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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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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