Jonathan Badger - Publications

University of California, Davis, Davis, CA 

66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Davar D, Dzutsev AK, McCulloch JA, Rodrigues RR, Chauvin JM, Morrison RM, Deblasio RN, Menna C, Ding Q, Pagliano O, Zidi B, Zhang S, Badger JH, Vetizou M, Cole AM, et al. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science (New York, N.Y.). 371: 595-602. PMID 33542131 DOI: 10.1126/science.abf3363  0.04
2020 Giordano R, Donthu RK, Zimin A, Julca Chavez IC, Gabaldon T, van Munster M, Hon L, Hall R, Badger J, Nguyen M, Flores A, Potter B, Giray T, Soto-Adames FN, Weber E, et al. Soybean Aphid Biotype 1 Genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. Insect Biochemistry and Molecular Biology. 103334. PMID 32109587 DOI: 10.1016/J.Ibmb.2020.103334  0.01
2020 Kumar M, Singh P, Murugesan S, Vetizou M, McCulloch J, Badger JH, Trinchieri G, Al Khodor S. Microbiome as an Immunological Modifier. Methods in Molecular Biology (Clifton, N.J.). 2055: 595-638. PMID 31502171 DOI: 10.1007/978-1-4939-9773-2_27  0.01
2019 Song H, Donthu RK, Hall R, Hon L, Weber E, Badger JH, Giordano R. Description of soybean aphid (Aphis glycines Matsumura) mitochondrial genome and comparative mitogenomics of Aphididae (Hemiptera: Sternorrhyncha). Insect Biochemistry and Molecular Biology. 103208. PMID 31422150 DOI: 10.1016/J.Ibmb.2019.103208  0.01
2019 Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, McCulloch JA, Anastasakis DG, Sarshad AA, Leonardi I, Collins N, Blatter JA, Han SJ, Tamoutounour S, Potapova S, et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science (New York, N.Y.). 365. PMID 31371577 DOI: 10.1126/Science.Aaw4361  0.01
2019 Badger J, LaRose E, Mayer J, Bashiri F, Page D, Peissig P. Machine Learning for Phenotyping Opioid Overdose Events. Journal of Biomedical Informatics. 103185. PMID 31028874 DOI: 10.1016/J.Jbi.2019.103185  0.01
2019 Davar D, Vetizou MA, Dzutsev A, Badger J, McCullogh J, Menna C, Pagliano O, Kirkwood JM, Trinchieri G, Zarour HM. Abstract IA38: Manipulating the gut microbiome to improve immunotherapy of melanoma Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-Ia38  0.01
2018 Fatkhullina AR, Peshkova IO, Dzutsev A, Aghayev T, McCulloch JA, Thovarai V, Badger JH, Vats R, Sundd P, Tang HY, Kossenkov AV, Hazen SL, Trinchieri G, Grivennikov SI, Koltsova EK. An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis. Immunity. PMID 30389414 DOI: 10.1016/J.Immuni.2018.09.011  0.01
2018 Kleiman RS, LaRose ER, Badger JC, Page D, Caldwell MD, Clay JA, Peissig PL. Using Machine Learning Algorithms to Predict Risk for Development of Calciphylaxis in Patients with Chronic Kidney Disease. Amia Joint Summits On Translational Science Proceedings. Amia Joint Summits On Translational Science. 2017: 139-146. PMID 29888059  0.01
2018 Bender SJ, Moran DM, McIlvin MR, Zheng H, McCrow JP, Badger J, DiTullio GR, Allen AE, Saito MA. Iron triggers colony formation in Phaeocystis antarctica : connecting molecular mechanisms with iron biogeochemistry Biogeosciences Discussions. 1-52. DOI: 10.5194/Bg-2017-558  1
2017 P Tafti A, Badger J, LaRose E, Shirzadi E, Mahnke A, Mayer J, Ye Z, Page D, Peissig P. Adverse Drug Event Discovery Using Biomedical Literature: A Big Data Neural Network Adventure. Jmir Medical Informatics. 5: e51. PMID 29222076 DOI: 10.2196/Medinform.9170  0.01
2017 Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K, Hickman HD, McCulloch JA, Badger JH, Ajami NJ, Trinchieri G, Pardo-Manuel de Villena F, Yewdell JW, Rehermann B. Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance. Cell. PMID 29056339 DOI: 10.1016/J.Cell.2017.09.016  0.01
2017 Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE. Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. Plos Genetics. 13: e1006688. PMID 28355217 DOI: 10.1371/journal.pgen.1006688  1
2017 Dzutsev A, Badger JH, Perez-Chanona E, Roy S, Salcedo R, Smith CK, Trinchieri G. Microbes and Cancer. Annual Review of Immunology. PMID 28142322 DOI: 10.1146/annurev-immunol-051116-052133  0.01
2016 Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE. Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. Plos Genetics. 12: e1006490. PMID 27973599 DOI: 10.1371/Journal.Pgen.1006490  1
2016 Hamilton EP, Kapusta A, Huvos PE, Bidwell SL, Zafar N, Tang H, Hadjithomas M, Krishnakumar V, Badger JH, Caler EV, Russ C, Zeng Q, Fan L, Levin JZ, Shea T, et al. Structure of the germline genome of Tetrahymenathermophila and relationship to the massively rearranged somatic genome. Elife. 5. PMID 27892853 DOI: 10.7554/Elife.19090  1
2016 Huguet-Tapia JC, Lefebure T, Badger JH, Guan D, Pettis GS, Stanhope MJ, Loria R. Genome content and phylogenomics reveal both ancestral and lateral evolutionary pathways in plant pathogenic Streptomyces species. Applied and Environmental Microbiology. PMID 26826232 DOI: 10.1128/Aem.03504-15  1
2015 Chen H, Brinkac LM, Mishra P, Li N, Lymperopoulou DS, Dickerson TL, Gordon-Bradley N, Williams HN, Badger JH. Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters. Standards in Genomic Sciences. 10: 11. PMID 26203326 DOI: 10.1186/1944-3277-10-11  0.01
2015 Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA. Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria). Genome Announcements. 3. PMID 25635017 DOI: 10.1128/Genomea.01490-14  1
2015 Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA. Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae). Genome Announcements. 3. PMID 25635016 DOI: 10.1128/Genomea.01489-14  1
2014 Holland-Moritz HE, Coil DA, Badger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen JA. Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1. Genome Announcements. 2. PMID 25146141 DOI: 10.1128/Genomea.00833-14  1
2014 Alexiev A, Coil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen JA. Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announcements. 2. PMID 24831154 DOI: 10.1128/Genomea.00470-14  1
2014 Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, ... ... Badger JH, et al. Functional tradeoffs underpin salinity-driven divergence in microbial community composition. Plos One. 9: e89549. PMID 24586863 DOI: 10.1371/Journal.Pone.0089549  1
2014 Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA. Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12. Genome Announcements. 2. PMID 24558247 DOI: 10.1128/Genomea.00109-14  1
2013 Grindberg RV, Yee-Greenbaum JL, McConnell MJ, Novotny M, O'Shaughnessy AL, Lambert GM, Araúzo-Bravo MJ, Lee J, Fishman M, Robbins GE, Lin X, Venepally P, Badger JH, Galbraith DW, Gage FH, et al. RNA-sequencing from single nuclei. Proceedings of the National Academy of Sciences of the United States of America. 110: 19802-7. PMID 24248345 DOI: 10.1073/Pnas.1319700110  1
2013 McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, et al. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences of the United States of America. 110: E2390-9. PMID 23754396 DOI: 10.1073/Pnas.1219809110  1
2013 McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, et al. 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: 867-77. PMID 23564253 DOI: 10.1101/Gr.150433.112  1
2013 Konotchick T, Dupont CL, Valas RE, Badger JH, Allen AE. Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season. The New Phytologist. 198: 398-407. PMID 23488966 DOI: 10.1111/Nph.12160  1
2012 Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM. The "most wanted" taxa from the human microbiome for whole genome sequencing. Plos One. 7: e41294. PMID 22848458 DOI: 10.1371/Journal.Pone.0041294  1
2012 Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, Fitzgerald MG, Fulton RS, Hallsworth-Pepin K, et al. A framework for human microbiome research Nature. 486: 215-221. PMID 22699610 DOI: 10.1038/Nature11209  1
2012 Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, Fitzgerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, et al. Structure, function and diversity of the healthy human microbiome Nature. 486: 207-214. PMID 22699609 DOI: 10.1038/Nature11234  1
2012 Ziemert N, Podell S, Penn K, Badger JH, Allen E, Jensen PR. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. Plos One. 7: e34064. PMID 22479523 DOI: 10.1371/Journal.Pone.0034064  1
2012 Zeigler Allen L, Allen EE, Badger JH, McCrow JP, Paulsen IT, Elbourne LD, Thiagarajan M, Rusch DB, Nealson KH, Williamson SJ, Venter JC, Allen AE. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. The Isme Journal. 6: 1403-14. PMID 22278668 DOI: 10.1038/Ismej.2011.201  1
2012 Cock JM, Sterck L, Ahmed S, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Arun A, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, et al. The Ectocarpus Genome and Brown Algal Genomics. The Ectocarpus Genome Consortium. Advances in Botanical Research. 64: 141-184. DOI: 10.1016/B978-0-12-391499-6.00005-0  1
2011 Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH, Kumar U, Saier M, Wang Y, Cai H, Gu J, et al. 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. PMID 22004680 DOI: 10.1186/Gb-2011-12-10-R100  1
2011 Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotechnology. 29: 915-21. PMID 21926975 DOI: 10.1038/Nbt.1966  1
2011 Chen Y, Stine OC, Badger JH, Gil AI, Nair GB, Nishibuchi M, Fouts DE. Comparative genomic analysis of Vibrio parahaemolyticus: Serotype conversion and virulence Bmc Genomics. 12. PMID 21645368 DOI: 10.1186/1471-2164-12-294  1
2011 Huguet-Tapia JC, Badger JH, Loria R, Pettis GS. Streptomyces turgidiscabies Car8 contains a modular pathogenicity island that shares virulence genes with other actinobacterial plant pathogens. Plasmid. 65: 118-24. PMID 21087627 DOI: 10.1016/J.Plasmid.2010.11.002  1
2011 Badger JH, Ng PC, Venter JC. The human genome, microbiomes, and disease Metagenomics of the Human Body. 1-14. DOI: 10.1007/978-1-4419-7089-3_1  1
2010 Cock JM, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature. 465: 617-21. PMID 20520714 DOI: 10.1038/Nature09016  1
2010 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, ... ... Badger J, et al. A catalog of reference genomes from the human microbiome. Science (New York, N.Y.). 328: 994-9. PMID 20489017 DOI: 10.1126/Science.1183605  1
2010 Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings Rd, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, ... Badger JH, et al. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. Plos One. 5: e9773. PMID 20333304 DOI: 10.1371/Journal.Pone.0009773  1
2010 Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, et al. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. Plos One. 5: e9605. PMID 20333302 DOI: 10.1371/Journal.Pone.0009605  1
2010 Losada L, Ronning CM, DeShazer D, Woods D, Fedorova N, Kim HS, Shabalina SA, Pearson TR, Brinkac L, Tan P, Nandi T, Crabtree J, Badger J, Beckstrom-Sternberg S, Saqib M, et al. Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biology and Evolution. 2: 102-16. PMID 20333227 DOI: 10.1093/Gbe/Evq003  1
2009 Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CA, Elshahawi S, ... ... Badger JH, et al. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). Plos One. 4: e6085. PMID 19568419 DOI: 10.1371/Journal.Pone.0006085  1
2009 Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, ... ... Badger JH, et al. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (New York, N.Y.). 324: 268-72. PMID 19359590 DOI: 10.1126/Science.1167222  1
2009 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, et al. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and Environmental Microbiology. 75: 2046-56. PMID 19201974 DOI: 10.1128/Aem.02294-08  1
2009 Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. Plos One. 4: e4207. PMID 19148287 DOI: 10.1371/Journal.Pone.0004207  1
2008 Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC. IDEA: Interactive Display for Evolutionary Analyses. Bmc Bioinformatics. 9: 524. PMID 19061522 DOI: 10.1186/1471-2105-9-524  1
2008 Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 456: 239-44. PMID 18923393 DOI: 10.1038/Nature07410  1
2008 van den Berg MA, Albang R, Albermann K, Badger JH, Daran JM, Driessen AJ, Garcia-Estrada C, Fedorova ND, Harris DM, Heijne WH, Joardar V, Kiel JA, Kovalchuk A, Martín JF, Nierman WC, et al. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nature Biotechnology. 26: 1161-8. PMID 18820685 DOI: 10.1038/Nbt.1498  1
2008 Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LF, Krogfelt KA, et al. Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. Plos Genetics. 4: e1000141. PMID 18654632 DOI: 10.1371/Journal.Pgen.1000141  1
2008 Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, et al. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. Plos Genetics. 4: e1000046. PMID 18404212 DOI: 10.1371/Journal.Pgen.1000046  1
2007 Myers GS, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, Deboy RT, Tettelin H, Boyce JD, McCarl VP, Han X, Nelson WC, Madupu R, et al. Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nature Biotechnology. 25: 569-75. PMID 17468768 DOI: 10.1038/nbt1302  1
2006 Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrázek J, Ren Q, Paulsen IT, Nelson KE, Khouri HM, Radune D, Sosa J, Dodson RJ, Sullivan SA, et al. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus Journal of Bacteriology. 188: 6841-6850. PMID 16980487 DOI: 10.1128/Jb.00111-06  1
2006 Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, et al. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proceedings of the National Academy of Sciences of the United States of America. 103: 13555-9. PMID 16938853 DOI: 10.1073/Pnas.0602963103  1
2006 Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Plos Biology. 4: e286. PMID 16933976 DOI: 10.1371/Journal.Pbio.0040286  1
2005 Fedorova ND, Badger JH, Robson GD, Wortman JR, Nierman WC. Comparative analysis of programmed cell death pathways in filamentous fungi. Bmc Genomics. 6: 177. PMID 16336669 DOI: 10.1186/1471-2164-6-177  1
2005 El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, ... ... Badger J, et al. Comparative genomics of trypanosomatid parasitic protozoa. Science (New York, N.Y.). 309: 404-9. PMID 16020724 DOI: 10.1126/Science.1112181  1
2005 Badger JH, Eisen JA, Ward NL. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. International Journal of Systematic and Evolutionary Microbiology. 55: 1021-6. PMID 15879228 DOI: 10.1099/Ijs.0.63510-0  1
2005 Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, ... ... Badger JH, et al. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. Plos Biology. 3: e15. PMID 15660156 DOI: 10.1371/Journal.Pbio.0030015  1
2004 Badger J, Kearney P, Li M, Tsang J, Jiang T. Selecting the branches for an evolutionary tree: a polynomial time approximation scheme Journal of Algorithms. 51: 1-14. DOI: 10.1016/S0196-6774(03)00086-5  1
2003 Vogl C, Badger J, Kearney P, Li M, Clegg M, Jiang T. Probabilistic analysis indicates discordant gene trees in chloroplast evolution Journal of Molecular Evolution. 56: 330-340. PMID 12612836 DOI: 10.1007/S00239-002-2404-3  1
2001 Wang H, Badger J, Kearney P, Li M. Analysis of Codon Usage Patterns of Bacterial Genomes Using the Self-Organizing Map Molecular Biology and Evolution. 18: 792-800. PMID 11319263 DOI: 10.1093/Oxfordjournals.Molbev.A003861  1
1999 Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, Olsen GJ. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proceedings of the National Academy of Sciences of the United States of America. 96: 3578-83. PMID 10097079 DOI: 10.1073/Pnas.96.7.3578  1
1997 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, ... ... Badger JH, et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 390: 364-70. PMID 9389475 DOI: 10.1038/37052  1
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