Graham Hatfull

Eberly Family Professor of Biotechnology, HHMI Professor

Phages and tuberculosis

Graham Hatfull
Office: (412) 624-6975
Lab: (412) 624-6976
376 Crawford Hall
4249 Fifth Avenue
Pittsburgh, PA 15260

Dr. Hatfull received his Ph.D. in 1981 with Willie Donachie at the University of Edinburgh, Scotland, performed postdoctoral studies with Nigel Grindley at Yale University and with Fred Sanger at the MRC, and joined the Department in 1988.

Mycobacterium tuberculosis kills more people than any other single infectious agent. Since antibiotics are available and the BCG vaccine is in widespread use, why do two million people die each year from TB? The answer, in part, is that we really don't understand this curious bacterium or what parts of its genetic instructions make this such a deadly pathogen. At the heart of our strategies to understand mycobacterial genetics is the mycobacteriophages - viruses that infect the mycobacteria. These are easy to grow and manipulate and offer advantages over working with the slow-growing mycobacteria (such as M. tuberculosis) that can take up to a month to produce a colony on an agar plate. Phages are also rich sources of  potential genetic and molecular tools that can be used to study - and to modify - their bacterial hosts.Corndog: Mycobacteriophage CorndogCorndog: Mycobacteriophage Corndog

Here's just a flavor of some of the current studies going on in the lab:

Exploring bacteriophage genomics. In collaboration with Dr. Hendrix we have spearheaded an initiative to understand viral diversity and evolution. Our specific focus is on the genomic characterization of mycobactriophages, and a collection of about 250 complete genome sequences have been determined. Many of these phages were isolated and sequenced through three programs in which phage discovery and genomics is a platform for integrating our science and educational missions. These are the Pittsburgh Phage Hunters Integrating Research and Education (PHIRE) program, the Howard Hughes Medical Institute Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEA-PHAGES) program, and a Univiersity of KwaZulu-Natal and KwaZulu-Nalat Research in TB and HIV (UKZN/K-RITH) workshop.  These studies have not only provided valuable insights into phage diveristy and evolution, but present a rich and easily-accessible reservoir of genetic and mechanistic novelty for further study. A database of mycobaectriophage genomic infomration is available at

Exploiting mycobacteriophages. We are dissecting the mycobacteriophages to understand the functional roles of the thousands of genes we have identified, and to deternine if and when they are expressed, and how this expression is regulated.  We are exploiting this information to develop tools and approaches that not only generate new tools for genetic manipulation for tuberculosis, but also to gain advances in diagnosis, prevention and treatment of the disease.

Site-specific recombination. Many if not most of the mycobacteriophages we have sequenced integrate their DNA into the host chromosome (and can excise them too). We are studying the mechanism of integrase-mediated site-specific recombination with a primary current focus on the serine-integrases.  We are partiualrly interested in understanding how recomibnational directionality is determine in phage integration systems.

Tools - Genetic and Clinical. Studying the mycobacteria and their phages has great potential for the development of novel tools for their genetics but also for a more direct clinical involvement. Two systems we have been involved in developing are multivalent recombinant BCG vaccines and Luciferase Reporter Phages, but there are numerous additional strategies awaiting further development!

Recent Publications
  • Pope, W.H., D.N. Biery, Z.T. Huff, A.B. Huynh, W.M. McFadden, J.S. Mouat, S.E. Schneiderman, H. Song, L.E. Szpak, M.S. Umbaugh, B.A. German, J.E. McDonnell, N. Mezghani, C.E. Schafer, P.K. Thompson, M.C. Ulbrich, V.J. Yu, E.C. Furbee, S.R. Grubb, M.H. Warner, M.T. Montgomery, R.A. Garlena, D.A. Russell, D. Jacobs-Sera & G.F. Hatfull, (2016) Genome Sequences of Gordonia terrae Phages Attis and SoilAssassin. Genome announcements 4, doi:10.1128/genomeA.00591-16.

  • Pope, W.H., M.S. Benczkowski, D.E. Green, M. Hwang, B. Kennedy, B. Kocak, E. Kruczek, L. Lin, M.L. Moretti, F.L. Onelangsy, N. Mezghani, K.A. Milliken, C.L. Toner, P.K. Thompson, M.C. Ulbrich, E.C. Furbee, S.R. Grubb, M.H. Warner, M.T. Montgomery, R.A. Garlena, D.A. Russell, D. Jacobs-Sera & G.F. Hatfull, (2016) Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha. Genome announcements 4, doi:10.1128/genomeA.00578-16.

  • Pope, W.H., A.F. Akbar, T.N. Ayers, S.G. Belohoubek, C.F. Chung, A.C. Hartman, T. Kayiti, C.M. Kessler, P.I. Koman, G.A. Kotovskiy, T.M. Morgan, R.M. Rohac, G.M. Silva, C.E. Willis, 3rd, K.A. Milliken, K.A. Shedlock, A.C. Stanton, C.L. Toner, E.C. Furbee, S.R. Grubb, M.H. Warner, M.T. Montgomery, R.A. Garlena, D.A. Russell, D. Jacobs-Sera & G.F. Hatfull, (2016) Genome Sequences of Gordonia Bacteriophages Obliviate, UmaThurman, and Guacamole. Genome announcements 4, doi:10.1128/genomeA.00595-16.

  • Dedrick, R.M., T.N. Mavrich, W.L. Ng, J.C. Cervantes Reyes, M.R. Olm, R.E. Rush, D. Jacobs-Sera, D.A. Russell & G.F. Hatfull, (2016) Function, expression, specificity, diversity, and incompatibility of actinobacteriophage parABS systems. Mol Microbiol In press, doi:10.1111/mmi.13414.

  • Bollivar, D.W., B. Bernardoni, M.R. Bockman, B.M. Miller, D.A. Russell, V.A. Delesalle, G.P. Krukonis, G.F. Hatfull, M.R. Cross, M.M. Szewczyk & A. Eppurath, (2016) Complete Genome Sequences of Five Bacteriophages That Infect Rhodobacter capsulatus. Genome announcements 4, doi:10.1128/genomeA.00051-16.

  • Pope, W.H., A.K. Brown, D.J. Fisher, N.H. Okwiya, K.A. Savage, B.A. German, J.E. McDonnell, C.E. Schafer, V.J. Yu, E.C. Furbee, S.R. Grubb, M.H. Warner, M.T. Montgomery, R.A. Garlena, D.A. Russell, D. Jacobs-Sera & G.F. Hatfull, (2016) Genome Sequence of Gordonia Bacteriophage Lucky10. Genome announcements 4, doi:10.1128/genomeA.00580-16.

  • Lima-Junior, J.D., C. Viana-Niero, D.V. Conde Oliveira, G.E. Machado, M.C. Rabello, J. Martins-Junior, L.F. Martins, L.A. Digiampietri, A.M. da Silva, J.C. Setubal, D.A. Russell, D. Jacobs-Sera, W.H. Pope, G.F. Hatfull & S.C. Leao, (2016) Characterization of mycobacteria and mycobacteriophages isolated from compost at the Sao Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U. BMC Microbiol 16: 111, doi:10.1186/s12866-016-0734-3.

  • Lunt, B.L. & G.F. Hatfull, (2016) Brujita Integrase: A Simple, Arm-Less, Directionless, and Promiscuous Tyrosine Integrase System. J Mol Biol 428: 2289-2306, doi:10.1016/j.jmb.2016.04.023.

  • Pope, W. H. & Hatfull, G. F. (2016). Adding pieces to the puzzle: New insights into bacteriophage diversity from integrated research-education programs.  Bacteriophage 5(4):e1084073.

  • Russell, D.A. & G.F. Hatfull, (2016) Complete Genome Sequence of Arthrobacter sp. ATCC 21022, a Host for Bacteriophage Discovery. Genome announcements 4, doi:10.1128/genomeA.00168-16.

  • Urdaniz, E., L. Rondon, M.A. Marti, G.F. Hatfull & M. Piuri, (2016) Rapid Whole-Cell Assay of Antitubercular Drugs Using Second-Generation Fluoromycobacteriophages. Antimicrob Agents Chemother 60: 3253-3256, doi:10.1128/AAC.03016-15.

  • Hatfull, G. F. (2016). In the Trenches of Microbial Warfare: Identification of Genes and Pathways Contributing to Bacteriophage Infection by Quantitative Selection Analysis. J. Mol. Biol. 428, 413-415.

  • Hanauer, D. I & Hatfull, G. F. (2015).  Measuring Networkign as an Outcome Variable in Undergraduate Research Experiecnes.  CBE Life Sci Educ. 14(4):ar38

  • Villanueva, V. M., Oldfield, L. M. &  Hatfull, G. F. (2015). An unusual phage repressor ecoded by mycobacteriophage BPs.  PLoSOne 10(9):e0137187

  • Petrova, Z. O., Broussard, G. W. and Hatfull, G. F. (2015). Mycobacteriophage-repressor mediated immunity as selectable genetic markers: Adephagia and BPs repressor-selection.  Microbiology In press.

  • Mehla, J., R.M. Dedrick, J.H. Caufield, R. Siefring, M. Mair, A. Johnson, G.F. Hatfull & P. Uetz, (2015) The protein interactome of mycobacteriophage Giles predicts functions for unknown proteins. J Bacteriol. 197, 2508-2516.

  • Pope, W.H., T. Ahmed, M.K. Drobitch, D.R. Early, S. Eljamri, N.S. Kasturiarachi, E.F. Klonicki, D.T. Manjooran, A.N. Ni Chochlain, A.O. Puglionesi, V. Rajakumar, K.A. Shindle, M.T. Tran, B.R. Brown, B.M. Churilla, K.L. Cohen, K.E. Wilkes, S.R. Grubb, M.H. Warner, C.A. Bowman, D.A. Russell & G.F. Hatfull, (2015) Genome Sequences of Mycobacteriophages Luchador and Nerujay. Genome announcements 3.

  • Pope, W.H., D.A. Augustine, D.C. Carroll, J.C. Duncan, K.M. Harwi, R. Howry, B. Jagessar, B.A. Lum, J.W. Meinert, J.S. Migliozzi, K.A. Milliken, C.J. Mitchell, A.S. Nalatwad, K.C. Orlandini, M.J. Rhein, V. Saravanan, B.A. Seese, J.G. Schiebel, K.B. Thomas, N.L. Adkins, K.L. Cohen, V.B. Iyengar, H. Kim, Z.J. Kramer, M.T. Montgomery, C.E. Schafer, K.E. Wilkes, S.R. Grubb, M.H. Warner, C.A. Bowman, D.A. Russell & G.F. Hatfull, (2015) Genome Sequences of Cluster G Mycobacteriophages Cambiare, FlagStaff, and MOOREtheMARYer. Genome announcements 3.

  • Pope, W.H., N.I. Bernstein, C.S. Fasolas, N. Mezghani, C.A. Pressimone, P. Selvakumar, A.C. Stanton, J.S. Lapin, A.K. Prout, S.R. Grubb, M.H. Warner, C.A. Bowman, D.A. Russell & G.F. Hatfull, (2015) Genome Sequence of Mycobacteriophage Mindy. Genome announcements 3.

  • Pope, W.H., E.A. Bina, I.S. Brahme, A.B. Hill, P.H. Himmelstein, S.M. Hunsicker, A.R. Ish, T.S. Le, M.M. Martin, C.N. Moscinski, S.A. Shetty, T. Swierzewski, V.B. Iyengar, H. Kim, C.E. Schafer, S.R. Grubb, M.H. Warner, C.A. Bowman, D.A. Russell & G.F. Hatfull, (2015) Genome Sequence of Mycobacteriophage Momo. Genome announcements 3.

  • Pope, W.H., M.E. Carbonara, H.M. Cioffi, T. Cruz, B.Q. Dang, A.N. Doyle, O.H. Fan, M. Gallagher, G.M. Gentile, B.A. German, M.E. Farrell, M. Gerwig, K.L. Hunter, V.E. Lefever, N.A. Marfisi, J.E. McDonnell, J.K. Monga, K.G. Quiroz, A.C. Pong, P.A. Rimple, M. Situ, P.C. Sohnen, A.N. Stockinger, P.K. Thompson, N.M. Torchio, C.L. Toner, M.C. Ulbrich, N.I. Vohra, A. Zakir, N.L. Adkins, B.R. Brown, B.M. Churilla, Z.J. Kramer, J.S. Lapin, M.T. Montgomery, A.K. Prout, S.R. Grubb, M.H. Warner, C.A. Bowman, D.A. Russell & G.F. Hatfull, (2015) Genome Sequences of Mycobacteriophages AlanGrant, Baee, Corofin, OrangeOswald, and Vincenzo, New Members of Cluster B. Genome announcements 3.

  • Pope, W.H., J.T. Carter, K.L. Dasher, M.C. Haynberg, A. Reddi, K.A. Shedlock, J.S. Lapin, A.K. Prout, S.R. Grubb, M.H. Warner, C.A. Bowman, D.A. Russell & G.F. Hatfull, (2015) Genome Sequence of a Newly Isolated Mycobacteriophage, ShedlockHolmes. Genome announcements 3.

  • Pope, W.H., E. Jacobetz, C.A. Johnson, B.L. Kihle, M.A. Sobeski, M.B. Werner, N.L. Adkins, Z.J. Kramer, M.T. Montgomery, S.R. Grubb, M.H. Warner, C.A. Bowman, D.A. Russell & G.F. Hatfull, (2015) Genome Sequence of Mycobacteriophage Phayonce. Genome announcements 3.

  • Hatfull, G.F. (2015). Dark matter of the biosphere: The amazing world of bacteriophage diversity. J. Virol. 89, 8107-8110.

  • Hatfull, G.F. (2015). Innovations in Undergraduate Science Education: Going Viral. J Virol. 89, 8111-8113.

  • Mehla, J., Dedrick, R.M., Caufield, J.H., Siefring, R., Mair, M., Johnson, A., Hatfull, G.F., and Uetz, P. (2015). The protein interactome of mycobacteriophage Giles predicts functions for unknown proteins. J. Bacteriol. pii: JB.00164-15

  • Pope, W.H., Bowman, C.A., Russell, D.A., Jacobs-Sera, D., Asai, D.J., Cresawn, S.G., Jacobs, W.R., Hendrix, R.W., Lawrence, J.G., Hatfull, G.F., et al. (2015). Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife 4.

  • Ojha, A. K., Jacobs, W R. Jr., and Hatfull, G. F.  (2015). Genetic Dissection of Mycobacterial Biofilms in Mycobacteria Protocols. Methods in Molecular Biology 1285, 215-226.

  • Casjens S. R., Jacobs-Sera, D., Hatfull, G. F., Hendrix, R. W. (2015) Genome sequence of Salmonella enterica phage Det7.  Genome Announc.  May 7;3(3). pii: e00279-15. doi: 10.1128/genomeA.00279-15.

  • Cresawn, S. G., Pope, W. H., Jacobs-Sera, D., Bowman, C. A., Russell, D. A., Dedrick, R. A., Adair, T., Anders, K. R., Ball, S., Bollivar, D., Breitenberger, C., Burnett, S. H., Butela, K., Byrnes, D., Carzo, S., Cornely, K. A., Cross, T., Daniels, R. L., Dunbar, D., Findley, A. M., Gissendanner, C. R., Golebiewska, U. P., Hartzog, G. A., Hatherill, J. R., Hughes, L. E., Jalloh, C. S., DeLosSantos, C., Ekanam, K., Khambule, S. L., King, R. A., King-Smith, C., Klyczek, K., Krukonis, G. P., Laing, C., Lapin, J. S., Lopez, A. J., Mkhwanazi, S. M., Molloy, S. D., Moran, D., Munsamy, V., Pacey, E., Plymale, R., Poxleitner, M., Reyna, N., Schildbach, J. F., Stukey, J., Taylor, S. E., Ware, V. C., Wellmann, A. L., Westholm, D., Wodarski, D., Zajko, M., Zikalala, T. S., Hendrix, R. W., and  Hatfull, G. F. (2015) Comparative Genomics of Cluster O Mycobacteriophages PLoS One 10:e0118725.

  • Hendrix, R. W., Ko, C. C., Jacobs-Sera, D., Hatfull, G. F., Erhardt, M., Hughes, K. T,, Casjensm S. R. (2015) Genome Sequence of Salmonella Phage χ. Genome Announc. 3. pii: e01229-14.

  • Pope, W. H., Jacobs-Sera, D., Russell, D. A., Rubin, D. H. F., Kajee, A., Msibi, Z. N. P., Larsen, M. H., Jacobs, W. R. Jr., Lawrence, J. G., Hendrix, R. W., & Hatfull, G. F. (2014). Genomics and proteomics of Mycobacteriophage Patience: An accidental tourist in the Mycobacterium neighborhood mBio pii: e02145-14. doi: 10.1128/mBio.02145-14.

  • Hatfull, G. F. (2014) Molecular Genetics of Mycobacteriophages. Microbiol Spectr.  2, 1-36.

  • Hatfull, G. F. and Racaniello, V. (2014). PHIRE and TWiV: Experiences in bringing virology to new audiences. Ann. Rev. Virology1, 37-53.

  • Dieterle, M. E., Bowman, C., Batthyany, C., Lanzarotti, E., Turjanski, A., Hatfull, G., Piuri, M. 2014. Exposing the secrets of two well known Lactobacillus casei phages: Genomic and structural analysis of J-1 and PL-1. Appl. Environ. Microbiol80, 7107-7021

  • Casjens, S. R., Leavitt, J. C., Hatfull, G. F., and Hendrix, R. W. 2014. Genome Sequence of Salmonella Phage 9NA. GenomeA pii: e00531-14

  • Hatfull G. F. & Jacobs W.R Jr.(eds)  Molecular Genetics of Mycobacteria.  (2014). Second edition. ASM Press.  Washington, DC.

  • Oldfield, L. M. and Hatfull, G. F. (2014). Mutational Analysis of the Mycobacteriophage BPs Promoter PR Reveals Context-Dependent Sequences for Mycobacterial Gene Expression. J. Bacteriol. 196, 3589-3597.

  • Hatfull, G. F. (2014). Molecular Genetics of Mycobacteriophages in Molecular Genetics of Mycobacteria, Second Edition. Eds. Hatfull, G. F. & Jacobs, W. R. Jr. ASM press, Washington, DC.

  • Tufariello, J. M., Malek, A. A., Vilchèze, C., Cole, L. E., Ratner, H. K., González, P. A., Jain, P., Hatfull, G. F., Larsen, M. H., and Jacobs, W. R. Jr. (2014) Enhanced specialized transduction using recombineering in Mycobacterium tuberculosis. mBio 5(3):e01179-14

  • Russell, D. A., Bowman, C. A., and Hatfull, G. F. (2014) Genome Sequence of Salmonella enterica subsp. enterica Strain Durban. Genome Announcements. 2(3). pii: e00399-14

  • Hatfull, G. F. (2014). Mycobacteriophages: Windows into tuberculosis.  PLoS Pathogens. 10(3):e1003953

  • Jordan,T. C., Burnett, S. H., Carson, S., Caruso, S. M., Clase, K., DeJong, R. J., Dennehy, J. J., Denver, D. R., Dunbar, D., Elgin, S. C. R., Findley A. M., Gissendanner, C. R., Golebiewska, U. P., Guild, N., Hartzog, G. A., Grillo, W. H., Hollowell, G. P., Hughes, L. E., Johnson, A., King, R. A., Lewis, L. O., Li,W., Rosenzweig, F., Rubin, M. R., Saha, M. S., Sandoz, J., Shaffer, C. D., Taylor, B., Temple,  L., Vazquez, E., Ware, V. C., Barker, L.P., Bradley, K. W., Jacobs-Sera, D., Pope, W. H., Russell, D. A., Cresawn, S. G., Lopatto, D., Bailey, C. P., Hatfull, G. F. (2014) A broadly implementable research course for first-year undergraduate students. mBio 5:e01051-01013.

  • Pope, W.H., Anders, K. R., Baird, M., Bowman, C.A., Boyle, M.M., Broussard, G.W., Chow, T., Clase, K.L., Cooper, S., Cornely, K.A., Dejong, R.J., Delesalle, V.A., Deng, L., Dunbar, D., Edgington, N.P., Ferreira, C.M., Hafer, K.W., Hartzog, G.A., Hatherill, J.R., Hughes, L.E., Ipapo, K., Krukonis, G.P., Meier, C.G., Monti, D.L., Olm, M.R., Page, S.T., Peebles, C.L., Rinehart, C.A., Rubin, M.R., Russell, D.A., Sanders, E.R.,Schoer, M., Shaffer, J., Wherley, C.D.,Vazquez,E., Yuan, H., Zhang, D., Cresawn, S.G., Jacobs-Sera, D., Hendrix, R.W. & Hatfull, G. F. (2014) Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes. J. Virol. 88, 2461-2480.

  • Dieterle, M. E., Jacobs-Sera, D., Russell, D., Hatfull, G., Piuri, M. (2014) Complete Genome Sequences of Lactobacillus Phages J-1 and PL-1. Genome Announc 2.

  • Singh, S., Plaks, S. G., Homa, N. J., Amrich, C. G., Heroux, A., Hatfull, G. F., & VanDemark, A. P. (2014). The structure of Xis reveals the basis for filament fomration and insight into DNA bending within a mycobacteriophage Intasome.  J. Mol. Biol., 426, 412-422.

  • Singh. S., Rockenbach, K., Dedrick, R. M., VanDemark, A. P., & Hatfull, G. F. (2014) Cross-talk between Diverse Serine Integrases. J Mol Biol 426, 318-331.

  • Smith, M. C., Hendrix, R. W., Dedrick, R., Mitchell, K., Ko, CC., Russell, D., Bell, E., Gregory, M., Bibb, M. J., Pethick, F., Jacobs-Sera, D., Herron, P., Buttner, M. J., and Hatull, G. F. (2013).  Evolutionary relationships within actinophages and a putative adaptation for growth in Streptomyces spp. J. Bacteriol. 195, 4924-4935.

  • Hatfull, G. F. Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) Mycobacterial Genetics Course, University of California Los Angeles  Research Immersion Laboratory in Virology, Phage Hunters Integrating Research and Education (PHIRE) program. (2013). The complete genome sequences of 63 mycobacteriophages.  GenomeA 1, doi:pii: e00847-13. 10.1128/genomeA.00847-13.

  • Piuri, M., Rondon, L., Urdaniz, E., and Hatfull, G. F. (2013). Generation of affinity-tagged fluoromycobacteriophages by mixed assembly of phage capsids. Appl Environ Microbiol. 79, 5608-5615.

  • Pope, W. H., Jacobs-Sera, D., Best, A. A., Broussard, G. W., Connerly, P. L., Dedrick, R. M., Kremer, T. A., Offner, S., Ogiefo, A. H., Pizzorno, M. C., Rockenbach, K., Russell, D. A., Stowe, E. L., Stukey, J., Thibault, S. A., Conway, J. F., Hendrix, R. W., Hatfull, G. F. (2013) Cluster J mycobacteriophages: intron splicing in capsid and tail genes. PLoS One 8:e69273.

  • Broussard, G. W. and Hatfull, G. F. (2013) Evolution of genetic switch complexity. Bacteriophage 3:e24186.

  • Singh, S., Ghosh, P., and Hatfull, G. F. (2013).  Attachment site selection and identity in Bxb1 serine integrase-mediated site-specific recombination.  PLoS Genetics9, e1003490

  • Sambandan, D., D.N. Dao, B.C. Weinrick, C. Vilcheze, S.S. Gurcha, A. Ojha, L. Kremer, G.S. Besra, G.F. Hatfull & W.R. Jacobs, Jr., (2013) Keto-mycolic acid-dependent pellicle formation confers tolerance to drug-sensitive Mycobacterium tuberculosis. MBio 4: e00222-00213.

  • Hatfull, G. F. (Ed). Recent Progress in Bacteriophage Research (2013).  Multidisciplinary Digital Publishing Institute, Basel.

  • Silva, J.L., M. Piuri, G. Broussard, L. Marinelli, G.M. Bastos, R.D. Hirata, G.F. Hatfull & M.H. Hirata, (2013) Application of BRED technology to construct recombinant D29 reporter phage expressing EGFP. FEMS Microbiol Lett. 344, 166-172.

  • Dedrick, R. M., Marinelli, L. J., Newton, G. L., Pogliano, K., Pogliano, J ., Hatfull, G. F. (2013). FUnctional requirements for bacetriophage growth: gene essentiality and expression in mycobacteriophage Giles. Mol. Microbiology  EPub head of print.   

  • Sencilo, A., Jacobs-Sera, D., Russell, D. A., Ko, C-C., Bowman, C. A., Atanasova, N., Österlund, E., Oksanen, H. M., Bamford, D. H., Hatfull, G. F., Roine, E., & Hendrix, R.W.  (2013).  Snapshot of haloarchaeal tailed virus genomes.  RNA Biology.  In Press

  • Broussard, G.W., L.M. Oldfield, V.M. Villanueva, B.L. Lunt, E.E. Shine & G.F. Hatfull, (2013) Integration-Dependent Bacteriophage Immunity Provides Insights into the Evolution of Genetic Switches. Mol Cell. 49, 237-248.

  • Jacobs-Sera, D., Marinelli, L. J., Bowman, C., Broussard, G. W., Guerrero Bustamante, C., Boyle, M. M., Petrova, Z. O., Dedrick, R. M., Pope, W. H., Science Education Alliance Phage Hunters Advancing, G., Evolutionary Science Sea-Phages, P., Modlin, R. L., Hendrix, R. W., and Hatfull, G. F. (2012) On the nature of mycobacteriophage diversity and host preference. Virology 434, 187-201.

  • Marinelli, L.J., Fitz-Gibbon, S., Hayes, C., Bowman, C., Inkeles, M., Loncaric, A., Russell, D.A., Jacobs-Sera, D., Cokus, S., Pellegrini, M., Kim, J., Miller, J. F., Hatfull, G. F., and Modlin, R. L. (2012). Propionibacterium acnes Bacteriophages Display Limited Genetic Diversity and Broad Killing Activity against Bacterial Skin Isolates. mBio 3. e00279-12

  • Bai, H., Kath, J.E., Zorgiebel, F.M., Sun, M., Ghosh, P., Hatfull, G.F., Grindley, N.D., and Marko, J.F. (2012). Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end. Proc Natl Acad Sci U S A. Epub

  • Marinelli, L. J. , Hatfull, G. F., Piuri, M. (2012) Recombineering: A powerful tool for modification of bacteriophage genomes.  Bacteriophage 2, 5-14. 

  • Payne, K.M., and Hatfull, G.F. (2012). Mycobacteriophage endolysins: diverse and modular enzymes with multiple catalytic activities. PLoS One 7, e34052

  • Mageeney, C., W. Pope, M. Harrison, D. Moran, T. Cross, D. Jacobs-Sera, R. W. Hendrix, D. Dunbar & G. F. Hatfull, (2012) Mycobacteriophage Marvin: A new singleton phage with an unusual genome organization. J Virol. 86:4762-75.

  • Hatfull (2012).  The Secret Lives of Mycobacteriophages. Advances in Virus Research. 82,179-288.

  • Hatfull, G. F., et al (2012) Complete genome sequences of 138 mycobacteriophages.  J. Virol. 86: 2382-2384.

  • Kulka, K., Hatfull, G., and Ojha, A.K. (2012). Growth of Mycobacterium tuberculosis biofilms. J. Vis. Exp. 15:3820

  • Savinov, A., Pan, J., Ghosh, P. and Hatfull, G. F. (2012) The Bxb1 gp47 recombination directionality factor is required not only for prophage excision but also for phage DNA replication.  Gene 495: 42-48.

  • Jain, P., Hartman, T.E., Eisenberg, N., O'Donnell, M. R., Kriakov, J., Govender, K., Makume, M., Thaler, D.S., Maiga, M., Timmins, G.S., Bishai, W.R., Hatfull, G.F., Sturm, A.W., Larsen, M.H., Moodley, P., and Jacobs, W.R. (2012) A high intensity fluorophage enables detection and rapid drug susceptibility testing of Mycobacterium tuberculosis directy from sputum samples.  J. Clin. Microbiol. 50, 1362-1369

  • Cresawn, S.G., Bogel, M., Day, N., Jacobs-Sera, D., Hendrix, R.W. and Hatfull, G.F. (2011) Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12:395.

  • Anderson, W.A., Amasino, R.M., Ares, M., Jr., Banerjee, U., Bartel, B., Corces, V.G., Drennan, C.L., Elgin, S.C., Epstein, I.R., Fanning, E., Guillette, L.J., Jr., Handelsman, J., Hatfull, G.F., Hoy, R.R., Kelley, D., Leinwand, L.A., Losick, R., Lu, Y., Lynn, D.G., Neuhauser, C., ODowd, D.K., Olivera, T., Pevzner, P., Richards-Kortum, R.R., Rine, J., Sah, R.L., Strobel, S.A., Walker, G.C., Walt, D.R., Warner, I.M., Wessler, S., Willard, H.F. and Zare, R.N. (2011) Competencies: a cure for pre-med curriculum. Science 334: 760-761

  • Pope, W.H., Ferreira, C.M., Jacobs-Sera, D., Benjamin, R.C., Davis, A.J., DeJong, R.J., Elgin, S.C.R., Guilfoile, F.R., Forsyth, M.H., Harris, A.D., Harvey, S.E., Hughes, L.E., Hynes, P.M., Jackson, A.S., Jalal, M.D., MacMurray, E.A., Manley, C.M., McDonough, M.J., Mosier, J.L., Osterbann, L.J., Rabinowitz, H.S., Rhyan, C.N., Russell, D.A., Saha, M.S., Shaffer, C.D., Simon, S.E., Sims, E.F., Tovar, I.G., Weisser, E.G., Wertz, J.T., Weston-Hafer, K.A., Williamson, K.E., Zhang, B., Cresawn, S.G., Jain, P., Piuri, M., Jacobs, W.R., Jr., Hendrix, R.W. and Hatfull, G.F. (2011) Cluster K Mycobacteriophages: Insights into the Evolutionary Origins of Mycobacteriophage TM4. PLoS ONE 6:e26750.

  • Hatfull, G.F. and Hendrix, R.W. (2011) Bacteriophages and their Genomes. Current Opinions in Virology 1: 298-303

  • Bai, H., Sun, M., Ghosh, P., Hatfull, G.F., Grindley, N.D. and Marko, J.F. (2011) Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase. Proc Natl Acad Sci U S A 108:7419-24.

  • Huang, J., Ghosh, P., Hatfull, G.F. and Hong, Y. (2011) Successive and targeted DNA integrations in the Drosophila genome by Bxb1 and phiC31 integrases. Genetics 189:391-5.

  • Marine, R., Polson, S.W., Ravel, J., Hatfull, G., Russell, D., Sullivan, M., Syed, F., Dumas, M. and Wommack, K.E. (2011) Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl Environ Microbiol 77:  8071-9.

  • Jain, P., Thaler, D.S., Maiga, M., Timmins, G.S., Bishai, W.R., Hatfull, G.F., Larsen, M.H. and Jacobs, W.R. (2011) Reporter phage and breath tests: emerging phenotypic assays for diagnosing active tuberculosis, antibiotic resistance, and treatment efficacy. J Infect Dis 204: 1142-1150.

  • Anderson, W.A., Banerjee, U., Drennan, C.L., Elgin, S.C., Epstein, I.R., Handelsman, J., Hatfull, G.F., Losick, R., ODowd, D.K., Olivera, B.M., Strobel, S.A., Walker, G.C. and Warner, I.M. (2011) Science education. Changing the culture of science education at research universities. Science 331:152-153.

  • Pope, W.H., D. Jacobs-Sera, D.A. Russell, C.L. Peebles, Z. Al-Atrache, T.A. Alcoser, L.M. Alexander, M.B. Alfano, S.T. Alford, N.E. Amy, M.D. Anderson, A.G. Anderson, A.A. Ang, J.r Ares M, A.J. Barber, L.P. Barker, J.M. Barrett, W.D. Barshop, C.M. Bauerle, I.M. Bayles, K.L. Belfield, A.A. Best, J.r Borjon A, C.A. Bowman, C.A. Boyer, K.W. Bradley, V.A. Bradley, L.N. Broadway, K. Budwal, K.N. Busby, I.W. Campbell, A.M. Campbell, A. Carey, S.M. Caruso, R.D. Chew, C.L. Cockburn, L.B. Cohen, J.M. Corajod, S.G. Cresawn, K.R. Davis, L. Deng, D.R. Denver, B.R. Dixon, S. Ekram, S.C. Elgin, A.E. Engelsen, B.E. English, M.L. Erb, C. Estrada, L.Z. Filliger, A.M. Findley, L. Forbes, M.H. Forsyth, T.M. Fox, M.J. Fritz, R. Garcia, Z.D. George, A.E. Georges, C.R. Gissendanner, S. Goff, R. Goldstein, K.C. Gordon, R.D. Green, S.L. Guerra, K.R. Guiney-Olsen, B.G. Guiza, L. Haghighat, G.V. Hagopian, C.J. Harmon, J.S. Harmson, G.A. Hartzog, S.E. Harvey, S. He, K.J. He, K.E. Healy, E.R. Higinbotham, E.N. Hildebrandt, J.H. Ho, G.M. Hogan, V.G. Hohenstein, N.A. Holz, V.J. Huang, E.L. Hufford, P.M. Hynes, A.S. Jackson, E.C. Jansen, J. Jarvik, P.G. Jasinto, T.C. Jordan, T. Kasza, M.A. Katelyn, J.S. Kelsey, L.A. Kerrigan, D. Khaw, J. Kim, J.Z. Knutter, C.C. Ko, G.V. Larkin, J.R. Laroche, A. Latif, K.D. Leuba, S.I. Leuba, L.O. Lewis, K.E. Loesser-Casey, C.A. Long, A.J. Lopez, N. Lowery, T.Q. Lu, V. Mac, I.R. Masters, J.J. McCloud, M.J. McDonough, A.J. Medenbach, A. Menon, R. Miller, B.K. Morgan, P.C. Ng, E. Nguyen, K.T. Nguyen, E.T. Nguyen, K.M. Nicholson, L.A. Parnell, C.E. Peirce, A.M. Perz, L.J. Peterson, R.E. Pferdehirt, S.V. Philip, K. Pogliano, J. Pogliano, T. Polley, E.J. Puopolo, H.S. Rabinowitz, M.J. Resiss, C.N. Rhyan, Y.M. Robinson, L.L. Rodriguez, A.C. Rose, J.D. Rubin, J.A. Ruby, M.S. Saha, J.W. Sandoz, J. Savitskaya, D.J. Schipper, C.E. Schnitzler, A.R. Schott, J.B. Segal, C.D. Shaffer, K.E. Sheldon, E.M. Shepard, J.W. Shepardson, M.K. Shroff, J.M. Simmons, E.F. Simms, B.M. Simpson, K.M. Sinclair, R.L. Sjoholm, I.J. Slette, B.C. Spaulding, C.L. Straub, J. Stukey, T. Sughrue, T.Y. Tang, L.M. Tatyana, S.B. Taylor, B.J. Taylor, L.M. Temple, J.V. Thompson, M.P. Tokarz, S.E. Trapani, A.P. Troum, J. Tsay, A.T. Tubbs, J.M. Walton, D.H. Wang, H. Wang, J.R. Warner, E.G. Weisser, S.C. Wendler, K.A. Weston-Hafer, H.M. Whelan, K.E. Williamson, A.N. Willis, H.S. Wirtshafter, T.W. Wong, P. Wu, Y. Yang, B.C. Yee, D.A. Zaidins, B. Zhang, M.Y. Zuniga, R.W. Hendrix, and G.F. Hatfull (2011) Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PLoS One 6:e16329e16329

  • Rondon, L., M. Piuri, J.r Jacobs WR, J. de Waard, G.F. Hatfull, and H. Takiff (2011) Evaluation of Fluoromycobacteriophages for detecting drug resistance in Mycobacterium tuberculosis. J Clin Microbiol :

  • Traag, B.A., A. Driks, P. Stragier, W. Bitter, G. Broussard, G. Hatfull, F. Chu, K.N. Adams, L. Ramakrishnan, and R. Losick (2010) Do mycobacteria produce endospores? Proc Natl Acad Sci U S A 107:878-881

  • Hatfull, G.F. (2010) Mycobacteriophages: genes and genomes. Annu Rev Microbiol 64:331-356

  • Alibaud, L., A. Alahari, X. Trivelli, A.K. Ojha, G.F. Hatfull, Y. Guerardel, and L. Kremer (2010) Temperature-dependent regulation of mycolic acid cyclopropanation in saprophytic mycobacteria: role of the Mycobacterium smegmatis 1351 gene (MSMEG_1351) in CIS-cyclopropanation of alpha-mycolates. J Biol Chem 285:21698-21707

  • Ojha, A.K., X. Trivelli, Y. Guerardel, L. Kremer, and G.F. Hatfull (2010) Enzymatic hydrolysis of trehalose dimycolate releases free mycolic acids during mycobacterial growth in biofilms. J Biol Chem 285:17380-17389

  • Sampson, T., G.W. Broussard, L.J. Marinelli, D. Jacobs-Sera, M. Ray, C.C. Ko, D. Russell, R.W. Hendrix, and G.F. Hatfull (2009) Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements. Microbiology 155:2962-2977

  • Payne, K., Q. Sun, J. Sacchettini, and G.F. Hatfull (2009) Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase. Mol. Microbiol. 73:367-381

  • Stewart, C.R., S.R. Casjens, S.G. Cresawn, J.M. Houtz, A.L. Smith, M.E. Ford, C.L. Peebles, G.F. Hatfull, R.W. Hendrix, W.M. Huang, and M.L. Pedulla (2009) The genome of Bacillus subtilis bacteriophage SPO1. J. Mol. Biol. 388:48-70

  • Comeau, A.M., G.F. Hatfull, H.M. Krisch, D. Lindell, N.H. Mann, and D. Prangishvili (2008) Exploring the prokaryotic virosphere. Res. Microbiol. 159:306-313

  • Hatfull, G.F., S.G. Cresawn, and R.W. Hendrix (2008) Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution. Res. Microbiol. 159:332-339

  • van Kessel, J.C., L.J. Marinelli, and G.F. Hatfull (2008) Recombineering mycobacteria and their phages. Nat. Rev. Microbiol. 6:851-857

  • Marinelli, L.J., M. Piuri, Z. Swigonova, A. Balachandran, L.M. Oldfield, K.e.s.s.e. van, and G.F. Hatfull (2008) BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes. PLoS ONE 3:e3957

  • van Kessel, J.C., and G.F. Hatfull (2008) Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: characterization of antimycobacterial drug targets. Mol. Microbiol. 67:1094-1107

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