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Paul M. Ruegger, Ph.D. - Publications

Affiliations: 
2011 Genetics, Genomics and Bioinformatics University of California, Riverside, Riverside, CA, United States 
Area:
Microbiology Biology, Bioinformatics Biology, Genetics
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44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Martinez-Lomeli J, Deol P, Deans JR, Jiang T, Ruegger P, Borneman J, Sladek FM. Impact of various high fat diets on gene expression and the microbiome across the mouse intestines. Scientific Reports. 13: 22758. PMID 38151490 DOI: 10.1038/s41598-023-49555-7  0.602
2023 Martinez-Lomeli J, Deol P, Deans JR, Jiang T, Ruegger P, Borneman J, Sladek FM. Impact of Various High Fat Diets on Gene Expression and the Microbiome Across the Mouse Intestines. Research Square. PMID 37886485 DOI: 10.21203/rs.3.rs-3401763/v1  0.602
2023 Smith Becker J, Ruegger PM, Borneman J, Becker JO. Indigenous populations of a biological control agent in agricultural field soils predicted suppression of a plant pathogen. Phytopathology. PMID 37698487 DOI: 10.1094/PHYTO-07-23-0221-R  0.51
2023 Deol P, Ruegger P, Logan GD, Shawki A, Li J, Mitchell JD, Yu J, Piamthai V, Radi SH, Hasnain S, Borkowski K, Newman JW, McCole DF, Nair MG, Hsiao A, et al. Diet high in linoleic acid dysregulates the intestinal endocannabinoid system and increases susceptibility to colitis in Mice. Gut Microbes. 15: 2229945. PMID 37400966 DOI: 10.1080/19490976.2023.2229945  0.607
2022 Jacobs JP, Goudarzi M, Lagishetty V, Li D, Mak T, Tong M, Ruegger P, Haritunians T, Landers C, Fleshner P, Vasiliauskas E, Ippoliti A, Melmed G, Shih D, Targan S, et al. Crohn's disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome. Genome Medicine. 14: 91. PMID 35971134 DOI: 10.1186/s13073-022-01099-7  0.609
2022 Hale AR, Ruegger PM, Rolshausen P, Borneman J, Yang JI. Fungi associated with the potato taste defect in coffee beans from Rwanda. Botanical Studies. 63: 17. PMID 35604510 DOI: 10.1186/s40529-022-00346-9  0.692
2022 Maier I, Ruegger PM, Deutschmann J, Helbich TH, Pietschmann P, Schiestl RH, Borneman J. Particle Radiation Side-Effects: Intestinal Microbiota Composition Shapes Interferon-γ-Induced Osteo-Immunogenicity. Radiation Research. 197: 184-192. PMID 35130347 DOI: 10.1667/RADE-21-00065.1  0.57
2021 McNamara MP, Singleton JM, Cadney MD, Ruegger PM, Borneman J, Garland T. Early-life effects of juvenile Western diet and exercise on adult gut microbiome composition in mice. The Journal of Experimental Biology. PMID 33431595 DOI: 10.1242/jeb.239699  0.567
2020 Ramakrishna C, Mendonca S, Ruegger PM, Kim JH, Borneman J, Cantin EM. Herpes simplex virus infection, Acyclovir and IVIG treatment all independently cause gut dysbiosis. Plos One. 15: e0237189. PMID 32760124 DOI: 10.1371/Journal.Pone.0237189  0.622
2020 Shawki A, Ramirez R, Spalinger MR, Ruegger PM, Sayoc-Becerra A, Santos AN, Chatterjee P, Canale V, Mitchell JD, Macbeth JC, Gries CM, Tremblay ML, Hsiao A, Borneman J, McCole DF. The autoimmune susceptibility gene, , restricts expansion of a novel mouse adherent-invasive . Gut Microbes. 1-20. PMID 32586195 DOI: 10.1080/19490976.2020.1775538  0.686
2020 Blacutt A, Ginnan N, Dang T, Bodaghi S, Vidalakis G, Ruegger P, Peacock B, Viravathana P, Campos Vieira F, Drozd C, Jablonska B, Borneman J, McCollum G, Cordoza J, Meloch J, et al. An pipeline to screen and select citrus-associated microbiota with potential anti- Liberibacter asiaticus properties. Applied and Environmental Microbiology. PMID 32086307 DOI: 10.1128/Aem.02883-19  0.607
2020 Shawki A, Spalinger MR, Santos AN, Canale V, Sayoc-Becerra A, Mitchell J, Macbeth J, Ruegger PM, Borneman J, Hsiao A, McCole DF. A Novel IBD‐Associated Mouse Pathobiont E. coli Causes Disease and Prevents Recovery from Colitis The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.06961  0.607
2020 McNamara MP, Cadney MD, Singleton JM, Ruegger PM, Borneman J, Garland T. Long‐lasting Effects of Early‐life Western Diet and Exercise on Adult Gut Microbiome Composition in Mice The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.02523  0.577
2019 Ramakrishna C, Corleto J, Ruegger PM, Logan GD, Peacock BB, Mendonca S, Yamaki S, Adamson T, Ermel R, McKemy D, Borneman J, Cantin EM. Dominant Role of the Gut Microbiota in Chemotherapy Induced Neuropathic Pain. Scientific Reports. 9: 20324. PMID 31889131 DOI: 10.1038/S41598-019-56832-X  0.594
2019 Kim JH, Yang B, Tedesco A, Lebig EGD, Ruegger PM, Xu K, Borneman J, Martins-Green M. High Levels of Oxidative Stress and Skin Microbiome are Critical for Initiation and Development of Chronic Wounds in Diabetic Mice. Scientific Reports. 9: 19318. PMID 31848388 DOI: 10.1038/S41598-019-55644-3  0.555
2019 Maier I, Liu J, Ruegger PM, Deutschmann J, Patsch JM, Helbich TH, Borneman J, Schiestl RH. Intestinal bacterial indicator phylotypes associate with impaired DNA double-stranded break sensors but augmented skeletal bone micro-structure. Carcinogenesis. PMID 31840161 DOI: 10.1093/Carcin/Bgz204  0.618
2019 Shawki A, Alvarez R, Krishnan M, Ruegger P, Li J, Spalinger MR, Nair MG, Borneman J, McCole DF. 694 – The IBD Candidate Gene, Ptpn2, Regulates Segmented Filamentous Bacteria Mediated Th17 Response and Intestinal Barrier Protection Against Adherent-Invasive E. Coli Gastroenterology. 156: S-151-S-152. DOI: 10.1016/S0016-5085(19)37168-9  0.609
2018 Cheng Z, Zhao L, Dhall D, Ruegger PM, Borneman J, Frykman PK. Bacterial Microbiome Dynamics in Post Pull-Through Hirschsprung-Associated Enterocolitis (HAEC): An Experimental Study Employing the Endothelin Receptor B-Null Mouse Model. Frontiers in Surgery. 5: 30. PMID 29682507 DOI: 10.3389/Fsurg.2018.00030  0.635
2018 Barr T, Sureshchandra S, Ruegger P, Zhang J, Ma W, Borneman J, Grant K, Messaoudi I. Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates. Gut Microbes. 1-44. PMID 29517944 DOI: 10.1080/19490976.2018.1441663  0.62
2018 Ginnan NA, Dang T, Bodaghi S, Ruegger PM, Peacock BB, McCollum G, England G, Vidalakis G, Roper C, Rolshausen P, Borneman J. Bacterial and Fungal Next Generation Sequencing Datasets and Metadata from Citrus Infected with ‘Candidatus Liberibacter asiaticus’ Phytobiomes Journal. 2: 64-70. DOI: 10.1094/PBIOMES-08-17-0032-A  0.581
2018 Shawki A, Alvarez R, Krishnan M, Ruegger P, Borneman J, McCole DF. Mo1950 - Increased Abundance of a Novel Adherent-Invasive E. Coli in PTPN2 -Deficient Mice Causes Altered Barrier Function and Tight Junction Remodeling Gastroenterology. 154: S-862. DOI: 10.1016/S0016-5085(18)32914-7  0.588
2017 Deyett E, Roper MC, Ruegger P, Yang J, Borneman J, Rolshausen PE. Microbial Landscape of the Grapevine Endosphere in the Context of Pierce’s Disease Phytobiomes Journal. 1: 138-149. DOI: 10.1094/PBIOMES-08-17-0033-R  0.71
2017 Jacobs J, Tong M, Ruegger P, Li D, Haritunians T, Fleshner P, Vasiliauskas E, Ippoliti A, Melmed G, Shih DQ, Targan SR, Borneman J, McGovern D, Braun J. Crohn's Disease, Obesity, and High Crohn's Disease Genetic Risk are Associated with Parallel Changes in the Microbiome of the Cecal and Sigmoid Mucosal-Luminal Interface Gastroenterology. 152: S111. DOI: 10.1016/S0016-5085(17)30712-6  0.607
2017 Barr T, Sureshchandra S, Ruegger P, Borneman J, Grant K, Messaoudi I. Chronic ethanol consumption disrupts intestinal microbiota and mucosal gene expression Alcohol. 59: 70. DOI: 10.1016/J.Alcohol.2016.10.015  0.596
2016 Jacobs JP, Goudarzi M, Singh N, Tong M, McHardy IH, Ruegger P, Asadourian M, Moon BH, Ayson A, Borneman J, McGovern DP, Fornace AJ, Braun J, Dubinsky M. A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients. Cellular and Molecular Gastroenterology and Hepatology. 2: 750-766. PMID 28174747 DOI: 10.1016/J.Jcmgh.2016.06.004  0.664
2016 Jacobs JP, Lin L, Goudarzi M, Ruegger P, McGovern DP, Fornace AJ, Borneman J, Xia L, Braun J. Microbial, metabolomic, and immunologic dynamics in a relapsing genetic mouse model of colitis induced by T-synthase deficiency. Gut Microbes. 0. PMID 27874308 DOI: 10.1080/19490976.2016.1257469  0.656
2016 Cheema AK, Maier I, Dowdy T, Wang Y, Singh R, Ruegger PM, Borneman J, Fornace AJ, Schiestl RH. Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis. Plos One. 11: e0151190. PMID 27073845 DOI: 10.1371/Journal.Pone.0151190  0.649
2016 Jacobs J, Lin L, Lagishetty V, Ruegger P, Borneman J, Braun J. Su1880 RORγt-Dependent CD4+ T Cells Garden the Mucosa-Associated Microbiome of the Small Intestine and Colon Gastroenterology. 150: S578. DOI: 10.1016/S0016-5085(16)31979-5  0.6
2015 Jacobs JP, Tong M, McHardy I, Goudarzi M, Ruegger P, McGovern D, Borneman J, Fornace AJ, Dubinsky M, Braun J. 1010 Disease-Associated Enterotypes and Metabotypes in Families With Pediatric Inflammatory Bowel Disease Gastroenterology. 148: S-190. DOI: 10.1016/S0016-5085(15)30633-8  0.554
2014 Ruegger PM, Clark RT, Weger JR, Braun J, Borneman J. Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer. Journal of Microbiological Methods. 105: 82-7. PMID 25034229 DOI: 10.1016/J.Mimet.2014.07.001  0.588
2014 Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, Li X, Graeber TG, Schwager E, Huttenhower C, Fornace AJ, Sonnenburg JL, McGovern DP, Borneman J, Braun J. Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. The Isme Journal. 8: 2193-206. PMID 24781901 DOI: 10.1038/Ismej.2014.64  0.64
2014 Jacobs JP, Tong M, Goudarzi M, McHardy I, Lin L, Ruegger P, Liu Z, Xia L, Fornace AJ, Borneman J, Braun J. Tu1750 Microbial, Metabolomic, and Immunologic Dynamics During Disease Onset, Remission, and Relapse in a Mouse Model of Colitis Involving a Genetically Impaired Mucus Barrier Gastroenterology. 146: S-833. DOI: 10.1016/S0016-5085(14)63026-2  0.624
2013 McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P, Braun J. HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota. Microbiome. 1: 26. PMID 24451087 DOI: 10.1186/2049-2618-1-26  0.565
2013 McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR, Graeber TG, Sonnenburg JL, Horvath S, Huttenhower C, McGovern DP, Fornace AJ, Borneman J, Braun J. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome. 1: 17. PMID 24450808 DOI: 10.1186/2049-2618-1-17  0.656
2013 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, et al. Intestinal bacteria modify lymphoma incidence and latency by affecting systemic inflammatory state, oxidative stress, and leukocyte genotoxicity. Cancer Research. 73: 4222-32. PMID 23860718 DOI: 10.1158/0008-5472.Can-13-0022  0.749
2013 McHardy I, Goudarzi M, Tong M, Ruegger P, Horvath S, Sonnenburg J, Graeber T, Huttenhower C, Borneman J, McGovern DP, Fornace A, Braun J. Tu1983 Comprehensive Inter-Omic Analysis Reveals Exquisite Metabolite-Driven Microbial Relationships Gastroenterology. 144: S-896-S-897. DOI: 10.1016/S0016-5085(13)63339-9  0.596
2013 Tong M, McHardy I, Ruegger P, Schwager E, Fleshner P, Li X, McGovern DP, Huttenhower C, Borneman J, Braun J. Sa1800 The Crohn's Disease Risk Locus FUT2 Selects for Microbial Functional Specialization in Normal Individuals That Predisposes to IBD Susceptibility Gastroenterology. 144: S-309. DOI: 10.1016/S0016-5085(13)61111-7  0.619
2012 Yang JI, Ruegger PM, McKenry MV, Becker JO, Borneman J. Correlations between root-associated microorganisms and peach replant disease symptoms in a California soil. Plos One. 7: e46420. PMID 23071565 DOI: 10.1371/Journal.Pone.0046420  0.699
2012 Ruegger PM, Bent E, Li W, Jeske DR, Cui X, Braun J, Jiang T, Borneman J. Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology. Journal of Microbiological Methods. 90: 235-40. PMID 22640891 DOI: 10.1016/J.Mimet.2012.05.013  0.585
2012 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, et al. Host-microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal-luminal interface. Inflammatory Bowel Diseases. 18: 409-17. PMID 21698720 DOI: 10.1002/Ibd.21793  0.702
2011 Ruegger PM, Della Vedova G, Jiang T, Borneman J. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences. Bmc Bioinformatics. 12: 394. PMID 21985453 DOI: 10.1186/1471-2105-12-394  0.569
2010 Yu H, Jeske DR, Ruegger P, Borneman J. Neutral Zone Classifiers Using a Decision-Theoretic Approach With Application to DNA Array Analyses. Journal of Agricultural, Biological, and Environmental Statistics. 15: 474-490. PMID 21769245 DOI: 10.1007/S13253-010-0034-6  0.547
2010 Li W, Ruegger PM, Borneman J, Jiang T. Polony identification using the EM algorithm based on a Gaussian mixture model 10th Ieee International Conference On Bioinformatics and Bioengineering 2010, Bibe 2010. 220-225. DOI: 10.1109/BIBE.2010.43  0.494
2008 Fu Q, Ruegger P, Bent E, Chrobak M, Borneman J. PRISE (PRImer SElector): software for designing sequence-selective PCR primers. Journal of Microbiological Methods. 72: 263-7. PMID 18221808 DOI: 10.1016/J.Mimet.2007.12.004  0.56
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