Early EBV genomic diversity and convergence towards the B95.8 genome in primary infection. Weiss ER, Lamers SL, Henderson JL, Melnikov A, Somasundaran M, Garber M, Selin L, Nusbaum C, Luzuriaga K. J Virol. 2017 Nov 1. pii: JVI.01466-17. doi: 10.1128/JVI.01466-17.

Insights into the Impact of CD8+ Immune Modulation on Human Immunodeficiency Virus Evolutionary Dynamics in Distinct Anatomical Compartments by Using Simian Immunodeficiency Virus-Infected Macaque Models of AIDS Progression. Rife Magalis B, Nolan DJ, Autissier P, Burdo TH, Williams KC, Salemi M.J Virol. 2017 Nov 14;91(23).

Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics. Dellicour S, Rose R, Faria NR, Vieira LFP, Bourhy H, Gilbert M, Lemey P, Pybus OG.Mol Biol Evol. 2017 Oct 1;34(10):2563-2571.

The spleen is an HIV-1 sanctuary during cART. Nolan D, Rose RR, Rodriguez P, Salemi M, Singer EJ, Lamers S, McGrath M. AIDS Res Hum Retroviruses. 2017 Oct 30.

Brain-specific HIV Nef identified in multiple patients with neurological disease. Lamers SL, Fogel GB, Liu ES, Barbier AE, Rodriguez CW, Singer EJ, Nolan DJ, Rose R, McGrath MS. J Neurovirol. 2017 Oct 23.

Eradication of HIV from Tissue Reservoirs: Challenges for the Cure. Rose R, Nolan DJ, Maidji E, Stoddart CA, Singer EJ, Lamers SL, McGrath MS. AIDS Res Hum Retroviruses. 2017 Aug 7.

Complete Genome Sequences of Identical Zika virus Isolates in a Nursing Mother and Her Infant.
Blohm GM, Lednicky JA, Márquez M, White SK, Loeb JC, Pacheco CA, Nolan DJ, Paisie T, Salemi M, Rodríguez-Morales AJ, Morris JG Jr, Pulliam JRC, Carrillo AS, Plaza JD, Paniz-Mondolfi AE.Genome Announc. 2017 Apr 27;5(17).

Predicted coreceptor usage at end-stage HIV disease in tissues derived from subjects on antiretroviral therapy with an undetectable plasma viral load. Lamers SL, Fogel GB, Liu ES, Nolan DJ, Salemi M, Barbier AE, Rose R, Singer EJ, McGrath MS. Infect Genet Evol. 2017 Apr 6

Paucity of Intact Non-Induced Provirus with Early, Long-Term Antiretroviral Therapy of Perinatal HIV Infection. Rainwater-Lovett K, Ziemniak C, Watson D, Luzuriaga K, Siberry G, Petru A, Chen Y, Uprety P, McManus M, Ho YC, Lamers SL, Persaud D.PLoS One. 2017 Feb

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. Mallard J, Papazian E, Soulas C, Nolan DJ, Salemi M, Williams KC.J Immunol Methods. 2017 Mar;442:59-63. doi: 10.1016/j.jim.2017.01.003. Epub 2017 Jan 14.

SERAPHIM: studying environmental rasters and phylogenetically-informed movements. S Dellicour, R Rose, N Faria, P Lemey, OG Pybus. Bioinformatics 32(20):3204-3206. (2016) PMID: 27334476

Challenges in the analysis of viral metagenomes. R Rose, A Tapinos, B Constanitis, D Robertson, M Prosperi (2016)  Virus Evolution 2 (2): vew022.

Identifying transmission clusters with Cluster Picker and HIV-TRACE. Rose R, Lamers SL, Dollar JJ, Grabowski M, Hodcroft EB, Ragonnet-Cronin M, Wertheim JO, Redd AD, German D, Laeyendecker O. AIDS Res Hum Retroviruses. 2016 Nov 8

Non-toxigenic environmental Vibrio cholerae O1 strain from Haiti provides evidence of pre-pandemic cholera in Hispaniola. 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. Sci Rep. 2016 Oct 27;6:36115. doi: 10.1038/srep36115.

Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection. Raghwani J, Rose R, Sheridan I, Lemey P, Suchard MA, Santantonio T, Farci P, Klenerman P, Pybus OG.PLoS Pathog. 2016 Sep 15;12(9):e1005894. doi: 10.1371/journal.ppat.1005894

Low Rates of Transmitted Drug Resistance among Newly Identified HIV-1 Seroconverters in Rural Rakai,Uganda. Reynolds SJ, Ssempijja V, Galiwango RM, Ndyanabo A, Nakigozi G, Lyagoba F, Nazziwa J, Redd AD, Lamers SL, Gray RH, Wawer MJ, Serwadda D, Quinn TC. AIDS Res Hum Retroviruses. 2016 Oct 31

HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi’s Sarcoma during AIDS. Lamers SL, Rose R, Nolan DJ, Fogel GB, Barbier AE, Salemi M, McGrath MS. Sarcoma. 2016;2016:4510483.

Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit. Azarian T, Maraqa NF, Cook RL, Johnson JA, Bailey C, Wheeler S, Nolan D, Rathore MH, Morris JG Jr, Salemi M. PLoS One. 2016 Oct 12;11(10):e0164397. doi: 10.1371/journal.pone.0164397. eCollection 2016.

HIV DNA is frequently present within pathologic tissues evaluated at autopsy from cART-treated patients with undetectable viral load. 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, Mathisen G, Donovan S, Shirimizu B, Stoddart CA, McGrath MS, Singer EJ.J Virol. 2016 Jul 27. pii: JVI.00674-16

HIV maintains an evolving and dispersed population among multiple tissues during suppressive cART with periods of rapid expansion corresponding to the onset of cancer. 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. J Virol. 2016 Jul 27. pii: JVI.00684-16.

Intrahost Evolution of Methicillin-Resistant Staphylococcus aureus USA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections. Azarian T, Daum RS, Petty LA, Steinbeck JL, Yin Z, Nolan D, Boyle-Vavra S, Hanage WP, Salemi M, David MZ. J Infect Dis. 2016 Sep 15;214(6):895-905. doi: 10.1093/infdis/jiw242. Epub 2016 Jun 10.

HIV-1 Sequence Data Coverage in Central East Africa from 1959 to 2013. Lamers SL, Barbier AE, Ratmann O2, Fraser C, Rose R, Laeyendecker, Grabowski MK. AIDS Res Hum Retroviruses. 2016 Aug 2

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. Rife BD, Nolan DJ, Lamers SL, Autissier P, Burdo T, Williams KC, Salemi M. J Virol. 2016 Apr 27. pii: JVI.00137-16.

Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. Dellicour S, Rose R, Pybus OG.BMC Bioinformatics. 2016 Feb 11;17:82. doi: 10.1186/s12859-016-0924-x.

Visual programming for next-generation sequencing data analytics. Milicchio F, Rose R, Bian J, Min J, Prosperi M.BioData Min. 2016 Apr 27;9:16. doi: 10.1186/s13040-016-0095-3. eCollection 2016. Review.

On the Physicochemical and Structural Modifications Associated with HIV-1 Subtype B Tropism Transition. Lamers SL, Fogel GB, Liu ES, Salemi M, McGrath MS. AIDS Res Hum Retroviruses. 2016 Apr 12. PMID: 27071630

The meningeal lymphatic system: a route for HIV brain migration? Lamers SL, Rose R, Ndhlovu LC, Nolan DJ, Salemi M, Maidji E, Stoddart CA, McGrath MS. J Neurovirol. 2015 Nov 16. PMID: 26572785

Identification of dual-tropic HIV-1 using evolved neural networks. Fogel GB, Lamers SL, Liu ES, Salemi M, McGrath MS. Biosystems. 2015 Sep 28. pii: S0303-2647(15)00158-6. doi: 10.1016/j.biosystems.2015.09.007.

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. Lamers SL, Nolan DJ, Rife BD, Fogel GB, McGrath MS, Burdo TH, Autissier P, Williams KC, Goodenow MM, Salemi M. J Virol. 2015 Jun 3. pii: JVI.01010-15.

Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2. Newman RM, Lamers SL, Weiner B, Ray SC, Colgrove RC, Diaz F, Jing L, Wang K, Saif S, Young S, Henn M, Laeyendecker O, Tobian AA, Cohen J, Koelle DM, Quinn TC, Knipe DM. J Virol. 2015 May 27. pii: JVI.01303-15.

Global Diversity Within and Between Human Herpes Virus 1 and 2 Glycoproteins. Lamers SL1, Newman R2, Laeyendecker O3, Tobian AA4, Colgrove RC5, Ray SC6, Koelle DM7, Cohen J4, Knipe DM8, Quinn TC9. J Virol. 2015 May 27. pii: JVI.01302-15.

Factors related to HIV-associated neurocognitive impairment differ with age. Fogel GB, Lamers SL, Levine AJ, Valdes-Sueiras M, McGrath MS, Shapshak P, Singer EJ. Journal of Neurovirology. 2014 Nov 18.

HIV-1 Persistence in Macrophage Reservoirs during Antiretroviral Therapy. Susanna L. Lamers and Michael S. McGrath. Austin Journal of Clinical Pathology. 2014. 1 (4).

Anti-α4 antibody treatment blocks virus traffic to the brain and gut early, and stabilizes CNS injury late in infection. Campbell JH, Ratai EM, Autissier P, Nolan DJ, Tse S, Miller AD, González RG, Salemi M, Burdo TH, Williams KC. PLoS Pathog. 2014 Dec 11;10(12):e1004533. doi: 10.1371/journal.ppat.1004533. eCollection 2014 Dec.

Spatiotemporal Dynamics of SIV Brain Infection in CD8+ Lymphocyte-Depleted Rhesus Macaques with NeuroAIDS. 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.J Gen Virol. 2014 Sep 9. pii: vir.0.070318-0. doi: 10.1099/vir.0.070318-0. PMID:25205684

HIV-associated neuropathogenesis: A systems biology perspective for modeling and therapy. Lamers SL, Fogel GB, Nolan DJ, McGrath MS, Salemi M. Biosystems. 2014 Apr 13. pii: S0303-2647(14)00043-4. doi:

Anti-α4 antibody treatment blocks virus traffic to the brain and gut early, and stabilizes CNS injury late in infection.Campbell JH, Ratai EM, Autissier P, Nolan DJ, Tse S, Miller AD, González RG, Salemi M, Burdo TH, Williams KC. PLoS Pathog. 2014 Dec 11;10(12):e1004533. doi: 10.1371/journal.ppat.1004533. eCollection 2014 Dec.

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges. Prosperi MC, Yin L, Nolan DJ, Lowe AD, Goodenow MM, et al.Scientific reports. 2013; 3:2837.

Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a crosssectional study. Prosperi M, Veras N, Azarian T, Rathore M, Nolan D, et al. Scientific reports. 2013; 3:1902.

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges. Prosperi MC, Yin L, Nolan DJ, Lowe AD, Goodenow MM, Salemi M.Sci Rep. 2013 Oct 3;3:2837. doi: 10.1038/srep02837.

Viral evolution explains the associations among hepatitis C virus genotype, clinical outcomes, and human genetic variation. R Rose, PV Markov, T Lam, OG Pybus (2013) Infection, Genetics and Evolution 20: 418–421.10.1016/j.biosystems.

Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS. Lamers SL, Nolan DJ, Strickland SL, Prosperi M, Fogel GB, Goodenow MM, Salemi M. J Gen Virol. 2013 Nov;94(Pt 11):2469-79. doi: 10.1099/vir.0.055335-0. Epub 2013 Aug 20.

The Virus whose family expanded. R Rose Gray, OG Pybus (2013) Nature 498:310-11.

Evolutionary analysis of hepatitis C virus gene sequences from 1953. R Rose Gray, Y Tanaka, Y Takebe, G Magiorkinis, Z Buskell, L Seeff, H Alter, OG Pybus (2013) Philosophical Transactions of the Royal Society Series B 368: 20130168.

High intrapatient HIV-1 evolutionary rate is associated with CCR5-to-CXCR4 coreceptor switch. M Mild*, R Rose Gray*, A Kvist, P Lemey, MM Goodenow, EM Fenyö, J Albert, M Salemi, J Esbjörnsson, P Medstrand (2013) Infection Genetics and Evolution 19:369-77.

HIV-1 Nef in macrophage-mediated disease pathogenesis. Lamers SL, Fogel GB, Singer EJ, Salemi M, Nolan DJ, Huysentruyt LC, McGrath MS. Int Rev Immunol. 2012 Dec;31(6):432-50. doi: 10.3109/08830185.2012.737073. Review.

Efficient transmission and persistence of low-frequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology. Strickland SL, Gray RR, Lamers SL, Burdo TH, Huenink E, Nolan DJ, Nowlin B, Alvarez X, Midkiff CC, Goodenow MM, Williams K, Salemi M. J Gen Virol. 2012 May;93(Pt 5):925-38. doi: 10.1099/vir.0.039586-0. Epub 2012 Feb 1.

HIV type 1 genetic variation in foreskin and blood from subjects in Rakai, Uganda. Galiwango RM, Lamers SL, Redd AD, Manucci J, Tobian AA, Sewankambo N, Kigozi G, Nakigozi G, Serwadda D, Boaz I, Nalugoda F, Sullivan DJ, Kong X, Wawer MJ, Gray RH, Quinn TC, Laeyendecker O; Rakai Health Sciences Program. AIDS Res Hum Retroviruses. 2012 Jul;28(7):729-33. doi: 10.1089/AID.2011.0176. Epub 2011 Sep 19.

A new evolutionary model for Hepatitis C virus chronic infection. R Rose Gray, M Salemi, P Klenerman, OG Pybus (2012) PLoS Pathogens. 8:e1002656.

Unexpected Maintenance of Hepatitis C Viral Diversity Following Liver Transplantation. R Rose Gray, S Strickland, NMC Veras, OG Pybus, MM Goodenow, DW Fried, SM Lemon, DR Nelson, M Salemi (2012) Journal of Virology 86:8432-9.

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. Duffy M, Salemi M, Sheehy N, Vandamme AM, Hegarty J, Curry M, Nolan N, Kelleher D, McKiernan S, Hall WW. Virology. 2002 Sep 30;301(2):354-64.

Integrative molecular phylogeography in the context of infectious diseases on the human-animal interface. R Rose Gray, M Salemi (2012) Parasitology 139:1939-51.

PhyloTempo: A set of R scripts for assessing and visualizing temporal clustering in genealogies inferred from serially sampled viral sequences. MM Norström, MC Prosperi, R Rose Gray, AC Karlsson, M Salemi (2012) Evolutionary Bioinformatics 8:261-269.

Spatial accessibility and the spread of HIV-1 subtypes and recombinants in sub-Saharan Africa. AJ Tatem, J Hemelaar, R Rose Gray, M Salemi (2012) AIDS 26:2351-60.

Unifying the spatial epidemiology and molecular evolution of emerging epidemics. OG Pybus, M Suchard, P Lemey, F Bernardin, A Rambaut, FW Crawford, R Rose Gray, N Arinaminpathy, S Stramer, MP Busch, E Delwart (2012) Proceedings of the National Academy of Sciences 109:15066-71.

Efficient Transmission and Persistence of Low Frequency SIVmac251 Variants in CD8-depleted Rhesus Macaques with Different Neuropathology. S Strickland, R Rose Gray, S Lamers, T Burdo, E Huenink, D Nolan, B Nowlin, X Alvarez, C Midkiff, MM Goodenow, K Williams, M Salemi (2012) Journal of General Virology 93:925-38.

HIV-1 Subtype distribution in Morocco based on national sentinel surveillance data 2004-2005. M Akrim, S Lemrabet, E Elharti, R Rose Gray, JC Tardy, RL Cook, M Salemi, P Andre, T Azarian and R El Aouad (2012) AIDS Research & Therapy. 93:925-38.

On counting the frequency distribution of string motifs in molecular sequences. MCF Prosperi, L Prosperi, R Rose Gray, M Salemi (2012) International Journal of Biomathematics 5: 1250055.

The mode and tempo of hepatitis C virus evolution within and among hosts. R Rose Gray, J Parker, P Lemey, M Salemi, A Katzourakis, OG Pybus (2011) BMC Evolutionary Biology 11:131.

Measuring the Temporal Structure in Serially-Sampled Phylogenies. R Rose Gray, OG Pybus, M Salemi (2011) Methods in Ecology and Evolution 2:437–445.

Testing Spatiotemporal Hypothesis Of Bacterial Evolution Using Methicillin-Resistant Staphylococcus Aureus ST239 Genome-Wide Data Within A Bayesian Framework. R Rose Gray, AJ Tatem, JA Johnson, AV Alekseyenko, OG Pybus, MA Suchard, M Salemi (2011) Molecular Biology and Evolution 28: 1593-1603.

Multiple independent lineages of HIV-1 persist in breast milk and plasma. R Rose Gray, M Salemi, A Lowe, KJ Nakamura, WD Decker, M Sinkala, C Kankasa, CJ Mulligan, D Thea, L Kuhn, G Aldrovandi, MM Goodenow (2011) AIDS 25:143-152.

High-Resolution Phylogenetics and Phylogeography of HIV-1 Subtype C Epidemic in South America. NM Véras, RR Gray, LF Brígido, R Rodrigues, M Salemi (2011) Journal of General Virology 92:1698-709.

Reconstruction of the evolutionary dynamics of the Hepatitis C virus 1b epidemic in Turkey. M Ciccozzi, AR Ciccaglione, A Lo Presti, T Yalcinkaya, MEquestre, A Costantino, R Bruni , E Ebranati, M Salemi, R Rose Gray, G Rezza, M Galli, G Zehender (2011) Infection, Genetics and Evolution 1:863-8.

Novel Methodology for Large-Scale Phylogeny Partition. M Prosperi, M Ciccozzi, I Fanti, F Saladini, M Pecorari ,V Borghi, S Di Giambenedetto, B Bruzzone, A Capetti, A Vivarelli, S Rusconi, M Re, MR Gismondo, L Sighinolfi, R Rose Gray, M Salemi, M Zazzi, A De Luca (2011) A Nature Communications 2:321.

Molecular Epidemiology of HIV-1 CRF02_AG in Cameroon and African Patients Living in Italy. NMC Véras, MM Santoro, R Rose Gray, AJ Tatem, A Lo Presti, F Olearo, G Cappelli, V Colizzi, D Takou, J Torimiro, G Russo, A Callegaro, R Salpini, R D’Arrigo, CF Perno, MM Goodenow, M Ciccozzi, M Salemi (2011) AIDS Research Human Retroviruses 27:1173-82.

Haplotype-Based Study of the Association of Alcohol Metabolizing Genes with Alcohol Dependence in Four Independent Populations. J Liu, Z Zhou, CA Hodgkinson, Q Yuan, P-H Shen, CJ Mulligan, A Wang, R Rose Gray, A Roy, M Virkkunen, D Goldman, M-A Enoch (2011) Alcoholism: Clinical & Experimental Research 35: 1-13.

Significant genetic heterogeneity of the SIVmac251 viral swarm derived from different sources. Strickland SL, Gray RR, Lamers SL, Burdo TH, Huenink E, Nolan DJ, Nowlin B, Alvarez X, Midkiff CC, Goodenow MM, Williams K, Salemi M. AIDS Res Hum Retroviruses. 2011 Dec;27(12):1327-32. doi: 10.1089/aid.2011.0100. Epub 2011 Jun 28.

HIV-1 nef protein structures associated with brain infection and dementia pathogenesis. Lamers SL, Poon AF, McGrath MS. PLoS One. 2011 Feb 9;6(2):e16659. doi: 10.1371/journal.pone.0016659.

Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms. Ng OT, Munshaw S, Lamers SL, Chew KK, Lin L, Redd AD, Manucci J, Quinn TC, Ray SC, Chua A, Leo YS,Laeyendecker O. AIDS Res Hum Retroviruses. 2011 Oct;27(10):1135-7. doi: 10.1089/AID.2010.0364. Epub 2011 Feb 14.

HIV-1 nef protein visits B-cells via macrophage nanotubes: a mechanism for AIDS-related lymphoma pathogenesis? Lamers SL, Fogel GB, Huysentruyt LC, McGrath MS. Curr HIV Res. 2010 Dec;8(8):638-40.

HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues. Lamers SL, Gray RR, Salemi M, Huysentruyt LC, McGrath MS. Infect Genet Evol. 2011 Jan;11(1):31-7. doi: 10.1016/j.meegid.2010.10.016. Epub 2010 Nov 3.

HIV-miR-H1 evolvability during HIV pathogenesis. Lamers SL, Fogel GB, McGrath MS. Biosystems. 2010 Aug;101(2):88-96. doi: 10.1016/j.biosystems.2010.05.001. Epub 2010 May 31.

Human immunodeficiency virus-1 evolutionary patterns associated with pathogenic processes in the brain. Lamers SL, Salemi M, Galligan DC, Morris A, Gray R, Fogel G, Zhao L, McGrath MS. J Neurovirol. 2010 May;16(3):230-41.

Evolutionary characterization of the West Nile virus complete genome. R Rose Gray, NMC Veras, LA Santos and M Salemi (2010) Molecular Phylogenetics and Evolution 56:195-200.

Genetically restricted HIV-1 sub populations are associated with and migrate within metastatic sites of AIDS-related lymphoma. MS McGrath,M Salemi, R Grey, D Galligan and SL Lamers. Infectious Agents and Cancer 2009, 4(Suppl 2):P27  doi:10.1186/1750-9378-4-S2-P27.

Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4. WM Switzer, M Salemi, SH Qari, H Jia, R Rose Gray, A Katzourakis, SJ Marriott, KN Pryor, ND Wolfe, DS Burke, TM Folks and W Heneine (2009) Retrovirology, 6:9.

Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma. Salemi M, Lamers SL, Huysentruyt LC, Galligan D, Gray RR, Morris A, McGrath MS. PLoS One. 2009 Dec 3;4(12):e8153.

Geographic HIV type 1 subtype distribution in Rakai district, Uganda. Collinson-Streng AN, Redd AD, Sewankambo NK, Serwadda D, Rezapour M, Lamers SL, Gray RH, Wawer MJ, Quinn TC, Laeyendecker O. AIDS Res Hum Retroviruses. 2009 Oct;25(10):1045-8. doi: 10.1089/aid.2009.0127.

Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. Gray RR, Tatem AJ, Lamers S, Hou W, Laeyendecker O, Serwadda D, Sewankambo N, Gray RH, Wawer M, Quinn TC, Goodenow MM, Salemi M. AIDS. 2009 Sep 10;23(14):F9-F17. doi: 10.1097/QAD.0b013e32832faf61.

High level HIV-1 DNA concentrations in brain tissues differentiate patients with post-HAART AIDS dementia complex or cardiovascular disease from those with AIDS. Zhao L, Galligan DC, Lamers SL, Yu S, Shagrun L, Salemi M, McGrath MS. Sci China C Life Sci. 2009 Jul;52(7):651-6. doi: 10.1007/s11427-009-0085-5. Epub 2009 Jul 30.

Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology. Lamers SL, Salemi M, Galligan DC, de Oliveira T, Fogel GB, Granier SC, Zhao L, Brown JN, Morris A, Masliah E, McGrath MS. PLoS One. 2009;4(3):e5065. doi: 10.1371/journal.pone.0005065. Epub 2009 Mar 31.

An exploratory algorithm to identify intra-host recombinant viral sequences. M Salemi, R Rose Gray, MM Goodenow (2008) Molecular Phylogenetics and Evolution 49:618-628.

Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks. Lamers SL, Salemi M, McGrath MS, Fogel GB. IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):291-300. doi: 10.1109/TCBB.2007.1074.

Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-Using quasispecies. M Salemi, BR Burkhardt, R Rose Gray, G Ghaffari, JW Sleasman, MM Goodenow (2007) PLoS One 2:e950.

Linkage disequilibrium and association analysis of alpha synuclein (SNCA) and alcohol and drug dependence in two American Indian populations. J Clarimon*, R Rose Gray*, L Williams, MA Enoch, R Robin, B Albaugh, A Singleton, D Goldman, CJ Mulligan (2007) Alcoholism: Clinical & Experimental Research 4:1-9.

Molecular evolution of the tprC, D, I, K, G, and J genes in the pathogenic genus Treponema. R Rose Gray, CJ Mulligan, BJ Molini, ES Sun, L Giacani, C Godornes, A Kitchen, SA Lukehart, and A Centurion-Lara (2006 Molecular Biology & Evolution 23:2220-2233.

Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. Salemi M, Lamers SL, Yu S, de Oliveira T, Fitch WM, McGrath MS. J Virol. 2005 Sep;79(17):11343-52.

Increased replication of non-syncytium-inducing HIV type 1 isolates in monocyte-derived macrophages is linked to advanced disease in infected children. Tuttle DL, Anders CB, Aquino-De Jesus MJ, Poole PP, Lamers SL, Briggs DR, Pomeroy SM, Alexander L, Peden KW, Andiman WA, Sleasman JW, Goodenow MM. AIDS Res Hum Retroviruses. 2002 Mar 20;18(5):353-62.

Human immunodeficiency virus type 1 protease genotype predicts immune and viral responses to combination therapy with protease inhibitors (PIs) in PI-naive patients. Perez EE, Rose SL, Peyser B, Lamers SL, Burkhardt B, Dunn BM, Hutson AD, Sleasman JW, Goodenow MM. J Infect Dis. 2001 Feb 15;183(4):579-88. Epub 2001 Jan 19.

Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants. Ping LH, Nelson JA, Hoffman IF, Schock J, Lamers SL, Goodman M, Vernazza P, Kazembe P, Maida M, Zimba D, Goodenow MM, Eron JJ Jr, Fiscus SA, Cohen MS, Swanstrom R. J Virol. 1999 Aug;73(8):6271-81.

Structure of a putative sodium channel from the sea anemone Aiptasia pallida. White GB, Pfahnl A, Haddock S, Lamers S, Greenberg RM, Anderson PA. Invert Neurosci. 1998 Mar;3(4):317-26.

Analysis of a large collection of natural HIV-1 integrase sequences, including those from long-term nonprogressors. Skinner LM, Lamers SL, Sanders JC, Eyster ME, Goodenow MM, Katzman M. J Acquir Immune Defic Syndr Hum Retrovirol. 1998 Oct 1;19(2):99-110.

A model for alignment of Env V1 and V2 hypervariable domains from human and simian immunodeficiency viruses. Lamers SL, Sleasman JW, Goodenow MM. AIDS Res Hum Retroviruses. 1996 Aug 10;12(12):1169-78.

Natural variation in HIV-1 protease, Gag p7 and p6, and protease cleavage sites within gag/pol polyproteins: amino acid substitutions in the absence of protease inhibitors in mothers and children infected by human immunodeficiency virus type 1. Barrie KA, Perez EE, Lamers SL, Farmerie WG, Dunn BM, Sleasman JW, Goodenow MM. Virology. 1996 May 15;219(2):407-16.

Persistence of multiple maternal genotypes of human immunodeficiency virus type I in infants infected by vertical transmission. Lamers SL, Sleasman JW, She JX, Barrie KA, Pomeroy SM, Barrett DJ, Goodenow MM. J Clin Invest. 1994 Jan;93(1):380-90.

Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo. Lamers SL, Sleasman JW, She JX, Barrie KA, Pomeroy SM, Barrett DJ, Goodenow MM. J Virol. 1993 Jul;67(7):3951-60.