Sydney Ramirez

Title(s)	Postdoctoral Scholar, Medicine
School	Vc-health Sciences-schools
Address	9500 Gilman Drive # La Jolla CA 92093
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Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.

SARS-CoV-2 monoclonal antibody treatment followed by vaccination shifts human memory B cell epitope recognition suggesting antibody feedback. bioRxiv. 2023 Nov 22. Coelho CH, Bloom N, Ramirez SI, Parikh UM, Heaps A, Sieg SF, Greninger A, Ritz J, Moser C, Eron JJ, Currier JS, Klekotka P, Wohl DA, Daar ES, Li J, Hughes MD, Chew KW, Smith DM, Crotty S, Accelerating COVID-19 Therapeutic Interventions and Vaccines–2/A5401 (ACTIV-2/A5401) Study Team. PMID: 38045374; PMCID: PMC10690233.

View in: PubMed Mentions:
YAP-Driven Malignant Reprogramming of Epithelial Stem Cells at Single Cell Resolution. Res Sq. 2023 Oct 27. Gutkind JS, Faraji F, Ramirez S, Clubb L, Sato K, Quiroz PA, Galloway W, Mikulski Z, Hoang T, Medetgul-Ernar K, Marangoni P, Jones K, Officer A, Molinolo A, Kim K, Sakaguchi K, Califano J, Smith Q, Klein O, Tamayo P. PMID: 37961717; PMCID: PMC10635308.

View in: PubMed Mentions:
Early antiviral CD4 and CD8 T cell responses are associated with upper respiratory tract clearance of SARS-CoV-2. bioRxiv. 2023 Oct 26. Ramirez SI, Lopez PG, Faraji F, Parikh UM, Heaps A, Ritz J, Moser C, Eron JJ, Wohl DA, Currier JS, Daar ES, Greninger AL, Klekotka P, Grifoni A, Weiskopf D, Sette A, Peters B, Hughes MD, Chew KW, Smith DM, Crotty S, ACTIV-2/A5401 Study Team. PMID: 37961119; PMCID: PMC10634820.

View in: PubMed Mentions:
High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma. Cell Rep Med. 2023 11 21; 4(11):101244. Arang N, Lubrano S, Ceribelli M, Rigiracciolo DC, Saddawi-Konefka R, Faraji F, Ramirez SI, Kim D, Tosto FA, Stevenson E, Zhou Y, Wang Z, Bogomolovas J, Molinolo AA, Swaney DL, Krogan NJ, Yang J, Coma S, Pachter JA, Aplin AE, Alessi DR, Thomas CJ, Gutkind JS. PMID: 37858338; PMCID: PMC10694608.

View in: PubMed Mentions: 1 Fields:
Med Medicine (General)
Translation:Animals
Direct reprogramming of oral epithelial progenitor cells to cancer stem cells at single cell resolution in vivo. bioRxiv. 2023 Jul 26. Faraji F, Ramirez SI, Clubb LM, Sato K, Quiroz PYA, Galloway WMG, Mikulski Z, Hoang TS, Medetgul-Ernar K, Marangoni P, Jones KB, Officer A, Molinolo AA, Kim K, Sakaguchi K, Califano JA, Smith Q, Klein OD, Tamayo P, Gutkind JS. PMID: 37546810; PMCID: PMC10402053.

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Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients. Cell Rep Med. 2023 02 21; 4(2):100935. Lam MTY, Duttke SH, Odish MF, Le HD, Hansen EA, Nguyen CT, Trescott S, Kim R, Deota S, Chang MW, Patel A, Hepokoski M, Alotaibi M, Rolfsen M, Perofsky K, Warden AS, Foley J, Ramirez SI, Dan JM, Abbott RK, Crotty S, Crotty Alexander LE, Malhotra A, Panda S, Benner CW, Coufal NG. PMID: 36758547; PMCID: PMC9874047.

View in: PubMed Mentions: 2 Fields:
Med Medicine (General)
Translation:Humans Cells
Bamlanivimab therapy for acute COVID-19 does not blunt SARS-CoV-2-specific memory T cell responses. JCI Insight. 2022 12 22; 7(24). Ramirez SI, Grifoni A, Weiskopf D, Parikh UM, Heaps A, Faraji F, Sieg SF, Ritz J, Moser C, Eron JJ, Currier JS, Klekotka P, Sette A, Wohl DA, Daar ES, Hughes MD, Chew KW, Smith DM, Crotty S, Accelerating COVID-19 Therapeutic Interventions and Vaccines–2/A5401 (ACTIV-2/A5401) Study Team. PMID: 36378539; PMCID: PMC9869965.

View in: PubMed Mentions: 2 Fields:
Med Medicine (General)
Translation:Humans Cells
Correction to: Increased Peripheral Blood Neutrophil Activation Phenotypes and Neutrophil Extracellular Trap Formation in Critically Ill Coronavirus Disease 2019 Patients: A Case Series and Review of the Literature. Clin Infect Dis. 2022 May 30; 74(10):1889-1890. Masso-Silva JA, Moshensky A, Lam MTY, Odish M, Patel A, Xu L, Hansen E, Trescott S, Nguyen C, Kim R, Perofsky K, Perera S, Ma L, Pham J, Rolfsen M, Olay J, Shin J, Dan JM, Abbott R, Ramirez S, Alexander TH, Lin GY, Fuentes AL, Advani I, Gunge D, Pretorius V, Malhotra A, Sun X, Duran J, Hepokoski M, Crotty S, Coufal NG, Meier A, Crotty Alexander LE. PMID: 35416961; PMCID: PMC9327099.

View in: PubMed Mentions: 4 Fields:
Com Communicable Diseases
Genomic Hippo Pathway Alterations and Persistent YAP/TAZ Activation: New Hallmarks in Head and Neck Cancer. Cells. 2022 04 18; 11(8). Faraji F, Ramirez SI, Anguiano Quiroz PY, Mendez-Molina AN, Gutkind JS. PMID: 35456049; PMCID: PMC9028246.

View in: PubMed Mentions: 12 Fields:
Bio Biophysics Cel Cell Biology Mol Molecular Biology
Translation:Humans Animals Cells
Increased Peripheral Blood Neutrophil Activation Phenotypes and Neutrophil Extracellular Trap Formation in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients: A Case Series and Review of the Literature. Clin Infect Dis. 2022 02 11; 74(3):479-489. Masso-Silva JA, Moshensky A, Lam MTY, Odish MF, Patel A, Xu L, Hansen E, Trescott S, Nguyen C, Kim R, Perofsky K, Perera S, Ma L, Pham J, Rolfsen M, Olay J, Shin J, Dan JM, Abbott RK, Ramirez S, Alexander TH, Lin GY, Fuentes AL, Advani I, Gunge D, Pretorius V, Malhotra A, Sun X, Duran J, Hepokoski M, Crotty S, Coufal NG, Meier A, Crotty Alexander LE. PMID: 33988226; PMCID: PMC8241438.

View in: PubMed Mentions: 60 Fields:
Com Communicable Diseases
Translation:Humans Cells
Development of a T cell-based immunodiagnostic system to effectively distinguish SARS-CoV-2 infection and COVID-19 vaccination status. Cell Host Microbe. 2022 03 09; 30(3):388-399.e3. Yu ED, Wang E, Garrigan E, Goodwin B, Sutherland A, Tarke A, Chang J, Gálvez RI, Mateus J, Ramirez SI, Rawlings SA, Smith DM, Filaci G, Frazier A, Weiskopf D, Dan JM, Crotty S, Grifoni A, Sette A, da Silva Antunes R. PMID: 35172129; PMCID: PMC8824221.

View in: PubMed Mentions: 20 Fields:
Mic Microbiology
Translation:Humans Cells PHPublic Health
Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19. bioRxiv. 2021 Aug 24. Lam MTY, Duttke SH, Odish MF, Le HD, Hansen EA, Nguyen CT, Trescott S, Kim R, Deota S, Chang MW, Patel A, Hepokoski M, Alotaibi M, Rolfsen M, Perofsky K, Warden AS, Foley J, Ramirez SI, Dan JM, Abbott RK, Crotty S, Crotty Alexander LE, Malhotra A, Panda S, Benner CW, Coufal NG. PMID: 34462742; PMCID: PMC8404884.

View in: PubMed Mentions: 3
Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals. Cell Rep Med. 2021 07 20; 2(7):100355. Tarke A, Sidney J, Methot N, Yu ED, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, Wang E, Frazier A, Ramirez SI, Rawlings SA, Smith DM, da Silva Antunes R, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A. PMID: 34230917; PMCID: PMC8249675.

View in: PubMed Mentions: 338 Fields:
Med Medicine (General)
Translation:Humans Cells
AI-guided discovery of the invariant host response to viral pandemics. EBioMedicine. 2021 Jun; 68:103390. Sahoo D, Katkar GD, Khandelwal S, Behroozikhah M, Claire A, Castillo V, Tindle C, Fuller M, Taheri S, Rogers TF, Beutler N, Ramirez SI, Rawlings SA, Pretorius V, Smith DM, Burton DR, Alexander LEC, Duran J, Crotty S, Dan JM, Das S, Ghosh P. PMID: 34127431; PMCID: PMC8193764.

View in: PubMed Mentions: 22 Fields:
Gen Genetics Med Medicine (General)
Translation:Humans Animals PHPublic Health
AI-guided discovery of the invariant host response to viral pandemics. bioRxiv. 2021 Apr 13. Sahoo D, Katkar GD, Khandelwal S, Behroozikhah M, Claire A, Castillo V, Tindle C, Fuller M, Taheri S, Rogers TF, Beutler N, Ramirez SI, Rawlings SA, Pretorius V, Smith DM, Burton DR, Alexander LEC, Duran J, Crotty S, Dan JM, Das S, Ghosh P. PMID: 32995790; PMCID: PMC7523116.

View in: PubMed Mentions:
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. Cell Rep Med. 2021 02 16; 2(2):100204. Tarke A, Sidney J, Kidd CK, Dan JM, Ramirez SI, Yu ED, Mateus J, da Silva Antunes R, Moore E, Rubiro P, Methot N, Phillips E, Mallal S, Frazier A, Rawlings SA, Greenbaum JA, Peters B, Smith DM, Crotty S, Weiskopf D, Grifoni A, Sette A. PMID: 33521695; PMCID: PMC7837622.

View in: PubMed Mentions: 274 Fields:
Med Medicine (General)
Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection. Science. 2021 02 05; 371(6529). Dan JM, Mateus J, Kato Y, Hastie KM, Yu ED, Faliti CE, Grifoni A, Ramirez SI, Haupt S, Frazier A, Nakao C, Rayaprolu V, Rawlings SA, Peters B, Krammer F, Simon V, Saphire EO, Smith DM, Weiskopf D, Sette A, Crotty S. PMID: 33408181; PMCID: PMC7919858.

View in: PubMed Mentions: 1394 Fields:
Sci Science
Translation:Humans Cells
Immunological memory to SARS-CoV-2 assessed for up to eight months after infection. bioRxiv. 2020 Dec 18. Dan JM, Mateus J, Kato Y, Hastie KM, Yu ED, Faliti CE, Grifoni A, Ramirez SI, Haupt S, Frazier A, Nakao C, Rayaprolu V, Rawlings SA, Peters B, Krammer F, Simon V, Saphire EO, Smith DM, Weiskopf D, Sette A, Crotty S. PMID: 33442687; PMCID: PMC7805444.

View in: PubMed Mentions: 10
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. bioRxiv. 2020 Dec 09. Tarke A, Sidney J, Kidd CK, Dan JM, Ramirez SI, Yu ED, Mateus J, da Silva Antunes R, Moore E, Rubiro P, Methot N, Phillips E, Mallal S, Frazier A, Rawlings SA, Greenbaum JA, Peters B, Smith DM, Crotty S, Weiskopf D, Grifoni A, Sette A. PMID: 33330869; PMCID: PMC7743077.

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Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity. Cell. 2020 11 12; 183(4):996-1012.e19. Rydyznski Moderbacher C, Ramirez SI, Dan JM, Grifoni A, Hastie KM, Weiskopf D, Belanger S, Abbott RK, Kim C, Choi J, Kato Y, Crotty EG, Kim C, Rawlings SA, Mateus J, Tse LPV, Frazier A, Baric R, Peters B, Greenbaum J, Ollmann Saphire E, Smith DM, Sette A, Crotty S. PMID: 33010815; PMCID: PMC7494270.

View in: PubMed Mentions: 964 Fields:
Cel Cell Biology
Translation:Humans Cells PHPublic Health
Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science. 2020 10 02; 370(6512):89-94. Mateus J, Grifoni A, Tarke A, Sidney J, Ramirez SI, Dan JM, Burger ZC, Rawlings SA, Smith DM, Phillips E, Mallal S, Lammers M, Rubiro P, Quiambao L, Sutherland A, Yu ED, da Silva Antunes R, Greenbaum J, Frazier A, Markmann AJ, Premkumar L, de Silva A, Peters B, Crotty S, Sette A, Weiskopf D. PMID: 32753554; PMCID: PMC7574914.

View in: PubMed Mentions: 629 Fields:
Sci Science
Translation:Humans Cells PHPublic Health
Post-transplant survey to assess patient experiences with donor-derived HCV infection. Transpl Infect Dis. 2020 Dec; 22(6):e13402. Prakash K, Ramirez-Sanchez C, Ramirez SI, Logan C, Law N, Mekeel K, Pretorius V, Aslam S. PMID: 32634289; PMCID: PMC10084045.

View in: PubMed Mentions: 5 Fields:
Tra Transplantation
Translation:Humans
Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science. 2020 08 21; 369(6506):956-963. Rogers TF, Zhao F, Huang D, Beutler N, Burns A, He WT, Limbo O, Smith C, Song G, Woehl J, Yang L, Abbott RK, Callaghan S, Garcia E, Hurtado J, Parren M, Peng L, Ramirez S, Ricketts J, Ricciardi MJ, Rawlings SA, Wu NC, Yuan M, Smith DM, Nemazee D, Teijaro JR, Voss JE, Wilson IA, Andrabi R, Briney B, Landais E, Sok D, Jardine JG, Burton DR. PMID: 32540903; PMCID: PMC7299280.

View in: PubMed Mentions: 827 Fields:
Sci Science
Translation:Humans Animals Cells PHPublic Health
Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell. 2020 06 25; 181(7):1489-1501.e15. Grifoni A, Weiskopf D, Ramirez SI, Mateus J, Dan JM, Moderbacher CR, Rawlings SA, Sutherland A, Premkumar L, Jadi RS, Marrama D, de Silva AM, Frazier A, Carlin AF, Greenbaum JA, Peters B, Krammer F, Smith DM, Crotty S, Sette A. PMID: 32473127; PMCID: PMC7237901.

View in: PubMed Mentions: 2032 Fields:
Cel Cell Biology
Translation:Humans Cells PHPublic Health
Mechanistic Insight into the Host Transcription Inhibition Function of Rift Valley Fever Virus NSs and Its Importance in Virulence. PLoS Negl Trop Dis. 2016 Oct; 10(10):e0005047. Terasaki K, Ramirez SI, Makino S. PMID: 27711108; PMCID: PMC5053439.

View in: PubMed Mentions: 7 Fields:
Tro Tropical Medicine
Translation:Humans Animals Cells
Middle East Respiratory Syndrome Coronavirus nsp1 Inhibits Host Gene Expression by Selectively Targeting mRNAs Transcribed in the Nucleus while Sparing mRNAs of Cytoplasmic Origin. J Virol. 2015 Nov; 89(21):10970-81. Lokugamage KG, Narayanan K, Nakagawa K, Terasaki K, Ramirez SI, Tseng CT, Makino S. PMID: 26311885; PMCID: PMC4621111.

View in: PubMed Mentions: 99 Fields:
Vir Virology
Translation:Humans Cells
Coronavirus nonstructural protein 1: Common and distinct functions in the regulation of host and viral gene expression. Virus Res. 2015 Apr 16; 202:89-100. Narayanan K, Ramirez SI, Lokugamage KG, Makino S. PMID: 25432065; PMCID: PMC4444399.

View in: PubMed Mentions: 115 Fields:
Vir Virology
Translation:Humans Animals Cells
Development of a novel, single-cycle replicable rift valley Fever vaccine. PLoS Negl Trop Dis. 2014 Mar; 8(3):e2746. Murakami S, Terasaki K, Ramirez SI, Morrill JC, Makino S. PMID: 24651859; PMCID: PMC3961198.

View in: PubMed Mentions: 11 Fields:
Tro Tropical Medicine
Translation:Animals Cells