Publications

For the most up-to-date publications, see Google Scholar.

^*, ^†, or ^‡ Equal contribution · ^# Corresponding author

2026

Nature

Tertiary lymphoid structures harbour stem-like tumour-specific T cells

Alexander B. Afeyan^*, Adi Nagler^*, Chloe R. Tu^*, Gabriel Roberti De Oliveira, Berkay Simsek, Maxwell D. Seager, Nourhan El Ahmar, Haley E. Sax, Emma Lin, Amit Sud, Mehdi Borji, Cleo Forman, Sophia Liu, Patrick A. Ott, Toni K. Choueiri, Jennifer G. Abelin, Richard Burack, Shuqiang Li, Kenneth J. Livak, Svitlana Tyekucheva, Derin B. Keskin, Fei Chen, Michael B. Atkins, Jeremy M. Simon, Sabina Signoretti, Giacomo Oliveira^#, David A. Braun^#, Catherine J. Wu^#

Immunity

Local antibody feedback enforces a checkpoint on affinity maturation in the germinal center and promotes epitope spreading

Yu Yan^*, Xuesong Wang^*, Zhenfei Xie^*, Daniel L. V. Bader^†, Ryan H. Lim^†, Krystal M. Ma, Christopher A. Cottrell, Jon M. Steichen, Liling Xu, Paula M. Villavicencio, Madhav Akauliya, Ja-Hyun Koo, Jacqueline M. Shen, Alexandra Vernich, Oleksandr Kalyuzhniy, Joel D. Allen, Ali A. Albowaidey, Anthony Alicea, Bingxian Chen, Erik Georgeson, Jordan Renae Ellis-Pugh, Nushin Alavi, Abigail Esposito, Hannah Naili, Nicole Phelps, Brendon Kelley, Michael Kubitz, Quynh Anh Phan, Alessia Liguori, Thavaleak Prum, Ryan Tingle, Danny Lu, Saman Eskandarzadeh, Xiaotie Liu, John E. Warner, Stephanie R. Weldon, Sunny Himansu, Max Crispin, Usha Nair, Sophia Liu^#, William R. Schief^#, Facundo D. Batista^#

Nature

Transient hepatic reconstitution of trophic factors enhances aged immunity

Mirco J. Friedrich, Julie Pham, Jiakun Tian, Hongyu Chen, Jiahao Huang, Niklas Kehl, Sophia Liu, Blake Lash, Fei Chen, Xiao Wang, Rhiannon K. Macrae, Feng Zhang^#

2025

Cell Metabolism

A metabolic atlas of mouse aging

Steven E. Pilley, Dominik Awad^*, Djakim Latumalea^*, Connie New, Edgar Esparza^*, Shuo Wang, Xuanyi Shi, Li Zhang, Maximilian Unfried, Jasinda H. Lee, Ernst Schmid, Ipsita Mohanty, Jenna L.E. Blum, Shivaanishaa Raventhiran, Esther Wong, Preeti R. Iyengar, Racheal Mulondo, Sriraksha Bharadwaj Kashyap, Darius Moaddeli, Peter Sajjakulnukit, Damien Sutton, Harrison K.A. Wong, Yaqi Gao, George Wang, Aeowynn J. Coakley, Gilberto Garcia, Ryo Higuchi-Sanabria, Anja Karlstaedt, Timothy L. Frankel, Marina Pasca di Magliano, Whitaker Cohn, Sophia Liu, Bingfei Yu, Pieter C. Dorrestein, Ernest Fraenkel, Shawn M. Davidson, William B. Tu, Brian K. Kennedy, Costas A. Lyssiotis^†^#, Peter J. Mullen^†^#

Cell

CRATER tumor niches facilitate CD8(+) T cell engagement and correspond with immunotherapy success

Aya Ludin^*, Georgia L. Stirtz^*, Asaf Tal, Ajit J. Nirmal, Kathleen L. Pfaff, Michael Manos, Naomi Besson, Nebiyat Eskndir, Billie Porter, Stephanie M. Jones, Hannah M. Faulkner, Qiyu Gong, Sophia Liu, Irving Barrera, Lijian Wu, Cecilia Pessoa Rodrigues, Aditi Sahu, Elizabeth Jerison, Joao V. Alessi, Biagio Ricciuti, Douglas S. Richardson, Jodi D. Weiss, Hadley M. Moreau, Meredith E. Stanhope, Alexander B. Afeyan, James Sefton, Wyatt D. McCall, Emily Formato, Song Yang, Yi Zhou, David P. Hoytema van Konijnenburg, Hannah L. Cole, Miguel Cordova, Liang Deng, Milind Rajadhyaksha, Stephen R. Quake, Mark M. Awad, Fei Chen, Kai W. Wucherpfennig, Peter K. Sorger, F. Stephen Hodi, Scott J. Rodig, George F. Murphy, Leonard I. Zon^#

First page of TissueMosaic: Self-supervised learning of tissue representations enables differential spatial transcriptomics across samples

Cell Systems

TissueMosaic: Self-supervised learning of tissue representations enables differential spatial transcriptomics across samples

Sandeep Kambhampati, Luca D’Alessio, Fedor Grab, Stephen Fleming, Sophia Liu, Ruth Raichur, Fei Chen^†^#, Mehrtash Babadi^†^#

Journal of Experimental Medicine · Viewpoint

Women in STEM becoming independent: People should feel free to be themselves and do great science

Sophia Liu, Margarida Saraiva, Caroline R. Bartman, Nathalie Saurat, Pamela C. Rosato, Paula Licona-Limon, Alejandra Mendoza, Jenna Guthmiller, Coraline Mlynarczyk, Emily Goldberg

bioRxiv · Preprint

Tissue architecture dynamics underlying immune development and decline in the thymus

Sophia Liu^*^#, Mirco J. Friedrich^*^#, Ruth Raichur^*, Dennis Gong, Niklas Kehl, Qiyu Gong, Bingxian Chen, Karin Gustafsson, Larissa L. Ma, David T. Scadden, Rhiannon K. Macrae, Feng Zhang, Fei Chen^#

2023

Nature

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

Andrew J. C. Russell^*, Jackson A. Weir^*, Naeem M. Nadaf^*, Matthew Shabet, Vipin Kumar, Sandeep Kambhampati, Ruth Raichur, Giovanni J. Marrero, Sophia Liu, Karol S. Balderrama, Charles R. Vanderburg, Vignesh Shanmugam, Luyi Tian, J. Bryan Iorgulescu, Charles H. Yoon, Catherine J. Wu, Evan Z. Macosko^†^#, Fei Chen^†^#

2022

First page of Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response

Immunity

Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response

Sophia Liu^*, J. Bryan Iorgulescu^*, Shuqiang Li^*, Mehdi Borji, Irving A. Barrera-Lopez, Vignesh Shanmugam, Haoxiang Lyu, Julia W. Morriss, Zoe N. Garcia, Evan Murray, David A. Reardon, Charles H. Yoon, David A. Braun, Kenneth J. Livak, Catherine J. Wu^#, Fei Chen^#

First page of Microfluidic Squeezing Enables MHC Class I Antigen Presentation by Diverse Immune Cells to Elicit CD8+ T Cell Responses with Antitumor Activity

Journal of Immunology

Microfluidic Squeezing Enables MHC Class I Antigen Presentation by Diverse Immune Cells to Elicit CD8+ T Cell Responses with Antitumor Activity

Matthew G Booty^*, Kelan A Hlavaty^*, Adam Stockmann, Emrah Ilker Ozay, Carolyne Smith, Lina Tian, Edylle How, Disha Subramanya, Anita Venkitaraman, Christian Yee, Olivia Pryor, Kelly Volk, Katarina Blagovic, Ildefonso Vicente-Suarez, Defne Yarar, Melissa Myint, Amy Merino, Jonathan Chow, Tarek Abdeljawad, Harry An, Sophia Liu, Shirley Mao, Megan Heimann, LeeAnn Talarico, Miye K Jacques, Eritza Chong, Lucas Pomerance, John T Gonzalez, Ulrich H von Andrian, Klavs F Jensen, Robert Langer, Hendrik Knoetgen, Christine Trumpfheller, Pablo Umaña, Howard Bernstein, Armon Sharei, Scott M Loughhead^#

2020

Nature Biotechnology

RNA timestamps identify the age of single molecules in RNA sequencing

Samuel G. Rodriques^*, Linlin M. Chen^*, Sophia Liu, Ellen D. Zhong, Joseph R. Scherrer, Edward S. Boyden^#, Fei Chen^#

2019

Nature Biotechnology

Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor

Haiqi Chen, Sophia Liu^*, Samuel Padula^*, Daniel Lesman, Kettner Griswold, Allen Lin, Tongtong Zhao, Jamie L. Marshall, Fei Chen^#

2015

PLOS ONE

Ex vivo cytosolic delivery of functional macromolecules to immune cells

Armon Sharei^*, Radiana Trifonova^*, Siddharth Jhunjhunwala^*, George C. Hartoularos, Alexandra T. Eyerman, Abigail Lytton-Jean, Mathieu Angin, Siddhartha Sharma, Roberta Poceviciute, Shirley Mao, Megan Heimann, Sophia Liu, Tanya Talkar, Omar F. Khan, Marylyn Addo, Ulrich H. von Andrian, Daniel G. Anderson, Robert Langer, Judy Lieberman^#, Klavs F. Jensen^#