S. Ray

O. Laeyendecker, S. Ray, Eshan U. Patel, 2020, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

The Brief Case: The Fly Who Cried Wohlf

S. Ray, P. Simner, Josh H. Gray, 2022, Journal of clinical microbiology.

An Update on SARS-CoV-2 Diversity in the United States National Capital Region: Evolution of Novel and Variants of Concern.

S. Ray, A. Pekosz, H. Mostafa, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Laser captured hepatocytes show association of butyrylcholinesterase gene loss and fibrosis progression in hepatitis C‐infected drug users

K. Hansen, S. Ray, M. Torbenson, 2012, Hepatology.

Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population.

O. Laeyendecker, S. Ray, R. Rose, 2018, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

IgM anti-ACE2 autoantibodies in severe COVID-19 activate complement and perturb vascular endothelial function

Jamie B. Spangler, S. Zeger, O. Laeyendecker, 2022, JCI insight.

Dynamics of SEN virus infection among injection drug users.

D. Vlahov, S. Ray, L. Wilson, 2001, The Journal of infectious diseases.

Prospective evaluation of community-acquired acute-phase hepatitis C virus infection.

D. Vlahov, S. Ray, S. Strathdee, 2005, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Analysis of HIV diversity using a high-resolution melting assay.

S. Ray, P. Musoke, C. Nakabiito, 2010, AIDS research and human retroviruses.

Inconsistent temporal patterns of genetic variation of HCV among high-risk subjects may impact inference of transmission networks.

O. Laeyendecker, S. Ray, R. Rose, 2019, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Towards real-time urinalysis with holographic lens-free imaging

Gregory N. McKay, Mason T. Chen, Nicholas J. Durr, 2022, BiOS.

Decreased Activated CD4+ T Cell Repertoire Diversity After Antiretroviral Therapy in HIV-1/HCV Coinfection Correlates with CD4+ T Cell Recovery.

R. El-Diwany, S. Ray, S. Wheelan, 2021, Viral immunology.

Hepatitis C Virus Immune Escape via Exploitation of a Hole in the T Cell Repertoire1

Todd M. Allen, J. Sidney, A. Sette, 2008, The Journal of Immunology.

Immunogenicity and Cross-Reactivity of a Representative Ancestral Sequence in Hepatitis C Virus Infection

J. Sidney, A. Sette, S. Ray, 2012, The Journal of Immunology.

Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region

Yunfan Fan, Winston Timp, Michael C Schatz, 2020, medRxiv.

No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues

S. Ray, R. Gifford, S. Lytras, 2021, Proceedings of the National Academy of Sciences.

CD4+ T-Cell-Dependent Reduction in Hepatitis C Virus-Specific Neutralizing Antibody Responses After Coinfection With Human Immunodeficiency Virus.

S. Ray, S. Mehta, G. Kirk, 2015, The Journal of infectious diseases.

Needlestick transmission of hepatitis C.

S. Ray, M. Sulkowski, David L. Thomas, 2002, JAMA.

The transhepatic endotoxin gradient is present despite liver cirrhosis and is attenuated after transjugular portosystemic shunt (TIPS).

S. Ray, A. Lohse, C. Gaydos, 2011, BMC gastroenterology.

Antiretroviral therapy, interferon sensitivity, and virologic setpoint in human immunodeficiency virus/hepatitis C virus coinfected patients

S. Ray, L. Eldred, M. Sulkowski, 2014, Hepatology.

The Role of Viral Introductions in Sustaining Community-Based HIV Epidemics in Rural Uganda: Evidence from Spatial Clustering, Phylogenetics, and Egocentric Transmission Models

D. Cummings, O. Laeyendecker, J. Lessler, 2014, PLoS medicine.

Human Immunodeficiency Virus Seroconversion and Evolution of the Hepatitis C Virus Quasispecies

D. Vlahov, O. Laeyendecker, J. Ticehurst, 2001, Journal of Virology.

An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern

S. Ray, A. Pekosz, H. Mostafa, 2021, Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America.

Kupffer cells are depleted with HIV immunodeficiency and partially recovered with antiretroviral immune reconstitution

Richard D Moore, S. Ray, M. Torbenson, 2009, AIDS.

Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial.

Lei Wang, James P Hughes, Kenneth H Mayer, 2011, The Journal of infectious diseases.

Recrudescence of treated neurosyphilis in a patient with human immunodeficiency virus.

S. Ray, D. A. Dibbern, 1999, Mayo Clinic proceedings.

Spatiotemporal Phylodynamics of Hepatitis C Among People Who Inject Drugs in India

T. Quinn, S. Ray, P. Duggal, 2021, Hepatology.

Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms.

O. Laeyendecker, T. Quinn, S. Ray, 2011, AIDS research and human retroviruses.

Healthy donor T-cell responses to common cold coronaviruses and SARS-CoV-2.

O. Laeyendecker, J. Blankson, S. Ray, 2020, The Journal of clinical investigation.

S3 Details on Simulation and Experimental Methods S3.1 Simulating Cluster Expansion S3.2 Precision of Sclcm Measurements

A. Perelson, S. Ray, R. Ribeiro, 2022 .

Repeated exposure to heterologous hepatitis C viruses associates with enhanced neutralizing antibody breadth and potency

G. Shaw, S. Ray, Shuyi Wang, 2022, The Journal of clinical investigation.

Comprehensive genetic and epigenetic analysis of occult hepatitis B from liver tissue samples.

S. Ray, M. Torbenson, P. Vivekanandan, 2008, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Maternal Neutralizing Antibody and Transmission of HCV to her Infant

S. Ray, R. Hershow, D. Thomas, 2009 .

Maternal neutralizing antibody and transmission of hepatitis C virus to infants.

S. Ray, R. Hershow, David L. Thomas, 2008, The Journal of infectious diseases.

Genetic epidemiology of hepatitis C virus throughout egypt.

D L Thomas, J. Bukh, S. Ray, 2000, The Journal of infectious diseases.

Determinants of the quantity of hepatitis C virus RNA.

D. Vlahov, O. Laeyendecker, S. Ray, 2000, The Journal of infectious diseases.

156 – Hepatitis C

S. Ray, David L. Thomas, 2015 .

Immune evasion by hepatitis C virus NS3/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF.

Stanley M Lemon, Michael Gale, Masanori Ikeda, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Acute hepatitis C

S. Ray, Anurag Maheshwari, P. Thuluvath, 2008, The Lancet.

Spontaneous clearance of primary acute hepatitis C virus infection correlated with high initial viral RNA level and rapid HVR1 evolution

S. Ray, Brian E. Fisher, D. Thomas, 2012, Hepatology.

Cross-Genotype Immunity to Hepatitis C Virus

S. Ray, R. Lanford, David L. Thomas, 2004, Journal of Virology.

Protection against persistence of hepatitis C

D. Vlahov, S. Ray, D. Hoover, 2002, The Lancet.

Ecchymoses and eschars at sites of injection

S. Ray, D. Pan, K. Hsu., 1997, The Lancet.

PCR Detection of Adenovirus in a Bone Marrow Transplant Recipient: Hemorrhagic Cystitis as a Presenting Manifestation of Disseminated Disease

S. Ray, J. Dumler, R. Ambinder, 1999, Journal of Clinical Microbiology.

Characterization of novel recombinant HIV-1 genomes using the branching index.

Jan Albert, Mika Salminen, S. Ray, 2003, Virology.

Continued Production of Drug-Sensitive Human Immunodeficiency Virus Type 1 in Children on Combination Antiretroviral Therapy Who Have Undetectable Viral Loads

Thomas C. Quinn, Douglas C. Watson, Robert F. Siliciano, 2004, Journal of Virology.

Intermittent HIV-1 viremia (Blips) and drug resistance in patients receiving HAART.

Tara L. Kieffer, Joel E Gallant, Charles Flexner, 2005, JAMA.

Letter to the Editor: Genetic Linkage of Hepatitis B Virus in Peripheral Blood Leukocytes Provides Evidence for Contamination

S. Ray, C. Thio, 2010, Journal of Virology.

Genetic Linkage of Hepatitis B Virus in Peripheral Blood Leukocytes Provides Evidence for Contamination

S. Ray, C. Thio, 2010, Journal of Virology.

Human immunodeficiency virus-related microbial translocation and progression of hepatitis C.

S. Ray, T. Block, S. Mehta, 2008, Gastroenterology.

Accurate Representation of the Hepatitis C Virus Quasispecies in 5.2-Kilobase Amplicons

O. Laeyendecker, J. Ticehurst, S. Ray, 2004, Journal of Clinical Microbiology.

Genetic Divergence of Hepatitis C Virus: The Role of HIV-Related Immunosuppression

S. Ray, R. Klein, D. Netski, 2008, Journal of acquired immune deficiency syndromes.

Analyses of HIV-1 drug-resistance profiles among infected adolescents experiencing delayed antiretroviral treatment switch after initial nonsuppressive highly active antiretroviral therapy.

J. Lindsey, S. Ray, S. Spector, 2008, AIDS patient care and STDs.

Early archiving and predominance of nonnucleoside reverse transcriptase inhibitor-resistant HIV-1 among recently infected infants born in the United States.

S. Ray, M. Purswani, D. Persaud, 2007, The Journal of infectious diseases.

Acute Hepatitis C Virus Structural Gene Sequences as Predictors of Persistent Viremia: Hypervariable Region 1 as a Decoy

O. Laeyendecker, J. Ticehurst, S. Ray, 1999, Journal of Virology.

Determinants of Viral Clearance and Persistence during Acute Hepatitis C Virus Infection

F. Chisari, S. Ray, Kyong‐Mi Chang, 2001, The Journal of experimental medicine.

Expanded cellular clones carrying replication-competent HIV-1 persist, wax, and wane

Jeffrey M. Gerold, R. Siliciano, J. Siliciano, 2018, Proceedings of the National Academy of Sciences.

Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore–Washington metropolitan area

M. Schatz, J. Lessler, Melanie Kirsche, 2021, JCI insight.

High diversity of hepatitis C viral quasispecies is associated with early virological response in patients undergoing antiviral therapy

S. Ray, A. D. Di Bisceglie, Xiaofeng Fan, 2009, Hepatology.

Durable SARS-CoV-2 B cell immunity after mild or severe disease.

S. Ray, S. Klein, M. Betenbaugh, 2021, The Journal of clinical investigation.

Durable SARS-CoV-2 B cell immunity after mild or severe disease

S. Ray, S. Klein, M. Betenbaugh, 2020, medRxiv.

Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) exposure investigations using genomic sequencing among healthcare workers and patients in a large academic center

S. Cosgrove, S. Ray, H. Mostafa, 2022, Infection Control & Hospital Epidemiology.

Evolution of the HIV-1 nef gene in HLA-B*57 Positive Elite Suppressors

R. Siliciano, J. Blankson, S. Ray, 2010, Retrovirology.

Control of HIV-1 in Elite Suppressors despite Ongoing Replication and Evolution in Plasma Virus

R. Siliciano, J. Blankson, S. Ray, 2010, Journal of Virology.

Transmission of Human Immunodeficiency Virus Type 1 from a Patient Who Developed AIDS to an Elite Suppressor

R. Siliciano, J. Blankson, S. Ray, 2008, Journal of Virology.

Intracellular HIV-1 RNA and CD4+ T-cell activation in patients starting antiretrovirals

R. El-Diwany, J. Blankson, S. Ray, 2017, AIDS.

Divergent and convergent evolution after a common-source outbreak of hepatitis C virus

Stuart C. Ray, S. Ray, David L. Thomas, 2005, The Journal of experimental medicine.

Prospective Characterization of Full-Length Hepatitis C Virus NS5A Quasispecies during Induction and Combination Antiviral Therapy

S. Ray, S. Polyak, D. Gretch, 2000, Journal of Virology.

Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression

S. Ray, R. Viscidi, S C Ray, 1995, Journal of virology.

Progression of Fibrosis during Chronic Hepatitis C Is Associated with Rapid Virus Evolution

S. Ray, M. Torbenson, S. Mehta, 2007, Journal of Virology.

Cellular immune selection with hepatitis C virus persistence in humans

J. Sidney, A. Sette, S. Ray, 2005, The Journal of experimental medicine.

This information is current as Cognate Antigen during Chronic Infection Persistence and Require Preservation of Acute Infection Are Associated with Viral Hepatitis C Virus-Specific T Cells during High-Programmed Death-1 Levels on

S. Ray, A. Korman, D. Pardoll, 2013 .

Constraints on Viral Evolution during Chronic Hepatitis C Virus Infection Arising from a Common-Source Exposure

S. Ray, E. Kenny‐Walsh, L. Fanning, 2012, Journal of Virology.

Immunogenicity and Cross-Reactivity of a Representative Ancestral Sequence in Hepatitis C Virus Infection

J. Sidney, A. Sette, S. Ray, 2012, The Journal of Immunology.

Acceleration of Hepatitis C Virus Envelope Evolution in Humans Is Consistent with Progressive Humoral Immune Selection during the Transition from Acute to Chronic Infection

Stuart C. Ray, S. Ray, Brian E. Fisher, 2010, Journal of Virology.

High-Programmed Death-1 Levels on Hepatitis C Virus-Specific T Cells during Acute Infection Are Associated with Viral Persistence and Require Preservation of Cognate Antigen during Chronic Infection1

J. Sidney, A. Sette, S. Ray, 2008, The Journal of Immunology.

Cognate Antigen during Chronic Infection Persistence and Require Preservation of Acute Infection Are Associated with Viral Hepatitis C Virus-Specific T Cells during High-Programmed Death-1 Levels on Sette

J. Sidney, A. Sette, S. Ray, 2008 .

Comprehensive analyses of CD8+ T cell responses during longitudinal study of acute human hepatitis C

G. Lauer, S. Ray, D. Pardoll, 2005, Hepatology.

Residual Human Immunodeficiency Virus Type 1 Viremia in Some Patients on Antiretroviral Therapy Is Dominated by a Small Number of Invariant Clones Rarely Found in Circulating CD4+ T Cells

Claus O. Wilke, Thomas C. Quinn, Tara L. Kieffer, 2006, Journal of Virology.

A Novel Assay Allows Genotyping of the Latent Reservoir for Human Immunodeficiency Virus Type 1 in the Resting CD4+ T Cells of Viremic Patients

Thomas C. Quinn, Yan Zhou, Tara L. Kieffer, 2005, Journal of Virology.

Neutralizing Antibodies Do Not Mediate Suppression of Human Immunodeficiency Virus Type 1 in Elite Suppressors or Selection of Plasma Virus Variants in Patients on Highly Active Antiretroviral Therapy

Thomas C. Quinn, Robert F. Siliciano, Stuart C. Ray, 2006, Journal of Virology.

Plasma virome and the risk of blood-borne infection in persons with substance use disorder

W. Timp, S. Ray, K. Ghanem, 2021, Nature Communications.

Factors associated with phylogenetic clustering of hepatitis C among people who inject drugs in Baltimore

O. Laeyendecker, S. Ray, C. Latkin, 2020, BMC Infectious Diseases.

Diversity of hepatitis C virus infection among HIV-infected people who inject drugs in India

D. Boon, S. Ray, D. Persaud, 2019, VirusDisease.

Acute Hepatitis C Virus Infection Induces Consistent Changes in Circulating MicroRNAs That Are Associated with Nonlytic Hepatocyte Release

R. El-Diwany, S. Ray, K. Witwer, 2015, Journal of Virology.

Selection pressure from neutralizing antibodies drives sequence evolution during acute infection with hepatitis C virus.

S. Ray, Xiao-hong Wang, Andrea L Cox, 2009, Gastroenterology.

Computational Reconstruction of Bole1a, a Representative Synthetic Hepatitis C Virus Subtype 1a Genome

S. Ray, S. Munshaw, J. Bailey, 2012, Journal of Virology.

Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes

Alan S. Perelson, David L. Thomas, Ruy M. Ribeiro, 2014, PLoS Comput. Biol..

Use of laser capture microdissection to map hepatitis C virus-positive hepatocytes in human liver.

Frederik Graw, Ashwin Balagopal, A. Perelson, 2013, Gastroenterology.

Clearance of hepatitis C infection is associated with the early appearance of broad neutralizing antibody responses

S. Ray, David L. Thomas, J. Bailey, 2014, Hepatology.

Presence in India of HIV type 1 similar to North American strains.

T. Quinn, R. Bollinger, S. Ray, 1994, AIDS research and human retroviruses.

of Both Single-and Double-Stranded DNAs Complexity by Electrophoretic Mobilities Assessment of Hepatitis C Virus Sequence

O. Laeyendecker, S. Ray, Yu-ming Wang, 2014 .

Identification of Ongoing Human Immunodeficiency Virus Type 1 (HIV-1) Replication in Residual Viremia during Recombinant HIV-1 Poxvirus Immunizations in Patients with Clinically Undetectable Viral Loads on Durable Suppressive Highly Active Antiretroviral Therapy

T. Greenough, S. Ray, D. Persaud, 2009, Journal of Virology.

Slow human immunodeficiency virus type 1 evolution in viral reservoirs in infants treated with effective antiretroviral therapy.

S. Gange, T. Quinn, J. Casazza, 2007, AIDS research and human retroviruses.

Persistence of Wild-Type Virus and Lack of Temporal Structure in the Latent Reservoir for Human Immunodeficiency Virus Type 1 in Pediatric Patients with Extensive Antiretroviral Exposure

Thomas C. Quinn, Roxann Ashworth, Robert F. Siliciano, 2002, Journal of Virology.

Hypervariable Region 1 Sequence Stability during Hepatitis C Virus Replication in Chimpanzees

O. Laeyendecker, S. Ray, R. Lanford, 2000, Journal of Virology.

Assessment of Hepatitis C Virus Sequence Complexity by Electrophoretic Mobilities of Both Single-and Double-Stranded DNAs

Oliver Laeyendecker, Stuart C. Ray, John R. Ticehurst, 1998, Journal of Clinical Microbiology.

Broadly neutralizing antibodies with few somatic mutations and hepatitis C virus clearance.

G. Learn, G. Shaw, S. Ray, 2017, JCI insight.

Molecular Epidemiology of HIV-1 Subtypes in Southern China

S. Lai, O. Laeyendecker, T. Quinn, 2005, Journal of acquired immune deficiency syndromes.

Autologous strain-specific cytolytic T lymphocyte responses directed against human immunodeficiency virus type 1 Env.

R. Siliciano, R. Bollinger, S. Ray, 1998, AIDS research and human retroviruses.

Characterization of a polyclonal cytolytic T lymphocyte response to human immunodeficiency virus in persons without clinical progression.

R. Siliciano, T. Quinn, R. Bollinger, 1997, The Journal of infectious diseases.

G→A Hypermutation in Protease and Reverse Transcriptase Regions of Human Immunodeficiency Virus Type 1 Residing in Resting CD4+ T Cells In Vivo

Tara L. Kieffer, R. Siliciano, S. Ray, 2005, Journal of Virology.

Lens Free Holographic Imaging for Urinary Tract Infection Screening

Gregory N. McKay, Mason T. Chen, Nicholas J. Durr, 2022, IEEE Transactions on Biomedical Engineering.

Sex and the genetic diversity of HIV-1

T. Quinn, S. Ray, 2000, Nature Medicine.

Hepatitis C virus resistance to broadly neutralizing antibodies measured using replication-competent virus and pseudoparticles.

S. Ray, J. Bailey, Lisa N. Wasilewski, 2016, The Journal of general virology.

IgM autoantibodies recognizing ACE2 are associated with severe COVID-19

Jamie B. Spangler, S. Zeger, O. Laeyendecker, 2020, medRxiv.

Broadly Neutralizing Antibody Mediated Clearance of Human Hepatitis C Virus Infection.

G. Learn, G. Shaw, S. Ray, 2018, Cell host & microbe.

Convergent antibody responses are associated with broad neutralization of hepatitis C virus

K. Schuebel, S. Ray, J. Crowe, 2023, Frontiers in Immunology.

Identification of nevirapine-resistant HIV-1 in the latent reservoir after single-dose nevirapine to prevent mother-to-child transmission of HIV-1.

R. Siliciano, B. Lau, O. Laeyendecker, 2009, The Journal of infectious diseases.

Hepatitis C virus infection of neuroepithelioma cell lines.

S. Ray, J. McKeating, J. Neyts, 2010, Gastroenterology.

Severe pruritus after completing pegylated interferon for hepatitis C.

S. Ray, Chistopher J Hoffman, 2008, The AIDS reader.

Hepatitis C virus epitope exposure and neutralization by antibodies is affected by time and temperature.

D. Fremont, M. Diamond, J. Bukh, 2012, Virology.

A sensitive genotyping assay for detection of drug resistance mutations in reverse transcriptase of HIV-1 subtypes B and C in samples stored as dried blood spots or frozen RNA extracts.

S. Ray, W. Moss, D. Persaud, 2006, Journal of virological methods.

B cell overexpression of FCRL5 and PD-1 is associated with low antibody titers in HCV infection

S. Ray, P. Bjorkman, J. Crowe, 2022, PLoS pathogens.

Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and

S. Ray, J. Dumler, Y. Rikihisa, 2001, International journal of systematic and evolutionary microbiology.

Hepatitis C virus NS3 serine protease variability and evolution are strongly constrained by the need for structural and functional conservation

F. Penin, S. Ray, J. Pawlotsky, 2002 .

Acute hepatitis C

S. Ray, Anurag Maheshwari, P. Thuluvath, 2008, The Lancet.

Challenge Inoculum for Hepatitis C Virus Controlled Human Infection Model.

J. Bukh, T. Liang, S. Ray, 2023, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Oral antibiotic treatment of right-sided staphylococcal endocarditis in injection drug users: prospective randomized comparison with parenteral therapy.

C Flexner, Stephen D. Sisson, S. Goodman, 1996, The American journal of medicine.

Rapid and sensitive detection of viral nucleic acids using silicon microchips.

M. Fauvart, S. Ray, P. Fiorini, 2018, The Analyst.

S. Ray, J. Dumler, A. Barbet, 2001, International journal of systematic and evolutionary microbiology.