For a complete list, including recent publications, please visit Google Scholar.

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 syndrome82019
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, 201712018
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 System12018
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 Monkeys12018
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 models42018
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 model22018
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 mice12018
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 diverticulosis32018
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 samples32018
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 mice22018
AR Rogala, AA Schoenborn, BE Fee, VA Cantillana, MJ Joyce, …
Disease Models & Mechanisms 11 (2), dmm031070
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 genes12017
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 consortium572017
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 cases112017
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 carcinogenesis52017
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 monkeys132017
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 perspective192017
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 measures12017
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 implications42017
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 obesity282016
EE Noble, TM Hsu, RB Jones, AA Fodor, MI Goran, SE Kanoski
The Journal of nutrition 147 (1), 20-28
K Kavanagh, AT Davis, R Jones, R Gharaibeh, A Fodor, C Shively
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
Gut microbiota and a selectively bred taste phenotype: a novel model of microbiome-behavior relationships112016
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 syndrome34*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 challenges612016
MCB Tsilimigras, AA Fodor
Annals of epidemiology 26 (5), 330-335
328 Human Colorectal Cancer-Associated Biofilms Promote Tumorigenesis in Susceptible Mice22016
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 macrophages122015
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 Study52015
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 Microbiota12015
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 evidence92015
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 period232015
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 pancreatitis52014
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 cancer1322014
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 Nod2792014
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 ecosystem72014
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 tract12013
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 model942013
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 cancer422013
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 primates662013
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 disease12013
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)32013
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 research142013
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:


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 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.

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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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