Publications

Approaches toward understanding human immunity

Immunity, 2025

Petter Brodin, Feng Wang, Bo Zhu, Timothy Hammond, Catherine P Lu, Florian Wimmers, Alexandra Zhernakova, Wanlu Liu, Kari Nadeau, Martin Prlic

Immunity

Study Design

Single-cell

System vaccinology analysis of predictors and mechanisms of antibody response durability to multiple vaccines in humans

Nature immunology, 2025

Mario Cortese, Thomas Hagan, Nadine Rouphael, Sheng-Yang Wu, Xia Xie, Dmitri Kazmin, Florian Wimmers, Shakti Gupta, Robbert van der Most, Margherita Coccia, Prabhu S. Aranuchalam, Helder I. Nakaya, Yating Wang, Elizabeth Coyle, Shu Horiuchi, Hanchih Wu, Mary Bower, Aneesh Mehta, Clifford Gunthel, Steve E. Bosinger, Yuri Kotliarov, Foo Cheung, Pamela L. Schwartzberg, Ronald N. Germain, John Tsang, Shuzhao Li, Randy Albrecht, Hideki Ueno, Shankar Subramaniam, Mark J. Mulligan, Surender Khurana, Hana Golding, Bali Pulendran.

Vaccines

Machine learning

Transcriptomics

Inhibition of glutaminase-1 in DLBCL potentiates venetoclax-induced antitumor activity by promoting oxidative stress

Blood Advances, 2023

Beatriz Gomez Solsona, Heike Horn, Anja Schmitt, Wendan Xu, Philip Bucher, Aylin Heinrich, Sabrina Kalmbach, Nina Kreienkamp, Maik Franke, Florian Wimmers, Laurentz Schuhknecht, Andreas Rosenwald, Mattia Zampieri, German Ott, Georg Lenz, Klaus Schulze-Osthoff, Stephan Hailfinger

Immunotherapy

Cancer

Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth

Cell, 2023

Florian Wimmers, Allison R Burrell, Yupeng Feng, Hong Zheng, Prabhu S Arunachalam, Mengyun Hu, Sara Spranger, Lindsay E Nyhoff, Devyani Joshi, Meera Trisal, Mayanka Awasthi, Lorenza Bellusci, Usama Ashraf, Sangeeta Kowli, Katherine C Konvinse, Emily Yang, Michael Blanco, Kathryn Pellegrini, Gregory Tharp, Thomas Hagan, R Sharon Chinthrajah, Tran T Nguyen, Alba Grifoni, Alessandro Sette, Kari C Nadeau, David B Haslam, Steven E Bosinger, Jens Wrammert, Holden T Maecker, Paul J Utz, Taia T Wang, Surender Khurana, Purvesh Khatri, Mary A Staat, Bali Pulendran

Immunity in infants

SARS-CoV-2

Multi-omics

SREBP signaling is essential for effective B cell responses

Nature immunology, 2023

Wei Luo, Julia Z Adamska, Chunfeng Li, Rohit Verma, Qing Liu, Thomas Hagan, Florian Wimmers, Shakti Gupta, Yupeng Feng, Wenxia Jiang, Jiehao Zhou, Erika Valore, Yanli Wang, Meera Trisal, Shankar Subramaniam, Timothy F Osborne, Bali Pulendran

Systems vaccinology

B cells

Humoral response

Ablation of Adar1 in myeloid cells imprints a global antiviral state in the lung and heightens early immunity against SARS-CoV-2

Cell report, 2023

Julia Z Adamska, Rohit Verma, Shakti Gupta, Thomas Hagan, Florian Wimmers, Katharine Floyd, Qin Li, Erika V Valore, Yanli Wang, Meera Trisal, José G Vilches-Moure, Shankar Subramaniam, Carl R Walkley, Mehul S Suthar, Jin Billy Li, Bali Pulendran

dsRNA sensing

SARS-CoV-2

Transcriptomics

Epigenetic adjuvants: durable reprogramming of the innate immune system with adjuvants

Current opinion in immunology, 2022

Audrey Lee, Florian Wimmers, Bali Pulendran

Cell programming

Epigenetics

Vaccines

Mechanisms of innate and adaptive immunity to the Pfizer-BioNTech BNT162b2 vaccine

Nature Immunology, 2022

Chunfeng Li, Audrey Lee, Lilit Grigoryan, Prabhu S Arunachalam, Madeleine KD Scott, Meera Trisal, Florian Wimmers, Mrinmoy Sanyal, Payton A Weidenbacher, Yupeng Feng, Julia Z Adamska, Erika Valore, Yanli Wang, Rohit Verma, Noah Reis, Diane Dunham, Ruth O’Hara, Helen Park, Wei Luo, Alexander D Gitlin, Peter Kim, Purvesh Khatri, Kari C Nadeau, Bali Pulendran

Innate & adaptive immunity

SARS-CoV-2

Vaccines

A molecular atlas of innate immunity to adjuvanted and live attenuated vaccines, in mice

Nature communications, 2022

Audrey Lee, Madeleine KD Scott, Florian Wimmers, Prabhu S Arunachalam, Wei Luo, Christopher B Fox, Mark Tomai, Purvesh Khatri, Bali Pulendran

Adjuvants

scRNA-seq

Vaccines

Systems vaccinology of the BNT162b2 mRNA vaccine in humans

Nature, 2021

Prabhu S Arunachalam, Madeleine KD Scott, Thomas Hagan, Chunfeng Li, Yupeng Feng, Florian Wimmers, Lilit Grigoryan, Meera Trisal, Venkata Viswanadh Edara, Lilin Lai, Sarah Esther Chang, Allan Feng, Shaurya Dhingra, Mihir Shah, Alexandra S Lee, Sharon Chinthrajah, Sayantani B Sindher, Vamsee Mallajosyula, Fei Gao, Natalia Sigal, Sangeeta Kowli, Sheena Gupta, Kathryn Pellegrini, Gregory Tharp, Sofia Maysel-Auslender, Sydney Hamilton, Hadj Aoued, Kevin Hrusovsky, Mark Roskey, Steven E Bosinger, Holden T Maecker, Scott D Boyd, Mark M Davis, Paul J Utz, Mehul S Suthar, Purvesh Khatri, Kari C Nadeau, Bali Pulendran

SARS-CoV-2

scRNA-seq

Vaccines

The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination

Cell, 2021

Florian Wimmers, Michele Donato, Alex Kuo, Tal Ashuach, Shakti Gupta, Chunfeng Li, Mai Dvorak, Mariko Hinton Foecke, Sarah E Chang, Thomas Hagan, Sanne E De Jong, Holden T Maecker, Robbert van der Most, Peggie Cheung, Mario Cortese, Steven E Bosinger, Mark Davis, Nadine Rouphael, Shankar Subramaniam, Nir Yosef, Paul J Utz, Purvesh Khatri, Bali Pulendran

Influenza

Epigenomics

Vaccines

Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans

Science, 2020

Prabhu S Arunachalam*, Florian Wimmers* (shared 1st), Chris Ka Pun Mok*, Ranawaka APM Perera*, Madeleine Scott, Thomas Hagan, Natalia Sigal, Yupeng Feng, Laurel Bristow, Owen Tak-Yin Tsang, Dhananjay Wagh, John Coller, Kathryn L Pellegrini, Dmitri Kazmin, Ghina Alaaeddine, Wai Shing Leung, Jacky Man Chun Chan, Thomas Shiu Hong Chik, Chris Yau Chung Choi, Christopher Huerta, Michele Paine McCullough, Huibin Lv, Evan Anderson, Srilatha Edupuganti, Amit A Upadhyay, Steve E Bosinger, Holden Terry Maecker, Purvesh Khatri, Nadine Rouphael, Malik Peiris, Bali Pulendran

SARS-CoV-2

Vaccines

Flow cytometry

Emerging technologies for systems vaccinology — multi-omics integration and single-cell (epi)genomic profiling

Current opinion in immunology, 2020

Florian Wimmers, Bali Pulendran

Systems vaccinology

Single-cell omics

Multi-omics

T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers

Nature medicine, 2020

Prabhu S Arunachalam, Tysheena P Charles, Vineet Joag, Venkata S Bollimpelli, Madeleine KD Scott, Florian Wimmers, Samantha L Burton, Celia C Labranche, Caroline Petitdemange, Sailaja Gangadhara, Tiffany M Styles, Clare F Quarnstrom, Korey A Walter, Thomas J Ketas, Traci Legere, Pradeep Babu Jagadeesh Reddy, Sudhir Pai Kasturi, Anthony Tsai, Bertrand Z Yeung, Shakti Gupta, Mark Tomai, John Vasilakos, George M Shaw, Chil-Yong Kang, John P Moore, Shankar Subramaniam, Purvesh Khatri, David Montefiori, Pamela A Kozlowski, Cynthia A Derdeyn, Eric Hunter, David Masopust, Rama R Amara, Bali Pulendran

HIV

scRNA-seq

Vaccines

A pipette-tip based method for seeding cells to droplet microfluidic platforms

Journal of Visualized Experiments, 2019

Nidhi Sinha*, Nikita Subedi*, Florian Wimmers* (shared 1st), Melf Soennichsen, Jurjen Tel

Single-cell

Microfluidics

Engineering

Naturally produced type I IFNs enhance human myeloid dendritic cell maturation and IL-12p70 production and mediate elevated effector functions in innate and adaptive immune cells

Cancer Immunology, Immunotherapy, 2018

Annette E Sköld, Till SM Mathan, Jasper JP van Beek, Georgina Flórez-Grau, Michelle D van den Beukel, Simone P Sittig, Florian Wimmers, Ghaith Bakdash, Gerty Schreibelt, I Jolanda M de Vries

Immunotherapy

Dendritic cells

Vaccines

Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells

Nature communications, 2018

Florian Wimmers, Nikita Subedi, Nicole van Buuringen, Daan Heister, Judith Vivié, Inge Beeren-Reinieren, Rob Woestenenk, Harry Dolstra, Aigars Piruska, Joannes FM Jacobs, Alexander van Oudenaarden, Carl G Figdor, Wilhelm TS Huck, I Jolanda M de Vries, Jurjen Tel

Dendritic cells

scRNA-seq

Cytokines

Monitoring of dynamic changes in Keyhole Limpet Hemocyanin (KLH)-specific B cells in KLH-vaccinated cancer patients

Scientific reports, 2017

Florian Wimmers, Nienke de Haas, Anja Scholzen, Gerty Schreibelt, Elles Simonetti, Marc J Eleveld, Huberdina MLM Brouwers, Marjo Beldhuis-Valkis, Irma Joosten, Marien I de Jonge, Winald R Gerritsen, I Jolanda M de Vries, Dimitri A Diavatopoulos, Joannes FM Jacobs

Flow cytometry

Dendritic cells

Vaccines

A membrane-anchored aptamer sensor for probing IFNγ secretion by single cells

Chemical Communications, 2017

Liping Qiu, Florian Wimmers, Jorieke Weiden, Hans A Heus, Jurjen Tel, Carl G Figdor

Single-cell

Cytokines

Microfluitics

Opportunities for immunotherapy in microsatellite instable colorectal cancer

Cancer Immunology, Immunotheraphy, 2016

Harm Westdorp, Felix L Fennemann, Robbert DA Weren, Tanya M Bisseling, Marjolijn JL Ligtenberg, Carl G Figdor, Gerty Schreibelt, Nicoline Hoogerbrugge, Florian Wimmers, I Jolanda M de Vries

Immunotherapy

Cancer

Neoantigens

Effective Clinical Responses in Metastatic Melanoma Patients after Vaccination with Primary Myeloid Dendritic Cells

Clinical cancer research, 2016

Gerty Schreibelt, Kalijn F Bol, Harm Westdorp, Florian Wimmers, Erik HJG Aarntzen, Tjitske Duiveman-de Boer, Mandy WMM Van De Rakt, Nicole M Scharenborg, Annemiek J De Boer, Jeanette M Pots, Michel AM Olde Nordkamp, Tom GM Van Oorschot, Jurjen Tel, Gregor Winkels, Katja Petry, Willeke AM Blokx, Michelle M Van Rossum, Marieke EB Welzen, Roel DM Mus, Sandra AJ Croockewit, Rutger HT Koornstra, Joannes FM Jacobs, Sander Kelderman, Christian U Blank, Winald R Gerritsen, Cornelis JA Punt, Carl G Figdor, I Jolanda M De Vries

Immunotherapy

Vaccines

Dendritic cells