Publications | UCSF CoLabs

Authors: Flynn Emily, Almonte-Loya Ana, Fragiadakis Gabriela K.

Journal:

Annual Review of Biomedical Data Science

May 2023

Glioblastoma remodelling of human neural circuits decreases survival

Authors: Krishna Saritha, Choudhury Abrar, Keough Michael B., Seo Kyounghee, Ni Lijun, Kakaizada Sofia, Lee Anthony, Aabedi Alexander, Popova Galina, Lipkin Benjamin, Cao Caroline, Nava Gonzales Cesar, Sudharshan Rasika, Egladyous Andrew, Almeida Nyle, Zhang Yalan, Molinaro Annette M., Venkatesh Humsa S., Da... See more

Journal:

Nature

May 2023

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 Ra... See more

March 2023

Hyperstabilization of T cell microvilli contacts by chimeric antigen receptors

Authors: Beppler Casey, Eichorst John, Marchuk Kyle, Cai En, Castellanos Carlos A., Sriram Venkataraman, Roybal Kole T., Krummel Matthew F.

Journal:

Journal of Cell Biology

March 2023

Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes

Authors: Rahim Maha K., Okholm Trine Line H., Jones Kyle B., McCarthy Elizabeth E., Liu Candace C., Yee Jacqueline L., Tamaki Stanley J., Marquez Diana M., Tenvooren Iliana, Wai Katherine, Cheung Alexander, Davidson Brittany R., Johri Vrinda, Samad Bushra, O’Gorman William E., Krummel Matthew F., van Zante A... See more

Journal:

Cell

March 2023

Polyunsaturated fatty acid-bound alpha-fetoprotein promotes immune suppression by altering human dendritic cell metabolism

Authors: Munson Paul V., Adamik Juraj, Hartmann Felix J., Favaro Patricia M. B., Ho Daniel, Bendall Sean C., Combes Alexis J., Krummel Matthew F., Zhang Karen, Kelley Robin K., Butterfield Lisa H.

Journal:

Cancer Research

February 2023

Patients with abdominal aortic aneurysms have reduced levels of microRNA 122-5p in circulating exosomes

Authors: Lopez Jose L., Ramirez Joel L., Phu Tuan Anh, Duong Phat, Bouchareychas Laura, Kuhrau Christina R., Lin Pei-Yu, Eckalbar Walter L., Barczak Andrea J., Rudolph Joshua D., Maliskova Lenka, Conte Michael S., Vartanian Shant M., Raffai Robert L., Oskowitz Adam Z., Subramanian Venkateswaran

Journal:

PLOS ONE

February 2023

Tissue-specific abundance of interferon-gamma drives regulatory T cells to restrain DC1-mediated priming of cytotoxic T cells against lung cancer

Authors: Zagorulya Maria, Yim Leon, Morgan Duncan M., Edwards Austin, Torres-Mejia Elen, Momin Noor, McCreery Chloe V., Zamora Izabella L., Horton Brendan L., Fox James G., Wittrup K. Dane, Love J. Christopher, Spranger Stefani

Journal:

Immunity

February 2023

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

Authors: 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... See more

Journal:

Stem Cell Reports

February 2023

Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet

Authors: Wastyk Hannah C., Perelman Dalia, Topf Madeline, Fragiadakis Gabriela K., Robinson Jennifer L., Sonnenburg Justin L., Gardner Christopher D., Sonnenburg Erica D.

Journal:

Gut Microbes

January 2023

Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma

Authors: Koh Kyung Duk, Bonser Luke R., Eckalbar Walter L., Yizhar-Barnea Ofer, Shen Jiangshan, Zeng Xiaoning, Hargett Kirsten L., Sun Dingyuan I., Zlock Lorna T., Finkbeiner Walter E., Ahituv Nadav, Erle David J.

Journal:

Cell Genomics

December 2022

Selective decrease of donor-reactive T after liver transplantation limits T therapy for promoting allograft tolerance in humans

Authors: Tang Qizhi, Leung Joey, Peng Yani, Sanchez-Fueyo Alberto, Lozano Juan-Jose, Lam Alice, Lee Karim, Greenland John R., Hellerstein Marc, Fitch Mark, Li Kelvin W., Esensten Jonathan H., Putnam Amy L., Lares Angela, Nguyen Vinh, Liu Weihong, Bridges Nancy D., Odim Jonah, Demetris Anthony J., Levitsky Jo... See more

Journal:

Science Translational Medicine

November 2022

Archetypes of checkpoint-responsive immunity

Authors: Im Kwok, Combes Alexis J., Spitzer Matthew H., Satpathy Ansuman T., Krummel Matthew F.

Journal:

Trends in Immunology

October 2022

Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells

Authors: Adamik Juraj, Munson Paul V., Hartmann Felix J., Combes Alexis J., Pierre Philippe, Krummel Matthew F., Bendall Sean C., Argüello Rafael J., Butterfield Lisa H.

Journal:

Nature Communications

September 2022

Tumor-Associated Macrophage Heterogeneity is Driven by Tissue Territories in Breast Cancer

Authors: Laviron Marie, Petit Maxime, Weber-Delacroix Eléonore, Combes Alexis J., Arkal Arjun Rao, Barthélémy Sandrine, Courau Tristan, Hume David A., Combadière Christophe, Krummel Matthew F., Boissonnas Alexandre

Journal:

Cell Reports

September 2022

T Cells Use Distinct Topographical and Membrane Receptor Scanning Strategies that Individually Coalesce During Receptor Recognition

Authors: Cai En, Beppler Casey, Eichorst John, Marchuk Kyle, Eastman Scott W., Krummel Matthew F.

Journal:

Proceedings of the National Academy of Sciences

August 2022

A Functional Circuit Formed by the Autonomic Nerves and Myofibroblasts Controls Mammalian Alveolar Formation for Gas Exchange

Authors: Zhang Kuan, Yao Erica, Wang Shao-An, Chuang Ethan, Wong Julia, Minichiello Liliana, Schroeder Andrew, Eckalbar Walter, Wolters Paul J., Chuang Pao-Tien

Journal:

Developmental Cell

July 2022

Spatiotemporal Co-Dependency Between Macrophages and Exhausted CD8+ T Cells in Cancer

Authors: Kersten Kelly, Hu Kenneth H., Combes Alexis J., Samad Bushra, Harwin Tory, Ray Arja, Rao Arjun Arkal, Cai En, Marchuk Kyle, Artichoker Jordan, Courau Tristan, Shi Quanming, Belk Julia, Satpathy Ansuman T., Krummel Matthew F.

Journal:

Cancer Cell

June 2022

Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis

Authors: 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,&... See more

June 2022

Deep Immunophenotyping Reveals Endometriosis is Marked by Dysregulation of the Mononuclear Phagocytic System in Endometrium and Peripheral Blood

Authors: Vallvé-Juanico Júlia, George Ashley F, Sen Sushmita, Thomas Reuben, Shin Min-Gyoung, Kushnoor Divyashree, Vásquez Joshua J, Vo Kim Chi, Irwin Juan C, Roan Nadia R, Combes Alexis J, Giudice Linda C. 

Journal:

BMC Medicine

April 2022