プロフィール詳細

プロジェクトを作成

★★★★★

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★★★★★

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Dr. Josephine G.に依頼

United States

PhD in immunology from Yale University | Expert in T cell exhaustion, single cell genomics, CRISPR, R analysis

プロフィール概要

I am currently a senior research investigator at the University of Pennsylvania. My overall research goal is to elucidate the epigenetic and transcriptional networks that control CD8 T cell differentiation. Specifically, my work focuses on CD8 T cell exhaustion in cancer and chronic infection. These studies combine mouse models of T cell differentiation and human immunology with next-generation sequencing, single cell genomics, high dimensional cytometry, CRISPR technologies, and computational analysis. I graduated from Mount Holyoke College summa cum laude in 2007, then earned a PhD from Yale University. My graduate work in the laboratory of Mark J. Shlomchik investigated T cell - B cell interaction in systemic autoimmune disease and resulted in a novel method for identifying and studying autoreactive T cells. In my postdoctoral position, I was awarded a Cancer Research Institute-Mark Foundation Fellow and published papers in Science, Immunity, Nature Immunology, Science Immunology, and others. I am available to consult at all stages for scientific projects: overall project conception and development, experimental design, assay development and optimization, analysis (flow cytometry, bulk and single cell genomics, R analysis), data visualization (R coding and Illustrator), manuscript writing/editing, and scientific presentations.

専門分野

• ★ Omics
• ★ Basic Immunology
• ★ Data Analysis
• ☆ Molecular Biology
• ☆ Transcriptomics
• ☆ Genomics
• ☆ Chromatin
• ☆ Epigenetics
• ☆ PCR
• ☆ Molecular Cloning
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ Gene Expression Analysis
• ☆ RNA Sequencing
• ☆ Cell Biology
• ☆ Data Processing
• ☆ Data Exploration
• ☆ Data Visualization
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Cytometry
• ☆ R
• ☆ Clinical Immunology
• ☆ Cancer Research
• ☆ Presentation Design
• ☆ Technical & Scientific Writing
• ☆ Manuscript & Journal Article Writing
• ☆ Experimental Protocols
• ☆ SOP & Protocol Writing

サービス

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Scientific and Technical Research

Consulting Scientific and Technical Consulting

Data & AI Data Visualization, Data Processing

職務経験

Trainee

University of Pennsylvania

- 現在

Senior Research Investigator

University of Pennsylvania

12月 2021 - 現在

学歴

PhD in Immunology

University of Pennsylvania

8月 2007 - 5月 2015

Bachelors

Mount Holyoke College

8月 2002 - 5月 2005

認定資格

• 認定資格の詳細は未入力です。

出版物

JOURNAL ARTICLE

Goel, R.R., Painter, M.M., Lundgreen, K.A., Apostolidis, S.A., Baxter, A.E., Giles, J.R., Mathew, D., Pattekar, A., Reynaldi, A., Khoury, D.S., et al.(2022). Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine . Cell. 185. (11). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1875-1887.e8.

Bucktrout, S.L., Banovich, N.E., Butterfield, L.H., Cimen-Bozkus, C., Giles, J.R., Good, Z., Goodman, D., Jonsson, V.D., Lareau, C., Marson, A., et al.(2022). Advancing T cell-based cancer therapy with single-cell technologies . Nature medicine. 28. (9). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1761-1764.

Daniel, B., Yost, K.E., Hsiung, S., Sandor, K., Xia, Y., Qi, Y., Hiam-Galvez, K.J., Black, M., J. Raposo, C., Shi, Q., et al.(2022). Divergent clonal differentiation trajectories of T cell exhaustion . Nature Immunology. 23. (11). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1614-1627.

Merenstein, C., Liang, G., Whiteside, S.A., Cobián-Güemes, A.G., Merlino, M.S., Taylor, L.J., Glascock, A., Bittinger, K., Tanes, C., Graham-Wooten, J., et al.(2022). Erratum: Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome(mBio 12:4 (e01777-21) DOI: 10.1128/mBio.01777-21) . mBio. 13. (5).

Giles, J.R., Manne, S., Freilich, E., Oldridge, D.A., Baxter, A.E., George, S., Chen, Z., Huang, H., Chilukuri, L., Carberry, M., et al.(2022). Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers . Immunity. 55. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 557-574.e7.

Giles, J.R., Ngiow, S.F., Manne, S., Baxter, A.E., Khan, O., Wang, P., Staupe, R., Abdel-Hakeem, M.S., Huang, H., Mathew, D., et al.(2022). Shared and distinct biological circuits in effector, memory and exhausted CD8⁺ T cells revealed by temporal single-cell transcriptomics and epigenetics . Nature Immunology. 23. (11). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1600-1613.

Apostolidis, S.A., Sarkar, A., Giannini, H.M., Goel, R.R., Mathew, D., Suzuki, A., Baxter, A.E., Greenplate, A.R., Alanio, C., Abdel-Hakeem, M., et al.(2022). Signaling Through FcγRIIA and the C5a-C5aR Pathway Mediate Platelet Hyperactivation in COVID-19 . Frontiers in Immunology. 13.

Abdel-Hakeem, M.S., Manne, S., Beltra, J.-C., Stelekati, E., Chen, Z., Nzingha, K., Ali, M.-A., Johnson, J.L., Giles, J.R., Mathew, D., et al.(2021). Author Correction: Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation (Nature Immunology, (2021), 22, 8, (1008-1019), 10.1038/s41590-021-00975-5) . Nature Immunology. 22. (11). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1465.

Bange, E.M., Han, N.A., Wileyto, P., Kim, J.Y., Gouma, S., Robinson, J., Greenplate, A.R., Hwee, M.A., Porterfield, F., Owoyemi, O., et al.(2021). CD8⁺ T cells contribute to survival in patients with COVID-19 and hematologic cancer . Nature Medicine. 27. (7). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1280-1289.

Vella, L.A., Giles, J.R., Baxter, A.E., Oldridge, D.A., Diorio, C., Kuri-Cervantes, L., Alanio, C., Pampena, M.B., Wu, J.E., Chen, Z., et al.(2021). Deep immune profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19 . Science Immunology. 6. (57).

Goel, R.R., Apostolidis, S.A., Painter, M.M., Mathew, D., Pattekar, A., Kuthuru, O., Gouma, S., Hicks, P., Meng, W., Rosenfeld, A.M., et al.(2021). Distinct antibody and memory B cell responses in SARSCoV-2 naïve and recovered individuals following mRNA vaccination . Science Immunology. 6. (58). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1-19.

Abdel-Hakeem, M.S., Manne, S., Beltra, J.-C., Stelekati, E., Chen, Z., Nzingha, K., Ali, M.-A., Johnson, J.L., Giles, J.R., Mathew, D., et al.(2021). Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation . Nature Immunology. 22. (8). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1008-1019.

Chen, Z., Arai, E., Khan, O., Zhang, Z., Ngiow, S.F., He, Y., Huang, H., Manne, S., Cao, Z., Baxter, A.E., et al.(2021). In vivo CD8⁺ T cell CRISPR screening reveals control by Fli1 in infection and cancer . Cell. 184. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1262-1280.e22.

Johnnidis, J.B., Muroyama, Y., Ngiow, S.F., Chen, Z., Manne, S., Cai, Z., Song, S., Platt, J.M., Schenkel, J.M., Abdel-Hakeem, M., et al.(2021). Inhibitory signaling sustains a distinct early memory CD8⁺ T cell precursor that is resistant to DNA damage . Science Immunology. 6. (55).

Diorio, C., Shraim, R., Vella, L.A., Giles, J.R., Baxter, A.E., Oldridge, D.A., Canna, S.W., Henrickson, S.E., McNerney, K.O., Balamuth, F., et al.(2021). Proteomic profiling of MIS-C patients indicates heterogeneity relating to interferon gamma dysregulation and vascular endothelial dysfunction . Nature Communications. 12. (1).

Painter, M.M., Mathew, D., Goel, R.R., Apostolidis, S.A., Pattekar, A., Kuthuru, O., Baxter, A.E., Herati, R.S., Oldridge, D.A., Gouma, S., et al.(2021). Rapid induction of antigen-specific CD4⁺ T cells is associated with coordinated humoral and cellular immunity to SARS-CoV-2 mRNA vaccination . Immunity. 54. (9). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2133-2142.e3.

Merenstein, C., Liang, G., Whiteside, S.A., Cobián-Güemes, A.G., Merlino, M.S., Taylor, L.J., Glascock, A., Bittinger, K., Tanes, C., Graham-Wooten, J., et al.(2021). Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome . mBio. 12. (4).

Goel, R.R., Painter, M.M., Apostolidis, S.A., Mathew, D., Meng, W., Rosenfeld, A.M., Lundgreen, K.A., Reynaldi, A., Khoury, D.S., Pattekar, A., et al.(2021). mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern . Science. 374. (6572).

Mathew, D., Giles, J.R., Baxter, A.E., Oldridge, D.A., Greenplate, A.R., Wu, J.E., Alanio, C., Kuri-Cervantes, H., Pampena, M.B., D'Andrea, K., et al.(2020). Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications . Science. 369. (6508).

Beltra, J.-C., Manne, S., Abdel-Hakeem, M.S., Kurachi, M., Giles, J.R., Chen, Z., Casella, V., Ngiow, S.F., Khan, O., Huang, Y.J., et al.(2020). Developmental Relationships of Four Exhausted CD8⁺ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms . Immunity. 52. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 825-841.e8.

Vella, L.A., Buggert, M., Manne, S., Herati, R.S., Sayin, I., Kuri-Cervantes, L., Brody, I.B., O’Boyle, K.C., Kaprielian, H., Giles, J.R., et al.(2019). T follicular helper cells in human efferent lymph retain lymphoid characteristics . Journal of Clinical Investigation. 129. (8). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 3185-3200.

Chen, Z., Ji, Z., Ngiow, S.F., Manne, S., Cai, Z., Huang, A.C., Johnson, J., Staupe, R.P., Bengsch, B., Xu, C., et al.(2019). TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision . Immunity. 51. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 840-855.e5.

Khan, O., Giles, J.R., McDonald, S., Manne, S., Ngiow, S.F., Patel, K.P., Werner, M.T., Huang, A.C., Alexander, K.A., Wu, J.E., et al.(2019). TOX transcriptionally and epigenetically programs CD8⁺ T cell exhaustion . Nature. 571. (7764). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 211-218.

Giles, J.R., Neves, A.T., Marshak-Rothstein, A., Shlomchik, M.J.(2017). Autoreactive helper T cells alleviate the need for intrinsic TLR signaling in autoreactive B cell activation . JCI Insight. 2. (4).

Huang, A.C., Postow, M.A., Orlowski, R.J., Mick, R., Bengsch, B., Manne, S., Xu, W., Harmon, S., Giles, J.R., Wenz, B., et al.(2017). T-cell invigoration to tumour burden ratio associated with anti-PD-1 response . Nature. 545. (7652). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 60-65.

Ols, M.L., Cullen, J.L., Turqueti-Neves, A., Giles, J., Shlomchik, M.J.(2016). Dendritic Cells Regulate Extrafollicular Autoreactive B Cells via T Cells Expressing Fas and Fas Ligand . Immunity. 45. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1052-1065.

Giles, J.R., Kashgarian, M., Koni, P.A., Shlomchik, M.J.(2015). B cell-specific MHC class II deletion reveals multiple nonredundant roles for B cell antigen presentation in murine lupus . Journal of Immunology. 195. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2571-2579.

OTHER

Goel, R.R., Painter, M.M., Lundgreen, K.A., Apostolidis, S.A., Baxter, A.E., Giles, J.R., Mathew, D., Pattekar, A., Reynaldi, A., Khoury, D.S., et al.(2022). Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine . bioRxiv.

Gustafson, C.E., Thomson, Z., He, Z., Swanson, E., Henderson, K., Pebworth, M.-P., Okada, L.Y., Heubeck, A.T., Roll, C.R., Hernandez, V., et al.(2022). Distinct Heterogeneity in the Naive T cell Compartments of Children and Adults . bioRxiv.

Beltra, J.-C., Abdel-Hakeem, M.S., Manne, S., Zhang, Z., Huang, H., Kurachi, M., Su, L., Picton, L., Muroyama, Y., Casella, V., et al.(2022). Enhanced STAT5a activation rewires exhausted CD8 T cells during chronic stimulation to acquire a hybrid durable effector like state . bioRxiv.

Giles, J.R., Ngiow, S.F., Manne, S., Baxter, A.E., Khan, O., Wang, P., Staupe, R., Abdel-Hakeem, M.S., Huang, H., Mathew, D., et al.(2022). Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates . bioRxiv.

Daniel, B., Yost, K.E., Sandor, K., Xia, Y., Qi, Y., Hiam-Galvez, K.J., Meier, S.L., Belk, J.A., Giles, J.R., Wherry, E.J., et al.(2021). Divergent clonal differentiation trajectories of T cell exhaustion . bioRxiv.

Diorio, C., Shraim, R., Vella, L.A., Giles, J.R., Baxter, A.E., Oldridge, D.A., Canna, S.W., Henrickson, S.E., McNerney, K.O., Balamuth, F., et al.(2021). Proteomic profiling of MIS-C patients reveals heterogeneity relating to interferon gamma dysregulation and vascular endothelial dysfunction . medRxiv.

Apostolidis, S.A., Sarkar, A., Giannini, H.M., Goel, R.R., Mathew, D., Suzuki, A., Baxter, A.E., Greenplate, A.R., Alanio, C., Abdel-Hakeem, M., et al.(2021). Signaling through FcgRIIA and the C5a-C5aR pathway mediates platelet hyperactivation in COVID-19 . bioRxiv.

Merenstein, C., Liang, G., Whiteside, S.A., Cobián-Güemes, A.G., Merlino, M.S., Taylor, L.J., Glascock, A., Bittinger, K., Tanes, C., Graham-Wooten, J., et al.(2021). Signatures of COVID-19 severity and immune response in the respiratory tract microbiome . medRxiv.

Goel, R.R., Apostolidis, S.A., Painter, M.M., Mathew, D., Pattekar, A., Kuthuru, O., Gouma, S., Kuri-Cervantes, L., Meng, W., Adamski, S., et al.(2021). Longitudinal analysis reveals distinct antibody and memory B cell responses in SARS-CoV2 Naïve and recovered individuals following mRNA vaccination . medRxiv.

Goel, R.R., Painter, M.M., Apostolidis, S.A., Mathew, D., Meng, W., Rosenfeld, A.M., Lundgreen, K.A., Reynaldi, A., Khoury, D.S., Pattekar, A., et al.(2021). mRNA vaccination induces durable immune memory to SARS-CoV-2 with continued evolution to variants of concern . bioRxiv.

Vella, L.A., Giles, J.R., Baxter, A.E., Oldridge, D.A., Diorio, C., Kuri-Cervantes, L., Alanio, C., Pampena, M.B., Wu, J.E., Chen, Z., et al.(2020). Deep Immune Profiling of MIS-C demonstrates marked but transient immune activation compared to adult and pediatric COVID-19 . medRxiv.

Mathew, D., Giles, J.R., Baxter, A.E., Greenplate, A.R., Wu, J.E., Alanio, C., Oldridge, D.A., Kuri-Cervantes, L., Pampena, M.B., D’Andrea, K., et al.(2020). Deep immune profiling of COVID-19 patients reveals patient heterogeneity and distinct immunotypes with implications for therapeutic interventions . bioRxiv.

Chen, Z., Arai, E., Khan, O., Zhang, Z., Ngiow, S.F., He, Y., Huang, H., Manne, S., Cao, Z., Baxter, A.E., et al.(2020). In vivo CRISPR screening identifies Fli1 as a transcriptional safeguard that restrains effector CD8 T cell differentiation during infection and cancer . bioRxiv.

Chen, Z., Arai, E., Khan, O., Zhang, Z., Ngiow, S.F., He, Y., Huang, H., Manne, S., Cao, Z., Baxter, A.E., et al.(2020). In vivo CRISPR Screening Identifies Fli1 as a Transcriptional Safeguard that Restrains Effector CD8 T Cell Differentiation during Infection and Cancer . SSRN.

Staupe, R.P., Vella, L.A., Manne, S., Giles, J.R., Meng, W., Herati, R.S., Khan, O., Wu, J.E., Baxter, A.E., Luning Prak, E.T., et al.(2019). Chronic viral infection promotes early germinal center exit of B cells and impaired antibody development . bioRxiv.