Publications | UCSF CoLabs

Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells

Authors: Mowery Cody T., Freimer Jacob W., Chen Zeyu, Casaní-Galdón Salvador, Umhoefer Jennifer M., Arce Maya M., Gjoni Ketrin, Daniel Bence, Sandor Katalin, Gowen Benjamin G., Nguyen Vinh, Simeonov Dimitre R., Garrido Christian M., Curie Gemma L., Schmidt Ralf, Steinhart Zachary, Satpathy Ansuman T., Pollar... See more

Journal:

Nature Genetics

May 2024

Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics

Authors: Rabadam Gabrielle, Wibrand Camilla, Flynn Emily, Hartoularos George C., Sun Yang, Madubata Chioma, Fragiadakis Gabriela K., Ye Chun Jimmie, Kim Susan, Gartner Zev J., Sirota Marina, Neely Jessica

Journal:

JCI Insight

May 2024

Regulatory T cell-derived enkephalin imparts pregnancy-induced analgesia

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

May 2024

Dysregulation of CD4 Array and CD8 Array resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis

Authors: He Jun Yan, Kim Yang-Joon, Mennillo Elvira, Rusu Iulia, Bain Jared, Rao Arjun A, Andersen Christopher, Law Karen, Yang Hai, Tsui Jessica, Shen Alan, Davidson Brittany, Kushnoor Divyashree, Shi Yimin, Fan Frances, Cheung Alexander, Zhang Li, Fong Lawrence, Combes Alexis J, Pisco Angela O, Kattah Mich... See more

Journal:

Journal for ImmunoTherapy of Cancer

April 2024

Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology

Authors: Phan Hoang Van, Tsitsiklis Alexandra, Maguire Cole P., Haddad Elias K., Becker Patrice M., Kim-Schulze Seunghee, Lee Brian, Chen Jing, Hoch Annmarie, Pickering Harry, van Zalm Patrick, Altman Matthew C., Augustine Alison D., Calfee Carolyn S., Bosinger Steve, Cairns Charles B., Eckalbar Walter, Guan... Phan Hoang Van, Tsitsiklis Alexandra, Maguire Cole P., Haddad Elias K., Becker Patrice M., Kim-Schulze Seunghee, Lee Brian, Chen Jing, Hoch Annmarie, Pickering Harry, van Zalm Patrick, Altman Matthew C., Augustine Alison D., Calfee Carolyn S., Bosinger Steve, Cairns Charles B., Eckalbar Walter, Guan Leying, Jayavelu Naresh Doni, Kleinstein Steven H., Krammer Florian, Maecker Holden T., Ozonoff Al, Peters Bjoern, Rouphael Nadine, Montgomery Ruth R., Reed Elaine, Schaenman Joanna, Steen Hanno, Levy Ofer, Diray-Arce Joann, Langelier Charles R., Erle David J., 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, Patel Ravi, Wilson Michael, Dandekar Ravi, Alvarenga Bonny, Rajan Jayant, Schroeder Andrew W., Fragiadakis Gabriela K., Mick Eran, Guerrero Yanedth Sanchez, Love Christina, Maliskova Lenka, Adkisson Michael, Ehrlich Lauren I. R., Melamed Esther, Rousseau Justin F., Hurley Kerin C., Geltman Janelle N., Siles Nadia, Rogers Jacob E., Kutzler Michele A., Bernui Mariana, Cusimano Gina, Connors Jennifer, Woloszczuk Kyra, Joyner David, Edwards Carolyn, 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, Holland Steven M., Rosen Lindsey B., Lee Serena, Vaysman Tatyana, Fernandez-Sesma Ana, Simon Viviana, Van Bakel Harm, Gonzalez-Reiche Ana Silvia, Qi Jingjing, 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, Bermúdez González Maria Carolina, Mulder Lubbertus C. F., Beach Katherine, Fatou Benoit, Smolen Kinga, Viode Arthur, van Haren Simon, Jha Meenakshi, Kho Alvin, Milliren Carly E., Chang Ana C., McEnaney Kerry, Barton Brenda, Lentucci Claudia, Murphy Maimouna, Saluvan Mehmet, Shaheen Tanzia, Liu Shanshan, Syphurs Caitlin, Albert Marisa, Hayati Arash Nemati, Bryant Robert, Abraham James, Salehi-Rad Ramin, Rivera Adreanne M., Sen Subha, Elashoff David, Ward Dawn C., Presnell Scott, Kohr Bernard, Arnett Azlann, Boddapati Arun K., Tharp Greg K., Pellegrini Kathryn L., Johnson Brandi, Panganiban Bernadine, Huerta Christopher, Anderson Evan J., Samaha Hady, Sevransky Jonathan, Bristow Laurel, Beagle Elizabeth, Cowan David, Hamilton Sydney, Hodder Thomas, Esserman Denise, Brito Anderson, Rothman Jessica, Grubaugh Nathan, Ko Albert I., Hafler David A., Shaw Albert C., Gygi Jeremy, 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, Pulendran Bali, Nadeau R. Kari C., Rosenberg-Hasson Yael, Leipold Michael, Sigal Natalia, Rogers Angela, Fernandez Andrea, Manohar Monali, Do Evan, Chang Iris, Vita Randi, Westendorf Kerstin, Corry David B., Kheradmand Farrah, Song Li-Zhen, Nelson Ebony, Baden Lindsey R., Mendez Kevin, Lasky-Su Jessica, Tong Alexandra, Rooks Rebecca, Sekaly Rafick-Pierre, Fourati Slim, McComsey Grace A., Harris Paul, Sieg Scott, Ribeiro Susan Pereira, Overton James A., Rahman Adeeb, Hutton Scott R., Michelotti Greg, Wong Kari, Seyfert-Margolis Vicki, Metcalf Jordan P., Agudelo Higuita Nelson I., Sinko Lauren, Booth J. Leland, Messer William B., Hough Catherine L., Siegel Sarah, Sullivan Peter, Lu Zhengchun, Kraft Monica, Bime Chris, Mosier Jarrod, Erickson Heidi, Schunk Ron, Kimura Hiroki, Conway Michelle, Atkinson Mark A., Brakenridge Scott C., Ungaro Ricardo F., Manning Brittany Roth, Oberhaus Jordan, Guirgis Faheem W., Borresen Brittany, Anderson Matthew L. See more

Journal:

Science Translational Medicine

April 2024

Proliferation-driven mechanical compression induces signalling centre formation during mammalian organ development

Authors: Shroff Neha Pincha, Xu Pengfei, Kim Sangwoo, Shelton Elijah R., Gross Ben J., Liu Yucen, Gomez Carlos O., Ye Qianlin, Drennon Tingsheng Yu, Hu Jimmy K., Green Jeremy B. A., Campàs Otger, Klein Ophir D.

Journal:

Nature Cell Biology

April 2024

IgG hexamers initiate complement-dependent acute lung injury

Authors: Cleary Simon J., Seo Yurim, Tian Jennifer J., Kwaan Nicholas, Bulkley David P., Bentlage Arthur E.H., Vidarsson Gestur, Boilard Éric, Spirig Rolf, Zimring James C., Looney Mark R.

Journal:

Journal of Clinical Investigation

March 2024

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains

Authors: Zwick Rachel K., Kasparek Petr, Palikuqi Brisa, Viragova Sara, Weichselbaum Laura, McGinnis Christopher S., McKinley Kara L., Rathnayake Asoka, Vaka Dedeepya, Nguyen Vinh, Trentesaux Coralie, Reyes Efren, Gupta Alexander R., Gartner Zev J., Locksley Richard M., Gardner James M., Itzkovitz Shalev, Bo... See more

Journal:

Nature Cell Biology

February 2024

Macrophage and CD8 T Cell Discordance are Associated with Acute Lung Allograft Dysfunction Progression

Authors: Calabrese Daniel R., Yellamilli Shivaram, Ekstrand Christina, Singer Jonathan P., Hays Steven R., Leard Lorriana E., Shah Rupal J., Venado Aida, Kolaitis Nicholas A., Perez Alyssa, Combes Alexis, Greenland John R.

Journal:

The Journal of Heart and Lung Transplantation

February 2024

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

Authors: Mennillo Elvira, Kim Yang Joon, Lee Gyehyun, Rusu Iulia, Patel Ravi K., Dorman Leah C., Flynn Emily, Li Stephanie, Bain Jared L., Andersen Christopher, Rao Arjun, Tamaki Stanley, Tsui Jessica, Shen Alan, Lotstein Madison L., Rahim Maha, Naser Mohammad, Bernard-Vazquez Faviola, Eckalbar Walter, Cho S... See more

January 2024

Regulatory T cells in skin mediate immune privilege of the hair follicle stem cell niche

Authors: Cohen Jarish N., Gouirand Victoire, Macon Courtney E., Lowe Margaret M., Boothby Ian C., Moreau Joshua M., Gratz Iris K., Stoecklinger Angelika, Weaver Casey T., Sharpe Arlene H., Ricardo-Gonzalez Roberto R., Rosenblum Michael D.

Journal:

Science Immunology

January 2024

Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study

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

Journal:

Nature Communications

January 2024

Mechanosensitive hormone signaling promotes mammary progenitor expansion and breast cancer risk

Authors: Northey Jason J., Hayward Mary-Kate, Yui Yoshihiro, Stashko Connor, Kai FuiBoon, Mouw Janna K., Thakar Dhruv, Lakins Jonathon N., Ironside Alastair J., Samson Susan, Mukhtar Rita A., Hwang E. Shelley, Weaver Valerie M.

Journal:

Cell Stem Cell

January 2024

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

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

December 2023

Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients

Authors: Langelier Charles, Pickering Harry, Schaenman Joanna, Phan Hoang, Maguire Cole, Tsitsiklis Alexandra, Rouphael Nadine, Higuita Nelson, Atkinson Mark, Breckenridge Scott, Fung Monica, Messer William, Network IMPACC, Salehi-rad Ramin, Altman Matthew, Becker Patrice, Bosinger Steven, Eckalbar Walter, H... See more

December 2023

Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes

Authors: Cutts Zachary, Patterson Sarah, Maliskova Lenka, Taylor Kimberly E., Ye Chun, Dall’Era Maria, Yazdany Jinoos, Criswell Lindsey, Fragiadakis Gabriela K., Langelier Charles, Capra John A., Sirota Marina, Lanata Cristina M

November 2023

Functional haematopoietic progenitor cells in the adult human lung

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

November 2023

Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants

Authors: Gygi Jeremy P., Maguire Cole, Patel Ravi K., Shinde Pramod, Konstorum Anna, Shannon Casey P., Xu Leqi, Hoch Annmarie, Jayavelu Naresh Doni, Network IMPACC, Haddad Elias K., Reed Elaine F., Kraft Monica, McComsey Grace A., Metcalf Jordan, Ozonoff Al, Esserman Denise, Cairns Charles B., Rouphael Nadin... See more

November 2023

Ikaros is a principal regulator of Aire + mTEC homeostasis, thymic mimetic cell diversity, and central tolerance

Authors: Sin Jun Hyung, Sucharov Juliana, Kashyap Sujit, Wang Yi, Proekt Irina, Liu Xian, Parent Audrey V., Gupta Alexander, Kastner Philippe, Chan Susan, Gardner James M., Ntranos Vasilis, Miller Corey N., Anderson Mark S., Schjerven Hilde, Waterfield Michael R.

Journal:

Science Immunology

October 2023

Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans

Authors: Locher Veronica, Park Sara, Bunis Daniel G., Makredes Stephanie, Mayer Margareta, Burt Trevor D., Fragiadakis Gabriela K., Halkias Joanna

Journal:

JCI Insight

October 2023