Characterizing cell-type spatial relationships across length scales in spatially resolved omics data

Authors: Rafael dos Santos Peixoto, Brendan F. Miller, Maigan A. Brusko, Gohta Aihara, Lyla Atta, Manjari Anant, Mark A. Atkinson, Todd M. Brusko, Clive H. Wasserfall, Jean Fan

Source: Nature Communications, Vol 16, Iss 1, Pp 1-14 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/e742b0d2c57b4301a591ae535aed15da

Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients

Authors: Harry Pickering, Joanna Schaenman, Hoang Van Phan, Cole Maguire, Alexandra Tsitsiklis, Nadine Rouphael, Nelson Iván Agudelo Higuita, Mark A. Atkinson, Scott Brakenridge, Monica Fung, William Messer, IMPACC Network, Ramin Salehi-rad, Matthew C. Altman, Patrice M. Becker, Steven E. Bosinger, Walter Eckalbar, Annmarie Hoch, Naresh Doni Jayavelu, Seunghee Kim-Schulze, Meagan Jenkins, Steven H. Kleinstein, Florian Krammer, Holden T. Maecker, Al Ozonoff, Joann Diray-Arce, Albert Shaw, Lindsey Baden, Ofer Levy, Elaine F. Reed, Charles R. Langelier

Source: Nature Communications, Vol 16, Iss 1, Pp 1-16 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/20b3ccc91d1c4a4d8f174764fa4ecf22

Type 1 diabetes prevention clinical trial simulator: Case reports of model‐informed drug development tool

Authors: Juan Francisco Morales, Marian Klose, Yannick Hoffert, Jagdeep T. Podichetty, Jackson Burton, Stephan Schmidt, Klaus Romero, Inish O'Doherty, Frank Martin, Martha Campbell‐Thompson, Michael J. Haller, Mark A. Atkinson, Sarah Kim

Source: CPT: Pharmacometrics & Systems Pharmacology, Vol 13, Iss 8, Pp 1309-1316 (2024)

Subject Terms: Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://doaj.org/toc/2163-8306

Access URL: https://doaj.org/article/8b4ca31b57414e94973b9675f895a590

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

Authors: Al Ozonoff, Naresh Doni Jayavelu, Shanshan Liu, Esther Melamed, Carly E. Milliren, Jingjing Qi, Linda N. Geng, Grace A. McComsey, Charles B. Cairns, Lindsey R. Baden, Joanna Schaenman, Albert C. Shaw, Hady Samaha, Vicki Seyfert-Margolis, Florian Krammer, Lindsey B. Rosen, Hanno Steen, Caitlin Syphurs, Ravi Dandekar, Casey P. Shannon, Rafick P. Sekaly, Lauren I. R. Ehrlich, David B. Corry, Farrah Kheradmand, Mark A. Atkinson, Scott C. Brakenridge, Nelson I. Agudelo Higuita, Jordan P. Metcalf, Catherine L. Hough, William B. Messer, Bali Pulendran, Kari C. Nadeau, Mark M. Davis, Ana Fernandez Sesma, Viviana Simon, Harm van Bakel, Seunghee Kim-Schulze, David A. Hafler, Ofer Levy, Monica Kraft, Chris Bime, Elias K. Haddad, Carolyn S. Calfee, David J. Erle, Charles R. Langelier, Walter Eckalbar, Steven E. Bosinger, IMPACC Network, Bjoern Peters, Steven H. Kleinstein, Elaine F. Reed, Alison D. Augustine, Joann Diray-Arce, Holden T. Maecker, Matthew C. Altman, Ruth R. Montgomery, Patrice M. Becker, Nadine Rouphael

Source: Nature Communications, Vol 15, Iss 1, Pp 1-17 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/ec0ddc29cd90460ca1ec27bea2b831b8

Impaired islet function and normal exocrine enzyme secretion occur with low inter-regional variation in type 1 diabetes

Authors: Denise M. Drotar, Ana Karen Mojica-Avila, Drew T. Bloss, Christian M. Cohrs, Cameron T. Manson, Amanda L. Posgai, MacKenzie D. Williams, Maigan A. Brusko, Edward A. Phelps, Clive H. Wasserfall, Stephan Speier, Mark A. Atkinson

Source: Cell Reports, Vol 43, Iss 6, Pp 114346- (2024)

Subject Terms: CP: Metabolism, CP: Immunology, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124724006740; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/fcfd2fb1042a446182c1c09a0ce0ffd8

Disease progression joint model predicts time to type 1 diabetes onset: Optimizing future type 1 diabetes prevention studies

Authors: Juan Francisco Morales, Rhoda Muse, Jagdeep T. Podichetty, Jackson Burton, Sarah David, Patrick Lang, Stephan Schmidt, Klaus Romero, Inish O'Doherty, Frank Martin, Martha Campbell‐Thompson, Michael J. Haller, Mark A. Atkinson, Sarah Kim

Source: CPT: Pharmacometrics & Systems Pharmacology, Vol 12, Iss 7, Pp 1016-1028 (2023)

Subject Terms: Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://doaj.org/toc/2163-8306

Access URL: https://doaj.org/article/f29e4953b25f4d88b03fbbb1b32d2233

An antigen-specific immunotherapeutic, AKS-107, deletes insulin-specific B cells and prevents murine autoimmune diabetes

Authors: David G. Alleva, Andrea R. Delpero, Thillainaygam Sathiyaseelan, Sylaja Murikipudi, Thomas M. Lancaster, Mark A. Atkinson, Clive H. Wasserfall, Liping Yu, Ramya Ragupathy, Rachel H. Bonami, Todd C. Zion

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: autoreactive B cell, autoimmunity, type 1 diabetes, Fc-fusion protein, antigen specific immunotherapeutic, insulin autoantigen, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1367514/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/b3f0b85106cd4df6a579f9f468414ba7

A genomic data archive from the Network for Pancreatic Organ donors with Diabetes

Authors: Daniel J. Perry, Melanie R. Shapiro, Sonya W. Chamberlain, Irina Kusmartseva, Srikar Chamala, Leandro Balzano-Nogueira, Mingder Yang, Jason O. Brant, Maigan Brusko, MacKenzie D. Williams, Kieran M. McGrail, James McNichols, Leeana D. Peters, Amanda L. Posgai, John S. Kaddis, Clayton E. Mathews, Clive H. Wasserfall, Bobbie-Jo M. Webb-Robertson, Martha Campbell-Thompson, Desmond Schatz, Carmella Evans-Molina, Alberto Pugliese, Patrick Concannon, Mark S. Anderson, Michael S. German, Chester E. Chamberlain, Mark A. Atkinson, Todd M. Brusko

Source: Scientific Data, Vol 10, Iss 1, Pp 1-16 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2052-4463

Access URL: https://doaj.org/article/0ad4cb66140840c5abd02c69201bad7b

Human immune phenotyping reveals accelerated aging in type 1 diabetes

Authors: Melanie R. Shapiro, Xiaoru Dong, Daniel J. Perry, James M. McNichols, Puchong Thirawatananond, Amanda L. Posgai, Leeana D. Peters, Keshav Motwani, Richard S. Musca, Andrew Muir, Patrick Concannon, Laura M. Jacobsen, Clayton E. Mathews, Clive H. Wasserfall, Michael J. Haller, Desmond A. Schatz, Mark A. Atkinson, Maigan A. Brusko, Rhonda Bacher, Todd M. Brusko

Source: JCI Insight, Vol 8, Iss 17 (2023)

Subject Terms: Autoimmunity, Immunology, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/2379-3708

Access URL: https://doaj.org/article/637333e5554a47dcb1444963f6436280

Responders to low-dose ATG induce CD4+ T cell exhaustion in type 1 diabetes

Authors: Laura M. Jacobsen, Kirsten Diggins, Lori Blanchfield, James McNichols, Daniel J. Perry, Jason Brant, Xiaoru Dong, Rhonda Bacher, Vivian H. Gersuk, Desmond A. Schatz, Mark A. Atkinson, Clayton E. Mathews, Michael J. Haller, S. Alice Long, Peter S. Linsley, Todd M. Brusko

Source: JCI Insight, Vol 8, Iss 16 (2023)

Subject Terms: Endocrinology, Immunology, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/2379-3708

Access URL: https://doaj.org/article/ad46bb6a2d254bafb3f6b3213915a443

Exploration of autoantibody responses in canine diabetes using protein arrays

Authors: Allison L. O’Kell, Mahasish Shome, Ji Qiu, Stacy Williams, Yunro Chung, Joshua LaBaer, Mark A. Atkinson, Clive Wasserfall

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-7 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/53d3d7788a9c4fbea56fbb4fc9a0b32c

Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study

Authors: Al Ozonoff, Joanna Schaenman, Naresh Doni Jayavelu, Carly E. Milliren, Carolyn S. Calfee, Charles B. Cairns, Monica Kraft, Lindsey R. Baden, Albert C. Shaw, Florian Krammer, Harm van Bakel, Denise A. Esserman, Shanshan Liu, Ana Fernandez Sesma, Viviana Simon, David A. Hafler, Ruth R. Montgomery, Steven H. Kleinstein, Ofer Levy, Christian Bime, Elias K. Haddad, David J. Erle, Bali Pulendran, Kari C. Nadeau, Mark M. Davis, Catherine L. Hough, William B. Messer, Nelson I. Agudelo Higuita, Jordan P. Metcalf, Mark A. Atkinson, Scott C. Brakenridge, David Corry, Farrah Kheradmand, Lauren I.R. Ehrlich, Esther Melamed, Grace A. McComsey, Rafick Sekaly, Joann Diray-Arce, Bjoern Peters, Alison D. Augustine, Elaine F. Reed, Matthew C. Altman, Patrice M. Becker, Nadine Rouphael, Chris Bime, Mark M Davis, Kerry McEnaney, Brenda Barton, Claudia Lentucci, Mehmet Saluvan, Ana C. Chang, Annmarie Hoch, Marisa Albert, Tanzia Shaheen, Alvin T. Kho, Sanya Thomas, Jing Chen, Maimouna D. Murphy, Mitchell Cooney, Scott Presnell, Gabriela K. Fragiadakis, Ravi Patel, Leying Guan, Jeremy Gygi, Shrikant Pawar, Anderson Brito, Zain Khalil, Cole Maguire, Slim Fourati, James A. Overton, Randi Vita, Kerstin Westendorf, Ramin Salehi-Rad, Aleksandra Leligdowicz, Michael A. Matthay, Jonathan P. Singer, Kirsten N. Kangelaris, Carolyn M. Hendrickson, Matthew F. Krummel, Charles R. Langelier, Prescott G. Woodruff, Debra L. Powell, James N. Kim, Brent Simmons, I. Michael Goonewardene, Cecilia M. Smith, Mark Martens, Jarrod Mosier, Hiroki Kimura, Amy C. Sherman, Stephen R. Walsh, Nicolas C. Issa, Charles Dela Cruz, Shelli Farhadian, Akiko Iwasaki, Albert I. Ko, Sharon Chinthrajah, Neera Ahuja, Angela J. Rogers, Maja Artandi, Sarah A.R. Siegel, Zhengchun Lu, Douglas A. Drevets, Brent R. Brown, Matthew L. Anderson, Faheem W. Guirgis, Rama V. Thyagarajan, Justin F. Rousseau, Dennis Wylie, Johanna Busch, Saurin Gandhi, Todd A. Triplett, George Yendewa, Olivia Giddings, Evan J. Anderson, Aneesh K. Mehta, Jonathan E. Sevransky, Bernard Khor, Adeeb Rahman, Daniel Stadlbauer, Jayeeta Dutta, Hui Xie, Seunghee Kim-Schulze, Ana Silvia Gonzalez-Reiche, Adriana van de Guchte, Keith Farrugia, Zenab Khan, Holden T. Maecker, David Elashoff, Jenny Brook, Estefania Ramires-Sanchez, Megan Llamas, Adreanne Rivera, Claudia Perdomo, Dawn C. Ward, Clara E. Magyar, Jennifer A. Fulcher, Yumiko Abe-Jones, Saurabh Asthana, Alexander Beagle, Sharvari Bhide, Sidney A. Carrillo, Suzanna Chak, Rajani Ghale, Ana Gonzalez, Alejandra Jauregui, Norman Jones, Tasha Lea, Deanna Lee, Raphael Lota, Jeff Milush, Viet Nguyen, Logan Pierce, Priya A. Prasad, Arjun Rao, Bushra Samad, Cole Shaw, Austin Sigman, Pratik Sinha, Alyssa Ward, Andrew Willmore, Jenny Zhan, Sadeed Rashid, Nicklaus Rodriguez, Kevin Tang, Luz Torres Altamirano, Legna Betancourt, Cindy Curiel, Nicole Sutter, Maria Tercero Paz, Gayelan Tietje-Ulrich, Carolyn Leroux, Jennifer Connors, Mariana Bernui, Michel A. Kutzler, Carolyn Edwards, Edward Lee, Edward Lin, Brett Croen, Nicholas C. Semenza, Brandon Rogowski, Nataliya Melnyk, Kyra Woloszczuk, Gina Cusimano, Mathew R. Bell, Sara Furukawa, Renee McLin, Pamela Marrero, Julie Sheidy, George P. Tegos, Crystal Nagle, Nathan Mege, Kristen Ulring, Vicki Seyfert-Margolis, Michelle Conway, Dave Francisco, Allyson Molzahn, Heidi Erickson, Connie Cathleen Wilson, Ron Schunk, Bianca Sierra, Trina Hughes, Kinga Smolen, Michael Desjardins, Simon van Haren, Xhoi Mitre, Jessica Cauley, Xiaofang Li, Alexandra Tong, Bethany Evans, Christina Montesano, Jose Humberto Licona, Jonathan Krauss, Jun Bai Park Chang, Natalie Izaguirre, Omkar Chaudhary, Andreas Coppi, John Fournier, Subhasis Mohanty, M. Catherine Muenker, Allison Nelson, Khadir Raddassi, Michael Rainone, William E. Ruff, Syim Salahuddin, Wade L. Schulz, Pavithra Vijayakumar, Haowei Wang, Elsio Wunder Jr., H. Patrick Young, Yujiao Zhao, Miti Saksena, Deena Altman, Erna Kojic, Komal Srivastava, Lily Q. Eaker, Maria C. Bermúdez-González, Katherine F. Beach, Levy A. Sominsky, Arman R. Azad, Juan Manuel Carreño, Gagandeep Singh, Ariel Raskin, Johnstone Tcheou, Dominika Bielak, Hisaaki Kawabata, Lubbertus CF Mulder, Giulio Kleiner, Alexandra S. Lee, Evan Do Do, Andrea Fernandes, Monali Manohar, Thomas Hagan, Catherine A. Blish, Hena Naz Din, Jonasel Roque, Samuel Yang, Amanda Brunton, Peter E. Sullivan, Matthew Strnad, Zoe L. Lyski, Felicity J. Coulter, J. Leland Booth, Lauren A. Sinko, Lyle L. Moldawer, Brittany Borresen, Brittney Roth-Manning, Li-Zhen Song, Ebony Nelson, Megan Lewis-Smith, Jacob Smith, Pablo Guaman Tipan, Nadia Siles, Sam Bazzi, Janelle Geltman, Kerin Hurley, Gio Gabriele, Scott Sieg, Tatyana Vaysman, Laurel Bristow, Laila Hussaini, Kieffer Hellmeister, Hady Samaha, Andrew Cheng, Christine Spainhour, Erin M. Scherer, Brandi Johnson, Amer Bechnak, Caroline R. Ciric, Lauren Hewitt, Erin Carter, Nina Mcnair, Bernadine Panganiban, Christopher Huerta, Jacob Usher, Susan Pereira Ribeiro

Source: EBioMedicine, Vol 83, Iss , Pp 104208- (2022)

Subject Terms: COVID-19, SARS-CoV-2, Viral load, Antibody, Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352396422003905; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/6bb1f29e485b44e3b837f1d761005a73

Islet sympathetic innervation and islet neuropathology in patients with type 1 diabetes

Authors: Martha Campbell-Thompson, Elizabeth A. Butterworth, J. Lucas Boatwright, Malavika A. Nair, Lith H. Nasif, Kamal Nasif, Andy Y. Revell, Alberto Riva, Clayton E. Mathews, Ivan C. Gerling, Desmond A. Schatz, Mark A. Atkinson

Source: Scientific Reports, Vol 11, Iss 1, Pp 1-17 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/06c0546e7343448f81538ebc42c845a0

Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes

Authors: Leandro Balzano-Nogueira, Ricardo Ramirez, Tatyana Zamkovaya, Jordan Dailey, Alexandria N. Ardissone, Srikar Chamala, Joan Serrano-Quílez, Teresa Rubio, Michael J. Haller, Patrick Concannon, Mark A. Atkinson, Desmond A. Schatz, Eric W. Triplett, Ana Conesa

Source: Genome Biology, Vol 22, Iss 1, Pp 1-27 (2021)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/222e6d8caa7d414bab3c617c18e90212

Evaluation for type 1 diabetes associated autoantibodies in diabetic and non-diabetic Australian terriers and Samoyeds

Authors: Allison L. O’Kell, Clive H. Wasserfall, Paula S. Henthorn, Mark A. Atkinson, Rebecka S. Hess

Source: Canine Medicine and Genetics, Vol 7, Iss 1, Pp 1-6 (2020)

Subject Terms: Canine, Diabetes, Autoantibodies, Veterinary medicine, SF600-1100

File Description: electronic resource

Relation: https://doaj.org/toc/2662-9380

Access URL: https://doaj.org/article/cf593e70d12f41d99cacc450c2eae419

Large-scale electron microscopy database for human type 1 diabetes

Authors: Pascal de Boer, Nicole M. Pirozzi, Anouk H. G. Wolters, Jeroen Kuipers, Irina Kusmartseva, Mark A. Atkinson, Martha Campbell-Thompson, Ben N. G. Giepmans

Source: Nature Communications, Vol 11, Iss 1, Pp 1-9 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b384446e156a477db4af65825afe3aac

α Cell dysfunction in islets from nondiabetic, glutamic acid decarboxylase autoantibody–positive individuals

Authors: Nicolai M. Doliba, Andrea V. Rozo, Jeffrey Roman, Wei Qin, Daniel Traum, Long Gao, Jinping Liu, Elisabetta Manduchi, Chengyang Liu, Maria L. Golson, Golnaz Vahedi, Ali Naji, Franz M. Matschinsky, Mark A. Atkinson, Alvin C. Powers, Marcela Brissova, Klaus H. Kaestner, Doris A. Stoffers, for the HPAP Consortium

Source: The Journal of Clinical Investigation, Vol 132, Iss 11 (2022)

Subject Terms: Endocrinology, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1558-8238

Access URL: https://doaj.org/article/ed4642c42951458c9cba96f40f54dcec

Substance Use Affects Type 1 Diabetes Pancreas Pathology: Implications for Future Studies

Authors: Brittany S. Bruggeman, Martha Campbell-Thompson, Stephanie L. Filipp, Matthew J. Gurka, Mark A. Atkinson, Desmond A. Schatz, Laura M. Jacobsen

Source: Frontiers in Endocrinology, Vol 12 (2021)

Subject Terms: islet amyloid polypeptide, islets of langerhans, pancreatitis, pathology, substance-related disorders, tissue donors, Diseases of the endocrine glands. Clinical endocrinology, RC648-665

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fendo.2021.778912/full; https://doaj.org/toc/1664-2392

Access URL: https://doaj.org/article/9fcb09c6bd724f0792d6b2f5202af3fe

Single-cell analysis of the human pancreas in type 2 diabetes using multi-spectral imaging mass cytometry

Authors: Minghui Wu, Michelle Y.Y. Lee, Varun Bahl, Daniel Traum, Jonathan Schug, Irina Kusmartseva, Mark A. Atkinson, Guanjie Fan, Klaus H. Kaestner

Source: Cell Reports, Vol 37, Iss 5, Pp 109919- (2021)

Subject Terms: imaging mass cytometry, immunolabeling, histopathology, type 2 diabetes, human pancreas, multiplexed imaging, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124721013929; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/a8c0452dd1184df08e2878403748613b

Genetic risk for autoimmunity is associated with distinct changes in the human gut microbiome

Authors: Jordan T. Russell, Luiz F. W. Roesch, Malin Ördberg, Jorma Ilonen, Mark A. Atkinson, Desmond A. Schatz, Eric W. Triplett, Johnny Ludvigsson

Source: Nature Communications, Vol 10, Iss 1, Pp 1-12 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b1c5abc6f37a4cff909ed60a09d13270