T. taxus - Jonathan Badger's Home on the Net

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Journal Articles

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

Amy Egan, Anup Mahurkar, Jonathan Crabtree, Jonathan H Badger, Jane M Carlton and Joana C Silva. IDEA: Interactive Display for Evolutionary Analyses. BMC Bioinformatics 9:524, 2008. PMID:19061522

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

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. PMID: 16336669
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. PMID: 16020724
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. PMID: 15879228
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

Jonathan Badger, Paul Kearney, Ming Li, John Tsang, Tao Jiang. Selecting the Branches for an Evolutionary Tree. A Polynomial Time Approximation Scheme. Journal of Algorithms, 51:1-14. 2004.

2003

Claus Vogl, Jonathan Badger, Paul Kearney, Ming Li, Michael Clegg, Tao Jiang. Probabilistic Analysis Indicates Discordant Gene Trees in Chloroplast Evolution. Journal of Molecular Evolution, 56(3):330-340. 2003. PMID: 12612836

2001

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. PMID: 11319263
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. PMID: 11238070

1999

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. PMID: 10097079
Jonathan H. Badger, Gary J. Olsen. CRITICA: Coding Region Identification Tool Invoking Comparative Analysis. Molecular Biology and Evolution, 16(4):512-524. 1999. PMID: 10331277

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

Michael Hu, Paul Kearney, Jonathan Badger. A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees. In Proceedings of the 3rd IEEE International Symposium on Bioinformatics and Bioengineering (BIBE), pp. 95-104, Washington DC, March 10-12 2003.

2001

Jonathan H. Badger, Paul Kearney. Picking Fruit from the Tree of Life: Comments on Taxonomic Sampling and Quartet Methods. In Proceedings of the 16th ACM Symposium on Applied Computing (SAC), pp. 61-67, Las Vegas, March 11-14 2001.