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The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

SEA-PHAGES Publications

Below is a list of publications that are based on data generated by participants in the SEA-PHAGES program and are authored by SEA-PHAGES students or faculty.

Excluding genome announcements from the list. Use the links above the table to change this.

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Journal

Title

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Undergrad Authors

Related Clusters or Subclusters
Hanauer et aliaDavid Hanauer, Tong Zhang, Mark Graham, Sandra Adams, Yesmi Patricia Ahumada-Santos, Richard Alvey, Mauricio Antunes, Mary Ayuk, María Elena Báez-Flores, Christa Bancroft, Tonya Bates, Meghan Bechman, Elizabeth Behr, Andrea Beyer, Rebecca Bortz, Dane Bowder, Laura Briggs, Victoria Brown-Kennerly, Michael Buckholt, Sharon Bullock, Kristen Butela, Christine Byrum, Steven Caruso, Catherine Chia, Rebecca Chong, Hui-Min Chung, Kari Clase, Sean Coleman, D. Parks Collins, Stephanie Conant, Brett Condon, Pamela Connerly, Bernadette Connors, Jennifer Cook-Easterwood, Katie Crump, Tom D'Elia, Megan Dennis, Linda DeVeaux, Lautaro Diacovich, Iain Duffy, Nicholas Edgington, Dustin Edwards, Tenny Egwuatu, Elvira Eivazova, Patricia Fallest-Strobl, Christy Fillman, Ann Findley, Emily Fisher, Matthew Fisher, Marie Fogarty, Amanda Freise, Victoria Frost, Maria Gainey, Amaya Garcia Costas, Atenea Garza, Hannah Gavin, Raffaella Ghittoni, Bryan Gibb, Urszula Golebiewska, Anna Grinath, Susan Gurney, Rebekah Hare, Steven Heninger, John Hinz, Lee Hughes, Pradeepa Jayachandran, Kristen Johnson, Allison Johnson, Michelle Kanther , Margaret Kenna, Bridgette Kirkpatrick, Karen Klyczek, Kathryn Kohl, Michael Kuchka, Amber LaPeruta , Julia Lee-Soety, Lynn Lewis, Heather Lindberg, Jaclyn Madden, Sergei Markov, Matthew Mastropaolo, Vinayak Mathur, Sean McClory, Evan Merkhofer, Julie Merkle, Scott Michael, Jon Mitchell, Sally Molloy, Denise Monti, María Alejandra Mussi, Holly Nance, Fernando Nieto-Fernandez, Jillian Nissen, Imade Nsa, Mary O'Donnell, Shallee Page, Andrea Panagakis, Jesús Ricardo Parra-Unda, Tara Pelletier, Tiara Perez Morales, Nick Peters, Vipaporn Phuntumart , Richard Pollenz, Mary Preuss, David Puthoff, Muideen Raifu, Nathan Reyna, Claire Rinehart, Jessica Rocheleau, Ombeline Rossier, Adam Rudner, Elizabeth Rueschhoff, Amy Ryan, Sanghamitra Saha, Christopher Shaffer, Mary Ann Smith, Amy Sprenkle, Christy Strong, C. Nicole Sunnen, Brian Tarbox, Louise Temple, Kara Thoemke, Michael Thomas, Deborah Tobiason, Sara Tolsma, Julie Torruellas Garcia, Megan Valentine, Edwin Vazquez, Robert Ward, Catherine Ward, Vassie Ware, Marcie Warner, Jacqueline Washington , Daniel Westholm, Keith Wheaton, Beth Wilkes, Elizabeth Williams, William Biederman, Steven Cresawn, Danielle Heller, Deborah Jacobs-Sera, Graham Hatfull, David Asai, Viknesh Sivanathan 2023 Frontiers in Education Models of classroom assessment for course-based research experiences No
Amaya et alIsabel Amaya, Kaylia Edwards, Bethany M Wise, Ankita Bhattacharyya, Clint H D Pablo, Ember Mushrush, Amber N Coats, Sara Dao, Grace Dittmar, Taylor Gore, Taiya M Jarva, Giorgi Kenkebashvili, Sudiksha Rathan-Kumar, Gabriella M Reyes, Garrett L Watts, Victoria Kalene Watts, Deena Dubrow, Gabrielle Lewis, Benjamin H Stone, Bingjie Xue, Steven G Cresawn, Dmitri Mavrodi, Viknesh Sivanathan, Danielle Heller 2023 G3 Genes|Genomes|Genetics A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy Howard Hughes Medical Institute
James Madison University
University of Maryland, Baltimore County
University of Southern Mississippi 		No K
K6
deCarvalho et al, 2023Tagide deCarvalho, Elia Mascolo, Steven M. Caruso, Júlia López-Pérez, Kathleen Weston-Hafer, Christopher Shaffer, and Ivan Erill 2023 The ISME Journal Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species University of Maryland, Baltimore County
Washington University in St. Louis 		No
Milhaven et alMark Milhaven, Cyril J. Versoza, Aman Garg, Lindsey Cai, Sanjana Cherian, Kamalei Johnson, Kevin Salas Perez, Madison Blanco, Jackelyn Lobatos, Corinne Mitra, Maria Strasser, Susanne P. Pfeifer 2023 Microorganisms Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions Arizona State University No EA
EA1, EA10, EA2, EA3, EA4, EA5, EA6, EA7, EA8, EA9
Kaylen Little, Yamere Lloyd, Melanie Hwalek, Victoria StraubKaylen Little, Yamere Lloyd, Melanie Hwalek, Victoria Straub, Stephanie B. Conant, Jacob D. Kagey 2022 Undergraduate and Community College Interventions The ReBUILDetroit program and SEA PHAGES increases student attitudes towards research and sense of belonging for both ReBUILDetroit Scholars and non-BUILD students No
Kapinos et alAndrew Kapinos, Pauline Aghamalian, Erika Capehart, Anya Alag, Heather Angel, Eddie Briseno, Byron Corado Perez, Emily Farag, Hilory Foster, Abbas Hakim, Daisy Hernandez-Casas, Calvin Huang, Derek Lam, Maya Mendez, Ashley Min, Nikki Nguyen, Alexa L. Omholt, Emily Ortiz, Lizbeth Shelly Saldivar, Jack Arthur Shannon, Rachel Smith, Mihika V. Sridhar, An Ta, Malavika C. Theophilus, Ryan Ngo, Canela Torres, Krisanavane Reddi, Amanda C. Freise, Jordan Moberg Parker 2022 PLOS ONE Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages 24
Vill et alAlbert C. Vill, Véronique A. Delesalle, Brianne E. Tomko, Katherine B. Lichty, Madison S. Strine, Alexandra A. Guffey, Elizabeth A. Burton, Natalie T. Tanke, and Greg P. Krukonis 2022 PHAGE Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States No
Richard S. Pollenz, Jackson Bland, Welkin H. PopeRichard S. Pollenz, Jackson Bland, Welkin H. Pope 2022 PLOS ONE Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta Chatham University
University of South Florida 		1
Ramsey et alJolene Ramsey, Brenley McIntosh, Daniel Renfro, Suzanne A. Aleksander, Sandra LaBonte, Curtis Ross ,Adrienne E. Zweifel, Nathan Liles, Shabnam Farrar, Jason J. Gill, Ivan Erill, Sarah Ades, Tanya Z. Berardini, Jennifer A. Bennett, Siobhan Brady, Robert Britton, Seth Carbon, Steven M. Caruso, Dave Clements, Ritu Dalia, Meredith Defelice, Erin L. Doyle, Iddo Friedberg, Susan M. R. Gurney, Lee Hughes, Allison Johnson, Jason M. Kowalski, Donghui Li, Ruth C. Lovering, Tamara L. Mans, Fiona McCarthy, Sean D. Moore, Rebecca Murphy, Timothy D. Paustian, Sarah Perdue, Celeste N. Peterson, Birgit M. Prüß, Margaret S. Saha, Robert R. Sheehy, John T. Tansey, Louise Temple, Alexander William Thorman, Saul Trevino, Amy Cheng Vollmer, Virginia Walbot, Joanne Willey, Deborah A. Siegele, James C. Hu 2022 PLOS Computational Biology Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) No
McGinnis et alReliza J. McGinnis, Chad A. Brambley, Brandon Stamey, William C. Green, Kimberly N. Gragg, Erin R. Cafferty, Thomas C. Terwilliger, Michal Hammel, Thomas J. Hollis, Justin M. Miller, Maria D. Gainey & Jamie R. Wallen 2022 nature communications A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence Western Carolina University No A
A2
Versoza et alCyril J Versoza, Abigail A Howell, Tanya Aftab, Madison Blanco, Akarshi Brar, Elaine Chaffee, Nicholas Howell, Willow Leach, Jackelyn Lobatos, Michael Luca, Meghna Maddineni, Ruchira Mirji, Corinne Mitra, Maria Strasser, Saige Munig, Zeel Patel, Minerva So, Makena Sy, Sarah Weiss, Susanne P Pfeifer 2022 Viruses Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages Arizona State University No DR
Heller et alDanielle Heller, Isabel Amaya, Aleem Mohamed, Ilzat Ali, Dmitri Mavrodi, Padraig Deighan, Viknesh Sivanathan 2022 G3 Genes|Genomes|Genetics Systematic overexpression of genes encoded by mycobacteriophage Waterfoul reveals novel inhibitors of mycobacterial growth Howard Hughes Medical Institute
University of Maryland, Baltimore County
University of Southern Mississippi 		No K
K5
Uylae Kim, Elizabeth S Paul, and Arturo DiazUylae Kim, Elizabeth S Paul, and Arturo Diaz 2022 International Journal of Molecular Sciences Characterization of Phages YuuY, KaiHaiDragon, and OneinaGillian Isolated from Microbacterium foliorum La Sierra University 2 EA, EC, EG
EA10
Hanauer et alDavid I. Hanauer, Mark J. Graham, Rachel J. Arnold, Mary A. Ayuk, Mitchell F. Balish, Andrea R. Beyer, Kristen A. Butela, Christine A. Byrum, Catherine P. Chia, Hui-Min Chung, Kari L. Clase, Stephanie Conant, Roy J. Coomans, Tom D’Elia, Jason Diaz, Arturo Diaz, Jean A. Doty, Nicholas P. Edgington, Dustin C. Edwards, Elvira Eivazova, Christine B. Emmons, Kayla M. Fast, Emily J. Fisher, Christine L. Fleischacker, Gregory D. Frederick, Amanda C. Freise, Maria D. Gainey, Chris R. Gissendanner, Urszula P. Golebiewska, Nancy A. Guild, Heather L. Hendrickson, Christopher D. Herren, Margaret S. Hopson-Fernandes Lee E. Hughes, Deborah Jacobs-Sera, Allison A. Johnson, Bridgette L. Kirkpatrick, Karen K. Klyczek, Ann P. Koga, Hari Kotturi, Janine LeBlanc-Straceski, Julia Y. Lee-Soety, Justin E. Leonard, Matthew D. Mastropaolo, Evan C. Merkhofer, Scott F. Michael, Jon C. Mitchell, Swarna Mohan, Denise L. Monti, Christos Noutsos, Imade Y. Nsa, Nick T. Peters, Ruth Plymale, Richard S. Pollenz, Megan L. Porter, Claire A. Rinehart, German Rosas-Acosta, Joseph F. Ross, Michael R. Rubin, Anne E. Scherer, Stephanie C. Schroeder, Christopher D. Shaffer, Amy B. Sprenkle, C. Nicole Sunnen, Sarah J. Swerdlow, Deborah Tobiason, Sara S. Tolsma, Philippos K. Tsourkas, Robert E. Ward, Vassie C. Ware, Marcie H. Warner, Jacqueline M. Washington, Kristi M. Westover, Simon J. White, JoAnn L. Whitefleet-Smith, Daniel C. Williams, Michael J. Wolyniak, Jill H. Zeilstra-Ryalls, David J. Asai, Graham F. Hatfull, and Viknesh Sivanathan 2022 CBE—Life Sciences Education Instructional Models for Course-Based Research Experience (CRE) Teaching No
Demo et alStephanie Demo, Andrew Kapinos, Aaron Bernardino, Kristina Guardino, Blake Hobbs, Kimberly Hoh, Edward Lee, Iphen Vuong, Krisanavane Reddi, Amanda C. Freise, Jordan Moberg Parker 2021 PLOS ONE BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE 8
Koert et alKoert, Matthew; López-Pérez, Júlia; Mattson, Courtney; Caruso, Steven; Erill, Ivan 2021 Peer Community Journal Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages 2
Crane et alAdele Crane, Cyril J Versoza, Tiana Hua, Rohan Kapoor, Lillian Lloyd, Rithik Mehta, Jueliet Menolascino, Abraham Morais, Saige Munig, Zeel Patel, Daniel Sackett, Brandon Schmit, Makena Sy, Susanne P Pfeifer 2021 G3 : Genes | Genomes | Genetics Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages No
Saha et alSurya Saha, Teresa D. Shippy, Susan J. Brown, Joshua B. Benoit, and Tom D’Elia 2021 Journal of Microbiology & Biology Education Undergraduate Virtual Engagement in Community Genome Annotation Provides Flexibility to Overcome Course Disruptions No
Mavrich et alMavrich T, Gauthier C, Abad L, Bowman C, Cresawn S, Hatfull G 2020 Bioinformatics pdm_utils: a SEA-PHAGES MySQL phage database management toolkit No
Jacobs-Sera et alDeborah Jacobs-Sera, Lawrence A. Abad, Richard M. Alvey, Kirk R. Anders, Haley G. Aull, Suparna S. Bhalla, Lawrence S. Blumer, David W. Bollivar, J. Alfred Bonilla, Kristen A. Butela, Roy J. Coomans, Steven G. Cresawn, Tom D'Elia, Arturo Diaz, Ashley M. Divens, Nicholas P. Edgington, Gregory D. Frederick, Maria D. Gainey, Rebecca A. Garlena, Kenneth W. Grant, Susan M. R. Gurney, Heather L. Hendrickson, Lee E. Hughes, Margaret A. Kenna, Karen K. Klyczek, Hari Kotturi, Travis N. Mavrich, Angela L. McKinney, Evan C. Merkhofer, Jordan Moberg Parker, Sally D. Molloy, Denise L. Monti, Dana A. Pape-Zambito, Richard S. Pollenz, Welkin H. Pope, Nathan S. Reyna, Claire A. Rinehart, Daniel A. Russell, Christopher D. Shaffer, Viknesh Sivanathan, Ty H. Stoner, Joseph Stukey, C. Nicole Sunnen, Sara S. Tolsma, Philippos K. Tsourkas, Jamie R. Wallen, Vassie C. Ware, Marcie H. Warner, Jacqueline M. Washington, Kristi M. Westover, JoAnn L. Whitefleet-Smith, Helen I. Wiersma-Koch, Daniel C. Williams, Kira M. Zack, Graham F. Hatfull 2020 PLoS ONE Genomic diversity of bacteriophages infecting Microbacterium spp No
Caruso et al.Steven M. Caruso, Tagide N. deCarvalho, Anthony Huynh, George Morcos, Nansen Kuo, Shabnam Parsa, and Ivan Erill 2019 Viruses A Novel Genus of Actinobacterial Tectiviridae University of Maryland, Baltimore County 4 BO
Etobayeva et alEtobayeva I, Linden SB, Alem F, Harb L, Rizkalla L, Mosier PD, Johnson AA, Temple L, Hakami RM, Nelson DC. 2018 Viruses Discovery and Biochemical Characterization of PlyP56, PlyN74, and PlyTB40-Bacillus Specific Endolysins. No
Arens et alDaniel K. Arens,T. Scott Brady,John L. Carter,Jenny A. Pape,David M. Robinson,Kerri A. Russell,Lyndsay A. Staley,Jason M. Stettler,Olivia B. Tateoka,Michelle H. Townsend,Kiara V. Whitley,Trevor M. Wienclaw,Taryn L. Williamson,Steven M. Johnson,Julianne H. Grose 2018 PLoS One Characterization of two related Erwinia myoviruses that are distant relatives of the PhiKZ-like Jumbo phages No
Laungani R. et alLaungani R 1 , Tanner C 2 , Brooks TD 1 , Clement B 1 , Clouse M 1 , Doyle E 1 , Dworak S 3 , Elder B 1 , Marley K 1 , Schofield B 1 2018 Journal of Microbiology & Biology Education Finding Some Good in an Invasive Species: Introduction and Assessment of a Novel CURE to Improve Experimental Design in Undergraduate Biology Classrooms. No
Russell et alDaniel A Russell Graham F Hatfull 2017 Bioinformatics PhagesDB: the actinobacteriophage database No
Mavrich TN, Hatfull GFMavrich TN, Hatfull GF 2017 Nat Microbiol. Bacteriophage evolution differs by host, lifestyle and genome No
Klyczek KK et al.Klyczek KK, Bonilla JA, Jacobs-Sera D, Adair TL, Afram P, Allen KG, Archambault ML, Aziz RM, Bagnasco FG, Ball SL, Barrett NA, Benjamin RC, Blasi CJ, Borst K, Braun MA, Broomell H, Brown CB, Brynell ZS, Bue AB, Burke SO, Casazza W, Cautela JA, Chen K, Chimalakonda NS, Chudoff D, Connor JA, Cross TS, Curtis KN, Dahlke JA, Deaton BM, Degroote SJ, DeNigris DM, DeRuff KC, Dolan M, Dunbar D, Egan MS, Evans DR, Fahnestock AK, Farooq A, Finn G, Fratus CR, Gaffney BL, Garlena RA, Garrigan KE, Gibbon BC, Goedde MA, Guerrero Bustamante CA, Harrison M, Hartwell MC, Heckman EL, Huang J, Hughes LE, Hyduchak KM, Jacob AE, Kaku M, Karstens AW, Kenna MA, Khetarpal S, King RA, Kobokovich AL, Kolev H, Konde SA, Kriese E, Lamey ME, Lantz CN, Lapin JS, Lawson TO, Lee IY, Lee SM, Lee-Soety JY, Lehmann EM, London SC, Lopez AJ, Lynch KC, Mageeney CM, Martynyuk T, Mathew KJ, Mavrich TN, McDaniel CM, McDonald H, McManus CJ, Medrano J, Mele FE, Menninger JE, Miller SN, Minick JE, Nabua CT, Napoli CK, Nkangabwa M, Oates EA, Ott CT, Pellerino SK, Pinamont WJ, Pirnie RT, Pizzorno MC, Plautz EJ, Pope WH, Pruett KM, Rickstrew G, Rimple PA, Rinehart CA, Robinson KM, Rose VA, Russell DA, Schick AM, Schlossman J, Schneider VM, Sells CA, Sieker JW, Silva MP, Silvi MM, Simon SE, Staples AK, Steed IL, Stowe EL, Stueven NA, Swartz PT, Sweet EA, Sweetman AT, Tender C, Terry K, Thomas C, Thomas DS, Thompson AR, Vanderveen L, Varma R, Vaught HL, Vo QD, Vonberg ZT, Ware VC, Warrad YM, Wathen KE, Weinstein JL, Wyper JF3, Yankauskas JR, Zhang C, Hatfull GF 2017 PLoS One. Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages. 4
Pope et al.Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, Russell DA, Warner MH; Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES), Hatfull GF 2017 MBio. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships No
Hanauer et al.Hanauer DI, Graham MJ; SEA-PHAGES, Betancur L, Bobrownicki A, Cresawn SG, Garlena RA, Jacobs-Sera D, Kaufmann N, Pope WH, Russell DA, Jacobs WR Jr, Sivanathan V, Asai DJ, Hatfull GF. 2017 Proc Natl Acad Sci U S A. An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning. No
Dedrick et al.Dedrick, R. M., Jacobs-Sera, D., Guerrero Bustamante, C. A., Garlena, R. A., Mavrich, T. N., Pope, W. H. , Reyes, J. C., Russell, D. A., Adair, T., Alvey, R., Bonilla, J. A., Bricker, J. S., Brown, B. R., Byrnes, D., Cresawn, S. G., Davis, W. B., Dickson, L. A., Edgington, N. P., Findley, A. M., Golebiewska, U., Grose, J. H., Hayes, C. F., Hughes, L. E., Hutchison, K. W., Isern, S., Johnson, A. A., Kenna, M. A., Klyczek, K. K, Mageeney, C. M., Michael, S. F., Molloy, S. D., Montgomery, M. T., Neitzel, J., Page, S. T., Pizzorno, M. C., Poxleitner, M. K., Rinehart, C. A., Robinson, C. J., Rubin, M. R., Teyim, J. N., Vazquez, E., Ware, V. C., Washington, J., and Hatfull, G. F. 2017 Nature Microbiology Prophage-mediated defence against viral attack and viral counter-defence. No
Berg JA et al.Berg JA, Merrill BD, Crockett JT, Esplin KP, Evans MR, Heaton KE, Hilton JA, Hyde JR, McBride MS, Schouten JT, Simister AR, Thurgood TL, Ward AT, Breakwell DP, Hope S, Grose JH. 2016 PLoS One. Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages. No
Dedrick et al.Dedrick RM, Mavrich TN, Ng WL, Cervantes Reyes JC, Olm MR, Rush RE, Jacobs-Sera D, Russell DA, Hatfull GF. 2016 Mol Microbiol. Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems. 3
Bradshaw JC, Gongola AB, Reyna NS.Bradshaw JC, Gongola AB, Reyna NS. 2016 J Vis Exp. Rapid Verification of Terminators Using the pGR-Blue Plasmid and Golden Gate Assembly. No
Staub NL et alStaub NL, Poxleitner M, Braley A, Smith-Flores H, Pribbenow CM, Jaworski L, Lopatto D, Anders KR. 2016 CBE—Life Sciences Education Scaling Up: Adapting a Phage-Hunting Course to Increase Participation of First-Year Students in Research. No
Delesalle VA, Tanke NT, Vill AC, Krukonis GP.Delesalle VA, Tanke NT, Vill AC, Krukonis GP. 2016 Bacteriophage. Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes. No
Kelley DS, Lennon CW; SEA-PHAGES, Belfort M, Novikova O.Kelley DS, Lennon CW; SEA-PHAGES, Belfort M, Novikova O. 2016 MBio. Mycobacteriophages as Incubators for Intein Dissemination and Evolution. No
Hanauer DI, Graham MJ, Hatfull GF.Hanauer DI, Graham MJ, Hatfull GF. 2016 CBE—Life Sciences Education A Measure of College Student Persistence in the Sciences (PITS). No
Merrill BD, Ward AT1, Grose JH, Hope S.Merrill BD, Ward AT1, Grose JH, Hope S. 2016 BMC Genomics. Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies No
Sauder et alSauder A.B., Quinn M.R., Brouillette A., Caruso S., Cresawn S., Erill I., Lewis L., Loesser-Casey K., Pate M., Scott C., Stockwell S., Temple L. 2016 Virology Genomic characterization and comparison of seven Myoviridae bacteriophage infecting Bacillus thuringiensis Yes
Hanauer DI, Hatfull G.Hanauer DI, Hatfull G. 2015 CBE—Life Sciences Education Measuring Networking as an Outcome Variable in Undergraduate Research Experiences. No
Siranosian B. et al.Siranosian B, Perera S, Williams E, Ye C, de Graffenried C, Shank P. 2015 F1000Res. Tetranucleotide usage highlights genomic heterogeneity among mycobacteriophages. No
Cross T et al.Cross T, Schoff C, Chudoff D, Graves L, Broomell H, Terry K, Farina J, Correa A, Shade D, Dunbar D. 2015 J Vis Exp. An optimized enrichment technique for the isolation of Arthrobacter bacteriophage species from soil sample isolates. No
Halleran et al.Halleran A, Clamons S, Saha M 2015 PLos One Transcriptomic Characterization of an Infection of Mycobacterium smegmatis by the Cluster A4 Mycobacteriophage Kampy. No
Pope, Bowman, Russell, et alPope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science; Phage Hunters Integrating Research and Education; Mycobacterial Genetics Course 2015 eLIFE Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity Yes
Cresawn SG, Pope WH, Jacobs-Sera D, Bowman CA, et alCresawn SG, Pope WH, Jacobs-Sera D, Bowman CA, Russell DA, Dedrick RM, Adair T, Anders KR, Ball S, Bollivar D, Breitenberger C, Burnett SH, Butela K, Byrnes D, Carzo S, Cornely KA, Cross T, Daniels RL, Dunbar D, Findley AM, Gissendanner CR, Golebiewska UP, Hartzog GA, Hatherill JR, Hughes LE, Jalloh CS, De Los Santos C, Ekanem K, Khambule SL, King RA, King-Smith C, Klyczek K, Krukonis GP, Laing C, Lapin JS, Lopez AJ, Mkhwanazi SM, Molloy SD, Moran D, Munsamy V, Pacey E, Plymale R, Poxleitner M, Reyna N, Schildbach JF, Stukey J, Taylor SE, Ware VC, Wellmann AL, Westholm D, Wodarski D, Zajko M, Zikalala TS, Hendrix RW, Hatfull GF 2015 PLoS One Comparative genomics of Cluster O mycobacteriophages Yes
Grose JH, et alGrose JH, Jensen GL, Burnett SH, Breakwell DP 2014 BMC Genomics Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity No
Merrill BD et alMerrill BD, Grose JH, Breakwell DP, Burnett SH 2014 BMC Genomics Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages No
Grose JH, et alGrose JH, Belnap DM, Jensen JD, Mathis AD, Prince JT, Merrill BD, Burnett SH, Breakwell DP 2014 Journal of Virology The genomes, proteomes, and structures of three novel phages that infect the Bacillus cereus group and carry putative virulence factors No
Gissendanner CR et alGissendanner CR, Wiedemeier AM, Wiedemeier PD, Minton RL, Bhuiyan S, Harmson JS, Findley AM 2014 Journal of Basic Microbiology A web-based restriction endonuclease tool for mycobacteriophage cluster prediction No
Jordan TC et alJordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, Dennehy JJ, Denver DR, Dunbar D, Elgin SC, Findley AM, Gissendanner CR, Golebiewska UP, Guild N, Hartzog GA, Grillo WH, Hollowell GP, Hughes LE, Johnson A, King RA, Lewis LO, Li W, Rosenzweig F, Rubin MR, Saha MS, Sandoz J, Shaffer CD, Taylor B, Temple L, Vazquez E, Ware VC, Barker LP, Bradley KW, Jacobs-Sera D, Pope WH, Russell DA, Cresawn SG, Lopatto D, Bailey CP, Hatfull GF. 2014 mBio A broadly implementable research course in phage discovery and genomics for first-year undergraduate students No
Pope WH et alPope WH, Anders KR, Baird M, Bowman CA, Boyle MM, Broussard GW, Chow T, Clase KL, Cooper S, Cornely KA, DeJong RJ, Delesalle VA, Deng L, Dunbar D, Edgington NP, Ferreira CM, Weston Hafer K, Hartzog GA, Hatherill JR, Hughes LE, Ipapo K, Krukonis GP, Meier CG, Monti DL, Olm MR, Page ST, Peebles CL, Rinehart CA, Rubin MR, Russell DA, Sanders ER, Schoer M, Shaffer CD, Wherley J, Vazquez E, Yuan H, Zhang D, Cresawn SG, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2014 Journal of Virology Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repetoires of tRNA isotypes Yes
Lorenz L, et alLorenz L, Lins B, Barrett J, Montgomery A, Trapani S, Schindler A, Christie GE, Cresawn SG, Temple L 2013 Virology Genomic characterization of six novel Bacillus pumilus bacteriophages Yes
Smith KC et alSmith KC, Castro-Nallar E, Fisher JN, Breakwell DP, Grose JH, Burnett SH. 2013 BMC Genomics Phage cluster relationships identified through single gene analysis No
Pope, WH et alPope WH, Jacobs-Sera D, Best AA, Broussard GW, Connerly PL, Dedrick RM, Kremer TA, Offner S, Ogiefo AH, Pizzorno MC, Rockenbach K, Russell DA, Stowe EL, Stukey J, Thibault SA, Conway JF, Hendrix RW, Hatfull GF. 2013 PLoS One Cluster J mycobacteriophages:intron splicing in capsid and tail genes Yes
Dunbar et alDunbar, David & Harrison, Melinda & Mageeney, Catherine & Catagnus, Christopher & Cimo, Amy & Beckowski, Catherine & Ratmansky, Linda 2012 Perspectives on Undergraduate Research and Mentoring The Rewards and Challenges of Undergraduate Peer Mentoring in Course-based Research: Student Perspectives from a Liberal Arts Institution. No
Hatfull et alHatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Program; KwaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course Students; Phage Hunters Integrating Research and Education Program 2012 Journal of Virology Complete genome sequences of 138 mycobacteriophages Yes
Jacobs-Sera, D., et alJacobs-Sera D, Marinelli LJ, Bowman C, Broussard GW, Guerrero Bustamante C, Boyle MM, Petrova ZO, Dedrick RM, Pope WH; Science Education Alliance Phage Hunters Advancing Genomics And Evolutionary Science Sea-Phages Program, Modlin RL, Hendrix RW, Hatfull GF. 2012 Virology On the nature of mycobacteriophage diversity and host preference Yes
Mageeney C, et al.Mageeney C, Pope WH, Harrison M, Moran D, Cross T, Jacobs-Sera D, Hendrix RW, Dunbar D, Hatfull GF. 2012 Journal of Virology Mycobacteriophage Marvin: a new singleton phage with an unusual genome organization. Yes
Harrison, Dunbar, Ratmansky, et alHarrison M, Dunbar D, Ratmansky L, Boyd K, Lopatto D 2011 CBE—Life Sciences Education Classroom-based science research at the introductory level: changes in career choices and attitude No
Cresawn SG, et al.Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfu 2011 BMC Bioinformatics Phamerator: a bioinformatic tool for comparative bacteriophage genomics. No
Pope WH, Ferreira CM, Jacobs-Sera D, et alPope WH, Ferreira CM, Jacobs-Sera D, Benjamin RC, Davis AJ, DeJong RJ, Elgin SC, Guilfoile FR, Forsyth MH, Harris AD, Harvey SE, Hughes LE, Hynes PM, Jackson AS, Jalal MD, MacMurray EA, Manley CM, McDonough MJ, Mosier JL, Osterbann LJ, Rabinowitz HS, Rhyan CN, Russell DA, Saha MS, Shaffer CD, Simon SE, Sims EF, Tovar IG, Weisser EG, Wertz JT, Weston-Hafer KA, Williamson KE, Zhang B, Cresawn SG, Jain P, Piuri M, Jacobs WR Jr, Hendrix RW, Hatfull GF. 2011 PLoS One Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4 Yes
Pope WH et alPope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, Alcoser TA, Alexander LM, Alfano MB, Alford ST, Amy NE, Anderson MD, Anderson AG, Ang AA, Ares M Jr, Barber AJ, Barker LP, Barrett JM, Barshop WD, Bauerle CM, Bayles IM, Belfield KL, Best AA, Borjon A Jr, Bowman CA, Boyer CA, Bradley KW, Bradley VA, Broadway LN, Budwal K, Busby KN, Campbell IW, Campbell AM, Carey A, Caruso SM, Chew RD, Cockburn CL, Cohen LB, Corajod JM, Cresawn SG, Davis KR, Deng L, Denver DR, Dixon BR, Ekram S, Elgin SC, Engelsen AE, English BE, Erb ML, Estrada C, Filliger LZ, Findley AM, Forbes L, Forsyth MH, Fox TM, Fritz MJ, Garcia R, George ZD, Georges AE, Gissendanner CR, Goff S, Goldstein R, Gordon KC, Green RD, Guerra SL, Guiney-Olsen KR, Guiza BG, Haghighat L, Hagopian GV, Harmon CJ, Harmson JS, Hartzog GA, Harvey SE, He S, He KJ, Healy KE, Higinbotham ER, Hildebrandt EN, Ho JH, Hogan GM, Hohenstein VG, Holz NA, Huang VJ, Hufford EL, Hynes PM, Jackson AS, Jansen EC, Jarvik J, Jasinto PG, Jordan TC, Kasza T, Katelyn MA, Kelsey JS, Kerrigan LA, Khaw D, Kim J, Knutter JZ, Ko CC, Larkin GV, Laroche JR, Latif A, Leuba KD, Leuba SI, Lewis LO, Loesser-Casey KE, Long CA, Lopez AJ, Lowery N, Lu TQ, Mac V, Masters IR, McCloud JJ, McDonough MJ, Medenbach AJ, Menon A, Miller R, Morgan BK, Ng PC, Nguyen E, Nguyen KT, Nguyen ET, Nicholson KM, Parnell LA, Peirce CE, Perz AM, Peterson LJ, Pferdehirt RE, Philip SV, Pogliano K, Pogliano J, Polley T, Puopolo EJ, Rabinowitz HS, Resiss MJ, Rhyan CN, Robinson YM, Rodriguez LL, Rose AC, Rubin JD, Ruby JA, Saha MS, Sandoz JW, Savitskaya J, Schipper DJ, Schnitzler CE, Schott AR, Segal JB, Shaffer CD, Sheldon KE, Shepard EM, Shepardson JW, Shroff MK, Simmons JM, Simms EF, Simpson BM, Sinclair KM, Sjoholm RL, Slette IJ, Spaulding BC, Straub CL, Stukey J, Sughrue T, Tang TY, Tatyana LM, Taylor SB, Taylor BJ, Temple LM, Thompson JV, Tokarz MP, Trapani SE, Troum AP, Tsay J, Tubbs AT, Walton JM, Wang DH, Wang H, Warner JR, Weisser EG, Wendler SC, Weston-Hafer KA, Whelan HM, Williamson KE, Willis AN, Wirtshafter HS, Wong TW, Wu P, Yang Y, Yee BC, Zaidins DA, Zhang B, Zúniga MY, Hendrix RW, Hatfull GF. 2011 PLoSOne Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution Yes
Hatfull et al.Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, Hoyte NN, Bowman CA, Tantoco AT, Paladin EC, Myers MS, Smith AL, Grace MS, Pham TT, O'Brien MB, Vogelsberger AM, Hryckowian AJ, Wynalek JL, Donis-Keller H, Bogel MW, Peebles CL, Cresawn SG, Hendrix RW. 2010 J Mol Biol. Comparative genomic analysis of sixty mycobacteriophage genomes: Genome clustering, gene acquisition and gene size No
Temple L, Cresawn SG, Monroe JD.Temple L, Cresawn SG, Monroe JD. 2010 Biochemistry and Molecular Biology Education Genomics and bioinformatics in undergraduate curricula: Contexts for hybrid laboratory/lecture courses for entering and advanced science students No
Caruso SM1, Sandoz J, Kelsey J.Caruso SM, Sandoz J, Kelsey J. 2009 CBE—Life Sciences Education Non-STEM undergraduates become enthusiastic phage-hunters No
Sampson T et alTimothy Sampson, Gregory W Broussard, Laura J Marinelli, Deborah Jacobs-Sera, Mondira Ray, Ching-Chung Ko, Daniel Russell, Roger W Hendrix, Graham F Hatfull 2009 Microbiology (Reading, England) Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements. No
Morris P et alPeter Morris, Laura J Marinelli, Deborah Jacobs-Sera, Roger W Hendrix, Graham F Hatfull 2008 Journal of bacteriology Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination. No
Pham TT et alThuy T Pham, Deborah Jacobs-Sera, Marisa L Pedulla, Roger W Hendrix, Graham F Hatfull 2007 Microbiology (Reading, England) Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria. No
Hanauer DI, et al.Hanauer DI, Jacobs-Sera D, Pedulla ML, Cresawn SG, Hendrix RW, Hatfull GF. 2006 Science Inquiry learning. Teaching scientific inquiry. No
Hatfull GF et alGraham F Hatfull, Marisa L Pedulla, Deborah Jacobs-Sera, Pauline M Cichon, Amy Foley, Michael E Ford, Rebecca M Gonda, Jennifer M Houtz, Andrew J Hryckowian, Vanessa A Kelchner, Swathi Namburi, Kostandin V Pajcini, Mark G Popovich, Donald T Schleicher, Brian Z Simanek, Alexis L Smith, Gina M Zdanowicz, Vanaja Kumar, Craig L Peebles, William R Jacobs, Jeffrey G Lawrence, Roger W Hendrix 2006 PLoS genetics Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. No
Pedulla ML et alMarisa L Pedulla, Michael E Ford, Jennifer M Houtz, Tharun Karthikeyan, Curtis Wadsworth, John A Lewis, Debbie Jacobs-Sera, Jacob Falbo, Joseph Gross, Nicholas R Pannunzio, William Brucker, Vanaja Kumar, Jayasankar Kandasamy, Lauren Keenan, Svetsoslav Bardarov, Jordan Kriakov, Jeffrey G Lawrence, William R Jacobs, Roger W Hendrix, Graham F Hatfull 2003 Cell Origins of highly mosaic mycobacteriophage genomes. No
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