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Items: 1 to 50 of 51

1.

Microbiome as an Immunological Modifier.

Kumar M, Singh P, Murugesan S, Vetizou M, McCulloch J, Badger JH, Trinchieri G, Al Khodor S.

Methods Mol Biol. 2020;2055:595-638. doi: 10.1007/978-1-4939-9773-2_27.

PMID:
31502171
2.

Description of soybean aphid (Aphis glycines Matsumura) mitochondrial genome and comparative mitogenomics of Aphididae (Hemiptera: Sternorrhyncha).

Song H, Donthu RK, Hall R, Hon L, Weber E, Badger JH, Giordano R.

Insect Biochem Mol Biol. 2019 Oct;113:103208. doi: 10.1016/j.ibmb.2019.103208. Epub 2019 Aug 15.

PMID:
31422150
3.

Laboratory mice born to wild mice have natural microbiota and model human immune responses.

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, Foster St Claire MB, Yuan W, Sen SK, Dreier MS, Hild B, Hafner M, Wang D, Iliev ID, Belkaid Y, Trinchieri G, Rehermann B.

Science. 2019 Aug 2;365(6452). pii: eaaw4361. doi: 10.1126/science.aaw4361. Epub 2019 Aug 1.

PMID:
31371577
4.

An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis.

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.

Immunity. 2018 Nov 20;49(5):943-957.e9. doi: 10.1016/j.immuni.2018.09.011. Epub 2018 Oct 30.

PMID:
30389414
5.

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance.

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.

Cell. 2017 Nov 16;171(5):1015-1028.e13. doi: 10.1016/j.cell.2017.09.016. Epub 2017 Oct 19.

6.

Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.

Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE.

PLoS Genet. 2017 Mar 29;13(3):e1006688. doi: 10.1371/journal.pgen.1006688. eCollection 2017 Mar.

7.

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.

Zeigler Allen L, McCrow JP, Ininbergs K, Dupont CL, Badger JH, Hoffman JM, Ekman M, Allen AE, Bergman B, Venter JC.

mSystems. 2017 Feb 14;2(1). pii: e00125-16. doi: 10.1128/mSystems.00125-16. eCollection 2017 Jan-Feb.

8.

Microbes and Cancer.

Dzutsev A, Badger JH, Perez-Chanona E, Roy S, Salcedo R, Smith CK, Trinchieri G.

Annu Rev Immunol. 2017 Apr 26;35:199-228. doi: 10.1146/annurev-immunol-051116-052133. Epub 2017 Jan 30. Review.

PMID:
28142322
9.

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.

Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE.

PLoS Genet. 2016 Dec 14;12(12):e1006490. doi: 10.1371/journal.pgen.1006490. eCollection 2016 Dec. Erratum in: PLoS Genet. 2017 Mar 29;13(3):e1006688.

10.

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome.

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, Young SK, Hegarty R, Daza R, Gujja S, Wortman JR, Birren BW, Nusbaum C, Thomas J, Carey CM, Pritham EJ, Feschotte C, Noto T, Mochizuki K, Papazyan R, Taverna SD, Dear PH, Cassidy-Hanley DM, Xiong J, Miao W, Orias E, Coyne RS.

Elife. 2016 Nov 28;5. pii: e19090. doi: 10.7554/eLife.19090.

11.

Genome Content and Phylogenomics Reveal both Ancestral and Lateral Evolutionary Pathways in Plant-Pathogenic Streptomyces Species.

Huguet-Tapia JC, Lefebure T, Badger JH, Guan D, Pettis GS, Stanhope MJ, Loria R.

Appl Environ Microbiol. 2016 Jan 29;82(7):2146-2155. doi: 10.1128/AEM.03504-15.

12.

Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters.

Chen H, Brinkac LM, Mishra P, Li N, Lymperopoulou DS, Dickerson TL, Gordon-Bradley N, Williams HN, Badger JH.

Stand Genomic Sci. 2015 Mar 24;10:11. doi: 10.1186/1944-3277-10-11. eCollection 2015.

13.

Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria).

Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA.

Genome Announc. 2015 Jan 29;3(1). pii: e01490-14. doi: 10.1128/genomeA.01490-14.

14.

Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae).

Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA.

Genome Announc. 2015 Jan 29;3(1). pii: e01489-14. doi: 10.1128/genomeA.01489-14.

15.

Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1.

Holland-Moritz HE, Coil DA, Badger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen JA.

Genome Announc. 2014 Aug 21;2(4). pii: e00833-14. doi: 10.1128/genomeA.00833-14.

16.

Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265.

Alexiev A, Coil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen JA.

Genome Announc. 2014 May 15;2(3). pii: e00470-14. doi: 10.1128/genomeA.00470-14.

17.

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

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, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B.

PLoS One. 2014 Feb 27;9(2):e89549. doi: 10.1371/journal.pone.0089549. eCollection 2014.

18.

Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12.

Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA.

Genome Announc. 2014 Feb 20;2(1). pii: e00109-14. doi: 10.1128/genomeA.00109-14.

19.

RNA-sequencing from single nuclei.

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, Lasken RS.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19802-7. doi: 10.1073/pnas.1319700110. Epub 2013 Nov 18.

20.

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.

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, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110. Epub 2013 Jun 10.

21.

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.

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, Torriani F, Nealson KH, Pevzner PA, Friedman R, Venter JC, Lasken RS.

Genome Res. 2013 May;23(5):867-77. doi: 10.1101/gr.150433.112. Epub 2013 Apr 5.

22.

Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season.

Konotchick T, Dupont CL, Valas RE, Badger JH, Allen AE.

New Phytol. 2013 Apr;198(2):398-407. doi: 10.1111/nph.12160. Epub 2013 Mar 13.

23.

The "most wanted" taxa from the human microbiome for whole genome sequencing.

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.

PLoS One. 2012;7(7):e41294. doi: 10.1371/journal.pone.0041294. Epub 2012 Jul 26.

24.

The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity.

Ziemert N, Podell S, Penn K, Badger JH, Allen E, Jensen PR.

PLoS One. 2012;7(3):e34064. doi: 10.1371/journal.pone.0034064. Epub 2012 Mar 29.

25.

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic.

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.

ISME J. 2012 Jul;6(7):1403-14. doi: 10.1038/ismej.2011.201. Epub 2012 Jan 26.

26.

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.

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, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG.

Genome Biol. 2011 Oct 17;12(10):R100. doi: 10.1186/gb-2011-12-10-r100.

27.

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.

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.

Nat Biotechnol. 2011 Sep 18;29(10):915-21. doi: 10.1038/nbt.1966.

28.

Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence.

Chen Y, Stine OC, Badger JH, Gil AI, Nair GB, Nishibuchi M, Fouts DE.

BMC Genomics. 2011 Jun 6;12:294. doi: 10.1186/1471-2164-12-294.

29.

Streptomyces turgidiscabies Car8 contains a modular pathogenicity island that shares virulence genes with other actinobacterial plant pathogens.

Huguet-Tapia JC, Badger JH, Loria R, Pettis GS.

Plasmid. 2011 Mar;65(2):118-24. doi: 10.1016/j.plasmid.2010.11.002. Epub 2010 Nov 16.

PMID:
21087627
30.

The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

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, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collén J, Corre E, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CM, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Küpper FC, Lang D, Le Bail A, Leblanc C, Lerouge P, Lohr M, Lopez PJ, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collén P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Ségurens B, Strittmatter M, Tonon T, Tregear JW, Valentin K, von Dassow P, Yamagishi T, Van de Peer Y, Wincker P.

Nature. 2010 Jun 3;465(7298):617-21. doi: 10.1038/nature09016.

PMID:
20520714
31.

Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.

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, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M.

PLoS One. 2010 Mar 19;5(3):e9773. doi: 10.1371/journal.pone.0009773.

32.

The complete genome sequence of Haloferax volcanii DS2, a model archaeon.

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, Eisen JA.

PLoS One. 2010 Mar 19;5(3):e9605. doi: 10.1371/journal.pone.0009605.

33.

The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).

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, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL.

PLoS One. 2009 Jul 1;4(7):e6085. doi: 10.1371/journal.pone.0006085.

34.

Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.

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, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV.

Science. 2009 Apr 10;324(5924):268-72. doi: 10.1126/science.1167222.

35.

Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.

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.

PLoS One. 2009;4(1):e4207. doi: 10.1371/journal.pone.0004207. Epub 2009 Jan 16.

36.

IDEA: Interactive Display for Evolutionary Analyses.

Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC.

BMC Bioinformatics. 2008 Dec 8;9:524. doi: 10.1186/1471-2105-9-524.

37.

The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

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, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kröger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jézéquel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV.

Nature. 2008 Nov 13;456(7219):239-44. doi: 10.1038/nature07410. Epub 2008 Oct 15.

PMID:
18923393
38.

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum.

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, Nijland JG, Pronk JT, Roubos JA, van der Klei IJ, van Peij NN, Veenhuis M, von Döhren H, Wagner C, Wortman J, Bovenberg RA.

Nat Biotechnol. 2008 Oct;26(10):1161-8. doi: 10.1038/nbt.1498. Epub 2008 Sep 28.

PMID:
18820685
39.

Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice.

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, Struve C, Triplett EW, Methé BA.

PLoS Genet. 2008 Jul 25;4(7):e1000141. doi: 10.1371/journal.pgen.1000141.

40.

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.

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, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC.

PLoS Genet. 2008 Apr 11;4(4):e1000046. doi: 10.1371/journal.pgen.1000046.

41.

Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.

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, Mohamoud Y, Holley T, Fedorova N, Khouri H, Bottomley SP, Whittington RJ, Adler B, Songer JG, Rood JI, Paulsen IT.

Nat Biotechnol. 2007 May;25(5):569-75. Epub 2007 Apr 29.

PMID:
17468768
42.

Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus.

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, Rosovitz MJ, Madupu R, Brinkac LM, Durkin AS, Daugherty SC, Kothari SP, Giglio MG, Zhou L, Haft DH, Selengut JD, Davidsen TM, Yang Q, Zafar N, Ward NL.

J Bacteriol. 2006 Oct;188(19):6841-50.

43.

Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.

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, Halpin R, Paulsen IT.

Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13555-9. Epub 2006 Aug 25.

44.

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

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, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E.

PLoS Biol. 2006 Sep;4(9):e286.

45.

Comparative analysis of programmed cell death pathways in filamentous fungi.

Fedorova ND, Badger JH, Robson GD, Wortman JR, Nierman WC.

BMC Genomics. 2005 Dec 8;6:177.

47.

Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.

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, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE.

PLoS Biol. 2005 Jan;3(1):e15. Epub 2005 Jan 4.

48.

An information-based sequence distance and its application to whole mitochondrial genome phylogeny.

Li M, Badger JH, Chen X, Kwong S, Kearney P, Zhang H.

Bioinformatics. 2001 Feb;17(2):149-54.

PMID:
11238070
49.

CRITICA: coding region identification tool invoking comparative analysis.

Badger JH, Olsen GJ.

Mol Biol Evol. 1999 Apr;16(4):512-24.

PMID:
10331277
50.

Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species.

Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, Olsen GJ.

Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3578-83.

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