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Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics.

Huebner KL, Martin JN, Weissend CJ, Holzer KL, Parker JK, Lakin SM, Doster E, Weinroth MD, Abdo Z, Woerner DR, Metcalf JL, Geornaras I, Bryant TC, Morley PS, Belk KE.

Sci Rep. 2019 Feb 22;9(1):2559. doi: 10.1038/s41598-019-39181-7.


Applications of the FIV Model to Study HIV Pathogenesis.

Miller C, Abdo Z, Ericsson A, Elder J, VandeWoude S.

Viruses. 2018 Apr 20;10(4). pii: E206. doi: 10.3390/v10040206. Review.


Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis.

Noyes N, Cho KC, Ravel J, Forney LJ, Abdo Z.

PLoS One. 2018 Jan 24;13(1):e0191625. doi: 10.1371/journal.pone.0191625. eCollection 2018.


Associations between Escherichia coli O157 shedding and the faecal microbiota of dairy cows.

Stenkamp-Strahm C, McConnel C, Magzamen S, Abdo Z, Reynolds S.

J Appl Microbiol. 2018 Mar;124(3):881-898. doi: 10.1111/jam.13679. Epub 2018 Feb 8.


Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.

Noyes NR, Weinroth ME, Parker JK, Dean CJ, Lakin SM, Raymond RA, Rovira P, Doster E, Abdo Z, Martin JN, Jones KL, Ruiz J, Boucher CA, Belk KE, Morley PS.

Microbiome. 2017 Oct 17;5(1):142. doi: 10.1186/s40168-017-0361-8.


Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease.

Owen JR, Noyes N, Young AE, Prince DJ, Blanchard PC, Lehenbauer TW, Aly SS, Davis JH, O'Rourke SM, Abdo Z, Belk K, Miller MR, Morley P, Van Eenennaam AL.

G3 (Bethesda). 2017 Sep 7;7(9):3059-3071. doi: 10.1534/g3.117.1137.


Determining the distribution of fitness effects using a generalized Beta-Burr distribution.

Joyce P, Abdo Z.

Theor Popul Biol. 2018 Jul;122:88-96. doi: 10.1016/j.tpb.2017.07.001. Epub 2017 Jul 12.


Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection.

Susta L, He Y, Hutcheson JM, Lu Y, West FD, Stice SL, Yu P, Abdo Z, Afonso CL.

Virol J. 2016 Dec 5;13(1):205.


MEGARes: an antimicrobial resistance database for high throughput sequencing.

Lakin SM, Dean C, Noyes NR, Dettenwanger A, Ross AS, Doster E, Rovira P, Abdo Z, Jones KL, Ruiz J, Belk KE, Morley PS, Boucher C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D574-D580. doi: 10.1093/nar/gkw1009. Epub 2016 Nov 28.


Subtyping of Salmonella enterica Subspecies I Using Single-Nucleotide Polymorphisms in Adenylate Cyclase.

Guard J, Abdo Z, Byers SO, Kriebel P, Rothrock MJ Jr.

Foodborne Pathog Dis. 2016 Jul;13(7):350-62. doi: 10.1089/fpd.2015.2088. Epub 2016 Apr 1.


Influence of commercial laying hen housing systems on the incidence and identification of Salmonella and Campylobacter.

Jones DR, Guard J, Gast RK, Buhr RJ, Fedorka-Cray PJ, Abdo Z, Plumblee JR, Bourassa DV, Cox NA, Rigsby LL, Robison CI, Regmi P, Karcher DM.

Poult Sci. 2016 May;95(5):1116-24. doi: 10.3382/ps/pew036. Epub 2016 Mar 14.


Draft Genome Sequence of Cercospora arachidicola, Causal Agent of Early Leaf Spot in Peanuts.

Orner VA, Cantonwine EG, Wang XM, Abouelleil A, Bochicchio J, Nusbaum C, Culbreath AK, Abdo Z, Arias RS.

Genome Announc. 2015 Nov 5;3(6). pii: e01281-15. doi: 10.1128/genomeA.01281-15.


Maize death acids, 9-lipoxygenase-derived cyclopente(a)nones, display activity as cytotoxic phytoalexins and transcriptional mediators.

Christensen SA, Huffaker A, Kaplan F, Sims J, Ziemann S, Doehlemann G, Ji L, Schmitz RJ, Kolomiets MV, Alborn HT, Mori N, Jander G, Ni X, Sartor RC, Byers S, Abdo Z, Schmelz EA.

Proc Natl Acad Sci U S A. 2015 Sep 8;112(36):11407-12. doi: 10.1073/pnas.1511131112. Epub 2015 Aug 24.


Mi-1-Mediated Nematode Resistance in Tomatoes is Broken by Short-Term Heat Stress but Recovers Over Time.

Marques de Carvalho L, Benda ND, Vaughan MM, Cabrera AR, Hung K, Cox T, Abdo Z, Allen LH, Teal PE.

J Nematol. 2015 Jun;47(2):133-40.


The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation.

Carmody LA, Zhao J, Kalikin LM, LeBar W, Simon RH, Venkataraman A, Schmidt TM, Abdo Z, Schloss PD, LiPuma JJ.

Microbiome. 2015 Apr 1;3:12. doi: 10.1186/s40168-015-0074-9. eCollection 2015.


Comparison of Resistance to Asiatic Citrus Canker Among Different Genotypes of Citrus in a Long-Term Canker-Resistance Field Screening Experiment in Brazil.

de Carvalho SA, de Carvalho Nunes WM, Belasque J Jr, Machado MA, Croce-Filho J, Bock CH, Abdo Z.

Plant Dis. 2015 Feb;99(2):207-218. doi: 10.1094/PDIS-04-14-0384-RE.


Impact of commercial housing systems and nutrient and energy intake on laying hen performance and egg quality parameters.

Karcher DM, Jones DR, Abdo Z, Zhao Y, Shepherd TA, Xin H.

Poult Sci. 2015 Mar;94(3):485-501. doi: 10.3382/ps/peu078. Epub 2015 Jan 28.


Evaluation of disinfectants to prevent mechanical transmission of viruses and a viroid in greenhouse tomato production.

Li R, Baysal-Gurel F, Abdo Z, Miller SA, Ling KS.

Virol J. 2015 Jan 27;12:5. doi: 10.1186/s12985-014-0237-5.


Microbiological impact of three commercial laying hen housing systems.

Jones DR, Cox NA, Guard J, Fedorka-Cray PJ, Buhr RJ, Gast RK, Abdo Z, Rigsby LL, Plumblee JR, Karcher DM, Robison CI, Blatchford RA, Makagon MM.

Poult Sci. 2015 Mar;94(3):544-51. doi: 10.3382/ps/peu010. Epub 2014 Dec 5.


Influence of brown stink bug feeding, planting date and sampling time on common smut infection of maize.

Ni X, Toews MD, Buntin GD, Carpenter JE, Huffaker A, Schmelz EA, Cottrell TE, Abdo Z.

Insect Sci. 2014 Oct;21(5):564-71. doi: 10.1111/1744-7917.12149. Epub 2014 Aug 20.


Effect of a commercial housing system on egg quality during extended storage.

Jones DR, Karcher DM, Abdo Z.

Poult Sci. 2014 May;93(5):1282-8. doi: 10.3382/ps.2013-03631.


Microbiota of the seminal fluid from healthy and infertile men.

Hou D, Zhou X, Zhong X, Settles ML, Herring J, Wang L, Abdo Z, Forney LJ, Xu C.

Fertil Steril. 2013 Nov;100(5):1261-9. doi: 10.1016/j.fertnstert.2013.07.1991. Epub 2013 Aug 29.


Effects of tampons and menses on the composition and diversity of vaginal microbial communities over time.

Hickey RJ, Abdo Z, Zhou X, Nemeth K, Hansmann M, Osborn TW 3rd, Wang F, Forney LJ.

BJOG. 2013 May;120(6):695-704; discussion 704-6. doi: 10.1111/1471-0528.12151. Epub 2013 Feb 11.


Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women.

Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, Forney LJ, Carlton JM, Abdo Z, Ravel J.

Sex Transm Dis. 2012 Oct;39(10):807-12.


The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation.

Hughes JM, Lohman BK, Deckert GE, Nichols EP, Settles M, Abdo Z, Top EM.

MBio. 2012 Jul 3;3(4):e00077-12. doi: 10.1128/mBio.00077-12. Print 2012.


mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

Copeland WK, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z.

Bioinformatics. 2012 Aug 15;28(16):2198-9. doi: 10.1093/bioinformatics/bts338. Epub 2012 Jun 12.


Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans.

Sanapareddy N, Legge RM, Jovov B, McCoy A, Burcal L, Araujo-Perez F, Randall TA, Galanko J, Benson A, Sandler RS, Rawls JF, Abdo Z, Fodor AA, Keku TO.

ISME J. 2012 Oct;6(10):1858-68. doi: 10.1038/ismej.2012.43. Epub 2012 May 24.


Temporal dynamics of the human vaginal microbiota.

Gajer P, Brotman RM, Bai G, Sakamoto J, Schütte UM, Zhong X, Koenig SS, Fu L, Ma ZS, Zhou X, Abdo Z, Forney LJ, Ravel J.

Sci Transl Med. 2012 May 2;4(132):132ra52. doi: 10.1126/scitranslmed.3003605.


Evaluation of methods for the extraction and purification of DNA from the human microbiome.

Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ.

PLoS One. 2012;7(3):e33865. doi: 10.1371/journal.pone.0033865. Epub 2012 Mar 23.


Characterization of the diversity and temporal stability of bacterial communities in human milk.

Hunt KM, Foster JA, Forney LJ, Schütte UM, Beck DL, Abdo Z, Fox LK, Williams JE, McGuire MK, McGuire MA.

PLoS One. 2011;6(6):e21313. doi: 10.1371/journal.pone.0021313. Epub 2011 Jun 17.


Contrasting codon usage patterns and purifying selection at the mating locus in putatively asexual alternaria fungal species.

Stewart JE, Kawabe M, Abdo Z, Arie T, Peever TL.

PLoS One. 2011;6(5):e20083. doi: 10.1371/journal.pone.0020083. Epub 2011 May 19.


Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth.

Zhou X, Brotman RM, Gajer P, Abdo Z, Schüette U, Ma S, Ravel J, Forney LJ.

Infect Dis Obstet Gynecol. 2010;2010:737425. doi: 10.1155/2010/737425. Epub 2010 Dec 9. Review.


Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas.

Shen XJ, Rawls JF, Randall T, Burcal L, Mpande CN, Jenkins N, Jovov B, Abdo Z, Sandler RS, Keku TO.

Gut Microbes. 2010 May-Jun;1(3):138-47. doi: 10.4161/gmic.1.3.12360. Epub 2010 May 13.


Vaginal microbiome of reproductive-age women.

Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4680-7. doi: 10.1073/pnas.1002611107. Epub 2010 Jun 3.


Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein.

Sota M, Yano H, Hughes JM, Daughdrill GW, Abdo Z, Forney LJ, Top EM.

ISME J. 2010 Dec;4(12):1568-80. doi: 10.1038/ismej.2010.72. Epub 2010 Jun 3.


Effects of parameter estimation on maximum-likelihood bootstrap analysis.

Ripplinger J, Abdo Z, Sullivan J.

Mol Phylogenet Evol. 2010 Aug;56(2):642-8. doi: 10.1016/j.ympev.2010.04.035. Epub 2010 Apr 29.


Bacterial diversity in a glacier foreland of the high Arctic.

Schütte UM, Abdo Z, Foster J, Ravel J, Bunge J, Solheim B, Forney LJ.

Mol Ecol. 2010 Mar;19 Suppl 1:54-66. doi: 10.1111/j.1365-294X.2009.04479.x.


The genetics of adaptation for eight microvirid bacteriophages.

Rokyta DR, Abdo Z, Wichman HA.

J Mol Evol. 2009 Sep;69(3):229-39. doi: 10.1007/s00239-009-9267-9. Epub 2009 Aug 20.


Bacterial succession in a glacier foreland of the High Arctic.

Schütte UM, Abdo Z, Bent SJ, Williams CJ, Schneider GM, Solheim B, Forney LJ.

ISME J. 2009 Nov;3(11):1258-68. doi: 10.1038/ismej.2009.71. Epub 2009 Jul 9.


Estimation of selection intensity under overdominance by Bayesian methods.

Buzbas EO, Joyce P, Abdo Z.

Stat Appl Genet Mol Biol. 2009;8:Article32. doi: 10.2202/1544-6115.1466. Epub 2009 Jun 30.


Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities.

Schütte UM, Abdo Z, Bent SJ, Shyu C, Williams CJ, Pierson JD, Forney LJ.

Appl Microbiol Biotechnol. 2008 Sep;80(3):365-80. doi: 10.1007/s00253-008-1565-4. Epub 2008 Jul 22. Review.


Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertainty.

Heuer H, Abdo Z, Smalla K.

FEMS Microbiol Ecol. 2008 Sep;65(3):361-71. doi: 10.1111/j.1574-6941.2008.00539.x. Epub 2008 Jul 8. Review.


Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women.

Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P, Foster JA, Forney LJ.

ISME J. 2007 Jun;1(2):121-33. Epub 2007 May 10.


Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes.

Abdo Z, Schüette UM, Bent SJ, Williams CJ, Forney LJ, Joyce P.

Environ Microbiol. 2006 May;8(5):929-38.


Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation.

Sullivan J, Abdo Z, Joyce P, Swofford DL.

Mol Biol Evol. 2005 Jun;22(6):1386-92. Epub 2005 Mar 9.


Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution.

Joyce P, Abdo Z, Ponciano JM, De Gelder L, Forney LJ, Top EM.

J Math Biol. 2005 Jun;50(6):645-62. Epub 2004 Dec 20.


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