Publications
For a complete list, including recent publications, please visit Google Scholar.
| TITLE | CITED BY | YEAR |
|---|---|---|
| Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic | 2019 | |
| S Tomkovich, CM Dejea, K Winglee, JL Drewes, L Chung, F Housseau, … | ||
| The Journal of clinical investigation 129 (4) | ||
| Whole Genome Sequencing detects Inter-Facility Transmission of Carbapenem-resistant Klebsiella pneumoniae | 2019 | |
| MD Spencer, K Winglee, C Passaretti, AM Earl, AL Manson, HP Mulder, … | ||
| Journal of Infection 78 (3), 187-199 | ||
| Rifaximin is associated with modest, transient decreases in multiple taxa in the gut microbiota of patients with diarrhoea-predominant irritable bowel syndrome | 8 | 2019 |
| AA Fodor, M Pimentel, WD Chey, A Lembo, PL Golden, RJ Israel, … | ||
| Gut microbes 10 (1), 22-33 | ||
| The Role of the Gut Microbiota in Sustained Weight Loss Following Roux-en-Y Gastric Bypass Surgery | 2019 | |
| F Fouladi, AE Brooks, AA Fodor, IM Carroll, EC Bulik-Sullivan, … | ||
| Obesity surgery, 1-9 | ||
| Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017 | 1 | 2018 |
| R Sinha, H Ahsan, M Blaser, JG Caporaso, JR Carmical, AT Chan, … | ||
| Microbiome 6 (1), 210 | ||
| Initial microbial community of the neonatal stomach immediately after birth | 2018 | |
| S Bajorek, L Parker, N Li, K Winglee, M Weaver, J Johnson, M Sioda, … | ||
| Gut microbes, 1-9 | ||
| Microbial Community Composition and Antibiotic Resistance Genes within a North Carolina Urban Water System | 1 | 2018 |
| K Lambirth, M Tsilimigras, A Lulla, J Johnson, A Al-Shaer, O Wynblatt, … | ||
| Water 10 (11), 1539 | ||
| Greater Microbial Translocation and Vulnerability to Metabolic Disease in Healthy Aged Female Monkeys | 1 | 2018 |
| QN Wilson, M Wells, AT Davis, C Sherrill, MCB Tsilimigras, RB Jones, … | ||
| Scientific reports 8 (1), 11373 | ||
| Environmental Factors Modify the Severity of Acute DSS Colitis in Caspase-11-Deficient Mice | 2018 | |
| TJ Fan, SY Tchaptchet, D Arsene, Y Mishima, B Liu, RB Sartor, IM Carroll, … | ||
| Inflammatory bowel diseases 24 (11), 2394-2403 | ||
| Measurement and comparison of the gut microbial communities in fecal, rectal swab, and mucosal samples | 2018 | |
| RB Jones, X Zhu, E Moan, HJ Murff, Q Dai, MJ Shrubsole, AA Fodor, … | ||
| Cancer Research 78 (13 Supplement), 3266-3266 | ||
| Intestinal microbiota enhances pancreatic carcinogenesis in preclinical models | 4 | 2018 |
| RM Thomas, RZ Gharaibeh, J Gauthier, M Beveridge, JL Pope, … | ||
| Carcinogenesis 39 (8), 1068-1078 | ||
| Interactions between stress and sex in microbial responses within the microbiota-gut-brain axis in a mouse model | 2 | 2018 |
| MCB Tsilimigras, RZ Gharaibeh, M Sioda, L Gray, AA Fodor, M Lyte | ||
| Psychosomatic medicine 80 (4), 361-369 | ||
| Microbiota-derived metabolic factors reduce campylobacteriosis in mice | 1 | 2018 |
| X Sun, K Winglee, RZ Gharaibeh, J Gauthier, Z He, P Tripathi, D Avram, … | ||
| Gastroenterology 154 (6), 1751-1763. e2 | ||
| An aberrant microbiota is not strongly associated with incidental colonic diverticulosis | 3 | 2018 |
| RB Jones, AA Fodor, AF Peery, MCB Tsilimigras, K Winglee, A McCoy, … | ||
| Scientific reports 8 (1), 4951 | ||
| Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples | 3 | 2018 |
| RB Jones, X Zhu, E Moan, HJ Murff, RM Ness, DL Seidner, S Sun, C Yu, … | ||
| Scientific reports 8 (1), 4139 | ||
| Environmental factors regulate Paneth cell phenotype and host susceptibility to intestinal inflammation in Irgm1-deficient mice | 2 | 2018 |
| AR Rogala, AA Schoenborn, BE Fee, VA Cantillana, MJ Joyce, … | ||
| Disease Models & Mechanisms 11 (2), dmm031070 | ||
| PSYCHOSOMATIC | 2018 | |
| DA Hackman, DCH Kuan, SB Manuck, PJ Gianaros, JF Hunter, … | ||
| Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes | 1 | 2017 |
| K Winglee, AG Howard, W Sha, RZ Gharaibeh, J Liu, D Jin, AA Fodor, … | ||
| Microbiome 5 (1), 121 | ||
| Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium | 57 | 2017 |
| R Sinha, G Abu-Ali, E Vogtmann, AA Fodor, B Ren, A Amir, E Schwager, … | ||
| Nature biotechnology 35 (11), 1077 | ||
| Daily changes in composition and diversity of the intestinal microbiota in patients with anorexia nervosa: a series of three cases | 11 | 2017 |
| SC Kleiman, EM Glenny, EC Bulik‐Sullivan, EY Huh, MCB Tsilimigras, … | ||
| European Eating Disorders Review 25 (5), 423-427 | ||
| Ibs microbiota and uses thereof | 2017 | |
| P Golden, A Fodor, E Bortey, W Forbes | ||
| US Patent App. 15/342,739 | ||
| Locoregional effects of microbiota in a preclinical model of colon carcinogenesis | 5 | 2017 |
| S Tomkovich, Y Yang, K Winglee, J Gauthier, M Mühlbauer, X Sun, … | ||
| Cancer research 77 (10), 2620-2632 | ||
| Reduced intestinal motility, mucosal barrier function, and inflammation in aged monkeys | 13 | 2017 |
| EL Mitchell, AT Davis, K Brass, M Dendinger, R Barner, R Gharaibeh, … | ||
| The journal of nutrition, health & aging 21 (4), 354-361 | ||
| Carcinogenesis and therapeutics: the microbiota perspective | 19 | 2017 |
| MCB Tsilimigras, A Fodor, C Jobin | ||
| Nature microbiology 2 (3), 17008 | ||
| The gut-brain axis in healthy females: lack of significant association between microbial composition and diversity with psychiatric measures | 1 | 2017 |
| SC Kleiman, EC Bulik-Sullivan, EM Glenny, SC Zerwas, EY Huh, … | ||
| PloS one 12 (1), e0170208 | ||
| Characterizing and functionally defining the gut microbiota: methodology and implications | 4 | 2017 |
| M Ellermann, JS Carr, AA Fodor, JC Arthur, IM Carroll | ||
| The microbiota in gastrointestinal pathophysiology, 15-25 | ||
| Early-life sugar consumption affects the rat microbiome independently of obesity | 28 | 2016 |
| EE Noble, TM Hsu, RB Jones, AA Fodor, MI Goran, SE Kanoski | ||
| The Journal of nutrition 147 (1), 20-28 | ||
| INTESTINAL BARRIER FUNCTION AND PHYSICAL FUNCTION IN HEALTHY OLD SARCOPENIC MONKEYS | 2016 | |
| K Kavanagh, AT Davis, R Jones, R Gharaibeh, A Fodor, C Shively | ||
| GERONTOLOGIST 56, 350-350 | ||
| Stool microbiota characterization in patients with diarrhea-predominant irritable bowel syndrome (IBS-D) receiving repeat Rifaximin | 2016 | |
| M Pimentel, AA Fodor, PL Golden, E Bortey, WP Forbes | ||
| NEUROGASTROENTEROLOGY AND MOTILITY 28, 100-100 | ||
| Gut microbiota and a selectively bred taste phenotype: a novel model of microbiome-behavior relationships | 11 | 2016 |
| M Lyte, AA Fodor, CD Chapman, GG Martin, E Perez-Chanona, C Jobin, … | ||
| Psychosomatic medicine 78 (5), 610-619 | ||
| Effects of rifaximin on transit, permeability, fecal microbiome, and organic acid excretion in irritable bowel syndrome | 34* | 2016 |
| A Acosta, M Camilleri, A Shin, SL Nord, J O’neill, AV Gray, AJ Lueke, … | ||
| Clinical and translational gastroenterology 7 (5), e173 | ||
| Compositional data analysis of the microbiome: fundamentals, tools, and challenges | 61 | 2016 |
| MCB Tsilimigras, AA Fodor | ||
| Annals of epidemiology 26 (5), 330-335 | ||
| 328 Human Colorectal Cancer-Associated Biofilms Promote Tumorigenesis in Susceptible Mice | 2 | 2016 |
| SE Tomkovich, C Craig, K Winglee, JL Pope, J Gauthier, D Ferraguti, … | ||
| Gastroenterology 150 (4), S77 | ||
| Su1389 Intestinal Microbiota Influences Pancreatic Cancer Development, Which Associates With Alterations of the Tumor Microenvironment | 2016 | |
| RM Thomas, M Beveridge, J Gauthier, X Sun, JL Pope, K Winglee, … | ||
| Gastroenterology 150 (4), S513 | ||
| Gut microbial dysbiosis due to helicobacter drives an increase in marginal zone B cells in the absence of IL-10 signaling in macrophages | 12 | 2015 |
| A Ray, S Basu, RZ Gharaibeh, LC Cook, R Kumar, EJ Lefkowitz, … | ||
| The Journal of Immunology 195 (7), 3071-3085 | ||
| Mo1268 Characterization of Stool Microbiota in Subjects With IBS-D Receiving Repeat Treatments With Rifaximin in the TARGET 3 Study | 5 | 2015 |
| M Pimentel, AA Fodor, P Golden, E Bortey, WP Forbes | ||
| Gastroenterology 148 (4), S-655 | ||
| Mo1769 The Susceptibility to Intestinal Inflammation in IRGM1-Deficient Mice Is Influenced by the Gut Microbiota | 1 | 2015 |
| AR Rogala, AA Schoenborn, V Cantillana, R Gharaibeh, AA Fodor, … | ||
| Gastroenterology 148 (4), S-707 | ||
| Utilizing Markov Chains to Model Ion Channel Sequence Variation and Kinetics | 2015 | |
| A Fodor | ||
| Handbook of Ion Channels, 118-126 | ||
| Intrinsic association between diet and the gut microbiome: Current evidence | 9 | 2015 |
| K Winglee, AA Fodor | ||
| Nutrition and dietary supplements 7, 69 | ||
| Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period | 23 | 2015 |
| JR Stokell, RZ Gharaibeh, TJ Hamp, MJ Zapata, AA Fodor, TR Steck | ||
| Journal of clinical microbiology 53 (1), 237-247 | ||
| Comparison of culture and molecular techniques for microbial community characterization in infected necrotizing pancreatitis | 5 | 2014 |
| EM Hanna, TJ Hamp, IH McKillop, F Bahrani-Mougeot, JB Martinie, … | ||
| journal of surgical research 191 (2), 362-369 | ||
| Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer | 132 | 2014 |
| JC Arthur, RZ Gharaibeh, M Mühlbauer, E Perez-Chanona, JM Uronis, … | ||
| Nature communications 5, 4724 | ||
| Methods and kits for detecting adenomas, colorectal cancer, and uses thereof | 2014 | |
| T Keku, A Fodor, N Sanapareddy | ||
| US Patent App. 14/124,443 | ||
| Mouse Paneth cell antimicrobial function is independent of Nod2 | 79 | 2014 |
| MT Shanahan, IM Carroll, E Grossniklaus, A White, RJ Von Furstenberg, … | ||
| Gut 63 (6), 903-910 | ||
| Covariance in protein multiple sequence alignments using groups of columns | 2014 | |
| KE Kreth, AA Fodor | ||
| arXiv preprint arXiv:1401.1141 | ||
| Utilizing “omics” tools to study the complex gut ecosystem | 7 | 2014 |
| A Fodor | ||
| Microbial Endocrinology: The Microbiota-Gut-Brain Axis in Health and Disease … | ||
| Reply to KN Litwak and S Levin | 2014 | |
| K Kavanagh, AT Wylie, KL Tucker, TJ Hamp, RZ Gharaibeh, AA Fodor, … | ||
| The American journal of clinical nutrition 99 (1), 210-210 | ||
| P-240 Host Colonization by Commensal and Pathogenic Bacteria is Unaffected by Nod2 Expression | 2013 | |
| M Shanahan, I Carroll, Z Poliacoff, A Schoenborn, J Galanko, A Fodor, … | ||
| Inflammatory Bowel Diseases 19 (suppl_1), S121-S122 | ||
| P103 Culture and culture independant identification of bacterial communities in the cystic fibrosis respiratory tract | 1 | 2013 |
| GG Einarsson, J McCaughan, AA Fodor, MC Wolfgang, MM Tunney, … | ||
| Thorax 68 (Suppl 3), A121-A121 | ||
| Reply to JS White | 2013 | |
| K Kavanagh, AT Wylie, KL Tucker, TJ Hamp, RZ Gharaibeh, AA Fodor, … | ||
| The American journal of clinical nutrition 98 (5), 1370-1370 | ||
| Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model | 94 | 2013 |
| J McCafferty, M Mühlbauer, RZ Gharaibeh, JC Arthur, E Perez-Chanona, … | ||
| The ISME journal 7 (11), 2116 | ||
| VSL# 3 probiotic modifies mucosal microbial composition but does not reduce colitis-associated colorectal cancer | 42 | 2013 |
| JC Arthur, RZ Gharaibeh, JM Uronis, E Perez-Chanona, W Sha, … | ||
| Scientific reports 3, 2868 | ||
| Dietary fructose induces endotoxemia and hepatic injury in calorically controlled primates | 66 | 2013 |
| K Kavanagh, AT Wylie, KL Tucker, TJ Hamp, RZ Gharaibeh, AA Fodor, … | ||
| The American journal of clinical nutrition 98 (2), 349-357 | ||
| WS8. 5 airway bacterial community structure and correlation during health and disease | 1 | 2013 |
| GG Einarsson, M Tunney, ER Klem, AA Fodor, MC Wolfgang, JS Elborn | ||
| Journal of Cystic Fibrosis 12, S17 | ||
| Sa1801 Local Environmental Conditions Override NOD2-Mediated Regulatory Effects on Mouse Intestinal Microbial Composition | 2013 | |
| IM Carroll, MT Shanahan, R Barner, AA Fodor, RB Sartor, AS Gulati | ||
| Gastroenterology 144 (5), S-309 | ||
| 317 Iron Supplemented Diet Protects Against Chronic Immune Mediated Colitis in IL-10 Deficient Mice | 2013 | |
| M Ellermann, N Maharshak, R Gharaibeh, W Sha, E Perez-Chanona, … | ||
| Gastroenterology 144 (5), S-66 | ||
| 825 intestinal inflammation targets E. coli NC101 transcriptome response and promotes development of colorectal cancer (CRC) | 3 | 2013 |
| M Muehlbauer, R Gharaibeh, JC Arthur, A Fodor, C Jobin | ||
| Gastroenterology 144 (5), S-144-S-145 | ||
| Highlights of the 2012 Research Workshop: Using nutrigenomics and metabolomics in clinical nutrition research | 14 | 2013 |
| SH Zeisel, RA Waterland, JM Ordovás, DM Muoio, W Jia, A Fodor | ||
| Journal of Parenteral and Enteral Nutrition 37 (2), 190-200 | ||
| deep Sequencing Analysis Of Microbial Dna In Infected Necrotizing Pancreatitis | 2013 | |
| EM Hanna, IH Mckillop, FK Bahrani-mougeot, A Fodor, T Hamp, … | ||
| The Official Journal of The International Hepato Pancreato Biliary … | ||
| P689 Iron supplemented diet protects against chronic immune mediated colitis in mice | 2013 | |
| N Maharshak, M Ellermann, R Gharaibeh, W Sha, E Perez-Chanona, … | ||
| Journal of Crohn’s and Colitis 7 (Supplement_1), S287-S287 |
Manually currated:
2012
Anthony A. Fodor, Erich R. Klem, Deirdre F. Gilpin, J. Stuart Elborn, Richard C. Boucher, Michael M. Tunney, Matthew C. Wolfgang. The Adult Cystic Fibrosis Airway Microbiota Is Stable over Time and Infection Type, and Highly Resilient to Antibiotic Treatment of Exacerbations. PLoS ONE 7(9)
Structure, Function and Diversity of the Human Microbiome in an Adult Reference Population. A.A. Fodor as part of The Human Microbiome Consortium. Nature 486, 207–214
A framework for human microbiome research. A.A. Fodor as part of The Human Microbiome Consortium. Nature 486, 215-221
N. Sanapareddy, R. Legge, B. Jovov, A. McCoy, L. Burcal, F.A. Perez, T.A. Randall, J.Galanko, A. Benson, R.S. Sandler, J.F. Rawls, Z.Abdo, A.A. Fodor, T.O. Keku. Increased microbial richness is associated with colorectal adenomas. The ISME Journal 6, 1858-1868 (October 2012)
S. M. Huse, Y. Ye, Y. Zhou, A.A. Fodor. A Core Human Microbiome as Viewed Through 16S rRNA Sequences Clusters. PLoS ONE 7(6)
S.H. Zeisel, R.A. Waterland, J.M. Ordovás, D.M. Muoio , W. Jia and A.A. Fodor. Highlights of the 2012 Research Workshop: Using Nutrigenomics and Metabolomics in Clinical Nutrition Research. (In Press. JPEN).
D.R. Livesay, K.E. Kreth, A.A. Fodor. A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms. Methods Mol Biol. 2012;796:385-98.
2011
A.A. Fodor and N. Talley. Bugs, stool and the irritable bowel syndrome– too much is as bad as too little? Invited editorial Gastroenterology. 2011 Nov;141(5):1555-9. Epub 2011 Sep 22.
M M Tunney, E R Klem, A A Fodor, D F Gilpin, T F Moriarty, S J McGrath, M S Muhlebach, R C Boucher, C Cardwell, G Doering, J S Elborn, M C Wolfgang. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax 2011;66:579-584 doi:10.1136/thx.2010.137281
Uronis JM, Arthur JC, Keku T, Fodor AA, Carroll IM, Cruz ML, De Simone C, Appleyard CB, Jobin C. Gut microbial diversity is reduced by the probiotic VSL#3 and correlates with decreased TNBS-induced colitis. Inflamm Bowel Dis. Volume 17, Number 1, January 2011
Melanie D. Spencer, Timothy J. Hamp, Robert W. Reid, Leslie M. Fischer, Steven H. Zeisel, Anthony A. Fodor. Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology Volume 140, Issue 3, March 2011, Pages 976-986.
2010
Gharaibeh, RZ, Fodor AA, Gibas CJ. 2010. Accurate Estimates of Microarray Target Concentration from a Simple Sequence-Independent Langmuir Model. PLoS ONE. 5(12):e14464.
Lightfoot JT, Leamy L, Pomp D, Turner MJ, Fodor AA, Knab A, Bowen RS, Ferguson D, Moore-Harrison T, Hamilton A. Strain screen and haplotype association mapping of wheel running in inbred mouse strains. J Appl Physiol 109: 623-634, 2010.
2009
T.J. Hamp, W.J. Jones, A.A. Fodor. The effects of experimental choices and analysis noise on surveys of the rare biosphere. Applied and Environmental Microbiology. 75(10):3263-70. 2009. PMCID: PMC2681628
A.A. Fodor and R.W. Aldrich. Convergent Evolution of Alternative Splices at Domain Boundaries of the BK Channel. Annual Review of Physiology, Vol. 71: 19-36 March, 2009. PMID: 18694345
N. Sanapereddy, T. Hamp, L. Gonzalez and H. Hilger, A.A. Fodor and S.M. Clinton. Molecular Diversity of a North Carolina Wastewater Treatment Plant As Revealed by Pyrosequencing. Applied and Environmental Microbiology. 75(6):1688-96. 2009. PMCID: PMC2655459
2008
R.W. Reid and A.A. Fodor. Determining gene expression on a single pair of microarrays. BMC Bioinformatics. BMC Bioinformatics 9:489. 2008. PMCID: PMC2605475
R.Z. Gharaibeh, A.A. Fodor and C. J. Gibas. Background correction using dinucleotide affinities improves the performance of GCRMA. BMC Bioinformatics 9:452. 2008. PMCID: PMC2579310
2007
A.A. Fodor, T.L. Tickle and C. Richardson. Towards the Uniform Distribution of Null p-values on Affymetrix Microarrays. Genome Biology. May 1;8(5):R69. 2007. PMCID: PMC1929139
R.Z. Gharaibeh, A.A. Fodor and C.J. Gibas. Using Probe Secondary Structure Information to Enhance Affymetrix GeneChip Background Estimates. Computational Biology and Chemistry. 2007. PMCID: PMC2043163
S.J. Pyott, A.L. Meredith, A.A. Fodor, AE. Vázquez, E.N. Yamoah and R.W. Aldrich. Cochlear function in mice lacking the bk channel alpha, beta-1, OR beta-4 Subunits. J. Biol. Chem., Vol. 282, Issue 5, 3312-3324, 2007. PMID: 17135251
2006
Andrea L Meredith, Steven W Wiler, Brooke H Miller, Joseph S Takahashi, Anthony A Fodor, Norman F Ruby, Richard W Aldrich.
BK calcium-activated potassium channels regulate circadian behavioral rhythms and pacemaker output. Nature Neuroscience. 9, 1041-1049, 2006
Anthony A. Fodor, Richard W. Aldrich. Statistical Limits to the Identification of Ion Channel Domains by Sequence Similarity. JGP 127(6), 755-766, 2006
2004
Anthony A. Fodor, Richard W. Aldrich. On Evolutionary Conservation of Thermodynamic Coupling in Proteins. JBC 279(18):19046-19050, 2004
John P. Dekker, Anthony Fodor, Richard Aldrich and Gary Yellen.
A pertubation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics 20:1565-1572, 2004
Anthony A. Fodor and Richard W. Aldrich. Influence of Conservation on Calculations of Amino Acid Covariance in Multiple Sequence Alignments. Proteins 56(2): 211-221, 2004
Pre-publication
Fodor AA, Kreth K, Livesay D. A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms. To appear in: Methods in Molecular Biology: Allostery, Methods and Protocols.