Publications | UCSF CoLabs

Single-nuclei UPR profiling by flow cytometry reveals bortezomib resistance mechanisms in multiple myeloma

Authors: Gigan Julien P, Garcia-Gonzalez Paulina, Pilotti Angelo, Galliot Lou, Reynaud Alexandre, Ghaffar Yoan, Flores-Santibáñez Felipe, Ghafoori Sara, Seillier Eve, Lavignolle-Heguy Rosario, Barros Daniela, Bret Caroline, Fichaux Sharon, Combes Alexis, Bani Alessandro, Rua Rejane, Gatti Evelina, Nal-Rogier... See more

Journal:

EMBO Molecular Medicine

June 2026

Programmed cycle-induced endometrial perturbations do not independently influence angiogenic imbalance or hypertensive disorders in pregnancy

Authors: Huang David, Flynn Emily, Davidson Brittany R., Irwin Juan C., Naser Mohammad, Almonte Ana Laura, Qin Jennifer, Song Yue, Rabara Fleurdeliza B., Wong Rebecca, Zablotska Lydia B., Rosen Mitchell P., Wittmann Torsten, Fragiadakis Gabriela K., Combes Alexis J., Sirota Marina, Cedars Marcelle I., Giudic... See more

Journal:

JCI Insight

June 2026

Spatial Orchestration of Skin Fibrosis by a CD8+ T cell-Myofibroblast Axis

Authors: Boothby Ian C., Gan Thomas C., Johri Vrinda, Flynn Emily, Kazmi Maha, Maliskova Lenka, Shaikh Saba, Yellamilli Shivaram, Fragiadakis Gabriela K., Neuhaus Isaac, Eckalbar Walter, Cohen Jarish N., Combes Alexis J., Haemel Anna, Rosenblum Michael D., Kinet Maxime J.

June 2026

Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks

Authors: Mennillo Elvira, Lotstein Madison L., Lee Gyehyun, Hou Julian H., Johri Vrinda, Leet Donna E., Ekstrand Christina A., Tsui Jessica, He Jun Yan, Mahadevan Uma, Eckalbar Walter, Gill Ryan M., Bowman Christopher J., Oh David Y., Fragiadakis Gabriela K., Kattah Michael G., Combes Alexis J.

Journal:

Journal of Clinical Investigation

June 2026

Congenital cytomegalovirus infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors

Authors: Levan Justine, Vaaben Anna V, Tsui Jessica, Davidson Brittany R, Olive Meagan E, Callaway Perri C, Nguyen Catherine B T, Ilala Mikias, Patel Ravi K, Hunter Riana D, Fragiadakis Gabriela K, Combes Alexis J, Nankya Felistas, Dorsey Grant, Kakuru Abel, Muhindo Mary, Feeney Margaret E

Journal:

The Journal of Immunology

June 2026

Differential assembly of mouse and human tumor microenvironments

Authors: Courau Tristan, Jaszczak Rebecca G., Samad Bushra, Flynn Emily, Chew Nayvin W., Reeder Gabriella C., Tsui Jessica, Teklu Semhar, Pass Lomax F., Edwards Austin W., Naser Mohammad, Ray Arja, Wismer Harrison, Bunis Daniel, Lupin-Jimenez Leonard, Gavil Noah V., Masopust David, Graham John P., Skelly Dan... See more

Journal:

Nature Immunology

May 2026

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

Authors: Jespersen Jillian M., Avanesyan Lia, Publicover Jean, Carey Nicholas D., Patel Ravi K., Edwards Austin W., Stenske Sarah, Shin Jae, Li Jiajing, Simone Margaret, Chew Nayvin W., Wong Nicholas, Trilok Suprita, Erickson Ann, Rao Arjun, Loo Christopher P., Stec Michael, Anderson Mark, Cloherty Gavin, Sa... See more

Journal:

Science Translational Medicine

April 2026

Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19

Journal:

Nature Microbiology

March 2026

Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19

Authors: Abigail Glascock, Cole Maguire, Hoang Van Phan, Emily C Lydon, Joanna Schaenman, Carolyn S Calfee, Esther Melamed, John Greenland, David B Corry, Farrah Kheradmand, Lindsey R Baden, Rafick Sekaly, Grace A McComsey, Elias K Haddad, Charles B Cairns, Linda N Geng, Bali Pulendran, Ana Fernandez-Sesma, ... See more

Journal:

Nature Microbiology

March 2026

Immune-microbiome coordination defines interferon setpoints in healthy humans

Authors: Babdor Joel, Patel Ravi K., Davidson Brittany, Koser Kelvin, Noecker Cecilia, Rahim Maha K., Bisanz Jordan E., Tenvooren Iliana, Marquez Diana, Calvo Maria, Johri Vrinda, McCarthy Elizabeth E., Shaheed Avneet, Ekstrand Christina, Weakley Allison M., Yu Feiqiao B., Krip Kristen, Shaikh Kashif A., Ama... See more

Journal:

Cell

March 2026

Commensal-myeloid crosstalk in neonatal skin regulates interleukin-1 signaling and cutaneous type 17 inflammation

Authors: Dhariwala Miqdad O., Carale Ricardo O., DeRogatis Andrea M., Rodriguez-Valbuena Henry, Okoro Joy N., Ekstrand Christina A., Weckel Antonin, Tran Victoria M., Habrylo Irek, Barrere-Cain Rio, Ojewumi Oluwasunmisola T., Tammen Allison E., Tsui Jessica, Shaikh Saba, Yellamilli Shivaram, Aladhami Ahmed K... See more

Journal:

Immunity

February 2026

Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors

Authors: Doni Jayavelu Naresh, Samaha Hady, Wimalasena Sonia Tandon, Hoch Annmarie, Gygi Jeremy P., Gabernet Gisela, Ozonoff Al, Liu Shanshan, Milliren Carly E., Levy Ofer, Baden Lindsey R., Melamed Esther, Ehrlich Lauren I. R., McComsey Grace A., Sekaly Rafick P., Cairns Charles B., Haddad Elias K., Schaenm... See more

Journal:

Communications Medicine

January 2026

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

TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity

Authors: Du Jacob, Wijayaratna Uthpala N., Wang Xinyue, Fung Jeffrey P., Huang Belinda, Farzaneh Farzin, Kohn Donald B., Combes Alexis J., Gaensler Karin M. L.

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

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

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