Publications | UCSF CoLabs

CCR2 deficiency alters activation of microglia subsets in traumatic brain injury

Authors: Somebang Kerri, Rudolph Joshua, Imhof Isabella, Li Luyi, Niemi Erene C., Shigenaga Judy, Tran Huy, Gill T. Michael, Lo Iris, Zabel Brian A., Schmajuk Gabriela, Wipke Brian T., Gyoneva Stefka, Jandreski Luke, Craft Michael, Benedetto Gina, Plowey Edward D., Charo Israel, Campbell James, Ye Chun Jimmi... See more

Journal:

Cell Reports

September 2021

Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study

Authors: Rouphael Nadine, Maecker Holden, Montgomery Ruth R., Diray-Arce Joann, Kleinstein Steven H., Altman Matthew C., Bosinger Steven E., Eckalbar Walter, Guan Leying, Hough Catherine L., Krammer Florian, Langelier Charles, Levy Ofer, McEnaney Kerry, Peters Bjoern, Rahman Adeeb, Rajan Jayant V., Sigelman ... See more

Journal:

Science Immunology

August 2021

The WAVE complex associates with sites of saddle membrane curvature

Authors: Pipathsouk Anne, Brunetti Rachel M., Town Jason P., Graziano Brian R., Breuer Artù, Pellett Patrina A., Marchuk Kyle, Tran Ngoc-Han T., Krummel Matthew F., Stamou Dimitrios, Weiner Orion D.

Journal:

Journal of Cell Biology

August 2021

Gut-microbiota-targeted diets modulate human immune status

Journal:

Cell

August 2021

Cbl-b deficiency prevents functional but not phenotypic T cell anergy

Authors: Nguyen Trang T.T., Wang Zhi-En, Shen Lin, Schroeder Andrew, Eckalbar Walter, Weiss Arthur

Journal:

Journal of Experimental Medicine

July 2021

Single-Cell Transcriptome Analysis Defines Heterogeneity of the Murine Pancreatic Ductal Tree

Authors: Hendley Audrey M, Rao Arjun A, Leonhardt Laura, Ashe Sudipta, Smith Jennifer A, Giacometti Simone, Peng Xianlu L, Jiang Honglin, Berrios David I, Pawlak Mathias, Li Lucia Y, Lee Jonghyun, Collisson Eric A, Anderson Mark S, Fragiadakis Gabriela K, Yeh Jen Jen, Ye Chun Jimmie, Kim Grace E, Weaver Vale... See more

Journal:

eLife

May 2021

DNGR-1 Limits Flt3L-Mediated Antitumor Immunity by Restraining Tumor-Infiltrating Type I Conventional Dendritic Cells

Authors: Cueto Francisco J, del Fresno Carlos, Brandi Paola, Combes Alexis J., Hernández-García Elena, Sánchez-Paulete Alfonso R, Enamorado Michel, Bromley Christian P, Gomez Manuel J, Conde-Garrosa Ruth, Mañes Santos, Zelenay Santiago, Melero Ignacio, Iborra Salvador, Krummel Matthew F., Sancho David

Journal:

Journal for ImmunoTherapy of Cancer

May 2021

Gut-Microbiota-Targeted Diets Modulate Human Immune Status

Authors: Wastyk Hannah C., Fragiadakis Gabriela K., Perelman Dalia, Dahan Dylan, Merrill Bryan D., Yu Feiqiao B., Topf Madeline, Gonzalez Carlos G., Van Treuren William, Han Shuo, Robinson Jennifer L., Elias Joshua E., Sonnenburg Erica D., Gardner Christopher D., Sonnenburg Justin L.

Journal:

Cell

May 2021

Transcriptomic Analysis of Immune Cells in a Multi-Ethnic Cohort of Systemic Lupus Erythematosus Patients Identifies Ethnicity- and Disease-Specific Expression Signatures

Authors: Andreoletti Gaia, Lanata Cristina M., Trupin Laura, Paranjpe Ishan, Jain Tia S., Nititham Joanne, Taylor Kimberly E., Combes Alexis J., Maliskova Lenka, Ye Chun Jimmie, Katz Patricia, Dall’Era Maria, Yazdany Jinoos, Criswell Lindsey A., Sirota Marina

Journal:

Communications Biology

April 2021

A Tumor-Specific Mechanism of T Enrichment Mediated by the Integrin αvβ8

Authors: Seed Robert I., Kobayashi Kenji, Ito Saburo, Takasaka Naoki, Cormier Anthony, Jespersen Jillian M., Publicover Jean, Trilok Suprita, Combes Alexis J., Chew Nayvin W., Chapman Jocelyne, Krummel Matthew F., Lou Jianlong, Marks James, Cheng Yifan, Baron Jody L., Nishimura Stephen L.

Journal:

Science Immunology

March 2021

The SIRPα–CD47 immune checkpoint in NK cells

Authors: Deuse Tobias, Hu Xiaomeng, Agbor-Enoh Sean, Jang Moon K., Alawi Malik, Saygi Ceren, Gravina Alessia, Tediashvili Grigol, Nguyen Vinh Q., Liu Yuan, Valantine Hannah, Lanier Lewis L., Schrepfer Sonja

Journal:

Journal of Experimental Medicine

March 2021

Flow-Cytometric Analysis and Purification of Airway Epithelial-Cell Subsets

Authors: Bonser Luke R., Koh Kyung Duk, Johansson Kristina, Choksi Semil P., Cheng Dan, Liu Leqian, Sun Dingyuan I., Zlock Lorna T., Eckalbar Walter L., Finkbeiner Walter E., Erle David J.

Journal:

American Journal of Respiratory Cell and Molecular Biology

March 2021

A “Data Sharing Trust” Model for Rapid, Collaborative Science

Authors: Chan Vincent, Gherardini Pier Federico, Krummel Matthew F., Fragiadakis Gabriela K.

Journal:

Cell

February 2021

Global Absence and Targeting of Protective Immune States in Severe COVID-19

Authors: Combes Alexis J., Courau Tristan, Kuhn Nicholas F., Hu Kenneth H., Ray Arja, Chen William S., Chew Nayvin W., Cleary Simon J., Kushnoor Divyashree, Reeder Gabriella C., Shen Alan, Tsui Jessica, Hiam-Galvez Kamir J., Muñoz-Sandoval Priscila, Zhu Wandi S., Lee David S., Sun Yang, You Ran, Magnen Mélia... See more

Journal:

Nature

January 2021

The Type 2 Asthma Mediator IL-13 Inhibits Severe Acute Respiratory Syndrome Coronavirus 2 Infection of Bronchial Epithelium

Authors: Bonser Luke R., Eckalbar Walter L., Rodriguez Lauren, Shen Jiangshan, Koh Kyung Duk, Ghias Khadija, Zlock Lorna T., Christenson Stephanie, Woodruff Prescott G., Finkbeiner Walter E., Erle David J.

Journal:

American Journal of Respiratory Cell and Molecular Biology

January 2021

Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit

Authors: Bunis Daniel G, Andrews Jared, Fragiadakis Gabriela K, BurtTrevor D, Sirota Marina

Journal:

Bioinformatics

December 2020

SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution

Authors: Argüello Rafael J., Combes Alexis J., Char Remy, Gigan Julien-Paul, Baaziz Ania I., Bousiquot Evens, Camosseto Voahirana, Samad Bushra, Tsui Jessica, Yan Peter, Boissonneau Sebastien, Figarella-Branger Dominique, Gatti Evelina, Tabouret Emeline, Krummel Matthew F., Pierre Philippe

Journal:

Cell Metabolism

December 2020

Asthma and its Relationship to Mitochondrial Copy Number: Results from the Asthma Translational Genomics Collaborative (ATGC) of the Trans-Omics for Precision Medicine (TOPMed) Program

Authors: Cocco Maxwell P., White Evan, Xiao Shujie, Hu Donglei, Mak Angel, Sleiman Patrick, Yang Mao, Bobbitt Kevin R., Gui Hongsheng, Levin Albert M., Hochstadt Samantha, Whitehouse Kyle, Rynkowski Dean, Barczak Andrea J., Abecasis Gonçalo, Blackwell Thomas W., Kang Hyun Min, Nickerson Deborah A., Germer So... See more

Journal:

PLOS ONE

November 2020

Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome

Authors: Makki Nadja, Zhao Jingjing, Liu Zhaoyang, Eckalbar Walter L, Ushiki Aki, Khanshour Anas M, Wu Joe, Rios Jonathan, Gray Ryan S, Wise Carol A, Ahituv Nadav

Journal:

Human Molecular Genetics

November 2020

A defect in COPI-mediated transport of STING causes immune dysregulation in COPA syndrome

Authors: Deng Zimu, Chong Zhenlu, Law Christopher S., Mukai Kojiro, Ho Frances O., Martinu Tereza, Backes Bradley J., Eckalbar Walter L., Taguchi Tomohiko, Shum Anthony K.

Journal:

Journal of Experimental Medicine

November 2020