Browsing by Author "Xavier, Ramnik J."

Now showing items 1-11 of 11

    • Akkermansia muciniphila phospholipid induces homeostatic immune responses 

      Bae, Munhyung; Cassilly, Chelsi D.; Liu, Xiaoxi; Park, Sung-Moo; Tusi, Betsabeh Khoramian; Chen, Xiangiun; Kwon, Jaeyoung; Filipcik, Pavel; Bolze, Andrew S.; Liu, Zehua; Vlamkis, Hera; Graham, Daniel B.; Buhrlage, Sara J.; Xavier, Ramnik J.; Clardy, Jon (Springer Science and Business Media LLC, 2022-07-27)
      Multiple studies have established associations between human gut bacteria and host physiology, but determining the molecular mechanisms underlying these associations has been challenging1–3. Akkermansia muciniphila has ...

    • Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense 

      Lassen, Kara G.; Kuballa, Petric; Conway, Kara L.; Patel, Khushbu K.; Becker, Christine E.; Peloquin, Joanna M.; Villablanca, Eduardo J.; Norman, Jason M.; Liu, Ta-Chiang; Heath, Robert J.; Becker, Morgan L.; Fagbami, Lola; Horn, Heiko; Mercer, Johnathan; Yilmaz, Omer H.; Jaffe, Jacob D.; Shamji, Alykhan F.; Bhan, Atul K.; Carr, Steven A.; Daly, Mark J.; Virgin, Herbert W.; Schreiber, Stuart L.; Stappenbeck, Thaddeus S.; Xavier, Ramnik J. (National Academy of Sciences, 2014)
      A coding polymorphism (Thr300Ala) in the essential autophagy gene, autophagy related 16-like 1 (ATG16L1), confers increased risk for the development of Crohn disease, although the mechanisms by which single disease-associated ...

    • Discovery of bioactive microbial gene products in inflammatory bowel disease 

      Zhang, Yancong; Bhosle, Amrisha; Bae, Sena; McIver, Lauren J.; Pishchany, Gleb; Accorsi, Emma K.; Thompson, Kelsey N.; Arze, Cesar; Wang, Ya; Subramanian, Ayshwarya; Kearney, Sean M.; Pawluk, April; Plichta, Damian R.; Rahnavard, Ali; Shafquat, Afrah; Xavier, Ramnik J.; Vlamakis, Hera; Garrett, Wendy S.; Krueger, Andy; Huttenhower, Curtis; Franzosa, Eric A. (Springer Science and Business Media LLC, 2022-05-25)
      Microbial communities and their associated bioactive compounds are often disrupted in conditions such as the inflammatory bowel diseases (IBD). However, even in well-characterized environments (e.g. the human gastrointestinal ...

    • Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans 

      Smeekens, Sanne P.; Ng, Aylwin; Kumar, Vinod; Johnson, Melissa D.; Plantinga, Theo S.; van Diemen, Cleo; Arts, Peer; Verwiel, Eugéne T.P.; Gresnigt, Mark S.; Fransen, Karin; van Sommeren, Suzanne; Oosting, Marije; Cheng, Shih-Chin; Joosten, Leo A.B.; Hoischen, Alexander; Kullberg, Bart-Jan; Scott, William K.; Perfect, John R.; van der Meer, Jos W.M.; Wijmenga, Cisca; Netea, Mihai G.; Xavier, Ramnik J. (2013)
      Candida albicans is the most common human fungal pathogen causing mucosal and systemic infections. However, human antifungal immunity remains poorly defined. Here, by integrating transcriptional analysis and functional ...

    • Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease 

      Lipinski, Marta M.; Zheng, Bin; Lu, Tao; Yan, Zhenyu; Py, Bénédicte F.; Ng, Aylwin; Xavier, Ramnik J.; Li, Cheng; Yankner, Bruce A.; Scherzer, Clemens R.; Yuan, Junying (National Academy of Sciences, 2010)
      Dysregulation of autophagy, a cellular catabolic mechanism essential for degradation of misfolded proteins, has been implicated in multiple neurodegenerative diseases. However, the mechanisms that lead to the autophagy ...

    • Growth Effects of N-Acylethanolamines on Gut Bacteria Reflect Altered Bacterial Abundances in Inflammatory Bowel Disease 

      Fornelos, Nadine; Franzosa, Eric; Bishai, Jason; Annand, John W.; Oka, Akihiko; Lloyd-Price, Jason; Arthur, Timothy D.; Garner, Ashley; Avila-Pacheco, Julian; Haiser, Henry J.; Tolonen, Andrew C.; Porter, Jeffrey A.; Clish, Clary B.; Sartor, R. Balfour; Huttenhower, Curtis; Vlamakis, Hera; Xavier, Ramnik J.; Xavier (Springer Science and Business Media LLC, 2020-01-20)
      Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain ...

    • Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics 

      Muus, Christoph; Luecken, Malte D.; Eraslan, Gökcen; Sikkema, Lisa; Waghray, Avinash; Heimberg, Graham; Kobayashi, Yoshihiko; Vaishnav, Eeshit Dhaval; Subramanian, Ayshwarya; Smillie, Christopher; Jagadeesh, Karthik A.; Duong, Elizabeth Thu; Fiskin, Evgenij; Torlai Triglia, Elena; Ansari, Meshal; Cai, Peiwen; Lin, Brian; Buchanan, Justin; Chen, Sijia; Shu, Jian; Haber, Adam L.; Chung, Hattie; Montoro, Daniel T.; Adams, Taylor; Aliee, Hananeh; Allon, Samuel J.; Andrusivova, Zaneta; Angelidis, Ilias; Ashenberg, Orr; Bassler, Kevin; Bécavin, Christophe; Benhar, Inbal; Bergenstråhle, Joseph; Bergenstråhle, Ludvig; Bolt, Liam; Braun, Emelie; Bui, Linh T.; Callori, Steven; Chaffin, Mark; Chichelnitskiy, Evgeny; Chiou, Joshua; Conlon, Thomas M.; Cuoco, Michael S.; Cuomo, Anna S. E.; Deprez, Marie; Duclos, Grant; Fine, Denise; Fischer, David S.; Ghazanfar, Shila; Gillich, Astrid; Giotti, Bruno; Gould, Joshua; Guo, Minzhe; Gutierrez, Austin J.; Habermann, Arun C.; Harvey, Tyler; He, Peng; Hou, Xiaomeng; Hu, Lijuan; Hu, Yan; Jaiswal, Alok; Ji, Lu; Jiang, Peiyong; Kapellos, Theodoros S.; Kuo, Christin S.; Larsson, Ludvig; Leney-Greene, Michael A.; Lim, Kyungtae; Litviňuková, Monika; Ludwig, Leif S.; Lukassen, Soeren; Luo, Wendy; Maatz, Henrike; Madissoon, Elo; Mamanova, Lira; Manakongtreecheep, Kasidet; Leroy, Sylvie; Mayr, Christoph H.; Mbano, Ian M.; McAdams, Alexi M.; Nabhan, Ahmad N.; Nyquist, Sarah K.; Penland, Lolita; Poirion, Olivier B.; Poli, Sergio; Qi, CanCan; Queen, Rachel; Reichart, Daniel; Rosas, Ivan; Schupp, Jonas C.; Shea, Conor V.; Shi, Xingyi; Sinha, Rahul; Sit, Rene V.; Slowikowski, Kamil; Slyper, Michal; Smith, Neal P.; Sountoulidis, Alex; Strunz, Maximilian; Sullivan, Travis B.; Sun, Dawei; Talavera-López, Carlos; Tan, Peng; Tantivit, Jessica; Travaglini, Kyle J.; Tucker, Nathan R.; Vernon, Katherine A.; Wadsworth, Marc H.; Waldman, Julia; Wang, Xiuting; Xu, Ke; Yan, Wenjun; Zhao, William; Ziegler, Carly G. K.; Deutsch, Gail H.; Dutra, Jennifer; Gaulton, Kyle J.; Holden-Wiltse, Jeanne; Huyck, Heidie L.; Mariani, Thomas J.; Misra, Ravi S.; Poole, Cory; Preissl, Sebastian; Pryhuber, Gloria S.; Rogers, Lisa; Sun, Xin; Wang, Allen; Whitsett, Jeffrey A.; Xu, Yan; Alladina, Jehan; Banovich, Nicholas E.; Barbry, Pascal; Beane, Jennifer E.; Bhattacharyya, Roby P.; Black, Katharine E.; Brazma, Alvis; Campbell, Joshua D.; Cho, Josalyn L.; Collin, Joseph; Conrad, Christian; de Jong, Kitty; Desai, Tushar; Ding, Diane Z.; Eickelberg, Oliver; Eils, Roland; Ellinor, Patrick T.; Faiz, Alen; Falk, Christine S.; Farzan, Michael; Gellman, Andrew; Getz, Gad; Glass, Ian A.; Greka, Anna; Haniffa, Muzlifah; Hariri, Lida P.; Hennon, Mark W.; Horvath, Peter; Hübner, Norbert; Hung, Deborah T.; Huyck, Heidie L.; Janssen, William J.; Juric, Dejan; Kaminski, Naftali; Koenigshoff, Melanie; Koppelman, Gerard H.; Krasnow, Mark A.; Kropski, Jonathan A.; Kuhnemund, Malte; Lafyatis, Robert; Lako, Majlinda; Lander, Eric S.; Lee, Haeock; Lenburg, Marc E.; Marquette, Charles-Hugo; Metzger, Ross J.; Linnarsson, Sten; Liu, Gang; Lo, Yuk Ming Dennis; Lundeberg, Joakim; Marioni, John C.; Mazzilli, Sarah A.; Medoff, Benjamin D.; Meyer, Kerstin B.; Miao, Zhichao; Misharin, Alexander V.; Nawijn, Martijn C.; Nikolić, Marko Z.; Noseda, Michela; Ordovas-Montanes, Jose; Oudit, Gavin Y.; Pe’er, Dana; Powell, Joseph E.; Quake, Stephen R.; Rajagopal, Jayaraj; Tata, Purushothama Rao; Rawlins, Emma L.; Regev, Aviv; Reid, Mary E.; Reyfman, Paul A.; Rieger-Christ, Kimberly M.; Rojas, Mauricio; Rozenblatt-Rosen, Orit; Saeb-Parsy, Kourosh; Samakovlis, Christos; Sanes, Joshua R.; Schiller, Herbert B.; Schultze, Joachim L.; Schwarz, Roland F.; Segre, Ayellet V.; Seibold, Max A.; Seidman, Christine E.; Seidman, Jon G.; Shalek, Alex K.; Shepherd, Douglas P.; Sinha, Rahul; Spence, Jason R.; Spira, Avrum; Sun, Xin; Sundström, Erik; Teichmann, Sarah A.; Theis, Fabian J.; Tsankov, Alexander M.; Vallier, Ludovic; van den Berge, Maarten; Van Zyl, Tave A.; Villani, Alexandra-Chloé; Weins, Astrid; Xavier, Ramnik J.; Yildirim, Ali Önder; Zaragosi, Laure-Emmanuelle; Zerti, Darin; Zhang, Hongbo; Zhang, Kun; Zhang, Xiaohui (Springer Science and Business Media LLC, 2021-03)
      ACE2 and accessory proteases (TMPRSS2, CTSL) are needed for SARS-CoV-2 cellular entry, and their expression may shed light on viral tropism and impact across the body. We assess the cell type-specific expression of ACE2, ...

    • Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells 

      Sundberg, Thomas B.; Choi, Hwan Geun; Song, Joo-Hye; Russell, Caitlin N.; Hussain, Mahmud M.; Graham, Daniel B.; Khor, Bernard; Gagnon, John; O’Connell, Daniel J.; Narayan, Kavitha; Dančík, Vlado; Perez, Jose R.; Reinecker, Hans-Christian; Gray, Nathanael S.; Schreiber, Stuart L.; Xavier, Ramnik J.; Shamji, Alykhan F. (National Academy of Sciences, 2014)
      Genetic alterations that reduce the function of the immunoregulatory cytokine IL-10 contribute to colitis in mouse and man. Myeloid cells such as macrophages (M Phi s) and dendritic cells (DCs) play an essential role in ...

    • The Scaffold Protein CNK1 Interacts with the Tumor Suppressor RASSF1A and Augments RASSF1A-induced Cell Death 

      Rabizadeh, Shahrooz; Xavier, Ramnik J.; Ishiguro, Kazuhiro; Bernabeortiz, Juliocesar; Lopez-Ilasaca, Marco; Khokhlatchev, Andrei; Mollahan, Pamela; Pfeifer, Gerd P.; Avruch, Joseph; Seed, Brian (American Society for Biochemistry and Molecular Biology, 2004)
      The connector enhancer of KSR (CNK) is a multidomain scaffold protein discovered in Drosophila, where it is necessary for Ras activation of the Raf kinase. Recent studies have shown that CNK1 also interacts with RalA and ...

    • Transmembrane Adaptor Protein PAG/CBP Is Involved in both Positive and Negative Regulation of Mast Cell Signaling 

      Draberova, Lubica; Bugajev, Viktor; Potuckova, Lucie; Halova, Ivana; Bambouskova, Monika; Polakovicova, Iva; Xavier, Ramnik J.; Seed, Brian; Draber, Petr (American Society for Microbiology, 2014)
      The transmembrane adaptor protein PAG/CBP (here, PAG) is expressed in multiple cell types. Tyrosine-phosphorylated PAG serves as an anchor for C-terminal SRC kinase, an inhibitor of SRC-family kinases. The role of PAG as ...

    • Wnt signaling regulates mitochondrial physiology and insulin sensitivity 

      Yoon, John C.; Ng, Aylwin; Kim, Brian H.; Bianco, Antonio; Xavier, Ramnik J.; Elledge, Stephen J. (Cold Spring Harbor Laboratory Press, 2010)
      Mitochondria serve a critical role in physiology and disease. The genetic basis of mitochondrial regulation in mammalian cells has not yet been detailed. We performed a large-scale RNAi screen to systematically identify ...