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Items: 1 to 50 of 95

1.

The pH sensing receptor AopalH plays important roles in the nematophagous fungus Arthrobotrys oligospora.

Li J, Wu R, Wang M, Borneman J, Yang J, Zhang KQ.

Fungal Biol. 2019 Jul;123(7):547-554. doi: 10.1016/j.funbio.2019.05.008. Epub 2019 May 18.

PMID:
31196524
2.

Malassezia Is Associated with Crohn's Disease and Exacerbates Colitis in Mouse Models.

Limon JJ, Tang J, Li D, Wolf AJ, Michelsen KS, Funari V, Gargus M, Nguyen C, Sharma P, Maymi VI, Iliev ID, Skalski JH, Brown J, Landers C, Borneman J, Braun J, Targan SR, McGovern DPB, Underhill DM.

Cell Host Microbe. 2019 Mar 13;25(3):377-388.e6. doi: 10.1016/j.chom.2019.01.007. Epub 2019 Mar 5.

PMID:
30850233
3.

A screen of Crohn's disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells.

Chang YL, Rossetti M, Vlamakis H, Casero D, Sunga G, Harre N, Miller S, Humphries R, Stappenbeck T, Simpson KW, Sartor RB, Wu G, Lewis J, Bushman F, McGovern DPB, Salzman N, Borneman J, Xavier R, Huttenhower C, Braun J.

Mucosal Immunol. 2019 Mar;12(2):457-467. doi: 10.1038/s41385-018-0022-7. Epub 2018 Apr 25.

4.

Bacterial Microbiome Dynamics in Post Pull-Through Hirschsprung-Associated Enterocolitis (HAEC): An Experimental Study Employing the Endothelin Receptor B-Null Mouse Model.

Cheng Z, Zhao L, Dhall D, Ruegger PM, Borneman J, Frykman PK.

Front Surg. 2018 Apr 6;5:30. doi: 10.3389/fsurg.2018.00030. eCollection 2018.

5.

Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates.

Barr T, Sureshchandra S, Ruegger P, Zhang J, Ma W, Borneman J, Grant K, Messaoudi I.

Gut Microbes. 2018 Jul 4;9(4):338-356. doi: 10.1080/19490976.2018.1441663. Epub 2018 Apr 27.

6.

Engineered nonlinear materials using gold nanoantenna array.

Drachev VP, Kildishev AV, Borneman JD, Chen KP, Shalaev VM, Yamnitskiy K, Norwood RA, Peyghambarian N, Marder SR, Padilha LA, Webster S, Ensley TR, Hagan DJ, Van Stryland EW.

Sci Rep. 2018 Jan 15;8(1):780. doi: 10.1038/s41598-017-19066-3.

7.

Information Transfer Capacity of Articulators in American Sign Language.

Malaia E, Borneman JD, Wilbur RB.

Lang Speech. 2018 Mar;61(1):97-112. doi: 10.1177/0023830917708461. Epub 2017 May 31.

PMID:
28565932
8.

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients.

Jacobs JP, Goudarzi M, Singh N, Tong M, McHardy IH, Ruegger P, Asadourian M, Moon BH, Ayson A, Borneman J, McGovern DP, Fornace AJ Jr, Braun J, Dubinsky M.

Cell Mol Gastroenterol Hepatol. 2016 Jul 2;2(6):750-766. doi: 10.1016/j.jcmgh.2016.06.004. eCollection 2016 Nov.

9.

Microbial, metabolomic, and immunologic dynamics in a relapsing genetic mouse model of colitis induced by T-synthase deficiency.

Jacobs JP, Lin L, Goudarzi M, Ruegger P, McGovern DP, Fornace AJ Jr, Borneman J, Xia L, Braun J.

Gut Microbes. 2017 Jan 2;8(1):1-16. doi: 10.1080/19490976.2016.1257469. Epub 2016 Nov 22.

10.

A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition.

Li D, Achkar JP, Haritunians T, Jacobs JP, Hui KY, D'Amato M, Brand S, Radford-Smith G, Halfvarson J, Niess JH, Kugathasan S, Büning C, Schumm LP, Klei L, Ananthakrishnan A, Aumais G, Baidoo L, Dubinsky M, Fiocchi C, Glas J, Milgrom R, Proctor DD, Regueiro M, Simms LA, Stempak JM, Targan SR, Törkvist L, Sharma Y, Devlin B, Borneman J, Hakonarson H, Xavier RJ, Daly M, Brant SR, Rioux JD, Silverberg MS, Cho JH, Braun J, McGovern DP, Duerr RH.

Gastroenterology. 2016 Oct;151(4):724-32. doi: 10.1053/j.gastro.2016.06.051. Epub 2016 Aug 1.

11.

Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis.

Cheema AK, Maier I, Dowdy T, Wang Y, Singh R, Ruegger PM, Borneman J, Fornace AJ Jr, Schiestl RH.

PLoS One. 2016 Apr 13;11(4):e0151190. doi: 10.1371/journal.pone.0151190. eCollection 2016.

12.

Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium.

Volkmann ER, Chang YL, Barroso N, Furst DE, Clements PJ, Gorn AH, Roth BE, Conklin JL, Getzug T, Borneman J, McGovern DP, Tong M, Jacobs JP, Braun J.

Arthritis Rheumatol. 2016 Jun;68(6):1483-92. doi: 10.1002/art.39572.

13.

PRISE2: software for designing sequence-selective PCR primers and probes.

Huang YT, Yang JI, Chrobak M, Borneman J.

BMC Bioinformatics. 2014 Sep 25;15:317. doi: 10.1186/1471-2105-15-317.

14.

Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer.

Ruegger PM, Clark RT, Weger JR, Braun J, Borneman J.

J Microbiol Methods. 2014 Oct;105:82-7. doi: 10.1016/j.mimet.2014.07.001. Epub 2014 Jul 15.

15.

Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism.

Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, Li X, Graeber TG, Schwager E, Huttenhower C, Fornace AJ Jr, Sonnenburg JL, McGovern DP, Borneman J, Braun J.

ISME J. 2014 Nov;8(11):2193-206. doi: 10.1038/ismej.2014.64. Epub 2014 Apr 29.

16.

HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota.

McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P, Braun J.

Microbiome. 2013 Oct 12;1(1):26. doi: 10.1186/2049-2618-1-26.

17.

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships.

McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR, Graeber TG, Sonnenburg JL, Horvath S, Huttenhower C, McGovern DP, Fornace AJ Jr, Borneman J, Braun J.

Microbiome. 2013 Jun 5;1(1):17. doi: 10.1186/2049-2618-1-17.

18.

Phylogeny-based classification of microbial communities.

Tanaseichuk O, Borneman J, Jiang T.

Bioinformatics. 2014 Feb 15;30(4):449-56. doi: 10.1093/bioinformatics/btt700. Epub 2013 Dec 24.

19.

A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease.

Tong M, Li X, Wegener Parfrey L, Roth B, Ippoliti A, Wei B, Borneman J, McGovern DP, Frank DN, Li E, Horvath S, Knight R, Braun J.

PLoS One. 2013 Nov 19;8(11):e80702. doi: 10.1371/journal.pone.0080702. eCollection 2013.

20.

Intestinal bacteria modify lymphoma incidence and latency by affecting systemic inflammatory state, oxidative stress, and leukocyte genotoxicity.

Yamamoto ML, Maier I, Dang AT, Berry D, Liu J, Ruegger PM, Yang JI, Soto PA, Presley LL, Reliene R, Westbrook AM, Wei B, Loy A, Chang C, Braun J, Borneman J, Schiestl RH.

Cancer Res. 2013 Jul 15;73(14):4222-32. doi: 10.1158/0008-5472.CAN-13-0022.

21.
22.

Population Dynamics of Dactylella oviparasitica and Heterodera schachtii: Toward a Decision Model for Sugar Beet Planting.

Yang JI, Benecke S, Jeske DR, Rocha FS, Smith Becker J, Timper P, Ole Becker J, Borneman J.

J Nematol. 2012 Sep;44(3):237-44.

23.

Correlations between root-associated microorganisms and peach replant disease symptoms in a California soil.

Yang JI, Ruegger PM, McKenry MV, Becker JO, Borneman J.

PLoS One. 2012;7(10):e46420. doi: 10.1371/journal.pone.0046420. Epub 2012 Oct 5.

24.

Separating metagenomic short reads into genomes via clustering.

Tanaseichuk O, Borneman J, Jiang T.

Algorithms Mol Biol. 2012 Sep 26;7(1):27. doi: 10.1186/1748-7188-7-27.

25.

The role of coral-associated bacterial communities in Australian Subtropical White Syndrome of Turbinaria mesenterina.

Godwin S, Bent E, Borneman J, Pereg L.

PLoS One. 2012;7(9):e44243. doi: 10.1371/journal.pone.0044243. Epub 2012 Sep 6.

26.

Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology.

Ruegger PM, Bent E, Li W, Jeske DR, Cui X, Braun J, Jiang T, Borneman J.

J Microbiol Methods. 2012 Sep;90(3):235-40. doi: 10.1016/j.mimet.2012.05.013. Epub 2012 May 25.

27.

Numerical modeling of plasmonic nanoantennas with realistic 3D roughness and distortion.

Kildishev AV, Borneman JD, Chen KP, Drachev VP.

Sensors (Basel). 2011;11(7):7178-87. doi: 10.3390/s110707178. Epub 2011 Jul 13.

28.

A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface.

Li X, LeBlanc J, Truong A, Vuthoori R, Chen SS, Lustgarten JL, Roth B, Allard J, Ippoliti A, Presley LL, Borneman J, Bigbee WL, Gopalakrishnan V, Graeber TG, Elashoff D, Braun J, Goodglick L.

PLoS One. 2011;6(11):e26542. doi: 10.1371/journal.pone.0026542. Epub 2011 Nov 21.

29.

Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences.

Ruegger PM, Della Vedova G, Jiang T, Borneman J.

BMC Bioinformatics. 2011 Oct 10;12:394. doi: 10.1186/1471-2105-12-394.

30.

Neutral Zone Classifiers Using a Decision-Theoretic Approach With Application to DNA Array Analyses.

Yu H, Jeske DR, Ruegger P, Borneman J.

J Agric Biol Environ Stat. 2010 Dec;15(4):474-490.

31.

Host-microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal-luminal interface.

Presley LL, Ye J, Li X, Leblanc J, Zhang Z, Ruegger PM, Allard J, McGovern D, Ippoliti A, Roth B, Cui X, Jeske DR, Elashoff D, Goodglick L, Braun J, Borneman J.

Inflamm Bowel Dis. 2012 Mar;18(3):409-17. doi: 10.1002/ibd.21793. Epub 2011 Jun 22.

32.

Clustering Scatter Plots Using Data Depth Measures.

Zhang Z, Cui X, Jeske DR, Li X, Braun J, Borneman J.

J Biom Biostat. 2011;Suppl 5:001.

33.

Functional diversity in resource use by fungi.

McGuire KL, Bent E, Borneman J, Majumder A, Allison SD, Tresederi KK.

Ecology. 2010 Aug;91(8):2324-32.

PMID:
20836454
34.

Drude relaxation rate in grained gold nanoantennas.

Chen KP, Drachev VP, Borneman JD, Kildishev AV, Shalaev VM.

Nano Lett. 2010 Mar 10;10(3):916-22. doi: 10.1021/nl9037246.

PMID:
20128610
35.

Commensal microbiota and CD8+ T cells shape the formation of invariant NKT cells.

Wei B, Wingender G, Fujiwara D, Chen DY, McPherson M, Brewer S, Borneman J, Kronenberg M, Braun J.

J Immunol. 2010 Feb 1;184(3):1218-26. doi: 10.4049/jimmunol.0902620. Epub 2010 Jan 4.

36.

Bacteria associated with immunoregulatory cells in mice.

Presley LL, Wei B, Braun J, Borneman J.

Appl Environ Microbiol. 2010 Feb;76(3):936-41. doi: 10.1128/AEM.01561-09. Epub 2009 Dec 11.

37.

Simplified model for periodic nanoantennae: linear model and inverse design.

Borneman J, Chen KP, Kildishev A, Shalaev V.

Opt Express. 2009 Jul 6;17(14):11607-17.

PMID:
19582077
38.

Investigations into peach seedling stunting caused by a replant soil.

Bent E, Loffredo A, Yang JI, McKenry MV, Becker JO, Borneman J.

FEMS Microbiol Ecol. 2009 May;68(2):192-200. doi: 10.1111/j.1574-6941.2009.00668.x.

39.

Cellular immune response to intrastriatally implanted allogeneic bone marrow stromal cells in a rat model of Parkinson's disease.

Camp DM, Loeffler DA, Farrah DM, Borneman JN, LeWitt PA.

J Neuroinflammation. 2009 Jun 5;6:17. doi: 10.1186/1742-2094-6-17.

40.

Bone marrow stromal cells increase oligodendrogenesis after stroke.

Zhang J, Li Y, Zhang ZG, Lu M, Borneman J, Buller B, Savant-Bhonsale S, Elias SB, Chopp M.

J Cereb Blood Flow Metab. 2009 Jun;29(6):1166-74. doi: 10.1038/jcbfm.2009.41. Epub 2009 Apr 22.

41.

Detection and Investigation of Soil Biological Activity against Meloidogyne incognita.

Bent E, Loffredo A, McKenry MV, Becker JO, Borneman J.

J Nematol. 2008 Jun;40(2):109-18.

42.
43.

Immunogenicity of allogeneic adipose-derived stem cells in a rat spinal fusion model.

McIntosh KR, Lopez MJ, Borneman JN, Spencer ND, Anderson PA, Gimble JM.

Tissue Eng Part A. 2009 Sep;15(9):2677-86. doi: 10.1089/ten.TEA.2008.0566.

44.

Bone marrow stromal cell therapy reduces proNGF and p75 expression in mice with experimental autoimmune encephalomyelitis.

Zhang J, Brodie C, Li Y, Zheng X, Roberts C, Lu M, Gao Q, Borneman J, Savant-Bhonsale S, Elias SB, Chopp M.

J Neurol Sci. 2009 Apr 15;279(1-2):30-8. doi: 10.1016/j.jns.2008.12.033. Epub 2009 Feb 3.

45.

Resident enteric microbiota and CD8+ T cells shape the abundance of marginal zone B cells.

Wei B, Su TT, Dalwadi H, Stephan RP, Fujiwara D, Huang TT, Brewer S, Chen L, Arditi M, Borneman J, Rawlings DJ, Braun J.

Eur J Immunol. 2008 Dec;38(12):3411-25. doi: 10.1002/eji.200838432.

46.

Suppression of the Plant-Parasitic Nematode Heterodera schachtii by the Fungus Dactylella oviparasitica.

Olatinwo R, Yin B, Becker JO, Borneman J.

Phytopathology. 2006 Jan;96(1):111-4. doi: 10.1094/PHYTO-96-0111.

47.

Identification of Fungal rDNA Associated with Soil Suppressiveness Against Heterodera schachtii Using Oligonucleotide Fingerprinting.

Yin B, Valinsky L, Gao X, Becker JO, Borneman J.

Phytopathology. 2003 Aug;93(8):1006-13. doi: 10.1094/PHYTO.2003.93.8.1006.

48.

Induction of Beet-Cyst Nematode Suppressiveness by the Fungi Dactylella oviparasitica and Fusarium oxysporum in Field Microplots.

Olatinwo R, Borneman J, Becker JO.

Phytopathology. 2006 Aug;96(8):855-9. doi: 10.1094/PHYTO-96-0855.

49.

Effect of Repetitive Applications of the Biocontrol Bacterium Pseudomonas putida 06909-rif/nal on Citrus Soil Microbial Communities.

Steddom K, Menge JA, Crowley D, Borneman J.

Phytopathology. 2002 Aug;92(8):857-62. doi: 10.1094/PHYTO.2002.92.8.857.

50.

Acceleration of spinal fusion using syngeneic and allogeneic adult adipose derived stem cells in a rat model.

Lopez MJ, McIntosh KR, Spencer ND, Borneman JN, Horswell R, Anderson P, Yu G, Gaschen L, Gimble JM.

J Orthop Res. 2009 Mar;27(3):366-73. doi: 10.1002/jor.20735.

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