Publications | UCSF CoLabs

Minimalistic transcriptomic signatures permit accurate early prediction of COVID-19 mortality

Authors: Narendra Rithwik, Lydon Emily C., Phan Hoang Van, Spottiswoode Natasha, Neyton Lucile P., Diray-Arce Joann, Becker Patrice M., Kim-Schulze Seunghee, Hoch Annmarie, Pickering Harry, van Zalm Patrick, Cairns Charles B., Altman Matthew C., Augustine Alison D., Bosinger Steve, Eckalbar Walter, Guan Leyi... See more

Journal:

JCI Insight

November 2025

Type 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort

Authors: Jayavelu Naresh Doni, Qi Jingjing, Milliren Carly E., Ozonoff Al, Liu Shanshan, Levy Ofer, Baden Lindsey R., Melamed Esther, McComsey Grace A., Cairns Charles B., Schaenman Joanna, Shaw Albert C., Hafler David A., Corry David B., Kheradmand Farrah, Atkinson Mark A., Brakenridge Scott C., Agudelo Hig... Jayavelu Naresh Doni, Qi Jingjing, Milliren Carly E., Ozonoff Al, Liu Shanshan, Levy Ofer, Baden Lindsey R., Melamed Esther, McComsey Grace A., Cairns Charles B., Schaenman Joanna, Shaw Albert C., Hafler David A., Corry David B., Kheradmand Farrah, Atkinson Mark A., Brakenridge Scott C., Agudelo Higuita Nelson I., Metcalf Jordan P., Hough Catherine L., Messer William B., Pulendran Bali, Nadeau Kari C., Davis Mark M., Geng Linda N., Sesma Ana Fernandez, Simon Viviana, Krammer Florian, Bime Chris, Calfee Carolyn S., Bosinger Steven E., Eckalbar Walter, Steen Hanno, Maecker Holden T., Becker Patrice M., Augustine Alison D., Holland Steven M., Rosen Lindsey B., Lee Serena, Vaysman Tatyana, Ozonoff Al, Diray-Arce Joann, Chen Jing, Kho Alvin, Milliren Carly E., Hoch Annmarie, Chang Ana C., McEnaney Kerry, Barton Brenda, Lentucci Claudia, Murphy Maimouna D., Saluvan Mehmet, Shaheen Tanzia, Liu Shanshan, Syphurs Caitlin, Albert Marisa, Hayati Arash Nemati, Bryant Robert, Abraham James, Thomas Sanya, Cooney Mitchell, Karoly Meagan, Altman Matthew C., Jayavelu Naresh Doni, Presnell Scott, Kohr Bernard, Jancsyk Tomasz, Arnett Azlann, Peters Bjoern, Overton James A., Vita Randi, Westendorf Kerstin, Overton James A., Levy Ofer, Steen Hanno, van Zalm Patrick, Fatou Benoit, Smolen Kinga K., Viode Arthur, van Haren Simon, Jha Meenakshi, Stevenson David, Odumade Oludare, Baden Lindsey R., Mendez Kevin, Lasky-Su Jessica, Tong Alexandra, Rooks Rebecca, Desjardins Michael, Sherman Amy C., Walsh Stephen R., Mitre Xhoi, Cauley Jessica, Li Xiofang, Evans Bethany, Montesano Christina, Licona Jose Humberto, Krauss Jonathan, Issa Nicholas C., Park Chang Jun Bai, Izaguirre Natalie, Hutton Scott R., Michelotti Greg, Wong Kari, Tebbutt Scott J., Shannon Casey P., Sekaly Rafick-Pierre, Fourati Slim, McComsey Grace A., Harris Paul, Sieg Scott, Ribeiro Susan Pereira, Cairns Charles B., Haddad Elias K., Kutzler Michele A., Bernui Mariana, Cusimano Gina, Connors Jennifer, Woloszczuk Kyra, Joyner David, Edwards Carolyn, Lee Edward, Lin Edward, Melnyk Nataliya, Powell Debra L., Kim James N., Goonewardene I. Michael, Simmons Brent, Smith Cecilia M., Martens Mark, Croen Brett, Semenza Nicholas C., Bell Mathew R., Furukawa Sara, McLin Renee, Tegos George P., Rogowski Brandon, Mege Nathan, Ulring Kristen, Schearer Pam, Sheidy Judie, Nagle Crystal, Seyfert-Margolis Vicki, Rouphael Nadine, Bosinger Steven E., Boddapati Arun K., Tharp Greg K., Pellegrini Kathryn L., Johnson Brandi, Panganiban Bernadine, Huerta Christopher, Anderson Evan J., Samaha Hady, Sevransky Jonathan E., Bristow Laurel, Beagle Elizabeth, Cowan David, Hamilton Sydney, Hodder Thomas, Bechnak Amer, Cheng Andrew, Mehta Aneesh, Ciric Caroline R., Spainhour Christine, Carter Erin, Scherer Erin M., Usher Jacob, Hellmeister Kieffer, Hussaini Laila, Hewitt Lauren, Mcnair Nina, Ribeiro Susan Pereira, Wimalasena Sonia, Fernandez-Sesma Ana, Simon Viviana, Krammer Florian, Van Bakel Harm, Kim-Schulze Seunghee, Gonzalez Reiche Ana Silvia, Qi Jingjing, Lee Brian, Carreño Juan Manuel, Singh Gagandeep, Raskin Ariel, Tcheou Johnstone, Khalil Zain, van de Guchte Adriana, Farrugia Keith, Khan Zenab, Kelly Geoffrey, Srivastava Komal, Eaker Lily Q., Bermúdez-González Maria C., Mulder Lubbertus C.F., Beach Katherine F., Saksena Miti, Altman Deena, Kojic Erna, Sominsky Levy A., Azad Arman, Bielak Dominika, Kawabata Hisaaki, Yellin Temima, Fried Miriam, Sullivan Leeba, Morris Sara, Kleiner Giulio, Stadlbauer Daniel, Dutta Jayeeta, Xie Hui, Patel Manishkumar, Nie Kai, Rahman Adeeb, Messer William B., Hough Catherine L., Siegel Sarah A.R., Sullivan Peter E., Lu Zhengchun, Brunton Amanda E., Strand Matthew, Lyski Zoe L., Coulter Felicity J., Micheleti Courtney, Maecker Holden, Pulendran Bali, Nadeau Kari C., Rosenberg-Hasson Yael, Leipold Michael, Sigal Natalia, Rogers Angela, Fernandes Andrea, Manohar Monali, Do Evan, Chang Iris, Lee Alexandra S., Blish Catherine, Din Henna Naz, Roque Jonasel, Geng Linda N., Artandi Maja, Davis Mark M., Ahuja Neera, Yang Samuel S., Chinthrajah Sharon, Hagan Thomas, Reed Elaine F., Schaenman Joanna, Salehi-Rad Ramin, Rivera Adreanne M., Pickering Harry C., Sen Subha, Elashoff David, Ward Dawn C., Brook Jenny, Sanchez Estefania Ramires, Llamas Megan, Perdomo Claudia, Magyar Clara E., Fulcher Jennifer, Erle David J., Calfee Carolyn S., Hendrickson Carolyn M., Kangelaris Kirsten N., Nguyen Viet, Lee Deanna, Chak Suzanna, Ghale Rajani, Gonzalez Ana, Jauregui Alejandra, Leroux Carolyn, Altamirano Luz Torres, Rashid Ahmad Sadeed, Willmore Andrew, Woodruff Prescott G., Krummel Matthew F., Carrillo Sidney, Ward Alyssa, Langelier Charles R., Patel Ravi, Wilson Michael, Dandekar Ravi, Alvarenga Bonny, Rajan Jayant, Eckalbar Walter, Schroeder Andrew W., Fragiadakis Gabriela K., Tsitsiklis Alexandra, Mick Eran, Guerrero Yanedth Sanchez, Love Christina, Maliskova Lenka, Adkisson Michael, Leligdowicz Aleksandra, Beagle Alexander, Rao Arjun, Sigman Austin, Samad Bushra, Curiel Cindy, Shaw Cole, Tietje-Ulrich Gayelan, Milush Jeff, Singer Jonathan, Vasquez Joshua J., Tang Kevin, Betancourt Legna, Santhosh Lekshmi, Pierce Logan, Paz Maria Tecero, Matthay Michael, Thakur Neeta, Rodriguez Nicklaus, Sutter Nicole, Jones Norman, Sinha Pratik, Prasad Priya, Lota Raphael, Rashid Sadeed, Asthana Saurabh, Bhide Sharvari, Lea Tasha, Abe-Jones Yumiko, Hafler David A., Montgomery Ruth R., Shaw Albert C., Kleinstein Steven H., Gygi Jeremy P., Pawar Shrikant, Konstorum Anna, Chen Ernie, Cotsapas Chris, Wang Xiaomei, Xu Leqi, Dela Cruz Charles, Iwasaki Akiko, Mohanty Subhasis, Nelson Allison, Zhao Yujiao, Farhadian Shelli, Asashima Hiromitsu, Chaudhary Omkar, Coppi Andreas, Fournier John, Muenker M. Catherine, Nelson Allison, Raddassi Khadir, Rainone Michael, Ruff William, Salahuddin Syim, Shulz Wade L., Vijayakumar Pavithra, Wang Haowei, Wunder Esio, Young H. Patrick, Ko Albert I., Wang Xiomei, Duchen Dylan, Esserman Denise, Guan Leying, Brito Anderson, Rothman Jessica, Grubaugh Nathan D., Corry David B., Kheradmand Farrah, Song Li-Zhen, Nelson Ebony, Metcalf Jordan P., Agudelo Higuita Nelson I., Sinko Lauren A., Booth J. Leland, Drevets Douglas A., Brown Brent R., Kraft Monica, Bime Chris, Mosier Jarrod, Erickson Heidi, Schunk Ron, Kimura Hiroki, Conway Michelle, Francisco Dave, Molzahn Allyson, Wilson Connie Cathleen, Schunk Ron, Hughes Trina, Sierra Bianca, Atkinson Mark A., Brakenridge Scott C., Ungaro Ricardo F., Manning Brittany Roth, Moldawer Lyle, Oberhaus Jordan, Guirgis Faheem W., Borresen Brittney, Anderson Matthew L., Ehrlich Lauren I.R., Melamed Esther, Maguire Cole, Wylie Dennis, Rousseau Justin F., Hurley Kerin C., Geltman Janelle N., Siles Nadia, Rogers Jacob E., Augustine Alison D., Diray-Arce Joann, Haddad Elias K., Sekaly Rafick-Pierre, Kraft Monica, Woodruff Prescott G., Erle David J., Ehrlich Lauren I.R., Montgomery Ruth R., Becker Patrice M., Altman Matthew C., Fourati Slim See more

Journal:

Journal of Allergy and Clinical Immunology: Global

November 2025

The coming era of nudge drugs for cancer

Authors: Courau Tristan, Desai Arpita, Wagner Allon, Combes Alexis J., Krummel Matthew F.

Journal:

Cancer Cell

November 2025

Discovery of tissue-specific proteomic signatures in juvenile dermatomyositis highlights pathways reflecting persistent disease activity, clinical heterogeneity, and myositis-specific autoantibody subtype

Authors: Neely Jessica, Sabbagh Sara E., Dvergsten Jeffrey, Madubata Chioma, Berthier Celine C., Zheng Zilan, Goudsmit Christine, Matossian Sophia, Ferris Sean P., Fragiadakis Gabriela K., Sirota Marina, Kahlenberg J. Michelle, Kim Hanna, Turnier Jessica L.

Journal:

Annals of the Rheumatic Diseases

November 2025

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

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

Journal:

The Journal of Heart and Lung Transplantation

September 2025

Myeloid-mesenchymal crosstalk drives ARG1-dependent profibrotic metabolism via ornithine in lung fibrosis

Authors: Yadav Preeti, Gómez Ortega Javier, Dabral Prerna, Tamaki Whitney, Chien Charles, Chang Kai-Chun, Biswas Nivedita, Pan Sixuan, Nilsson Julia, Yin Xiaoyang, Bhattacharyya Aritra, Boostanpour Kaveh, Jujaray Tanay, Wang Jasper T., Tsukui Tatsuya, Molina Christopher J., Auyeung Vincent C., Sheppard Dean,... See more

Journal:

Journal of Clinical Investigation

August 2025

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

Authors: Karra Laila, Finger Anna-Marie, Shechtman Lauren A, Krush Milana, Meng-Yao Huang Rita, Prinz Morgan, Tennvooren Iliana, Bahl Kriti, Hysienaj Lisiena, Garcia-Gonzalez Paulina, Combes Alexis J, Gonzalez Hugo, Argüello Rafael Jose, Spitzer Mathew H, Roose Jeroen P.

Journal:

Blood Advances

July 2025

Single-Cell Profiling Reveals Altered Endometrial Cellular Features Across the Menstrual Cycle in Endometriosis Patients

Authors: Almonte-Loya Ana, Wang Wanxin, Houshdaran Sahar, Tang Xinyu, Flynn Emily, Liu Binya, Kushnoor Divyashree, Nezhat Camran, Vilella Felipe, Simon Carlos, Vo Kim Chi, Casillas Amber, Khan Umair, Peredas Carlota, Oskotsky Tomiko T., Huang David, Vallvé-Juanico Júlia, Irwin Juan, Combes Alexis, Sirota Mar... See more

July 2025

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

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

Journal:

Science Immunology

July 2025

Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study

Authors: Hou Jintong, Haslund-Gourley Benjamin, Diray-Arce Joann, Hoch Annmarie, Rouphael Nadine, Becker Patrice M., Augustine Alison D., Ozonoff Al, Guan Leying, Kleinstein Steven H., Peters Bjoern, Reed Elaine, Altman Matt, Langelier Charles R., Maecker Holden, Kim Seunghee, Montgomery Ruth R., Krammer Flo... See more

Journal:

Frontiers in Medicine

July 2025

MICBG406A polymorphism reduces risk of mechanical ventilation and death during viral acute lung injury

Authors: Pickering Harry, Alipanah-Lechner Narges, Chen Ernie, Duchen Dylan, Maecker Holden T., Kim-Schulze Seunghee, Montgomery Ruth R., Cotsapas Chris, Steen Hanno, Krammer Florian, Langelier Charles R., Levy Ofer, Baden Lindsey R., Melamed Esther, Ehrlich Lauren I.R., McComsey Grace A., Sekaly Rafick P., ... See more

Journal:

JCI Insight

July 2025

Transient Dietary Changes Modulate Inflammatory Disease Trajectory in the Lean State

Authors: Jiang Zewen, Tayeri John M., Tabuchi Chihiro, Gayer Sarah G., Yoo Arum, Sun Im-Hong, Wang Jiaxi, Yin Han, Chuah Shin Shyan, Deshpande Preetal, Johri Vrinda, Davidson Brittany, Tsui Jessica, Kuhn Nicholas F., Courau Tristan, Combes Alexis J., Gardner James M., Bapat Sagar P.

June 2025

Empiric Azithromycin in COVID-19 Impacts the Respiratory Microbiome and Antimicrobial Resistome without Anti-inflammatory Benefit

Authors: Langelier Charles, Glascock Abigail, Maguire Cole, Phan Hoang Van, Lydon Emily, Calfee Carolyn, Network IMPACC, Corry David, Kheradmand Farrah, Baden Lindsey, Sekaly Rafick-Pierre, McComsey Grace, Haddad Elias, Cairns Charles, Pulendran Bali, Fernandez-Sesma Ana, Simon Viviana, Metcalf Jordan, Higui... See more

June 2025

Tumor cell heterogeneity drives spatial organization of the intratumoral immune response

Authors: 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.

Journal:

Journal of Experimental Medicine

June 2025

Meningeal regulatory T cells inhibit nociception in female mice

Authors: Midavaine Élora, Moraes Beatriz C., Benitez Jorge, Rodriguez Sian R., Braz Joao M., Kochhar Nathan P., Eckalbar Walter L., Tian Lin, Domingos Ana I., Pintar John E., Basbaum Allan I., Kashem Sakeen W.

Journal:

Science

April 2025

Identification of a conserved subset of cold tumors responsive to immune checkpoint blockade

Authors: Moore Jade, Gkantalis Jim, Guix Ines, Chou William, Yuen Kobe, Lazar Ann A, Spitzer Matthew, Combes Alexis, Barcellos-Hoff Mary Helen

Journal:

Journal for ImmunoTherapy of Cancer

March 2025

KDM6B-dependent epigenetic programming of uterine fibroblasts in early pregnancy regulates parturition timing in mice

Authors: McIntyre Tara I., Valdez Omar, Kochhar Nathan P., Davidson Brittany, Samad Bushra, Qiu Longhui, Hu Kenneth, Combes Alexis J., Erlebacher Adrian

Journal:

Cell

March 2025

Decoding functional hematopoietic progenitor cells in the adult human lung

Authors: Conrad Catharina, Magnen Melia, Tsui Jessica, Wismer Harrison Jacob, Naser Mohammad, Venkataramani Urmila, Samad Bushra, Cleary Simon J, Qiu Longhui, Tian Jennifer J, De Giovanni Marco, Mende Nicole, Leavitt Andrew D, Passegue Emmanuelle, Laurenti Elisa, Combes Alexis J, Looney Mark R.

Journal:

Blood

February 2025

Peripheral blood mononuclear cell transcriptomic trajectories reveal dynamic regulation of inflammatory actors in delirium

Authors: LaHue Sara C., Takegami Naoki, Simmasalam Rubinee, Baqai Abiya, Munoz Elena, Sikri Anya, de Courson Thibault du Buisson, Singhal Nilika S., Eckalbar Walter, Langelier Charles R., Hendrickson Carolyn M., Calfee Carolyn S., Erle David J., Krummel Matthew F., Woodruff Prescott G., Oskotsky Tomiko, Siro... See more

February 2025

Identification of a multi-omics factor predictive of long COVID in the IMPACC study

Authors: Gabernet Gisela, Maciuch Jessica, Gygi Jeremy P., Moore John F., Hoch Annmarie, Syphurs Caitlin, Chu Tianyi, Jayavelu Naresh Doni, Corry David B., Kheradmand Farrah, Baden Lindsey R., Sekaly Rafick-Pierre, McComsey Grace A., Haddad Elias K., Cairns Charles B., Rouphael Nadine, Fernandez-Sesma Ana, S... See more

February 2025