Bookmark and Share

Michelle G Giglio
 

Michelle G Giglio Ph.D.

Academic Title: Assistant Professor
Primary Appointment: Medicine
mgiglio@som.umaryland.edu
Location: BioPark II, 651
Phone: (410) 706-7694

Personal History:

I received my Bachelor of Science degree in Biology from the University of Maryland College Park.  I went on to get my Ph.D. at Johns Hopkins School of Medicine in the laboratory of Dr. Hamilton Smith where I worked on natural transformation in Haemophilus influenzae. I then moved to The Institute for Genomic Research in Rockville, MD where I spent nearly 10 years as a Staff Scientist engaged in prokaryotic genome annotation, pipeline development, and ontology development. I joined the Institute for Genome Sciences here at the University of Maryland School of Medicine in 2007 shortly after the institute was formed. Below is a description of my research interests at IGS.

Research Interests:

The Analysis Engine, a prokaryotic analysis resource

I have worked in aspects of prokaryotic genome annotation and analysis for over 15 years. During that time I have contributed to the development of automatic annotation pipelines that attempt to mimic the decision processes made during manual curation by a human. In addition I have been involved in the development of the annotation visualization and curation tool Manatee. Many years ago we realized that there was a large and growing population of researchers who needed access to such analysis tools but who lacked the resources to develop them. We wished to bring these tools to those researchers. Starting in 2007 I received funding from NIGMS to offer a prokaryotic annotation service called the Annotation Engine. This service provides free access to the IGS prokaryotic annotation pipeline to any researcher with a prokaryotic genome of interest. The Annotation Engine has been extremely successful and to date has processed nearly 1000 prokaryotic genomes for our users. I recently received renewal funding to expand the services provided by the Annotation Engine and transform it into the Analysis Engine. The newly expanded Analysis Engine service remains free to users and continues to provide genome annotation but now also provides comparative analysis, transcriptome analysis, and more. We are working to more fully integrate the tools and output of the Analysis Engine with other third-party tools to increase the usefulness of the service.

Microbiome analysis

The Human Microbiome Project (HMP), a large-scale collaboration funded by the NIH Common Fund, provided baseline information on microbial community composition and function at 5 major human body sites and investigated the role of these communities in human health. My role in the project was as part of the HMP Data Analysis and Coordination Center located here at IGS and led by PI Owen White. I coordinated DACC activities associated with the analysis of the many terabytes of sequence data produced by the project including reference genome functional annotation, metagenome functional annotation, Gene Ontology analysis, metadata capture/standardization, standardized protocol development, and walkthrough production. Walkthroughs are HMP analysis pipelines made available as virtual machines with associated step-by-step instructions for easy use by the research community. The datasets produced and/or provided by the DACC on our web resource have been accessed by thousands of researchers each year.

Ontology development

The ability to capture biological information in a standardized, consistent manor is absolutely essential for the ability to effectively mine the vast quantities of sequence and analysis data. Controlled vocabularies and ontologies provide an excellent mechanism for standardized information capture. I have been part of the Gene Ontology consortium since 2001 and have contributed significantly to the expansion of the GO to include terms for prokaryotic biology, in particular host-microbe interactions.  More recently I have become a lead editor of the Evidence Code Ontology. In addition, I have received funding along with Dr. James Hu (Texas A&M) to develop an Ontology of Microbial Phenotypes (OMP).

Training and Outreach

As the IGS Academic and Outreach Coordinator I organize multiple training and outreach events each year. I have been heavily involved in curriculum development for the Genome Biology track of the GPLS Molecular Medicine graduate program. In addition, I have developed a professional development program consisting of five different training workshops offered throughout each year. These multi-day events are attended by researchers from all over the world and focus on a variety of genomics and bioinformatics related topics. Finally, I am involved in many kinds of K-12 outreach. We have hosted or participated in many events for middle school children, hosted field trips for high school students, and engaged in outreach to high school teachers.


Publications:

Fischer A, Santana-Cruz I, Giglio M, Nadendla S, Drabek E, Vilei EM, Frey J, Jores J.Genome Sequence of Mycoplasma feriruminatoris sp. Nov., a Fast-Growing Mycoplasma species. Genome Announc. 2013 Jan;1(1).

Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D’Eustachio, Robert Finn, Michelle Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch Mizrachi, Monica Munoz-Torres, Darren Natale, Claire O’Donovan, Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul Schofield, Granger Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy Wu, Jasmine Young, Raja Mazumder. Recent advances in biocuration: Meeting Report from the 5th International Biocuration Conference. Database, 2012 Oct. 29.

Witzel K, Gwinn-Giglio M, Nadendla S, Shefchek K, Ruppel S. Genome Sequence of Enterobacter radicincitans DSM16656T, a Plant Growth-Promoting Endophyte. J Bacteriol. 2012 Oct;194(19):5469.

The Human Microbiome Project Consortium (Giglio, 11th out of 248 authors). Structure, function and diversity of the healthy human microbiome. Nature, June 2012, 486, 207-214.

The Human Microbiome Project Consortium (Giglio, 5th out of 248 authors). A framework for human microbiome research. Nature, June 2012, 486, 215–221.

Cecilia Arighi, Phoebe Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle Gwinn Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E. Thomas, Luca Toldo, Lynette Hirschman and Cathy H Wu. BioCreative III Interactive Task: an Overview. BMC Bioinformatics, October 2011, 12(Suppl 8):S4.

Kevin Galens, Joshua Orvis, Sean Daugherty, Heather H. Creasy, Sam Angiuoli, Owen White, Jennifer Wortman, Anup Mahurkar, Michelle Gwinn Giglio. The IGS Standard Operating Procedure for Automated Prokaryotic Annotation. SIGS 2011 Apr:Vol 4, No 2

Trudy Torto-Alalibo, Candace W. Collmer, Michelle Gwinn-Giglio, Magdalen Lindeberg, Shaowu Meng, Marcus C. Chibucos, Tsai-Tien Tseng, Jane Lomax, Bryan Biehl, Amelia Ireland, David Bird, Ralph A. Dean, Jeremy D. Glasner, Nicole Perna, Joao C. Setubal, Alan Collmer, and Brett M. Tyler. Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology.
Microbiol. Mol. Biol. Rev. December 2010 74: 479-503

Human Microbiome Jumpstart Reference Strains Consortium: Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D. A catalog of reference genomes from the human microbiome. Science. 2010 May 21;328(5981):994-9. PMCID:PMC2940224

Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5.

Giglio MG, Collmer CW, Lomax J, Ireland A.  Applying the Gene Ontology in Microbial Annotation. Trends Microbiol. 2009 Jul;17(7):262-8.

Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol. 2009 Apr;75(7):2046-56.

Chibucos MC, Collmer CW, Torto-Alalibo T, Gwinn-Giglio M, Lindeberg M, Li D, Tyler BM. Programmed cell death in host-symbiont associations, viewed through the Gene Ontology. BMC Microbiol. 2009 Feb 19;9 Suppl 1:S5.

Torto-Alalibo T, Collmer CW, Gwinn-Giglio M. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions. BMC Microbiol. 2009 Feb 19;9 Suppl 1:S1.

The Gene Ontology Consortium (includes: Midori A. Harris, Jennifer I. Deegan (née Clark), Amelia Ireland, Jane Lomax, Michael Ashburner, Susan Tweedie, Seth Carbon, Suzanna Lewis, Chris Mungall, John Day-Richter, Karen Eilbeck, Judith A. Blake, Carol Bult, Alexander D. Diehl, Mary Dolan, Harold Drabkin, Janan T. Eppig, David P. Hill, Li Ni, Martin Ringwald, Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Karen R. Christie, Maria C. Costanzo, Qing Dong, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Eurie L. Hong, Cynthia J. Krieger, Stuart R. Miyasato, Robert S. Nash, Julie Park, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kathy K. Zhu, David Botstein, Kara Dolinski, Michael S. Livstone, Rose Oughtred, Tanya Berardini, Donghui Li, Seung Y. Rhee, Rolf Apweiler, Daniel Barrell, Evelyn Camon, Emily Dimmer, Rachael Huntley, Nicola Mulder, Varsha K. Khodiyar, Ruth C. Lovering, Sue Povey, Rex Chisholm, Petra Fey, Pascale Gaudet, Warren Kibbe, Ranjana Kishore, Erich M. Schwarz, Paul Sternberg, Kimberly Van Auken, Michelle Gwinn Giglio, Linda Hannick, Jennifer Wortman, Martin Aslett, Matthew Berriman, Valerie Wood, Howard Jacob, Stan Laulederkind, Victoria Petri, Mary Shimoyama, Jennifer Smith, Simon Twigger, Pankaj Jaiswal, Trent Seigfried, Doug Howe, Monte Westerfield, Candace Collmer, Trudy Torto-Alalibo, Erika Feltrin, Giorgio Valle, Susan Bromberg, Shane Burgess, Fiona McCarthy). The Gene Ontology Project in 2008. Nucleic Acids Res. 2008 Jan;36 (Database issue):D440-4. Epub 2007 Nov 4.

Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4. Epub 2006 Dec 6.

Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrazek J, Ren Q Paulsen IT, Nelson KE, Khouri HM, Radune D, Sosa J, Dodson RJ, Sullivan SA, Rosovitz MJ, Madupu R, Brinkac LM, Durkin AS, Daugherty SC, Kothari SP, Giglio MG, Zhou L, Haft DH, Selengut JD, Davidsen TM, Yang Q, Zafar N, Ward NL. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. J Bacteriol. 2006 Oct;188(19):6841-50

Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet. 2006 Feb;2(2):e21. Epub 2006 Feb 17.

Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5. Epub 2005 Sep 19. Erratum in: Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16530.

Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol. 2005 Sep;187(18):6488-98.

Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS 3rd, Thomashow LS, Loper JE. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol. 2005 Jul;23(7):873-8. Epub 2005 Jun 26. Erratum in: Nat Biotechnol. 2006 Apr;24(4):466.

Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, Deboy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM. Structural flexibility in the Burkholderia mallei genome. Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14246-51. Epub 2004 Sep 17.

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.

Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM. Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments. Science. 2003 Dec 12;302(5652):1967-9.

Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Daugherty S, Brinkac L, Beanan MJ, Haft DH, Nelson WC, Davidsen T, Zafar N, Zhou L, Liu J, Yuan Q, Khouri H, Fedorova N, Tran B, Russell D, Berry K, Utterback T, Van Aken SE, Feldblyum TV, D'Ascenzo M, Deng WL, Ramos AR, Alfano JR, Cartinhour S, Chatterjee AK, Delaney TP, Lazarowitz SG, Martin GB, Schneider DJ, Tang X, Bender CL, White O, Fraser CM, Collmer A. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A. 2003 Sep 2;100(18):10181-6. Epub 2003 Aug 19.

Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM. Complete genome sequence of the oral pathogenic Bacterium Porphyromonas gingivalis strain W83. J Bacteriol. 2003 Sep;185(18):5591-601. Erratum in: J Bacteriol. 2004 Jan;186(2):593.

Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 2003 May 1;423(6935):81-6.

Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs Jr WR Jr, Venter JC, Fraser CM. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol. 2002 Oct;184(19):5479-90.

Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9509-14. Epub 2002 Jul 1.

Fouts DE, Abramovitch RB, Alfano JR, Baldo AM, Buell CR, Cartinhour S, Chatterjee AK, D'Ascenzo M, Gwinn ML, Lazarowitz SG, Lin NC, Martin GB, Rehm AH, Schneider DJ, van Dijk K, Tang X, Collmer A Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2275-80.

Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science. 2001 Jul 20;293(5529):498-506.

Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, Heidelberg JF, Alley MR, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C, Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A, Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM. Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):4136-41.

Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 2000 Aug 3;406(6795):477 83.

Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen J, Fraser CM. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 2000 Mar 15;28(6):1397-406.

Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 2000 Mar 10;287(5459):1809-15.

Casjens S, Palmer N, van Vugt R, Huang WM, Stevenson B, Rosa P, Lathigra R, Sutton G, Peterson J, Dodson RJ, Haft D, Hickey E, Gwinn M, White O, Fraser CM. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol Microbiol. 2000 Feb;35(3):490-516.

Smith HO, Gwinn ML, Salzberg SL. DNA uptake signal sequences in naturally transformable bacteria. Res Microbiol. 1999 Nov-Dec;150(9-10):603-16.

White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science. 1999 Nov 19;286(5444):1571-7.

Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 1999 May 27;399(6734):323-9.

Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, Sodergren E, Hardham JM, McLeod MP, Salzberg S, Peterson J, Khalak H, Richardson D, Howell JK, Chidambaram M, Utterback T, McDonald L, Artiach P, Bowman C, Cotton MD, Fujii C, Garland S, Hatch B, Horst K, Roberts K, Sandusky M, Weidman J, Smith HO, Venter JC. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science. 1998 Jul 17;281(5375):375-88.

Gwinn ML, Ramanathan R, Smith HO, Tomb JF. A new transformation-deficient mutant of Haemophilus influenzae Rd with normal DNA uptake. J Bacteriol. 1998 Feb;180(3):746-8

Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, van Vugt R, Palmer N, Adams MD, Gocayne J, Weidman J, Utterback T, Watthey L, McDonald L, Artiach P, Bowman C, Garland S, Fuji C, Cotton MD, Horst K, Roberts K, Hatch B, Smith HO, Venter JC. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 1997 Dec 11;390(6660):580-6.

Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 1997 Nov 27;390(6658):364-70. Erratum in: Nature 1998 Jul 2;394(6688):101.

Gwinn ML, Stellwagen AE, Craig NL, Tomb JF, Smith HO. In vitro Tn7 mutagenesis of Haemophilus influenzae Rd and characterization of the role of atpA in transformation. J Bacteriol.1997 Dec;179(23):7315-20.

Gwinn ML, Yi D, Smith HO, Tomb JF. Role of the two-component signal transduction and the phosphoenolpyruvate: carbohydrate phosphotransferase systems in competence development of Haemophilus influenzae Rd. J Bacteriol. 1996 Nov;178(21):6366-8.