Search Results - "Davis, Fred P."

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain by Mo, Alisa, Mukamel, Eran A., Davis, Fred P., Luo, Chongyuan, Henry, Gilbert L., Picard, Serge, Urich, Mark A., Nery, Joseph R., Sejnowski, Terrence J., Lister, Ryan, Eddy, Sean R., Ecker, Joseph R., Nathans, Jeremy

“…Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate…”
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Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality by Shih, Han-Yu, Sciumè, Giuseppe, Mikami, Yohei, Guo, Liying, Sun, Hong-Wei, Brooks, Stephen R., Urban, Joseph F., Davis, Fred P., Kanno, Yuka, O’Shea, John J.

“…Innate lymphoid cells (ILCs) play key roles in host defense, barrier integrity, and homeostasis and mirror adaptive CD4+ T helper (Th) cell subtypes in both…”
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A genetic, genomic, and computational resource for exploring neural circuit function by Davis, Fred P, Nern, Aljoscha, Picard, Serge, Reiser, Michael B, Rubin, Gerald M, Eddy, Sean R, Henry, Gilbert L

“…The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we…”
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Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report by Kim, Doyoung, Kobayashi, Tetsuro, Voisin, Benjamin, Jo, Jay-Hyun, Sakamoto, Keiko, Jin, Seon-Pil, Kelly, Michael, Pasieka, Helena B., Naff, Jessica L., Meyerle, Jon H., Ikpeama, Ijeoma D., Fahle, Gary A., Davis, Fred P., Rosenzweig, Sergio D., Alejo, Julie C., Pittaluga, Stefania, Kong, Heidi H., Freeman, Alexandra F., Nagao, Keisuke

“…Drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms (DiHS/DRESS) is a potentially fatal multiorgan inflammatory…”
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Odorant binding protein 69a connects social interaction to modulation of social responsiveness in Drosophila by Bentzur, Assa, Shmueli, Anat, Omesi, Liora, Ryvkin, Julia, Knapp, Jon-Michael, Parnas, Moshe, Davis, Fred P, Shohat-Ophir, Galit

“…Living in a social environment requires the ability to respond to specific social stimuli and to incorporate information obtained from prior interactions into…”
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Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells by Villarino, Alejandro V, Sciumè, Giuseppe, Davis, Fred P, Iwata, Shigeru, Zitti, Beatrice, Robinson, Gertraud W, Hennighausen, Lothar, Kanno, Yuka, O'Shea, John J

“…Innate lymphoid cells (ILCs) patrol environmental interfaces to defend against infection and protect barrier integrity. Using a genetic tuning model, we…”
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Cell type-specific genomics of Drosophila neurons by Henry, Gilbert L, Davis, Fred P, Picard, Serge, Eddy, Sean R

“…Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the…”
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Evolved Repression Overcomes Enhancer Robustness by Preger-Ben Noon, Ella, Davis, Fred P., Stern, David L.

“…Biological systems display extraordinary robustness. Robustness of transcriptional enhancers results mainly from clusters of binding sites for the same…”
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MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23 by Mikami, Yohei, Philips, Rachael L., Sciumè, Giuseppe, Petermann, Franziska, Meylan, Françoise, Nagashima, Hiroyuki, Yao, Chen, Davis, Fred P., Brooks, Stephen R., Sun, Hong-Wei, Takahashi, Hayato, Poholek, Amanda C., Shih, Han-Yu, Afzali, Behdad, Muljo, Stefan A., Hafner, Markus, Kanno, Yuka, O’Shea, John J.

“…MicroRNAs are important regulators of immune responses. Here, we show miR-221 and miR-222 modulate the intestinal Th17 cell response. Expression of miR-221 and…”
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Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of NK Cells by Sciumè, Giuseppe, Mikami, Yohei, Jankovic, Dragana, Nagashima, Hiroyuki, Villarino, Alejandro V., Morrison, Tasha, Yao, Chen, Signorella, Sadie, Sun, Hong-Wei, Brooks, Stephen R., Fang, Difeng, Sartorelli, Vittorio, Nakayamada, Shingo, Hirahara, Kiyoshi, Zitti, Beatrice, Davis, Fred P., Kanno, Yuka, O’Shea, John J., Shih, Han-Yu

“…Innate immune responses rely on rapid and precise gene regulation mediated by accessibility of regulatory regions to transcription factors (TFs). In natural…”
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Retinoic Acid Receptor Alpha Represses a Th9 Transcriptional and Epigenomic Program to Reduce Allergic Pathology by Schwartz, Daniella M., Farley, Taylor K., Richoz, Nathan, Yao, Chen, Shih, Han-Yu, Petermann, Franziska, Zhang, Yuan, Sun, Hong-Wei, Hayes, Erika, Mikami, Yohei, Jiang, Kan, Davis, Fred P., Kanno, Yuka, Milner, Joshua D., Siegel, Richard, Laurence, Arian, Meylan, Françoise, O’Shea, John J.

“…CD4+ T helper (Th) differentiation is regulated by diverse inputs, including the vitamin A metabolite retinoic acid (RA). RA acts through its receptor RARα to…”
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A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency by Xie, Liangqi, Torigoe, Sharon E, Xiao, Jifang, Mai, Daniel H, Li, Li, Davis, Fred P, Dong, Peng, Marie-Nelly, Herve, Grimm, Jonathan, Lavis, Luke, Darzacq, Xavier, Cattoglio, Claudia, Liu, Zhe, Tjian, Robert

“…Transcription factor (TF)-directed enhanceosome assembly constitutes a fundamental regulatory mechanism driving spatiotemporal gene expression programs during…”
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Epigenomic landscapes of retinal rods and cones by Mo, Alisa, Luo, Chongyuan, Davis, Fred P, Mukamel, Eran A, Henry, Gilbert L, Nery, Joseph R, Urich, Mark A, Picard, Serge, Lister, Ryan, Eddy, Sean R, Beer, Michael A, Ecker, Joseph R, Nathans, Jeremy

“…Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide…”
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A Metabolic Switch for Th17 Pathogenicity by Davis, Fred P., Kanno, Yuka, O’Shea, John J.

“…T helper 17 (Th17) cells are critical for host defense but can also drive autoimmunity. This divergent behavior is explored by Gaublomme et al. and Wang…”
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The overlap of small molecule and protein binding sites within families of protein structures by Davis, Fred P, Sali, Andrej

“…Protein-protein interactions are challenging targets for modulation by small molecules. Here, we propose an approach that harnesses the increasing structural…”
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Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma by Dolgalev, Igor, Zhou, Hua, Murrell, Nina, Le, Hortense, Sakellaropoulos, Theodore, Coudray, Nicolas, Zhu, Kelsey, Vasudevaraja, Varshini, Yeaton, Anna, Goparaju, Chandra, Li, Yonghua, Sulaiman, Imran, Tsay, Jun-Chieh J., Meyn, Peter, Mohamed, Hussein, Sydney, Iris, Shiomi, Tomoe, Ramaswami, Sitharam, Narula, Navneet, Kulicke, Ruth, Davis, Fred P., Stransky, Nicolas, Smolen, Gromoslaw A., Cheng, Wei-Yi, Cai, James, Punekar, Salman, Velcheti, Vamsidhar, Sterman, Daniel H., Poirier, J. T., Neel, Ben, Wong, Kwok-Kin, Chiriboga, Luis, Heguy, Adriana, Papagiannakopoulos, Thales, Nadorp, Bettina, Snuderl, Matija, Segal, Leopoldo N., Moreira, Andre L., Pass, Harvey I., Tsirigos, Aristotelis

“…Approximately 30% of early-stage lung adenocarcinoma patients present with disease progression after successful surgical resection. Despite efforts of mapping…”
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Host–pathogen protein interactions predicted by comparative modeling by Davis, Fred P., Barkan, David T., Eswar, Narayanan, McKerrow, James H., Sali, Andrej

“…Pathogens have evolved numerous strategies to infect their hosts, while hosts have evolved immune responses and other defenses to these foreign challenges. The…”
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Phosphorylation at the Interface by Davis, Fred P.

“…Proteomic studies have identified thousands of eukaryotic phosphorylation sites (phosphosites), but few are functionally characterized. Nishi et al., in this…”
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Transcription factors that convert adult cell identity are differentially polycomb repressed by Davis, Fred P, Eddy, Sean R

“…Transcription factors that can convert adult cells of one type to another are usually discovered empirically by testing factors with a known developmental role…”
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Proteome-wide prediction of overlapping small molecule and protein binding sites using structure by Davis, Fred P

“…Small molecules that modulate protein-protein interactions are of great interest for chemical biology and therapeutics. Here I present a structure-based…”
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