The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, Crécy-Lagard V de, Diaz NN, Disz T, Edwards R, Fonstein M, et al. (2005)
Nucleic Acids Research 33(17): 5691-5702.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Overbeek, Ross; Begley, Tadhg; Butler, Ralph M.; Choudhuri, Jomuna V.; Chuang, Han-Yu; Cohoon, Matthew; Crécy-Lagard, Valérie de; Diaz, Naryttza N.; Disz, Terry; Edwards, Robert; Fonstein, Michael; Frank, Ed D.
Abstract / Bemerkung
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.
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Overbeek R, Begley T, Butler RM, et al. The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes. Nucleic Acids Research. 2005;33(17):5691-5702.
Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H. - Y., Cohoon, M., Crécy-Lagard, V. de, et al. (2005). The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes. Nucleic Acids Research, 33(17), 5691-5702.
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, Crécy-Lagard, Valérie de, et al. 2005. “The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes”. Nucleic Acids Research 33 (17): 5691-5702.
Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H. - Y., Cohoon, M., Crécy-Lagard, V. de, Diaz, N. N., Disz, T., Edwards, R., et al. (2005). The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes. Nucleic Acids Research 33, 5691-5702.
Overbeek, R., et al., 2005. The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes. Nucleic Acids Research, 33(17), p 5691-5702.
R. Overbeek, et al., “The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes”, Nucleic Acids Research, vol. 33, 2005, pp. 5691-5702.
Overbeek, R., Begley, T., Butler, R.M., Choudhuri, J.V., Chuang, H.-Y., Cohoon, M., Crécy-Lagard, V. de, Diaz, N.N., Disz, T., Edwards, R., Fonstein, M., Frank, E.D., Gerdes, S., Glass, E.M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., Krause, L., Kubal, M., Larsen, N., Linke, B., McHardy, A.C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy, V., Pusch, G.D., Rodionov, D.A., Rückert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O., Vonstein, V.: The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes. Nucleic Acids Research. 33, 5691-5702 (2005).
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, Crécy-Lagard, Valérie de, Diaz, Naryttza N., Disz, Terry, Edwards, Robert, Fonstein, Michael, Frank, Ed D., Gerdes, Svetlana, Glass, Elizabeth M., Goesmann, Alexander, Hanson, Andrew, Iwata-Reuyl, Dirk, Jensen, Roy, Jamshidi, Neema, Krause, Lutz, Kubal, Michael, Larsen, Niels, Linke, Burkhard, McHardy, Alice C., Meyer, Folker, Neuweger, Heiko, Olsen, Gary, Olson, Robert, Osterman, Andrei, Portnoy, Vasiliy, Pusch, Gordon D., Rodionov, Dmitry A., Rückert, Christian, Steiner, Jason, Stevens, Rick, Thiele, Ines, Vassieva, Olga, Ye, Yuzhen, Zagnitko, Olga, and Vonstein, Veronika. “The subsystems approach to genome annotation and its use in the Project to Annotate 1000 Genomes”. Nucleic Acids Research 33.17 (2005): 5691-5702.
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PA5339, a RidA Homolog, Is Required for Full Growth in Pseudomonas aeruginosa.
Irons J, Hodge-Hanson KM, Downs DM., J Bacteriol 200(22), 2018
PMID: 30181125
Evolutionary History of Copper Membrane Monooxygenases.
Khadka R, Clothier L, Wang L, Lim CK, Klotz MG, Dunfield PF., Front Microbiol 9(), 2018
PMID: 30420840
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.
Niu SY, Yang J, McDermaid A, Zhao J, Kang Y, Ma Q., Brief Bioinform 19(6), 2018
PMID: 28481971
Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi.
Nho SW, Abdelhamed H, Paul D, Park S, Mauel MJ, Karsi A, Lawrence ML., Front Microbiol 9(), 2018
PMID: 30524416
Adaptions of Lichen Microbiota Functioning Under Persistent Exposure to Arsenic Contamination.
Cernava T, Vasfiu Q, Erlacher A, Aschenbrenner IA, Francesconi K, Grube M, Berg G., Front Microbiol 9(), 2018
PMID: 30555453
Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota.
Biggs MB, Medlock GL, Moutinho TJ, Lees HJ, Swann JR, Kolling GL, Papin JA., ISME J 11(2), 2017
PMID: 27824342
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.
Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RM, Thiele I., Nat Biotechnol 35(1), 2017
PMID: 27893703
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.
Vallenet D, Calteau A, Cruveiller S, Gachet M, Lajus A, Josso A, Mercier J, Renaux A, Rollin J, Rouy Z, Roche D, Scarpelli C, Médigue C., Nucleic Acids Res 45(d1), 2017
PMID: 27899624
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL., Nucleic Acids Res 45(d1), 2017
PMID: 27899627
Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals.
Singh C, Glaab E, Linster CL., J Biol Chem 292(3), 2017
PMID: 27909055
Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics.
Fahrenfeld NL, Delos Reyes H, Eramo A, Akob DM, Mumford AC, Cozzarelli IM., Sci Total Environ 580(), 2017
PMID: 28034542
Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites.
Hadadi N, Hafner J, Soh KC, Hatzimanikatis V., Biotechnol J 12(1), 2017
PMID: 27897385
High diversity of airborne fungi in the hospital environment as revealed by meta-sequencing-based microbiome analysis.
Tong X, Xu H, Zou L, Cai M, Xu X, Zhao Z, Xiao F, Li Y., Sci Rep 7(), 2017
PMID: 28045065
Unraveling the microbial processes of black band disease in corals through integrated genomics.
Sato Y, Ling EY, Turaev D, Laffy P, Weynberg KD, Rattei T, Willis BL, Bourne DG., Sci Rep 7(), 2017
PMID: 28094312
Key Impact of an Uncommon Plasmid on Bacillus amyloliquefaciens subsp. plantarum S499 Developmental Traits and Lipopeptide Production.
Molinatto G, Franzil L, Steels S, Puopolo G, Pertot I, Ongena M., Front Microbiol 8(), 2017
PMID: 28154555
Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens.
Uehling J, Gryganskyi A, Hameed K, Tschaplinski T, Misztal PK, Wu S, Desirò A, Vande Pol N, Du Z, Zienkiewicz A, Zienkiewicz K, Morin E, Tisserant E, Splivallo R, Hainaut M, Henrissat B, Ohm R, Kuo A, Yan J, Lipzen A, Nolan M, LaButti K, Barry K, Goldstein AH, Labbé J, Schadt C, Tuskan G, Grigoriev I, Martin F, Vilgalys R, Bonito G., Environ Microbiol 19(8), 2017
PMID: 28076891
Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1.
Henry CS, Rotman E, Lathem WW, Tyo KE, Hauser AR, Mandel MJ., J Infect Dis 215(suppl_1), 2017
PMID: 28375518
Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics.
Zallot R, Ross R, Chen WH, Bruner SD, Limbach PA, de Crécy-Lagard V., ACS Chem Biol 12(3), 2017
PMID: 28128549
The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ₀) Transport.
Zallot R, Yuan Y, de Crécy-Lagard V., Biomolecules 7(1), 2017
PMID: 28208705
Insight into the Genome of Brochothrix thermosphacta, a Problematic Meat Spoilage Bacterium.
Stanborough T, Fegan N, Powell SM, Tamplin M, Chandry PS., Appl Environ Microbiol 83(5), 2017
PMID: 27986732
Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species.
Yasuike M, Nishiki I, Iwasaki Y, Nakamura Y, Fujiwara A, Shimahara Y, Kamaishi T, Yoshida T, Nagai S, Kobayashi T, Katoh M., PLoS One 12(3), 2017
PMID: 28257489
Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses.
Motlagh AM, Bhattacharjee AS, Coutinho FH, Dutilh BE, Casjens SR, Goel RK., Front Microbiol 8(), 2017
PMID: 28316597
Comparative analysis of metagenomes of Italian top soil improvers.
Gigliucci F, Brambilla G, Tozzoli R, Michelacci V, Morabito S., Environ Res 155(), 2017
PMID: 28214713
A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation.
Dufault-Thompson K, Jian H, Cheng R, Li J, Wang F, Zhang Y., mSystems 2(2), 2017
PMID: 28382331
Intraspecies comparative genomics of three strains of Orientia tsutsugamushi with different antibiotic sensitivity.
Liao HM, Chao CC, Lei H, Li B, Tsai S, Hung GC, Ching WM, Lo SC., Genom Data 12(), 2017
PMID: 28393016
Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.
Wang Y, Hatt JK, Tsementzi D, Rodriguez-R LM, Ruiz-Pérez CA, Weigand MR, Kizer H, Maresca G, Krishnan R, Poretsky R, Spain JC, Konstantinidis KT., Appl Environ Microbiol 83(8), 2017
PMID: 28258138
Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria.
Muthusamy S, Lundin D, Mamede Branca RM, Baltar F, González JM, Lehtiö J, Pinhassi J., Environ Microbiol 19(6), 2017
PMID: 28371138
Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration.
Kumaresan D, Cross AT, Moreira-Grez B, Kariman K, Nevill P, Stevens J, Allcock RJN, O'Donnell AG, Dixon KW, Whiteley AS., Sci Rep 7(1), 2017
PMID: 28373716
Bacterial communities on facial skin of teenage and elderly Thai females.
Somboonna N, Wilantho A, Srisuttiyakorn C, Assawamakin A, Tongsima S., Arch Microbiol 199(7), 2017
PMID: 28391505
A geographically-diverse collection of 418 human gut microbiome pathway genome databases.
Hahn AS, Altman T, Konwar KM, Hanson NW, Kim D, Relman DA, Dill DL, Hallam SJ., Sci Data 4(), 2017
PMID: 28398290
A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer.
Cameron SJS, Lewis KE, Huws SA, Hegarty MJ, Lewis PD, Pachebat JA, Mur LAJ., PLoS One 12(5), 2017
PMID: 28542458
MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.
Gacesa R, Zucko J, Petursdottir SK, Gudmundsdottir EE, Fridjonsson OH, Diminic J, Long PF, Long PF, Cullum J, Hranueli D, Hreggvidsson GO, Starcevic A., Food Technol Biotechnol 55(2), 2017
PMID: 28867956
Functional metagenomics of oil-impacted mangrove sediments reveals high abundance of hydrolases of biotechnological interest.
Ottoni JR, Cabral L, de Sousa STP, Júnior GVL, Domingos DF, Soares Junior FL, da Silva MCP, Marcon J, Dias ACF, de Melo IS, de Souza AP, Andreote FD, de Oliveira VM., World J Microbiol Biotechnol 33(7), 2017
PMID: 28593475
Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice.
Boyd BM, Allen JM, Nguyen NP, Vachaspati P, Quicksall ZS, Warnow T, Mugisha L, Johnson KP, Reed DL., Mol Biol Evol 34(7), 2017
PMID: 28419279
Genome Sequence of Oxalobacter formigenes Strain HC-1.
Hatch M, Allison MJ, Yu F, Farmerie W., Genome Announc 5(27), 2017
PMID: 28684568
Genome Sequence of Oxalobacter formigenes Strain OXCC13.
Hatch M, Allison MJ, Yu F, Farmerie W., Genome Announc 5(28), 2017
PMID: 28705966
Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived Consortia.
Leyn SA, Maezato Y, Romine MF, Rodionov DA., Front Microbiol 8(), 2017
PMID: 28751880
A curated genome-scale metabolic model of Bordetella pertussis metabolism.
Fyson N, King J, Belcher T, Preston A, Colijn C., PLoS Comput Biol 13(7), 2017
PMID: 28715411
Deciphering functional diversification within the lichen microbiota by meta-omics.
Cernava T, Erlacher A, Aschenbrenner IA, Krug L, Lassek C, Riedel K, Grube M, Berg G., Microbiome 5(1), 2017
PMID: 28724401
Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology.
Marine RL, Nasko DJ, Wray J, Polson SW, Wommack KE., ISME J 11(11), 2017
PMID: 28731469
Draft Genome Sequence of the Deep-Sea Bacterium Moritella sp. JT01 and Identification of Biotechnologically Relevant Genes.
Freitas RC, Odisi EJ, Kato C, da Silva MAC, Lima AOS., Mar Biotechnol (NY) 19(5), 2017
PMID: 28733934
First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile.
Serrano AE, Escudero LV, Tebes-Cayo C, Acosta M, Encalada O, Fernández-Moroso S, Demergasso C., Stand Genomic Sci 12(), 2017
PMID: 28770028
Association of the gut microbiota mobilome with hospital location and birth weight in preterm infants.
Ravi A, Estensmo ELF, Abée-Lund TML, Foley SL, Allgaier B, Martin CR, Claud EC, Rudi K., Pediatr Res 82(5), 2017
PMID: 28665922
Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry.
Petrovska L, Tang Y, Jansen van Rensburg MJ, Cawthraw S, Nunez J, Sheppard SK, Ellis RJ, Whatmore AM, Crawshaw TR, Irvine RM., Front Cell Infect Microbiol 7(), 2017
PMID: 28848714
Microbial communities in the reef water at Kham Island, lower Gulf of Thailand.
Somboonna N, Wilantho A, Monanunsap S, Chavanich S, Tangphatsornruang S, Tongsima S., PeerJ 5(), 2017
PMID: 28828243
Aura-biomes are present in the water layer above coral reef benthic macro-organisms.
Walsh K, Haggerty JM, Doane MP, Hansen JJ, Morris MM, Moreira APB, de Oliveira L, Leomil L, Garcia GD, Thompson F, Dinsdale EA., PeerJ 5(), 2017
PMID: 28828261
Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems.
Imchen M, Kumavath R, Barh D, Azevedo V, Ghosh P, Viana M, Wattam AR., Sci Rep 7(1), 2017
PMID: 28821820
Restriction and modification of deoxyarchaeosine (dG+)-containing phage 9 g DNA.
Tsai R, Corrêa IR, Xu MY, Xu SY., Sci Rep 7(1), 2017
PMID: 28827753
Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight.
Niehaus TD, Elbadawi-Sidhu M, de Crécy-Lagard V, Fiehn O, Hanson AD., J Biol Chem 292(39), 2017
PMID: 28830929
A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
Michalik S, Depke M, Murr A, Gesell Salazar M, Kusebauch U, Sun Z, Meyer TC, Surmann K, Pförtner H, Hildebrandt P, Weiss S, Palma Medina LM, Gutjahr M, Hammer E, Becher D, Pribyl T, Hammerschmidt S, Deutsch EW, Bader SL, Hecker M, Moritz RL, Mäder U, Völker U, Schmidt F., Sci Rep 7(1), 2017
PMID: 28887440
Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars.
Pontefract A, Zhu TF, Walker VK, Hepburn H, Lui C, Zuber MT, Ruvkun G, Carr CE., Front Microbiol 8(), 2017
PMID: 29018418
Novel archaeal thermostable cellulases from an oil reservoir metagenome.
Lewin A, Zhou J, Pham VTT, Haugen T, Zeiny ME, Aarstad O, Liebl W, Wentzel A, Liles MR., AMB Express 7(1), 2017
PMID: 28963711
Bacterial strategies along nutrient and time gradients, revealed by metagenomic analysis of laboratory microcosms.
Song HK, Song W, Kim M, Tripathi BM, Kim H, Jablonski P, Adams JM., FEMS Microbiol Ecol 93(10), 2017
PMID: 28962015
Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas.
Rathour R, Gupta J, Kumar M, Hiloidhari M, Mehrotra AK, Thakur IS., Genome Announc 5(40), 2017
PMID: 28982995
Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema.
Oh S, Yap GC, Hong PY, Huang CH, Aw MM, Shek LP, Liu WT, Lee BW., PLoS One 12(10), 2017
PMID: 29049378
Heat Resistance Mediated by pLM58 Plasmid-Borne ClpL in Listeria monocytogenes.
Pöntinen A, Aalto-Araneda M, Lindström M, Korkeala H., mSphere 2(6), 2017
PMID: 29104933
Microbial Community Composition and Functional Capacity in a Terrestrial Ferruginous, Sulfate-Depleted Mud Volcano.
Tu TH, Wu LW, Lin YS, Imachi H, Lin LH, Wang PL., Front Microbiol 8(), 2017
PMID: 29163423
Kullback Leibler divergence in complete bacterial and phage genomes.
Akhter S, Aziz RK, Kashef MT, Ibrahim ES, Bailey B, Edwards RA., PeerJ 5(), 2017
PMID: 29204318
Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh.
Dong X, Shulzhenko N, Lemaitre J, Greer RL, Peremyslova K, Quamruzzaman Q, Rahman M, Hasan OS, Joya SA, Golam M, Christiani DC, Morgun A, Kile ML., PLoS One 12(12), 2017
PMID: 29211769
Subspecies in the global human gut microbiome.
Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P., Mol Syst Biol 13(12), 2017
PMID: 29242367
Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization.
Meneghine AK, Nielsen S, Varani AM, Thomas T, Carareto Alves LM., PLoS One 12(12), 2017
PMID: 29267397
Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.
Carda-Diéguez M, Ghai R, Rodríguez-Valera F, Amaro C., Microbiome 5(1), 2017
PMID: 29268781
Brucella, nitrogen and virulence.
Ronneau S, Moussa S, Barbier T, Conde-Álvarez R, Zuniga-Ripa A, Moriyon I, Letesson JJ., Crit Rev Microbiol 42(4), 2016
PMID: 25471320
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.
Silva GG, Green KT, Dutilh BE, Edwards RA., Bioinformatics 32(3), 2016
PMID: 26454280
Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea.
Alzubaidy H, Essack M, Malas TB, Bokhari A, Motwalli O, Kamanu FK, Jamhor SA, Mokhtar NA, Antunes A, Simões MF, Alam I, Bougouffa S, Lafi FF, Bajic VB, Archer JA., Gene 576(2 pt 1), 2016
PMID: 26475934
Metabolic network-guided binning of metagenomic sequence fragments.
Biggs MB, Papin JA., Bioinformatics 32(6), 2016
PMID: 26568626
EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.
Eichinger V, Nussbaumer T, Platzer A, Jehl MA, Arnold R, Rattei T., Nucleic Acids Res 44(d1), 2016
PMID: 26590402
The MG-RAST metagenomics database and portal in 2015.
Wilke A, Bischof J, Gerlach W, Glass E, Harrison T, Keegan KP, Paczian T, Trimble WL, Bagchi S, Grama A, Chaterji S, Meyer F., Nucleic Acids Res 44(d1), 2016
PMID: 26656948
Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity.
Calusinska M, Marynowska M, Goux X, Lentzen E, Delfosse P., Environ Microbiol 18(4), 2016
PMID: 26568175
An evaluation of the accuracy and speed of metagenome analysis tools.
Lindgreen S, Adair KL, Gardner PP., Sci Rep 6(), 2016
PMID: 26778510
A Bacterial Quorum-Sensing Precursor Induces Mortality in the Marine Coccolithophore, Emiliania huxleyi.
Harvey EL, Deering RW, Rowley DC, El Gamal A, Schorn M, Moore BS, Johnson MD, Mincer TJ, Whalen KE., Front Microbiol 7(), 2016
PMID: 26870019
Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation.
Gómez-Lunar Z, Hernández-González I, Rodríguez-Torres MD, Souza V, Olmedo-Álvarez G., Front Microbiol 7(), 2016
PMID: 26903955
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.
Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD, Shukla M, Vonstein V, Wattam AR, Yoo H., Front Microbiol 7(), 2016
PMID: 26903996
Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome.
Babujia LC, Silva AP, Nakatani AS, Cantão ME, Vasconcelos AT, Visentainer JV, Hungria M., Transgenic Res 25(4), 2016
PMID: 26873023
Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome.
Lopes FA, Catão EC, Santana RH, Cabral Ade S, Paranhos R, Rangel TP, de Rezende CE, Edwards RA, Thompson CC, Thompson FL, Kruger RH., PLoS One 11(2), 2016
PMID: 26881432
Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps.
Yamazaki Y, Meirelles PM, Mino S, Suda W, Oshima K, Hattori M, Thompson FL, Sakai Y, Sawabe T, Sawabe T., Sci Rep 6(), 2016
PMID: 26905381
Novel genomic island modifies DNA with 7-deazaguanine derivatives.
Thiaville JJ, Kellner SM, Yuan Y, Hutinet G, Thiaville PC, Jumpathong W, Mohapatra S, Brochier-Armanet C, Letarov AV, Hillebrand R, Malik CK, Rizzo CJ, Dedon PC, de Crécy-Lagard V., Proc Natl Acad Sci U S A 113(11), 2016
PMID: 26929322
Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge.
Cao H, Dong C, Bougouffa S, Li J, Zhang W, Shao Z, Bajic VB, Qian PY., Sci Rep 6(), 2016
PMID: 26953077
Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island.
Fadeev E, De Pascale F, Vezzi A, Hübner S, Aharonovich D, Sher D., Front Microbiol 7(), 2016
PMID: 27014193
Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?
Souza RC, Mendes IC, Reis-Junior FB, Carvalho FM, Nogueira MA, Vasconcelos AT, Vicente VA, Hungria M., BMC Microbiol 16(), 2016
PMID: 26983403
Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data.
Faria JP, Overbeek R, Taylor RC, Conrad N, Vonstein V, Goelzer A, Fromion V, Rocha M, Rocha I, Henry CS., Front Microbiol 7(), 2016
PMID: 27047450
Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB).
Thiaville JJ, Frelin O, García-Salinas C, Harrison K, Hasnain G, Horenstein NA, Díaz de la Garza RI, Henry CS, Hanson AD, de Crécy-Lagard V., Front Microbiol 7(), 2016
PMID: 27065985
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.
Granger BR, Chang YC, Wang Y, DeLisi C, Segrè D, Hu Z., PLoS Comput Biol 12(4), 2016
PMID: 27081850
Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean.
Tavares TC, Normando LR, de Vasconcelos AT, Gerber AL, Agnez-Lima LF, Melo VM., Sci Total Environ 557-558(), 2016
PMID: 27088626
Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree.
Finkel OM, Delmont TO, Post AF, Belkin S., Appl Environ Microbiol 82(9), 2016
PMID: 26944845
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics.
Jovel J, Patterson J, Wang W, Hotte N, O'Keefe S, Mitchel T, Perry T, Kao D, Mason AL, Madsen KL, Wong GK., Front Microbiol 7(), 2016
PMID: 27148170
Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics.
Meziti A, Tsementzi D, Ar Kormas K, Karayanni H, Konstantinidis KT., Environ Microbiol 18(12), 2016
PMID: 27001690
Evolution and adaptation of SAR11 and Cyanobium in a saline Tibetan lake.
Oh S, Zhang R, Wu QL, Liu WT., Environ Microbiol Rep 8(5), 2016
PMID: 27084571
Draft Genome Sequence of Bacillus licheniformis CG-B52, a Highly Virulent Bacterium of Pacific White Shrimp (Litopenaeus vannamei), Isolated from a Colombian Caribbean Aquaculture Outbreak.
Gálvez EJ, Carrillo-Castro K, Zárate L, Güiza L, Pieper DH, García-Bonilla E, Salazar M, Junca H., Genome Announc 4(3), 2016
PMID: 27174263
A single gene of a commensal microbe affects host susceptibility to enteric infection.
Yoon MY, Min KB, Lee KM, Yoon Y, Kim Y, Oh YT, Lee K, Chun J, Kim BY, Yoon SH, Lee I, Kim CY, Yoon SS., Nat Commun 7(), 2016
PMID: 27173141
Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling.
Ferrarini MG, Siqueira FM, Mucha SG, Palama TL, Jobard É, Elena-Herrmann B, R Vasconcelos AT, Tardy F, Schrank IS, Zaha A, Sagot MF., BMC Genomics 17(), 2016
PMID: 27178561
Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee.
Messina E, Sorokin DY, Kublanov IV, Toshchakov S, Lopatina A, Arcadi E, Smedile F, La Spada G, La Cono V, Yakimov MM., Stand Genomic Sci 11(), 2016
PMID: 27182430
Two Bacterial Genera, Sodalis and Rickettsia, Associated with the Seal Louse Proechinophthirus fluctus (Phthiraptera: Anoplura).
Boyd BM, Allen JM, Koga R, Fukatsu T, Sweet AD, Johnson KP, Reed DL., Appl Environ Microbiol 82(11), 2016
PMID: 26994086
Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing.
Festa S, Macchi M, Cortés F, Morelli IS, Coppotelli BM., FEMS Microbiol Ecol 92(8), 2016
PMID: 27279417
Draft Genome Sequence of Carbaryl-Degrading Soil Isolate Pseudomonas sp. Strain C5pp.
Trivedi VD, Jangir PK, Sharma R, Phale PS., Genome Announc 4(3), 2016
PMID: 27284139
A family of metal-dependent phosphatases implicated in metabolite damage-control.
Huang L, Khusnutdinova A, Nocek B, Brown G, Xu X, Cui H, Petit P, Flick R, Zallot R, Balmant K, Ziemak MJ, Shanklin J, de Crécy-Lagard V, Fiehn O, Gregory JF, Joachimiak A, Savchenko A, Yakunin AF, Hanson AD., Nat Chem Biol 12(8), 2016
PMID: 27322068
Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges.
Bruder K, Malki K, Cooper A, Sible E, Shapiro JW, Watkins SC, Putonti C., Evol Bioinform Online 12(suppl 1), 2016
PMID: 27375355
Systematic identification and analysis of frequent gene fusion events in metabolic pathways.
Henry CS, Lerma-Ortiz C, Gerdes SY, Mullen JD, Colasanti R, Zhukov A, Frelin O, Thiaville JJ, Zallot R, Niehaus TD, Hasnain G, Conrad N, Hanson AD, de Crécy-Lagard V., BMC Genomics 17(), 2016
PMID: 27342196
Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure.
Colombo LT, de Oliveira MN, Carneiro DG, de Souza RA, Alvim MC, Dos Santos JC, da Silva CC, Vidigal PM, da Silveira WB, Passos FM., Antonie Van Leeuwenhoek 109(9), 2016
PMID: 27350392
Natural diversity of cellulases, xylanases, and chitinases in bacteria.
Talamantes D, Biabini N, Dang H, Abdoun K, Berlemont R., Biotechnol Biofuels 9(), 2016
PMID: 27366206
An automated system for evaluation of the potential functionome: MAPLE version 2.1.0.
Takami H, Taniguchi T, Arai W, Takemoto K, Moriya Y, Goto S., DNA Res (), 2016
PMID: 27374611
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.
Hiraoka S, Yang CC, Iwasaki W., Microbes Environ 31(3), 2016
PMID: 27383682
Comparative genomics and evolution of transcriptional regulons in Proteobacteria.
Leyn SA, Suvorova IA, Kazakov AE, Ravcheev DA, Stepanova VV, Novichkov PS, Rodionov DA., Microb Genom 2(7), 2016
PMID: 28348857
CtaM Is Required for Menaquinol Oxidase aa3 Function in Staphylococcus aureus.
Hammer ND, Schurig-Briccio LA, Gerdes SY, Gennis RB, Skaar EP., MBio 7(4), 2016
PMID: 27406563
Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica.
Buelow HN, Winter AS, Van Horn DJ, Barrett JE, Gooseff MN, Schwartz E, Takacs-Vesbach CD., Front Microbiol 7(), 2016
PMID: 27486436
A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples.
Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FS, Isaac-Renton J, Prystajecky NA, Tang P., Microbiome 4(1), 2016
PMID: 27391119
Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes.
Seston SL, Beinart RA, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ., Front Microbiol 7(), 2016
PMID: 27486438
Iron and Fur in the life cycle of the zoonotic pathogen Vibrio vulnificus.
Pajuelo D, Hernández-Cabanyero C, Sanjuan E, Lee CT, Silva-Hernández FX, Hor LI, MacKenzie S, Amaro C., Environ Microbiol 18(11), 2016
PMID: 27348505
A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein.
Wheatley NM, Eden KD, Ngo J, Rosinski JS, Sawaya MR, Cascio D, Collazo M, Hoveida H, Hubbell WL, Yeates TO., J Mol Biol 428(20), 2016
PMID: 27464895
Gene set-based integrative analysis of ovarian clear cell carcinoma.
Chang CM, Chiou SH, Yang MJ, Yen MS, Wang PH., Taiwan J Obstet Gynecol 55(4), 2016
PMID: 27590381
Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms.
Shiba T, Watanabe T, Kachi H, Koyanagi T, Maruyama N, Murase K, Takeuchi Y, Maruyama F, Izumi Y, Nakagawa I., Sci Rep 6(), 2016
PMID: 27499042
Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type.
Ibarbalz FM, Orellana E, Figuerola EL, Erijman L., Appl Environ Microbiol 82(17), 2016
PMID: 27316957
Genomic Sequencing of Orientia tsutsugamushi Strain Karp, an Assembly Comparable to the Genome Size of the Strain Ikeda.
Liao HM, Chao CC, Lei H, Li B, Tsai S, Hung GC, Ching WM, Lo SC., Genome Announc 4(4), 2016
PMID: 27540052
Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient.
Saghaï A, Zivanovic Y, Moreira D, Benzerara K, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P., Environ Microbiol 18(12), 2016
PMID: 27422734
Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil).
Walter JM, Tschoeke DA, Meirelles PM, de Oliveira L, Leomil L, Tenório M, Valle R, Salomon PS, Thompson CC, Thompson FL., PLoS One 11(8), 2016
PMID: 27548380
Functional Annotations of Paralogs: A Blessing and a Curse.
Zallot R, Harrison KJ, Kolaczkowski B, de Crécy-Lagard V., Life (Basel) 6(3), 2016
PMID: 27618105
Functional Characteristics of the Gut Microbiome in C57BL/6 Mice Differentially Susceptible to Plasmodium yoelii.
Stough JM, Dearth SP, Denny JE, LeCleir GR, Schmidt NW, Campagna SR, Wilhelm SW., Front Microbiol 7(), 2016
PMID: 27729904
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions.
Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C., Database (Oxford) 2016(), 2016
PMID: 27694208
Adaptation to Potassium-Limitation Is Essential for Acinetobacter baumannii Pneumonia Pathogenesis.
Samir R, Hussein SH, Elhosseiny NM, Khattab MS, Shawky AE, Attia AS., J Infect Dis 214(12), 2016
PMID: 27923956
Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota.
Kristoffersen C, Jensen RB, Avershina E, Austbø D, Tauson AH, Rudi K., Microbes Environ 31(4), 2016
PMID: 27773914
Constraint-based stoichiometric modelling from single organisms to microbial communities.
Gottstein W, Olivier BG, Bruggeman FJ, Teusink B., J R Soc Interface 13(124), 2016
PMID: 28334697
Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges.
Li Z, Wang Y, Li J, Liu F, He L, He Y, Wang S., Mar Biotechnol (NY) 18(6), 2016
PMID: 27819120
Genome Sequence of Formosa haliotis Strain MA1, a Brown Alga-Degrading Bacterium Isolated from the Gut of Abalone Haliotis gigantea.
Tanaka R, Mizutani Y, Shibata T, Miyake H, Iehata S, Mori T, Kuroda K, Ueda M., Genome Announc 4(6), 2016
PMID: 27856598
Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis.
Richards MA, Lie TJ, Zhang J, Ragsdale SW, Leigh JA, Price ND., J Bacteriol 198(24), 2016
PMID: 27736793
Draft Genome Sequence of Lysinibacillus xylanilyticus SR-86.
Loscar ME, Huptas C, Wenning M, Sieber V, Schmid J., Genome Announc 4(6), 2016
PMID: 27881544
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.
Faria JP, Davis JJ, Edirisinghe JN, Taylor RC, Weisenhorn P, Olson RD, Stevens RL, Rocha M, Rocha I, Best AA, DeJongh M, Tintle NL, Parrello B, Overbeek R, Henry CS., Front Microbiol 7(), 2016
PMID: 27933038
Genome sequence of a commensal bacterium, Enterococcus faecalis CBA7120, isolated from a Korean fecal sample.
Kim JY, Song HS, Kim YB, Kwon J, Choi JS, Cho YJ, Kim BY, Rhee JK, Myoung J, Nam YD, Roh SW., Gut Pathog 8(), 2016
PMID: 27924153
Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes.
Voronina OL, Kunda MS, Ryzhova NN, Aksenova EI, Semenov AN, Romanova YM, Gintsburg AL., Biomed Res Int 2016(), 2016
PMID: 28070515
Glycoside Hydrolases across Environmental Microbial Communities.
Berlemont R, Martiny AC., PLoS Comput Biol 12(12), 2016
PMID: 27992426
Characterization of saliva microbiota's functional feature based on metagenomic sequencing.
Yang F, Ning K, Zeng X, Zhou Q, Su X, Yuan X., Springerplus 5(1), 2016
PMID: 28053828
Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequences' mobility.
Voronina OL, Kunda MS, Aksenova EI, Semenov AN, Ryzhova NN, Lunin VG, Gintsburg AL., BMC Genomics 17(suppl 14), 2016
PMID: 28105923
Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties.
Castelhano Santos N, Pereira MO, Lourenço A., Brief Bioinform 16(1), 2015
PMID: 24106130
Enabling comparative modeling of closely related genomes: example genus Brucella.
Faria JP, Edirisinghe JN, Davis JJ, Disz T, Hausmann A, Henry CS, Olson R, Overbeek RA, Pusch GD, Shukla M, Vonstein V, Wattam AR., 3 Biotech 5(1), 2015
PMID: 28324362
Evidence that glutamine transaminase and omega-amidase potentially act in tandem to close the methionine salvage cycle in bacteria and plants.
Ellens KW, Richardson LG, Frelin O, Collins J, Ribeiro CL, Hsieh YF, Mullen RT, Hanson AD., Phytochemistry 113(), 2015
PMID: 24837359
Association of biodiversity with the rates of micropollutant biotransformations among full-scale wastewater treatment plant communities.
Johnson DR, Helbling DE, Lee TK, Park J, Fenner K, Kohler HP, Ackermann M., Appl Environ Microbiol 81(2), 2015
PMID: 25398862
Microbial community composition and ultrastructure of granules from a full-scale anammox reactor.
Gonzalez-Gil G, Sougrat R, Behzad AR, Lens PN, Saikaly PE., Microb Ecol 70(1), 2015
PMID: 25501888
News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals.
Deusch S, Tilocca B, Camarinha-Silva A, Seifert J., Comput Struct Biotechnol J 13(), 2015
PMID: 26900430
Ancient and modern environmental DNA.
Pedersen MW, Overballe-Petersen S, Ermini L, Sarkissian CD, Haile J, Hellstrom M, Spens J, Thomsen PF, Bohmann K, Cappellini E, Schnell IB, Wales NA, Carøe C, Campos PF, Schmidt AM, Gilbert MT, Hansen AJ, Orlando L, Willerslev E., Philos Trans R Soc Lond B Biol Sci 370(1660), 2015
PMID: 25487334
The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius.
Frank J, Dingemanse C, Schmitz AM, Vossen RH, van Ommen GJ, den Dunnen JT, Robanus-Maandag EC, Anvar SY., Front Microbiol 6(), 2015
PMID: 26779178
Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary.
Jeffries TC, Schmitz Fontes ML, Harrison DP, Van-Dongen-Vogels V, Eyre BD, Ralph PJ, Seymour JR., Front Microbiol 6(), 2015
PMID: 26858690
Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks.
Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N., Gut 64(11), 2015
PMID: 25614621
Genomic potential for polysaccharide deconstruction in bacteria.
Berlemont R, Martiny AC., Appl Environ Microbiol 81(4), 2015
PMID: 25527556
Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin.
Dailey HA, Gerdes S, Dailey TA, Burch JS, Phillips JD., Proc Natl Acad Sci U S A 112(7), 2015
PMID: 25646457
Metatranscriptomic evidence for co-occurring top-down and bottom-up controls on toxic cyanobacterial communities.
Steffen MM, Belisle BS, Watson SB, Boyer GL, Bourbonniere RA, Wilhelm SW., Appl Environ Microbiol 81(9), 2015
PMID: 25662977
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.
Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA, Stevens R, Vonstein V, Wattam AR, Xia F., Sci Rep 5(), 2015
PMID: 25666585
Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L.
Erlacher A, Cernava T, Cardinale M, Soh J, Sensen CW, Grube M, Berg G., Front Microbiol 6(), 2015
PMID: 25713563
Metagenomic analysis of the bacterial community associated with the taproot of sugar beet.
Tsurumaru H, Okubo T, Okazaki K, Hashimoto M, Kakizaki K, Hanzawa E, Takahashi H, Asanome N, Tanaka F, Sekiyama Y, Ikeda S, Minamisawa K., Microbes Environ 30(1), 2015
PMID: 25740621
Comparative genomic analysis of seven Mycoplasma hyosynoviae strains.
Bumgardner EA, Kittichotirat W, Bumgarner RE, Lawrence PK., Microbiologyopen 4(2), 2015
PMID: 25693846
First draft genome sequence of Aureimonas altamirensis, isolated from patient blood culture.
Eshaghi A, Shahinas D, Patel SN, Kus JV., FEMS Microbiol Lett 362(6), 2015
PMID: 25714548
Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs.
Menzel P, Gudbergsdóttir SR, Rike AG, Lin L, Zhang Q, Contursi P, Moracci M, Kristjansson JK, Bolduc B, Gavrilov S, Ravin N, Mardanov A, Bonch-Osmolovskaya E, Young M, Krogh A, Peng X., Microb Ecol 70(2), 2015
PMID: 25712554
Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii.
Wang J, McIntosh F, Radomski N, Dewar K, Simeone R, Enninga J, Brosch R, Rocha EP, Veyrier FJ, Behr MA., Genome Biol Evol 7(3), 2015
PMID: 25716827
An event-driven approach for studying gene block evolution in bacteria.
Ream DC, Bankapur AR, Friedberg I., Bioinformatics 31(13), 2015
PMID: 25717195
Influence of a non-hospital medical care facility on antimicrobial resistance in wastewater.
Bäumlisberger M, Youssar L, Schilhabel MB, Jonas D., PLoS One 10(3), 2015
PMID: 25821977
BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies.
Oliveira JS, Araújo W, Lopes Sales AI, Brito Guerra Ad, Silva Araújo SC, de Vasconcelos AT, Agnez-Lima LF, Freitas AT., Database (Oxford) 2015(), 2015
PMID: 25833955
Distinct circular single-stranded DNA viruses exist in different soil types.
Reavy B, Swanson MM, Cock PJ, Dawson L, Freitag TE, Singh BK, Torrance L, Mushegian AR, Taliansky M., Appl Environ Microbiol 81(12), 2015
PMID: 25841004
Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus.
Leis B, Angelov A, Mientus M, Li H, Pham VT, Lauinger B, Bongen P, Pietruszka J, Gonçalves LG, Santos H, Liebl W., Front Microbiol 6(), 2015
PMID: 25904908
Comparative accessory gene fingerprinting of surface water Escherichia coli reveals genetically diverse naturalized population.
Tymensen LD, Pyrdok F, Coles D, Koning W, McAllister TA, Jokinen CC, Dowd SE, Neumann NF., J Appl Microbiol 119(1), 2015
PMID: 25816691
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes.
Magnúsdóttir S, Ravcheev D, de Crécy-Lagard V, Thiele I., Front Genet 6(), 2015
PMID: 25941533
Soil microbiome responses to the short-term effects of Amazonian deforestation.
Navarrete AA, Tsai SM, Mendes LW, Faust K, de Hollander M, Cassman NA, Raes J, van Veen JA, Kuramae EE., Mol Ecol 24(10), 2015
PMID: 25809788
Effect of lake water on algal biomass and microbial community structure in municipal wastewater-based lab-scale photobioreactors.
Krustok I, Truu J, Odlare M, Truu M, Ligi T, Tiirik K, Nehrenheim E., Appl Microbiol Biotechnol 99(15), 2015
PMID: 25895091
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.
Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C., Nat Rev Microbiol 13(6), 2015
PMID: 25915636
Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine.
Arntzen MØ, Karlskås IL, Skaugen M, Eijsink VG, Mathiesen G., PLoS One 10(4), 2015
PMID: 25915650
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists.
Dong X, Yambartsev A, Ramsey SA, Thomas LD, Shulzhenko N, Morgun A., Bioinform Biol Insights 9(), 2015
PMID: 25983554
Unraveling interactions in microbial communities - from co-cultures to microbiomes.
Tan J, Zuniga C, Zengler K., J Microbiol 53(5), 2015
PMID: 25935300
Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi.
Moon JS, Choi HS, Shin SY, Noh SJ, Jeon CO, Han NS., J Microbiol 53(5), 2015
PMID: 25935305
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I., Bioinform Biol Insights 9(), 2015
PMID: 25983555
Complete Genome Sequence of Martelella endophytica YC6887, Which Has Antifungal Activity Associated with a Halophyte.
Khan A, Khan H, Chung EJ, Hossain MT, Chung YR., Genome Announc 3(3), 2015
PMID: 25953177
Draft Genome Sequence of Bordetella bronchiseptica KU1201, the First Isolation Source of Arylmalonate Decarboxylase.
Yoshida S, Enoki J, Hemmi R, Kourist R, Kawakami N, Miyamoto K., Genome Announc 3(3), 2015
PMID: 25953178
Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family.
Niehaus TD, Gerdes S, Hodge-Hanson K, Zhukov A, Cooper AJ, ElBadawi-Sidhu M, Fiehn O, Downs DM, Hanson AD., BMC Genomics 16(), 2015
PMID: 25975565
Databases for Microbiologists.
Zhulin IB., J Bacteriol 197(15), 2015
PMID: 26013493
FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples.
Lee J, Lee HT, Hong WY, Jang E, Kim J., J Microbiol Methods 115(), 2015
PMID: 26027543
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome.
Bikel S, Valdez-Lara A, Cornejo-Granados F, Rico K, Canizales-Quinteros S, Soberón X, Del Pozo-Yauner L, Ochoa-Leyva A., Comput Struct Biotechnol J 13(), 2015
PMID: 26137199
Biodiversity and distribution of polar freshwater DNA viruses.
Aguirre de Cárcer D, López-Bueno A, Pearce DA, Alcamí A., Sci Adv 1(5), 2015
PMID: 26601189
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.
Pérez-Losada M, Castro-Nallar E, Bendall ML, Freishtat RJ, Crandall KA., PLoS One 10(6), 2015
PMID: 26125632
Functional Screening of Hydrolytic Activities Reveals an Extremely Thermostable Cellulase from a Deep-Sea Archaeon.
Leis B, Heinze S, Angelov A, Pham VT, Thürmer A, Jebbar M, Golyshin PN, Streit WR, Daniel R, Liebl W., Front Bioeng Biotechnol 3(), 2015
PMID: 26191525
Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System.
Takami H, Arai W, Takemoto K, Uchiyama I, Taniguchi T., PLoS One 10(7), 2015
PMID: 26196861
Metaproteomic analysis using the Galaxy framework.
Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ., Proteomics 15(20), 2015
PMID: 26058579
Nitrogen Cycling Potential of a Grassland Litter Microbial Community.
Nelson MB, Berlemont R, Martiny AC, Martiny JB., Appl Environ Microbiol 81(20), 2015
PMID: 26231641
Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.
Islam MA, Zengler K, Edwards EA, Mahadevan R, Stephanopoulos G., Integr Biol (Camb) 7(8), 2015
PMID: 25994252
Proteins of Unknown Biochemical Function: A Persistent Problem and a Roadmap to Help Overcome It.
Niehaus TD, Thamm AM, de Crécy-Lagard V, Hanson AD., Plant Physiol 169(3), 2015
PMID: 26269542
STAC--A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems.
Korycinski M, Albrecht R, Ursinus A, Hartmann MD, Coles M, Martin J, Dunin-Horkawicz S, Lupas AN., J Mol Biol 427(20), 2015
PMID: 26321252
Mapping high-growth phenotypes in the flux space of microbial metabolism.
Güell O, Massucci FA, Font-Clos F, Sagués F, Serrano MÁ., J R Soc Interface 12(110), 2015
PMID: 26289659
In silico analyses of metagenomes from human atherosclerotic plaque samples.
Mitra S, Drautz-Moses DI, Alhede M, Maw MT, Liu Y, Purbojati RW, Yap ZH, Kushwaha KK, Gheorghe AG, Bjarnsholt T, Hansen GM, Sillesen HH, Hougen HP, Hansen PR, Yang L, Tolker-Nielsen T, Schuster SC, Givskov M., Microbiome 3(), 2015
PMID: 26334731
Draft Genome Sequence of the Shellfish Larval Probiotic Bacillus pumilus RI06-95.
Hamblin M, Spinard E, Gomez-Chiarri M, Nelson DR, Rowley DC., Genome Announc 3(5), 2015
PMID: 26337873
Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides.
Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N, Henrissat B, Osterman AL, Gordon JI., Science 350(6256), 2015
PMID: 26430127
Web Resources for Metagenomics Studies.
Dudhagara P, Bhavsar S, Bhagat C, Ghelani A, Bhatt S, Patel R., Genomics Proteomics Bioinformatics 13(5), 2015
PMID: 26602607
General Stress Signaling in the Alphaproteobacteria.
Fiebig A, Herrou J, Willett J, Crosson S., Annu Rev Genet 49(), 2015
PMID: 26442844
Structural genomics for drug design against the pathogen Coxiella burnetii.
Franklin MC, Cheung J, Rudolph MJ, Burshteyn F, Cassidy M, Gary E, Hillerich B, Yao ZK, Carlier PR, Totrov M, Love JD., Proteins 83(12), 2015
PMID: 26033498
Remobilization of Phytol from Chlorophyll Degradation Is Essential for Tocopherol Synthesis and Growth of Arabidopsis.
Vom Dorp K, Hölzl G, Plohmann C, Eisenhut M, Abraham M, Weber AP, Hanson AD, Dörmann P., Plant Cell 27(10), 2015
PMID: 26452599
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.
Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A., BMC Syst Biol 9(), 2015
PMID: 26452770
Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family.
Han SJ, Song T, Cho YJ, Kim JS, Choi SY, Bang HE, Chun J, Bai GH, Cho SN, Shin SJ., Stand Genomic Sci 10(), 2015
PMID: 26473025
COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets.
Bose T, Haque MM, Reddy C, Mande SS., PLoS One 10(11), 2015
PMID: 26561344
Complete genome sequence of Novosphingobium pentaromativorans US6-1(T).
Choi DH, Kwon YM, Kwon KK, Kim SJ., Stand Genomic Sci 10(), 2015
PMID: 26594308
Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes.
López-López O, Knapik K, Cerdán ME, González-Siso MI., Front Microbiol 6(), 2015
PMID: 26635759
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.
Bauer E, Laczny CC, Magnusdottir S, Wilmes P, Thiele I., Microbiome 3(), 2015
PMID: 26617277
Networks of energetic and metabolic interactions define dynamics in microbial communities.
Embree M, Liu JK, Al-Bassam MM, Zengler K., Proc Natl Acad Sci U S A 112(50), 2015
PMID: 26621749
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach.
Ponce-de-Leon M, Calle-Espinosa J, Peretó J, Montero F., PLoS One 10(12), 2015
PMID: 26629901
Functional overlap of the Arabidopsis leaf and root microbiota.
Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P., Nature 528(7582), 2015
PMID: 26633631
Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality.
Van Rossum T, Peabody MA, Uyaguari-Diaz MI, Cronin KI, Chan M, Slobodan JR, Nesbitt MJ, Suttle CA, Hsiao WW, Tang PK, Prystajecky NA, Brinkman FS., Front Microbiol 6(), 2015
PMID: 26733955
Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.
Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ., Microbiome 3(), 2015
PMID: 26684897
The microbial communities in two apparently physically separated deep subsurface oil reservoirs show extensive DNA sequence similarities.
Lewin A, Johansen J, Wentzel A, Kotlar HK, Drabløs F, Valla S., Environ Microbiol 16(2), 2014
PMID: 23827055
In search of genome annotation consistency: solid gene clusters and how to use them.
Davis JJ, Olsen GJ, Overbeek R, Vonstein V, Xia F., 3 Biotech 4(3), 2014
PMID: 28324432
Physiologic and metagenomic attributes of the rhodoliths forming the largest CaCO3 bed in the South Atlantic Ocean.
Cavalcanti GS, Gregoracci GB, dos Santos EO, Silveira CB, Meirelles PM, Longo L, Gotoh K, Nakamura S, Iida T, Sawabe T, Rezende CE, Francini-Filho RB, Moura RL, Amado-Filho GM, Thompson FL., ISME J 8(1), 2014
PMID: 23985749
Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone.
Ganesh S, Parris DJ, DeLong EF, Stewart FJ., ISME J 8(1), 2014
PMID: 24030599
Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers.
Singh KM, Shah TM, Reddy B, Deshpande S, Rank DN, Joshi CG., J Appl Genet 55(1), 2014
PMID: 24136777
Software platforms to facilitate reconstructing genome-scale metabolic networks.
Hamilton JJ, Reed JL., Environ Microbiol 16(1), 2014
PMID: 24148076
The Structure-Function Linkage Database.
Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC., Nucleic Acids Res 42(database issue), 2014
PMID: 24271399
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R., Nucleic Acids Res 42(database issue), 2014
PMID: 24293654
DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data.
Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A, Bazzicalupo M, Benedetti A, Mocali S., Genomics 103(1), 2014
PMID: 24316132
Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir.
Dong Y, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann IK, Flynn TM, Sanford RA, Krapac IG, Locke RA, Hong PY, Tamaki H, Liu WT, Mackie RI, Hernandez AG, Wright CL, Mikel MA, Walker JL, Sivaguru M, Fried G, Yannarell AC, Fouke BW., Environ Microbiol 16(6), 2014
PMID: 24238218
Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments.
Port JA, Cullen AC, Wallace JC, Smith MN, Faustman EM., Environ Health Perspect 122(3), 2014
PMID: 24334622
Soil microbial community responses to a decade of warming as revealed by comparative metagenomics.
Luo C, Rodriguez-R LM, Johnston ER, Wu L, Cheng L, Xue K, Tu Q, Deng Y, He Z, Shi JZ, Yuan MM, Sherry RA, Li D, Luo Y, Schuur EA, Chain P, Tiedje JM, Zhou J, Konstantinidis KT., Appl Environ Microbiol 80(5), 2014
PMID: 24375144
Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.).
Yun JH, Cho YJ, Chun J, Hyun DW, Bae JW., Stand Genomic Sci 9(3), 2014
PMID: 25197435
ITEP: an integrated toolkit for exploration of microbial pan-genomes.
Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND., BMC Genomics 15(), 2014
PMID: 24387194
Comparative genomics of cultured and uncultured strains suggests genes essential for free-living growth of Liberibacter.
Fagen JR, Leonard MT, McCullough CM, Edirisinghe JN, Henry CS, Davis MJ, Triplett EW., PLoS One 9(1), 2014
PMID: 24416233
Vibrio coralliilyticus strain OCN008 is an etiological agent of acute Montipora white syndrome.
Ushijima B, Videau P, Burger AH, Shore-Maggio A, Runyon CM, Sudek M, Aeby GS, Callahan SM., Appl Environ Microbiol 80(7), 2014
PMID: 24463971
Meta'omic analytic techniques for studying the intestinal microbiome.
Morgan XC, Huttenhower C., Gastroenterology 146(6), 2014
PMID: 24486053
Variability in microbial community composition and function between different niches within a coral reef.
Tout J, Jeffries TC, Webster NS, Stocker R, Ralph PJ, Seymour JR., Microb Ecol 67(3), 2014
PMID: 24477921
Characterization of bacterial NMN deamidase as a Ser/Lys hydrolase expands diversity of serine amidohydrolases.
Sorci L, Brunetti L, Cialabrini L, Mazzola F, Kazanov MD, D'Auria S, Ruggieri S, Raffaelli N., FEBS Lett 588(6), 2014
PMID: 24530526
Structure and expression of propanediol utilization microcompartments in Acetonema longum.
Tocheva EI, Matson EG, Cheng SN, Chen WG, Leadbetter JR, Jensen GJ., J Bacteriol 196(9), 2014
PMID: 24532773
Metabolic and bactericidal effects of targeted suppression of NadD and NadE enzymes in mycobacteria.
Rodionova IA, Schuster BM, Guinn KM, Sorci L, Scott DA, Li X, Kheterpal I, Shoen C, Cynamon M, Locher C, Rubin EJ, Osterman AL., MBio 5(1), 2014
PMID: 24549842
Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism.
Goh KM, Gan HM, Chan KG, Chan GF, Shahar S, Chong CS, Kahar UM, Chai KP., PLoS One 9(6), 2014
PMID: 24603481
Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants.
Yang Y, Yu K, Xia Y, Lau FT, Tang DT, Fung WC, Fang HH, Zhang T., Appl Microbiol Biotechnol 98(12), 2014
PMID: 24633414
Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus spongiarum".
Gao ZM, Wang Y, Tian RM, Wong YH, Batang ZB, Al-Suwailem AM, Bajic VB, Qian PY., MBio 5(2), 2014
PMID: 24692632
Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil.
Pacchioni RG, Carvalho FM, Thompson CE, Faustino AL, Nicolini F, Pereira TS, Silva RC, Cantão ME, Gerber A, Vasconcelos AT, Agnez-Lima LF., Microbiologyopen 3(3), 2014
PMID: 24706600
Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.
Somboonna N, Wilantho A, Jankaew K, Assawamakin A, Sangsrakru D, Tangphatsornruang S, Tongsima S., PLoS One 9(4), 2014
PMID: 24710002
Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics.
Fernández AB, Ghai R, Martin-Cuadrado AB, Sánchez-Porro C, Rodriguez-Valera F, Ventosa A., FEMS Microbiol Ecol 88(3), 2014
PMID: 24661078
Functional genomic characterization of virulence factors from necrotizing fasciitis-causing strains of Aeromonas hydrophila.
Grim CJ, Kozlova EV, Ponnusamy D, Fitts EC, Sha J, Kirtley ML, van Lier CJ, Tiner BL, Erova TE, Joseph SJ, Read TD, Shak JR, Joseph SW, Singletary E, Felland T, Baze WB, Horneman AJ, Chopra AK., Appl Environ Microbiol 80(14), 2014
PMID: 24795370
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, Väremo L, Nookaew I, Nielsen J., Nucleic Acids Res 42(web server issue), 2014
PMID: 24792167
Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes.
Grosjean H, Breton M, Sirand-Pugnet P, Tardy F, Thiaucourt F, Citti C, Barré A, Yoshizawa S, Fourmy D, de Crécy-Lagard V, Blanchard A., PLoS Genet 10(5), 2014
PMID: 24809820
Large-scale metagenomic-based study of antibiotic resistance in the environment.
Nesme J, Cécillon S, Delmont TO, Monier JM, Vogel TM, Simonet P., Curr Biol 24(10), 2014
PMID: 24814145
Characterization of tetA-like gene encoding for a major facilitator superfamily efflux pump in Streptococcus thermophilus.
Arioli S, Guglielmetti S, Amalfitano S, Viti C, Marchi E, Decorosi F, Giovannetti L, Mora D., FEMS Microbiol Lett 355(1), 2014
PMID: 24766488
Human and environmental impacts on river sediment microbial communities.
Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA., PLoS One 9(5), 2014
PMID: 24841417
A mesophilic, autotrophic, ammonia-oxidizing archaeon of thaumarchaeal group I.1a cultivated from a deep oligotrophic soil horizon.
Jung MY, Park SJ, Kim SJ, Kim JG, Sinninghe Damsté JS, Jeon CO, Rhee SK., Appl Environ Microbiol 80(12), 2014
PMID: 24705324
Rapidly expanding knowledge on the role of the gut microbiome in health and disease.
Cénit MC, Matzaraki V, Tigchelaar EF, Zhernakova A., Biochim Biophys Acta 1842(10), 2014
PMID: 24882755
Comparative genomic characterization of a Thailand-Myanmar isolate, MS6, of Vibrio cholerae O1 El Tor, which is phylogenetically related to a "US Gulf Coast" clone.
Okada K, Na-Ubol M, Natakuathung W, Roobthaisong A, Maruyama F, Nakagawa I, Chantaroj S, Hamada S., PLoS One 9(6), 2014
PMID: 24887199
Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis.
Kopac S, Wang Z, Wiedenbeck J, Sherry J, Wu M, Cohan FM., Appl Environ Microbiol 80(16), 2014
PMID: 24907327
Complete genome sequence of Kosakonia sacchari type strain SP1(T.).
Chen M, Zhu B, Lin L, Yang L, Li Y, An Q., Stand Genomic Sci 9(3), 2014
PMID: 25197499
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.
Seaver SM, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LM, Zallot R, Hasnain G, Niehaus TD, El Yacoubi B, Pasternak S, Olson R, Pusch G, Overbeek R, Stevens R, de Crécy-Lagard V, Ware D, Hanson AD, Henry CS., Proc Natl Acad Sci U S A 111(26), 2014
PMID: 24927599
Comparative genomics and evolution of regulons of the LacI-family transcription factors.
Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA., Front Microbiol 5(), 2014
PMID: 24966856
Promiscuity of Exiguobacterium sp. AT1b o-succinylbenzoate synthase illustrates evolutionary transitions in the OSBS family.
Brizendine AM, Odokonyero D, McMillan AW, Zhu M, Hull K, Romo D, Glasner ME., Biochem Biophys Res Commun 450(1), 2014
PMID: 24937446
Draft Genome Sequence of Kitasatospora cheerisanensis KCTC 2395, Which Produces Plecomacrolide against Phytopathogenic Fungi.
Hwang JY, Kim SH, Oh HR, Cho YJ, Chun J, Chung YR, Nam DH., Genome Announc 2(3), 2014
PMID: 24948770
Microbial community degradation of widely used quaternary ammonium disinfectants.
Oh S, Kurt Z, Tsementzi D, Weigand MR, Kim M, Hatt JK, Tandukar M, Pavlostathis SG, Spain JC, Konstantinidis KT., Appl Environ Microbiol 80(19), 2014
PMID: 24951783
Draft Genome Sequence of Kozakia baliensis SR-745, the First Sequenced Kozakia Strain from the Family Acetobacteraceae.
Schmid J, Koenig S, Pick A, Steffler F, Yoshida S, Miyamoto K, Sieber V., Genome Announc 2(3), 2014
PMID: 24970826
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.
Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS., Brief Bioinform 15(4), 2014
PMID: 23422247
Promiscuous and adaptable enzymes fill "holes" in the tetrahydrofolate pathway in Chlamydia species.
Adams NE, Thiaville JJ, Proestos J, Juárez-Vázquez AL, McCoy AJ, Barona-Gómez F, Iwata-Reuyl D, de Crécy-Lagard V, Maurelli AT., MBio 5(4), 2014
PMID: 25006229
Revealing microbial functional activities in the Red Sea sponge Stylissa carteri by metatranscriptomics.
Moitinho-Silva L, Seridi L, Ryu T, Voolstra CR, Ravasi T, Hentschel U., Environ Microbiol 16(12), 2014
PMID: 24920529
Structural and functional diversity of free-living microorganisms in reef surface, Kra island, Thailand.
Somboonna N, Wilantho A, Assawamakin A, Monanunsap S, Sangsrakru D, Tangphatsornruang S, Tongsima S., BMC Genomics 15(), 2014
PMID: 25037613
Gut microbes of mammalian herbivores facilitate intake of plant toxins.
Kohl KD, Weiss RB, Cox J, Dale C, Dearing MD., Ecol Lett 17(10), 2014
PMID: 25040855
Discovery of the β-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs.
Kimura S, Miyauchi K, Ikeuchi Y, Thiaville PC, Crécy-Lagard Vd, Suzuki T., Nucleic Acids Res 42(14), 2014
PMID: 25063302
Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae.
Dittami SM, Barbeyron T, Boyen C, Cambefort J, Collet G, Delage L, Gobet A, Groisillier A, Leblanc C, Michel G, Scornet D, Siegel A, Tapia JE, Tonon T., Front Genet 5(), 2014
PMID: 25120558
Computational integration of genomic traits into 16S rDNA microbiota sequencing studies.
Keller A, Horn H, Förster F, Schultz J., Gene 549(1), 2014
PMID: 25084126
Handling temperature bursts reaching 464°C: different microbial strategies in the sisters peak hydrothermal chimney.
Perner M, Gonnella G, Kurtz S, LaRoche J., Appl Environ Microbiol 80(15), 2014
PMID: 24837379
Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells.
Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, Shteynberg D, Kusebauch U, Moritz RL, Wollscheid B, Lalk M, Völker U, Schmidt F., Front Microbiol 5(), 2014
PMID: 25136337
VibrioBase: a model for next-generation genome and annotation database development.
Choo SW, Heydari H, Tan TK, Siow CC, Beh CY, Wee WY, Mutha NV, Wong GJ, Ang MY, Yazdi AH., ScientificWorldJournal 2014(), 2014
PMID: 25243218
Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions.
Dutilh BE, Thompson CC, Vicente AC, Marin MA, Lee C, Silva GG, Schmieder R, Andrade BG, Chimetto L, Cuevas D, Garza DR, Okeke IN, Aboderin AO, Spangler J, Ross T, Dinsdale EA, Thompson FL, Harkins TT, Edwards RA., BMC Genomics 15(), 2014
PMID: 25096633
Molecular analysis of the cold tolerant Antarctic nematode, Panagrolaimus davidi.
Thorne MA, Kagoshima H, Clark MS, Marshall CJ, Wharton DA., PLoS One 9(8), 2014
PMID: 25098249
MediaDB: a database of microbial growth conditions in defined media.
Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, Price ND., PLoS One 9(8), 2014
PMID: 25098325
Potential drivers of microbial community structure and function in Arctic spring snow.
Maccario L, Vogel TM, Larose C., Front Microbiol 5(), 2014
PMID: 25147550
Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.
Kumar A, Punta M, Axelrod HL, Das D, Farr CL, Grant JC, Chiu HJ, Miller MD, Coggill PC, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA., Protein Sci 23(10), 2014
PMID: 25044324
Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca.
Vanee N, Brooks JP, Spicer V, Shamshurin D, Krokhin O, Wilkins JA, Deng Y, Fong SS., BMC Syst Biol 8(), 2014
PMID: 25115351
NAD homeostasis in the bacterial response to DNA/RNA damage.
Sorci L, Ruggieri S, Raffaelli N., DNA Repair (Amst) 23(), 2014
PMID: 25127744
A tree of cellular life inferred from a genomic census of molecular functions.
Kim KM, Nasir A, Hwang K, Caetano-Anollés G., J Mol Evol 79(5-6), 2014
PMID: 25128982
Draft Genome Sequence of Falsirhodobacter sp. Strain alg1, an Alginate-Degrading Bacterium Isolated from Fermented Brown Algae.
Mori T, Takahashi M, Tanaka R, Shibata T, Kuroda K, Ueda M, Takeyama H., Genome Announc 2(4), 2014
PMID: 25146138
Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut.
Gupta A, Gopal M, Thomas GV, Manikandan V, Gajewski J, Thomas G, Seshagiri S, Schuster SC, Rajesh P, Gupta R., PLoS One 9(8), 2014
PMID: 25162593
Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum.
Zhang L, Nie X, Ravcheev DA, Rodionov DA, Sheng J, Gu Y, Yang S, Jiang W, Yang C., J Bacteriol 196(22), 2014
PMID: 25182496
The characteristics of ubiquitous and unique Leptospira strains from the collection of Russian centre for leptospirosis.
Voronina OL, Kunda MS, Aksenova EI, Ryzhova NN, Semenov AN, Petrov EM, Didenko LV, Lunin VG, Ananyina YV, Gintsburg AL., Biomed Res Int 2014(), 2014
PMID: 25276806
Evolution and comparative genomics of Campylobacter jejuni ST-677 clonal complex.
Kivistö RI, Kovanen S, Skarp-de Haan A, Schott T, Rahkio M, Rossi M, Hänninen ML., Genome Biol Evol 6(9), 2014
PMID: 25193305
The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions.
Bragina A, Oberauner-Wappis L, Zachow C, Halwachs B, Thallinger GG, Müller H, Berg G., Mol Ecol 23(18), 2014
PMID: 25113243
Statistical approach of functional profiling for a microbial community.
An L, Pookhao N, Jiang H, Xu J., PLoS One 9(9), 2014
PMID: 25198674
Archaeal populations in two distinct sedimentary facies of the subsurface of the Dead Sea.
Thomas C, Ionescu D, Ariztegui D, DSDDP Scientific Team., Mar Genomics 17(), 2014
PMID: 25224966
Draft Genome Sequence of the Shellfish Bacterial Pathogen Vibrio sp. Strain B183.
Schreier HJ, Schott EJ., Genome Announc 2(5), 2014
PMID: 25237023
Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine.
Zallot R, Yazdani M, Goyer A, Ziemak MJ, Guan JC, McCarty DR, de Crécy-Lagard V, Gerdes S, Garrett TJ, Benach J, Hunt JF, Shintani DK, Hanson AD., Biochem J 463(1), 2014
PMID: 25014715
Plant-driven repurposing of the ancient S-adenosylmethionine repair enzyme homocysteine S-methyltransferase.
Bradbury LM, Ziemak MJ, El Badawi-Sidhu M, Fiehn O, Hanson AD., Biochem J 463(2), 2014
PMID: 25046177
Discovering the secondary metabolite potential encoded within entomopathogenic fungi.
Gibson DM, Donzelli BG, Krasnoff SB, Keyhani NO., Nat Prod Rep 31(10), 2014
PMID: 25148015
Dynamic flux balance analysis for synthetic microbial communities.
Henson MA, Hanly TJ., IET Syst Biol 8(5), 2014
PMID: 25257022
Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities.
Fernandez L, Mercader JM, Planas-Fèlix M, Torrents D., BMC Genomics 15(), 2014
PMID: 25294412
Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models.
Benedict MN, Mundy MB, Henry CS, Chia N, Price ND., PLoS Comput Biol 10(10), 2014
PMID: 25329157
The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV.
Anvar SY, Frank J, Pol A, Schmitz A, Kraaijeveld K, den Dunnen JT, Op den Camp HJ., BMC Genomics 15(), 2014
PMID: 25331649
Complete Genome Assembly of Corynebacterium sp. Strain ATCC 6931.
Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Li PE, Meincke L, Munk AC, Palacios GF, Redden CL, Johnson SL., Genome Announc 2(5), 2014
PMID: 25342684
Species-specific viromes in the ancestral holobiont Hydra.
Grasis JA, Lachnit T, Anton-Erxleben F, Lim YW, Schmieder R, Fraune S, Franzenburg S, Insua S, Machado G, Haynes M, Little M, Kimble R, Rosenstiel P, Rohwer FL, Bosch TC., PLoS One 9(10), 2014
PMID: 25343582
From microbial gene essentiality to novel antimicrobial drug targets.
Mobegi FM, van Hijum SA, Burghout P, Bootsma HJ, de Vries SP, van der Gaast-de Jongh CE, Simonetti E, Langereis JD, Hermans PW, de Jonge MI, Zomer A., BMC Genomics 15(), 2014
PMID: 25373505
Draft Genome Sequence of a Novel SAR11 Clade Species Abundant in a Tibetan Lake.
Oh S, Zhang R, Wu QL, Liu WT., Genome Announc 2(6), 2014
PMID: 25377713
Integrative workflows for metagenomic analysis.
Ladoukakis E, Kolisis FN, Chatziioannou AA., Front Cell Dev Biol 2(), 2014
PMID: 25478562
Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria.
Leyn SA, Suvorova IA, Kholina TD, Sherstneva SS, Novichkov PS, Gelfand MS, Rodionov DA., PLoS One 9(11), 2014
PMID: 25411846
Cellulolytic potential under environmental changes in microbial communities from grassland litter.
Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JB, Martiny AC., Front Microbiol 5(), 2014
PMID: 25505459
Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria.
Lynch RC, Darcy JL, Kane NC, Nemergut DR, Schmidt SK., Front Microbiol 5(), 2014
PMID: 25566214
Non-contiguous finished genome sequence and description of the gliding bacterium Flavobacterium seoulense sp. nov.
Shin SK, Goo H, Cho YJ, Kwon S, Yong D, Yi H., Stand Genomic Sci 9(), 2014
PMID: 25584140
Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan-Vavilov Deep.
Smedile F, Messina E, La Cono V, Tsoy O, Monticelli LS, Borghini M, Giuliano L, Golyshin PN, Mushegian A, Yakimov MM., Environ Microbiol 15(1), 2013
PMID: 22827264
MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A., J Biotechnol 167(2), 2013
PMID: 23026555
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.
Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL, Noirot P., Nucleic Acids Res 41(1), 2013
PMID: 23109554
Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park.
Kozubal MA, Romine M, Jennings Rd, Jay ZJ, Tringe SG, Rusch DB, Beam JP, McCue LA, Inskeep WP., ISME J 7(3), 2013
PMID: 23151644
TIGRFAMs and Genome Properties in 2013.
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E., Nucleic Acids Res 41(database issue), 2013
PMID: 23197656
Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics.
Burow LC, Woebken D, Marshall IP, Lindquist EA, Bebout BM, Prufert-Bebout L, Hoehler TM, Tringe SG, Pett-Ridge J, Weber PK, Spormann AM, Singer SW., ISME J 7(4), 2013
PMID: 23190731
Quinolinate salvage and insights for targeting NAD biosynthesis in group A streptococci.
Sorci L, Blaby IK, Rodionova IA, De Ingeniis J, Tkachenko S, de Crécy-Lagard V, Osterman AL., J Bacteriol 195(4), 2013
PMID: 23204464
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.
Kazanov MD, Li X, Gelfand MS, Osterman AL, Rodionov DA., Nucleic Acids Res 41(2), 2013
PMID: 23209028
genetic determinants of intrinsic colistin tolerance in Acinetobacter baumannii.
Hood MI, Becker KW, Roux CM, Dunman PM, Skaar EP., Infect Immun 81(2), 2013
PMID: 23230287
Phylogenetic conservatism of functional traits in microorganisms.
Martiny AC, Treseder K, Pusch G., ISME J 7(4), 2013
PMID: 23235290
Phylogenetic distribution of potential cellulases in bacteria.
Berlemont R, Martiny AC., Appl Environ Microbiol 79(5), 2013
PMID: 23263967
Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen.
Poulsen M, Schwab C, Jensen BB, Engberg RM, Spang A, Canibe N, Højberg O, Milinovich G, Fragner L, Schleper C, Weckwerth W, Lund P, Schramm A, Urich T., Nat Commun 4(), 2013
PMID: 23385573
Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.
Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K., Nat Commun 4(), 2013
PMID: 23612296
Applying Shannon's information theory to bacterial and phage genomes and metagenomes.
Akhter S, Bailey BA, Salamon P, Aziz RK, Edwards RA., Sci Rep 3(), 2013
PMID: 23301154
Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages.
Nelson CE, Goldberg SJ, Wegley Kelly L, Haas AF, Smith JE, Rohwer F, Carlson CA., ISME J 7(5), 2013
PMID: 23303369
Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes.
Zimmerman AE, Martiny AC, Allison SD., ISME J 7(6), 2013
PMID: 23303371
Exploring the diversity of Arcobacter butzleri from cattle in the UK using MLST and whole genome sequencing.
Merga JY, Williams NJ, Miller WG, Leatherbarrow AJ, Bennett M, Hall N, Ashelford KE, Winstanley C., PLoS One 8(2), 2013
PMID: 23405126
Computational tools for the secondary analysis of metabolomics experiments.
Booth SC, Weljie AM, Turner RJ., Comput Struct Biotechnol J 4(), 2013
PMID: 24688685
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria.
Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov PS, Rodionov DA., BMC Genomics 14(), 2013
PMID: 23398941
Improving microbial genome annotations in an integrated database context.
Chen IM, Markowitz VM, Chu K, Anderson I, Mavromatis K, Kyrpides NC, Ivanova NN., PLoS One 8(2), 2013
PMID: 23424620
Structure and function of a cyanophage-encoded peptide deformylase.
Frank JA, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards RA, Segall AM, Burgin AB., ISME J 7(6), 2013
PMID: 23407310
Novel inositol catabolic pathway in Thermotoga maritima.
Rodionova IA, Leyn SA, Burkart MD, Boucher N, Noll KM, Osterman AL, Rodionov DA., Environ Microbiol 15(8), 2013
PMID: 23441918
Metagenomic analysis of viral communities in (hado)pelagic sediments.
Yoshida M, Takaki Y, Eitoku M, Nunoura T, Takai K., PLoS One 8(2), 2013
PMID: 23468952
A polyphasic approach for assessing the suitability of bioremediation for the treatment of hydrocarbon-impacted soil.
Adetutu EM, Smith RJ, Weber J, Aleer S, Mitchell JG, Ball AS, Juhasz AL., Sci Total Environ 450-451(), 2013
PMID: 23454909
Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.
Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber AP., Science 339(6124), 2013
PMID: 23471408
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.
Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov PS, Rodionov DA., J Bacteriol 195(11), 2013
PMID: 23504016
Phylogenetic analysis and metabolic potential of microbial communities in an industrial bagasse collection site.
Kanokratana P, Mhuantong W, Laothanachareon T, Tangphatsornruang S, Eurwilaichitr L, Pootanakit K, Champreda V., Microb Ecol 66(2), 2013
PMID: 23504022
Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l.
Singer E, Heidelberg JF, Dhillon A, Edwards KJ., Front Microbiol 4(), 2013
PMID: 23518919
Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production.
Verbeke TJ, Zhang X, Henrissat B, Spicer V, Rydzak T, Krokhin OV, Fristensky B, Levin DB, Sparling R., PLoS One 8(3), 2013
PMID: 23555660
MGcV: the microbial genomic context viewer for comparative genome analysis.
Overmars L, Kerkhoven R, Siezen RJ, Francke C., BMC Genomics 14(), 2013
PMID: 23547764
Identification and characterization of five new molecular serogroups of Cronobacter spp.
Jarvis KG, Yan QQ, Grim CJ, Power KA, Franco AA, Hu L, Gopinath G, Sathyamoorthy V, Kotewicz ML, Kothary MH, Lee C, Sadowski J, Fanning S, Tall BD., Foodborne Pathog Dis 10(4), 2013
PMID: 23566272
Multivariate analysis of functional metagenomes.
Dinsdale EA, Edwards RA, Bailey BA, Tuba I, Akhter S, McNair K, Schmieder R, Apkarian N, Creek M, Guan E, Hernandez M, Isaacs K, Peterson C, Regh T, Ponomarenko V., Front Genet 4(), 2013
PMID: 23579547
Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis.
Macklaim JM, Fernandes AD, Di Bella JM, Hammond JA, Reid G, Gloor GB., Microbiome 1(1), 2013
PMID: 24450540
A preliminary metagenomic study of puer tea during pile fermentation.
Lyu C, Chen C, Ge F, Liu D, Zhao S, Chen D., J Sci Food Agric 93(13), 2013
PMID: 23553377
Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes.
Davis JJ, Xia F, Overbeek RA, Olsen GJ., Int J Syst Evol Microbiol 63(pt 7), 2013
PMID: 23606477
Characterization of Aeromonas hydrophila wound pathotypes by comparative genomic and functional analyses of virulence genes.
Grim CJ, Kozlova EV, Sha J, Fitts EC, van Lier CJ, Kirtley ML, Joseph SJ, Read TD, Burd EM, Tall BD, Joseph SW, Horneman AJ, Chopra AK, Shak JR., MBio 4(2), 2013
PMID: 23611906
Metabolic network modeling approaches for investigating the "hungry cancer".
Sharma AK, König R., Semin Cancer Biol 23(4), 2013
PMID: 23680724
Computational meta'omics for microbial community studies.
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C., Mol Syst Biol 9(), 2013
PMID: 23670539
Draft Genome Sequence of Cesiribacter andamanensis Strain AMV16T, Isolated from a Soil Sample from a Mud Volcano in the Andaman Islands, India.
Shivaji S, Ara S, Begum Z, Srinivas TN, Singh A, Kumar Pinnaka A., Genome Announc 1(3), 2013
PMID: 23682146
Two multidrug-resistant clinical isolates of Bacteroides fragilis carry a novel metronidazole resistance nim gene (nimJ).
Husain F, Veeranagouda Y, Hsi J, Meggersee R, Abratt V, Wexler HM., Antimicrob Agents Chemother 57(8), 2013
PMID: 23716049
Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation.
Grim CJ, Kotewicz ML, Power KA, Gopinath G, Franco AA, Jarvis KG, Yan QQ, Jackson SA, Sathyamoorthy V, Hu L, Pagotto F, Iversen C, Lehner A, Stephan R, Fanning S, Tall BD., BMC Genomics 14(), 2013
PMID: 23724777
Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T)).
Hyun DW, Whon TW, Cho YJ, Chun J, Kim MS, Jung MJ, Shin NR, Kim JY, Kim PS, Yun JH, Lee J, Oh SJ, Bae JW., Stand Genomic Sci 8(2), 2013
PMID: 23991257
Life on human surfaces: skin metagenomics.
Mathieu A, Delmont TO, Vogel TM, Robe P, Nalin R, Simonet P., PLoS One 8(6), 2013
PMID: 23776466
Genomics-guided analysis of NAD recycling yields functional elucidation of COG1058 as a new family of pyrophosphatases.
Cialabrini L, Ruggieri S, Kazanov MD, Sorci L, Mazzola F, Orsomando G, Osterman AL, Raffaelli N., PLoS One 8(6), 2013
PMID: 23776507
Comparative Genomic Analyses of Streptococcus pseudopneumoniae Provide Insight into Virulence and Commensalism Dynamics.
Shahinas D, Thornton CS, Tamber GS, Arya G, Wong A, Jamieson FB, Ma JH, Alexander DC, Low DE, Pillai DR., PLoS One 8(6), 2013
PMID: 23840352
MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information.
Konwar KM, Hanson NW, Pagé AP, Hallam SJ., BMC Bioinformatics 14(), 2013
PMID: 23800136
Metagenomic Analysis of the Dynamic Changes in the Gut Microbiome of the Participants of the MARS-500 Experiment, Simulating Long Term Space Flight.
Mardanov AV, Babykin MM, Beletsky AV, Grigoriev AI, Zinchenko VV, Kadnikov VV, Kirpichnikov MP, Mazur AM, Nedoluzhko AV, Novikova ND, Prokhortchouk EB, Ravin NV, Skryabin KG, Shestakov SV., Acta Naturae 5(3), 2013
PMID: 24303207
Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules.
Williams KJ, Bryant WA, Jenkins VA, Barton GR, Witney AA, Pinney JW, Robertson BD., BMC Genomics 14(), 2013
PMID: 23819599
Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants.
Claud EC, Keegan KP, Brulc JM, Lu L, Bartels D, Glass E, Chang EB, Meyer F, Antonopoulos DA., Microbiome 1(1), 2013
PMID: 24450928
Metagenomic insights into metabolic capacities of the gut microbiota in a fungus-cultivating termite (Odontotermes yunnanensis).
Liu N, Zhang L, Zhou H, Zhang M, Yan X, Wang Q, Long Y, Xie L, Wang S, Huang Y, Zhou Z., PLoS One 8(7), 2013
PMID: 23874908
Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine Bacterium.
Yasuike M, Nakamura Y, Kai W, Fujiwara A, Fukui Y, Satomi M, Sano M., Genome Announc 1(4), 2013
PMID: 23868120
Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes.
Jakobsen TH, Hansen MA, Jensen PØ, Hansen L, Riber L, Cockburn A, Kolpen M, Rønne Hansen C, Ridderberg W, Eickhardt S, Hansen M, Kerpedjiev P, Alhede M, Qvortrup K, Burmølle M, Moser C, Kühl M, Ciofu O, Givskov M, Sørensen SJ, Høiby N, Bjarnsholt T., PLoS One 8(7), 2013
PMID: 23894309
Function and X-ray crystal structure of Escherichia coli YfdE.
Mullins EA, Sullivan KL, Kappock TJ., PLoS One 8(7), 2013
PMID: 23935849
Functional profiling of the gut microbiome in disease-associated inflammation.
Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C., Genome Med 5(7), 2013
PMID: 23906180
Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities.
Seifert J, Herbst FA, Halkjaer Nielsen P, Planes FJ, Jehmlich N, Ferrer M, von Bergen M., Proteomics 13(18-19), 2013
PMID: 23625762
Mercury methylation by the methanogen Methanospirillum hungatei.
Yu RQ, Reinfelder JR, Hines ME, Barkay T., Appl Environ Microbiol 79(20), 2013
PMID: 23934484
Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives.
Khosravi Y, Rehvathy V, Wee WY, Wang S, Baybayan P, Singh S, Ashby M, Ong J, Amoyo AA, Seow SW, Choo SW, Perkins T, Chua EG, Tay A, Marshall BJ, Loke MF, Goh KL, Pettersson S, Vadivelu J., Gut Pathog 5(), 2013
PMID: 23957912
Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.
Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL., Front Microbiol 4(), 2013
PMID: 23986752
The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S., PLoS Biol 11(8), 2013
PMID: 24013487
A cross-kingdom Nudix enzyme that pre-empts damage in thiamin metabolism.
Goyer A, Hasnain G, Frelin O, Ralat MA, Gregory JF, Hanson AD., Biochem J 454(3), 2013
PMID: 23834287
Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility.
Yan Q, Power KA, Cooney S, Fox E, Gopinath GR, Grim CJ, Tall BD, McCusker MP, Fanning S., Front Microbiol 4(), 2013
PMID: 24032028
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.
Sun EI, Leyn SA, Kazanov MD, Saier MH, Novichkov PS, Rodionov DA., BMC Genomics 14(), 2013
PMID: 24060102
Exploration and prediction of interactions between methanotrophs and heterotrophs.
Stock M, Hoefman S, Kerckhof FM, Boon N, De Vos P, De Baets B, Heylen K, Waegeman W., Res Microbiol 164(10), 2013
PMID: 24012541
High throughput sequencing methods and analysis for microbiome research.
Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G., J Microbiol Methods 95(3), 2013
PMID: 24029734
Comparative evaluation of rumen metagenome community using qPCR and MG-RAST.
Nathani NM, Patel AK, Dhamannapatil PS, Kothari RK, Singh KM, Joshi CG., AMB Express 3(1), 2013
PMID: 24025701
A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities.
Thureborn P, Lundin D, Plathan J, Poole AM, Sjöberg BM, Sjöling S., PLoS One 8(9), 2013
PMID: 24086414
Draft Genome Sequence of Exopolysaccharide-Producing Thermophilic Bacterium Brevibacillus thermoruber Strain 423.
Yasar Yildiz S, Kambourova M, Arga KY, Toksoy Oner E., Genome Announc 1(5), 2013
PMID: 24072869
Analytical tools and databases for metagenomics in the next-generation sequencing era.
Kim M, Lee KH, Yoon SW, Kim BS, Chun J, Yi H., Genomics Inform 11(3), 2013
PMID: 24124405
Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant.
Wang Z, Zhang XX, Huang K, Miao Y, Shi P, Liu B, Long C, Li A., PLoS One 8(10), 2013
PMID: 24098424
A preliminary metagenomic study of puer tea during pile fermentation
Lyu C, Chen C, Ge F, Liu D, Zhao S, Chen D., J Sci Food Agric 93(13), 2013
PMID: IND500690354
Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing.
Mitra S, Förster-Fromme K, Damms-Machado A, Scheurenbrand T, Biskup S, Huson DH, Bischoff SC., BMC Genomics 14 Suppl 5(), 2013
PMID: 24564472
A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves.
Thompson CE, Beys-da-Silva WO, Santi L, Berger M, Vainstein MH, Guima Rães JA, Vasconcelos AT., AMB Express 3(1), 2013
PMID: 24160319
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.
Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA., BMC Genomics 14(), 2013
PMID: 24175918
Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment.
Garcia JC, Urakawa H, Le VQ, Stein LY, Klotz MG, Nielsen JL., Genome Announc 1(6), 2013
PMID: 24201205
Comparative genome analysis of Megasphaera sp. reveals niche specialization and its potential role in the human gut.
Shetty SA, Marathe NP, Lanjekar V, Ranade D, Shouche YS., PLoS One 8(11), 2013
PMID: 24260205
Combining de novo and reference-guided assembly with scaffold_builder.
Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA., Source Code Biol Med 8(1), 2013
PMID: 24267787
Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content.
Vandroemme J, Cottyn B, Baeyen S, De Vos P, Maes M., BMC Genomics 14(), 2013
PMID: 24274055
Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria.
Rodionova IA, Li X, Thiel V, Stolyar S, Stanton K, Fredrickson JK, Bryant DA, Osterman AL, Best AA, Rodionov DA., Front Microbiol 4(), 2013
PMID: 24391637
Genome Sequence of the Pigment-Producing Bacterium Pseudogulbenkiania ferrooxidans, Isolated from Loktak Lake.
Puranik S, Talkal R, Qureshi A, Khardenavis A, Kapley A, Purohit HJ., Genome Announc 1(6), 2013
PMID: 24371207
Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study.
Singh KM, Ahir VB, Tripathi AK, Ramani UV, Sajnani M, Koringa PG, Jakhesara S, Pandya PR, Rank DN, Murty DS, Kothari RK, Joshi CG., Mol Biol Rep 39(4), 2012
PMID: 21947953
Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals.
Jeanguenin L, Lara-Núñez A, Rodionov DA, Osterman AL, Komarova NY, Rentsch D, Gregory JF, Hanson AD., Funct Integr Genomics 12(1), 2012
PMID: 21953179
Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.
Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA., Environ Microbiol 14(1), 2012
PMID: 22004549
Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems.
Smith RJ, Jeffries TC, Roudnew B, Fitch AJ, Seymour JR, Delpin MW, Newton K, Brown MH, Mitchell JG., Environ Microbiol 14(1), 2012
PMID: 22004107
Functional promiscuity of the COG0720 family.
Phillips G, Grochowski LL, Bonnett S, Xu H, Bailly M, Blaby-Haas C, El Yacoubi B, Iwata-Reuyl D, White RH, de Crécy-Lagard V., ACS Chem Biol 7(1), 2012
PMID: 21999246
Diversity of archaeosine synthesis in crenarchaeota.
Phillips G, Swairjo MA, Gaston KW, Bailly M, Limbach PA, Iwata-Reuyl D, de Crécy-Lagard V., ACS Chem Biol 7(2), 2012
PMID: 22032275
Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli.
Shepard SM, Danzeisen JL, Isaacson RE, Seemann T, Achtman M, Johnson TJ., J Bacteriol 194(2), 2012
PMID: 22081385
Evidence that the folate-dependent proteins YgfZ and MnmEG have opposing effects on growth and on activity of the iron-sulfur enzyme MiaB.
Waller JC, Ellens KW, Hasnain G, Alvarez S, Rocca JR, Hanson AD., J Bacteriol 194(2), 2012
PMID: 22081392
Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the High Arctic.
Varin T, Lovejoy C, Jungblut AD, Vincent WF, Corbeil J., Appl Environ Microbiol 78(2), 2012
PMID: 22081564
UniPathway: a resource for the exploration and annotation of metabolic pathways.
Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A., Nucleic Acids Res 40(database issue), 2012
PMID: 22102589
Exploration of community traits as ecological markers in microbial metagenomes.
Barberán A, Fernández-Guerra A, Bohannan BJ, Casamayor EO., Mol Ecol 21(8), 2012
PMID: 22121910
MOPED: Model Organism Protein Expression Database.
Kolker E, Higdon R, Haynes W, Welch D, Broomall W, Lancet D, Stanberry L, Kolker N., Nucleic Acids Res 40(database issue), 2012
PMID: 22139914
Functional bias of positively selected genes in Streptococcus genomes.
Suzuki H, Stanhope MJ., Infect Genet Evol 12(2), 2012
PMID: 22155358
Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus.
Kimes NE, Grim CJ, Johnson WR, Hasan NA, Tall BD, Kothary MH, Kiss H, Munk AC, Tapia R, Green L, Detter C, Bruce DC, Brettin TS, Colwell RR, Morris PJ., ISME J 6(4), 2012
PMID: 22158392
Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins.
Shlykov MA, Zheng WH, Chen JS, Saier MH., Biochim Biophys Acta 1818(3), 2012
PMID: 22192777
Grounding annotations in published literature with an emphasis on the functional roles used in metabolic models.
Binter E, Binter S, Disz T, Kalmanek E, Powers A, Pusch GD, Turgeon J., 3 Biotech 2(2), 2012
PMID: PMC3376863
Ribulokinase and transcriptional regulation of arabinose metabolism in Clostridium acetobutylicum.
Zhang L, Leyn SA, Gu Y, Jiang W, Rodionov DA, Yang C., J Bacteriol 194(5), 2012
PMID: 22194461
Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex.
Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov PS, Osterman AL, Rodionov DA., J Bacteriol 194(5), 2012
PMID: 22210771
Decoding in Candidatus Riesia pediculicola, close to a minimal tRNA modification set?
de Crécy-Lagard V, Marck C, Grosjean H., Trends Cell Mol Biol 7(), 2012
PMID: 23308034
Genomic arrangement of regulons in bacterial genomes.
Zhang H, Yin Y, Olman V, Xu Y., PLoS One 7(1), 2012
PMID: 22235300
Frontiers in metabolic reconstruction and modeling of plant genomes.
Seaver SM, Henry CS, Hanson AD., J Exp Bot 63(6), 2012
PMID: 22238452
A metabolic network approach for the identification and prioritization of antimicrobial drug targets.
Chavali AK, D'Auria KM, Hewlett EL, Pearson RD, Papin JA., Trends Microbiol 20(3), 2012
PMID: 22300758
Draft genome sequences of the Pseudomonas fluorescens biocontrol strains Wayne1R and Wood1R.
Rong X, Gurel FB, Meulia T, McSpadden Gardener BB., J Bacteriol 194(3), 2012
PMID: 22247526
Draft genome sequence of Pantoea ananatis B1-9, a nonpathogenic plant growth-promoting bacterium.
Kim HJ, Lee JH, Kang BR, Rong X, McSpadden Gardener BB, Ji HJ, Park CS, Kim YC., J Bacteriol 194(3), 2012
PMID: 22247529
Draft genome sequences of the biocontrol bacterium Mitsuaria sp. strain H24L5A.
Rong X, Gurel FB, Meulia T, McSpadden Gardener BB., J Bacteriol 194(3), 2012
PMID: 22247532
Structure, fluctuation and magnitude of a natural grassland soil metagenome.
Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, Le Paslier D, Simonet P, Vogel TM., ISME J 6(9), 2012
PMID: 22297556
Metaproteogenomic analysis of a community of sponge symbionts.
Liu M, Fan L, Zhong L, Kjelleberg S, Thomas T., ISME J 6(8), 2012
PMID: 22297557
Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study.
Steven B, Gallegos-Graves LV, Starkenburg SR, Chain PS, Kuske CR., Environ Microbiol Rep 4(2), 2012
PMID: 23757280
A novel protein kinase-like domain in a selenoprotein, widespread in the tree of life.
Dudkiewicz M, Szczepińska T, Grynberg M, Pawłowski K., PLoS One 7(2), 2012
PMID: 22359664
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.
Dwivedi B, Schmieder R, Goldsmith DB, Edwards RA, Breitbart M., BMC Bioinformatics 13(), 2012
PMID: 22385976
Insights into the bovine rumen plasmidome.
Brown Kav A, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, Mizrahi I., Proc Natl Acad Sci U S A 109(14), 2012
PMID: 22431592
Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria.
Babujee L, Apodaca J, Balakrishnan V, Liss P, Kiley PJ, Charkowski AO, Glasner JD, Perna NT., BMC Genomics 13(), 2012
PMID: 22439737
A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum--cellular behavior in adaptation to n-butanol.
Schwarz KM, Kuit W, Grimmler C, Ehrenreich A, Kengen SW., J Biotechnol 161(3), 2012
PMID: 22484128
Prevalence of avian-pathogenic Escherichia coli strain O1 genomic islands among extraintestinal and commensal E. coli isolates.
Johnson TJ, Wannemuehler Y, Kariyawasam S, Johnson JR, Logue CM, Nolan LK., J Bacteriol 194(11), 2012
PMID: 22467781
Population genomics of early events in the ecological differentiation of bacteria.
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ., Science 336(6077), 2012
PMID: 22491847
Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142.
Vu TT, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, Brown RN, Lipton MS, Osterman A, Fredrickson JK, Konopka AE, Beliaev AS, Reed JL., PLoS Comput Biol 8(4), 2012
PMID: 22529767
A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response.
Schwartz S, Friedberg I, Ivanov IV, Davidson LA, Goldsby JS, Dahl DB, Herman D, Wang M, Donovan SM, Chapkin RS., Genome Biol 13(4), 2012
PMID: 22546241
Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes.
Dos Santos PC, Fang Z, Mason SW, Setubal JC, Dixon R., BMC Genomics 13(), 2012
PMID: 22554235
The major facilitator superfamily (MFS) revisited.
Reddy VS, Shlykov MA, Castillo R, Sun EI, Saier MH., FEBS J 279(11), 2012
PMID: 22458847
Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.
Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P., Mol Syst Biol 8(), 2012
PMID: 22569339
Identification of a third osmoprotectant transport system, the osmU system, in Salmonella enterica.
Frossard SM, Khan AA, Warrick EC, Gately JM, Hanson AD, Oldham ML, Sanders DA, Csonka LN., J Bacteriol 194(15), 2012
PMID: 22609924
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.
Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K., Nucleic Acids Res 40(15), 2012
PMID: 22638584
In vitro and in vivo characterization and strain safety of Lactobacillus reuteri NCIMB 30253 for probiotic applications.
Sulemankhil I, Parent M, Jones ML, Feng Z, Labbé A, Prakash S., Can J Microbiol 58(6), 2012
PMID: 22642667
Deep sequencing of the oral microbiome reveals signatures of periodontal disease.
Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S., PLoS One 7(6), 2012
PMID: 22675498
Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts.
Fan L, Reynolds D, Liu M, Stark M, Kjelleberg S, Webster NS, Thomas T., Proc Natl Acad Sci U S A 109(27), 2012
PMID: 22699508
Identification and characterization of Cronobacter iron acquisition systems.
Grim CJ, Kothary MH, Gopinath G, Jarvis KG, Beaubrun JJ, McClelland M, Tall BD, Franco AA., Appl Environ Microbiol 78(17), 2012
PMID: 22706064
Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosynthetic organisms.
Bradbury LM, Shumskaya M, Tzfadia O, Wu SB, Kennelly EJ, Wurtzel ET., Proc Natl Acad Sci U S A 109(27), 2012
PMID: 22706644
Glutamine versus ammonia utilization in the NAD synthetase family.
De Ingeniis J, Kazanov MD, Shatalin K, Gelfand MS, Osterman AL, Sorci L., PLoS One 7(6), 2012
PMID: 22720044
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools.
Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F., BMC Bioinformatics 13(), 2012
PMID: 22720753
Metagenomics and development of the gut microbiota in infants.
Vallès Y, Gosalbes MJ, de Vries LE, Abellán JJ, Francino MP., Clin Microbiol Infect 18 Suppl 4(), 2012
PMID: 22647043
Comparative metagenomics of two microbial mats at Cuatro Ciénegas Basin I: ancient lessons on how to cope with an environment under severe nutrient stress.
Peimbert M, Alcaraz LD, Bonilla-Rosso G, Olmedo-Alvarez G, García-Oliva F, Segovia L, Eguiarte LE, Souza V., Astrobiology 12(7), 2012
PMID: 22920515
In silico method for modelling metabolism and gene product expression at genome scale.
Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO., Nat Commun 3(), 2012
PMID: 22760628
Functional assignment of metagenomic data: challenges and applications.
Prakash T, Taylor TD., Brief Bioinform 13(6), 2012
PMID: 22772835
RNase Y of Staphylococcus aureus and its role in the activation of virulence genes.
Marincola G, Schäfer T, Behler J, Bernhardt J, Ohlsen K, Goerke C, Wolz C., Mol Microbiol 85(5), 2012
PMID: 22780584
Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing.
Wirth R, Kovács E, Maróti G, Bagi Z, Rákhely G, Kovács KL., Biotechnol Biofuels 5(), 2012
PMID: 22673110
Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales.
Swithers KS, Petrus AK, Secinaro MA, Nesbø CL, Gogarten JP, Noll KM, Butzin NC., Genome Biol Evol 4(8), 2012
PMID: 22798452
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome.
Cong Q, Kinch LN, Kim BH, Grishin NV., PLoS One 7(7), 2012
PMID: 22815919
VIROME: a standard operating procedure for analysis of viral metagenome sequences.
Wommack KE, Bhavsar J, Polson SW, Chen J, Dumas M, Srinivasiah S, Furman M, Jamindar S, Nasko DJ., Stand Genomic Sci 6(3), 2012
PMID: 23407591
Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.
Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang YJ, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, Brumm P., Stand Genomic Sci 6(3), 2012
PMID: 23408395
Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches.
Logares R, Haverkamp TH, Kumar S, Lanzén A, Nederbragt AJ, Quince C, Kauserud H., J Microbiol Methods 91(1), 2012
PMID: 22849829
Pleiotropic functions of catabolite control protein CcpA in Butanol-producing Clostridium acetobutylicum.
Ren C, Gu Y, Wu Y, Zhang W, Yang C, Yang S, Jiang W., BMC Genomics 13(), 2012
PMID: 22846451
The ABC transporters in Candidatus Liberibacter asiaticus.
Li W, Cong Q, Pei J, Kinch LN, Grishin NV., Proteins 80(11), 2012
PMID: 22807026
Are we ready for genome-scale modeling in plants?
Collakova E, Yen JY, Senger RS., Plant Sci 191-(), 2012
PMID: IND44785982
A comparison of computational methods for identifying virulence factors.
Zheng LL, Li YX, Ding J, Guo XK, Feng KY, Wang YJ, Hu LL, Cai YD, Hao P, Chou KC., PLoS One 7(8), 2012
PMID: 22880014
Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data.
Tintle NL, Sitarik A, Boerema B, Young K, Best AA, Dejongh M., BMC Bioinformatics 13(), 2012
PMID: 22873695
Diversity and versatility of the Thermotoga maritima sugar kinome.
Rodionova IA, Yang C, Li X, Kurnasov OV, Best AA, Osterman AL, Rodionov DA., J Bacteriol 194(20), 2012
PMID: 22885293
Plant B vitamin pathways and their compartmentation: a guide for the perplexed.
Gerdes S, Lerma-Ortiz C, Frelin O, Seaver SM, Henry CS, de Crécy-Lagard V, Hanson AD., J Exp Bot 63(15), 2012
PMID: 22915736
Analysis of gene expression from the Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis.
Darby AC, Armstrong SD, Bah GS, Kaur G, Hughes MA, Kay SM, Koldkjær P, Rainbow L, Radford AD, Blaxter ML, Tanya VN, Trees AJ, Cordaux R, Wastling JM, Makepeace BL., Genome Res 22(12), 2012
PMID: 22919073
Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima.
Rodionova IA, Scott DA, Grishin NV, Osterman AL, Rodionov DA., Environ Microbiol 14(11), 2012
PMID: 22925190
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides.
Berendzen J, Bruno WJ, Cohn JD, Hengartner NW, Kuske CR, McMahon BH, Wolinsky MA, Xie G., BMC Res Notes 5(), 2012
PMID: 22925230
Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate.
de Crécy-Lagard V, Phillips G, Grochowski LL, El Yacoubi B, Jenney F, Adams MW, Murzin AG, White RH., ACS Chem Biol 7(11), 2012
PMID: 22931285
Sialic acid utilization by the soil bacterium Corynebacterium glutamicum.
Gruteser N, Marin K, Krämer R, Thomas GH., FEMS Microbiol Lett 336(2), 2012
PMID: 22924979
Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage.
de Crécy-Lagard V, Forouhar F, Brochier-Armanet C, Tong L, Hunt JF., Biol Direct 7(), 2012
PMID: 23013770
A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens).
Hildebrand F, Ebersbach T, Nielsen HB, Li X, Sonne SB, Bertalan M, Dimitrov P, Madsen L, Qin J, Wang J, Wang J, Raes J, Kristiansen K, Licht TR., BMC Genomics 13(), 2012
PMID: 23020652
Global probabilistic annotation of metabolic networks enables enzyme discovery.
Plata G, Fuhrer T, Hsiao TL, Sauer U, Vitkup D., Nat Chem Biol 8(10), 2012
PMID: 22960854
MESSA: MEta-Server for protein Sequence Analysis.
Cong Q, Grishin NV., BMC Biol 10(), 2012
PMID: 23031578
Real time metagenomics: using k-mers to annotate metagenomes.
Edwards RA, Olson R, Disz T, Pusch GD, Vonstein V, Stevens R, Overbeek R., Bioinformatics 28(24), 2012
PMID: 23047562
Automatic assignment of prokaryotic genes to functional categories using literature profiling.
Torrieri R, Oliveira FS, Oliveira G, Coimbra RS., PLoS One 7(10), 2012
PMID: 23077617
Microbial virus genome annotation-mustering the troops to fight the sequence onslaught.
Brister JR, Le Mercier P, Hu JC., Virology 434(2), 2012
PMID: 23084289
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.
Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F., PLoS One 7(10), 2012
PMID: 23110173
Dryland biological soil crust cyanobacteria show unexpected decreases in abundance under long-term elevated CO2.
Steven B, Gallegos-Graves LV, Yeager CM, Belnap J, Evans RD, Kuske CR., Environ Microbiol 14(12), 2012
PMID: 23116182
Phenomenological model for predicting the catabolic potential of an arbitrary nutrient.
Seaver SM, Sales-Pardo M, Guimerà R, Amaral LA., PLoS Comput Biol 8(11), 2012
PMID: 23133365
Metagenomic analysis of the microbiota from the crop of an invasive snail reveals a rich reservoir of novel genes.
Cardoso AM, Cavalcante JJ, Cantão ME, Thompson CE, Flatschart RB, Glogauer A, Scapin SM, Sade YB, Beltrão PJ, Gerber AL, Martins OB, Garcia ES, de Souza W, Vasconcelos AT., PLoS One 7(11), 2012
PMID: 23133637
Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations.
Cordero OX, Ventouras LA, DeLong EF, Polz MF., Proc Natl Acad Sci U S A 109(49), 2012
PMID: 23169633
Draft genome sequence of the cyanide-utilizing bacterium Pseudomonas fluorescens strain NCIMB 11764.
Vilo CA, Benedik MJ, Kunz DA, Dong Q., J Bacteriol 194(23), 2012
PMID: 23144379
Genome sequence of Janibacter hoylei MTCC8307, isolated from the stratospheric air.
Pawar SP, Dhotre DP, Shetty SA, Chowdhury SP, Chaudhari BL, Shouche YS., J Bacteriol 194(23), 2012
PMID: 23144385
Metagenomic analysis of a southern maritime antarctic soil.
Pearce DA, Newsham KK, Thorne MA, Calvo-Bado L, Krsek M, Laskaris P, Hodson A, Wellington EM., Front Microbiol 3(), 2012
PMID: 23227023
CINPER: an interactive web system for pathway prediction for prokaryotes.
Mao X, Chen X, Zhang Y, Pangle S, Xu Y., PLoS One 7(12), 2012
PMID: 23236458
A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences.
Boulund F, Johnning A, Pereira MB, Larsson DG, Kristiansson E., BMC Genomics 13(), 2012
PMID: 23231464
Evaluation method for the potential functionome harbored in the genome and metagenome.
Takami H, Taniguchi T, Moriya Y, Kuwahara T, Kanehisa M, Goto S., BMC Genomics 13(), 2012
PMID: 23234305
Chapter 12: Human microbiome analysis.
Morgan XC, Huttenhower C., PLoS Comput Biol 8(12), 2012
PMID: 23300406
Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara.
Quaiser A, Zivanovic Y, Moreira D, López-García P., ISME J 5(2), 2011
PMID: 20668488
Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis.
Kanokratana P, Uengwetwanit T, Rattanachomsri U, Bunterngsook B, Nimchua T, Tangphatsornruang S, Plengvidhya V, Champreda V, Eurwilaichitr L., Microb Ecol 61(3), 2011
PMID: 21057783
TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog.
Zhang Q, Zmasek CM, Cai X, Godzik A., Dev Comp Immunol 35(4), 2011
PMID: 21110998
Role of a Zn-independent DksA in Zn homeostasis and stringent response.
Blaby-Haas CE, Furman R, Rodionov DA, Artsimovitch I, de Crécy-Lagard V., Mol Microbiol 79(3), 2011
PMID: 21255113
Metagenomic analyses: past and future trends.
Simon C, Daniel R., Appl Environ Microbiol 77(4), 2011
PMID: 21169428
Phylogenetic characterization of transport protein superfamilies: superiority of SuperfamilyTree programs over those based on multiple alignments.
Chen JS, Reddy V, Chen JH, Shlykov MA, Zheng WH, Cho J, Yen MR, Saier MH., J Mol Microbiol Biotechnol 21(3-4), 2011
PMID: 22286036
Metagenomic analysis of 0.2-μm-passable microorganisms in deep-sea hydrothermal fluid.
Nakai R, Abe T, Takeyama H, Naganuma T., Mar Biotechnol (NY) 13(5), 2011
PMID: 21279410
Probabilistic pathway construction.
Yousofshahi M, Lee K, Hassoun S., Metab Eng 13(4), 2011
PMID: 21292021
Quantitative metagenomic analyses based on average genome size normalization.
Frank JA, Sørensen SJ., Appl Environ Microbiol 77(7), 2011
PMID: 21317268
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.
Satish Kumar V, Ferry JG, Maranas CD., BMC Syst Biol 5(), 2011
PMID: 21324125
Pathway-based functional analysis of metagenomes.
Sharon I, Bercovici S, Pinter RY, Shlomi T., J Comput Biol 18(3), 2011
PMID: 21385050
Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis.
Oberhardt MA, Puchałka J, Martins dos Santos VA, Papin JA., PLoS Comput Biol 7(3), 2011
PMID: 21483480
Mining high-throughput experimental data to link gene and function.
Blaby-Haas CE, de Crécy-Lagard V., Trends Biotechnol 29(4), 2011
PMID: 21310501
Host specific diversity in Lactobacillus johnsonii as evidenced by a major chromosomal inversion and phage resistance mechanisms.
Guinane CM, Kent RM, Norberg S, Hill C, Fitzgerald GF, Stanton C, Ross RP., PLoS One 6(4), 2011
PMID: 21533100
The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage.
Karpowicz SJ, Prochnik SE, Grossman AR, Merchant SS., J Biol Chem 286(24), 2011
PMID: 21515685
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence.
Ravcheev DA, Best AA, Tintle N, Dejongh M, Osterman AL, Novichkov PS, Rodionov DA., J Bacteriol 193(13), 2011
PMID: 21531804
A 5-formyltetrahydrofolate cycloligase paralog from all domains of life: comparative genomic and experimental evidence for a cryptic role in thiamin metabolism.
Pribat A, Blaby IK, Lara-Núñez A, Jeanguenin L, Fouquet R, Frelin O, Gregory JF, Philmus B, Begley TP, de Crécy-Lagard V, Hanson AD., Funct Integr Genomics 11(3), 2011
PMID: 21538139
Comparative fecal metagenomics unveils unique functional capacity of the swine gut.
Lamendella R, Domingo JW, Ghosh S, Martinson J, Oerther DB., BMC Microbiol 11(), 2011
PMID: 21575148
GCView: the genomic context viewer for protein homology searches.
Grin I, Linke D., Nucleic Acids Res 39(web server issue), 2011
PMID: 21609955
Discovery of a gene involved in a third bacterial protoporphyrinogen oxidase activity through comparative genomic analysis and functional complementation.
Boynton TO, Gerdes S, Craven SH, Neidle EL, Phillips JD, Dailey HA., Appl Environ Microbiol 77(14), 2011
PMID: 21642412
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset.
Larsen PE, Collart FR, Field D, Meyer F, Keegan KP, Henry CS, McGrath J, Quinn J, Gilbert JA., Microb Inform Exp 1(1), 2011
PMID: 22587810
Synergistic use of plant-prokaryote comparative genomics for functional annotations.
Gerdes S, El Yacoubi B, Bailly M, Blaby IK, Blaby-Haas CE, Jeanguenin L, Lara-Núñez A, Pribat A, Waller JC, Wilke A, Overbeek R, Hanson AD, de Crécy-Lagard V., BMC Genomics 12 Suppl 1(), 2011
PMID: 21810204
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.
Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS., BMC Genomics 12 Suppl 1(), 2011
PMID: 21810205
Integrative analysis of environmental sequences using MEGAN4.
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC., Genome Res 21(9), 2011
PMID: 21690186
Metagenomic biomarker discovery and explanation.
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C., Genome Biol 12(6), 2011
PMID: 21702898
Yersinia enterocolitica palearctica serobiotype O:3/4--a successful group of emerging zoonotic pathogens.
Batzilla J, Antonenka U, Höper D, Heesemann J, Rakin A., BMC Genomics 12(), 2011
PMID: 21733159
Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.
Tripp HJ, Hewson I, Boyarsky S, Stuart JM, Zehr JP., Nucleic Acids Res 39(20), 2011
PMID: 21771858
SEAS: a system for SEED-based pathway enrichment analysis.
Mao X, Zhang Y, Xu Y., PLoS One 6(7), 2011
PMID: 21799897
CAMBer: an approach to support comparative analysis of multiple bacterial strains.
Wozniak M, Wong L, Tiuryn J., BMC Genomics 12 Suppl 2(), 2011
PMID: 21989220
Chlamydia psittaci genetic variants differ in virulence by modulation of host immunity.
Miyairi I, Laxton JD, Wang X, Obert CA, Arva Tatireddigari VR, van Rooijen N, Hatch TP, Byrne GI., J Infect Dis 204(4), 2011
PMID: 21791668
Bacterial community assembly based on functional genes rather than species.
Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T., Proc Natl Acad Sci U S A 108(34), 2011
PMID: 21825123
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052.
Milne CB, Eddy JA, Raju R, Ardekani S, Kim PJ, Senger RS, Jin YS, Blaschek HP, Price ND., BMC Syst Biol 5(), 2011
PMID: 21846360
Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis.
Leyn SA, Li X, Zheng Q, Novichkov PS, Reed S, Romine MF, Fredrickson JK, Yang C, Osterman AL, Rodionov DA., J Biol Chem 286(41), 2011
PMID: 21849503
Substrate type determines metagenomic profiles from diverse chemical habitats.
Jeffries TC, Seymour JR, Gilbert JA, Dinsdale EA, Newton K, Leterme SS, Roudnew B, Smith RJ, Seuront L, Mitchell JG., PLoS One 6(9), 2011
PMID: 21966446
Identification of nicotinamide mononucleotide deamidase of the bacterial pyridine nucleotide cycle reveals a novel broadly conserved amidohydrolase family.
Galeazzi L, Bocci P, Amici A, Brunetti L, Ruggieri S, Romine M, Reed S, Osterman AL, Rodionov DA, Sorci L, Raffaelli N., J Biol Chem 286(46), 2011
PMID: 21953451
The coenzyme A disulphide reductase of Borrelia burgdorferi is important for rapid growth throughout the enzootic cycle and essential for infection of the mammalian host.
Eggers CH, Caimano MJ, Malizia RA, Kariu T, Cusack B, Desrosiers DC, Hazlett KR, Claiborne A, Pal U, Radolf JD., Mol Microbiol 82(3), 2011
PMID: 21923763
Genome sequence of Lentibacillus jeotgali Grbi(T), isolated from traditional Korean salt-fermented seafood.
Jung MJ, Roh SW, Kim MS, Whon TW, Bae JW., J Bacteriol 193(22), 2011
PMID: 22038972
Genome sequence of Brachybacterium squillarum M-6-3(T), isolated from salt-fermented seafood.
Park SK, Roh SW, Whon TW, Bae JW., J Bacteriol 193(22), 2011
PMID: 22038973
In vivo and in silico determination of essential genes of Campylobacter jejuni.
Metris A, Reuter M, Gaskin DJ, Baranyi J, van Vliet AH., BMC Genomics 12(), 2011
PMID: 22044676
The Escherichia coli protein YfeX functions as a porphyrinogen oxidase, not a heme dechelatase.
Dailey HA, Septer AN, Daugherty L, Thames D, Gerdes S, Stabb EV, Dunn AK, Dailey TA, Phillips JD., MBio 2(6), 2011
PMID: 22068980
Draft genome sequence of the biocontrol bacterium Pseudomonas putida B001, an oligotrophic bacterium that induces systemic resistance to plant diseases.
Park JY, Han SH, Lee JH, Han YS, Lee YS, Rong X, McSpadden Gardener BB, Park HS, Kim YC., J Bacteriol 193(23), 2011
PMID: 22072649
Genome sequence of Bifidobacterium breve DPC 6330, a strain isolated from the human intestine.
Guinane CM, Barrett E, Fitzgerald GF, van Sinderen D, Ross RP, Stanton C., J Bacteriol 193(23), 2011
PMID: 22072651
Draft genome sequence of Bacteroides faecis MAJ27T, a strain isolated from human feces.
Kim MS, Whon TW, Roh SW, Shin NR, Bae JW., J Bacteriol 193(23), 2011
PMID: 22072652
Draft genome sequence of the biocontrol bacterium Chromobacterium sp. strain C-61.
Kim HJ, Park JY, Han SH, Lee JH, Rong X, McSpadden Gardener BB, Park SK, Kim YC., J Bacteriol 193(23), 2011
PMID: 22072653
Purine biosynthesis in archaea: variations on a theme.
Brown AM, Hoopes SL, White RH, Sarisky CA., Biol Direct 6(), 2011
PMID: 22168471
The FGGY carbohydrate kinase family: insights into the evolution of functional specificities.
Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A., PLoS Comput Biol 7(12), 2011
PMID: 22215998
The novel polysaccharide deacetylase homologue Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae.
Milani CJ, Aziz RK, Locke JB, Dahesh S, Nizet V, Buchanan JT., Microbiology 156(pt 2), 2010
PMID: 19762441
Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris.
Axelrod HL, Kozbial P, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Carlton D, Caruthers J, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Tien HJ, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Zubieta C, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA., Acta Crystallogr Sect F Struct Biol Cryst Commun 66(pt 10), 2010
PMID: 20944231
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA., Nucleic Acids Res 38(database issue), 2010
PMID: 19884135
FolX and FolM are essential for tetrahydromonapterin synthesis in Escherichia coli and Pseudomonas aeruginosa.
Pribat A, Blaby IK, Lara-Núñez A, Gregory JF, de Crécy-Lagard V, Hanson AD., J Bacteriol 192(2), 2010
PMID: 19897652
Automatic policing of biochemical annotations using genomic correlations.
Hsiao TL, Revelles O, Chen L, Sauer U, Vitkup D., Nat Chem Biol 6(1), 2010
PMID: 19935659
Network analyses structure genetic diversity in independent genetic worlds.
Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E., Proc Natl Acad Sci U S A 107(1), 2010
PMID: 20007769
Modal codon usage: assessing the typical codon usage of a genome.
Davis JJ, Olsen GJ., Mol Biol Evol 27(4), 2010
PMID: 20018979
Biochemical networks: the evolution of gene annotation.
Kasif S, Steffen M., Nat Chem Biol 6(1), 2010
PMID: 20016491
Reservoir of bacterial exotoxin genes in the environment.
Casas V, Magbanua J, Sobrepeña G, Kelley ST, Maloy SR., Int J Microbiol 2010(), 2010
PMID: 21318166
Machine learning methods for metabolic pathway prediction.
Dale JM, Popescu L, Karp PD., BMC Bioinformatics 11(), 2010
PMID: 20064214
Short clones or long clones? A simulation study on the use of paired reads in metagenomics.
Mitra S, Schubach M, Huson DH., BMC Bioinformatics 11 Suppl 1(), 2010
PMID: 20122183
Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community.
Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P., PLoS One 5(1), 2010
PMID: 20098679
Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA.
Phillips G, Chikwana VM, Maxwell A, El-Yacoubi B, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V., J Biol Chem 285(17), 2010
PMID: 20129918
An archaeal order with multiple minichromosome maintenance genes.
Walters AD, Chong JP., Microbiology 156(pt 5), 2010
PMID: 20133362
Viral and microbial community dynamics in four aquatic environments.
Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, Breitbart M, Buchanan J, Desnues C, Dinsdale E, Edwards R, Felts B, Haynes M, Liu H, Lipson D, Mahaffy J, Martin-Cuadrado AB, Mira A, Nulton J, Pasić L, Rayhawk S, Rodriguez-Mueller J, Rodriguez-Valera F, Salamon P, Srinagesh S, Thingstad TF, Tran T, Thurber RV, Willner D, Youle M, Rohwer F., ISME J 4(6), 2010
PMID: 20147985
Census of the viral metagenome within an activated sludge microbial assemblage.
Parsley LC, Consuegra EJ, Thomas SJ, Bhavsar J, Land AM, Bhuiyan NN, Mazher MA, Waters RJ, Wommack KE, Harper WF, Liles MR., Appl Environ Microbiol 76(8), 2010
PMID: 20154108
Transposases are the most abundant, most ubiquitous genes in nature.
Aziz RK, Breitbart M, Edwards RA., Nucleic Acids Res 38(13), 2010
PMID: 20215432
Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome.
Yin Y, Zhang H, Olman V, Xu Y., Proc Natl Acad Sci U S A 107(14), 2010
PMID: 20308592
Brucella abortus ure2 region contains an acid-activated urea transporter and a nickel transport system.
Sangari FJ, Cayón AM, Seoane A, García-Lobo JM., BMC Microbiol 10(), 2010
PMID: 20380737
Microevolution of group A streptococci in vivo: capturing regulatory networks engaged in sociomicrobiology, niche adaptation, and hypervirulence.
Aziz RK, Kansal R, Aronow BJ, Taylor WL, Rowe SL, Kubal M, Chhatwal GS, Walker MJ, Kotb M., PLoS One 5(4), 2010
PMID: 20418946
Reconstruction of xylose utilization pathway and regulons in Firmicutes.
Gu Y, Ding Y, Ren C, Sun Z, Rodionov DA, Zhang W, Yang S, Yang C, Jiang W., BMC Genomics 11(), 2010
PMID: 20406496
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.
Schellenberger J, Park JO, Conrad TM, Palsson BØ., BMC Bioinformatics 11(), 2010
PMID: 20426874
Using comparative genome analysis to identify problems in annotated microbial genomes.
Poptsova MS, Gogarten JP., Microbiology 156(pt 7), 2010
PMID: 20430813
A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life.
Waller JC, Alvarez S, Naponelli V, Lara-Nuñez A, Blaby IK, Da Silva V, Ziemak MJ, Vickers TJ, Beverley SM, Edison AS, Rocca JR, Gregory JF, de Crécy-Lagard V, Hanson AD., Proc Natl Acad Sci U S A 107(23), 2010
PMID: 20489182
Phylogenetic evidence for lateral gene transfer in the intestine of marine iguanas.
Nelson DM, Cann IK, Altermann E, Mackie RI., PLoS One 5(5), 2010
PMID: 20520734
Construction and preliminary analysis of a deep-sea sediment metagenomic fosmid library from Qiongdongnan Basin, South China Sea.
Hu Y, Fu C, Yin Y, Cheng G, Lei F, Yang X, Li J, Ashforth EJ, Zhang L, Zhu B., Mar Biotechnol (NY) 12(6), 2010
PMID: 20514504
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I., Nucleic Acids Res 38(web server issue), 2010
PMID: 20542910
Accessing the SEED genome databases via Web services API: tools for programmers.
Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA., BMC Bioinformatics 11(), 2010
PMID: 20546611
Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae.
Kube M, Migdoll AM, Gehring I, Heitmann K, Mayer Y, Kuhl H, Knaust F, Geider K, Reinhardt R., BMC Genomics 11(), 2010
PMID: 20565991
Genome (re-)annotation and open-source annotation pipelines.
Siezen RJ, van Hijum SA., Microb Biotechnol 3(4), 2010
PMID: 21255336
Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation.
Guinane CM, Ben Zakour NL, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay JA, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penadés JR, Fitzgerald JR., Genome Biol Evol 2(), 2010
PMID: 20624747
454-pyrosequencing: a molecular battiscope for freshwater viral ecology.
Rooks DJ, Smith DL, McDonald JE, Woodward MJ, McCarthy AJ, Allison HE., Genes (Basel) 1(2), 2010
PMID: 24710042
Some considerations for analyzing biodiversity using integrative metagenomics and gene networks.
Bittner L, Halary S, Payri C, Cruaud C, de Reviers B, Lopez P, Bapteste E., Biol Direct 5(), 2010
PMID: 20673351
Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.
Yeoman CJ, Yildirim S, Thomas SM, Durkin AS, Torralba M, Sutton G, Buhay CJ, Ding Y, Dugan-Rocha SP, Muzny DM, Qin X, Gibbs RA, Leigh SR, Stumpf R, White BA, Highlander SK, Nelson KE, Wilson BA., PLoS One 5(8), 2010
PMID: 20865041
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus.
Rodionov DA, Yang C, Li X, Rodionova IA, Wang Y, Obraztsova AY, Zagnitko OP, Overbeek R, Romine MF, Reed S, Fredrickson JK, Nealson KH, Osterman AL., BMC Genomics 11(), 2010
PMID: 20836887
SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes.
Gulig PA, de Crécy-Lagard V, Wright AC, Walts B, Telonis-Scott M, McIntyre LM., BMC Genomics 11(), 2010
PMID: 20863407
TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures.
Krishna SS, Weekes D, Bakolitsa C, Elsliger MA, Wilson IA, Godzik A, Wooley J., Acta Crystallogr Sect F Struct Biol Cryst Commun 66(pt 10), 2010
PMID: 20944203
Systematizing the generation of missing metabolic knowledge.
Orth JD, Palsson BØ., Biotechnol Bioeng 107(3), 2010
PMID: 20589842
Genomics-driven reconstruction of acinetobacter NAD metabolism: insights for antibacterial target selection.
Sorci L, Blaby I, De Ingeniis J, Gerdes S, Raffaelli N, de Crécy Lagard V, Osterman A., J Biol Chem 285(50), 2010
PMID: 20926389
Moonlighting glutamate formiminotransferases can functionally replace 5-formyltetrahydrofolate cycloligase.
Jeanguenin L, Lara-Núñez A, Pribat A, Mageroy MH, Gregory JF, Rice KC, de Crécy-Lagard V, Hanson AD., J Biol Chem 285(53), 2010
PMID: 20952389
Functional Promiscuity of Homologues of the Bacterial ArsA ATPases.
Castillo R, Saier MH., Int J Microbiol 2010(), 2010
PMID: 20981284
A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins.
Pawłowski K, Muszewska A, Lenart A, Szczepińska T, Godzik A, Grynberg M., BMC Genomics 11(), 2010
PMID: 20964819
Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by gammaproteobacteria and bacteroidetes.
Edwards JL, Smith DL, Connolly J, McDonald JE, Cox MJ, Joint I, Edwards C, McCarthy AJ., Genes (Basel) 1(3), 2010
PMID: 24710093
Size Does Matter: Application-driven Approaches for Soil Metagenomics.
Kakirde KS, Parsley LC, Liles MR., Soil Biol Biochem 42(11), 2010
PMID: 21076656
Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing.
Xie G, Chain PS, Lo CC, Liu KL, Gans J, Merritt J, Qi F., Mol Oral Microbiol 25(6), 2010
PMID: 21040513
BIGSdb: Scalable analysis of bacterial genome variation at the population level.
Jolley KA, Maiden MC., BMC Bioinformatics 11(), 2010
PMID: 21143983
Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico.
Breitbart M, Hoare A, Nitti A, Siefert J, Haynes M, Dinsdale E, Edwards R, Souza V, Rohwer F, Hollander D., Environ Microbiol 11(1), 2009
PMID: 18764874
Evaluation of functional gene enrichment in a soil metagenomic clone library.
Demanèche S, David MM, Navarro E, Simonet P, Vogel TM., J Microbiol Methods 76(1), 2009
PMID: 18922230
Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria.
Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS., J Bacteriol 191(1), 2009
PMID: 18820024
A novel class of modular transporters for vitamins in prokaryotes.
Rodionov DA, Hebbeln P, Eudes A, ter Beek J, Rodionova IA, Erkens GB, Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, Eitinger T., J Bacteriol 191(1), 2009
PMID: 18931129
Genome-scale models of bacterial metabolism: reconstruction and applications.
Durot M, Bourguignon PY, Schachter V., FEMS Microbiol Rev 33(1), 2009
PMID: 19067749
Mutations in ampG and lytic transglycosylase genes affect the net release of peptidoglycan monomers from Vibrio fischeri.
Adin DM, Engle JT, Goldman WE, McFall-Ngai MJ, Stabb EV., J Bacteriol 191(7), 2009
PMID: 19074387
Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing.
Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM., Appl Environ Microbiol 75(6), 2009
PMID: 19114525
Reconstruction of biochemical networks in microorganisms.
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ., Nat Rev Microbiol 7(2), 2009
PMID: 19116616
Characterization of the LacI-type transcriptional repressor RbsR controlling ribose transport in Corynebacterium glutamicum ATCC 13032.
Nentwich SS, Brinkrolf K, Gaigalat L, Hüser AT, Rey DA, Mohrbach T, Marin K, Pühler A, Tauch A, Kalinowski J., Microbiology 155(pt 1), 2009
PMID: 19118356
Pathway-BasedFeature Selection Algorithm for Cancer Microarray Data.
Bandyopadhyay N, Kahveci T, Goodison S, Sun Y, Ranka S., Adv Bioinformatics (), 2009
PMID: 20204186
Metagenomics: Facts and Artifacts, and Computational Challenges*
Wooley JC, Ye Y., J Comput Sci Technol 25(1), 2009
PMID: 20648230
Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.
Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA., Proc Natl Acad Sci U S A 106(6), 2009
PMID: 19181843
Methods for comparative metagenomics.
Huson DH, Richter DC, Mitra S, Auch AF, Schuster SC., BMC Bioinformatics 10 Suppl 1(), 2009
PMID: 19208111
Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization.
Pinchuk GE, Rodionov DA, Yang C, Li X, Osterman AL, Dervyn E, Geydebrekht OV, Reed SB, Romine MF, Collart FR, Scott JH, Fredrickson JK, Beliaev AS., Proc Natl Acad Sci U S A 106(8), 2009
PMID: 19196979
Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis.
Sorci L, Martynowski D, Rodionov DA, Eyobo Y, Zogaj X, Klose KE, Nikolaev EV, Magni G, Zhang H, Osterman AL., Proc Natl Acad Sci U S A 106(9), 2009
PMID: 19204287
TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW., BMC Bioinformatics 10(), 2009
PMID: 19210774
The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA.
El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crécy-Lagard V., Nucleic Acids Res 37(9), 2009
PMID: 19287007
Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation.
Podzelinska K, He SM, Wathier M, Yakunin A, Proudfoot M, Hove-Jensen B, Zechel DL, Jia Z., J Biol Chem 284(25), 2009
PMID: 19366688
ACID: annotation of cassette and integron data.
Joss MJ, Koenig JE, Labbate M, Polz MF, Gillings MR, Stokes HW, Doolittle WF, Boucher Y., BMC Bioinformatics 10(), 2009
PMID: 19383137
Metagenomic analysis of stressed coral holobionts.
Vega Thurber R, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F., Environ Microbiol 11(8), 2009
PMID: 19397678
6-pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria.
Pribat A, Jeanguenin L, Lara-Núñez A, Ziemak MJ, Hyde JE, de Crécy-Lagard V, Hanson AD., J Bacteriol 191(13), 2009
PMID: 19395485
Visual and statistical comparison of metagenomes.
Mitra S, Klar B, Huson DH., Bioinformatics 25(15), 2009
PMID: 19515961
IMG ER: a system for microbial genome annotation expert review and curation.
Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC., Bioinformatics 25(17), 2009
PMID: 19561336
Controlled vocabularies for microbial virulence factors.
Korves T, Colosimo ME., Trends Microbiol 17(7), 2009
PMID: 19577471
Acinetobacter baylyi ADP1 as a model for metabolic system biology.
de Berardinis V, Durot M, Weissenbach J, Salanoubat M., Curr Opin Microbiol 12(5), 2009
PMID: 19709925
Microbial NAD metabolism: lessons from comparative genomics.
Gazzaniga F, Stebbins R, Chang SZ, McPeek MA, Brenner C., Microbiol Mol Biol Rev 73(3), 2009
PMID: 19721089
Three-dimensional structural view of the central metabolic network of Thermotoga maritima.
Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A., Science 325(5947), 2009
PMID: 19762644
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family.
Staroń A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, Mascher T., Mol Microbiol 74(3), 2009
PMID: 19737356
Furanose-specific sugar transport: characterization of a bacterial galactofuranose-binding protein.
Horler RS, Müller A, Williamson DC, Potts JR, Wilson KS, Thomas GH., J Biol Chem 284(45), 2009
PMID: 19744923
Achievements and new knowledge unraveled by metagenomic approaches.
Simon C, Daniel R., Appl Microbiol Biotechnol 85(2), 2009
PMID: 19760178
FIGfams: yet another set of protein families.
Meyer F, Overbeek R, Rodriguez A., Nucleic Acids Res 37(20), 2009
PMID: 19762480
CO dehydrogenase genes found in metagenomic fosmid clones from the deep mediterranean sea.
Martin-Cuadrado AB, Ghai R, Gonzaga A, Rodriguez-Valera F., Appl Environ Microbiol 75(23), 2009
PMID: 19801465
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.
Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F., PLoS One 4(10), 2009
PMID: 19816605
A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life.
Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS, de Crécy-Lagard V., BMC Genomics 10(), 2009
PMID: 19822009
MicroScope: a platform for microbial genome annotation and comparative genomics.
Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C., Database (Oxford) 2009(), 2009
PMID: 20157493
Genomic variations on a CoA biosynthetic theme.
Osterman AL., Nat Chem Biol 5(12), 2009
PMID: 19915531
'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.
Hanson AD, Pribat A, Waller JC, de Crécy-Lagard V., Biochem J 425(1), 2009
PMID: 20001958
The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species.
Descorps-Declère S, Lemoine F, Sculo Q, Lespinet O, Labedan B., Biochimie 90(4), 2008
PMID: 17961904
Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways.
Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL., J Bacteriol 190(5), 2008
PMID: 18156253
Bacterial carbon processing by generalist species in the coastal ocean.
Mou X, Sun S, Edwards RA, Hodson RE, Moran MA., Nature 451(7179), 2008
PMID: 18223640
Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms.
Naponelli V, Noiriel A, Ziemak MJ, Beverley SM, Lye LF, Plume AM, Botella JR, Loizeau K, Ravanel S, Rébeillé F, de Crécy-Lagard V, Hanson AD., Plant Physiol 146(4), 2008
PMID: 18245455
Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism.
Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H., Structure 16(2), 2008
PMID: 18275811
The RAST Server: rapid annotations using subsystems technology.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O., BMC Genomics 9(), 2008
PMID: 18261238
Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators.
Rodionov DA, De Ingeniis J, Mancini C, Cimadamore F, Zhang H, Osterman AL, Raffaelli N., Nucleic Acids Res 36(6), 2008
PMID: 18276643
Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon.
Rodionov DA, Li X, Rodionova IA, Yang C, Sorci L, Dervyn E, Martynowski D, Zhang H, Gelfand MS, Osterman AL., Nucleic Acids Res 36(6), 2008
PMID: 18276644
Large-scale prediction of drug-target relationships.
Kuhn M, Campillos M, González P, Jensen LJ, Bork P., FEBS Lett 582(8), 2008
PMID: 18291108
Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes.
Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ., Appl Environ Microbiol 74(8), 2008
PMID: 18296538
Microbial ecology of four coral atolls in the Northern Line Islands.
Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, Wegley L, Hatay M, Hall D, Brown E, Haynes M, Krause L, Sala E, Sandin SA, Thurber RV, Willis BL, Azam F, Knowlton N, Rohwer F., PLoS One 3(2), 2008
PMID: 18301735
Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities.
Bonner CA, Disz T, Hwang K, Song J, Vonstein V, Overbeek R, Jensen RA., Microbiol Mol Biol Rev 72(1), 2008
PMID: 18322033
On application of directons to functional classification of genes in prokaryotes.
Wu H, Mao F, Olman V, Xu Y., Comput Biol Chem 32(3), 2008
PMID: 18440870
Functional metagenomic profiling of nine biomes.
Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F., Nature 452(7187), 2008
PMID: 18337718
Genome-enabled approaches shed new light on plant metabolism.
DellaPenna D, Last RL., Science 320(5875), 2008
PMID: 18436775
The minimum information about a genome sequence (MIGS) specification.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A., Nat Biotechnol 26(5), 2008
PMID: 18464787
Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions.
Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, Talla E, López-García P., ISME J 2(8), 2008
PMID: 18463691
GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways.
Martinez-Guerrero CE, Ciria R, Abreu-Goodger C, Moreno-Hagelsieb G, Merino E., Nucleic Acids Res 36(web server issue), 2008
PMID: 18511460
Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers.
Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P, Genomic Standards Consortium., OMICS 12(2), 2008
PMID: 18479205
Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification.
Martin C, Diaz NN, Ontrup J, Nattkemper TW., Bioinformatics 24(14), 2008
PMID: 18535082
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome.
Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC., PLoS One 3(6), 2008
PMID: 18575584
Towards environmental systems biology of Shewanella.
Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM., Nat Rev Microbiol 6(8), 2008
PMID: 18604222
The type III pantothenate kinase encoded by coaX is essential for growth of Bacillus anthracis.
Paige C, Reid SD, Hanna PC, Claiborne A., J Bacteriol 190(18), 2008
PMID: 18641144
Identification and characterization of genes underlying chitinolysis in Collimonas fungivorans Ter331.
Fritsche K, de Boer W, Gerards S, van den Berg M, van Veen JA, Leveau JH., FEMS Microbiol Ecol 66(1), 2008
PMID: 18671744
Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter.
Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F., ISME J 2(12), 2008
PMID: 18670397
Annotation of metagenome short reads using proxygenes.
Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, Markowitz VM., Bioinformatics 24(16), 2008
PMID: 18689842
Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome.
Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, Joens LA, Konkel ME, Angly F, Dinsdale EA, Edwards RA, Nelson KE, White BA., PLoS One 3(8), 2008
PMID: 18698407
Identification of genes encoding the folate- and thiamine-binding membrane proteins in Firmicutes.
Eudes A, Erkens GB, Slotboom DJ, Rodionov DA, Naponelli V, Hanson AD., J Bacteriol 190(22), 2008
PMID: 18776013
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA., BMC Bioinformatics 9(), 2008
PMID: 18803844
Rise and persistence of global M1T1 clone of Streptococcus pyogenes.
Aziz RK, Kotb M., Emerg Infect Dis 14(10), 2008
PMID: 18826812
An introduction to metabolic networks and their structural analysis.
Lacroix V, Cottret L, Thébault P, Sagot MF., IEEE/ACM Trans Comput Biol Bioinform 5(4), 2008
PMID: 18989046
MetaSim: a sequencing simulator for genomics and metagenomics.
Richter DC, Ott F, Auch AF, Schmid R, Huson DH., PLoS One 3(10), 2008
PMID: 18841204
RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.
Grosjean H, Gaspin C, Marck C, Decatur WA, de Crécy-Lagard V., BMC Genomics 9(), 2008
PMID: 18844986
Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP cyclohydrolase I.
Phillips G, El Yacoubi B, Lyons B, Alvarez S, Iwata-Reuyl D, de Crécy-Lagard V., J Bacteriol 190(24), 2008
PMID: 18931107
Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources.
Blom EJ, Breitling R, Hofstede KJ, Roerdink JB, van Hijum SA, Kuipers OP., BMC Genomics 9(), 2008
PMID: 18939968
MetaMine--a tool to detect and analyse gene patterns in their environmental context.
Bohnebeck U, Lombardot T, Kottmann R, Glöckner FO., BMC Bioinformatics 9(), 2008
PMID: 18957118
Gene set analyses for interpreting microarray experiments on prokaryotic organisms.
Tintle NL, Best AA, DeJongh M, Van Bruggen D, Heffron F, Porwollik S, Taylor RC., BMC Bioinformatics 9(), 2008
PMID: 18986519
A bioinformatician's guide to metagenomics.
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P., Microbiol Mol Biol Rev 72(4), 2008
PMID: 19052320
SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes.
Lemoine F, Labedan B, Lespinet O., BMC Bioinformatics 9(), 2008
PMID: 19087285
OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes.
Thybert D, Avner S, Lucchetti-Miganeh C, Chéron A, Barloy-Hubler F., BMC Genomics 9(), 2008
PMID: 19117520
CutDB: a proteolytic event database.
Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, Godzik A., Nucleic Acids Res 35(database issue), 2007
PMID: 17142225
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R., Nucleic Acids Res 35(database issue), 2007
PMID: 17145713
Accurate phylogenetic classification of variable-length DNA fragments.
McHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I., Nat Methods 4(1), 2007
PMID: 17179938
GISMO--gene identification using a support vector machine for ORF classification.
Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F., Nucleic Acids Res 35(2), 2007
PMID: 17175534
GOing from functional genomics to biological significance.
McCarthy FM, Bridges SM, Burgess SC., Cytogenet Genome Res 117(1-4), 2007
PMID: 17675869
The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum.
Brune I, Jochmann N, Brinkrolf K, Hüser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Pühler A, Tauch A., J Bacteriol 189(7), 2007
PMID: 17259312
Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module.
Hebbeln P, Rodionov DA, Alfandega A, Eitinger T., Proc Natl Acad Sci U S A 104(8), 2007
PMID: 17301237
Structure of the type III pantothenate kinase from Bacillus anthracis at 2.0 A resolution: implications for coenzyme A-dependent redox biology.
Nicely NI, Parsonage D, Paige C, Newton GL, Fahey RC, Leonardi R, Jackowski S, Mallett TC, Claiborne A., Biochemistry 46(11), 2007
PMID: 17323930
Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate.
Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL., Proc Natl Acad Sci U S A 104(11), 2007
PMID: 17360515
Toward the automated generation of genome-scale metabolic networks in the SEED.
DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A., BMC Bioinformatics 8(), 2007
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Microbial genome data resources.
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