(You can click on the titles to download the papers)

Journal Articles

2024

• Diwakar Davar, Robert M. Morrison, Amiran K. Dzutsev, Arivarasan Karunamurthy, Joe-Marc Chauvin, Florent Amatore, Julie S. Deutsch, Rodrigo X. Das Neves, Richard R. Rodrigues, John A. McCulloch, Hong Wang, Douglas J. Hartman, Jonathan H. Badger, Miriam R. Fernandes, Yulong Bai, Jie Sun, Alicia M. Cole, Poonam Aggarwal, Jennifer R. Fang, Christopher Deitrick, Riyue Bao, Umamaheswar Duvvuri, Shaum S. Sridharan, Seungwon W. Kim, Haroon A. Choudry, Matthew P. Holtzman, James F. Pingpank, James Patrick O'Toole, Richelle DeBlasio, Yang Jin, Quanquan Ding, Wentao Gao, Christopher Groetsch, Ornella Pagliano, Amy Rose, Corey Urban, Jagjit Singh, Prajan Divarkar, David Mauro, Dmitri Bobilev, James Wooldridge, Arthur M. Krieg, Matthew G. Fury, Jeffrey R. Whiteaker, Lei Zhao, Amanda G. Paulovich, Yana G. Najjar, Jason J. Luke, John M. Kirkwood, Janis M. Taube, Hyun Jung Park, Giorgio Trinchieri, and Hassane M. Zarour. Neoadjuvant vidutolimod and nivolumab in high-risk resectable melanoma: A prospective phase II trial. Cancer Cell. https://doi.org/10.1016/j.ccell.2024.10.007. PMID:39486411/

• Francesca Benedetti, Emmanuel F. Mongodin, Jonathan H. Badger, Arshi Munawwar, Ashley Cellini, Weirong Yuan, Giovannino Silvestri, Carl N. Kraus, Simone Marini, Chozha V. Rathinam, Marco Salemi, Hervé Tettelin, Robert C. Gallo, Davide Zella. Bacterial DnaK reduces the activity of anti-cancer drugs cisplatin and 5FU. Journal of Translational Medicine. 22:269 2024. PMID:38475767/

2023

• Natasha R Soares, José C Huguet-Tapia, Dongli Guan, Christopher A Clark, Kuei-Ting Yang, Olivia R Kluchka, Raju S Thombal, Rendy Kartika, Jonathan H Badger, Gregg S Pettis. Comparative genomics of the niche-specific plant pathogen Streptomyces ipomoeae reveal novel genome content and organization. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.00308-23 2023. PMID:38009923

• Jonathan H Badger, Rosanna Giordano, Aleksey Zimin, Robert Wappel,Senem M Eskipehlivan, Stephanie Muller, Ravikiran Donthu, Felipe Soto-Adames, Paulo Vieira, Inga Zasada, Sara Goodwin. Direct sequencing of insect symbionts via nanopore adaptive sampling . Current Opinion in Insect Science. https://doi.org/10.1016/j.cois.2023.101135 2023. PMID:37926187

2022

• John A. McCulloch, Diwakar Davar, Richard R. Rodrigues, Jonathan H. Badger, Jennifer R. Fang, Alicia M. Cole, Ascharya K. Balaji, Marie Vetizou, Stephanie M. Prescott, Miriam R. Fernandes, Raquel G. F. Costa, Wuxing Yuan, Rosalba Salcedo, Erol Bahadiroglu, Soumen Roy, Richelle N. DeBlasio, Robert M. Morrison, Joe-Marc Chauvin, Quanquan Ding, Bochra Zidi, Ava Lowin, Saranya Chakka, Wentao Gao, Ornella Pagliano, Scarlett J. Ernst, Amy Rose, Nolan K. Newman, Andrey Morgun, Hassane M. Zarour, Giorgio Trinchieri, Amiran K. Dzutsev. Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. Nature Medicine. https://doi.org/10.1038/s41591-022-01698-2 2022. PMID:35228752

2021

• Christine N Spencer, Jennifer L McQuade, Vancheswaran Gopalakrishnan, John A McCulloch, Marie Vetizou, Alexandria P Cogdill, Md A Wadud Khan, Xiaotao Zhang, Michael G White, Christine B Peterson, Matthew C Wong, Golnaz Morad, Theresa Rodgers, Jonathan H Badger, Beth A Helmink, Miles C Andrews, Richard R Rodrigues, Andrey Morgun, Young S Kim, Jason Roszik, Kristi L Hoffman, Jiali Zheng, Yifan Zhou, Yusra B Medik, Laura M Kahn, Sarah Johnson, Courtney W Hudgens, Khalida Wani, Pierre-Olivier Gaudreau, Angela L Harris, Mohamed A Jamal, Erez N Baruch, Eva Perez-Guijarro, Chi-Ping Day, Glenn Merlino, Barbara Pazdrak, Brooke S Lochmann, Robert A Szczepaniak-Sloane, Reetakshi Arora, Jaime Anderson, Chrystia M Zobniw, Eliza Posada, Elizabeth Sirmans, Julie Simon, Lauren E Haydu, Elizabeth M Burton, Linghua Wang, Minghao Dang, Karen Clise-Dwyer, Sarah Schneider, Thomas Chapman, Nana-Ama A S Anang, Sheila Duncan, Joseph Toker, Jared C Malke, Isabella C Glitza, Rodabe N Amaria, Hussein A Tawbi, Adi Diab, Michael K Wong, Sapna P Patel, Scott E Woodman, Michael A Davies, Merrick I Ross, Jeffrey E Gershenwald, Jeffrey E Lee, Patrick Hwu, Vanessa Jensen, Yardena Samuels, Ravid Straussman, Nadim J Ajami, Kelly C Nelson, Luigi Nezi, Joseph F Petrosino, P Andrew Futreal, Alexander J Lazar, Jianhua Hu, Robert R Jenq, Michael T Tetzlaff, Yan Yan, Wendy S Garrett, Curtis Huttenhower, Padmanee Sharma, Stephanie S Watowich, James P Allison, Lorenzo Cohen, Giorgio Trinchieri, Carrie R Daniel, Jennifer A Wargo. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science. 374:1632-1640. 2021. PMID:34941392

• Benedikt Hild, Matthew S. Dreier, Ji Hoon Oh, John A. McCulloch, Jonathan H. Badger, Juen Guo, Claire E. Thefaine, Regina Umarova, Kevin D. Hall, Oksana Gavrilova, Stephan P. Rosshart, Giorgio Trinchieri, Barbara Rehermann. Neonatal exposure to a wild-derived microbiome protects mice against diet-induced obesity. Nature Metabolism. 8:1042-1057. 2021. PMID:34417593

• Diwakar Davar, Amiran K. Dzutsev, John A. McCulloch, Richard R. Rodrigues, Joe-Marc Chauvin1, Robert M. Morrison1, Richelle N. Deblasio, Carmine Menna, Quanquan Ding, Ornella Pagliano, Bochra Zidi, Shuowen Zhang, Jonathan H. Badger, Marie Vetizou, Alicia M. Cole, Miriam R. Fernandes, Stephanie Prescott, Raquel G. F. Costa, Ascharya K. Balaji, Andrey Morgun, Ivan Vujkovic-Cvijin, Hong Wang, Amir A. Borhani, Marc B. Schwartz, Howard M. Dubner, Scarlett J. Ernst, Amy Rose, Yana G. Najjar, Yasmine Belkaid, John M. Kirkwood, Giorgio Trinchieri, Hassane M. Zarour. Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients. Science. 371:595-602. 2021. PMID:33542131

2020

• Rosanna Giordano, Ravi Kiran Donthu, Aleksey V Zimin, Irene Consuelo Julca Chavez, Toni Gabaldon, Manuella van Munster, Lawrence Hon, Richard Hall, Jonathan H Badger, Minh Nguyen, Alejandra Flores, Bruce Potter, Tugrul Giray, Felipe N Soto-Adames, Everett Weber, Jose A P Marcelino, Christopher J Fields, David J Voegtlin, Curt B Hill, Glen L Hartman. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. Insect Biochemistry and Molecular Biology. 120:103334. 2020. PMID:32109587

2019

• Hojun Song, Ravi Kiran Donthu, Richard Hall, Lawrence Hon, Everett Weber, Jonathan H. Badger, Rosanna Giordano. Description of soybean aphid (Aphis glycines Matsumura) mitochondrial genome and comparative mitogenomics of Aphididae (Hemiptera: Sternorrhyncha). Insect Biochemistry and Molecular Biology. 113:103208. 2019. PMID:31422150

• Stephan P. Rosshart, Jasmin Herz, Brian G. Vassallo, Ashli Hunter, Morgan K. Wall, Jonathan H. Badger, John A. McCulloch, Dimitrios G. Anastasakis, Aishe A. Sarshad, Irina Leonardi, Nicholas Collins, Joshua A. Blatter, Seong-Ji Han, Samira Tamoutounour, Svetlana Potapova, Mark B. Foster St. Claire, Wuxing Yuan, Shurjo K. Sen, Matthew S. Dreier, Benedikt Hild, Markus Hafner, David Wang, Iliyan D. Iliev, Yasmine Belkaid, Giorgio Trinchieri, Barbara Rehermann. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 365(6452):eaaw4361. 2019. PMID:31371577

2018

• Aliia R. Fatkhullina, Iuliia O. Peshkova, Amiran Dzutsev, Turan Aghayev, John A. McCulloch, Vishal Thovarai, Jonathan H.Badger, Ravi Vats Prithu Sundd, Hsin-Yao Tang. Andrew V. Kossenkov, Stanley L. Hazen, Giorgio Trinchieri, Sergei I. Grivennikov, Ekaterina K. Koltsova. An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis. Immunity. 49(5):943-957. 2018. PMID:30389414

• Teizo Yoshimura, Mairi H. McLean, Amiran K. Dzutsev, Xiaohong Yao, Keqiang Chen, Jiaqiang Huang, Wanghua Gong, Jiamin Zhou, Yi Xiang, Jonathan H. Badger, Colm O hUigin, Vishal Thovarai, Lino Tessarollo, Scott K. Durum, Giorgio Trinchieri, Xiu-wu Bian, Ji Ming Wang. The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance. Journal of Immunology. 200(6):2174-2185. 2018. PMID:29440355

• Sara J. Bender, Dawn M. Moran, Matthew R. McIlvin, Hong Zheng, John P. McCrow, Jonathan Badger, Giacomo R. DiTullio, Andrew E. Allen, Mak A. Saito. Colony formation in Phaeocystis antarctica: connecting molecular mechanisms with iron biogeochemistry. Biogeosciences. 15:4923-4942. 2018.

2017

• Stephan P. Rosshart, Brian G. Vassallo, Davide Angeletti, Diane S. Hutchinson, Andrew P. Morgan, Kazuyo Takeda, Heather D. Hickman, John A. McCulloch, Jonathan H. Badger, Nadim J. Ajami, Giorgio Trinchieri, Fernando Pardo-Manuel de Villena, Jonathan W. Yewdell, Barbara Rehermann. Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance. Cell 171(5):1015-1028. 2017. PMID:29056339

• Lisa Zeigler Allen, John P. McCrow, Karolina Ininbergs, Christopher L. Dupont, Jonathan H. Badger, Jeffery M. Hoffman, Martin Ekman, Andrew E. Allen, Birgitta Bergman, J. Craig Venter. The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses. mSystems 2:e00125-16. 2017. PMID:28217745

• Amiran Dzutsev, Jonathan H. Badger, Ernesto Perez-Chanona, Soumen Roy, Rosalba Salcedo, Carolyne K. Smith, Giorgio Trinchieri. Microbes and Cancer. Annual Review of Immunology 35:199-228. 2017. PMID:28142322

2016

• Sarah R. Smith, Jeroen T. F. Gillard, Adam B. Kustka, John P. McCrow, Jonathan H. Badger, Hong Zheng, Ashley M. New, Chris L. Dupont, Toshihiro Obata, Alisdair R. Fernie, Andrew E. Allen. Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. PLOS Genetics. 12:e1006490. 2016. PMID:27973599

• Eileen P Hamilton, Aurélie Kapusta, Piroska E Huvos, Shelby L Bidwell, Nikhat Zafar, Haibao Tang, Michalis Hadjithomas, Vivek Krishnakumar, Jonathan H Badger, Elisabet V Caler, Carsten Russ, Qiandong Zeng, Lin Fan, Joshua Z Levin, Terrance Shea, Sarah K Young, Ryan Hegarty, Riza Daza, Sharvari Gujja, Jennifer R Wortman, Bruce W Birren, Chad Nusbaum, Jainy Thomas, Clayton M Carey, Ellen J Pritham, Cédric Feschotte, Tomoko Noto, Kazufumi Mochizuki, Romeo Papazyan, Sean D Taverna, Paul H Dear, Donna M Cassidy-Hanley, Jie Xiong, Wei Miao, Eduardo Orias, Robert S Coyne. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome. eLife. 10.7554/eLife.19090. 2016. PMID:27892853

• Jose C. Huguet-Tapia, Tristan Lefebure, Jonathan H. Badger, Dongli Guan, Gregg S. Pettis, Michael J. Stanhope, Rosemary Loria. Genome Content and Phylogenomics Reveal both Ancestral and Lateral Evolutionary Pathways in Plant-Pathogenic Streptomyces Species. Applied and Environmental Microbiology. 82:2146-2155. 2016. PMID:26826232

2015

• Huan Chen, Lauren M. Brinkac, Pamela Mishra, Nan Li, Despoina S. Lymperopoulou, Tamar L. Dickerson, Nadine Gordon-Bradley, Henry N. Williams, and Jonathan H. Badger. Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters. Stand Genomic Sci. 10:11, 2015. PMID:26203326

• Srijak Bhatnagar, Jonathan H. Badger, Ramana Madupu, Hoda M. Khouri, Elizabeth M. O'Connor, Frank T. Robb, Naomi L. Ward, and Jonathan A. Eisen. Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria). Genome Announc. 3:e01490-14, 2015. PMID:25635017

• Srijak Bhatnagar, Jonathan H. Badger, Ramana Madupu, Hoda M. Khouri, Elizabeth M. O'Connor, Frank T. Robb, Naomi L. Ward, and Jonathan A. Eisen. Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae). Genome Announc. 3:e01489-14, 2015. PMID:25635016

2014

• Alexandra Alexiev, David A. Coil, Jonathan H. Badger, Julie Enticknap, Naomi Ward, Frank T. Robb, and Jonathan A. Eisen. Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announc. 2:e00470-14, 2014. PMID:24831154

• Chris L. Dupont, John Larsson, Shibu Yooseph, Karolina Ininbergs, Johannes Goll, Johannes Asplund-Samuelsson, John P. McCrow, Narin Celepli, Lisa Zeigler Allen, Martin Ekman, Andrew J. Lucas, Åke Hagström, Mathangi Thiagarajn, Björn Brindefalk, Alexander R. Richter, Anders F. Andersson, Aaron Tenney, Daniel Lundin, Andrey Tovchigrechko, Johan A. A. Nylander, Daniel Brami, Jonathan H. Badger, Andrew E. Allen, Douglas B. Rusch, Jeff Hoffman, Erling Norrby, Robert Friedman, Jarone Pinhassi, J. Craig Venter, and Birgitta Bergman. Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition. PLOS ONE 9:e89549, 2014. PMID:24586863

• David A. Coil, Jonathan H. Badger, Heather C. Forberger, Florenta Riggs, Ramana Madupu, Nadia Fedorova, Naomi Ward, Frank T. Robb, and Jonathan A. Eisen. Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12. Genome Announc. 2:e00109-14, 2014. PMID:24558247

• Hannah E. Holland-Moritz, David A. Coil, Jonathan H. Badger, George I. Dmitrov, Hoda Khouri, Naomi L. Ward, Frank T. Robb, and Jonathan A. Eisen. Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1. Genome Announc. 2:e00833-14, 2014. PMID:25146141

2013

• Jeffrey S. McLean, Mary-Jane Lombardo, Jonathan H. Badger, Anna Edlund, Mark Novotny, Joyclyn Yee-Greenbaum, Nikolay Vyahhi, Adam P. Hall, Youngik Yang, Christopher L. Dupont, Michael G. Ziegler, Hamidreza Chitsaz, Andrew E. Allen, Shibu Yooseph, Glenn Tesler, Pavel A. Pevzner, Robert M. Friedman, Kenneth H. Nealson, J. Craig Venter, and Roger S. Lasken. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences, USA 110:E2390-E2399, 2013. PMID:23754396

• Jeffrey S. McLean, Mary-Jane Lombardo, Michael G. Ziegler,Mark Novotny, Joyclyn Yee-Greenbaum, Jonathan H. Badger, Glenn Tesler, Sergey Nurk, Valery Lesin, Daniel Brami, Adam P. Hall, Anna Edlund, Lisa Z. Allen, Scott Durkin, Sharon Reed, Francesca Torriani, Kenneth H. Nealson, Pavel A. Pevzner, Robert Friedman, J. Craig Venter and Roger S. Lasken. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Research 23(5):867-877. 2013 PMID:23564253

• Talina Konotchick, Christopher L. Dupont, Ruben E. Valas, Jonathan H. Badger, and Andrew E. Allen. Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season. New Phytologist 198(2):398-407. 2013. PMID:23488966

• Rashel V. Grindberg, Joyclyn L. Yee-Greenbaum, Michael J. McConnell, Mark Novotny, Andy L. O'Shaughnessy, Georgina M. Lambert, Marcos J. Araúzo-Bravo, Jun Lee, Max Fishman, Gillian E. Robbins, Xiaoying Lin, Pratap Venepally, Jonathan H. Badger, David W. Galbraith, Fred H. Gage, and Roger S. Lasken. RNA-sequencing from single nuclei. Proceedings of the National Academy of Sciences, USA 110:19802-19807. 2013. PMID: 24248345

2012

• Anthony A. Fodor, Todd Z. DeSantis, Kristine M. Wylie, Jonathan H. Badger, Yuzhen Ye, Theresa Hepburn, Ping Hu, Erica Sodergren, Konstantinos Liolios, Heather Huot-Creasy, Bruce W. Birren and Ashlee M. Earl. The "Most Wanted" Taxa from the Human Microbiome for Whole Genome Sequencing. PLOS ONE 7:e41294, 2012. PMID:22848458

• The Human Microbiome Consortium: Barbara A. Methé, Karen E. Nelson, Mihai Pop, Heather H. Creasy, Michelle G. Giglio, Curtis Huttenhower, Dirk Gevers, Joseph F. Petrosino, Sahar Abubucker, Jonathan H. Badger, Asif T. Chinwalla, Ashlee M. Earl, et al. A framework for human microbiome research. Nature 486:215-221, 2012. PMID:22699610

• The Human Microbiome Consortium: Curtis Huttenhower, Dirk Gevers, Rob Knight, Sahar Abubucker, Jonathan H. Badger, Asif T. Chinwalla, Heather H. Creasy, Ashlee M. Earl, et al. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214, 2012. PMID:22699609

• Nadine Ziemert, Sheila Podell, Kevin Penn, Jonathan H. Badger, Eric Allen, Paul R. Jensen. The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity. PLOS ONE 7:e34064, 2012. PMID:22479523

• 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 6:1403-1414, 2012. PMID:22278668

2011

• 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

• 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

• Yuansha Chen, O. Colin Stine, Jonathan H. Badger, Ana I. Gil, G. Balakrish Nair, Mitsuaki Nishibuchi and Derrick E. Fouts. Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence BMC Genomics 12:294, 2011. PMID:21645368

• José C. Huguet-Tapia, Jonathan H. Badger, Rosemary Loria, Gregg S. Pettis. Streptomyces turgidiscabies Car8 contains a modular pathogenicity island that shares virulence genes with other actinobacterial plant pathogens Plasmid 65:118-124, 2011. PMID:21087627

2010

• 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, Methé 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

• 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

Book Chapters

2011

• Jonathan H. Badger, Pauline C. Ng, and J. Craig Venter. The Human Genome, Microbiomes, and Disease. In Metagenomics of the Human Body, Karen E. Nelson, editor, pp. 1-14. Springer 2011

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.