2020
  • Putonti C, Shapiro JW, Ene A, Tsibere O, Wolfe AJ. Comparative genomic study of Lactobacillus jensenii and the newly defined Lactobacillus mulieris species identifies species-specific functionality. mSphere, 2020, In Press. 
  • Miller-Ensminger T, Garretto A, Stark N, Putonti C. Mimicking prophage induction in the body: Protocol for induction in the lab with pH gradients. PeerJ, 2020, In Press. 
  • Miller-Ensminger T, Mormando R, Maskeri L, Shapiro JW, Wolfe AJ, Putonti C. Introducing Lu-1, a novel Lactobacillus jensenii phage abundant in the urogenital tract. PLoS One, 2020, 15:e0234159. (Open Access)
  • Shapiro JW, Putonti C. UPphi phages, a new group of filamentous phages found in several members of Enterobacteriales. Virus Evol, 2020, 6:veaa030 (Open Access).
  • Brassil B, Mores CR, Wolfe AJ, Putonti C. Characterization and spontaneous induction of urinary tract Streptococcus anginosus prophages. J Gen Virol, 2020, 101:685-691. (Open Access)
  • Hilt EE, Putonti C, Thomas-White K, Lewis AL, Visick KL, Gilbert NM, Wolfe AJ. Aerococcus urinae isolated from women with lower urinary tract symptoms: in vitro aggregation and genome analysis. J Bacteriol, 2020, 202:e00170-20. (Open Access) (Commentary in UroToday)
Genome Announcements:
  • Belmonte M, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Escherichia coli UMB9246, isolated from the bladder of a woman with recurrent urinary tract infection. Microbiol Resour Announc, 2020, 9:e00437-20. (Open Access)
  • Truckenbrod A, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Staphylococcus epidermidis UMB8493, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00419-20. (Open Access)
  • Crawford T, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Escherichia coli UMB1353, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00416-20. (Open Access)
  • Scott T, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Streptococcus anginosus UMB0839, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00411-20. (Open Access)
  • Khan F, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Lactobacillus crispatus UMB1163, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00404-20. (Open Access)
  • Markovic T, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Actinomyces neuii UMB1295, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00402-20. (Open Access)
  • Eskandar S, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Corynebacterium aurimucosum UMB7769, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00391-20. (Open Access)
  • Kalski M, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Enterococcus faecalis UMB7780, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00400-20. (Open Access)
  • Schwartz A, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Enterococcus faecalis UMB1309, isolated from catheterized urine. Microbiol Resour Announc, 2020, 9:e00406-20. (Open Access)
  • Miller S, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Streptococcus anginosus UMB7768, isolated from a woman with recurrent UTI symptoms. Microbiol Resour Announc, 2020, 9:e00418-20. (Open Access)
  • Rivera I, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Lactobacillus jensenii UMB0836, isolated from the female bladder. Microbiol Resour Announc, 2020, 9:e00410-20. (Open Access)
  • Tsibere O, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Lactobacillus mulieris UMB7784, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00403-20. (Open Access)
  • Gallian N, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Proteus mirabilis UMB0038, isolated from the female bladder. Microbiol Resour Announc, 2020, 9:e00401-20. (Open Access)
  • Giannattasio-Ferraz S, Maskeri L, Oliveira AP, Barbosa-Stancioli E, Putonti C. Three draft genome sequences of Staphylococcus species isolated from the urine of healthy bovine heifers (Gyr breed). Microbiol Resour Announc, 2020, 9:e00389-20. (Open Access)
  • Giannattasio-Ferraz S, Maskeri L, Oliveira AP, Barbosa-Stancioli E, Putonti C. Draft genome sequence of Enterobacter asburiae UFMG-H9, isolated from urine from a healthy bovine heifer (Gyr breed). Microbiol Resour Announc, 2020, 9:e00385-20. (Open Access)
  • Giannattasio-Ferraz S, Maskeri L, Oliveira AP, Barbosa-Stancioli E, Putonti C. Draft genome sequences of three Enterococcus casseliflavus strains isolated from the urine of healthy bovine heifers (Gyr breed). Microbiol Resour Announc, 2020, 9:e00386-20. (Open Access)
  • Allen O, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Proteus mirabilis UMB1310, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00390-20. (Open Access)
  • Miller-Ensminger T, Wolfe AJ, Putonti C. Draft genome sequence of Lactobacillus jensenii strain UMB7766, isolated from the female bladder. Microbiol Resour Announc, 2020, 9:e00392-20. (Open Access)
  • Ali Khan A, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Corynebacterium coyleae UMB8490, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00393-20. (Open Access)
  • West-Pelak E, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Lactobacillus jensenii UMB0847, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00395-20. (Open Access)
  • Bhimalli P, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Klebsiella pneumoniae UMB7779, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00396-20. (Open Access)
  • Gondi S, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Klebsiella pneumoniae UMB8492, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00405-20. (Open Access)
  • Purta N, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of antibiotic-resistant Enterococcus faecalis strain UMB0843, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00407-20. (Open Access)
  • Ramotowski L, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Lactobacillus mulieris UMB9245, isolated from the female bladder. Microbiol Resour Announc, 2020, 9:e00408-20. (Open Access)
  • Temelkova S, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Streptococcus anginosus UMB1296, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00409-20. (Open Access)
  • Kemper L, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Staphylococcus epidermidis UMB7765, isolated from the urobiome of a woman with recurrent urinary tract infection. Microbiol Resour Announc, 2020, 9:e00417-20. (Open Access)
  • Salgado LM, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Streptococcus agalactiae UMB7782, isolated from the female urinary tract. Microbiol Resour Announc, 2020, 9:e00423-20. (Open Access)
  • Balce E, Miller-Ensminger T, Voukadinova A, Wolfe AJ, Putonti C. Draft genome sequence of Klebsiella pneumoniae UMB7783, isolated from the female bladder. Microbiol Resour Announc, 2020, 9:e00394-20. (Open Access)
  • Giannattasio-Ferraz S, Maskeri L, Penido A, Barbosa-Stancioli EF, Putonti C. Draft genome sequence of Aeromonas caviae UFMG-H8, isolated from urine from a healthy bovine heifer (Gyr breed). Microbiol Resour Announc, 2020, 9:e00388-20. (Open Access)
  • Giannattasio-Ferraz S, Maskeri L, Penido A, Barbosa-Stancioli EF, Putonti C. Draft genome sequence of Citrobacter freundii UFMG-H9, isoalted from urine from a healthy bovine heifer (Gyr breed). Microbiol Resour Announc, 2020, 9:e00387-20. (Open Access)
  • Johnson G, Mores CR, Wolfe AJ, Putonti C. Draft genome sequences of two Pseudomonas aeruginosa isolates from the female urinary urogenital tract. Microbiol Resour Announc, 2020, 9:e01378-19. (Open Access)
  • Mores CR, Price TK, Brassil B, Putonti C, Wolfe AJ. Complete genome sequences of Streptococcus mitis strains isolated from the oral cavity and urogenital tract of a woman and her male sexual partner. Microbiol Resour Announc, 2020, 9:e01379-19. (Open Access)

2019
  • Johnson G*, Stark N*, Wolfe AJ, Putonti C. Complete genome sequence of Pseudomonas aeruginosa isolate from a kidney stone. Microbiol Resour Announc, 2019, 8:e01073-19​. (*authors contributed equally) (Open Access)
  • Putonti C, Akhnoukh V, Anagnostopoulos Z, Bilek M, Colgan J, El Idrissi S, Magnuszewski K, Marino S, Szymulewski M, Tyahla M, Yanchuk V, Miller-Ensminger T, Batrich M, Brassil B, Mormando R, Johnson G, Wolfe AJ. Draft genome sequences of 6 Lactobacillus gasseri and 3 Lactobacillus paragasseri strains isolated from the female bladder. Microbiol Resour Announc, 2019, 8:e00973-19. (Open Access)
  • Putonti C, Ahmad A, Baddoo G, Diaz J, Do M, Gallian N, Lorentzen C, Mohammed H, Murphy J, Olu-Ajeigbe A, Yang T, Miller-Ensminger T, Stark N, Maskeri L, Van Dusen J, Wolfe AJ. Draft genomes of 11 Lactobacillus jensenii strains isolated from the female bladder. Microbiol Resour Announc, 2019, 8:e00970-19. (Open Access)
  • Johnson G, Putonti C. Genome sequence of Pseudomonas phage UMP151 from the female bladder microbiota. Microbiol Resour Announc, 2019, 8: e00853-19. (Open Access)
  • Garretto A, Miller-Ensminger T, Wolfe AJ, Putonti C. Bacteriophages of the lower urinary tract. Nat Rev Urol, 2019, 16: 422-432. (Online)
  • Zilliox MJ, Schreckenberger PC, Putonti C. Draft genome sequence of clinical isolate Alcaligenaceae sp. strain 429. Microbiol Resour Announc, 2019, 8: e00439-19. (Open Access)
  • Garretto A, Hatzopoulos T, Putonti C. virMine: Automated detection of viral sequences from complex metagenomic samples. PeerJ, 2019, 7: e6695. (Open Access)
  • Batrich M, Maskeri L, Schubert R, Ho B, Kohout M, Abdeljaber M, Abuhasna A, Kholoki M, Psihogios P, Razzaq T, Sawhney S, Siddiqui S, Xoubi E, Cooper A, Hatzopoulos T, Putonti C. Pseudomonas diversity within urban freshwaters. Front Microbiol, 2019, 10: 195. ​(Open Access)
  • Johnson G, Wolfe AJ, Putonti C. Characterization of the φCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota. Access Microbiology, 2019, 1. (Open Access)
  • Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, ThurberRV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol, 2019, 37: 29-37. (Open Access)

2018
  • Kooistra RL, David R, Ruiz AC, Powers SW, Haselton KJ, Kiernan K, Blagborough AM, Solamen L, Olsen KW, Putonti C, Kanzok SM. Characterization of a protozoan Phosducin-like protein-3 (PhLP-3) reveals conserved redox activity. PLoS ONE, 2018, 13: e0209699 (Open Access).
  • Putonti C, Diener Z, Watkins SC. Freshwater viromes: From sampling to evaluation. Methods Mol Biol, 2018, 1849: 17-27. (Online)
  • Kalesinskas L, Cudone E, Fofanov Y, Putonti C. S-plot2: Rapid visual and statistical analysis of genomic sequences. Evol Bioinform Online, 2018, 14: 1176934318797354. (Open Access)
  • Watkins SC, Sible E, Putonti C. Pseudomonas PB1-like phages: whole genomes from metagenomes offer insight into an abundant group of bacteriophages. Viruses, 2018, 10: E331. (Open Access)
  • Garretto A, Thomas-White K, Wolfe AJ, Putonti C. Detecting viral genomes in the female urinary microbiome. J Gen Virology, 2018, 99: 1141-1146. (Online)
  • Kula A, Saelens J, Cox J, Schubert AM, Travisano M, Putonti C. The evolution of molecular comparability between viruses and their hosts. Sci Reports, 2018, 8: 8350. (Open Access)
  • Thomas-White K, Forster SC, Kumar N, Van Kuiken M, Putonti C, Stares MD, Hilt EE, Price TK, Wolfe AJ, Lawley TD. Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nat Comm, 2018, 9: 1557. (Open Access)
  • Shapiro J, Putonti C. Gene co-occurrence networks reflect bacteriophage ecology and evolution. mBio, 2018, 9: e01870-17. (Open Access)
  • Miller-Ensminger T, Garretto A, Brenner J, Thomas-White K, Zambom A, Wolfe AJ, Putonti C. Bacteriophages of the urinary microbiome. J Bacteriol, 2018, 200: e00738-17. (Online)
  • Castignetti D, Polley N, Putonti C. Draft genome sequence of the siderophore-degrading soil bacterium Mesorhizobium loti LU. Genome Announc, 2018, 6: e00029-18. (Open Access)
  • Putonti C, Polley N, Castignetti D. Draft genome sequence of an active heterotrophic nitrifier-denitrifier, Cupriavidus pauculus UM1. Genome Announc, 2018, 6: e00028-18. (Open Access)

2017
  • Dimitrova D, Engelbrecht KC, Putonti C, Koenig DW, Wolfe AJ. Draft genome sequence of Escherichia coli K-12 (ATCC 10798). Genome Announc, 2017, 5: e00573-17. (Open Access)
  • Engelbrecht KC, Putonti C, Koenig DW, Wolfe AJ. Draft genome sequence Escherichia coli K-12 (ATCC 29425). Genome Announc, 2017, 5, e00574-17. (Open Access)
  • Putonti C, Kalesinskas L, Cudone E, Engelbrecht KC, Koenig DW, Wolfe AJ. Draft genome sequence of Enterococcus faecalis (ATCC BAA-2128). Genome Announc, 2017, 5: e00575-17. (Open Access)
  • Putonti C, Cudone E, Kalesinskas L, Engelbrecht KC, Koenig DW, Wolfe AJ. Draft genome sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698). Genome Announc, 2017, 5: e00576-17. (Open Access)
  • Putonti C, Kalesinskas L, Cudone E, Engelbrecht KC, Koenig DW, Wolfe AJ. Draft genome sequences of two ATCC Staphylococcus aureus subsp. aureus strains. Genome Announc, 2017, 5: e00618-17. (Open Access)
  • Putonti C, Kalesinskas L, Cudone E, Engelbrecht KC, Koenig DW, Wolfe AJ. Staphylococcus epidermidis (Winslow and Winslow) Evans (ATCC 14990) draft genome. Genome Announc, 2017, 5: e00619-17. (Open Access)
  • Watkins S, Putonti C. The use of Informativity in the development of robust viromics-based examinations. PeerJ, 2017, 5: e3281. (Open Access)

2016
  • Malki K, Shapiro JW, Price TK, Hilt EE, Thomas-White K, Sircar T, Rosenfeld AB, Kuffel G, Zilliox MJ, Wolfe AJ, Putonti C. Genomes of Gardnerella strains reveal an abundance of prophages within the bladder microbiome. PLoS ONE, 2016, 11: e0166757. (Open Access)
  • Malki K, Sible E, Cooper A, Garretto A, Bruder K, Watkins S, Putonti C. Seven bacteriophages isolated from the female urinary microbiota. Genome Announc, 2016, 4: e01003-16. (Open Access)
  • Price TK, Shaheen M, Kalesinskas L, Malki K, Hilt EE, Putonti C, Wolfe AJ. Draft genome for a urinary isolate of Lactobacillus crispatus. Genome Announc, 2016, 4: e01278-16. (Open Access)
  • Price TK, Mehtash A, Kalesinskas L, Malki K, Hilt EE, Putonti C, Wolfe AJ. Genome sequences and annotation of two urinary isolates of E. coli.​ Stand Genomic Sci, 2016, 11: 79. (Open Access)
  • Hilt EE, Price TK, Diebel K, Putonti C, Wolfe AJ. Draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae. Genome Announc, 2016, 4: e01248-16. (Open Access)
  • Ziccardi W, Zhao C, Shepelev V, Uralsky L, Alexandrov I, Andreeva T, Rogaev E, Bun C, Miller E, Putonti C, Doering J. Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers. Chromosome Res, 2016, 24: 421-36. (Link)
  • Bruder K, Malki K, Cooper A, Sible E, Shapiro JW, Watkins SC, Putonti C. Freshwater metaviromics and bacteriophages: A current assessment of the state of the art in relation to bioinformatic challenges. Evol Bioinform Online, 2016, 12: 25-33. (Open Access)
  • Hatzopoulos T, Watkins S, Putonti C. PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets. MGen, 2016, 2. (Open Access)
  • ​Reisman S, Hatzopoulos T, Laufer K, Thiruvathukal G, Putonti C. A polyglot approach to bioinformatics data integration: a phylogenetic analysis of HIV-1. Evol Bioinform, 2016, 12: 23-27. (Open Access)
  • Searle D, Sible E, Cooper A, Putonti C. 18S rDNA dataset profiling microeukaryotic populations within Chicago area nearshore waters. Data Brief, 2016, 6: 526-529. (Open Access)

2015
  • Boyd K, Highland E, Misch A, Hu A, Reddy S, Putonti C. Finding function in the unknown. Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015, 1098-1099. (Open Access)
  • Brenner J, Putonti C. HAsh-MaP-ERadicator: Filtering non-target sequences from next generation sequencing reads. Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015, 1100-1101​. (Open Access)
  • Malki K, Kula A, Bruder K, Sible E, Hatzopolous T, Steidel S, Watkins SC, Putonti C. An examination of four bacteriophages isolated from Lake Michigan capable of infecting across bacterial phyla. Virol J, 2015, 12: 164. (Open Access)
  • Watkins SC, Kuehnle N, Ruggeri CA, Malki K, Bruder K, Elayyan J, Damisch K, Vahora N, O’Malley P, Ruggles-Sage B, Romer Z, Putonti C. Assessment of a metaviromic dataset generated from nearshore Lake Michigan. Marine Fresh Res, 2015, 67: 1700-1708. (Author's accepted version of manuscript)
  • Malki K, Bruder K, Putonti C. Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches. Data Brief, 2015, 5: 556-559. (Open Access)
  • Sible E, Cooper A, Malki K, Bruder K, Hatzopoulos T, Watkins SC, Putonti C. Assessment of microbial populations within Chicago area nearshore waters and interfaces with river systems. Data Brief, 2015, 5: 305-308. (Open Access)
  • Sible E, Cooper A, Malki K, Bruder K, Watkins SC, Fofanov Y, Putonti C. Survey of viral populations within Lake Michigan nearshore waters at four Chicago area beaches. Data Brief, 2015, 5: 9-12. (Open Access)

2013
  • Putonti C, Nowicki B, Shaffer M, Fofanov Y, Nowicki S. Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus. BMC Evol Biol, 2013, 13: 184.  (Open Access)
  • Putonti C, Quach B, Kooistra RL, Kanzok S. The evolution and putative function of phosducin-like proteins in the malaria parasite Plasmodium. Infect Genet Evol, 2013, 13: 49-55.

2012
  • Bun C, Ziccardi W, Doering J, Putonti C. MiIP: The monomer identification and isolation program. Evol Bioinform, 2012, 8: 293-300. (Open Access)
  • Hilterbrand A, Saelens J, Putonti C. CBDB: The codon bias database. BMC Bioinformatics, 2012, 13: 62. (Open Access)
​
2011
  • Reynoso V, Putonti C. Mapping short sequencing reads to distant relatives. Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM, New York, NY, USA, 420-424.

2010
  • Cox J, Schubert A, Travisano M, Putonti C. Adaptive evolution and inherent tolerance to extreme thermal environments. BMC Evol Biol, 2010, 10: 75. (Open Access)
  • Cox J, Putonti C. Mechanisms responsible for a phiX174-mutant's ability to infect E. coli by phosphorylation. J Virol 2010, 84: 4860-4863. 
  • Dasu S, Williams A, Fofanov Y, Putonti C. csPCR: A computational tool for the simulation of the Polymerase Chain Reaction. Online J Bioinform, 2010, 11: 34-37. 
  • Schubert A, Putonti C. Evolution of the sequence composition of Flaviviruses. Infect Genet Evol, 2010, 10: 129-136. 


For a additional publications by Dr. Putonti, please see PubMed.