, Pages: 1669-1670, ISSN: 1367-4803
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- Citations: 329
Cordey S, Junier T, Gerlach D, et al., 2010, Rhinovirus Genome Evolution during Experimental Human Infection, PLOS ONE, Vol: 5, ISSN: 1932-6203
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- Citations: 40
Hovatta O, Jaconi M, Tohonen V, et al., 2010, A Teratocarcinoma-Like Human Embryonic Stem Cell (hESC) Line and Four hESC Lines Reveal Potentially Oncogenic Genomic Changes, PLOS ONE, Vol: 5, ISSN: 1932-6203
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- Citations: 38
Hunt BG, Wyder S, Elango N, et al., 2010, Sociality Is Linked to Rates of Protein Evolution in a Highly Social Insect, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 27, Pages: 497-500, ISSN: 0737-4038
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- Citations: 48
Werren JH, Richards S, Desjardins CA, et al., 2010, Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species, SCIENCE, Vol: 327, Pages: 343-348, ISSN: 0036-8075
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- Citations: 640
Kim J, Cunningham R, James B, et al., 2010, Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances, PLOS COMPUTATIONAL BIOLOGY, Vol: 6, ISSN: 1553-734X
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- Citations: 23
Yerly S, Junier T, Gayet-Ageron A, et al., 2009, The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection, AIDS, Vol: 23, Pages: 1415-1423, ISSN: 0269-9370
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- Citations: 92
Gatfield D, Le Martelot G, Vejnar CE, et al., 2009, Integration of microRNA miR-122 in hepatic circadian gene expression, GENES & DEVELOPMENT, Vol: 23, Pages: 1313-1326, ISSN: 0890-9369
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- Citations: 289
Tapparel C, Junier T, Gerlach D, et al., 2009, New Respiratory Enterovirus and Recombinant Rhinoviruses among Circulating Picornaviruses, EMERGING INFECTIOUS DISEASES, Vol: 15, Pages: 719-726, ISSN: 1080-6040
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- Citations: 112
Elsik CG, Tellam RL, Worley KC, et al., 2009, The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution, SCIENCE, Vol: 324, Pages: 522-528, ISSN: 0036-8075
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- Citations: 858
Papaioannou MD, Pitetti J-L, Ro S, et al., 2009, Sertoli cell Dicer is essential for spermatogenesis in mice, DEVELOPMENTAL BIOLOGY, Vol: 326, Pages: 250-259, ISSN: 0012-1606
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- Citations: 146
Matsui T, Yamamoto T, Wyder S, et al., 2009, Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates, BMC GENOMICS, Vol: 10, ISSN: 1471-2164
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- Citations: 4
Gerlach D, Kriventseva EV, Rahman N, et al., 2009, miROrtho: computational survey of microRNA genes, NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: D111-D117, ISSN: 0305-1048
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- Citations: 54
Lemay DG, Lynn DJ, Martin WF, et al., 2009, The bovine lactation genome: insights into the evolution of mammalian milk, GENOME BIOLOGY, Vol: 10, ISSN: 1474-760X
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- Citations: 145
Yerly S, Junier T, Gayet-Ageron A, et al., 2009, Impact of newly HIV diagnosed individuals on the transmission of drug resistance, 18th International HIV Drug Resistance Workshop, Publisher: INT MEDICAL PRESS LTD, Pages: A40-A40, ISSN: 1359-6535
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