Publications | UCSF CoLabs

Macrophage-fibroblast crosstalk drives Arg1-dependent lung fibrosis via ornithine loading

Authors: Yadav Preeti, Ortega Javier Gómez, Tamaki Whitney, Chien Charles, Chang Kai-chun, Biswas Nivedita, Pan Sixuan, Nilsson Julia, Yin Xiaoyang, Bhattacharyya Aritra, Boostanpour Kaveh, Jujaray Tanay, Wang Jasper, Tsukui Tatsuya, Sheppard Dean, Li Baosheng, Maishan Mazharul, Taenaka Hiroki, Matthay Micha... See more

September 2023

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

Authors: 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 Stewa... See more

Journal:

Frontiers in Immunology

September 2023

Organic Matrix Derived from Host–Microbe Interplay Contributes to Pathological Renal Biomineralization

Authors: Bai Yushi, Wang Yongmei, Kang Misun, Gabe Claire M., Srirangapatanam Sudarshan, Edwards Austin, Stoller Marshall, Green Stefan J., Aloni Shaul, Tamura Nobumichi, Beniash Elia, Hardt Markus, Ho Sunita P.

Journal:

ACS Nanoscience Au

July 2023

A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer

Authors: Stashko Connor, Hayward Mary-Kate, Northey Jason J., Pearson Neil, Ironside Alastair J., Lakins Johnathon N., Oria Roger, Goyette Marie-Anne, Mayo Lakyn, Russnes Hege G., Hwang E. Shelley, Kutys Matthew L., Polyak Kornelia, Weaver Valerie M.

Journal:

Nature Communications

June 2023

Defining and using immune archetypes to classify and treat cancer

Authors: Combes Alexis J., Samad Bushra, Krummel Matthew F.

Journal:

Nature Reviews Cancer

June 2023

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

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

Journal:

Cell Stem Cell

June 2023

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients

Authors: Diray-Arce Joann, Fourati Slim, Doni Jayavelu Naresh, Patel Ravi, Maguire Cole, Chang Ana C., Dandekar Ravi, Qi Jingjing, Lee Brian H., van Zalm Patrick, Schroeder Andrew, Chen Ernie, Konstorum Anna, Brito Anderson, Gygi Jeremy P., Kho Alvin, Chen Jing, Pawar Shrikant, Gonzalez-Reiche Ana Silvia, Ho... Diray-Arce Joann, Fourati Slim, Doni Jayavelu Naresh, Patel Ravi, Maguire Cole, Chang Ana C., Dandekar Ravi, Qi Jingjing, Lee Brian H., van Zalm Patrick, Schroeder Andrew, Chen Ernie, Konstorum Anna, Brito Anderson, Gygi Jeremy P., Kho Alvin, Chen Jing, Pawar Shrikant, Gonzalez-Reiche Ana Silvia, Hoch Annmarie, Milliren Carly E., Overton James A., Westendorf Kerstin, Cairns Charles B., Rouphael Nadine, Bosinger Steven E., Kim-Schulze Seunghee, Krammer Florian, Rosen Lindsey, Grubaugh Nathan D., van Bakel Harm, Wilson Michael, Rajan Jayant, Steen Hanno, Eckalbar Walter, Cotsapas Chris, Langelier Charles R., Levy Ofer, Altman Matthew C., Maecker Holden, Montgomery Ruth R., Haddad Elias K., Sekaly Rafick P., Esserman Denise, Ozonoff Al, Becker Patrice M., Augustine Alison D., Guan Leying, Peters Bjoern, Kleinstein Steven H., Abraham James, Adkisson Michael, Albert Marisa, Altamirano Luz Torres, Alvarenga Bonny, Anderson Matthew L., Anderson Evan J., Arnett Azlann, Asashima Hiromitsu, Atkinson Mark A., Baden Lindsey R., Barton Brenda, Beach Katherine, Beagle Elizabeth, Becker Patrice M., Bell Matthew R., Bernui Mariana, Bime Christian, Boddapati Arun Kumar, Booth J. Leland, Borresen Brittney, Brakenridge Scott C., Bristow Laurel, Bryant Robert, Calfee Carolyn S., Carreño Juan Manuel, Carrillo Sidney, Chak Suzanna, Chang Iris, Connors Jennifer, Conway Michelle, Corry David B., Cowan David, Croen Brett, Dela Cruz Charles S., Cusimano Gina, Eaker Lily, Edwards Carolyn, Ehrlich Lauren I.R., Elashoff David, Erickson Heidi, Erle David J., Farhadian Shelli, Farrugia Keith, Fatou Benoit, Fernandes Andrea, Fernandez-Sesma Ana, Fragiadakis Gabriela K., Furukawa Sara, Geltman Janelle N., Ghale Rajani, Bermúdez González Maria Carolina, Goonewardene I. Michael, Guerrero Estella Sanchez, Guirgis Faheem W., Hafler David A., Hamilton Sydney, Harris Paul, Hayati Arash Nemati, Hendrickson Carolyn M., Agudelo Higuita Nelson I., Hodder Thomas, Holland Steven M., Hough Catherine L., Huerta Christopher, Hurley Kerin C., Hutton Scott R., Iwasaki Akiko, Jauregui Alejandra, Jha Meenakshi, Johnson Brandi, Joyner David, Kangelaris Kirsten N., Kelly Geoffrey, Khalil Zain, Khan Zenab, Kheradmand Farrah, Kim James N., Kimura Hiroki, Ko Albert I., Kohr Bernard, Kraft Monica, Krummel Matthew, Kutzler Michele A., Lasky-Su Jessica, Lee Serena, Lee Deanna, Leipold Michael, Lentucci Claudia, Leroux Carolyn, Lin Edward, Liu Shanshan, Love Christina, Lu Zhengchun, Maliskova Lenka, Manning Brittany Roth, Manohar Monali, Martens Mark, McComsey Grace A., McEnaney Kerry, McLin Renee, Melamed Esther, Melnyk Nataliya, Mendez Kevin, Messer William B., Metcalf Jordan P., Michelotti Gregory, Mick Eran, Mohanty Subhasis, Mosier Jarrod, Mulder Lubbertus C.F., Murphy Maimouna, Nadeau Kari R.C., Nelson Ebony, Nelson Allison, Nguyen Viet, Oberhaus Jordan, Panganiban Bernadine, Pellegrini Kathryn L., Pickering Harry C., Powell Debra L., Presnell Scott, Pulendran Bali, Rahman Adeeb H., Rashid Ahmad Sadeed, Raskin Ariel, Reed Elaine F., Ribeiro Susan Pereira, Rivera Adreanne M., Rogers Jacob E., Rogers Angela, Rogowski Brandon, Rooks Rebecca, Rosenberg-Hasson Yael, Rothman Jessica, Rousseau Justin F., Salehi-Rad Ramin, Saluvan Mehmet, Samaha Hady, Schaenman Joanna, Schunk Ron, Semenza Nicholas C., Sen Subha, Sevransky Jonathan, Seyfert-Margolis Vicki, Shaheen Tanzia, Shaw Albert C., Sieg Scott, Siegel Sarah A.R., Sigal Natalia, Siles Nadia, Simmons Brent, Simon Viviana, Singh Gagandeep, Sinko Lauren, Smith Cecilia M., Smolen Kinga K., Song Li-Zhen, Srivastava Komal, Sullivan Peter, Syphurs Caitlin, Tcheou Johnstone, Tegos George P., Tharp Greg K., Tong Alexandra, Tsitsiklis Alexandra, Ungaro Ricardo F., Vaysman Tatyana, Viode Arthur, Vita Randi, Wang Xiaomei, Ward Alyssa, Ward Dawn C., Willmore Andrew, Woloszczuk Kyra, Wong Kari, Woodruff Prescott G., Xu Leqi, van Haren Simon, van de Guchte Adriana, Zhao Yujiao See more

Journal:

Cell Reports Medicine

June 2023

Single-Cell Multiomics

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