Publications | UCSF CoLabs

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

Loss of PPARγ activity characterizes early protumorigenic stromal reprogramming and dictates the therapeutic window of opportunity

Authors: Caruso Joseph A., Wang Xianhong, Murrow Lyndsay M., Rodriguez Carlos Ivan, Chen-Tanyolac Chira, Vu Lisa, Chen Yunn-Yi, Gascard Philippe, Gartner Zev J., Kerlikowske Karla, Tlsty Thea D.

Journal:

Proceedings of the National Academy of Sciences

October 2023

A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling

Authors: Hackney Jason A., Shivram Haridha, Vander Heiden Jason, Overall Chris, Orozco Luz, Gao Xia, Kim Eugene, West Nathan, Qamra Aditi, Chang Diana, Chakrabarti Arindam, Choy David F., Combes Alexis J., Courau Tristan, Fragiadakis Gabriela K., Rao Arjun Arkal, Ray Arja, Tsui Jessica, Hu Kenneth, Kuhn Nich... See more

Journal:

iScience

October 2023

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