Marco Salemi

Summary

Affiliation: University of Florida
Country: USA

Publications

  1. pmc Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4
    William M Switzer
    Laboratory Branch, Division of HIV AIDS Prevention, National Center for HIV AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
    Retrovirology 6:9. 2009
  2. pmc The mode and tempo of hepatitis C virus evolution within and among hosts
    Rebecca R Gray
    Department of Zoology, Oxford University, South Parks Road, UK
    BMC Evol Biol 11:131. 2011
  3. pmc Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-using quasispecies
    Marco Salemi
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
    PLoS ONE 2:e950. 2007
  4. pmc Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma
    Marco Salemi
    Department of Pathology Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
    PLoS ONE 4:e8153. 2009
  5. pmc An exploratory algorithm to identify intra-host recombinant viral sequences
    Marco Salemi
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, College of Medicine, 1376 Mowry Road, P O Box 106633, Gainesville, FL 32610, USA
    Mol Phylogenet Evol 49:618-28. 2008
  6. pmc High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania
    Marco Salemi
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
    PLoS ONE 3:e1390. 2008
  7. pmc Efficient transmission and persistence of low-frequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology
    Samantha L Strickland
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
    J Gen Virol 93:925-38. 2012
  8. pmc The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries
    Marco Salemi
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA
    AIDS Res Hum Retroviruses 24:771-9. 2008
  9. doi request reprint Spatial accessibility and the spread of HIV-1 subtypes and recombinants
    Andrew J Tatem
    Department of Geography, University of Florida, Gainesville, USA
    AIDS 26:2351-60. 2012
  10. pmc Spatial phylodynamics of HIV-1 epidemic emergence in east Africa
    Rebecca R Gray
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA
    AIDS 23:F9-F17. 2009

Detail Information

Publications40

  1. pmc Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4
    William M Switzer
    Laboratory Branch, Division of HIV AIDS Prevention, National Center for HIV AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
    Retrovirology 6:9. 2009
    ..Analysis of full-length genomes can provide basic information on the evolutionary history and replication and pathogenic potential of new viruses...
  2. pmc The mode and tempo of hepatitis C virus evolution within and among hosts
    Rebecca R Gray
    Department of Zoology, Oxford University, South Parks Road, UK
    BMC Evol Biol 11:131. 2011
    ..We use a powerful Bayesian inference framework that incorporates both among-lineage rate heterogeneity and phylogenetic uncertainty into estimates of evolutionary parameters...
  3. pmc Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-using quasispecies
    Marco Salemi
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
    PLoS ONE 2:e950. 2007
    ..Virtually no studies have evaluated the HIV-1 quasispecies present in vivo within thymic and lymphoid tissues or the evolutionary relationship between R5 and X4 viruses in tissues and peripheral blood...
  4. pmc Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma
    Marco Salemi
    Department of Pathology Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
    PLoS ONE 4:e8153. 2009
    ..Moreover, the study indicates that HIV could be used as an effective marker to study the origin and dissemination of lymphomas in vivo...
  5. pmc An exploratory algorithm to identify intra-host recombinant viral sequences
    Marco Salemi
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, College of Medicine, 1376 Mowry Road, P O Box 106633, Gainesville, FL 32610, USA
    Mol Phylogenet Evol 49:618-28. 2008
    ....
  6. pmc High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania
    Marco Salemi
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
    PLoS ONE 3:e1390. 2008
    ..In Albania, where a recent study estimated a ten-fold increase of AIDS incidence during the last six years, subtype A and B account for 90% of the know infections...
  7. pmc Efficient transmission and persistence of low-frequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology
    Samantha L Strickland
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
    J Gen Virol 93:925-38. 2012
    ....
  8. pmc The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries
    Marco Salemi
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA
    AIDS Res Hum Retroviruses 24:771-9. 2008
    ....
  9. doi request reprint Spatial accessibility and the spread of HIV-1 subtypes and recombinants
    Andrew J Tatem
    Department of Geography, University of Florida, Gainesville, USA
    AIDS 26:2351-60. 2012
    ..We sought to address the question of whether accessibility has been a significant factor in HIV-1 spread across mainland Africa through spatial analyses of molecular epidemiology, transport network and land cover data...
  10. pmc Spatial phylodynamics of HIV-1 epidemic emergence in east Africa
    Rebecca R Gray
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA
    AIDS 23:F9-F17. 2009
    ..In order to characterize the demographic history of HIV-1 subtypes A and D in east Africa, we examined molecular epidemiology, geographical and historical data...
  11. pmc Molecular epidemiology of HIV type 1 CRF02_AG in Cameroon and African patients living in Italy
    Nazle Mendonça Collaço Véras
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, USA
    AIDS Res Hum Retroviruses 27:1173-82. 2011
    ..The evaluation of the spread of CRF02_AG may provide significant insight about the future dynamics of the Italian and European epidemic...
  12. pmc High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems
    Li Yin
    Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, 2033 Mowry Road, PO Box 103633, Gainesville, FL 32610 3633, USA
    Retrovirology 9:108. 2012
    ....
  13. pmc Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks
    Susanna L Lamers
    BioInfoExperts, Gainesville, FL 32606, USA
    IEEE/ACM Trans Comput Biol Bioinform 5:291-300. 2008
    ..We demonstrate the use of artificial neural networks trained via evolutionary computation to predict viral co-receptor usage. The results indicate identification of R5X4 viruses with predictive accuracy of 75.5%...
  14. pmc Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework
    Rebecca R Gray
    Emerging Pathogens Institute, University of Florida, FL, USA
    Mol Biol Evol 28:1593-603. 2011
    ..Future applications of this approach to other bacterial strains may provide valuable epidemiological insights that may justify the cost of genome-wide typing...
  15. pmc Multiple independent lineages of HIV-1 persist in breast milk and plasma
    Rebecca R Gray
    Department of Pathology, Immunology and Laboratory Medicine, USA
    AIDS 25:143-52. 2011
    ....
  16. doi request reprint A novel methodology for large-scale phylogeny partition
    Mattia C F Prosperi
    Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy
    Nat Commun 2:321. 2011
    ..Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics...
  17. pmc Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study
    Mattia Prosperi
    College of Medicine, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Jacksonville, FL, USA
    Sci Rep 3:1902. 2013
    ..Phylodynamic analysis provides a powerful framework to investigate MRSA transmission between the community and hospitals, an understanding of which is essential for control...
  18. pmc QuRe: software for viral quasispecies reconstruction from next-generation sequencing data
    Mattia C F Prosperi
    Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610 3633, USA
    Bioinformatics 28:132-3. 2012
    ..QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions...
  19. pmc Significant genetic heterogeneity of the SIVmac251 viral swarm derived from different sources
    Samantha L Strickland
    Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, USA
    AIDS Res Hum Retroviruses 27:1327-32. 2011
    ..This finding highlights the importance of characterizing the exact source and genetic makeup of the infecting inoculum to achieve controlled experimental conditions and enable meaningful comparisons across studies...
  20. pmc HIV-1 Subtype distribution in morocco based on national sentinel surveillance data 2004-2005
    Mohammed Akrim
    Department of Epidemiology and Emerging Pathogens Institute, University of Florida, Gainesville, USA
    AIDS Res Ther 9:5. 2012
    ..abstract:..
  21. pmc U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains
    Kenneth E Robbins
    Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    J Virol 77:6359-66. 2003
    ..Furthermore, the estimated epidemic growth curve shows a period of exponential growth that preceded most of the early documented cases and also indicates a leveling of prevalence rates in the recent past...
  22. ncbi request reprint Site stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non-clock-like behavior on viral phylogenetic reconstructions
    Philippe Lemey
    Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B 3000, Leuven, Belgium
    FEMS Immunol Med Microbiol 39:125-32. 2003
    ..Our method was able to rapidly recover clock-like behavior and to indicate the presence and direction of a bias when estimates of divergence times using the unstripped data were flawed...
  23. pmc Severe acute respiratory syndrome coronavirus sequence characteristics and evolutionary rate estimate from maximum likelihood analysis
    Marco Salemi
    J Virol 78:1602-3. 2004
  24. pmc Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design?
    Tulio de Oliveira
    HIV Molecular Virology and Bioinformatics Laboratory, Africa Centre for Health and Population Studies, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu Natal, Durban 4013, South Africa
    Genetics 167:1047-58. 2004
    ..Understanding the relationship between host-driven positive selection and antigenic variation may lead to the development of novel vaccine strategies that preempt the escape process...
  25. ncbi request reprint Different epidemic potentials of the HIV-1B and C subtypes
    Marco Salemi
    Department of Ecology and Evolutionary Biology, University of California at Irvine, 92664, USA
    J Mol Evol 60:598-605. 2005
    ....
  26. ncbi request reprint Human retroviruses (HIV and HTLV) in Brazilian Indians: seroepidemiological study and molecular epidemiology of HTLV type 2 isolates
    Nice Shindo
    Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, Bahia 40295 001, Brazil
    AIDS Res Hum Retroviruses 18:71-7. 2002
    ..We also report for the first time HIV-1 infection among Brazilian Amerindians...
  27. ncbi request reprint An outbreak of HIV-1 subtype G among Italian injecting drug users
    Massimo Ciccozzi
    Epidemiology Unit, Department of Infectious, Parasite and Immune mediated Diseases, Istituto Superiore di Sanita, Rome, Italy
    AIDS 21:1213-5. 2007
    ..All G subtypes but one were found among IDU. The phylogenetic analysis indicated that the outbreak was of monophyletic origin and was caused by HIV-1 strains similar to those from western Africa...
  28. ncbi request reprint Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak
    Tulio de Oliveira
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Nature 444:836-7. 2006
    ....
  29. ncbi request reprint Hepatitis C virus evolutionary patterns studied through analysis of full-genome sequences
    Marco Salemi
    Rega Institute for Medical Research, KULeuven, Minderbroedersstraat 10, B 3000 Leuven, Belgium
    J Mol Evol 54:62-70. 2002
    ..These results offer a general guideline for the future of HCV phylogenetic analysis and also provide important insights on HCV origin and evolution...
  30. ncbi request reprint Phylogenetic classification of TT virus groups based on the N22 region is unreliable
    Philippe Lemey
    Rega Institute for Medical Research, KULeuven, Minderbroedersstraat 10, B 3000, Belgium
    Virus Res 85:47-59. 2002
    ..We suggest that care should be taken in future TTV phylogenetic analysis, in particular, larger and more conserved regions should be sequenced to allow between group comparisons...
  31. pmc Characterization of a novel simian immunodeficiency virus with a vpu gene from greater spot-nosed monkeys (Cercopithecus nictitans) provides new insights into simian/human immunodeficiency virus phylogeny
    Valerie Courgnaud
    UR36, Institut de Recherche pour le Developpement, and University of Montpellier I, France
    J Virol 76:8298-309. 2002
    ..The complex genomic structure of SIVgsn, the presence of a vpu gene, and its relatedness to SIVcpz in the envelope suggest a link between SIVgsn and SIVcpz and provide new insights about the origin of SIVcpz in chimpanzees...
  32. ncbi request reprint Comparative rates of nucleotide sequence variation in the hypervariable region of E1/E2 and the NS5b region of hepatitis C virus in patients with a spectrum of liver disease resulting from a common source of infection
    Margaret Duffy
    Department of Medical Microbiology, University College Dublin, Belfield, Dublin, 4, Ireland
    Virology 301:354-64. 2002
    ..These findings suggest that other factors, either additional viral or host, may be important in the pathogenesis and clinical outcome of chronic hepatitis C virus infection...
  33. ncbi request reprint An index of substitution saturation and its application
    Xuhua Xia
    Department of Biology, University of Ottawa, Ottawa, Ont, Canada
    Mol Phylogenet Evol 26:1-7. 2003
    ..We illustrate the index by applying it to an analysis of the aligned sequences of the elongation factor-1alpha gene originally used to resolve the deep phylogeny of major arthropod groups. The method has been implemented in DAMBE...
  34. pmc Tracing the origin and history of the HIV-2 epidemic
    Philippe Lemey
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
    Proc Natl Acad Sci U S A 100:6588-92. 2003
    ....
  35. pmc Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses
    Marco Salemi
    Rega Institute for Medical Research, KULeuven, Leuven, Belgium
    J Virol 77:7202-13. 2003
    ..Our findings not only imply that the six so-called pure PLV lineages have in fact mosaic genomes but also make more unlikely the hypothesis of cospeciation of SIVs and their simian hosts...
  36. ncbi request reprint Brazilian HTLV type 2a strains from intravenous drug users (IDUs) appear to have originated from two sources: Brazilian Amerindians and European/North American IDUs
    Luiz C J Alcantara
    Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil
    AIDS Res Hum Retroviruses 19:519-23. 2003
    ..Interestingly, we demonstrated for the first time in Brazil the presence of a subtype 2a in IDUs that is closely related to the prototype Mo but distinct from the Brazilian 2a molecular variant...
  37. ncbi request reprint Ancient co-speciation of simian foamy viruses and primates
    William M Switzer
    HIV and Retrovirology Branch, Division of HIV AIDS Prevention, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G 19, Atlanta, Georgia 30333, USA
    Nature 434:376-80. 2005
    ..These results indicate that SFVs might have co-speciated with Old World primates for at least 30 million years, making them the oldest known vertebrate RNA viruses...
  38. pmc Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS
    Marco Salemi
    Department of Ecology and Evolutionary Biology, University of California at Irvine, USA
    J Virol 79:11343-52. 2005
    ....
  39. ncbi request reprint Evidence for host-driven selection of the HIV type 1 vpr gene in vivo during HIV disease progression in a transfusion-acquired cohort
    Leon Cali
    Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Monash, VIC 3800, Australia
    AIDS Res Hum Retroviruses 21:728-33. 2005
    ....
  40. ncbi request reprint H5N1 influenza virus evolution: a comparison of different epidemics in birds and humans (1997-2004)
    Laura Campitelli
    Department of Infectious, Parasitic and Immune Mediated Diseases, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome, Italy
    J Gen Virol 87:955-60. 2006
    ..Positive-selection analysis performed on single-codon sites might be helpful in clarifying the driving force of avian and human influenza virus evolution and in selecting specific targets for vaccines and antiviral drugs...

Research Grants2

  1. Viral evolution in peropheral macrophages and brain during progression to AIDS
    Marco Salemi; Fiscal Year: 2009
    ..The result will be a description of the genetic basis for the onset of dementia in patients with AIDS leading the way to the development of new diagnostic and therapeutic tools. ..
  2. Viral evolution in peropheral macrophages and brain during progression to AIDS
    Marco Salemi; Fiscal Year: 2010
    ..The result will be a description of the genetic basis for the onset of dementia in patients with AIDS leading the way to the development of new diagnostic and therapeutic tools. ..