Jeffrey Martin, MD, MPH

Professor & Director UCSF TICR
M_Epidemiology & Biostatistics

Dr. Martin is Professor and Chief of the Division of Clinical Epidemiology and Health Services Research in the Department of Epidemiology and Biostatistics at the University of California, San Francisco (UCSF). His clinical training is in internal medicine and infectious diseases, and he has served as attending physician at the San Francisco General Hospital HIV/AIDS program clinic. He is formally trained in clinical and epidemiologic research methods at UC Berkeley, where he earned a master of public health degree with concentration in epidemiology. He is the former director of UCSF's Training in Clinical Research (TICR) program (https://ticr.ucsf.edu), in which he served as director of the UCSF Advanced Training in Clinical Research (ATCR) certificate program and founding director of the UCSF Master's Degree Program in Clinical Research. In the UCSF Graduate Division, Dr. Martin directs the foundational introductory course, Epidemiologic Methods (EPI 203). He is also one of the main architects of the epidemiology and biostatistics curriculum for the UCSF School of Medicine.

Dr. Martin's research methodology is best characterized as using the methods of epidemiology and biostatistics to derive biologic and clinical inferences. His substantive areas of interest are infectious diseases and cancer, with a special focus on HIV infection and its complications, notably Kaposi's sarcoma (KS), Kaposi's sarcoma–associated herpesvirus (KSHV) infection and cervical cancer. All of his work is collaborative and multidisciplinary; indeed, all of his projects are built specifically as robust platforms to support a variety of collaborative projects. Because of the compelling nature of the HIV epidemic in Africa, much of his work is centered there. In the COVID-19 era, Dr. Martin has pivoted some of his portfolio to focus on aspects of both acute-phase and post-acute phase of SARS-CoV-2 infection.

Dr. Martin's principal domestic research involves direction, along with Dr. Steven Deeks, of the NIH-sponsored Study of the Consequences of the Protease Inhibitor Era (SCOPE), a prospective cohort of HIV-infected adults. SCOPE was established to conduct translational research related to HIV, with the overarching objective to provide research access to a group of well-characterized, contemporary HIV-infected patients of diverse demographic and clinical status (https://cfar.ucsf.edu/cores/clinical-and-population-sciences). SCOPE, which contributes to the North American International Epidemiologic Databases to Evaluate AIDS (IeDEA) consortium, also serves as a fertile training ground, with many faculty members owning NIH K awards that depend on the cohort. Dr. Martin also directs the Specimen Core of the eight-site Center for AIDS Research Network of Integrated Clinical Systems (CNICS) Cohort (https://www.uab.edu/cnics). CNICS has documented the routine course of clinical care from over 40,000 HIV-infected adults and collected serial biological specimens from a large fraction. The Specimen Core supports projects which seek to discover causal or predictive determinants of various clinical phenotypes as well as to describe various human host or pathogen-related parameters in a large nationally representative in-care population. Most recently, Dr. Martin has contributed to the study of both the acute phase of SARS-CoV-2 infection (along with Dr. Dan Kelly of UCSF) and the post-acute phase (along with Drs. Deeks, Michael Peluso and other investigators of the NIH RECOVER Initiative).

In international research, Dr. Martin leads several NIH-sponsored ongoing projects in Africa. The first, performed in collaboration with the East Africa IeDEA network and Infectious Diseases Institute (IDI) in Uganda, is one of the first uses of rapid case ascertainment to study cancer in Africa. Dr. Martin’s group is performing RCA to study various aspects of Kaposi’s sarcoma, including incidence, pathway to diagnosis, stage of disease at diagnosis, and survival. The second project, in collaboration with Cornell University and the IDI, is developing a nucleic acid amplification-based device for the point-of-care diagnosis of KS. The work is slated to have field sites in Uganda, Kenya, Rwanda, Tanzania, Botswana, and Malawi. A third project, performed in collaboration with Duke University and the IDI, is developing a public health approach to the prevention and early detection of cervical cancer. This approach features community-based self-administered HPV screening and mobile treatment provision. A fourth project is the Uganda AIDS Rural Treatment Outcomes (UARTO) cohort, which followed 744 HIV-infected adults who initiated antiretroviral therapy in Mbarara, Uganda. Patterned after the SCOPE cohort, UARTO features rigorous research-level questionnaires and biological specimen collection; the focus is translational research. Finally, in Liberia, Dr. Martin and Dr. Krysia Lindan lead an NIH Fogarty International Center-sponsored training program in clinical and epidemiologic research in which Liberian scholars receive formal didactic training at UCSF and then perform mentored research in their home country.

Publications

SARS-CoV-2 infectious shedding and rebound among adults with and without oral antiviral use: two case-ascertained prospective household studies.

The Lancet. Microbe

Shah MM, Abedi GR, Lu S, Garcia-Knight M, Pineda-Ramirez J, Goldberg SA, Grijalva CG, Keipp Talbot H, Schmitz J, Lutrick K, Ellingson KD, Stockwell MS, Sano E, Nguyen HQ, Rao S, Asturias EJ, Suthar MS, Mellis AM, Deeks SG, Martin JN, Peluso MJ, Andino R, Rolfes MA, Kirking HL, Smith-Jeffcoat SE, Midgley CM, Hagen MB, Kelly JD, Respiratory Virus Transmission Network–Sentinel Study Group, UCSF FindCOVID Study Group

Long COVID trajectories in the prospectively followed RECOVER-Adult US cohort.

Nature communications

Thaweethai T, Donohue SE, Martin JN, Hornig M, Mosier JM, Shinnick DJ, Ashktorab H, Atieh O, Blomkalns A, Brim H, Chen Y, Cortez MM, Erdmann NB, Flaherman V, Goepfert P, Goldman JD, Hamburg NM, Han JE, Heath JR, Jacoby V, Jolley SE, Kelly JD, Kelly SW, Kim C, Krishnan JA, Letts R, Levitan EB, Modes ME, McComsey GA, Metz TD, Mullington JM, Ofotokun I, Okumura MJ, Paredes CC, Patterson TF, Peluso MJ, Reece R, Sherif ZA, Simhan HN, Simmons C, Singh U, Taylor BS, Taylor BD, Trinity JD, Troxel AB, Utz PJ, Vasey AJ, Weinberger E, Wiley Z, Wisnivesky J, Yee LM, Horwitz L, Foulkes AS, Levy BD, RECOVER-Adult Consortium

Changes in the Prevalence of Non-AIDS Conditions Among Hospitalized Persons With HIV in the United States and Canada, 2008-2018.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Davy-Mendez T, Napravnik S, Hogan BC, Eron JJ, Gebo KA, Althoff KN, Moore RD, Silverberg MJ, Horberg MA, Gill MJ, Colasanti JA, Nijhawan A, Karris MY, Klein MB, Lang R, Lesko CR, Yendewa GA, Kirk GD, McGinnis KA, Berry SA, North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of the International Epi

Olfactory Dysfunction After SARS-CoV-2 Infection in the RECOVER Adult Cohort.

JAMA network open

Horwitz LI, Becker JH, Huang W, Akintonwa T, Hornig-Rohan MM, Maranga G, Adams DR, Albers MW, Ayache M, Berry J, Brim H, Bryan TW, Charney AW, Clark RA, Cortez MM, D'Anza B, Davis H, Donohue SE, Erdmann N, Flaherman V, Fong TG, Frontera JA, Goldberg MP, Goldman JD, Harkins MS, Hodder SL, Jacoby VL, Jagannathan P, Jia X, Kelly JD, Krishnan JA, Kumar A, Laiyemo AO, Levitan EB, Martin JN, McCaffrey KM, McComsey GA, Metz TD, Murthy G, Nguyen H, Okumura M, Parry S, Parthasarathy S, Patterson TF, Peluso MJ, Sorochinsky C, Walker T, Wiegand SL, Wiley Z, Wisnivesky J, Ashktorab H, Foulkes A, Lee-Iannotti JK, Researching COVID to Enhance Recovery Consortium

Social Determinants of Health and Risk for Long COVID in the U.S. RECOVER-Adult Cohort.

Annals of internal medicine

Feldman CH, Santacroce L, Bassett IV, Thaweethai T, Alicic R, Atchley-Challenner R, Chung A, Goldberg MP, Horowitz CR, Jacobson KB, Kelly JD, Knight S, Lutrick K, Mudumbi P, Parthasarathy S, Prendergast H, Quintana Y, Sharareh N, Shellito J, Sherif ZA, Taylor BD, Taylor E, Tsevat J, Wiley Z, Williams NJ, Yee L, Aponte-Soto L, Baissary J, Berry J, Charney AW, Costantine MM, Duven AM, Erdmann N, Ernst KC, Feuerriegel EM, Flaherman VJ, Go M, Hawkins K, Jacoby V, John J, Kelly S, Kindred E, Laiyemo A, Levitan EB, Levy BD, Logue JK, Marathe JG, Martin JN, McComsey GA, Metz TD, Minor T, Montgomery AP, Mullington JM, Ofotokun I, Okumura MJ, Peluso MJ, Pogreba-Brown K, Raissy H, Rosas JM, Singh U, VanWagoner T, Clark CR, Karlson EW

Sex Differences in Long COVID.

JAMA network open

Shah DP, Thaweethai T, Karlson EW, Bonilla H, Horne BD, Mullington JM, Wisnivesky JP, Hornig M, Shinnick DJ, Klein JD, Erdmann NB, Brosnahan SB, Lee-Iannotti JK, Metz TD, Maughan C, Ofotokun I, Reeder HT, Stiles LE, Shaukat A, Hess R, Ashktorab H, Bartram L, Bassett IV, Becker JH, Brim H, Charney AW, Chopra T, Clifton RG, Deeks SG, Erlandson KM, Fierer DS, Flaherman VJ, Fonseca V, Gander JC, Hodder SL, Jacoby VL, Kotini-Shah P, Krishnan JA, Kumar A, Levy BD, Lieberman D, Lin JJ, Martin JN, McComsey GA, Moukabary T, Okumura MJ, Peluso MJ, Rosen CJ, Saade G, Shah PK, Sherif ZA, Taylor BS, Tuttle KR, Urdaneta AE, Wallick JA, Wiley Z, Zhang D, Horwitz LI, Foulkes AS, Singer NG, RECOVER Consortium

Measurement of circulating viral antigens post-SARS-CoV-2 infection in a multicohort study.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

Swank Z, Borberg E, Chen Y, Senussi Y, Chalise S, Manickas-Hill Z, Yu XG, Li JZ, Alter G, Henrich TJ, Kelly JD, Hoh R, Goldberg SA, Deeks SG, Martin JN, Peluso MJ, Talla A, Li X, Skene P, Bumol TF, Torgerson TR, Czartoski JL, McElrath MJ, Karlson EW, Walt DR, RECOVER consortium authors

Early biological markers of post-acute sequelae of SARS-CoV-2 infection.

Nature communications

Lu S, Peluso MJ, Glidden DV, Davidson MC, Lugtu K, Pineda-Ramirez J, Tassetto M, Garcia-Knight M, Zhang A, Goldberg SA, Chen JY, Fortes-Cobby M, Park S, Martinez A, So M, Donovan A, Viswanathan B, Hoh R, Donohue K, McIlwain DR, Gaudiliere B, Anglin K, Yee BC, Chenna A, Winslow JW, Petropoulos CJ, Deeks SG, Briggs-Hagen M, Andino R, Midgley CM, Martin JN, Saydah S, Kelly JD

Tissue-based T cell activation and viral RNA persist for up to 2 years after SARS-CoV-2 infection.

Science translational medicine

Peluso MJ, Ryder D, Flavell RR, Wang Y, Levi J, LaFranchi BH, Deveau TM, Buck AM, Munter SE, Asare KA, Aslam M, Koch W, Szabo G, Hoh R, Deswal M, Rodriguez AE, Buitrago M, Tai V, Shrestha U, Lu S, Goldberg SA, Dalhuisen T, Vasquez JJ, Durstenfeld MS, Hsue PY, Kelly JD, Kumar N, Martin JN, Gambhir A, Somsouk M, Seo Y, Deeks SG, Laszik ZG, VanBrocklin HF, Henrich TJ

Plasma-based antigen persistence in the post-acute phase of COVID-19.

The Lancet. Infectious diseases

Peluso MJ, Swank ZN, Goldberg SA, Lu S, Dalhuisen T, Borberg E, Senussi Y, Luna MA, Chang Song C, Clark A, Zamora A, Lew M, Viswanathan B, Huang B, Anglin K, Hoh R, Hsue PY, Durstenfeld MS, Spinelli MA, Glidden DV, Henrich TJ, Kelly JD, Deeks SG, Walt DR, Martin JN

Biological and Clinical Implications of the Vascular Endothelial Growth Factor Coreceptor Neuropilin-1 in Human Immunodeficiency Virus.

Open forum infectious diseases

Schnittman SR, Kolossváry M, Beck-Engeser G, Fitch KV, Ambayec GC, Nance RM, Zanni MV, Diggs M, Chan F, McCallum S, Toribio M, Bamford L, Fichtenbaum CJ, Eron JJ, Jacobson JM, Mayer KH, Malvestutto C, Bloomfield GS, Moore RD, Umbleja T, Saag MS, Aberg JA, Currier JS, Delaney JAC, Martin JN, Lu MT, Douglas PS, Ribaudo HJ, Crane HM, Hunt PW, Grinspoon SK

Multimodal Molecular Imaging Reveals Tissue-Based T Cell Activation and Viral RNA Persistence for Up to 2 Years Following COVID-19.

medRxiv : the preprint server for health sciences

Peluso MJ, Ryder D, Flavell R, Wang Y, Levi J, LaFranchi BH, Deveau TM, Buck AM, Munter SE, Asare KA, Aslam M, Koch W, Szabo G, Hoh R, Deswal M, Rodriguez A, Buitrago M, Tai V, Shrestha U, Lu S, Goldberg SA, Dalhuisen T, Durstenfeld MS, Hsue PY, Kelly JD, Kumar N, Martin JN, Gambir A, Somsouk M, Seo Y, Deeks SG, Laszik ZG, VanBrocklin HF, Henrich TJ

A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.

Nature

Augusto DG, Murdolo LD, Chatzileontiadou DSM, Sabatino JJ, Yusufali T, Peyser ND, Butcher X, Kizer K, Guthrie K, Murray VW, Pae V, Sarvadhavabhatla S, Beltran F, Gill GS, Lynch KL, Yun C, Maguire CT, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Vierra-Green CA, Spellman SR, Langton DJ, Dewar-Oldis MJ, Smith C, Barnard PJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Maiers M, Gras S, Hollenbach JA

Researching COVID to Enhance Recovery (RECOVER) adult study protocol: Rationale, objectives, and design.

PloS one

Horwitz LI, Thaweethai T, Brosnahan SB, Cicek MS, Fitzgerald ML, Goldman JD, Hess R, Hodder SL, Jacoby VL, Jordan MR, Krishnan JA, Laiyemo AO, Metz TD, Nichols L, Patzer RE, Sekar A, Singer NG, Stiles LE, Taylor BS, Ahmed S, Algren HA, Anglin K, Aponte-Soto L, Ashktorab H, Bassett IV, Bedi B, Bhadelia N, Bime C, Bind MC, Black LJ, Blomkalns AL, Brim H, Castro M, Chan J, Charney AW, Chen BK, Chen LQ, Chen P, Chestek D, Chibnik LB, Chow DC, Chu HY, Clifton RG, Collins S, Costantine MM, Cribbs SK, Deeks SG, Dickinson JD, Donohue SE, Durstenfeld MS, Emery IF, Erlandson KM, Facelli JC, Farah-Abraham R, Finn AV, Fischer MS, Flaherman VJ, Fleurimont J, Fonseca V, Gallagher EJ, Gander JC, Gennaro ML, Gibson KS, Go M, Goodman SN, Granger JP, Greenway FL, Hafner JW, Han JE, Harkins MS, Hauser KSP, Heath JR, Hernandez CR, Ho O, Hoffman MK, Hoover SE, Horowitz CR, Hsu H, Hsue PY, Hughes BL, Jagannathan P, James JA, John J, Jolley S, Judd SE, Juskowich JJ, Kanjilal DG, Karlson EW, Katz SD, Kelly JD, Kelly SW, Kim AY, Kirwan JP, Knox KS, Kumar A, Lamendola-Essel MF, Lanca M, Lee-Lannotti JK, Lefebvre RC, Levy BD, Lin JY, Logarbo BP, Logue JK, Longo MT, Luciano CA, Lutrick K, Malakooti SK, Mallett G, Maranga G, Marathe JG, Marconi VC, Marshall GD, Martin CF, Martin JN, May HT, McComsey GA, McDonald D, Mendez-Figueroa H, Miele L, Mittleman MA, Mohandas S, Mouchati C, Mullington JM, Nadkarni GN, Nahin ER, Neuman RB, Newman LT, Nguyen A, Nikolich JZ, Ofotokun I, Ogbogu PU, Palatnik A, Palomares KTS, Parimon T, Parry S, Parthasarathy S, Patterson TF, Pearman A, Peluso MJ, Pemu P, Pettker CM, Plunkett BA, Pogreba-Brown K, Poppas A, Porterfield JZ, Quigley JG, Quinn DK, Raissy H, Rebello CJ, Reddy UM, Reece R, Reeder HT, Rischard FP, Rosas JM, Rosen CJ, Rouphael NG, Rouse DJ, Ruff AM, Saint Jean C, Sandoval GJ, Santana JL, Schlater SM, Sciurba FC, Selvaggi C, Seshadri S, Sesso HD, Shah DP, Shemesh E, Sherif ZA, Shinnick DJ, Simhan HN, Singh U, Sowles A, Subbian V, Sun J, Suthar MS, Teunis LJ, Thorp JM, Ticotsky A, Tita ATN, Tragus R, Tuttle KR, Urdaneta AE, Utz PJ, VanWagoner TM, Vasey A, Vernon SD, Vidal C, Walker T, Ward HD, Warren DE, Weeks RM, Weiner SJ, Weyer JC, Wheeler JL, Whiteheart SW, Wiley Z, Williams NJ, Wisnivesky JP, Wood JC, Yee LM, Young NM, Zisis SN, Foulkes AS

Association of culturable-virus detection and household transmission of SARS-CoV-2 - California and Tennessee, 2020-2022.

The Journal of infectious diseases

Deyoe JE, Kelly JD, Grijalva CG, Bonenfant G, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Briggs Hagen M, Saydah S, Abedi GR, Goldberg SA, Tassetto M, Zhang A, Donohue KC, Davidson MC, Diaz Sanchez R, Djomaleu M, Mathur S, Shak JR, Deeks SG, Peluso MJ, Chiu CY, Zhu Y, Halasa NB, Chappell JD, Mellis A, Reed C, Andino R, Martin JN, Zhou B, Talbot HK, Midgley CM, Rolfes MA

Chronic viral coinfections differentially affect the likelihood of developing long COVID.

The Journal of clinical investigation

Peluso MJ, Deveau TM, Munter SE, Ryder D, Buck A, Beck-Engeser G, Chan F, Lu S, Goldberg SA, Hoh R, Tai V, Torres L, Iyer NS, Deswal M, Ngo LH, Buitrago M, Rodriguez A, Chen JY, Yee BC, Chenna A, Winslow JW, Petropoulos CJ, Deitchman AN, Hellmuth J, Spinelli MA, Durstenfeld MS, Hsue PY, Kelly JD, Martin JN, Deeks SG, Hunt PW, Henrich TJ

Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Nucleocapsid Antigen in the Blood as a Diagnostic Test for Infection and Infectious Viral Shedding.

Open forum infectious diseases

Mathur S, Davidson MC, Anglin K, Lu S, Goldberg SA, Garcia-Knight M, Tassetto M, Zhang A, Romero M, Pineda-Ramirez J, Diaz-Sanchez R, Rugart P, Chen JY, Donohue K, Shak JR, Chenna A, Winslow JW, Petropoulos CJ, Yee BC, Lambert J, Glidden DV, Rutherford GW, Deeks SG, Peluso MJ, Andino R, Martin JN, Kelly JD

Magnitude and determinants of SARS-CoV-2 household transmission: a longitudinal cohort study.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Daniel Kelly J, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Goldberg SA, Tassetto M, Zhang A, Donohue K, Davidson MC, Romero M, Sanchez RD, Djomaleu M, Mathur S, Chen JY, Forman CA, Servellita V, Montejano RD, Shak JR, Rutherford GW, Deeks SG, Abedi GR, Rolfes MA, Saydah S, Briggs-Hagen M, Peluso MJ, Chiu C, Midgley CM, Andino R, Martin JN

Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study.

PLoS pathogens

Garcia-Knight M, Anglin K, Tassetto M, Lu S, Zhang A, Goldberg SA, Catching A, Davidson MC, Shak JR, Romero M, Pineda-Ramirez J, Diaz-Sanchez R, Rugart P, Donohue K, Massachi J, Sans HM, Djomaleu M, Mathur S, Servellita V, McIlwain D, Gaudiliere B, Chen J, Martinez EO, Tavs JM, Bronstone G, Weiss J, Watson JT, Briggs-Hagen M, Abedi GR, Rutherford GW, Deeks SG, Chiu C, Saydah S, Peluso MJ, Midgley CM, Martin JN, Andino R, Kelly JD

Current Antiretroviral Treatment Among People With Human Immunodeficiency Virus in the United States: Findings from the Centers for AIDS Research Network of Integrated Clinic Systems Cohort.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Ma J, Nance RM, Delaney JAC, Whitney BM, Bamford L, Gravett RM, Moore RD, Napravnik S, Mayer KH, Jacobson JM, Christopoulos K, Burkholder GA, Keruly J, Eron JJ, Martin J, Cachay ER, Saag MS, Crane HM, Kitahata MM

Racial and ethnic disparities in coronavirus disease 2019 disease incidence independent of comorbidities, among people with HIV in the United States.

AIDS (London, England)

Bender Ignacio RA, Shapiro AE, Nance RM, Whitney BM, Delaney JAC, Bamford L, Wooten D, Karris MY, Mathews WC, Kim HN, Keruly J, Burkholder G, Napravnik S, Mayer KH, Jacobson J, Saag M, Moore RD, Eron JJ, Willig AL, Christopoulos KA, Martin J, Hunt PW, Crane HM, Kitahata MM, Cachay ER, Centers for AIDS Research Network of Integrated Clinical Systems (CNICS)

Persistence, Magnitude, and Patterns of Postacute Symptoms and Quality of Life Following Onset of SARS-CoV-2 Infection: Cohort Description and Approaches for Measurement.

Open forum infectious diseases

Peluso MJ, Kelly JD, Lu S, Goldberg SA, Davidson MC, Mathur S, Durstenfeld MS, Spinelli MA, Hoh R, Tai V, Fehrman EA, Torres L, Hernandez Y, Williams MC, Arreguin MI, Ngo LH, Deswal M, Munter SE, Martinez EO, Anglin KA, Romero MD, Tavs J, Rugart PR, Chen JY, Sans HM, Murray VW, Ellis PK, Donohue KC, Massachi JA, Weiss JO, Mehdi I, Pineda-Ramirez J, Tang AF, Wenger MA, Assenzio MT, Yuan Y, Krone MR, Rutishauser RL, Rodriguez-Barraquer I, Greenhouse B, Sauceda JA, Gandhi M, Scheffler AW, Hsue PY, Henrich TJ, Deeks SG, Martin JN

SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay.

Science advances

Peluso MJ, Takahashi S, Hakim J, Kelly JD, Torres L, Iyer NS, Turcios K, Janson O, Munter SE, Thanh C, Donatelli J, Nixon CC, Hoh R, Tai V, Fehrman EA, Hernandez Y, Spinelli MA, Gandhi M, Palafox MA, Vallari A, Rodgers MA, Prostko J, Hackett J, Trinh L, Wrin T, Petropoulos CJ, Chiu CY, Norris PJ, DiGermanio C, Stone M, Busch MP, Elledge SK, Zhou XX, Wells JA, Shu A, Kurtz TW, Pak JE, Wu W, Burbelo PD, Cohen JI, Rutishauser RL, Martin JN, Deeks SG, Henrich TJ, Rodriguez-Barraquer I, Greenhouse B

Rapid implementation of a cohort for the study of post-acute sequelae of SARS-CoV-2 infection/COVID-19.

medRxiv : the preprint server for health sciences

Peluso MJ, Kelly JD, Lu S, Goldberg SA, Davidson MC, Mathur S, Durstenfeld MS, Spinelli MA, Hoh R, Tai V, Fehrman EA, Torres L, Hernandez Y, Williams MC, Arreguin MI, Bautista JA, Ngo LH, Deswal M, Munter SE, Martinez EO, Anglin KA, Romero MD, Tavs J, Rugart PR, Chen JY, Sans HM, Murray VW, Ellis PK, Donohue KC, Massachi JA, Weiss JO, Mehdi I, Pineda-Ramirez J, Tang AF, Wenger M, Assenzio M, Yuan Y, Krone M, Rutishauser RL, Rodriguez-Barraquer I, Greenhouse B, Sauceda JA, Gandhi M, Hsue PY, Henrich TJ, Deeks SG, Martin JN

SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay.

medRxiv : the preprint server for health sciences

Peluso MJ, Takahashi S, Hakim J, Kelly JD, Torres L, Iyer NS, Turcios K, Janson O, Munter SE, Thanh C, Nixon CC, Hoh R, Tai V, Fehrman EA, Hernandez Y, Spinelli MA, Gandhi M, Palafox MA, Vallari A, Rodgers MA, Prostko J, Hackett J, Trinh L, Wrin T, Petroplolous CJ, Chiu CY, Norris PJ, DiGermanio C, Stone M, Busch MP, Elledge SK, Zhou XX, Wells JA, Shu A, Kurtz TW, Pak JE, Wu W, Burbelo PD, Cohen JI, Rutishauser RL, Martin JN, Deeks SG, Henrich TJ, Rodriguez-Barraquer I, Greenhouse B

Long-Term SARS-CoV-2-Specific Immune and Inflammatory Responses Across a Clinically Diverse Cohort of Individuals Recovering from COVID-19.

medRxiv : the preprint server for health sciences

Peluso MJ, Deitchman AN, Torres L, Iyer NS, Nixon CC, Munter SE, Donatelli J, Thanh C, Takahashi S, Hakim J, Turcios K, Janson O, Hoh R, Tai V, Hernandez Y, Fehrman E, Spinelli MA, Gandhi M, Trinh L, Wrin T, Petropoulos CJ, Aweeka FT, Rodriguez-Barraquer I, Kelly JD, Martin JN, Deeks SG, Greenhouse B, Rutishauser RL, Henrich TJ

TCF-1 regulates HIV-specific CD8+ T cell expansion capacity.

JCI insight

Rutishauser RL, Deguit CDT, Hiatt J, Blaeschke F, Roth TL, Wang L, Raymond KA, Starke CE, Mudd JC, Chen W, Smullin CP, Matus-Nicodemos R, Hoh R, Krone MR, Hecht FM, Pilcher CD, Martin JN, Koup RA, Douek DC, Brenchley JM, Sékaly RP, Pillai SK, Marson A, Deeks SG, McCune JM, Hunt PW

Kaposi sarcoma.

Nature reviews. Disease primers

Cesarman E, Damania B, Krown SE, Martin J, Bower M, Whitby D

HLA-C downregulation by HIV-1 adapts to host HLA genotype.

PLoS pathogens

Bachtel ND, Umviligihozo G, Pickering S, Mota TM, Liang H, Del Prete GQ, Chatterjee P, Lee GQ, Thomas R, Brockman MA, Neil S, Carrington M, Bwana B, Bangsberg DR, Martin JN, Kallas EG, Donini CS, Cerqueira NB, O'Doherty UT, Hahn BH, Jones RB, Brumme ZL, Nixon DF, Apps R

Mast Cell Activation and KSHV Infection in Kaposi Sarcoma.

Clinical cancer research : an official journal of the American Association for Cancer Research

Ayers LW, Barbachano-Guerrero A, McAllister SC, Ritchie JA, Asiago-Reddy E, Bartlett LC, Cesarman E, Wang D, Rochford R, Martin JN, King CA

As-Needed Vs Immediate Etoposide Chemotherapy in Combination With Antiretroviral Therapy for Mild-to-Moderate AIDS-Associated Kaposi Sarcoma in Resource-Limited Settings: A5264/AMC-067 Randomized Clinical Trial.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Hosseinipour MC, Kang M, Krown SE, Bukuru A, Umbleja T, Martin JN, Orem J, Godfrey C, Hoagland B, Mwelase N, Langat D, Nyirenda M, MacRae J, Borok M, Samaneka W, Moses A, Mngqbisa R, Busakhala N, Martínez-Maza O, Ambinder R, Dittmer DP, Nokta M, Campbell TB

Differential Immunodominance Hierarchy of CD8+ T-Cell Responses in HLA-B*27:05- and -B*27:02-Mediated Control of HIV-1 Infection.

Journal of virology

Adland E, Hill M, Lavandier N, Csala A, Edwards A, Chen F, Radkowski M, Kowalska JD, Paraskevis D, Hatzakis A, Valenzuela-Ponce H, Pfafferott K, Williams I, Pellegrino P, Borrow P, Mori M, Rockstroh J, Prado JG, Mothe B, Dalmau J, Martinez-Picado J, Tudor-Williams G, Frater J, Stryhn A, Buus S, Teran GR, Mallal S, John M, Buchbinder S, Kirk G, Martin J, Michael N, Fellay J, Deeks S, Walker B, Avila-Rios S, Cole D, Brander C, Carrington M, Goulder P

Increased Risk of Myocardial Infarction in HIV-Infected Individuals in North America Compared With the General Population.

Journal of acquired immune deficiency syndromes (1999)

Drozd DR, Kitahata MM, Althoff KN, Zhang J, Gange SJ, Napravnik S, Burkholder GA, Mathews WC, Silverberg MJ, Sterling TR, Heckbert SR, Budoff MJ, Van Rompaey S, Delaney JAC, Wong C, Tong W, Palella FJ, Elion RA, Martin JN, Brooks JT, Jacobson LP, Eron JJ, Justice AC, Freiberg MS, Klein DB, Post WS, Saag MS, Moore RD, Crane HM

The Causal Effect of Tracing by Peer Health Workers on Return to Clinic Among Patients Who Were Lost to Follow-up From Antiretroviral Therapy in Eastern Africa: A "Natural Experiment" Arising From Surveillance of Lost Patients.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Bershetyn A, Odeny TA, Lyamuya R, Nakiwogga-Muwanga A, Diero L, Bwana M, Braitstein P, Somi G, Kambugu A, Bukusi E, Hartogensis W, Glidden DV, Wools-Kaloustian K, Yiannoutsos C, Martin J, Geng EH

Epigenetic mechanisms, T-cell activation, and CCR5 genetics interact to regulate T-cell expression of CCR5, the major HIV-1 coreceptor.

Proceedings of the National Academy of Sciences of the United States of America

Gornalusse GG, Mummidi S, Gaitan AA, Jimenez F, Ramsuran V, Picton A, Rogers K, Manoharan MS, Avadhanam N, Murthy KK, Martinez H, Molano Murillo A, Chykarenko ZA, Hutt R, Daskalakis D, Shostakovich-Koretskaya L, Abdool Karim S, Martin JN, Deeks SG, Hecht F, Sinclair E, Clark RA, Okulicz J, Valentine FT, Martinson N, Tiemessen CT, Ndung'u T, Hunt PW, He W, Ahuja SK

CD41 T cell recovery during suppression of HIV replication: an international comparison of the immunological efficacy of antiretroviral therapy in North America, Asia and Africa.

International journal of epidemiology

Geng EH, Neilands TB, Thièbaut R, Bwana MB, Nash D, Moore RD, Wood R, Zannou DM, Althoff KN, Lim PL, Nachega JB, Easterbrook PJ, Kambugu A, Little F, Nakigozi G, Nakanjako D, Kiggundu V, Ki Li PC, Bangsberg DR, Fox MP, Prozesky H, Hunt PW, Davies MA, Reynolds SJ, Egger M, Yiannoutsos CT, Vittinghoff EV, Deeks SG, Martin JN

Trends and disparities in antiretroviral therapy initiation and virologic suppression among newly treatment-eligible HIV-infected individuals in North America, 2001-2009.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Hanna DB, Buchacz K, Gebo KA, Hessol NA, Horberg MA, Jacobson LP, Kirk GD, Kitahata MM, Korthuis PT, Moore RD, Napravnik S, Patel P, Silverberg MJ, Sterling TR, Willig JH, Lau B, Althoff KN, Crane HM, Collier AC, Samji H, Thorne JE, Gill MJ, Klein MB, Martin JN, Rodriguez B, Rourke SB, Gange SJ

Risk of anal cancer in HIV-infected and HIV-uninfected individuals in North America.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Silverberg MJ, Lau B, Justice AC, Engels E, Gill MJ, Goedert JJ, Kirk GD, D'Souza G, Bosch RJ, Brooks JT, Napravnik S, Hessol NA, Jacobson LP, Kitahata MM, Klein MB, Moore RD, Rodriguez B, Rourke SB, Saag MS, Sterling TR, Gebo KA, Press N, Martin JN, Dubrow R

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation.

Science (New York, N.Y.)

Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Ripke S, Brumme CJ, Pulit SL, Carrington M, Kadie CM, Carlson JM, Heckerman D, Graham RR, Plenge RM, Deeks SG, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Gao X, Qi Y, Yuki Y, Piechocka-Trocha A, Cutrell E, Rosenberg R, Moss KL, Lemay P, O'Leary J, Schaefer T, Verma P, Toth I, Block B, Baker B, Rothchild A, Lian J, Proudfoot J, Alvino DM, Vine S, Addo MM, Allen TM, Altfeld M, Henn MR, Le Gall S, Streeck H, Haas DW, Kuritzkes DR, Robbins GK, Shafer RW, Gulick RM, Shikuma CM, Haubrich R, Riddler S, Sax PE, Daar ES, Ribaudo HJ, Agan B, Agarwal S, Ahern RL, Allen BL, Altidor S, Altschuler EL, Ambardar S, Anastos K, Anderson B, Anderson V, Andrady U, Antoniskis D, Bangsberg D, Barbaro D, Barrie W, Bartczak J, Barton S, Basden P, Basgoz N, Bazner S, Bellos NC, Benson AM, Berger J, Bernard NF, Bernard AM, Birch C, Bodner SJ, Bolan RK, Boudreaux ET, Bradley M, Braun JF, Brndjar JE, Brown SJ, Brown K, Brown ST, Burack J, Bush LM, Cafaro V, Campbell O, Campbell J, Carlson RH, Carmichael JK, Casey KK, Cavacuiti C, Celestin G, Chambers ST, Chez N, Chirch LM, Cimoch PJ, Cohen D, Cohn LE, Conway B, Cooper DA, Cornelson B, Cox DT, Cristofano MV, Cuchural G, Czartoski JL, Dahman JM, Daly JS, Davis BT, Davis K, Davod SM, DeJesus E, Dietz CA, Dunham E, Dunn ME, Ellerin TB, Eron JJ, Fangman JJ, Farel CE, Ferlazzo H, Fidler S, Fleenor-Ford A, Frankel R, Freedberg KA, French NK, Fuchs JD, Fuller JD, Gaberman J, Gallant JE, Gandhi RT, Garcia E, Garmon D, Gathe JC, Gaultier CR, Gebre W, Gilman FD, Gilson I, Goepfert PA, Gottlieb MS, Goulston C, Groger RK, Gurley TD, Haber S, Hardwicke R, Hardy WD, Harrigan PR, Hawkins TN, Heath S, Hecht FM, Henry WK, Hladek M, Hoffman RP, Horton JM, Hsu RK, Huhn GD, Hunt P, Hupert MJ, Illeman ML, Jaeger H, Jellinger RM, John M, Johnson JA, Johnson KL, Johnson H, Johnson K, Joly J, Jordan WC, Kauffman CA, Khanlou H, Killian RK, Kim AY, Kim DD, Kinder CA, Kirchner JT, Kogelman L, Kojic EM, Korthuis PT, Kurisu W, Kwon DS, LaMar M, Lampiris H, Lanzafame M, Lederman MM, Lee DM, Lee JM, Lee MJ, Lee ET, Lemoine J, Levy JA, Llibre JM, Liguori MA, Little SJ, Liu AY, Lopez AJ, Loutfy MR, Loy D, Mohammed DY, Man A, Mansour MK, Marconi VC, Markowitz M, Marques R, Martin JN, Martin HL, Mayer KH, McElrath MJ, McGhee TA, McGovern BH, McGowan K, McIntyre D, Mcleod GX, Menezes P, Mesa G, Metroka CE, Meyer-Olson D, Miller AO, Montgomery K, Mounzer KC, Nagami EH, Nagin I, Nahass RG, Nelson MO, Nielsen C, Norene DL, O'Connor DH, Ojikutu BO, Okulicz J, Oladehin OO, Oldfield EC, Olender SA, Ostrowski M, Owen WF, Pae E, Parsonnet J, Pavlatos AM, Perlmutter AM, Pierce MN, Pincus JM, Pisani L, Price LJ, Proia L, Prokesch RC, Pujet HC, Ramgopal M, Rathod A, Rausch M, Ravishankar J, Rhame FS, Richards CS, Richman DD, Rodes B, Rodriguez M, Rose RC, Rosenberg ES, Rosenthal D, Ross PE, Rubin DS, Rumbaugh E, Saenz L, Salvaggio MR, Sanchez WC, Sanjana VM, Santiago S, Schmidt W, Schuitemaker H, Sestak PM, Shalit P, Shay W, Shirvani VN, Silebi VI, Sizemore JM, Skolnik PR, Sokol-Anderson M, Sosman JM, Stabile P, Stapleton JT, Starrett S, Stein F, Stellbrink HJ, Sterman FL, Stone VE, Stone DR, Tambussi G, Taplitz RA, Tedaldi EM, Telenti A, Theisen W, Torres R, Tosiello L, Tremblay C, Tribble MA, Trinh PD, Tsao A, Ueda P, Vaccaro A, Valadas E, Vanig TJ, Vecino I, Vega VM, Veikley W, Wade BH, Walworth C, Wanidworanun C, Ward DJ, Warner DA, Weber RD, Webster D, Weis S, Wheeler DA, White DJ, Wilkins E, Winston A, Wlodaver CG, van't Wout A, Wright DP, Yang OO, Yurdin DL, Zabukovic BW, Zachary KC, Zeeman B, Zhao M

Late presentation for human immunodeficiency virus care in the United States and Canada.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Althoff KN, Gange SJ, Klein MB, Brooks JT, Hogg RS, Bosch RJ, Horberg MA, Saag MS, Kitahata MM, Justice AC, Gebo KA, Eron JJ, Rourke SB, Gill MJ, Rodriguez B, Sterling TR, Calzavara LM, Deeks SG, Martin JN, Rachlis AR, Napravnik S, Jacobson LP, Kirk GD, Collier AC, Benson CA, Silverberg MJ, Kushel M, Goedert JJ, McKaig RG, Van Rompaey SE, Zhang J, Moore RD

Trends in multidrug treatment failure and subsequent mortality among antiretroviral therapy-experienced patients with HIV infection in North America.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Deeks SG, Gange SJ, Kitahata MM, Saag MS, Justice AC, Hogg RS, Eron JJ, Brooks JT, Rourke SB, Gill MJ, Bosch RJ, Benson CA, Collier AC, Martin JN, Klein MB, Jacobson LP, Rodriguez B, Sterling TR, Kirk GD, Napravnik S, Rachlis AR, Calzavara LM, Horberg MA, Silverberg MJ, Gebo KA, Kushel MB, Goedert JJ, McKaig RG, Moore RD

Effect of early versus deferred antiretroviral therapy for HIV on survival.

The New England journal of medicine

Kitahata MM, Gange SJ, Abraham AG, Merriman B, Saag MS, Justice AC, Hogg RS, Deeks SG, Eron JJ, Brooks JT, Rourke SB, Gill MJ, Bosch RJ, Martin JN, Klein MB, Jacobson LP, Rodriguez B, Sterling TR, Kirk GD, Napravnik S, Rachlis AR, Calzavara LM, Horberg MA, Silverberg MJ, Gebo KA, Goedert JJ, Benson CA, Collier AC, Van Rompaey SE, Crane HM, McKaig RG, Lau B, Freeman AM, Moore RD