Publications

Complete list of Dr. Cooper's publications (in reverse chronological order):

University of Arizona Faculty Publications

Garcia Bardales PF, Schiaffino F, Huynh S, Paredes M, Penataro Yori P, Pinedo Vasquez T, Manzanares Villaneuva K, Curico Huansi GE, Shapiama Lopez WV, Cooper KK, Parker CT, Kosek MN. 2022. Prevalence of “Candidatus Campylobacter infans” in fecal samples of children under the age of 2 in Peru. PLoS Negl Trop Dis. Oct 17:16(10):e0010869. DOI: 10.1371/journal.pntd.0010869.
Parker CT, Schiaffino F, Huynh S, Paredes Olortegui M, Penataro Yori P, Garcia Bardales PF, Pinedo Vasquez T, Curico Huansi GE, Manzanares Villanueva K, Shapiama Lopez WV, Cooper KK, Kosek MN. 2022. Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species. PLoS Negl Trop Dis. Oct 4:16(10):e0010815. DOI: 10.1371/journal.pntd.0010815.
Sen A, Goforth M, Cooper KK, Anakk S. 2022. Deletion of constitutive Androstane Receptor led to intestinal alterations and increased Imidacloprid in murine liver. J Endocrine Society. 6(12):1-9. DOI: 10.1210/jendso/bvac145.
Austhof E, Bell ML, Riddle MS, Catalfamo C, McFadden C, Cooper K, Scallan Walter E, Jacobs E, Pogreba-Brown K. 2022. Persisting gastrointestinal symptoms and post-infectious bowel syndrome following SARS-CoV-2 infection: results from the Arizona CoVHORT. Epidemiol Infect. Jul 8:150:e136. DOI: 10.1017/ S0950268822001200.
Luna E, Parkar S, Kirmiz N, Hartel S, Hearn E, Hossine M, Kurdian A, Mendoza C, Orr K, Padilla L, Ramirez K, Salcedo P, Serrano E, Choudhry B, Paulchakrabarti M, Parker C, Cooper K, Flores G. 2021. Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent. Appl Envrion Microbiol. Oct 20: AEM0148721. DOI: 10.1128/AEM.01487-21.
Heikema AP, Strepis N, Horst-Kreft D, Huynh S, Zomer AL, Kelly DJ, Cooper KK, Parker CT. 2021. Biomolecule sulfation and novel methylations related to Guillain-Barre syndrome-associated C. jejuni serotype HS:19. Microb Genom. Nov. 7(11). DOI: 10.1099/mgen.0.000660.
Achtman M, Van den Broeck F, Cooper KK, Lemey P, Parker CT, Zhou Z, et al. 2021. Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. PLoS Genet. 17(9):e1009820. DOI: 10.1371/journal.pgen.1009820.
Katiyar N, Ramadoss N, Gupta D, Pakala, SB, Cooper K, Basu C. 2021. Transcriptomic profiling of Paulownia elongata in response to heat stress. Plant Gene. 28:100330. DOI: 10.1016/j.plgene.2021.100330.
Crippen C, Zhou B, Andresen S, Patry R, Muszynski A, Parker C, Cooper KK, Szymanski C. 2021. RNA and sugars, unique properties of bacteriophages infecting multidrug resistant Acinetobacter radioresistens strain LH6. Viruses. 13(8):1652. DOI: 10.3390/v13081652.
Parker CT, Huynh S, Alexander A, Oliver AS, Cooper KK. 2021. Genomic characterization of Salmonella Typhimurium DT104 strains associated with cattle and beef products. Pathogens. 10(5):529. DOI: 10.3390/pathogens10050529.
Parker CT, Cooper KK, Schiaffino F, Miller WG, Huynh S, Gray HK, Olortegui MP, Bardales PG, Trigoso DR, Penataro-Yori P, Kosek MN. 2021. Genomic characterization of Campylobacter jejuni adapted to the guinea pig (Cavia porcellus) host. Front Cell Infect Microbiol. 11:607747. DOI: 10.3389/fcimb.2021.607747.
Arias DB, Gomez Pinto KA, Cooper KK, Summers ML. 2020. Transcriptomic analysis of cyanobacterial alkane overproduction reveals stress-related genes and inhibitors of lipid droplet formation. Microb Genom. 6(10):mgen000432. DOI: 10.1099/mgen.0.000432.
Pascoe B, Schiaffino F, Murray S, Méric G, Bayliss SC, Hitchings MD, Mourkas E, Calland JK, Burga R, Yori PP, Jolley KA, Cooper KK, Parker CT, Olortegui MP, Kosek MN, Sheppard SK. 2020. Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. PLoS Negl Trop Dis. 14(8):e0008533. DOI:10.1371/journal.pntd.0008533.
Bian X, Garber JM, Cooper KK, Huynh S, Jones J, Mills MK, Rafala D, Nasrin D, Kotloff KL, Parker CT, Tennant SM, Miller WG, Szymanski CM. 2019. Campylobacter abundance in breastfed infants and identification of a new species in the Global Enterics Multicenter Study. mSphere. 5(1):e00735-19. DOI:10.1129/mSphere.00735-19.
Ruiz C, McCarley A, Espejo ML, Cooper KK, Harmon DE. 2019. Comparative genomics reveals a well conserved intrinsic resistome in the emerging multidrug-resistant pathogen Cupriavidus gilardii. mSphere. 4(5):e00631-19. DOI:10.1128/mSphere.00631-19.
Parker CT, Cooper KK, Huynh S, Smith TP, Bono JL, Cooley M. 2018. Genome sequences of eight Shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California. Microbiol Resour Announc. 7(1):e00807-18. DOI: 10.1128/MRA.00807-18.
Oliver A, Kay M, Cooper KK. 2018. Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics. 19(1):310. DOI: 10.1186/s12864-018-4635-8.
Seuylemezian A, Vaishampayan P, Cooper K, Venkateswaran K. 2018. Draft genome sequences of Acinetobacter and Bacillus strains isolated from spacecraft-associated surfaces. Genome Announc. 6(6):e01554-17. DOI: 10.1128/genomeA.01554-17.
Seuylemezian A, Cooper K, Schubert W, Vaishampayan P. 2018. Draft genome sequences of 12 dry-heat-resistant Bacillus strains isolated from the cleanrooms where the Viking Spacecraft were assembled. Genome Announc. 6(12):e00094-18. DOI: 10.1128/genomeA.00094-18.
Gorski L, Huynh S, Cooper KK, Parker CT. 2017. Complete genomic sequences of two Salmonella enterica subsp. enterica Serogroup C2 (O:6:8) strains from Central California. Genome Announc. 5(46):e01234-17. DOI: 10.1128/genomeA.01234-17.

Non-University of Arizona Faculty Publications

Pinoargote G, Flores G, Cooper K, Ravishankar S. 2018. Effects on survival and bacterial community composition of the aquaculture water and gastrointestinal tract of shrimp (Litopenaeus vannamei) exposed to probiotic treatments after an induced infection of acute hepatopancreatic necrosis disease. Aquacult Res. 49:3270-3288. DOI: 10.1111/are.13791.
Pascoe B, Meric G, Yahara K, Wimalarathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MCJ, McCarthy ND, Didelot X, Parker CT, Sheppard SK. 2017. Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations. Mol Ecol. 26(17):4497-4508. DOI: 10.1111/mec.14176.
Chaires M, Gupta D, Joshee N, Cooper KK, Basu C. 2017. RNA-seq analysis of the salt stress-induced transcripts in fast-growing bioenergy tree, Paulownia elongate. J Plant Inter. 12(1):128-136. DOI: 10.1080/17429145.2017.1298851.
Parker CT, Huynh S, Gorski L, Cooper KK, Miller WG. 2015. Complete genome sequences of two outbreak strains of Salmonella enterica subsp. enterica serovar Thompson associated with cilantro. Genome Annouc. 3(6):e01365-15. DOI: 10.1128/genomeA.01365-15.
Parker CT, Huynh S, Heikema AP, Cooper KK, Miller WG. 2015. Complete genome sequences of Campylobacter jejuni strains RM3196 (233.94) and RM3197 (308.95) isolated from patients with Guillain-Barre Syndrome. Genome Announc. 3(6):e01312-15. DOI: 10.1128/genomeA.01312-15.
Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ. 2014. Complete genome sequences of two Escherichia coli O145:H28 outbreak strains of food origin. Genome Announc. 2(3):e00483-14. DOI: 10.1128/genomeA.00482-14.
Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ. 2014. Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. BMC Genomics. 15:17. DOI: 10.1186/1471-2164-15-17.
Cooper KK, Bueschel DM, Songer JG. 2013. Presence of Clostridium perfringens in retail chicken livers. Anaerobe. 21:67-8. DOI: 10.1016/j.anaerobe.2013.03.013.
Cooper KK, Songer JG, Uzal F. 2013. Diagnosing clostridial enteric disease in poultry. J Vet Diagn Invest. 25(3):314-27. DOI: 10.1177/1040638713483468.
Cooper KK, Cooper MA, Zuccolo A, Joens LA. 2013. Re-sequencing of virulent strain of Campylobacter jejuni NCTC11168 reveals potential virulence factors. Res Microbiol. 164:6-11. DOI: 10.1016/j.resmic.2012.10.002.
Theoret JR, Cooper KK, Zekarias B, Roland K, Law BF, Curtiss III R, Joens LA. 2012. The Campylobacter jejuni Dps homologue is important for in vitro biofilm formation and cecal colonization of poultry, and may serve as a protective antigen for vaccination. Clin Vaccine Immunol. 19(9):1426-31. DOI: 10.1128/CVI.00151-12.
Coursodon CF, Glock RD, Moore RL, Cooper KK, Songer JG. 2012. TpeL-producing strains of Clostridium perfringens type A are highly virulent for broiler chicks. Anaerobe. 18(1):117-21. DOI: 10.1016/j.anaerobe.2011.10.001.
Theoret JR, Cooper KK, Glock RD, Joens LA. 2011. A Campylobacter jejuni Dps homologue has a role in intracellular survival and in the development of campylobacteriosis in neonate piglets. Foodborne Pathog Dis. 8(12):1263-8. DOI: 10.1089/fpd.2011.0892.
Cooper KK, Cooper MA, Zuccolo A, Law B, Joens LA. 2011. The complete genome sequence of Campylobacter jejuni strain S3. J. Bacteriol. 193(6):1491-2. DOI: 10.1128/JB.01475-10.
Cooper KK, Theoret JR, Stewart BA, Trinh HT, Glock RD, Songer JG. 2010. Virulence for chickens of Clostridium perfringens isolated from poultry and other sources. Anaerobe. 16(3)289-92. DOI: 10.1016/j.anaerobe.2010.02.006.
Cooper KK, Songer JG. 2010. Virulence of Clostridium perfringens in an experimental model of poultry necrotic enteritis. Vet Microbiol. 142(3-4):323-8. DOI: 10.1016/j.vetmic.2009.09.065.
Cooper KK, Songer JG. 2009. Necrotic enteritis in poultry: A paradigm of enteric infection by Clostridium perfringens type A. Anaerobe. 15(1-2):55-60. DOI: 10.1016/j.anaerobe.2009.01/006.
Cooper KK, Trinh HT, Songer JG. 2009. Immunization with recombinant alpha toxin partially protects broiler chicks against experimental challenge with Clostridium perfringens. Vet Microbiol. 133(1-2):92-7. DOI: 10.1016/j.vetmic.2008.06.001.

Dr. Kerry Cooper

Complete list of Dr. Cooper's publications (in reverse chronological order):

University of Arizona Faculty Publications

Sen A, Goforth M, Cooper KK, Anakk S. 2022. Deletion of constitutive Androstane Receptor led to intestinal alterations and increased Imidacloprid in murine liver. J Endocrine Society. 6(12):1-9. DOI: 10.1210/jendso/bvac145.

Heikema AP, Strepis N, Horst-Kreft D, Huynh S, Zomer AL, Kelly DJ, Cooper KK, Parker CT. 2021. Biomolecule sulfation and novel methylations related to Guillain-Barre syndrome-associated C. jejuni serotype HS:19. Microb Genom. Nov. 7(11). DOI: 10.1099/mgen.0.000660.

Achtman M, Van den Broeck F, Cooper KK, Lemey P, Parker CT, Zhou Z, et al. 2021. Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. PLoS Genet. 17(9):e1009820. DOI: 10.1371/journal.pgen.1009820.

Katiyar N, Ramadoss N, Gupta D, Pakala, SB, Cooper K, Basu C. 2021. Transcriptomic profiling of Paulownia elongata in response to heat stress. Plant Gene. 28:100330. DOI: 10.1016/j.plgene.2021.100330.

Crippen C, Zhou B, Andresen S, Patry R, Muszynski A, Parker C, Cooper KK, Szymanski C. 2021. RNA and sugars, unique properties of bacteriophages infecting multidrug resistant Acinetobacter radioresistens strain LH6. Viruses. 13(8):1652. DOI: 10.3390/v13081652.

Parker CT, Huynh S, Alexander A, Oliver AS, Cooper KK. 2021. Genomic characterization of Salmonella Typhimurium DT104 strains associated with cattle and beef products. Pathogens. 10(5):529. DOI: 10.3390/pathogens10050529.

Arias DB, Gomez Pinto KA, Cooper KK, Summers ML. 2020. Transcriptomic analysis of cyanobacterial alkane overproduction reveals stress-related genes and inhibitors of lipid droplet formation. Microb Genom. 6(10):mgen000432. DOI: 10.1099/mgen.0.000432.

Ruiz C, McCarley A, Espejo ML, Cooper KK, Harmon DE. 2019. Comparative genomics reveals a well conserved intrinsic resistome in the emerging multidrug-resistant pathogen Cupriavidus gilardii. mSphere. 4(5):e00631-19. DOI:10.1128/mSphere.00631-19.

Parker CT, Cooper KK, Huynh S, Smith TP, Bono JL, Cooley M. 2018. Genome sequences of eight Shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California. Microbiol Resour Announc. 7(1):e00807-18. DOI: 10.1128/MRA.00807-18.

Oliver A, Kay M, Cooper KK. 2018. Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics. 19(1):310. DOI: 10.1186/s12864-018-4635-8.

Seuylemezian A, Vaishampayan P, Cooper K, Venkateswaran K. 2018. Draft genome sequences of Acinetobacter and Bacillus strains isolated from spacecraft-associated surfaces. Genome Announc. 6(6):e01554-17. DOI: 10.1128/genomeA.01554-17.

Seuylemezian A, Cooper K, Schubert W, Vaishampayan P. 2018. Draft genome sequences of 12 dry-heat-resistant Bacillus strains isolated from the cleanrooms where the Viking Spacecraft were assembled. Genome Announc. 6(12):e00094-18. DOI: 10.1128/genomeA.00094-18.

Gorski L, Huynh S, Cooper KK, Parker CT. 2017. Complete genomic sequences of two Salmonella enterica subsp. enterica Serogroup C2 (O:6:8) strains from Central California. Genome Announc. 5(46):e01234-17. DOI: 10.1128/genomeA.01234-17.

Non-University of Arizona Faculty Publications

Chaires M, Gupta D, Joshee N, Cooper KK, Basu C. 2017. RNA-seq analysis of the salt stress-induced transcripts in fast-growing bioenergy tree, Paulownia elongate. J Plant Inter. 12(1):128-136. DOI: 10.1080/17429145.2017.1298851.

Parker CT, Huynh S, Gorski L, Cooper KK, Miller WG. 2015. Complete genome sequences of two outbreak strains of Salmonella enterica subsp. enterica serovar Thompson associated with cilantro. Genome Annouc. 3(6):e01365-15. DOI: 10.1128/genomeA.01365-15.

Parker CT, Huynh S, Heikema AP, Cooper KK, Miller WG. 2015. Complete genome sequences of Campylobacter jejuni strains RM3196 (233.94) and RM3197 (308.95) isolated from patients with Guillain-Barre Syndrome. Genome Announc. 3(6):e01312-15. DOI: 10.1128/genomeA.01312-15.

Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ. 2014. Complete genome sequences of two Escherichia coli O145:H28 outbreak strains of food origin. Genome Announc. 2(3):e00483-14. DOI: 10.1128/genomeA.00482-14.

Cooper KK, Bueschel DM, Songer JG. 2013. Presence of Clostridium perfringens in retail chicken livers. Anaerobe. 21:67-8. DOI: 10.1016/j.anaerobe.2013.03.013.

Cooper KK, Songer JG, Uzal F. 2013. Diagnosing clostridial enteric disease in poultry. J Vet Diagn Invest. 25(3):314-27. DOI: 10.1177/1040638713483468.

Cooper KK, Cooper MA, Zuccolo A, Joens LA. 2013. Re-sequencing of virulent strain of Campylobacter jejuni NCTC11168 reveals potential virulence factors. Res Microbiol. 164:6-11. DOI: 10.1016/j.resmic.2012.10.002.

Coursodon CF, Glock RD, Moore RL, Cooper KK, Songer JG. 2012. TpeL-producing strains of Clostridium perfringens type A are highly virulent for broiler chicks. Anaerobe. 18(1):117-21. DOI: 10.1016/j.anaerobe.2011.10.001.

Theoret JR, Cooper KK, Glock RD, Joens LA. 2011. A Campylobacter jejuni Dps homologue has a role in intracellular survival and in the development of campylobacteriosis in neonate piglets. Foodborne Pathog Dis. 8(12):1263-8. DOI: 10.1089/fpd.2011.0892.

Cooper KK, Cooper MA, Zuccolo A, Law B, Joens LA. 2011. The complete genome sequence of Campylobacter jejuni strain S3. J. Bacteriol. 193(6):1491-2. DOI: 10.1128/JB.01475-10.

Cooper KK, Theoret JR, Stewart BA, Trinh HT, Glock RD, Songer JG. 2010. Virulence for chickens of Clostridium perfringens isolated from poultry and other sources. Anaerobe. 16(3)289-92. DOI: 10.1016/j.anaerobe.2010.02.006.

Cooper KK, Songer JG. 2010. Virulence of Clostridium perfringens in an experimental model of poultry necrotic enteritis. Vet Microbiol. 142(3-4):323-8. DOI: 10.1016/j.vetmic.2009.09.065.

Cooper KK, Songer JG. 2009. Necrotic enteritis in poultry: A paradigm of enteric infection by Clostridium perfringens type A. Anaerobe. 15(1-2):55-60. DOI: 10.1016/j.anaerobe.2009.01/006.

Cooper KK, Trinh HT, Songer JG. 2009. Immunization with recombinant alpha toxin partially protects broiler chicks against experimental challenge with Clostridium perfringens. Vet Microbiol. 133(1-2):92-7. DOI: 10.1016/j.vetmic.2008.06.001.