(You can click on the titles to download the papers)
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.
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.
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.
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.
Natalie D Fedorova, Jonathan H Badger, Geoff D Robson, Jennifer R Wortman, William C Nierman. Comparative analysis of programmed cell death pathways in filamentous fungi, BMC Genomics 6:177, 2005.
Michael Hu, Paul Kearney, Jonathan Badger. A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees, International Journal of Artificial Intelligence Tools, 14:717-731, 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.
Jonathan H Badger, Jonathan A Eisen and Naomi L Ward. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA-based phylogenetic analysis; implications for the taxonomy of the orders Rhodobacterales and Caulobacterales, International Journal of Evolutionary and Systematic Microbiology, 55:1021-1026, 2005.
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.
Huai-Chun Wang, Jonathan Badger, Paul Kearney, Ming Li. Analysis of Codon Usage Patterns of Bacterial Genomes Using the Self-Organizing Map. Molecular Biology and Evolution, 18(5):792-800. 2001.
Ming Li, Jonathan H. Badger, Chen Xin, Sam Kwong, Paul Kearney, Haoyong Zhang. An Information Based Sequence Distance and Its Application to Whole Mitochondrial Genome Phylogeny. Bioinformatics, 17(2):149-154. 2001.
Paul J. Haney, Jonathan H. Badger, Gerry L. Buldak, Claudia I. Reich, Carl R. Woese, Gary J. Olsen. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proceedings of the National Academy of Sciences, USA, 96(7):3578-3583. 1999.
Jonathan H. Badger, Gary J. Olsen. CRITICA: Coding Region Identification Tool Invoking Comparative Analysis. Molecular Biology and Evolution, 16(4):512-524. 1999.