| Year |
Citation |
Score |
| 2023 |
Elbadry MA, Efstathion CA, Qualls WA, Tagliamonte MS, Alam MM, Khan MSR, Ryan SJ, Xue RD, Charrel RN, Bangonan L, Salemi M, Ayhan N, Lednicky JA, Morris JG. Diversity and Genetic Reassortment of Keystone Virus in Mosquito Populations in Florida. The American Journal of Tropical Medicine and Hygiene. PMID 37127267 DOI: 10.4269/ajtmh.22-0594 |
0.324 |
|
| 2023 |
Ramirez-Mata AS, Ostrov D, Salemi M, Marini S, Magalis BR. Machine Learning Prediction and Phyloanatomic Modeling of Viral Neuroadaptive Signatures in the Macaque Model of HIV-Mediated Neuropathology. Microbiology Spectrum. e0308622. PMID 36847516 DOI: 10.1128/spectrum.03086-22 |
0.36 |
|
| 2022 |
Rich SN, Prosperi MCF, Dellicour S, Vrancken B, Cook RL, Spencer EC, Salemi M, Mavian C. Molecular Epidemiology of HIV-1 Subtype B Infection across Florida Reveals Few Large Superclusters with Metropolitan Origin. Microbiology Spectrum. e0188922. PMID 36222706 DOI: 10.1128/spectrum.01889-22 |
0.33 |
|
| 2022 |
Hendricks CM, Cash MN, Tagliamonte MS, Riva A, Brander C, Llano A, Salemi M, Stevenson M, Mavian C. Discordance between HIV-1 Population in Plasma at Rebound after Structured Treatment Interruption and Archived Provirus Population in Peripheral Blood Mononuclear Cells. Microbiology Spectrum. e0135322. PMID 35699458 DOI: 10.1128/spectrum.01353-22 |
0.315 |
|
| 2022 |
Alexiev I, Mavian C, Paisie T, Ciccozzi M, Dimitrova R, Gancheva A, Kostadinova A, Seguin-Devaux C, Salemi M. Analysis of the Origin and Dissemination of HIV-1 Subtype C in Bulgaria. Viruses. 14. PMID 35215855 DOI: 10.3390/v14020263 |
0.312 |
|
| 2021 |
Lednicky JA, Tagliamonte MS, White SK, Blohm GM, Alam MM, Iovine NM, Salemi M, Mavian C, Morris JG. Isolation of a Novel Recombinant Canine Coronavirus from a Visitor to Haiti: Further Evidence of Transmission of Coronaviruses of Zoonotic Origin to Humans. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 34718467 DOI: 10.1093/cid/ciab924 |
0.311 |
|
| 2020 |
Lednicky JA, Shankar SN, Elbadry MA, Gibson JC, Alam MM, Stephenson CJ, Eiguren-Fernandez A, Morris JG, Mavian CN, Salemi M, Clugston JR, Wu CY. Collection of SARS-CoV-2 Virus from the Air of a Clinic Within a University Student Health Care Center and Analyses of the Viral Genomic Sequence. Aerosol and Air Quality Research. 20: 1167-1171. PMID 33424954 DOI: 10.4209/Aaqr.2020.05.0202 |
0.41 |
|
| 2020 |
Rich SN, Richards VL, Mavian CN, Switzer WM, Rife Magalis B, Poschman K, Geary S, Broadway SE, Bennett SB, Blanton J, Leitner T, Boatwright JL, Stetten NE, Cook RL, Spencer EC, ... Salemi M, et al. Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study. Viruses. 12. PMID 32842636 DOI: 10.3390/V12090921 |
0.382 |
|
| 2020 |
Rich SN, Poschman K, Hu H, Mavian C, Cook RL, Salemi M, Spencer EC, Prosperi M. Sociodemographic, ecological, and spatiotemporal factors associated with HIV drug resistance in Florida: a retrospective analysis. The Journal of Infectious Diseases. PMID 32644119 DOI: 10.1093/Infdis/Jiaa413 |
0.371 |
|
| 2020 |
Mavian C, Marini S, Prosperi M, Salemi M. A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis. Jmir Public Health and Surveillance. 6. PMID 32412415 DOI: 10.2196/19170 |
0.357 |
|
| 2020 |
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, ... ... Salemi M, et al. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proceedings of the National Academy of Sciences of the United States of America. PMID 32381734 DOI: 10.1073/Pnas.2007295117 |
0.397 |
|
| 2020 |
RifeMagalis B, Strickland SL, Shank SD, Autissier P, Schuetz A, Sithinamsuwan P, Lerdlum S, Fletcher JLK, de Souza M, Ananworanich J, Valcour V, Williams KC, Kosakovsky Pond SL, RattoKim S, ... Salemi M, et al. Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host. Virus Evolution. 6: veaa005. PMID 32355568 DOI: 10.1093/Ve/Veaa005 |
0.459 |
|
| 2020 |
Scharf L, Tauriainen J, Buggert M, Hartogensis W, Nolan DJ, Deeks SG, Salemi M, Hecht FM, Karlsson AC. Delayed Expression of PD-1 and TIGIT on HIV-Specific CD8 T Cells in Untreated HLA-B*57:01 Individuals Followed from Early Infection. Journal of Virology. 94. PMID 32350076 DOI: 10.1128/Jvi.02128-19 |
0.355 |
|
| 2020 |
Andrade VM, Mavian C, Babic D, Cordeiro T, Sharkey M, Barrios L, Brander C, Martinez-Picado J, Dalmau J, Llano A, Li JZ, Jacobson J, Lavine CL, Seaman MS, Salemi M, et al. A minor population of macrophage-tropic HIV-1 variants is identified in recrudescing viremia following analytic treatment interruption. Proceedings of the National Academy of Sciences of the United States of America. PMID 32300019 DOI: 10.1073/Pnas.1917034117 |
0.397 |
|
| 2020 |
Mavian C, Paisie TK, Alam MT, Browne C, Beau De Rochars VM, Nembrini S, Cash MN, Nelson EJ, Azarian T, Ali A, Morris JG, Salemi M. Toxigenic evolution and establishment of reservoirs in aquatic ecosystems. Proceedings of the National Academy of Sciences of the United States of America. PMID 32229557 DOI: 10.1073/Pnas.1918763117 |
0.32 |
|
| 2020 |
Fontana C, Angeletti S, Mirandola W, Cella E, Alessia L, Zehender G, Favaro M, Leoni D, Rose DD, Gherardi G, Florio L, Salemi M, Andreoni M, Sarmati L, Ciccozzi M. Whole genome sequencing of carbapenem-resistant : evolutionary analysis for outbreak investigation. Future Microbiology. 15: 203-212. PMID 32056447 DOI: 10.2217/Fmb-2019-0074 |
0.369 |
|
| 2019 |
Abid N, Chillemi G, Salemi M. Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach Genes. 11: 28. PMID 31878331 DOI: 10.3390/Genes11010028 |
0.33 |
|
| 2019 |
Blohm GM, Márquez-Colmenarez MC, Lednicky JA, Bonny TS, Mavian C, Salemi M, Delgado-Noguera L, Morris JG, Paniz-Mondolfi AE. Isolation of Mayaro Virus from a Venezuelan Patient with Febrile Illness, Arthralgias, and Rash: Further Evidence of Regional Strain Circulation and Possible Long-Term Endemicity. The American Journal of Tropical Medicine and Hygiene. PMID 31595869 DOI: 10.4269/Ajtmh.19-0357 |
0.387 |
|
| 2019 |
Durães-Carvalho R, Ludwig-Begall LF, Salemi M, Lins RD, Marques ETA. Influence of directional positive Darwinian selection-driven evolution on arboviruses Dengue and Zika virulence and pathogenesis Molecular Phylogenetics and Evolution. 140: 106607. PMID 31473337 DOI: 10.1016/J.Ympev.2019.106607 |
0.368 |
|
| 2019 |
Blohm G, A Elbadry M, Mavian C, Stephenson C, Loeb J, White S, Telisma T, Chavannes S, De Rochar VMB, Salemi M, Lednicky JA, Glenn Morris J. Mayaro as a Caribbean traveler: Evidence for multiple introductions and transmission of the virus into Haiti. International Journal of Infectious Diseases : Ijid : Official Publication of the International Society For Infectious Diseases. PMID 31382049 DOI: 10.1016/J.Ijid.2019.07.031 |
0.401 |
|
| 2019 |
Ny S, Sandegren L, Salemi M, Giske CG. Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference. Scientific Reports. 9: 10291. PMID 31312006 DOI: 10.1038/S41598-019-46580-3 |
0.338 |
|
| 2019 |
Wilkinson E, Junqueira DM, Lessells R, Engelbrecht S, Zyl Gv, Oliveira Td, Salemi M. The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis Scientific Reports. 9: 2640. PMID 30804361 DOI: 10.1038/S41598-018-37749-3 |
0.406 |
|
| 2019 |
Lednicky JA, White SK, Mavian CN, El Badry MA, Telisma T, Salemi M, OKech BA, Beau De Rochars VM, Morris JG. Emergence of Madariaga virus as a cause of acute febrile illness in children, Haiti, 2015-2016. Plos Neglected Tropical Diseases. 13: e0006972. PMID 30629592 DOI: 10.1371/Journal.Pntd.0006972 |
0.42 |
|
| 2019 |
Rich SN, Mavian C, Richards V, Cook R, Prosperi M, Salemi M. Integrating Phylodynamic Techniques for Next-generation HIV Surveillance in Florida Online Journal of Public Health Informatics. 11. DOI: 10.5210/Ojphi.V11I1.9759 |
0.429 |
|
| 2018 |
Prakoso D, Dark MJ, Barbet AF, Salemi M, Barr KL, Liu JJ, Wenzlow N, Waltzek TB, Long MT. Viral Enrichment Methods Affect the Detection but Not Sequence Variation of West Nile Virus in Equine Brain Tissue. Frontiers in Veterinary Science. 5: 318. PMID 30619900 DOI: 10.3389/Fvets.2018.00318 |
0.388 |
|
| 2018 |
Lin SYC, Magalis BR, Salemi M, Liu HF. Origin and Dissemination of Hepatitis B Virus Genotype C in East Asia Revealed by Phylodynamic Analysis and Historical Correlates. Journal of Viral Hepatitis. PMID 30199591 DOI: 10.1111/Jvh.13006 |
0.366 |
|
| 2018 |
Fogolari M, Mavian C, Angeletti S, Salemi M, Lampel KA, Maurelli AT. Distribution and characterization of Shiga toxin converting temperate phages carried by Shigella flexneri in Hispaniola. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 30075254 DOI: 10.1016/J.Meegid.2018.07.038 |
0.351 |
|
| 2018 |
Séraphin MN, Didelot X, Nolan DJ, May JR, Khan MSR, Murray ER, Salemi M, Morris JG, Lauzardo M. Genomic Investigation of a Outbreak Involving Prison and Community Cases in Florida, United States. The American Journal of Tropical Medicine and Hygiene. PMID 29987998 DOI: 10.4269/Ajtmh.17-0700 |
0.314 |
|
| 2018 |
Rife Magalis B, Kosakovsky Pond SL, Summers MF, Salemi M. Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts. Virus Evolution. 4: vey018. PMID 29951250 DOI: 10.1093/Ve/Vey018 |
0.383 |
|
| 2018 |
White SK, Mavian C, Elbadry MA, Beau De Rochars VM, Paisie T, Telisma T, Salemi M, Lednicky JA, Morris JG. Detection and phylogenetic characterization of arbovirus dual-infections among persons during a chikungunya fever outbreak, Haiti 2014. Plos Neglected Tropical Diseases. 12: e0006505. PMID 29851952 DOI: 10.1371/Journal.Pntd.0006505 |
0.415 |
|
| 2018 |
Singh G, Rife BD, Seufzer B, Salemi M, Rendahl A, Boris-Lawrie K. Identification of conserved, primary sequence motifs that direct retrovirus RNA fate. Nucleic Acids Research. PMID 29846681 DOI: 10.1093/Nar/Gky369 |
0.338 |
|
| 2018 |
White SK, Mavian C, Salemi M, Morris JG, Elbadry MA, Okech BA, Lednicky JA, Dunford JC. A new "American" subgroup of African-lineage Chikungunya virus detected in and isolated from mosquitoes collected in Haiti, 2016. Plos One. 13: e0196857. PMID 29746539 DOI: 10.1371/Journal.Pone.0196857 |
0.417 |
|
| 2018 |
Blohm GM, Lednicky JA, White SK, Mavian CN, Márquez MC, González-García KP, Salemi M, Morris JG, Paniz-Mondolfi AE. Madariaga Virus: Identification of a Lineage III Strain in a Venezuelan Child With Acute Undifferentiated Febrile Illness, in the Setting of a Possible Equine Epizootic. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 29718127 DOI: 10.1093/Cid/Ciy224 |
0.377 |
|
| 2018 |
Durães-Carvalho R, Salemi M. In-depth phylodynamics, evolutionary analysis and in silico predictions of universal epitopes of Influenza A subtypes and Influenza B viruses. Molecular Phylogenetics and Evolution. 121: 174-182. PMID 29355604 DOI: 10.1016/J.Ympev.2018.01.008 |
0.358 |
|
| 2018 |
Cella E, Giovanetti M, Milano T, Fogolari M, Garilli F, Alexiev I, Bazzardi R, Salemi M, Alcantara LCJ, Angeletti S, Pascarella S, Ciccozzi M. Mayaro virus infection, the next epidemic wave after Zika? Evolutionary and structural analysis Asian Pacific Journal of Tropical Medicine. 11: 194. DOI: 10.4103/1995-7645.228433 |
0.362 |
|
| 2018 |
Cella E, Ciccozzi M, Fogolari M, Azarian T, Prosperi M, Dicuonzo G, Salemi M, Angeletti S. A66 Multi-drug-resistant Klebsiella pneumoniae strains circulating in hospital setting: Whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations. Virus Evolution. 4. DOI: 10.1093/Ve/Vey010.065 |
0.323 |
|
| 2017 |
Blohm GM, Lednicky JA, Márquez M, White SK, Loeb JC, Pacheco CA, Nolan DJ, Paisie T, Salemi M, Rodríguez-Morales AJ, Glenn Morris J, Pulliam JRC, Paniz-Mondolfi AE. Evidence for Mother-to-Child Transmission of Zika Virus Through Breast Milk. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 29300859 DOI: 10.1093/Cid/Cix968 |
0.359 |
|
| 2017 |
Rife BD, Mavian C, Chen X, Ciccozzi M, Salemi M, Min J, Prosperi MC. Phylodynamic applications in 21st century global infectious disease research. Global Health Research and Policy. 2: 13. PMID 29202081 DOI: 10.1186/S41256-017-0034-Y |
0.308 |
|
| 2017 |
Cella E, Riva E, Salemi M, Spoto S, Vita S, Fogolari M, Angeletti S, Ciccozzi M. The new Chikungunya virus outbreak in Italy possibly originated from a single introduction from Asia. Pathogens and Global Health. 1-3. PMID 29182057 DOI: 10.1080/20477724.2017.1406565 |
0.371 |
|
| 2017 |
Nolan D, Rose RR, Rodriguez P, Salemi M, Singer EJ, Lamers S, McGrath M. The spleen is an HIV-1 sanctuary during cART. Aids Research and Human Retroviruses. PMID 29084441 DOI: 10.1089/Aid.2017.0254 |
0.451 |
|
| 2017 |
Elbadry MA, White SK, Loeb JC, Tagliamonte MS, Salemi M, Beau De Rochars VM, Telisma T, Rashid M, Morris JG, Lednicky JA. Complete Genomic Sequence of Dengue Virus Serotype 4 Isolated from Plasma Collected from a Haitian Child in 2014. Genome Announcements. 5. PMID 28983011 DOI: 10.1128/Genomea.01160-17 |
0.441 |
|
| 2017 |
Bonny TS, Driver JP, Paisie T, Salemi M, Morris JG, Shender LA, Smith L, Enloe C, Oxenrider K, Gore JA, Loeb JC, Wu CY, Lednicky JA. Detection of Alphacoronavirus vRNA in the Feces of Brazilian Free-Tailed Bats (Tadarida brasiliensis) from a Colony in Florida, USA. Diseases (Basel, Switzerland). 5. PMID 28933360 DOI: 10.3390/Diseases5010007 |
0.377 |
|
| 2017 |
Rife Magalis B, Nolan DJ, Autissier P, Burdo TH, Williams KC, Salemi M. Insights into the impact of CD8+ immune modulation on HIV evolutionary dynamics in distinct anatomical compartments using SIV-infected macaque models of AIDS progression. Journal of Virology. PMID 28931681 DOI: 10.1128/Jvi.01162-17 |
0.44 |
|
| 2017 |
Mavian C, Rife BD, Dollar JJ, Cella E, Ciccozzi M, Prosperi MCF, Lednicky J, Morris JG, Capua I, Salemi M. Emergence of recombinant Mayaro virus strains from the Amazon basin. Scientific Reports. 7: 8718. PMID 28821712 DOI: 10.1038/S41598-017-07152-5 |
0.444 |
|
| 2017 |
Claytor SC, Subramaniam K, Landrau-Giovannetti N, Chinchar VG, Gray MJ, Miller DL, Mavian C, Salemi M, Wisely S, Waltzek TB. Ranavirus phylogenomics: Signatures of recombination and inversions among bullfrog ranaculture isolates. Virology. PMID 28803676 DOI: 10.1016/J.Virol.2017.07.028 |
0.401 |
|
| 2017 |
Cella E, Ciccozzi M, Presti AL, Fogolari M, Azarian T, Prosperi M, Salemi M, Equestre M, Antonelli F, Conti A, Cesaris M, Spoto S, Incalzi RA, Coppola R, Dicuonzo G, et al. Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations. Scientific Reports. 7: 3534. PMID 28615687 DOI: 10.1038/S41598-017-03581-4 |
0.344 |
|
| 2017 |
Blohm GM, Lednicky JA, Márquez M, White SK, Loeb JC, Pacheco CA, Nolan DJ, Paisie T, Salemi M, Rodríguez-Morales AJ, Morris JG, Pulliam JRC, Carrillo AS, Plaza JD, Paniz-Mondolfi AE. Complete Genome Sequences of Identical Zika virus Isolates in a Nursing Mother and Her Infant. Genome Announcements. 5. PMID 28450510 DOI: 10.1128/Genomea.00231-17 |
0.342 |
|
| 2017 |
Lamers SL, Fogel GB, Liu ES, Nolan DJ, Salemi M, Barbier AE, Rose R, Singer EJ, McGrath MS. Predicted coreceptor usage at end-stage HIV disease in tissues derived from subjects on antiretroviral therapy with an undetectable plasma viral load. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 28392467 DOI: 10.1016/J.Meegid.2017.04.004 |
0.395 |
|
| 2017 |
Mallard J, Papazian E, Soulas C, Nolan DJ, Salemi M, Williams KC. A method for obtaining simian immunodeficiency virus RNA sequences from laser capture microdissected and immune captured CD68+ and CD163+ macrophages from frozen tissue sections of bone marrow and brain. Journal of Immunological Methods. PMID 28093272 DOI: 10.1016/J.Jim.2017.01.003 |
0.321 |
|
| 2017 |
Zhou S, Cella E, Zhou W, Kong WH, Liu MQ, Liu PL, Ciccozzi M, Salemi M, Chen XG. Population dynamics of HCV subtypes in injecting drug-users on methadone maintenance treatment in China associated with economic and health reform. Journal of Viral Hepatitis. PMID 28092412 DOI: 10.1111/Jvh.12677 |
0.318 |
|
| 2016 |
Min J, Cella E, Ciccozzi M, Pelosi A, Salemi M, Prosperi M. The global spread of Middle East respiratory syndrome: an analysis fusing traditional epidemiological tracing and molecular phylodynamics Global Health Research and Policy. 1: 14-14. PMID 29202063 DOI: 10.1186/S41256-016-0014-7 |
0.428 |
|
| 2016 |
Cherabuddi K, Iovine NM, Shah K, White SK, Paisie T, Salemi M, Morris JG, Lednicky JA. Zika and Chikungunya virus co-infection in a traveller returning from Colombia, 2016: virus isolation and genetic analysis. Jmm Case Reports. 3: e005072. PMID 28348794 DOI: 10.1099/Jmmcr.0.005072 |
0.402 |
|
| 2016 |
Beau De Rochars VM, Lednicky J, White S, Loeb J, Elbadry MA, Telisma T, Chavannes S, Anilis MG, Cella E, Ciccozzi M, Okech BA, Salemi M, Morris JG. Isolation of Coronavirus NL63 from Blood from Children in Rural Haiti: Phylogenetic Similarities with Recent Isolates from Malaysia. The American Journal of Tropical Medicine and Hygiene. PMID 27799635 DOI: 10.4269/Ajtmh.16-0585 |
0.327 |
|
| 2016 |
Azarian T, Ali A, Johnson JA, Jubair M, Cella E, Ciccozzi M, Nolan DJ, Farmerie W, Rashid MH, Sinha-Ray S, Alam MT, Morris JG, Salemi M. Non-toxigenic environmental Vibrio cholerae O1 strain from Haiti provides evidence of pre-pandemic cholera in Hispaniola. Scientific Reports. 6: 36115. PMID 27786291 DOI: 10.1038/Srep36115 |
0.331 |
|
| 2016 |
Lednicky J, De Rochars VM, Elbadry M, Loeb J, Telisma T, Chavannes S, Anilis G, Cella E, Ciccozzi M, Okech B, Salemi M, Morris JG. Mayaro Virus in Child with Acute Febrile Illness, Haiti, 2015. Emerging Infectious Diseases. 22: 2000-2002. PMID 27767924 DOI: 10.3201/Eid2211.161015 |
0.386 |
|
| 2016 |
Azarian T, Maraqa NF, Cook RL, Johnson JA, Bailey C, Wheeler S, Nolan D, Rathore MH, Morris JG, Salemi M. Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit. Plos One. 11: e0164397. PMID 27732618 DOI: 10.1371/Journal.Pone.0164397 |
0.325 |
|
| 2016 |
Iovine N, Lednicky J, Cherabuddi K, Crooke H, White SK, Loeb JC, Cella E, Ciccozzi M, Salemi M, Morris JG. Co-Infection with Zika and Dengue-2 Viruses in a Traveler Returning from Haiti, 2016: Clinical Presentation and Genetic Analysis. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 27694479 DOI: 10.1093/Cid/Ciw667 |
0.421 |
|
| 2016 |
Lamers SL, Rose R, Nolan DJ, Fogel GB, Barbier AE, Salemi M, McGrath MS. HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi's Sarcoma during AIDS. Sarcoma. 2016: 4510483. PMID 27651732 DOI: 10.1155/2016/4510483 |
0.391 |
|
| 2016 |
Lamers SL, Rose R, Maidji E, Agsalda-Garcia M, Nolan DJ, Fogel GB, Salemi M, Garcia DL, Bracci P, Yong W, Commins D, Said J, Khanlou N, Hinkin CH, Valdes Sueiras M, et al. HIV DNA is frequently present within pathologic tissues evaluated at autopsy from cART-treated patients with undetectable viral load. Journal of Virology. PMID 27466426 DOI: 10.1128/Jvi.00674-16 |
0.376 |
|
| 2016 |
Rose R, Lamers SL, Nolan DJ, Maidji E, Faria NR, Pybus OG, Dollar JJ, Maruniak SA, McAvoy AC, Salemi M, Stoddart C, Singer E, McGrath MS. HIV maintains an evolving and dispersed population among multiple tissues during suppressive cART with periods of rapid expansion corresponding to the onset of cancer. Journal of Virology. PMID 27466425 DOI: 10.1128/Jvi.00684-16 |
0.44 |
|
| 2016 |
Rife BD, Nolan DJ, Lamers SL, Autissier P, Burdo T, Williams KC, Salemi M. Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brain of Rhesus Macaques with SIV-Associated Encephalitis. Journal of Virology. PMID 27122578 DOI: 10.1128/Jvi.00137-16 |
0.442 |
|
| 2016 |
Lednicky J, Beau De Rochars VM, El Badry M, Loeb J, Telisma T, Chavannes S, Anilis G, Cella E, Ciccozzi M, Rashid M, Okech B, Salemi M, Morris JG. Zika Virus Outbreak in Haiti in 2014: Molecular and Clinical Data. Plos Neglected Tropical Diseases. 10: e0004687. PMID 27111294 DOI: 10.1371/Journal.Pntd.0004687 |
0.396 |
|
| 2016 |
Cella E, Gabrielli I, Zehender G, Giovanetti M, Lo Presti A, Lai A, Dicuonzo G, Angeletti S, Salemi M, Ciccozzi M. Phylogeny of Murray Valley encephalitis virus in Australia and Papua New Guinea. Asian Pacific Journal of Tropical Medicine. 9: 385-9. PMID 27086158 DOI: 10.1016/J.Apjtm.2016.03.006 |
0.371 |
|
| 2016 |
Salemi M, Rife B. Phylogenetics and Phyloanatomy of HIV/SIV Intra-Host Compartments and Reservoirs: The Key Role of the Central Nervous System. Current Hiv Research. 14: 110-20. PMID 26511341 DOI: 10.2174/1570162x13666151029102413 |
0.36 |
|
| 2016 |
Salemi M, Rife B. Phylogenetics and phyloanatomy of HIV/SIV intra-host compartments and reservoirs: The key role of the central nervous system Current Hiv Research. 14: 110-120. DOI: 10.2174/1570162X13666151029102413 |
0.469 |
|
| 2015 |
Jain N, Morgan CE, Rife BD, Salemi M, Tolbert BS. Solution Structure of the HIV-1 Intron Splicing Silencer and its Interactions with the UP1 Domain of hnRNP A1. The Journal of Biological Chemistry. PMID 26607354 DOI: 10.1074/Jbc.M115.674564 |
0.337 |
|
| 2015 |
Fogel GB, Lamers SL, Liu ES, Salemi M, McGrath MS. Identification of dual-tropic HIV-1 using evolved neural networks. Bio Systems. PMID 26419858 DOI: 10.1016/J.Biosystems.2015.09.007 |
0.422 |
|
| 2015 |
Chan PA, Hogan JW, Huang A, DeLong A, Salemi M, Mayer KH, Kantor R. Phylogenetic Investigation of a Statewide HIV-1 Epidemic Reveals Ongoing and Active Transmission Networks Among Men Who Have Sex With Men. Journal of Acquired Immune Deficiency Syndromes (1999). 70: 428-35. PMID 26258569 DOI: 10.1097/Qai.0000000000000786 |
0.392 |
|
| 2015 |
Santos LA, Gray RR, Monteiro-Cunha JP, Rodrigues ES, Santos ES, Araujo TH, Gonçalves MS, Salemi M, Alcantara LC. Phylodynamics analysis of the Human Immunodeficiency Virus type 1 (HIV-1) envelope gene in mother and child pairs. Aids Research and Human Retroviruses. PMID 26123053 DOI: 10.1089/AID.2014.0352 |
0.365 |
|
| 2015 |
Lamers SL, Nolan DJ, Rife BD, Fogel GB, McGrath MS, Burdo TH, Autissier P, Williams KC, Goodenow MM, Salemi M. Tracking the emergence of host-specific SIV env and nef populations reveals nef early adaptation and convergent evolution in brain of naturally progressing Rhesus macaques. Journal of Virology. PMID 26041280 DOI: 10.1128/Jvi.01010-15 |
0.463 |
|
| 2015 |
Keane SC, Heng X, Lu K, Kharytonchyk S, Ramakrishnan V, Carter G, Barton S, Hosic A, Florwick A, Santos J, Bolden NC, McCowin S, Case DA, Johnson BA, Salemi M, et al. RNA structure. Structure of the HIV-1 RNA packaging signal. Science (New York, N.Y.). 348: 917-21. PMID 25999508 DOI: 10.1126/Science.Aaa9266 |
0.314 |
|
| 2015 |
Azarian T, Cook RL, Johnson JA, Guzman N, McCarter YS, Gomez N, Rathore MH, Morris JG, Salemi M. Whole-Genome Sequencing for Outbreak Investigations of Methicillin-Resistant Staphylococcus aureus in the Neonatal Intensive Care Unit: Time for Routine Practice? Infection Control and Hospital Epidemiology. 36: 777-85. PMID 25998499 DOI: 10.1017/Ice.2015.73 |
0.353 |
|
| 2015 |
Azarian T, Lo Presti A, Giovanetti M, Cella E, Rife B, Lai A, Zehender G, Ciccozzi M, Salemi M. Impact of spatial dispersion, evolution, and selection on Ebola Zaire Virus epidemic waves. Scientific Reports. 5: 10170. PMID 25973685 DOI: 10.1038/Srep10170 |
0.396 |
|
| 2015 |
Durães-Carvalho R, Caserta LC, Barnabé AC, Martini MC, Simas PV, Santos MM, Salemi M, Arns CW. Phylogenetic and phylogeographic mapping of the avian coronavirus spike protein-encoding gene in wild and synanthropic birds. Virus Research. 201: 101-12. PMID 25771408 DOI: 10.1016/J.Virusres.2015.03.002 |
0.367 |
|
| 2015 |
Cortés-Hinojosa G, Gulland FM, Goldstein T, Venn-Watson S, Rivera R, Waltzek TB, Salemi M, Wellehan JF. Phylogenomic characterization of California sea lion adenovirus-1. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 31: 270-6. PMID 25660039 DOI: 10.1016/J.Meegid.2015.01.024 |
0.415 |
|
| 2015 |
Rife B, Salemi M. On the early dynamics and spread of HIV-1 Trends in Microbiology. 23: 3-4. PMID 25465351 DOI: 10.1016/J.Tim.2014.11.004 |
0.424 |
|
| 2015 |
Azarian T, Petty L, Yin Z, Boyle-Vavra S, Salemi M, Daum RS, David MZ, Steinbeck JL. Whole-Genome Sequencing (WGS) of 19 Methicillin-Resistant Staphylococcus aureus (MRSA) Isolates From Recurrent Infections in 4 Patients: USA300 Strain Replacement Open Forum Infectious Diseases. 2. DOI: 10.1093/Ofid/Ofv133.836 |
0.339 |
|
| 2015 |
Lamers SL, Rose R, Ndhlovu LC, Nolan DJ, Salemi M, Maidji E, Stoddart CA, McGrath MS. The meningeal lymphatic system: a route for HIV brain migration? Journal of Neurovirology. DOI: 10.1007/S13365-015-0399-Y |
0.367 |
|
| 2014 |
Azarian T, Ali A, Johnson JA, Mohr D, Prosperi M, Veras NM, Jubair M, Strickland SL, Rashid MH, Alam MT, Weppelmann TA, Katz LS, Tarr CL, Colwell RR, Morris JG, ... Salemi M, et al. Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection. Mbio. 5. PMID 25538191 DOI: 10.1128/Mbio.01824-14 |
0.348 |
|
| 2014 |
Campbell JH, Ratai EM, Autissier P, Nolan DJ, Tse S, Miller AD, González RG, Salemi M, Burdo TH, Williams KC. Anti-α4 antibody treatment blocks virus traffic to the brain and gut early, and stabilizes CNS injury late in infection. Plos Pathogens. 10: e1004533. PMID 25502752 DOI: 10.1371/Journal.Ppat.1004533 |
0.326 |
|
| 2014 |
Salemi M, Vandamme AM. Bioinformatics tools for the investigation of viral evolution and molecular epidemiology Infection, Genetics and Evolution. 28: 349-350. PMID 25471675 DOI: 10.1016/J.Meegid.2014.11.017 |
0.343 |
|
| 2014 |
Strickland SL, Rife BD, Lamers SL, Nolan DJ, Veras NM, Prosperi MC, Burdo TH, Autissier P, Nowlin B, Goodenow MM, Suchard MA, Williams KC, Salemi M. Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS. The Journal of General Virology. 95: 2784-95. PMID 25205684 DOI: 10.1099/Vir.0.070318-0 |
0.471 |
|
| 2014 |
Norström MM, Veras NM, Huang W, Proper MC, Cook J, Hartogensis W, Hecht FM, Karlsson AC, Karlsoon AC, Salemi M. Baseline CD4+ T cell counts correlates with HIV-1 synonymous rate in HLA-B*5701 subjects with different risk of disease progression. Plos Computational Biology. 10: e1003830. PMID 25187947 DOI: 10.1371/Journal.Pcbi.1003830 |
0.412 |
|
| 2014 |
Buggert M, Norström MM, Salemi M, Hecht FM, Karlsson AC. Functional avidity and IL-2/perforin production is linked to the emergence of mutations within HLA-B*5701-restricted epitopes and HIV-1 disease progression Journal of Immunology. 192: 4685-4696. PMID 24740510 DOI: 10.4049/Jimmunol.1302253 |
0.341 |
|
| 2014 |
Lamers SL, Fogel GB, Nolan DJ, McGrath MS, Salemi M. HIV-associated neuropathogenesis: A systems biology perspective for modeling and therapy Biosystems. 119: 53-61. PMID 24732754 DOI: 10.1016/J.Biosystems.2014.04.002 |
0.384 |
|
| 2014 |
Chan PA, Reitsma MB, DeLong A, Boucek B, Nunn A, Salemi M, Kantor R. Phylogenetic and geospatial evaluation of HIV-1 subtype diversity at the largest HIV center in Rhode Island. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 28: 358-66. PMID 24721515 DOI: 10.1016/J.Meegid.2014.03.027 |
0.42 |
|
| 2014 |
Rollins C, Levengood JD, Rife BD, Salemi M, Tolbert BS. Thermodynamic and phylogenetic insights into hnRNP A1 recognition of the HIV-1 exon splicing silencer 3 element. Biochemistry. 53: 2172-84. PMID 24628426 DOI: 10.1021/Bi500180P |
0.316 |
|
| 2014 |
Hickman D, Jones MK, Zhu S, Kirkpatrick E, Ostrov DA, Wang X, Ukhanova M, Sun Y, Mai V, Salemi M, Karst SM. The effect of malnutrition on norovirus infection. Mbio. 5: e01032-13. PMID 24595373 DOI: 10.1128/Mbio.01032-13 |
0.337 |
|
| 2013 |
Salemi M. The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective. Infectious Disease Reports. 5: e3. PMID 24470967 DOI: 10.4081/idr.2013.s1.e3 |
0.382 |
|
| 2013 |
Prosperi MC, Yin L, Nolan DJ, Lowe AD, Goodenow MM, Salemi M. Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges. Scientific Reports. 3: 2837. PMID 24089188 DOI: 10.1038/Srep02837 |
0.403 |
|
| 2013 |
Lamers SL, Nolan DJ, Strickland SL, Prosperi M, Fogel GB, Goodenow MM, Salemi M. Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS Journal of General Virology. 94: 2469-2479. PMID 23963535 DOI: 10.1099/Vir.0.055335-0 |
0.393 |
|
| 2013 |
Prosperi M, Veras N, Azarian T, Rathore M, Nolan D, Rand K, Cook RL, Johnson J, Morris JG, Salemi M. Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study. Scientific Reports. 3: 1902. PMID 23712667 DOI: 10.1038/Srep01902 |
0.308 |
|
| 2013 |
Mild M, Gray RR, Kvist A, Lemey P, Goodenow MM, Fenyö EM, Albert J, Salemi M, Esbjörnsson J, Medstrand P. High intrapatient HIV-1 evolutionary rate is associated with CCR5-to-CXCR4 coreceptor switch. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 19: 369-77. PMID 23672855 DOI: 10.1016/J.Meegid.2013.05.004 |
0.432 |
|
| 2013 |
Murillo W, Veras N, Prosperi M, de Rivera IL, Paz-Bailey G, Morales-Miranda. S, Juarez SI, Yang C, DeVos J, Marín. JP, Mild M, Albert J, Salemi M. A single early introduction of HIV-1 subtype b into central america accounts for most current cases Journal of Virology. 87: 7463-7470. PMID 23616665 DOI: 10.1128/Jvi.01602-12 |
0.449 |
|
| 2013 |
Lin JH, Chiu SC, Lin YC, Cheng JC, Wu HS, Salemi M, Liu HF. Exploring the molecular epidemiology and evolutionary dynamics of influenza A virus in Taiwan. Plos One. 8: e61957. PMID 23613982 DOI: 10.1371/Journal.Pone.0061957 |
0.38 |
|
| 2013 |
Salemi M. The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: A phylogenetic perspective Infectious Disease Reports. 5: 8-14. DOI: 10.4081/Idr.2013.S1.E3 |
0.48 |
|
| 2012 |
Yin L, Liu L, Sun Y, Hou W, Lowe AC, Gardner BP, Salemi M, Williams WB, Farmerie WG, Sleasman JW, Goodenow MM. High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology. 9: 108. PMID 23244298 DOI: 10.1186/1742-4690-9-108 |
0.436 |
|
| 2012 |
Lamers SL, Fogel GB, Singer EJ, Salemi M, Nolan DJ, Huysentruyt LC, McGrath MS. HIV-1 Nef in macrophage-mediated disease pathogenesis. International Reviews of Immunology. 31: 432-50. PMID 23215766 DOI: 10.3109/08830185.2012.737073 |
0.37 |
|
| 2012 |
Ciccozzi M, Madeddu G, Presti AL, Cella E, Giovanetti M, Budroni C, Babudieri S, Mura MSA, Zehender G, Salemi M. HIV type 1 origin and transmission dynamics among different risk groups in sardinia: molecular epidemiology within the close boundaries of an Italian island. Aids Research and Human Retroviruses. 29: 404-410. PMID 22985362 DOI: 10.1089/Aid.2012.0209 |
0.437 |
|
| 2012 |
Tatem AJ, Hemelaar J, Gray RR, Salemi M. Spatial accessibility and the spread of HIV-1 subtypes and recombinants. Aids (London, England). 26: 2351-60. PMID 22951637 DOI: 10.1097/Qad.0B013E328359A904 |
0.368 |
|
| 2012 |
Gray RR, Salemi M. Integrative molecular phylogeography in the context of infectious diseases on the human-animal interface. Parasitology. 139: 1939-51. PMID 22931895 DOI: 10.1017/S0031182012001102 |
0.333 |
|
| 2012 |
Norström MM, Buggert M, Tauriainen J, Hartogensis W, Prosperi MC, Wallet MA, Hecht FM, Salemi M, Karlsson AC. Combination of immune and viral factors distinguishes low-risk versus high-risk HIV-1 disease progression in HLA-B*5701 subjects. Journal of Virology. 86: 9802-16. PMID 22761389 DOI: 10.1128/Jvi.01165-12 |
0.401 |
|
| 2012 |
Norström MM, Prosperi MC, Gray RR, Karlsson AC, Salemi M. PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences. Evolutionary Bioinformatics Online. 8: 261-9. PMID 22745529 DOI: 10.4137/Ebo.S9738 |
0.372 |
|
| 2012 |
Gray RR, Strickland SL, Veras NM, Goodenow MM, Pybus OG, Lemon SM, Fried MW, Nelson DR, Salemi M. Unexpected maintenance of hepatitis C viral diversity following liver transplantation. Journal of Virology. 86: 8432-9. PMID 22623804 DOI: 10.1128/Jvi.00749-12 |
0.33 |
|
| 2012 |
Gray RR, Salemi M, Klenerman P, Pybus OG. A new evolutionary model for hepatitis C virus chronic infection. Plos Pathogens. 8: e1002656. PMID 22570609 DOI: 10.1371/Journal.Ppat.1002656 |
0.377 |
|
| 2012 |
Akrim M, Lemrabet S, Elharti E, Gray RR, Tardy JC, Cook RL, Salemi M, Andre P, Azarian T, Aouad RE. HIV-1 Subtype distribution in morocco based on national sentinel surveillance data 2004-2005. Aids Research and Therapy. 9: 5. PMID 22333070 DOI: 10.1186/1742-6405-9-5 |
0.392 |
|
| 2012 |
Strickland SL, Gray RR, Lamers SL, Burdo TH, Huenink E, Nolan DJ, Nowlin B, Alvarez X, Midkiff CC, Goodenow MM, Williams K, Salemi M. Efficient transmission and persistence of lowfrequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology Journal of General Virology. 93: 925-938. PMID 22302881 DOI: 10.1099/Vir.0.039586-0 |
0.404 |
|
| 2012 |
Prosperi MCF, Salemi M. QuRe: Software for viral quasispecies reconstruction from next-generation sequencing data Bioinformatics. 28: 132-133. PMID 22088846 DOI: 10.1093/Bioinformatics/Btr627 |
0.386 |
|
| 2012 |
Prosperi MCF, Meloni S, Fanti I, Panzieri S, Ulivi G, Salemi M. Characterization of de novo assemblies of quasispecies from next-generation sequencing via complex network modeling Scientific Research and Essays. 7: 2997-3009. DOI: 10.5897/Sre12.242 |
0.324 |
|
| 2011 |
Lin JH, Chiu SC, Cheng JC, Chang HW, Hsiao KL, Lin YC, Wu HS, Salemi M, Liu HF. Phylodynamics and molecular evolution of influenza A virus nucleoprotein genes in Taiwan between 1979 and 2009. Plos One. 6: e23454. PMID 21858124 DOI: 10.1371/Journal.Pone.0023454 |
0.39 |
|
| 2011 |
Khanani MR, Somani M, Rehmani SS, Veras NM, Salemi M, Ali SH. The spread of HIV in Pakistan: bridging of the epidemic between populations. Plos One. 6: e22449. PMID 21799857 DOI: 10.1371/Journal.Pone.0022449 |
0.407 |
|
| 2011 |
Prosperi MC, Ciccozzi M, Fanti I, Saladini F, Pecorari M, Borghi V, Di Giambenedetto S, Bruzzone B, Capetti A, Vivarelli A, Rusconi S, Re MC, Gismondo MR, Sighinolfi L, Gray RR, ... Salemi M, et al. A novel methodology for large-scale phylogeny partition. Nature Communications. 2: 321. PMID 21610724 DOI: 10.1038/Ncomms1325 |
0.358 |
|
| 2011 |
Gray RR, Parker J, Lemey P, Salemi M, Katzourakis A, Pybus OG. The mode and tempo of hepatitis C virus evolution within and among hosts Bmc Evolutionary Biology. 11. PMID 21595904 DOI: 10.1186/1471-2148-11-131 |
0.378 |
|
| 2011 |
Strickland SL, Gray RR, Lamers SL, Burdo TH, Huenink E, Nolan DJ, Nowlin B, Alvarez X, Midkiff CC, Goodenow MM, Williams K, Salemi M. Significant genetic heterogeneity of the SIVmac251 viral swarm derived from different sources Aids Research and Human Retroviruses. 27: 1327-1332. PMID 21524235 DOI: 10.1089/Aid.2011.0100 |
0.48 |
|
| 2011 |
Véras NM, Santoro MM, Gray RR, Tatem AJ, Lo Presti A, Olearo F, Cappelli G, Colizzi V, Takou D, Torimiro J, Russo G, Callegaro A, Salpini R, D'Arrigo R, Perno CF, ... ... Salemi M, et al. Molecular epidemiology of HIV type 1 CRF02_AG in Cameroon and African patients living in Italy. Aids Research and Human Retroviruses. 27: 1173-82. PMID 21453131 DOI: 10.1089/Aid.2010.0333 |
0.423 |
|
| 2011 |
Véras NM, Gray RR, Brígido LF, Rodrigues R, Salemi M. High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America. The Journal of General Virology. 92: 1698-709. PMID 21450946 DOI: 10.1099/Vir.0.028951-0 |
0.459 |
|
| 2011 |
Salemi M. Toward a robust monitoring of HIV subtypes distribution worldwide Aids. 25: 713-714. PMID 21368591 DOI: 10.1097/Qad.0B013E32834543E7 |
0.355 |
|
| 2011 |
Ciccozzi M, Ciccaglione A, Presti AL, Yalcinkaya T, Taskan ZP, Equestre M, Costantino A, Bruni R, Ebranati E, Salemi M, Gray R, Rezza G, Galli M, Zehender G. Reconstruction of the evolutionary dynamics of the hepatitis C virus 1b epidemic in Turkey. Infection, Genetics and Evolution. 11: 863-868. PMID 21324382 DOI: 10.1016/J.Meegid.2011.02.006 |
0.388 |
|
| 2011 |
Callegaro A, Svicher V, Alteri C, Presti AL, Valenti D, Goglio A, Salemi M, Cella E, Perno CF, Ciccozzi M, Maggiolo F. Epidemiological network analysis in HIV-1 B infected patients diagnosed in Italy between 2000 and 2008. Infection, Genetics and Evolution. 11: 624-632. PMID 21292031 DOI: 10.1016/J.Meegid.2011.01.019 |
0.386 |
|
| 2011 |
Gray RR, Salemi M, Lowe A, Nakamura KJ, Decker WD, Sinkala M, Kankasa C, Mulligan CJ, Thea DM, Kuhn L, Aldrovandi G, Goodenow MM. Multiple independent lineages of HIV-1 persist in breast milk and plasma. Aids (London, England). 25: 143-52. PMID 21173592 DOI: 10.1097/Qad.0B013E328340Fdaf |
0.385 |
|
| 2011 |
Gray RR, Tatem AJ, Johnson JA, Alekseyenko AV, Pybus OG, Suchard MA, Salemi M. Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework. Molecular Biology and Evolution. 28: 1593-603. PMID 21112962 DOI: 10.1093/Molbev/Msq319 |
0.369 |
|
| 2011 |
Lamers SL, Gray RR, Salemi M, Huysentruyt LC, McGrath MS. HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 31-7. PMID 21055482 DOI: 10.1016/J.Meegid.2010.10.016 |
0.412 |
|
| 2011 |
Prosperi MCF, Switzer WM, Heneine W, Salemi M. Murine leukemia viruses (MuLV) and Xenotropic MuLV-related viruses exhibit inter-tropic complex recombination patterns Retrovirology. 8: 1-1. DOI: 10.1186/1742-4690-8-S1-A235 |
0.403 |
|
| 2011 |
Gray RR, Pybus OG, Salemi M. Measuring the temporal structure in serially sampled phylogenies Methods in Ecology and Evolution. 2: 437-445. DOI: 10.1111/J.2041-210X.2011.00102.X |
0.319 |
|
| 2010 |
Prosperi MCF, de Luca A, Di Giambenedetto S, Bracciale L, Fabbiani M, Cauda R, Salemi M. The threshold bootstrap clustering: A new approach to find families or transmission clusters within molecular quasispecies Plos One. 5. PMID 21049051 DOI: 10.1371/Journal.Pone.0013619 |
0.362 |
|
| 2010 |
Lamers SL, Salemi M, Galligan DC, Morris A, Gray R, Fogel G, Zhao L, McGrath MS. Human immunodeficiency virus-1 evolutionary patterns associated with pathogenic processes in the brain Journal of Neurovirology. 16: 230-241. PMID 20367240 DOI: 10.3109/13550281003735709 |
0.401 |
|
| 2010 |
Gray RR, Veras NMC, Santos LA, Salemi M. Evolutionary characterization of the West Nile Virus complete genome Molecular Phylogenetics and Evolution. 56: 195-200. PMID 20102743 DOI: 10.1016/J.Ympev.2010.01.019 |
0.415 |
|
| 2009 |
Salemi M, Lamers SL, Huysentruyt LC, Galligan D, Gray RR, Morris A, McGrath MS. Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma. Plos One. 4: e8153. PMID 19997510 DOI: 10.1371/Journal.Pone.0008153 |
0.41 |
|
| 2009 |
Gray RR, Tatem AJ, Lamers S, Hou W, Laeyendecker O, Serwadda D, Sewankambo N, Gray RH, Wawer M, Quinn TC, Goodenow MM, Salemi M. Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. Aids (London, England). 23: F9-F17. PMID 19644346 DOI: 10.1097/Qad.0B013E32832Faf61 |
0.414 |
|
| 2009 |
Zhao L, Galligan DC, Lamers SL, Yu S, Shagrun L, Salemi M, McGrath MS. High level HIV-1 DNA concentrations in brain tissues differentiate patients with post-HAART AIDS dementia complex or cardiovascular disease from those with AIDS Science in China, Series C: Life Sciences. 52: 651-656. PMID 19641870 DOI: 10.1007/S11427-009-0085-5 |
0.353 |
|
| 2009 |
Lamers SL, Salemi M, Galligan DC, de Oliveira T, Fogel GB, Granier SC, Zhao L, Brown JN, Morris A, Masliah E, McGrath MS. Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology. Plos One. 4: e5065. PMID 19333384 DOI: 10.1371/Journal.Pone.0005065 |
0.433 |
|
| 2009 |
Switzer WM, Salemi M, Qari SH, Jia H, Gray RR, Katzourakis A, Marriott SJ, Pryor KN, Wolfe ND, Burke DS, Folks TM, Heneine W. Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4. Retrovirology. 6: 9. PMID 19187529 DOI: 10.1186/1742-4690-6-9 |
0.414 |
|
| 2009 |
McGrath, Salemi M, Grey R, Galligan D, Lamers S. Genetically restricted HIV-1 sub populations are associated with and migrate within metastatic sites of AIDS-related lymphoma. Infectious Agents and Cancer. 4: 27. DOI: 10.1186/1750-9378-4-S2-P27 |
0.336 |
|
| 2008 |
Salemi M, Gray RR, Goodenow MM. An exploratory algorithm to identify intra-host recombinant viral sequences. Molecular Phylogenetics and Evolution. 49: 618-28. PMID 18801446 DOI: 10.1016/J.Ympev.2008.08.017 |
0.43 |
|
| 2008 |
Salemi M, Goodenow MM, Montieri S, de Oliveira T, Santoro MM, Beshkov D, Alexiev I, Elenkov I, Elenkov I, Yakimova T, Varleva T, Rezza G, Ciccozzi M. The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries. Aids Research and Human Retroviruses. 24: 771-9. PMID 18544022 DOI: 10.1089/Aid.2007.0181 |
0.439 |
|
| 2008 |
Lamers SL, Salemi M, McGrath MS, Fogel GB. Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. 5: 291-300. PMID 18451438 DOI: 10.1109/TCBB.2007.1074 |
0.318 |
|
| 2008 |
Salemi M, de Oliveira T, Ciccozzi M, Rezza G, Goodenow MM. High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania. Plos One. 3: e1390. PMID 18167549 DOI: 10.1371/Journal.Pone.0001390 |
0.401 |
|
| 2008 |
Lamers SL, Salemi M, McGrath MS, Fogel GB. Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks Ieee/Acm Transactions On Computational Biology and Bioinformatics. 5: 291-299. DOI: 10.1109/Tcbb.2007.1074 |
0.427 |
|
| 2007 |
Salemi M, Burkhardt BR, Gray RR, Ghaffari G, Sleasman JW, Goodenow MM. Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-using quasispecies. Plos One. 2: e950. PMID 17895991 DOI: 10.1371/Journal.Pone.0000950 |
0.392 |
|
| 2007 |
Ciccozzi M, Montieri S, Salemi M, Oliveira TD, Dorrucci M, Sinicco A, Luca AD, Giuliani M, Balotta C, Rezza G. An outbreak of HIV-1 subtype G among Italian injecting drug users. Aids. 21: 1213-1215. PMID 17502735 DOI: 10.1097/Qad.0B013E32813Aee1A |
0.406 |
|
| 2006 |
de Oliveira T, Pybus OG, Rambaut A, Salemi M, Cassol S, Ciccozzi M, Rezza G, Gattinara GC, D'Arrigo R, Amicosante M, Perrin L, Colizzi V, Perno CF. Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature. 444: 836-7. PMID 17171825 DOI: 10.1038/444836A |
0.429 |
|
| 2006 |
Campitelli L, Ciccozzi M, Salemi M, Taglia F, Boros S, Donatelli I, Rezza G. H5N1 influenza virus evolution: A comparison of different epidemics in birds and humans (1997-2004) Journal of General Virology. 87: 955-960. PMID 16528045 DOI: 10.1099/Vir.0.81397-0 |
0.379 |
|
| 2005 |
Cali L, Wang B, Mikhail M, Gill MJ, Beckthold B, Salemi M, Jans DA, Piller SC, Saksena NK. Evidence for host-driven selection of the HIV type 1 vpr gene in vivo during HIV disease progression in a transfusion-acquired cohort. Aids Research and Human Retroviruses. 21: 728-33. PMID 16131313 DOI: 10.1089/Aid.2005.21.728 |
0.418 |
|
| 2005 |
Salemi M, Lamers SL, Yu S, de Oliveira T, Fitch WM, McGrath MS. Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. Journal of Virology. 79: 11343-52. PMID 16103186 DOI: 10.1128/Jvi.79.17.11343-11352.2005 |
0.478 |
|
| 2005 |
Switzer WM, Salemi M, Shanmugam V, Gao F, Cong ME, Kuiken C, Bhullar V, Beer BE, Vallet D, Gautier-Hion A, Tooze Z, Villinger F, Holmes EC, Heneine W. Ancient co-speciation of simian foamy viruses and primates. Nature. 434: 376-80. PMID 15772660 DOI: 10.1038/Nature03341 |
0.352 |
|
| 2005 |
McGrath M, Salemi M, Lamers S. Genetic Analysis of HIV in AIDS Malignancies Retrovirology. 2: 1-1. DOI: 10.1186/1742-4690-2-S1-S54 |
0.397 |
|
| 2004 |
de Oliveira T, Salemi M, Gordon M, Vandamme AM, van Rensburg EJ, Engelbrecht S, Coovadia HM, Cassol S. Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design? Genetics. 167: 1047-58. PMID 15280222 DOI: 10.1534/Genetics.103.018135 |
0.357 |
|
| 2004 |
Salemi M, Fitch WM, Ciccozzi M, Ruiz-Alvarez MJ, Rezza G, Lewis MJ. Severe acute respiratory syndrome coronavirus sequence characteristics and evolutionary rate estimate from maximum likelihood analysis. Journal of Virology. 78: 1602-3. PMID 14722315 DOI: 10.1128/Jvi.78.3.1602-1603.2004 |
0.431 |
|
| 2003 |
Lemey P, Salemi M, Wang B, Duffy M, Hall WH, Saksena NK, Vandamme AM. Site stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non-clock-like behavior on viral phylogenetic reconstructions. Fems Immunology and Medical Microbiology. 39: 125-32. PMID 14625095 DOI: 10.1016/S0928-8244(03)00239-6 |
0.33 |
|
| 2003 |
Salemi M, De Oliveira T, Courgnaud V, Moulton V, Holland B, Cassol S, Switzer WM, Vandamme AM. Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses Journal of Virology. 77: 7202-7213. PMID 12805419 DOI: 10.1128/Jvi.77.13.7202-7213.2003 |
0.404 |
|
| 2003 |
Lemey P, Pybus OG, Wang B, Saksena NK, Salemi M, Vandamme AM. Tracing the origin and history of the HIV-2 epidemic. Proceedings of the National Academy of Sciences of the United States of America. 100: 6588-92. PMID 12743376 DOI: 10.1073/Pnas.0936469100 |
0.413 |
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| 2003 |
Robbins KE, Lemey P, Pybus OG, Jaffe HW, Youngpairoj AS, Brown TM, Salemi M, Vandamme AM, Kalish ML. U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. Journal of Virology. 77: 6359-66. PMID 12743293 DOI: 10.1128/Jvi.77.11.6359-6366.2003 |
0.452 |
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| 2002 |
Duffy M, Salemi M, Sheehy N, Vandamme AM, Hegarty J, Curry M, Nolan N, Kelleher D, McKiernan S, Hall WW. 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. Virology. 301: 354-64. PMID 12359437 DOI: 10.1006/Viro.2002.1597 |
0.348 |
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| 2002 |
Courgnaud V, Salemi M, Pourrut X, Mpoudi-Ngole E, Abela B, Auzel P, Bibollet-Ruche F, Hahn B, Vandamme A, Delaporte E, Peeters M. 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 Journal of Virology. 76: 8298-8309. PMID 12134035 DOI: 10.1128/Jvi.76.16.8298-8309.2002 |
0.485 |
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| 2002 |
Lewis MJ, Sheehy N, Salemi M, VanDamme AM, Hall WW. Comparison of CREB- and NF-kappaB-mediated transactivation by human T lymphotropic virus type II (HTLV-II) and type I (HTLV-I) tax proteins. Virology. 295: 182-9. PMID 12033776 DOI: 10.1006/Viro.2002.1357 |
0.318 |
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| 2002 |
Lemey P, Salemi M, Bassit L, Vandamme AM. Phylogenetic classification of TT virus groups based on the N22 region is unreliable Virus Research. 85: 47-59. PMID 11955638 DOI: 10.1016/S0168-1702(02)00017-5 |
0.336 |
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| 2002 |
Shindo N, Alcantara LCJ, Dooren SV, Salemi M, Costa MCR, Kashima S, Covas DT, Teva A, Pellegrini M, Brito I, Vandamme A, Galvão-Castro B. Human retroviruses (HIV and HTLV) in Brazilian Indians: seroepidemiological study and molecular epidemiology of HTLV type 2 isolates. Aids Research and Human Retroviruses. 18: 71-77. PMID 11804558 DOI: 10.1089/088922202753394736 |
0.458 |
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| 2001 |
Dooren SV, Salemi M, Pourrut X, Peeters M, Delaporte E, Ranst MV, Vandamme AM. Evidence for a second simian T-Cell lymphotropic virus type 3 in Cercopithecus nictitans from cameroon Journal of Virology. 75: 11939-11941. PMID 11708284 DOI: 10.1128/Jvi.75.23.11939-11941.2001 |
0.41 |
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| 2001 |
Van Dooren S, Salemi M, Vandamme AM. Dating the origin of the African human T-Cell lymphotropic virus type-I (HTLV-I) subtypes Molecular Biology and Evolution. 18: 661-671. PMID 11264418 DOI: 10.1093/Oxfordjournals.Molbev.A003846 |
0.411 |
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| 2001 |
Salemi M, Strimmer K, Hall WW, Duffy M, Delaporte E, Mboup S, Peeters M, Vandamme AM. Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution The Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 15: 276-278. PMID 11156935 DOI: 10.1096/Fj.00-0449Fje |
0.447 |
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| 2000 |
Vandamme AM, Bertazzoni U, Salemi M. Evolutionary strategies of human T-cell lymphotropic virus type II Gene. 261: 171-180. PMID 11164048 DOI: 10.1016/S0378-1119(00)00473-X |
0.421 |
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| 2000 |
Lewis MJ, Novoa P, Ishak R, Ishak M, Salemi M, Vandamme AM, Kaplan MH, Hall WW. Isolation, cloning, and complete nucleotide sequence of a phenotypically distinct Brazilian isolate of human T-lymphotropic virus type II (HTLV-II). Virology. 271: 142-54. PMID 10814579 DOI: 10.1006/Viro.2000.0284 |
0.414 |
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| 2000 |
Salemi M, Desmyter J, Vandamme AM. Tempo and mode of human and simian T-lymphotropic virus (HTLV/STLV) evolution revealed by analyses of full-genome sequences Molecular Biology and Evolution. 17: 374-386. PMID 10723738 DOI: 10.1093/Oxfordjournals.Molbev.A026317 |
0.397 |
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| 1999 |
Salemi M, Lewis M, Egan JF, Hall WW, Desmyter J, Vandamme AM. Different population dynamics of human T cell lymphotropic virus type II in intravenous drug users compared with endemically infected tribes Proceedings of the National Academy of Sciences of the United States of America. 96: 13253-13258. PMID 10557307 DOI: 10.1073/Pnas.96.23.13253 |
0.416 |
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| 1999 |
Van Brussel M, Salemi M, Liu HF, Goubau P, Desmyter J, Vandamme AM. The discovery of two new divergent STLVs has implications for the evolution and epidemiology of HTLVs Reviews in Medical Virology. 9: 155-170. PMID 10479777 DOI: 10.1002/(Sici)1099-1654(199907/09)9:3<155::Aid-Rmv242>3.0.Co;2-3 |
0.409 |
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| 1999 |
Salemi M, Vandamme AM, Desmyter J, Casoli C, Bertazzoni U. The origin and evolution of human T-cell lymphotropic virus type II (HTLV-II) and the relationship with its replication strategy Gene. 234: 11-21. PMID 10393234 DOI: 10.1016/S0378-1119(99)00169-9 |
0.386 |
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| 1998 |
Vandamme AM, Salemi M, Desmyter J. The simian origins of the pathogenic human T-cell lymphotropic virus type I Trends in Microbiology. 6: 477-483. PMID 10036726 DOI: 10.1016/S0966-842X(98)01406-1 |
0.365 |
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| 1998 |
Dooren SV, Gotuzzo E, Salemi M, Watts D, Audenaert E, Duwe S, Ellerbrok H, Grassmann R, Hagelberg E, Desmyter J, Vandamme AM. Evidence for a post-Columbian introduction of human T-cell lymphotropic virus [type I] [corrected] in Latin America. Journal of General Virology. 79: 2695-2708. PMID 9820145 DOI: 10.1099/0022-1317-79-11-2695 |
0.372 |
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| 1998 |
Ellerbrok H, Fleischer C, Salemi M, Reinhardt P, Ludwig WD, Vandamme AM, Pauli G. Sequence analysis of the first HTLV-I infection in Germany without relations to endemic areas. Aids Research and Human Retroviruses. 14: 1199-203. PMID 9737591 DOI: 10.1089/Aid.1998.14.1199 |
0.374 |
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| 1998 |
Salemi M, Van Dooren S, Audenaert E, Delaporte E, Goubau P, Desmyter J, Vandamme AM. Two new human T-lymphotropic virus type I phylogenetic subtypes in seroindeterminates, a Mbuti pygmy and a gabonese, have closest relatives among African STLV-l strains Virology. 246: 277-287. PMID 9657946 DOI: 10.1006/Viro.1998.9215 |
0.336 |
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| 1998 |
Van Brussel M, Salemi M, Liu HF, Gabriëls J, Goubau P, Desmyter J, Vandamme AM. The Simian T-lymphotropic virus STLV-PP1664 from Pan paniscus is distinctly related to HTLV-2 but differs in genomic organization Virology. 243: 366-379. PMID 9568035 DOI: 10.1006/Viro.1998.9075 |
0.43 |
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| 1998 |
Vandamme AM, Salemi M, Van Brussel M, Liu HF, Van Laethem K, Van Ranst M, Michels L, Desmyter J, Goubau P. African origin of human T-lymphotropic virus type 2 (HTLV-2) supported by a potential new HTLV-2d subtype in Congolese Bambuti Efe Pygmies. Journal of Virology. 72: 4327-40. PMID 9557723 DOI: 10.1128/Jvi.72.5.4327-4340.1998 |
0.39 |
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| 1998 |
Salemi M, Vandamme A, Gradozzi C, Laethem KV, Cattaneo E, Taylor G, Casoli C, Goubau P, Desmyter J, Bertazzoni U. Evolutionary Rate And Genetic Heterogeneity Of Human T-Cell Lymphotropic Virus Type Ii (Htlv-Ii) Using Isolates From European Injecting Drug Users Journal of Molecular Evolution. 46: 602-611. PMID 9545470 DOI: 10.1007/Pl00006340 |
0.362 |
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| 1996 |
Salemi M, Vandamme AM, Guano F, Gradozzi C, Cattaneo E, Casoli C, Bertazzoni U. Complete nucleotide sequence of the Italian human T-cell lymphotropic virus type II isolate Gu and phylogenetic identification of a possible origin of South European epidemics Journal of General Virology. 77: 1193-1201. PMID 8683207 DOI: 10.1099/0022-1317-77-6-1193 |
0.395 |
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| 1995 |
Salemi M, Cattaneo E, Casoli C, Bertazzoni U. Identification of IIa and IIb molecular subtypes of human T-cell lymphotropic virus type II among Italian injecting drug users Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology. 8: 516-520. PMID 7697450 DOI: 10.1097/00042560-199504120-00013 |
0.4 |
|
| 1993 |
Zella D, Cavicchini A, Salemi M, Casoli C, Lori F, Achilli G, Cattaneo E, Landini V, Bertazzoni U. Molecular characterization of two isolates of human T cell leukaemia virus type II from Italian drug abusers and comparison of genome structure with other isolates Journal of General Virology. 74: 437-444. PMID 8445366 DOI: 10.1099/0022-1317-74-3-437 |
0.391 |
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