(You can click on the titles to download the papers)
Book Chapters
2011
Journal Articles
2012
- Lisa Zeigler Allen, Eric E. Allen, Jonathan H. Badger, John P. McCrow, Ian T. Paulsen, Liam D.H. Elbourne, Mathangi Thiagarajan, Doug B. Rusch, Kenneth H. Nealson, Shannon J. Williamson, J. Craig Venter and Andrew E. Allen. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME Journal 6, 2012. PMID:22278668
2011
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Robert S. Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B. Hostetler,
Daniel Brami, Vinita S. Joardar, Justin Johnson, Diana Radune,
Irtisha Singh, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai,
Jianying Gu, Michael W. Mather, Akhil B. Vaidya, David E. Wilkes,
Vidyalakshmi Rajagopalan, David J. Asai, Chad G. Pearson, Robert C. Findly,
Harry W. Dickerson, Jonathan H. Badger, Martin Wu, Cindy Martens,
Yves Van de Peer, David S. Roos, Donna M. Cassidy-Hanley and Theodore G. Clark.
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Genome Biology 12:R100, 2011. PMID:22004680
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Hamidreza Chitsaz, Joyclyn L. Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo,
Christopher L. Dupont, Jonathan H. Badger, Mark Novotny,
Douglas B. Rusch, Louise J. Fraser, Niall A. Gormley, Ole Schulz-Trieglaff,
Geoffrey P. Smith, Dirk J. Evers, Pavel A. Pevzner and Roger S. Lasken.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets Nature Biotechnology 29:915-921, 2011. PMID:21926975
2010
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J. Mark Cock, Lieven Sterck, Pierre Rouzé, Delphine Scornet,
Andrew E. Allen, Grigoris Amoutzias, Veronique Anthouard, Francois
Artiguenave, Jean-Marc Aury, Jonathan H. Badger, Bank Beszteri,
Kenny Billiau, Eric Bonnet, John H. Bothwell, Chris Bowler, Catherine
Boyen, Colin Brownlee, Carl J. Carrano, Bénédicte
Charrier, Ga Youn Cho, Susana M. Coelho, Jonas Collen, Erwan Corre,
Corinne Da Silva, Ludovic Delage, Nicolas Delaroque, Simon M. Dittami,
Sylvie Doulbeau, Marek Elias, Garry Farnham, Claire M. M. Gachon,
Bernhard Gschloessl, Svenja Heesch, Kamel Jabbari, Claire Jubin,
Hiroshi Kawai, Kei Kimura, Bernard Kloareg, Frithjof C. Küpper,
Daniel Lang, Aude Le Bail, Catherine Leblanc, Patrice Lerouge, Martin
Lohr, Pascal J. Lopez, Cindy Martens, Florian Maumus, Gurvan Michel,
Diego Miranda-Saavedra, Julia Morales, Hervé Moreau, Taizo
Motomura, Chikako Nagasato, Carolyn A. Napoli, David R. Nelson, Pi
Nyvall-Collén, Akira F. Peters, Cyril Pommier, Philippe Potin,
Julie Poulain, Hadi Quesneville, Betsy Read, Stefan A. Rensing,
Andrés Ritter, Sylvie Rousvoal, Manoj Samanta, Gaelle Samson,
Declan C. Schroeder, Béatrice Ségurens, Martina
Strittmatter, Thierry Tonon, James W. Tregear, Klaus Valentin, Peter
von Dassow, Takahiro Yamagishi, Yves Van de Peer, and Patrick Wincker.
The
Ectocarpus genome and the independent evolution of multicellularity in
brown alga Nature 465:617-621, 2010. PMID:20520714
- The 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 328:994-999, 2010. PMID:20489017
- William P. Inskeep, Douglas B. Rusch, Zackary J. Jay,
Markus J. Herrgard, Mark A. Kozubal, Toby H. Richardson, Richard
E. Macur, Natsuko Hamamura, Ryan deM. Jennings, Bruce W. Fouke,
Anna-Louise Reysenbach, Frank Roberto, Mark Young, Ariel Schwartz,
Eric S. Boyd. Jonathan H. Badger, Eric J. Mathur, Alice
C. Ortmann, Mary Bateson, Gill Geesey, Marvin Frazier. Metagenomes
from high-temperature chemotrophic systems reveal geochemical controls
on microbial community structure and function. PLoS ONE
5:e9773, 2010. PMID:20333304
- Amber L. Hartman, Cédric Norais, Jonathan
H. Badger, Stéphane Delmas, Sam Haldenby, Ramana Madupu,
Jeffrey Robinson, Hoda Khouri, Qinghu Ren, Todd M. Lowe, Julie
Maupin-Furlow, Mecky Pohlschroder, Charles Daniels, Friedhelm
Pfeiffer, Thorsten Allers, Jonathan A. Eisen. The
Complete Genome Sequence of Haloferax volcanii DS2, a Model
Archaeon. PLoS ONE 5:e9605, 2010. PMID:20333302
- Liliana Losada, Catherine M. Ronning, David DeShazer,
Donald Woods, Natalie Fedorova, H. Stanley Kim, Svetlana A. Shabalina,
Talima R. Pearson, Lauren Brinkac, Patrick Tan, Tannistha Nandi,
Jonathan Crabtree, Jonathan Badger, Steve Beckstrom-Sternberg,
Muhammad Saqib, Steven E. Schutzer, Paul Keim, and William
C. Nierman. Continuing
Evolution of Burkholderia mallei Through Genome Reduction and
Large-Scale Rearrangements. Genome Biology and Evolution
2010:102-116, 2010. PMID:20333227
2009
- Joyce C. Yang, Ramana Madupu, A. Scott Durkin, Nathan A. Ekborg, Chandra S. Pedamallu, Jessica B. Hostetler, Diana Radune, Bradley S. Toms, Bernard Henrissat, Pedro M. Coutinho, Sandra Schwarz, Lauren Field, Amaro E. Trindade-Silva, Carlos A. G. Soares, Sherif Elshahawi, Amro Hanora, Eric W. Schmidt, Margo G. Haygood, Janos Posfai, Jack Benner, Catherine Madinger, John Nove, Brian Anton, Kshitiz Chaudhary, Jeremy Foster, Alex Holman, Sanjay Kumar, Philip A Lessard, Yvette A. Luyten,, Barton Slatko, Nicole Wood, Bo Wu, Max Teplitski, Joseph D. Mougous, Naomi Ward, Jonathan A. Eisen, Jonathan H. Badger, Daniel L. Distel. The Complete Genome of Teredinibacter turnerae T7901: An Intracellular Endosymbiont of Marine Wood-Boring Bivalves (Shipworms). PLoS ONE 4:e6085, 2009. PMID:
19568419
- Alexandra Z. Worden, Jae-Hyeok Lee, Thomas Mock, Pierre
Rouzé, Melinda P. Simmons, Andrea L. Aerts, Andrew E. Allen,
Marie L. Cuvelier, Evelyne Derelle, Meredith V. Everett, Elodie
Foulon, Jane Grimwood, Heidrun Gundlach, Bernard Henrissat, Carolyn
Napoli, Sarah M. McDonald, Micaela S. Parker, Stephane Rombauts, Aasf
Salamov, Peter Von Dassow, Jonathan H. Badger, Pedro
M. Coutinho, Elif Demir, Inna Dubchak, Chelle Gentemann, Wenche
Eikrem, Jill E. Gready, Uwe John, William Lanier, Erika A. Lindquist,
Susan Lucas, Klaus F. X. Mayer, Herve Moreau, Fabrice Not, Robert
Otillar, Olivier Panaud, Jasmyn Pangilinan, Ian Paulsen, Benoit Piegu,
Aaron Poliakov, Steven Robbens, Jeremy Schmutz, Eve Toulza, Tania
Wyss, Alexander Zelensky, Kemin Zhou, E. Virginia Armbrust, Debashish
Bhattacharya, Ursula W. Goodenough, Yves Van de Peer, and Igor
V. Grigoriev. Green
Evolution and Dynamic Adaptations Revealed by Genomes of the Marine
Picoeukaryotes Micromonas. Science 324:268-272,
2009. PMID:
19359590
- Naomi L. Ward, Jean F.Challacombe, Peter H. Janssen,
Bernard Henrissat, Pedro M. Coutinho, Martin Wu, Gary Xie, Daniel
H. Haft, Michelle Sait, Jonathan Badger, Ravi D. Barabote,
Brent Bradley, Thomas S. Brettin, Lauren M. Brinkac, David Bruce, Todd
Creasy, Sean C. Daugherty, Tanja M Davidsen, Robert T. DeBoy, J. Chris
Detter, Robert J. Dodson, A. Scott Durkin, Anuradha Ganapathy,
Michelle Gwinn-Giglio, Cliff S. Han, Hoda Khouri, Hajnalka Kiss, Sagar
P. Kothari, Ramana Madupu, Karen Nelson, William C. Nelson, Ian
Paulsen, Kevin Penn, Qinghu Ren, M.J. Rosovitz, Jeremy D. Selengut,
Susmita Shrivastava, Steven A. Sullivan, Roxanne Tapia, L. Sue
Thompson, Kisha L. Watkins, Qi Yang, Chunhui Yu, Nikhat Zafar, Liwei
Zhou, and Cheryl R. Kuske. Three
genomes from the phylum Acidobacteria provide insight into their
lifestyles in soils. Appl Environ Microbiol 75:2046-2056, 2009. PMID:
19201974
- Dongying Wu, Jason
Raymond, Martin Wu, Sourav Chatterji, Qinghu Ren, Joel E. Graham,
Donald A. Bryant, Frank Robb, Albert Colman, Luke J. Tallon,
Jonathan H. Badger, Ramana Madupu, Naomi L. Ward and Jonathan
A. Eisen. Complete Genome
Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium
roseum. PLoS ONE 4:e4207, 2009. PMID:
19148287
2008
- Chris Bowler, Andrew E. Allen, Jonathan H. Badger,
Jane Grimwood, Kamel Jabbari, Alan Kuo, Uma Maheswari, Cindy Martens,
Florian Maumus, Robert P. Otillar, Edda Rayko, Asaf Salamov, Klaas
Vandepoele, Bank Beszteri, Ansgar Gruber, Marc Heijde, Michael
Katinka, Thomas Mock, Klaus Valentin, Fréderic Verret, John
A. Berges, Colin Brownlee, Jean-Paul Cadoret, Anthony Chiovitti, Chang
Jae Choi, Sacha Coesel, Alessandra De Martino, J. Chris Detter,
Colleen Durkin, Angela Falciatore, Jérome Fournet, Miyoshi
Haruta, Marie J. J. Huysman, Bethany D. Jenkins, Katerina Jiroutova,
Richard E. Jorgensen, Yolaine Joubert, Aaron Kaplan, Nils Kröger,
Peter G. Kroth, Julie La Roche, Erica Lindquist, Markus Lommer,
Véronique Martin–Jézéquel, Pascal J. Lopez,
Susan Lucas, Manuela Mangogna, Karen McGinnis, Linda K. Medlin, Anton
Montsant, Marie-Pierre Oudot–Le Secq, Carolyn Napoli, Miroslav
Obornik, Micaela Schnitzler Parker, Jean-Louis Petit, Betina
M. Porcel, Nicole Poulsen, Matthew Robison, Leszek Rychlewski, Tatiana
A. Rynearson, Jeremy Schmutz, Harris Shapiro, Magali Siaut, Michele
Stanley, Michael R. Sussman, Alison R. Taylor, Assaf Vardi, Peter von
Dassow, Wim Vyverman, Anusuya Willis, Lucjan S. Wyrwicz, Daniel
S. Rokhsar, Jean Weissenbach, E. Virginia Armbrust, Beverley R. Green,
Yves Van de Peer & Igor V. Grigoriev The
Phaeodactylum genome reveals the evolutionary history of diatom
genomes. Nature 456:239-244, 2008. PMID: 18923393
- Marco A van den Berg, Richard Albang, Kaj Albermann,
Jonathan H Badger, Jean-Marc Daran, Arnold J M Driessen, Carlos
Garcia-Estrada, Natalie D Fedorova, Diana M Harris, Wilbert H M
Heijne, Vinita Joardar, Jan A K W Kiel, Andriy Kovalchuk, Juan F
Martin, William C Nierman, Jeroen G Nijland, Jack T Pronk, Johannes A
Roubos, Ida J van der Klei, Noël N M E van Peij, Marten Veenhuis,
Hans von Döhren, Christian Wagner, Jennifer Wortman, Roel A L
Bovenberg Genome
sequencing and analysis of the filamentous fungus Penicillium
chrysogenum. Nature Biotechnology 26:1161-1168, 2008. PMID: 18820685
- Derrick E. Fouts, Heather L. Tyler, Robert T. DeBoy, Sean
Daugherty, Qinghu Ren, Jonathan H. Badger, Anthony S. Durkin,
Heather Huot, Susmita Shrivastava, Sagar Kothari, Robert J. Dodson,
Yasmin Mohamoud, Hoda Khouri, Luiz F. W. Roesch, Karen A. Krogfelt,
Carsten Struve, Eric W. Triplett, Barbara A. Methé Complete
genome sequence of the N2-fixing broad host range endophyte Klebsiella
pneumoniae 342 and virulence predictions verified in
mice. PLoS Genetics 4:e1000141, 2008. PMID: 18654632
- Natalie D. Fedorova, Nora Khaldi, Vinita S. Joardar, Rama
Maiti, Paolo Amedeo, Michael J. Anderson, Jonathan Crabtree, Joana
C. Silva, Jonathan H. Badger, Ahmed Albarraq, Sam Angiuoli,
Howard Bussey, Paul Bowyer, Peter J. Cotty, Paul S. Dyer, Amy Egan,
Kevin Galens, Claire M. Fraser-Liggett, Brian J. Haas, Jason
M. Inman, Richard Kent, Sebastien Lemieux, Iran Malavazi, Joshua
Orvis, Terry Roemer, Catherine M. Ronning, Jaideep P. Sundaram,
Granger Sutton, Geoff Turner, J. Craig Venter, Owen R. White, Brett
R. Whitty, Phil Youngman, Kenneth H. Wolfe, Gustavo H. Goldman,
Jennifer R. Wortman, Bo Jiang, David W. Denning, William C. Nierman
Genomic
Islands in the Pathogenic Filamentous Fungus Aspergillus
fumigatus PLoS Genetics 4:e1000046, 2008. PMID: 18404212
2007
- Garry S. A. Myers, Dane Parker, Keith Al-Hasani, Ruth
M. Kennan, Torsten Seemann, Qinghu Ren, Jonathan H. Badger,
Jeremy D. Selengut, Robert T. DeBoy, Herve Tettelin, John D. Boyce,
Victoria P. McCarl, Xiaoyan Han, William C. Nelson, Ramana Madupu,
Yasmin Mohamoud, Tara Holley, Nadia Fedorova, Hoda Khouri, Steven
P. Bottomley, Richard J. Whittington, Ben Adler, J. Glenn Songer,
Julian I. Rood and Ian T. Paulsen
Genome sequence and identification of candidate vaccine antigens
from the animal pathogen Dichelobacter nodosus Nature
Biotechnology 25:569-575, 2007. PMID: 17468768
2006
- Jonathan H. Badger, Timothy R. Hoover, Yves V. Brun,
Ronald M. Weiner, Michael T. Laub, Gladys Alexandre, Jan Mrazek, Qinghu
Ren, Ian T. Paulsen, Karen E. Nelson, Hoda M. Khouri, Diana Radune,
Julia Sosa, Robert J. Dodson, Steven A. Sullivan, M. J. Rosovitz,
Ramana Madupu, Lauren M. Brinkac, A. Scott Durkin, Sean C. Daugherty,
Sagar P. Kothari, Michelle Gwinn Giglio, Liwei Zhou, Daniel H. Haft,
Jeremy D. Selengut, Tanja M. Davidsen, Qi Yang, Nikhat Zafar, and Naomi
L. Ward Comparative
Genomic Evidence for a Close Relationship between the Dimorphic
Prosthecate Bacteria Hyphomonas neptunium and Caulobacter crescentus Journal of Bacteriology, 188(19): 6841-6850, 2006. PMID: 16980487
- Brian Palenik, Qinghu Ren, Chris L. Dupont, Garry S. Myers, John F. Heidelberg, Jonathan H. Badger,
Ramana Madupu, William C. Nelson, Lauren M. Brinkac, Robert J. Dodson,
A. Scott Durkin, Sean C. Daugherty, Stephen A. Sullivan, Hoda Khouri,
Yasmin Mohamoud, Rebecca Halpin, and Ian T. Paulsen. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proceedings of the National Academy of Sciences, USA, 103(36):13555–13559. 2006.PMID: 16938853
- Jonathan A. Eisen, Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R. Wortman, Jonathan H. Badger,
Qinghu Ren, Paolo Amedeo, Kristie M. Jones, Luke J. Tallon, Arthur L.
Delcher, Steven L. Salzberg, Joana C. Silva, Brian J. Haas, William H.
Majoros, Maryam Farzad, Jane M. Carlton, Roger K. Smith Jr., Jyoti
Garg, Ronald E. Pearlman, Kathleen M. Karrer, Lei Sun, Gerard Manning,
Nels C. Elde, Aaron P. Turkewitz, David J. Asai, David E. Wilkes,
Yufeng Wang, Hong Cai, Kathleen Collins, B. Andrew Stewart, Suzanne R.
Lee, Katarzyna Wilamowska, Zasha Weinberg, Walter L. Ruzzo, Dorota
Wloga, Jacek Gaertig, Joseph Frankel, Che-Chia Tsao, Martin A.
Gorovsky, Patrick J. Keeling, Ross F. Waller, Nicola J. Patron, J.
Michael Cherry, Nicholas A. Stover, Cynthia J. Krieger, Christina del
Toro, Hilary F. Ryder, Sondra C. Williamson, Rebecca A. Barbeau, Eileen
P. Hamilton, Eduardo Orias. Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLoS Biology 4:e286. 2006. PMID: 16933976
2005
- Najib M. El-Sayed, Peter J. Myler, Gaëlle Blandin, Matthew
Berriman, Jonathan Crabtree, Gautam Aggarwal, Elisabet Caler, Hubert
Renauld, Elizabeth A. Worthey, Christiane Hertz-Fowler, Elodie Ghedin,
Christopher Peacock, Daniella C. Bartholomeu, Brian J. Haas, Anh-Nhi
Tran, Jennifer R. Wortman, U. Cecilia M. Alsmark, Samuel Angiuoli,
Atashi Anupama, Jonathan Badger, Frederic Bringaud, Eithon
Cadag, Jane M. Carlton, Gustavo C. Cerqueira, Todd Creasy, Arthur L.
Delcher, Appolinaire Djikeng, T. Martin Embley, Christopher Hauser,
Alasdair C. Ivens, Sarah K. Kummerfeld, Jose B. Pereira-Leal, Daniel
Nilsson, Jeremy Peterson, Steven L. Salzberg, Joshua Shallom, Joana C.
Silva, Jaideep Sundaram, Scott Westenberger, Owen White, Sara E.
Melville, John E. Donelson, Björn Andersson, Kenneth D. Stuart, Neil
Hall. Comparative Genomics of Trypanosomatid Parasitic Protozoa, Science, 309:404-409, 2005. PMID: 16020724
- Derrick E. Fouts, Emmanuel F. Mongodin, Robert E. Mandrell,
William G. Miller, David A. Rasko, Jacques Ravel, Lauren M. Brinkac,
Robert T. DeBoy, Craig T. Parker, Sean C. Daugherty, Robert J. Dodson,
A. Scott Durkin, Ramana Madupu, Steven A. Sullivan, Jyoti U. Shetty,
Mobolanle A. Ayodeji, Alla Shvartsbeyn, Michael C. Schatz, Jonathan H. Badger, Claire M. Fraser, and Karen E. Nelson. Major Structural Differences and Novel Potential Virulence Mechanisms from the Genomes of Multiple Campylobacter Species. PLoS Biology 3:e15. 2005.PMID: 15660156
2004
2003
2001
1999
1997
- Hans-Peter Klenk, Rebecca A. Clayton, Jean-Francois Tomb, Owen
White, Karen E. Nelson, Karen A. Ketchum, Robert J. Dodson, Michelle
Gwinn, Erin K. Hickey, Jeremy D. Peterson, Delwood L. Richardson,
Anthony R. Kerlavage, David E. Graham, Nikos C. Kyrpides, Robert D.
Fleischmann, John Quackenbush, Norman H. Lee, Granger G. Sutton, Steven
Gill, Ewen F. Kirkness, Brian A. Dougherty, Keith Mckenney, Mark D.
Adams, Brendan Loftus, Scott Peterson, Claudia I. Reich, Leslie K.
Mcneil, Jonathan H. Badger, Anna Glodek, Lixin Zhou, Ross
Overbeek, Jeannine D. Gocayne, Janice F. Weidman, Lisa Mcdonald, Teresa
Utterback, Matthew D. Cotton, Tracy Spriggs, Patricia Artiach, Brian P.
Kaine, Sean M. Sykes, Paul W. Sadow, Kurt P. D'Andrea, Cheryl Bowman,
Claire Fujii, Stacey A. Garland, Tanya M. Mason, Gary J. Olsen, Claire
M. Fraser, Hamilton O. Smith, Carl R. Woese, J. Craig Venter. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature, 390:364-370. 1997. PMID: 9389475
Peer Reviewed Conference Articles
2003
2001