Theses/Dissertations from 2024
The Effect of Environmental Pollutants on the Spotted Turtle Gut Microbiota, Roza Gawin
Regulation of Spermatogenesis by the BTB Transcription Factor Ribbon, Madeline Kyung Hee Hakala
Exploring Evolutionary Relationships of New World Astragalus through Phylogenomic Analyses, Victoria Martinez
Neurogenomics of Competition and Parental Care in a Socially Polyandrous Shorebird, Tessa Mathur Patton
Lactobacillus-Mediated Phage Induction and Inhibition of Growth of Escherichia coli, Natalie Stegman
Transcriptome-Wide Association Study of the Plasma Proteme Reveals Cis and Trans Regulatory Mechanisms Underlying Complex Traits, Henry Wittich
Theses/Dissertations from 2023
Incorporating Sex Chromosomes in Transcriptome Prediction Models and Improving Cross-Population Prediction Performance, Daniel S. Araujo
Exploring the Genotypic and Phenotypic Differences Distinguishing Lactobacillus jensenii and Lactobacillus mulieris, Adriana Ene, Swarnali Banerjee, Alan J. Wolfe, and Catherine Putonti
A Population Level Examination of the Incredible Fruit Diversity in Astragalus Lentiginosus, Quinn Thomas
Theses/Dissertations from 2022
Unveiling Bacterial Hitchhikers in the Urobiome, Genevieve Baddoo
Interplay between Human Microbiota and Celiac Disease, John James Colgan
Cataloging and Engineering Temperate Coliphages of the Human Urinary Microbiome, Elias Crum
Exploring the Role of Lactobacillus Jensenii and Lactobacillus Mulieris in the Urogenital Tract, Adriana Daniela Ene
Polyomavirus JCPyV and Its Role in the Urinary Tract, Rita Lauren Mormando
Integrating Current Analyses of the Breast Cancer Microbiome, Sidra Sohail
Theses/Dissertations from 2021
Population-Matched Transcriptome Prediction Increases Discovery and Replication Rate in TWAS, Elyse Geoffroy
Pseudomonas Aeruginosa Prophages and Engineered Temperate Phages, Genevieve Johnson
Lactobacillus Metabolite-Mediated Induction of Bacteriophage, Taylor Miller-Ensminger
The Utilization and Optimization of Omics Trait Prediction Models Within and Across Diverse Populations, Ashley Mulford
Submissions from 2020
Draft Genome Sequence of Corynebacterium coyleae UMB8490, Isolated from the Female Urinary Tract, Abbas Ali Khan, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Proteus mirabilis UMB1310, Isolated from the Female Urinary Tract, Olivia Allen, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection, Mikalina Belmonte, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Klebsiella pneumoniae UMB7779, Isolated from the Female Urinary Tract, Pavan Bhimalli, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Characterization and Spontaneous Induction of Urinary Tract Streptococcus anginosus Prophages, Bridget Brassil, Carine R. Mores, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Escherichia coli UMB1353, Isolated from the Female Urinary Tract, Tanea Crawford, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements, Julie C. Dunning Hotopp, David A. Baltrus, Vincent M. Bruno, John J. Dennehy, Steven R. Gill, Julia A. Maresca, Jelle Matthijnssens, Irene L. G. Newton, Catherine Putonti, David A. Rasko, Antonis Rokas, Simon Roux, Jason E. Stajich, Kenneth M. Stedman, Frank J. Stewart, and J. Cameron Thrash
Draft Genome Sequence of Corynebacterium aurimucosum UMB7769, Isolated from the Female Urinary Tract, Samantha Eskandar, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Proteus mirabilis Strain UMB0038, Isolated from the Female Bladder, Noreen Gallian, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms, Andrea Garretto, Taylor Miller-Ensminger, Adriana Ene, Zubia Merchant, Aashaka Shah, Athina Gerodias, Anthony Biancofiori, Stacey Canchola, Stephanie Canchola, Emanuel Castillo, Tasnim Chowdhury, Nikita Gandhi, Sarah Hamilton, Kyla Hatton, Syed Hyder, Koty Krull, Demetrios Lagios, Thinh Lam, Kennedy Mitchell, Christine Mortensen, Amber Murphy, Joseph Richburg, Meghan Rokas, Suzanne Ryclik, Pauline Sulit, Thomas Szwajnos, Manuel Widuch, Jessica Willis, Mary Woloszyn, Bridget Brassil, Genevieve Johnson, Rita Mormando, Laura Maskeri, Mary Batrich, Nicole Stark, Jason W. Shapiro, Cesar Montelongo Hernandez, Swarnali Banerjee, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Aeromonas caviae UFMG-H8, Isolated from Urine from a Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, and Catherine Putonti
Draft Genome Sequence of Citrobacter freundii UFMG-H9, Isolated from Urine from a Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, and Catherine Putonti
Draft Genome Sequences of Three Enterococcus casseliflavus Strains Isolated from the Urine of Healthy Bovine Heifers (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, and Catherine Putonti
Three Draft Genome Sequences of Staphylococcus Species Isolated from the Urine of Healthy Bovine Heifers (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, and Catherine Putonti
Draft Genome Sequence of Enterobacter asburiae UFMG-H9, Isolated from Urine from a Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Klebsiella pneumoniae UMB8492, Isolated from the Female Urinary Tract, Suma Gondi, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Aerococcus urinae Isolated from Women with Lower Urinary Tract Symptoms: In Vitro Aggregation and Genome Analysis, Evann E. Hilt, Catherine Putonti, Krystal Thomas-White, Amanda L. Lewis, Karen L. Visick, Nicole M. Gilbert, and Alan J. Wolfe
Draft Genome Sequences of Two Pseudomonas aeruginosa Isolates from the Female Urogenital Tract, Genevieve Johnson, Carine R. Mores, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Enterococcus faecalis UMB7780, Isolated from the Female Urinary Tract, Martin Kalski, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Staphylococcus epidermidis UMB7765, Isolated from the Urobiome of a Woman with Recurrent Urinary Tract Infection, Lucy Kemper, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Lactobacillus crispatus UMB1163, Isolated from the Female Urinary Tract, Fabeiha Khan, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Effects of Pharmaceutical Contamination on Sedment Microbial Communities in Streams, Benjamin Joseph Lorentz
Draft Genome Sequence of Actinomyces neuii UMB1295, Isolated from the Female Urinary Tract, Tijana Markovic, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Mimicking prophage induction in the body: induction in the lab with pH gradients, Taylor Miller-Ensminger, Andrea Garretto, Nicole Stark, and Catherine Putonti
Introducing Lu-1, a Novel Lactobacillus jensenii Phage Abundant in the Urogenital Tract, Taylor Miller-Ensminger, Rita Mormando, Laura Maskeri, Jason W. Shapiro, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Lactobacillus jensenii Strain UMB7766, Isolated from the Female Bladder, Taylor Miller-Ensminger, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Streptococcus anginosus UMB7768, Isolated from a Woman with Recurrent UTI Symptoms, Sarah Miller, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Complete Genome Sequences of Streptococcus mitis Strains Isolated from the Oral Cavity and Urogenital Tract of a Woman and Her Male Sexual Partner, Carine R. Mores, Travis K. Price, Bridget Brassil, Catherine Putonti, and Alan J. Wolfe
Optimizing Gene Expression Prediction and Omics Integration in Populations of African Ancestry, Paul Chukwuebuka Okoro
Draft Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract, Natalia Purta, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Comparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality, Catherine Putonti, Jason W. Shapiro, Adriana Ene, Oleksandra Tsibere, and Alan J. Wolfe
Draft Genome Sequence of Lactobacillus mulieris UMB9245, Isolated from the Female Bladder, Lidia Ramotowski, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Lactobacillus jensenii UMB0836, Isolated from the Female Bladder, Isaac Rivera, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Enterococcus faecalis UMB1309, Isolated from Catheterized Urine, Adam Schwartz, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Streptococcus anginosus UMB0839, Isolated from the Female Urinary Tract, Thomas Scott, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
UPΦ phages, a new group of filamentous phages found in several members of Enterobacteriales, Jason Shapiro and Catherine Putonti
Draft Genome Sequence of Streptococcus anginosus UMB1296, Isolated from the Female Urinary Tract, Sara Temelkova, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Staphylococcus epidermidis UMB8493, Isolated from the Female Urinary Tract, Anthony Truckenbrod, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Staphylococcus epidermidis UMB8493, Isolated from the Female Urinary Tract, Anthony Truckenbrod, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Lactobacillus mulieris UMB7784, Isolated from the Female Urinary Tract, Oleksandra Tsibere, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Draft Genome Sequence of Lactobacillus jensenii UMB0847, Isolated from the Female Urinary Tract, Ella West-Pelak, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, and Catherine Putonti
Submissions from 2019
Pseudomonas Diversity Within Urban Freshwaters, Mary Batrich, Laura Maskeri, Ryan Schubert, Brian Ho, Melanie Kohout, Malik Abdeljaber, Ahmed Abuhasna, Mutah Kholoki, Penelope Psihogios, Tahir Razzaq, Samrita Sawhney, Salah Siddiqui, Eyad Xoubi, Alexandria Cooper, Thomas Hatzopoulos, and Catherine Putonti
Bacteriophages of the Lower Urinary Tract, Andrea Garretto, Taylor Miller-Ensminger, Alan J. Wolfe, and Catherine Putonti
Characterization of the φCTX-like Pseudomonas aeruginosa Phage Dobby Isolated from the Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, and Catherine Putonti
Characterization of the φCTX-like Pseudomonas aeruginosa phage Dobby Isolated from the Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, and Catherine Putonti
virMine: Automated Detection of Viral Sequences from Complex Metagenomic Samples, Catherine Putonti, Andrea Garretto, and Thomas Hatzopoulos
Genome Sequence of Pseudomonas Phage UMP151, Isolated from the Female Bladder Microbiota, Catherine Putonti and Genevieve Johnson
Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp. Strain 429, Catherine Putonti, Michael Zilliox, and Paul Schreckenberger
Submissions from 2018
Gene-Based Association Study for Lipid Traits in Diverse Cohorts Implicates BACE1 and SIDT2 Regulation in Triglyceride Levels, Angela Andaleon, Lauren S. Mogil, and Heather Wheeler
Draft Genome Sequence of the Siderophore-Degrading Soil Bacterium Mesorhizobium loti Strain LU, Domenic Castignetti, Nathaniel Polley, and Catherine Putonti
Detecting Viral Genomes in the Female Urinary Microbiome, Andrea Garretto, Krystal Thomas-White, Alan J. Wolfe, and Catherine Putonti
S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences, Laurynas Kalensinskas, Evan Cudone, Yuriy Fofanov, and Catherine Putonti
S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences, Laurynas Kalesinskas, Evan Cudone, Yuriy Fofanov, and Catherine Putonti
Characterization of a Protozoan Phosducin-like Protein-3 (PhLP-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W. Olsen, Catherine Putonti, and Stefan M. Kanzok
Characterization of a protozoan Phosducin-like protein-3 (PhLP-3) reveals conserved redox activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ken W. Olsen, Catherine Putonti, and Stefan M. Kanzok
Characterization of a Protozoan Phosducin-like Protein-3 (PhLP-3) Reveals Conserved Redox Activity, Rachel L. Kooistra; Robin David; Ana C. Ruiz; Sean W. Powers; Kyle J. Haselton; Kaitlyn Kiernan; Andrew M. Blagborough; Ligin Solamen; Kenneth W, Olsen; Catherine Putonti; and Stefan M. Kanzok
The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host, Alexander Kula, Joseph Saelens, Alyxandria M. Schubert, Michael Travisano, and Catherine Putonti
Bacteriophages of the Urinary Microbiome, Taylor Miller-Ensminger, Andrea Garretto, Jonathon Brenner, Krystal Thomas-White, Adriano Zambom, Alan J. Wolfe, and Catherine Putonti
Genetic Architecture of Gene Expression Traits Across Diverse Populations, Lauren S. Mogil, Angela Andaleon, Alexa Badalamenti, Scott P. Dickinson, Xiuqing Guo, Jerome I. Rotter, W. C. Johnson, Hae Kyung Im, Yongmei Liu, and Heather E. Wheeler
Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1, Catherine Putonti, Nathaniel Polley, and Domenic Castignetti
Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1, Catherine Putonti, Nathaniel Polley, and Domenic Castignetti
Minimum Information about an Uncultivated Virus Genome (MIUViG), Simon Roux, Evelien M. Adriaenssens, Bas E. Dutilh, Eugene V. Koonin, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, Rob Lavigne, J Rodney Brister, Arvind Varsani, Clara Amid, Ramy K. Aziz, Seth R. Bordenstein, Peer Bork, Mya Breitbart, Guy R. Cochrane, Rebecca A. Daly, Christelle Desnues, Melissa B. Duhaime, Joanne B. Emerson, François Enault, Jed A. Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L. Hurwitz, Natalie N. Ivanova, Jessica M. Labonté, Kyung-Bum Lee, Rex R. Malmstrom, Manuel Martinez-Garcia, Ilene Karsch Mizrachi, Hiroyuki Ogata, David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F. Steward, Matthew B. Sullivan, Shinichi Sunagawa, Curtis A. Suttle, Ben Temperton, Susannah G. Tringe, Rebecca Vega Thurber, Nicole S. Webster, Katrine L. Whiteson, Steven W. Whilhelm, K Eric Wommack, Tanja Woyke, Kelly C. Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J. Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C. Kyrpides, and Emiley A. Eloe-Fadrosh
Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution, Jason W. Shapiro and Catherine Putonti
Culturing of Female Bladder Bacteria Reveals an Interconnected Urogenital Microbiota, Krystal Thomas-White, Samuel C. Forster, Nitin Kumar, Michelle Van Kuiken, Catherine Putonti, Mark D. Stares, Evann E. Hilt, Travis K. Price, Alan J. Wolfe, and Trevor D. Lawley
Culturing of Female Bladder Bacteria Reveals an Interconnected Urogenital Microbiota, Krystal Thomas-White, Samuel C. Forster, Nitin Kumar, Michelle Van Kuiken, Catherine Putonti, Mark D. Stares, Evann E. Hilt, Travis K. Price, Alan J. Wolfe, and Trevor D. Lawley
Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages, Siobhan C. Watkins, Emily Sible, and Catherine Putonti
Submissions from 2017
Genetic Variants Contributing to Colistin Cytotoxicity: Identification of TGIF1 and HOXD10 Using a Population Genomics Approach, Michael T. Eadon, Ronald J. Hause, Amy L. Stark, Ying-Hua Cheng, Heather E. Wheeler, Kimberly S. Burgess, Eric A. Benson, Patrick N. Cunningham, Robert L. Bacallao, Pierre C. Dagher, Todd C. Skaar, and M. Eileen Dolan
Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698), Catherine Putonti, Evan Cudone, Laurynas Kalesinskas, Kathleen C. Engelbrecht, David W. Koenig, and Alan J. Wolfe
Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798), Catherine Putonti, Daniela Dimitrova, Kathleen C. Engelbrecht, David W. Koenig, and Alan J. Wolfe
Draft Genome Sequence of Escherichia coli K-12 (ATCC 29425), Catherine Putonti, Kathleen C. Engelbrecht, David W. Koenig, and Alan J. Wolfe
Draft Genome Sequence of Enterococcus faecalis ATCC BAA-2128, Catherine Putonti, Laurynas Kalesinskas, Evan Cudone, Kathleen C. Engelbrecht, David W. Koenig, and Alan J. Wolfe
Draft Genome Sequences of Two ATCC Staphylococcus aureus subsp. aureus Strains, Catherine Putonti, Laurynas Kalesinskas, Evan Cudone, Kathleen C. Engelbrecht, David W. Koenig, and Alan J. Wolfe
Draft Genome Sequence of Staphylococcus epidermidis (Winslow and Winslow) Evans (ATCC 14990), Catherine Putonti, Laurynas Kalesinskas, Evan Cudone, Alan J. Wolfe, Kathleen C. Engelbrecht, and David W. Koenig
The Role of Phage tRNAs in the Evolution of Codon Usage Biases in Giant Pseudomonas Phage phiKZ and EL, Stephanie Steidel
The Use of Informativity in the Development of Robust Viromics-based Examinations, Siobhan C. Watkins and Catherine Putonti
Clinical and Genome-Wide Analysis of Cisplatin-Induced Peripheral Neuropathy in Survivors of Adult-Onset Cancer, Heather E. Wheeler
Application of Stem Cell Derived Neuronal Cells to Evaluate Neurotoxic Chemotherapy, Claudia Wing, Masaaki Komatsu, Shannon M. Delaney, Matthew Krause, Heather E. Wheeler, and M. Eileen Dolan
Submissions from 2016
Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges, Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins, and Catherine Putonti
Comprehensive Audiometric Analysis of Hearing Impairment and Tinnitus After Cisplatin-Based Chemotherapy in Survivors of Adult-Onset Cancer., Robert D. Frisina, Heather E. Wheeler, Sophie D. Fossa, Sarah L. Kerns, Chunkit Fung, Howard D. Sesso, Patrick O. Monahan, Darren R. Feldman, Robert Hamilton, David J. Vaughn, Clair J. Beard, Amy Budnick, Eileen M. Johnson, Shirin Ardeshir-Rouhani-Fard, Lawrence H. Einhorn, Steven E. Lipshultz, M. Eileen Dolan, and Lois B. Travis
PhagePhisher: a Pipeline for the Discovery of Covert Viral Sequences in Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, and Catherine Putonti
