Publication resources
Each project in the Data Library generates publications from its data. These publications represent the culmination of work within each project, while also serving as a foundation for future research, allowing others to reuse and reanalyze the data to drive new discoveries and additional publications.
Publications
Local gene editing of fibroblasts in tumors reveals a new cancer-associated fibroblast state
Authors
Nicholas F. Kuhn , Itzia Zaleta-Linares , Kenneth H. Hu , Tristan Courau , Brittany Davidson , Tammie Tam , Chih-Wei Chu , Maxime J. Kinet , Michael D. Rosenblum , Alexis J. Combes , William A. Nyberg , Justin Eyquem , Matthew F. Krummel
Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states
Authors
Joel Babdor, Ravi Patel, Brittany Davidson, Alexis J Combes, Gabriela K Fradgiadakis, Matthew H Spitzer
Differential Assembly of Mouse and Human Tumor Microenvironments
Authors
Tristan Courau, Rebecca G. Jaszczak, Bushra Samad, Emily Flynn, Nayvin W. Chew, Gabriella C. Reeder, Jessica Tsui, Arja Ray, Harrison Wismer, Daniel Bunis, Leonard Lupin-Jimenez, Noah V. Gavil, David Masopust, John P. Graham, Daniel A. Skelly, Xavier Vesco, Edison T. Liu, Gabriela K. Fragiadakis, Alexis J. Combes, Matthew F. Krummel
Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of robust CD4+ T cell responses
Authors
Jillian M. Jespersen J, Lia Avanesyan, Jean Publicover, Nicholas D. Carey, Ravi K. Patel, Austin W. Edwards, Sarah Stenske, Jae Shin, Jiajing Li, Margaret Simone, Nayvin W. Chew, Nicholas Wong, Suprita Trilok, Ann Erickson, Arjun Rao, Christopher P. Loo, Michael Stec, Mark Anderson, Gavin Cloherty, Monika Sarkar, Alexis J. Combes, Adil E. Wakil, Mark R. Segal, Gabriela K. Fragiadakis, Stewart Cooper, Jody L. Baron
Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis.
Year2024
ProjectImmunoprofiling of Ulcerative Colitis Patients on Anti-Integrin Therapy
JournalNature
Open linkAuthors
Elvira Mennillo, Yang Joon Kim, Iulia Rusu, Gyehyun Lee, Leah C Dorman, Faviola Bernard-Vazquez, Jared L Bain, Ravi Patel, Christopher Andersen, Arjun Rao, Stanley Tamaki, Jessica Tsui, Alan Shen, Mohammad Naser, Walter Eckalbar, Soo-jin Cho, Kendall Beck, Najwa El-Nachef, Sara Lewin, Daniel R Selvig, Jonathan P Terdiman, Uma Mahadevan, David Oh, Gabriela K Fragiadakis, Angela Pisco, Alexis Combes, Michael G Kattah
Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes
Authors
Maha K Rahim, Trine Line H Okholm, Kyle B Jones, Elizabeth E McCarthy, Candace C Liu, Jacqueline L Yee, Stanley J Tamaki, Diana M Marquez, Iliana Tenvooren, Katherine Wai, Alexander Cheung, Brittany R Davidson, Vrinda Johri, Bushra Samad, William E O'Gorman, Matthew F Krummel, Annemieke van Zante, Alexis J Combes, Michael Angelo, Lawrence Fong, Alain P Algazi, Patrick Ha, Matthew H Spitzer
Transcriptional space-time mapping identifies concerted immune and stromal cell patterns and gene programs in wound healing and cancer
Authors
Kenneth H.Hu, Nicholas F.Kuhn,Tristan Courau,Jessica Tsui, Bushra Samad, Patrick Ha, Johannes R.Kratz, Alexis J.Combes, Matthew F.Krummel
SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants
Authors
Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP
Macrophage and CD8 T cell Discordance are Associated with Acute Lung Allograft Dysfunction Progression
Authors
Daniel R. Calabrese, Christina A. Ekstrand, Shivaram Yellamilli, Jonathan P. Singer, Steven R. Hays, Lorriana E. Leard, Rupal J. Shah, Aida Venado, Nicholas A. Kolaitis, Alyssa Perez, Alexis Combes, and John R. Greenland
High-dimensional immune cell profiling of cerebrospinal fluid from patients with metastatic breast cancer and leptomeningeal disease
Authors
K. W. Im, L. A. Huppert,L. Malevanchik,H. S. Rugo,A. J. Combes,M. J. Campbell,M. F. Krummel & M. E. Melisko
Astroglial toxicity promotes synaptic degeneration in the thalamocortical circuit in frontotemporal dementia with GRN mutations
Authors
Elise Marsan, Dmitry Velmeshev, Arren Ramsey, Ravi K Patel, Jiasheng Zhang, Mark Koontz, Madeline G Andrews, Martina de Majo, Cristina Mora, Jessica Blumenfeld, Alissa N Li, Salvatore Spina, Lea T Grinberg, William W Seeley, Bruce L Miller, Erik M Ullian, Matthew F Krummel, Arnold R Kriegstein, Eric J Huang
Transcriptional space-time mapping identifies concerted immune and stromal cell patterns and gene programs in wound healing and cancer
Authors
Kenneth H. Hu, Nicholas F. Kuhn, Tristan Courau, Jessica Tsui, Bushra Samad, Patrick Ha, Johannes R. Kratz, Alexis J. Combes, Matthew F. Krummel
Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data
Authors
Ravi K Patel, Rebecca G Jaszczak, Im Kwok, Nicholas D Carey, Tristan Courau, Daniel Bunis, Bushra Samad, Lia Avanesyan, Nayvin W Chew, Sarah Stenske, Jillian M Jespersen, Jean Publicover, Austin Edwards, Mohammad Naser, Arjun A Rao, Leonard Lupin-Jimenez, Matthew F Krummel, Stewart Cooper, Jody Baron, Alexis J Combes, Gabriela K Fragiadakis
Discovering dominant tumor immune archetypes in a pan-cancer census
Authors
Alexis J Combes, Bushra Samad, Jessica Tsui, Nayvin W Chew, Peter Yan, Gabriella C Reeder, Divyashree Kushnoor, Alan Shen, Brittany Davidson, Andrea J Barczak, Michael Adkisson, Austin Edwards, Mohammad Naser, Kevin C Barry, Tristan Courau, Taymour Hammoudi, Rafael J Arguello, Arjun Arkal Rao, Adam B Olshen, Matthew Spitzer, Lawrence Fong, Amanda Nelson, Raj Kumar, Justin Lee, Arun Burra, Joy Hsu, Caroline Hackett, Karen Tolentino, Jasmine Sjarif, Peter Johnson, Evans Shao, Darrell Abrau, Leonard Lupin, Cole Shaw, Zachary Collins, Tasha Lea, Carlos Corvera, Eric Nakakura, Julia Carnevale, Michael Alvarado, Kimberley Loo, Lawrence Chen, Melissa Chow, Jennifer Grandis, Will Ryan, Ivan El-Sayed, David Jablons, Gavitt Woodard, Maxwell W Meng, Sima P Porten, Hideho Okada, Margaret Tempero, Andrew Ko, Kim Kirkwood, Scott Vandenberg, Denise Guevarra, Erica Oropeza, Chris Cyr, Pat Glenn, Jennifer Bolen, Amanda Morton, Walter Eckalbar, Cathy Cai, Jenny Zhan, Katelyn C Davis, Robin K Kelley, Jocelyn S Chapman, Chloe E Atreya, Amar Patel, Adil I Daud, Patrick Ha, Aaron A Diaz, Johannes R Kratz, Eric A Collisson, Gabriela K Fragiadakis, David J Erle, Alexandre Boissonnas, Saurabh Asthana, Vincent Chan, Matthew F Krummel
Holistic characterization of tumor monocyte-to-macrophage differentiation integrates distinct immune phenotypes in kidney cancer
Authors
Adriana M Mujal, Alexis J Combes, Arjun A Rao, Mikhail Binnewies, Bushra Samad, Jessica Tsui, Alexandre Boissonnas, Joshua L Pollack, Rafael J Arguello, Maxwell V Meng, Sima P Porten, Megan K Ruhland, Kevin C Barry, Vincent Chan, Matthew F Krummel
Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer
Authors
Kelly Kersten, Kenneth H Hu, Alexis J Combes, Bushra Samad, Tory Harwin, Arja Ray, Arjun Arkal Rao, En Cai, Kyle Marchuk, Jordan Artichoker, Tristan Courau, Quanming Shi, Julia Belk, Ansuman T Satpathy, Matthew F Krummel
Mass cytometry reveals a conserved immune trajectory of recovery in hospitalized COVID-19 patients
Authors
Burnett CE, Okholm TLH, Tenvooren I, Marquez DM, Tamaki S, Munoz Sandoval P, Willmore A; UCSF COMET Consortium; Hendrickson CM, Kangelaris KN, Langelier CR, Krummel MF, Woodruff PG, Calfee CS, Erle DJ, Ansel KM, Spitzer MH
Plasma SARS-CoV-2 nucleocapsid antigen levels are associated with progression to severe disease in hospitalized COVID-19
Authors
Wick KD, Leligdowicz A, Willmore A, Carrillo SA, Ghale R, Jauregui A, Chak SS, Nguyen V, Lee D, Jones C, Dewar R, Lane HC, Kangelaris KN, Hendrickson CM, Liu KD, Sinha P, Erle DJ, Langelier CR, Krummel MF, Woodruff PG, Calfee CS, Matthay MA; COMET Consortium
Deep immunophenotyping reveals endometriosis is marked by dysregulation of the mononuclear phagocytic system in endometrium and peripheral blood
Authors
Julia Vallve-Juanico, Ashley F George, Sushmita Sen, Reuben Thomas, Min-Gyoung Shin, Divyashree Kushnoor, Joshua J Vasquez, Kim Chi Vo, Juan C Irwin, Nadia R Roan, Alexis J Combes, Linda C Giudice
Activating immune recognition in pancreatic ductal adenocarcinoma via autophagy inhibition, MEK blockade, and CD40 agonism
Authors
Honglin Jiang, Tristan Courau, Joseph Borison, Alexa J Ritchie, Aaron T Mayer, Matthew F Krummel, Eric A Collisson
A tumor-specific mechanism of Treg enrichment mediated by the integrin _v_8
Authors
Robert I Seed, Kenji Kobayashi, Saburo Ito, Naoki Takasaka, Anthony Cormier, Jillian M Jespersen, Jean Publicover, Suprita Trilok, Alexis J Combes, Nayvin W Chew, Jocelyne Chapman, Matthew F Krummel, Jianlong Lou, James Marks, Yifan Cheng, Jody L Baron, Stephen L Nishimura
Active surveillance characterizes human intratumoral T cell exhaustion
Authors
Ran You, Jordan Artichoker, Adam Fries, Austin W Edwards, Alexis J Combes, Gabriella C Reeder, Bushra Samad, Matthew F Krummel
Global Absence and Targeting of Protective Immune States in Severe COVID-19
Authors
Alexis J Combes, Tristan Courau, Nicholas F Kuhn, Kenneth H Hu, Arja Ray, William S Chen, Nayvin W Chew, Simon J Cleary, Divyashree Kushnoor, Gabriella C Reeder, Alan Shen, Jessica Tsui, Kamir J Hiam-Galvez, Priscila Munoz-Sandoval, Wandi S Zhu, David S Lee, Yang Sun, Ran You, Melia Magnen, Lauren Rodriguez, KW Im, Nina K Serwas, Aleksandra Leligdowicz, Colin R Zamecnik, Rita P Loudermilk, Michael R Wilson, Chun J Ye, Gabriela K Fragiadakis, Mark R Looney, Vincent Chan, Alyssa Ward, Sidney Carrillo, Michael Matthay, David J Erle, Prescott G Woodruff, Charles Langelier, Kirsten Kangelaris, Carolyn M Hendrickson, Carolyn Calfee, Arjun Arkal Rao, Matthew F Krummel
Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19
Authors
Monique GP van der Wijst, Sara E Vazquez, George C Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno, David S Lee, John R Greenland, Yang Sun, Richard Perez, Anton Ogorodnikov, Alyssa Ward, Sabrina A Mann, Kara L Lynch, Cassandra Yun, Diane V Havlir, Gabriel Chamie, Carina Marquez, Bryan Greenhouse, Michail S Lionakis, Philip J Norris, Larry J Dumont, Kathleen Kelly, Peng Zhang, Qian Zhang, Adrian Gervais, Tom Le Voyer, Alexander Whatley, Yichen Si, Ashley Byrne, Alexis J Combes, Arjun Arkal Rao, Yun S Song, Gabriela K Fragiadakis, Kirsten Kangelaris, Carolyn S Calfee, David J Erle, Carolyn Hendrickson, Matthew F Krummel, Prescott G Woodruff, Charles R Langelier, Jean-Laurent Casanova, Joseph L Derisi, Mark S Anderson, Chun Jimmie Ye, UCSF COMET consortium
Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS
Authors
Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F, Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA; COMET Consortium; Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR
The intersection of COVID-19 and autoimmunity
Authors
Jason S Knight, Roberto Caricchio, Jean-Laurent Casanova, Alexis J Combes, Betty Diamond, Sharon E Fox, David A Hanauer, Judith A James, Yogendra Kanthi, Virginia Ladd, Puja Mehta, Aaron M Ring, Ignacio Sanz, Carlo Selmi, Russell P Tracy, Paul J Utz, Catriona A Wagner, Julia Y Wang, William J McCune
A "data sharing trust" model for rapid, collaborative science
Authors
Vincent Chan, Pier Federico Gherardini, Matthew F Krummel, Gabriela K Fragiadakis
Genetic and immunologic features of recurrent stage I lung adenocarcinoma
Authors
Johannes R Kratz, Jack Z Li, Jessica Tsui, Jen C Lee, Vivianne W Ding, Arjun A Rao, Michael J Mann, Vincent Chan, Alexis J Combes, Matthew F Krummel, David M Jablons
SCENITH: a flow cytometry-based method to functionally profile energy metabolism with single-cell resolution
Authors
Rafael J Arguello, Alexis J Combes, Remy Char, Julien-Paul Gigan, Ania I Baaziz, Evens Bousiquot, Voahirana Camosseto, Bushra Samad, Jessica Tsui, Peter Yan, Sebastien Boissonneau, Dominique Figarella-Branger, Evelina Gatti, Emeline Tabouret, Matthew F Krummel, Philippe Pierre
Unleashing type-2 dendritic cells to drive protective antitumor CD4+ T cell immunity
Authors
Mikhail Binnewies, Adriana M Mujal, Joshua L Pollack, Alexis J Combes, Emily A Hardison, Kevin C Barry, Jessica Tsui, Megan K Ruhland, Kelly Kersten, Marwan A Abushawish, Marko Spasic, Jonathan P Giurintano, Vincent Chan, Adil I Daud, Patrick Ha, J Ye Chun, Edward W Roberts, Matthew F Krummel
A natural killer dendritic cell axis defines checkpoint therapy responsive tumor microenvironments
Authors
Kevin C Barry, Joy Hsu, Miranda L Broz, Francisco J Cueto, Mikhail Binnewies, Alexis J Combes, Amanda E Nelson, Kimberly Loo, Raj Kumar, Michael D Rosenblum, Michael D Alvarado, Denise M Wolf, Dusan Bogunovic, Nina Bhardwaj, Adil I Daud, Patrick K Ha, William R Ryan, Joshua L Pollack, Bushra Samad, Saurabh Asthana, Vincent Chan, Matthew F Krummel