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Items: 25

1.

Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model.

Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver PA, Gerber GK.

Cell Host Microbe. 2019 Jun 12;25(6):803-814.e5. doi: 10.1016/j.chom.2019.05.001. Epub 2019 Jun 4.

2.

Quorum Sensing Can Be Repurposed To Promote Information Transfer between Bacteria in the Mammalian Gut.

Kim S, Kerns SJ, Ziesack M, Bry L, Gerber GK, Way JC, Silver PA.

ACS Synth Biol. 2018 Sep 21;7(9):2270-2281. doi: 10.1021/acssynbio.8b00271. Epub 2018 Aug 31.

PMID:
30125499
3.

Computer-guided design of optimal microbial consortia for immune system modulation.

Stein RR, Tanoue T, Szabady RL, Bhattarai SK, Olle B, Norman JM, Suda W, Oshima K, Hattori M, Gerber GK, Sander C, Honda K, Bucci V.

Elife. 2018 Apr 17;7. pii: e30916. doi: 10.7554/eLife.30916.

4.

Macrophage dysfunction initiates colitis during weaning of infant mice lacking the interleukin-10 receptor.

Redhu NS, Bakthavatchalu V, Conaway EA, Shouval DS, Tsou A, Goettel JA, Biswas A, Wang C, Field M, Muller W, Bleich A, Li N, Gerber GK, Bry L, Fox JG, Snapper SB, Horwitz BH.

Elife. 2017 Jul 5;6. pii: e27652. doi: 10.7554/eLife.27652.

5.

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation.

Riglar DT, Giessen TW, Baym M, Kerns SJ, Niederhuber MJ, Bronson RT, Kotula JW, Gerber GK, Way JC, Silver PA.

Nat Biotechnol. 2017 Jul;35(7):653-658. doi: 10.1038/nbt.3879. Epub 2017 May 29.

6.

Regulation of Glucose Uptake and Enteroendocrine Function by the Intestinal Epithelial Insulin Receptor.

Ussar S, Haering MF, Fujisaka S, Lutter D, Lee KY, Li N, Gerber GK, Bry L, Kahn CR.

Diabetes. 2017 Apr;66(4):886-896. doi: 10.2337/db15-1349. Epub 2017 Jan 17.

7.

Alterations of the human gut microbiome in multiple sclerosis.

Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, Mazzola MA, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topçuolu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L, Weiner HL.

Nat Commun. 2016 Jun 28;7:12015. doi: 10.1038/ncomms12015.

8.

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses.

Bucci V, Tzen B, Li N, Simmons M, Tanoue T, Bogart E, Deng L, Yeliseyev V, Delaney ML, Liu Q, Olle B, Stein RR, Honda K, Bry L, Gerber GK.

Genome Biol. 2016 Jun 3;17(1):121. doi: 10.1186/s13059-016-0980-6.

9.

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles.

Allegretti JR, Kearney S, Li N, Bogart E, Bullock K, Gerber GK, Bry L, Clish CB, Alm E, Korzenik JR.

Aliment Pharmacol Ther. 2016 Jun;43(11):1142-53. doi: 10.1111/apt.13616. Epub 2016 Apr 18.

10.

Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics.

Yaung SJ, Deng L, Li N, Braff JL, Church GM, Bry L, Wang HH, Gerber GK.

Mol Syst Biol. 2015 Mar;11(3):788.

11.

Computational Pathology: A Path Ahead.

Louis DN, Feldman M, Carter AB, Dighe AS, Pfeifer JD, Bry L, Almeida JS, Saltz J, Braun J, Tomaszewski JE, Gilbertson JR, Sinard JH, Gerber GK, Galli SJ, Golden JA, Becich MJ.

Arch Pathol Lab Med. 2016 Jan;140(1):41-50. doi: 10.5858/arpa.2015-0093-SA. Epub 2015 Jun 22.

12.

Diet dominates host genotype in shaping the murine gut microbiota.

Carmody RN, Gerber GK, Luevano JM Jr, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ.

Cell Host Microbe. 2015 Jan 14;17(1):72-84. doi: 10.1016/j.chom.2014.11.010. Epub 2014 Dec 18.

13.

Computational pathology: an emerging definition.

Louis DN, Gerber GK, Baron JM, Bry L, Dighe AS, Getz G, Higgins JM, Kuo FC, Lane WJ, Michaelson JS, Le LP, Mermel CH, Gilbertson JR, Golden JA.

Arch Pathol Lab Med. 2014 Sep;138(9):1133-8. doi: 10.5858/arpa.2014-0034-ED. No abstract available.

PMID:
25171694
14.

Dynamics of the microbiota in response to host infection.

Belzer C, Gerber GK, Roeselers G, Delaney M, DuBois A, Liu Q, Belavusava V, Yeliseyev V, Houseman A, Onderdonk A, Cavanaugh C, Bry L.

PLoS One. 2014 Jul 11;9(7):e95534. doi: 10.1371/journal.pone.0095534. eCollection 2014.

15.

The dynamic microbiome.

Gerber GK.

FEBS Lett. 2014 Nov 17;588(22):4131-9. doi: 10.1016/j.febslet.2014.02.037. Epub 2014 Feb 28. Review.

16.

A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis.

Noval Rivas M, Burton OT, Wise P, Zhang YQ, Hobson SA, Garcia Lloret M, Chehoud C, Kuczynski J, DeSantis T, Warrington J, Hyde ER, Petrosino JF, Gerber GK, Bry L, Oettgen HC, Mazmanian SK, Chatila TA.

J Allergy Clin Immunol. 2013 Jan;131(1):201-12. doi: 10.1016/j.jaci.2012.10.026. Epub 2012 Nov 30.

17.

Inferring dynamic signatures of microbes in complex host ecosystems.

Gerber GK, Onderdonk AB, Bry L.

PLoS Comput Biol. 2012;8(8):e1002624. doi: 10.1371/journal.pcbi.1002624. Epub 2012 Aug 2.

18.

Discovering homotypic binding events at high spatial resolution.

Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S.

Bioinformatics. 2010 Dec 15;26(24):3028-34. doi: 10.1093/bioinformatics/btq590. Epub 2010 Oct 21.

19.

Automated discovery of functional generality of human gene expression programs.

Gerber GK, Dowell RD, Jaakkola TS, Gifford DK.

PLoS Comput Biol. 2007 Aug;3(8):e148. Epub 2007 Jun 13.

20.

High-resolution computational models of genome binding events.

Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2006 Aug;24(8):963-70. Erratum in: Nat Biotechnol. 2006 Oct;24(10):1293.

PMID:
16900145
21.

Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide.

Schreiber J, Jenner RG, Murray HL, Gerber GK, Gifford DK, Young RA.

Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5899-904. Epub 2006 Apr 4.

22.

Computational discovery of gene modules and regulatory networks.

Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2003 Nov;21(11):1337-42. Epub 2003 Oct 12.

23.

Continuous representations of time-series gene expression data.

Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I.

J Comput Biol. 2003;10(3-4):341-56.

PMID:
12935332
24.

Transcriptional regulatory networks in Saccharomyces cerevisiae.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA.

Science. 2002 Oct 25;298(5594):799-804.

25.

Occurrence and function of a high-Km hexokinase in immature red blood cells.

Gerber GK, Schultze M, Rapoport SM.

Eur J Biochem. 1970 Dec;17(3):445-9. No abstract available.

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