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  1.  Genome Sequences of Salmonella enterica subsp. enterica Serovar  Lubbock Strains Isolated from Liver Abscesses of Feedlot Cattle.  Amachawadi RG, Thomas M, Nagaraja TG, Scaria J.Genome Announc. 2016 May  5;4(3). pii: e00319-16. doi: 10.1128/genomeA.00319-16. PMID:27151794
  2. Draft Genome Sequences of 37 Salmonella enterica Strains Isolated  from Poultry Sources in Nigeria. Useh NM, Ngbede EO, Akange N, Thomas M,  Foley A, Keena MC, Nelson E, Christopher-Hennings J, Tomita M, Suzuki  H, Scaria J.Genome Announc. 2016 May 5;4(3). pii: e00315-16. doi:  10.1128/genomeA.00315-16.PMID:27151793
  3. Draft Genome Sequences of Three Flavobacterium psychrophilum Strains  Isolated from Coldwater Disease Outbreaks at Three Production  Hatcheries. Neiger R, Thomas M, Das S, Barnes M, Fletcher B, Snekvik K,  Thompson J, Scaria J.Genome Announc. 2016 Mar 10;4(2). pii: e00035-16.  doi: 10.1128/genomeA.00035-16.PMID: 26966210
  4. Distribution and factors associated with Salmonella enterica  genotypes in a diverse population of humans and animals in Qatar using  multi-locus sequence typing (MLST).Chang YC, Scaria J, Ibraham M,  Doiphode S, Chang YF, Sultan A, Mohammed HO. J Infect Public Health.  2016 May-Jun;9(3):315-23. doi: 10.1016/j.jiph.2015.10.013.PMID:26631436
  5. Complete Genome Sequence of a Highly Pathogenic Avian Influenza Virus  (H5N2) Associated with an Outbreak in Commercial Chickens, Iowa, USA,  2015. Clement T, Kutish GF, Nezworski J, Scaria J, Nelson E,  Christopher-Hennings J, Diel DG. Genome Announc. 2015 Jun 11;3(3). pii:  e00613-15. doi: 10.1128/genomeA.00613-15.PMID: 26067961
  6. High-Throughput Screening for Biomarker Discovery. Janvilisri T,  Suzuki H, Scaria J, Chen JW, Charoensawan V. Dis Markers.  2015;2015:108064. doi: 10.1155/2015/108064. PMID: 26060333
  7. Comparative genomic and phenomic analysis of Clostridium difficile  and Clostridium sordellii, two related pathogens with differing host  tissue preference.
    Scaria J, Suzuki H, Ptak CP, Chen JW, Zhu Y, Guo XK, Chang YF. BMC  Genomics. 2015 Jun 10;16:448. doi:  10.1186/s12864-015-1663-5.PMID:26059449
  8. Comparative nutritional and chemical phenome of Clostridium difficile  isolates determined using phenotype microarrays. Scaria J, Chen JW,  Useh N, He H, McDonough SP, Mao C, Sobral B, Chang YF. Int J Infect  Dis. 2014 Oct;27:20-5. doi: 10.1016/j.ijid.2014.06.018.PMID:25130165
  9. Differential stress transcriptome landscape of historic and recently  emerged hypervirulent strains of Clostridium difficile strains  determined using RNA-seq. Scaria J, Mao C, Chen JW, McDonough SP,  Sobral B, Chang YF. PLoS One. 2013 Nov 7;8(11):e78489. doi:  10.1371/journal.pone.0078489.PMID:24244315
  10. Advances in molecular diagnostics. Janvilisri T, Bhunia AK, Scaria  J.Biomed Res Int. 2013;2013:172521. doi: 10.1155/2013/172521.  PMID:23781497
  11. Proteomic comparison of historic and recently emerged hypervirulent  Clostridium difficile strains. Chen JW, Scaria J, Mao C, Sobral B,  Zhang S, Lawley T, Chang YF. J Proteome Res. 2013 Mar 1;12(3):1151-61.  doi: 10.1021/pr3007528.PMID:23298230
  12. Temporal differential proteomes of Clostridium difficile in the pig  ileal-ligated loop model. Janvilisri T, Scaria J, Teng CH, McDonough SP,  Gleed RD, Fubini SL, Zhang S, Akey B, Chang YF. PLoS One.  2012;7(9):e45608. doi: 10.1371/journal.pone.0045608.PMID:23029131
  13. Phenotypic and transcriptomic response of auxotrophic Mycobacterium  avium subsp. paratuberculosis leuD mutant under environmental  stress.Chen JW, Scaria J, Chang YF. PLoS One. 2012;7(6):e37884. doi:  10.1371/journal.pone.0037884.PMID:22675497
  14. Immunogenicity and protective efficacy of the Mycobacterium avium  subsp. paratuberculosis attenuated mutants against challenge in a mouse  model. Chen JW, Faisal SM, Chandra S, McDonough SP, Moreira MA, Scaria  J, Chang CF, Bannantine JP, Akey B, Chang YF. Vaccine. 2012 Apr  19;30(19):3015-25. doi: 10.1016/j.vaccine.2011.11.029. PMID: 22107851
  15. Identification of Escherichia coli genes associated with urinary  tract infections.Mao BH, Chang YF, Scaria J, Chang CC, Chou LW, Tien N,  Wu JJ, Tseng CC, Wang MC, Chang CC, Hsu YM, Teng CH.J Clin Microbiol.  2012 Feb;50(2):449-56. doi: 10.1128/JCM.00640-11.PMID:22075599
  16. Clostridium difficile transcriptome analysis using pig ligated loop  model reveals modulation of pathways not modulated in vitro.Scaria J,  Janvilisri T, Fubini S, Gleed RD, McDonough SP, Chang YF.J Infect Dis.  2011 Jun 1;203(11):1613-20. doi: 10.1093/infdis/jir112.PMID:21592991
  17. Analysis of Escherichia coli O157 clinical isolates by multilocus  sequence typing.Rajkhowa S, Scaria J, Garcia DL, Musser KA, Akey BL,  Chang YF.BMC Res Notes. 2010 Dec 21;3:343. doi:  10.1186/1756-0500-3-343.PMID:21176142
  18. Analysis of ultra low genome conservation in Clostridium  difficile.Scaria J, Ponnala L, Janvilisri T, Yan W, Mueller LA, Chang  YF. PLoS One. 2010 Dec 8;5(12):e15147. doi:  10.1371/journal.pone.0015147.PMID: 21170335
  19. Comparison of phenotypic and genotypic antimicrobial profiles in  Escherichia coli and Salmonella enterica from the same dairy cattle  farms.Scaria J, Warnick LD, Kaneene JB, May K, Teng CH, Chang YF. Mol  Cell Probes. 2010 Dec;24(6):325-45. doi:  10.1016/j.mcp.2010.07.004.PMID:20688154
  20. Transcriptional profiling of Clostridium difficile and Caco-2 cells  during infection. Janvilisri T, Scaria J, Chang YF.J Infect Dis. 2010  Jul 15;202(2):282-90. doi: 10.1086/653484.PMID: 20521945
  21. Development of a microarray for identification of pathogenic  Clostridium spp.Janvilisri T, Scaria J, Gleed R, Fubini S, Bonkosky MM,  Gröhn YT, Chang YF. Diagn Microbiol Infect Dis. 2010 Feb;66(2):140-7.  doi: 10.1016/j.diagmicrobio.2009.09.014.PMID:19879710
  22. Microarray identification of Clostridium difficile core components  and divergent regions associated with host origin. Janvilisri T, Scaria  J, Thompson AD, Nicholson A, Limbago BM, Arroyo LG, Songer JG, Gröhn  YT, Chang YF. J Bacteriol. 2009 Jun;191(12):3881-91. doi:  10.1128/JB.00222-09.PMID:19376880
  23. Microbial Diagnostic Array Workstation (MDAW): a web server for  diagnostic array data storage, sharing and analysis.Scaria J, Sreedharan  A, Chang YF.Source Code Biol Med. 2008 Sep 23;3:14. doi:  10.1186/1751-0473-3-14.PMID:18811969
  24. Microarray for molecular typing of Salmonella enterica  serovars.Scaria J, Palaniappan RU, Chiu D, Phan JA, Ponnala L, McDonough  P, Grohn YT, Porwollik S, McClelland M, Chiou CS, Chu C, Chang YF.Mol  Cell Probes. 2008 Aug;22(4):238-43. doi:  10.1016/j.mcp.2008.04.002.PMID:18554865