Kylie Kavanagh, Ashley T Wylie, Kelly L Tucker, Timothy J Hamp, Raad Z Gharaibeh, Anthony A Fodor, and John M Cullen. Dietary fructose induces endotoxemia and hepatic injury in calorically controlled primates. The American Journal of Clinical Nutrition Aug 2013; 98: 2 349-357

Michael T Shanahan, Ian M Carroll, Emily Grossniklaus, Andrew White, Richard J von Furstenberg, Roshonda Barner, Anthony A Fodor, Susan J Henning, R Balfour Sartor, Ajay S Gulati. Mouse Paneth cell antimicrobial function is independent of Nod2. Gut 19 March 2013

Jonathan McCafferty, Marcus Mühlbauer, Raad Z Gharaibeh, Janelle C Arthur, Ernesto Perez-Chanona, Wei Sha, Christian Jobin and Anthony A Fodor. Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model. The ISME Journal July 2013


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.

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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 fibrosisThorax 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.

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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.

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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

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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

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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

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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

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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

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.

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