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Items: 32

1.

Retinoic Acid Receptor Alpha Represses a Th9 Transcriptional and Epigenomic Program to Reduce Allergic Pathology.

Schwartz DM, Farley TK, Richoz N, Yao C, Shih HY, Petermann F, Zhang Y, Sun HW, Hayes E, Mikami Y, Jiang K, Davis FP, Kanno Y, Milner JD, Siegel R, Laurence A, Meylan F, O'Shea JJ.

Immunity. 2019 Jan 15;50(1):106-120.e10. doi: 10.1016/j.immuni.2018.12.014.

PMID:
30650370
2.

Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute the Drosophila Mushroom Bodies.

Shih MM, Davis FP, Henry GL, Dubnau J.

G3 (Bethesda). 2019 Jan 9;9(1):81-94. doi: 10.1534/g3.118.200726.

3.

Odorant binding protein 69a connects social interaction to modulation of social responsiveness in Drosophila.

Bentzur A, Shmueli A, Omesi L, Ryvkin J, Knapp JM, Parnas M, Davis FP, Shohat-Ophir G.

PLoS Genet. 2018 Apr 9;14(4):e1007328. doi: 10.1371/journal.pgen.1007328. eCollection 2018 Apr.

4.

A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency.

Xie L, Torigoe SE, Xiao J, Mai DH, Li L, Davis FP, Dong P, Marie-Nelly H, Grimm J, Lavis L, Darzacq X, Cattoglio C, Liu Z, Tjian R.

Genes Dev. 2017 Sep 1;31(17):1795-1808. doi: 10.1101/gad.303321.117.

5.

Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells.

Villarino AV, Sciumè G, Davis FP, Iwata S, Zitti B, Robinson GW, Hennighausen L, Kanno Y, O'Shea JJ.

J Exp Med. 2017 Oct 2;214(10):2999-3014. doi: 10.1084/jem.20150907. Epub 2017 Sep 15.

6.

The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells.

Iwata S, Mikami Y, Sun HW, Brooks SR, Jankovic D, Hirahara K, Onodera A, Shih HY, Kawabe T, Jiang K, Nakayama T, Sher A, O'Shea JJ, Davis FP, Kanno Y.

Immunity. 2017 Jun 20;46(6):983-991.e4. doi: 10.1016/j.immuni.2017.05.005. Epub 2017 Jun 13.

7.

BACH2 immunodeficiency illustrates an association between super-enhancers and haploinsufficiency.

Afzali B, Grönholm J, Vandrovcova J, O'Brien C, Sun HW, Vanderleyden I, Davis FP, Khoder A, Zhang Y, Hegazy AN, Villarino AV, Palmer IW, Kaufman J, Watts NR, Kazemian M, Kamenyeva O, Keith J, Sayed A, Kasperaviciute D, Mueller M, Hughes JD, Fuss IJ, Sadiyah MF, Montgomery-Recht K, McElwee J, Restifo NP, Strober W, Linterman MA, Wingfield PT, Uhlig HH, Roychoudhuri R, Aitman TJ, Kelleher P, Lenardo MJ, O'Shea JJ, Cooper N, Laurence ADJ.

Nat Immunol. 2017 Jul;18(7):813-823. doi: 10.1038/ni.3753. Epub 2017 May 22.

8.

Evolved Repression Overcomes Enhancer Robustness.

Preger-Ben Noon E, Davis FP, Stern DL.

Dev Cell. 2016 Dec 5;39(5):572-584. doi: 10.1016/j.devcel.2016.10.010. Epub 2016 Nov 10.

9.

Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality.

Shih HY, Sciumè G, Mikami Y, Guo L, Sun HW, Brooks SR, Urban JF Jr, Davis FP, Kanno Y, O'Shea JJ.

Cell. 2016 May 19;165(5):1120-1133. doi: 10.1016/j.cell.2016.04.029. Epub 2016 May 5.

10.

Epigenomic landscapes of retinal rods and cones.

Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J.

Elife. 2016 Mar 7;5:e11613. doi: 10.7554/eLife.11613.

11.

A Metabolic Switch for Th17 Pathogenicity.

Davis FP, Kanno Y, O'Shea JJ.

Cell. 2015 Dec 3;163(6):1308-10. doi: 10.1016/j.cell.2015.11.033.

12.

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J.

Neuron. 2015 Jun 17;86(6):1369-84. doi: 10.1016/j.neuron.2015.05.018.

13.

NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species.

Striedter GF, Belgard TG, Chen CC, Davis FP, Finlay BL, Güntürkün O, Hale ME, Harris JA, Hecht EE, Hof PR, Hofmann HA, Holland LZ, Iwaniuk AN, Jarvis ED, Karten HJ, Katz PS, Kristan WB, Macagno ER, Mitra PP, Moroz LL, Preuss TM, Ragsdale CW, Sherwood CC, Stevens CF, Stüttgen MC, Tsumoto T, Wilczynski W.

Brain Behav Evol. 2014;83(1):1-8. doi: 10.1159/000360152. Epub 2014 Feb 28.

14.

NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species.

Striedter GF, Belgard TG, Chen CC, Davis FP, Finlay BL, Güntürkün O, Hale ME, Harris JA, Hecht EE, Hof PR, Hofmann HA, Holland LZ, Iwaniuk AN, Jarvis ED, Karten HJ, Katz PS, Kristan WB, Macagno ER, Mitra PP, Moroz LL, Preuss TM, Ragsdale CW, Sherwood CC, Stevens CF, Stüttgen MC, Tsumoto T, Wilczynski W.

J Comp Neurol. 2014 May 1;522(7):1445-53. doi: 10.1002/cne.23568.

PMID:
24596113
15.

Transcription factors that convert adult cell identity are differentially polycomb repressed.

Davis FP, Eddy SR.

PLoS One. 2013 May 1;8(5):e63407. doi: 10.1371/journal.pone.0063407. Print 2013.

16.

Cell type-specific genomics of Drosophila neurons.

Henry GL, Davis FP, Picard S, Eddy SR.

Nucleic Acids Res. 2012 Oct;40(19):9691-704. doi: 10.1093/nar/gks671. Epub 2012 Aug 1.

17.

Phosphorylation at the interface.

Davis FP.

Structure. 2011 Dec 7;19(12):1726-7. doi: 10.1016/j.str.2011.11.006.

18.

Gene expression analysis in the parvalbumin-immunoreactive PV1 nucleus of the mouse lateral hypothalamus.

Girard F, Meszar Z, Marti C, Davis FP, Celio M.

Eur J Neurosci. 2011 Dec;34(12):1934-43. doi: 10.1111/j.1460-9568.2011.07918.x. Epub 2011 Dec 1.

PMID:
22128821
19.

Proteome-wide prediction of overlapping small molecule and protein binding sites using structure.

Davis FP.

Mol Biosyst. 2011 Feb;7(2):545-57. doi: 10.1039/c0mb00200c. Epub 2010 Nov 24.

PMID:
21103609
20.

The overlap of small molecule and protein binding sites within families of protein structures.

Davis FP, Sali A.

PLoS Comput Biol. 2010 Feb 5;6(2):e1000668. doi: 10.1371/journal.pcbi.1000668.

21.

A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.

Davis FP, Eddy SR.

Bioinformatics. 2009 Jul 1;25(13):1647-54. doi: 10.1093/bioinformatics/btp288. Epub 2009 May 4.

22.

MODBASE, a database of annotated comparative protein structure models and associated resources.

Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54. doi: 10.1093/nar/gkn791. Epub 2008 Oct 23.

23.

Host pathogen protein interactions predicted by comparative modeling.

Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A.

Protein Sci. 2007 Dec;16(12):2585-96. Epub 2007 Oct 26.

24.

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.

Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S4.

25.

DBAli tools: mining the protein structure space.

Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W393-7. Epub 2007 May 3.

26.

Structural modeling of protein interactions by analogy: application to PSD-95.

Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A.

PLoS Comput Biol. 2006 Nov 10;2(11):e153. Epub 2006 Oct 4.

27.

Protein complex compositions predicted by structural similarity.

Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS.

Nucleic Acids Res. 2006 May 31;34(10):2943-52. Print 2006.

28.

MODBASE: a database of annotated comparative protein structure models and associated resources.

Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D291-5.

29.

Localization of protein-binding sites within families of proteins.

Korkin D, Davis FP, Sali A.

Protein Sci. 2005 Sep;14(9):2350-60. Epub 2005 Aug 4.

30.

PIBASE: a comprehensive database of structurally defined protein interfaces.

Davis FP, Sali A.

Bioinformatics. 2005 May 1;21(9):1901-7. Epub 2005 Jan 18.

PMID:
15657096
31.

A structural perspective on protein-protein interactions.

Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A.

Curr Opin Struct Biol. 2004 Jun;14(3):313-24. Review.

PMID:
15193311
32.

MODBASE, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22.

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