Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas von Moncada, Reuben, Barkley, Dalia, Wagner, Florian, Chiodin, Marta, Devlin, Joseph C., Baron, Maayan, Hajdu, Cristina H., Simeone, Diane M., Yanai, Itai

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Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition von Lin, Jian-Da, Devlin, Joseph C., Yeung, Frank, McCauley, Caroline, Leung, Jacqueline M., Chen, Ying-Han, Cronkite, Alex, Hansen, Christina, Drake-Dunn, Charlotte, Ruggles, Kelly V., Cadwell, Ken, Graham, Andrea L., Loke, P’ng

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Bacterial contact induces polar plug disintegration to mediate whipworm egg hatching von Robertson, Amicha, Sall, Joseph, Venzon, Mericien, Olivas, Janet J, Zheng, Xuhui, Cammer, Michael, Antao, Noelle, Zhou, Chunyi, Devlin, Joseph C, Saes Thur, Rafaela, Bethony, Jeffrey, Nejsum, Peter, Shopsin, Bo, Torres, Victor J, Liang, Feng-Xia, Cadwell, Ken

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Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease von Liu, Menghan, Devlin, Joseph C., Hu, Jiyuan, Volkova, Angelina, Battaglia, Thomas W., Ho, Melody, Asplin, John R., Byrd, Allyson, Loke, P'ng, Li, Huilin, Ruggles, Kelly, Tsirigos, Aristotelis, Blaser, Martin J., Nazzal, Lama

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WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data von Devlin, Joseph C, Battaglia, Thomas, Blaser, Martin J, Ruggles, Kelly V

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A Comparative Analysis of SARS-CoV-2 Antivirals Characterizes 3CLpro Inhibitor PF-00835231 as a Potential New Treatment for COVID-19 von de Vries, Maren, Mohamed, Adil S, Prescott, Rachel A, Valero-Jimenez, Ana M, Desvignes, Ludovic, O’Connor, Rebecca, Steppan, Claire, Devlin, Joseph C, Ivanova, Ellie, Herrera, Alberto, Schinlever, Austin, Loose, Paige, Ruggles, Kelly, Koralov, Sergei B, Anderson, Annaliesa S, Binder, Joseph, Dittmann, Meike

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mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection von Ivanova, Ellie N., Shwetar, Jasmine, Devlin, Joseph C., Buus, Terkild B., Gray-Gaillard, Sophie, Koide, Akiko, Cornelius, Amber, Samanovic, Marie I., Herrera, Alberto, Mimitou, Eleni P., Zhang, Chenzhen, Karmacharya, Trishala, Desvignes, Ludovic, Ødum, Niels, Smibert, Peter, Ulrich, Robert J., Mulligan, Mark J., Koide, Shohei, Ruggles, Kelly V., Herati, Ramin S., Koralov, Sergei B.

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Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization von Yeung, Frank, Chen, Ying-Han, Lin, Jian-Da, Leung, Jacqueline M., McCauley, Caroline, Devlin, Joseph C., Hansen, Christina, Cronkite, Alex, Stephens, Zac, Drake-Dunn, Charlotte, Fulmer, Yi, Shopsin, Bo, Ruggles, Kelly V., Round, June L., Loke, P’ng, Graham, Andrea L., Cadwell, Ken

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Single-Cell Transcriptional Survey of Ileal-Anal Pouch Immune Cells From Ulcerative Colitis Patients von Devlin, Joseph C., Axelrad, Jordan, Hine, Ashley M., Chang, Shannon, Sarkar, Suparna, Lin, Jian-Da, Ruggles, Kelly V., Hudesman, David, Cadwell, Ken, Loke, P’ng

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Recruitment and Maintenance of CX3CR1+CD4+ T Cells during Helminth Infection von Loredan, Denis G, Devlin, Joseph C, Khanna, Kamal M, Loke, P'ng

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Staphylococcus aureus induces a muted host response in human blood that blunts the recruitment of neutrophils von Zwack, Erin E, Chen, Ze, Devlin, Joseph C, Li, Zhi, Zheng, Xuhui, Weinstock, Ada, Lacey, Keenan A, Fisher, Edward A, Fenyö, David, Ruggles, Kelly V, Loke, P'ng, Torres, Victor J

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The γδ IEL effector API5 masks genetic susceptibility to Paneth cell death von Matsuzawa-Ishimoto, Yu, Yao, Xiaomin, Koide, Akiko, Ueberheide, Beatrix M., Axelrad, Jordan E., Reis, Bernardo S., Parsa, Roham, Neil, Jessica A., Devlin, Joseph C., Rudensky, Eugene, Dewan, M. Zahidunnabi, Cammer, Michael, Blumberg, Richard S., Ding, Yi, Ruggles, Kelly V., Mucida, Daniel, Koide, Shohei, Cadwell, Ken

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Targeting leukocidin-mediated immune evasion protects mice from Staphylococcus aureus bacteremia von Tam, Kayan, Lacey, Keenan A., Devlin, Joseph C., Coffre, Maryaline, Sommerfield, Alexis, Chan, Rita, O'Malley, Aidan, Koralov, Sergei B., Loke, P'ng, Torres, Victor J.

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Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice von Zhang, Xue-Song, Yin, Yue Sandra, Wang, Jincheng, Battaglia, Thomas, Krautkramer, Kimberly, Li, Wei Vivian, Li, Jackie, Brown, Mark, Zhang, Meifan, Badri, Michelle H., Armstrong, Abigail J.S., Strauch, Christopher M., Wang, Zeneng, Nemet, Ina, Altomare, Nicole, Devlin, Joseph C., He, Linchen, Morton, Jamie T., Chalk, John Alex, Needles, Kelly, Liao, Viviane, Mount, Julia, Li, Huilin, Ruggles, Kelly V., Bonneau, Richard A., Dominguez-Bello, Maria Gloria, Bäckhed, Fredrik, Hazen, Stanley L., Blaser, Martin J.

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Single-Cell Analysis of CX3CR1+ Cells Reveals a Pathogenic Role for BIRC5+ Myeloid Proliferating Cells Driven by Staphylococcus aureus Leukotoxins von Loredan, Denis G, Devlin, Joseph C, Lacey, Keenan A, Howard, Nina, Chen, Ze, Zwack, Erin E, Lin, Jian-Da, Ruggles, Kelly V, Khanna, Kamal M, Torres, Victor J, Loke, P'ng

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Distinct Features of Human Myeloid Cell Cytokine Response Profiles Identify Neutrophil Activation by Cytokines as a Prognostic Feature during Tuberculosis and Cancer von Devlin, Joseph C., Zwack, Erin E., Tang, Mei San, Li, Zhi, Fenyo, David, Torres, Victor J., Ruggles, Kelly V., Loke, P'ng

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Author Correction: Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas von Moncada, Reuben, Barkley, Dalia, Wagner, Florian, Chiodin, Marta, Devlin, Joseph C., Baron, Maayan, Hajdu, Cristina H., Simeone, Diane M., Yanai, Itai

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Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species von Sargsian, Shushan, Chen, Ze, Lee, Soo Ching, Robertson, Amicha, Thur, Rafaela Saes, Sproch, Julia, Devlin, Joseph C., Tee, Mian Zi, Er, Yi Xian, Copin, Richard, Heguy, Adriana, Pironti, Alejandro, Torres, Victor J., Ruggles, Kelly V., Lim, Yvonne A.L., Bethony, Jeffrey, Loke, P’ng, Cadwell, Ken

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Increased weight gain by C-section: Functional significance of the primordial microbiome von Martinez, 2nd, Keith A, Devlin, Joseph C, Lacher, Corey R, Yin, Yue, Cai, Yi, Wang, Jincheng, Dominguez-Bello, Maria G

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TRAPnSeq allows high-throughput profiling of antigen-specific antibody-secreting cells von Asrat, Seblewongel, Devlin, Joseph C., Vecchione, Andrea, Klotz, Brian, Setliff, Ian, Srivastava, Devin, Limnander, Andre, Rafique, Ashique, Adler, Christina, Porter, Stephen, Murphy, Andrew J., Atwal, Gurinder S., Sleeman, Matthew A., Lim, Wei Keat, Orengo, Jamie M.

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