Alexis J. Combes - Publications, H-index & Citations

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Alexis J. Combes

UCSF

27H-index

148Paper Count

5.1KCitation Count

Published Papers 40

Publication Date

Differential assembly of mouse and human tumor microenvironments

Nature Immunology

IF27.6

2026-05-19

OAAI

Tristan Courau; Rebecca G. Jaszczak; Bushra Samad; Emily Flynn; Nayvin W. Chew; Gabriella C. Reeder; Jessica Tsui; Semhar Teklu; Lomax F. Pass; Austin W. Edwards; Mohammad Naser; 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

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Clinical cure of chronic hepatitis B is associated with priming and perpetuation of hepatic CD4+ T cell responses

Science Translational Medicine

IF14.6

2026-04-29

PREAI

Jillian M. Jespersen; 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; Stephen L. Nishimura; Alexis J. Combes; Adil E. Wakil; Mark R. Segal; Gabriela K. Fragiadakis; Stewart L. Cooper; Jody L. Baron

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Single-cell spatiotemporal dissection of the human maternal–fetal interface

Nature

IF48.5

2026-04-08

OAAI

Cheng Wang; Yan Zhou; Yuejun Wang; Tuhin Kumar Guha; Zhida Luo; Anxhela Mustafaraj; Tara I. McIntyre; Marisa E. Schwab; Brittany R. Davidson; Gabriella C. Reeder; Ronald J. Wong; Sarah K. England; Juan M. Gonzalez; Robert Blelloch; Alexis J. Combes; Linda C. Giudice; Adrian Erlebacher; Tippi C. MacKenzie; David K. Stevenson; Gary M. Shaw; Michael P. Snyder; Xiaofei Sun; Virginia D. Winn; Susan J. Fisher; Jingjing Li

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The coming era of nudge drugs for cancer

Cancer Cell

IF44.5

2025-09-11

PREAI

Tristan Courau; Arpita Desai; Allon Wagner; Alexis J. Combes; Matthew F. Krummel

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Anticlustering for sample allocation to minimize batch effects

Cell Reports Methods

IF4.5

2025-08-18

OAAI

Martin Papenberg; Cheng Wang; Maïgane Diop; Syed Hassan Bukhari; Boris Oskotsky; Brittany R. Davidson; Kim Chi Vo; Binya Liu; Juan C. Irwin; Alexis J. Combes; Brice Gaudilliere; Jingjing Li; David K. Stevenson; Gunnar W. Klau; Linda C. Giudice; Marina Sirota; Tomiko T. Oskotsky

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Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions.

Blood Advances

IF7.1

2025-08-05

OAAI

Laila Karra; Anna-Marie Finger; Lauren Shechtman; Milana Krush; Rita Meng-Yao Huang; Morgan Prinz; Iliana Tennvooren; Kriti Bahl; Lisiena Hysienaj; Paulina G. Gonzalez; Alexis J. Combes; Hugo Gonzalez; Rafael J. Argüello; Matthew H. Spitzer; Jeroen P. Roose

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Multimodal delineation of a layer of effector function among exhausted CD8 T cells in tumors

Science Immunology

IF16.3

2025-07-11

PREAI

Arja Ray; Molly Bassette; Kenneth H. Hu; Lomax F. Pass; Tristan Courau; Bushra Samad; Alexis J. Combes; Vrinda Johri; Brittany Davidson; Katherine Wai; Patrick Ha; Grace Hernandez; Itzia Zaleta-Linares; Matthew F. Krummel

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Persistent and progressive acute lung allograft dysfunction is linked to cell compositional and transcriptional changes in small airways

heart and lung transplantation

IF0

2025-04-28

OAAI

Elsa Brunet-Ratnasingham; Shivaram Yellamilli; Ruyin Guo; Rashmi Prava Mohanty; Allen Duong; Nicholas A. Kolaitis; Steven R. Hays; Rupal J. Shah; Aida Venado; Julia A. Maheshwari; Mary Ellen Kleinhenz; Lorriana E. Leard; John McDyer; Tereza Martinu; Alexis J. Combes; Daniel R. Calabrese; Jonathan P. Singer; John R. Greenland

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Tumor cell heterogeneity drives spatial organization of the intratumoral immune response

JOURNAL OF EXPERIMENTAL MEDICINE

IF10.6

2025-04-01

PREAI

Tanaka, Miho; Lum, Lotus; Hu, Kenneth H.; Chaudhary, Piyush; Hughes, Savannah; Ledezma-Soto, Cecilia; Samad, Bushra; Superville, Daphne; Ng, Kenneth; Chumber, Arun; Benson, Ciara; Adams, Zoe N.; Kersten, Kelly; Aguilar, Oscar A.; Fong, Lawrence; Combes, Alexis J.; Krummel, Matthew F.; Reeves, Melissa Q.

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Targeting CD206+ macrophages disrupts the establishment of a key antitumor immune axis

JOURNAL OF EXPERIMENTAL MEDICINE

IF10.6

2024-11-27

PREAI

Ray, Arja; Hu, Kenneth H.; Kersten, Kelly; Courau, Tristan; Kuhn, Nicholas F.; Zaleta-Linares, Itzia; Samad, Bushra; Combes, Alexis J.; Krummel, Matthew F.

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Chromatin Remodeling Drives Immune-Fibroblast Cell Communication in Heart Failure

CIRCULATION

IF38.6

2024-11-12

PREAI

Alexanian, Michael; Padmanabhan, Arun; Nishino, Tomohiro; Travers, Joshua; Ye, Lin; Angelo, Pelonero; Lee, Clara; Sadagopan, Nandhini; Huang, Yu; Auclair, Kirsten; Zhu, Ada; An, Yuqian; Ekstrand, Christina; Martinez, Cassandra; Teran, Barbara Gonzalez; Flanigan, Will; Kim, Charis Kee-Seon; Conradson, Devon; Gardner, Zachary; Li, Li; Costa, Mauro; Jain, Rajan; Charo, Israel; Combes, Alexis; Haldar, Saptarsi; Pollard, Katherine; Vagnozzi, Ronald; McKinsey, Timothy; Przytycki, Pawel; Srivastava, Deepak

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Macrophage and CD8 T cell discordance are associated with acute lung allograft dysfunction progression

JOURNAL OF HEART AND LUNG TRANSPLANTATION

IF6

2024-07-01

OAAI

Calabrese, Daniel R.; Ekstrand, Christina A.; Yellamilli, Shivaram; Singer, Jonathan P.; Hays, Steven R.; Leard, Lorriana E.; Shah, Rupal J.; Venado, Aida; Kolaitis, Nicholas A.; Perez, Alyssa; Combes, Alexis; Greenland, John R.

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Tumor-associated macrophages restrict CD8+ T cell function through collagen deposition and metabolic reprogramming of the breast cancer microenvironment

NATURE CANCER

IF28.5

2024-06-03

PREAI

Tharp, Kevin M.; Kersten, Kelly; Maller, Ori; Timblin, Greg A.; Stashko, Connor; Canale, Fernando P.; Menjivar, Rosa E.; Hayward, Mary-Kate; Berestjuk, Ilona; ten Hoeve, Johanna; Samad, Bushra; Ironside, Alastrair J.; di Magliano, Marina Pasca; Muir, Alexander; Geiger, Roger; Combes, Alexis J.; Weaver, Valerie M.

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Leukemia inhibitory factor creates an immune suppressive tumor microenvironment and fosters tumor growth in KRAS-driven pancreatic ductal adenocarcinoma

CANCER RESEARCH

IF16.6

2024-03-22

PREAI

Miller-Phillips, Lisa; Hanafi, Imene Boukhalfa; Combes, Alexis J.; Bano, Shabana; Hysenaj, Lisiena; Roose, Jeroen P.; Olshen, Adam; Kiemen, Ashley; Umetsu, Sarah; Wang, Man-Tzu; Collisson, Eric A.

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Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

NATURE COMMUNICATIONS

IF15.7

2024-02-19

OAAI

Mennillo, Elvira; Kim, Yang Joon; Lee, Gyehyun; Rusu, Iulia; Patel, Ravi K.; Dorman, Leah C.; Flynn, Emily; Li, Stephanie; Bain, Jared L.; Andersen, Christopher; Rao, Arjun; Tamaki, Stanley; Tsui, Jessica; Shen, Alan; Lotstein, Madison L.; Rahim, Maha; Naser, Mohammad; Bernard-Vazquez, Faviola; Eckalbar, Walter; Cho, Soo-jin; Beck, Kendall; El-Nachef, Najwa; Lewin, Sara; Selvig, Daniel R.; Terdiman, Jonathan P.; Mahadevan, Uma; Oh, David Y.; Fragiadakis, Gabriela K.; Pisco, Angela; Combes, Alexis J.; Kattah, Michael G.

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Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data

FRONTIERS IN IMMUNOLOGY

IF5.9

2023-09-04

OAAI

Patel, Ravi K.; Jaszczak, Rebecca G.; Im, Kwok; Carey, Nicholas D.; Courau, Tristan; Bunis, Daniel G.; Samad, Bushra; Avanesyan, Lia; Chew, Nayvin W.; Stenske, Sarah; Jespersen, Jillian M.; Publicover, Jean; Edwards, Austin W.; Naser, Mohammad; Rao, Arjun A.; Lupin-Jimenez, Leonard; Krummel, Matthew F.; Cooper, Stewart; Baron, Jody L.; Combes, Alexis J.; Fragiadakis, Gabriela K.

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Defining and using immune archetypes to classify and treat cancer

NATURE REVIEWS CANCER

IF66.8

2023-06-05

PREAI

Combes, Alexis J.; Samad, Bushra; Krummel, Matthew F.

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Transcriptional space-time mapping identifies concerted immune and stromal cell patterns and gene programs in wound healing and cancer

CELL STEM CELL

IF20.4

2023-06-01

OAAI

Hu, Kenneth H.; Kuhn, Nicholas F.; Courau, Tristan; Tsui, Jessica; Samad, Bushra; Ha, Patrick; Kratz, Johannes R.; Combes, Alexis J.; Krummel, Matthew F.

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High-dimensional immune cell profiling of cerebrospinal fluid from patients with metastatic breast cancer and leptomeningeal disease

NPJ BREAST CANCER

IF7.6

2023-04-07

OAAI

Im, K. W.; Huppert, L. A.; Malevanchik, L.; Rugo, H. S.; Combes, A. J.; Campbell, M. J.; Krummel, M. F.; Melisko, M. E.

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SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants

STEM CELL REPORTS

IF5.1

2023-03-01

OAAI

Hysenaj, Lisiena; Little, Samantha; Kulhanek, Kayla; Magnen, Melia; Bahl, Kriti; Gbenedio, Oghenekevwe M.; Prinz, Morgan; Rodriguez, Lauren; Andersen, Christopher; Rao, Arjun Arkal; Shen, Alan; Lone, Jean-Christophe; Lupin-Jimenez, Leonard C.; Bonser, Luke R.; Serwas, Nina K.; Mick, Eran; Khalid, Mir M.; Taha, Taha Y.; Kumar, Renuka; Li, Jack Z.; Ding, Vivianne W.; Matsumoto, Shotaro; Maishan, Mazharul; Sreekumar, Bharath; Simoneau, Camille; Nazarenko, Irina; Tomlinson, Michael G.; Khan, Khajida; von Gottberg, Anne; Sigal, Alex; Looney, Mark R.; Fragiadakis, Gabriela K.; Jablons, David M.; Langelier, Charles R.; Matthay, Michael; Krummel, Matthew; Erle, David J.; Combes, Alexis J.; Sil, Anita; Ott, Melanie; Kratz, Johannes R.; Roose, Jeroen P.

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Research Directions