James M. TIEDJE, Ph.D. - Publications

Affiliations: 
Michigan State University, East Lansing, MI 
Area:
Environmental Microbiology

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

Year Citation  Score
2019 Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, ... ... Tiedje JM, et al. Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology. PMID 31086312 DOI: 10.1038/s41564-019-0426-5  0.44
2019 Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, ... ... Tiedje JM, et al. Consent insufficient for data release-Response. Science (New York, N.Y.). 364: 446. PMID 31048484 DOI: 10.1126/science.aax7509  0.96
2019 Pärnänen KMM, Narciso-da-Rocha C, Kneis D, Berendonk TU, Cacace D, Do TT, Elpers C, Fatta-Kassinos D, Henriques I, Jaeger T, Karkman A, Martinez JL, Michael SG, Michael-Kordatou I, O'Sullivan K, ... ... Tiedje JM, et al. Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Science Advances. 5: eaau9124. PMID 30944853 DOI: 10.1126/sciadv.aau9124  0.32
2019 Guo X, Zhou X, Hale L, Yuan M, Ning D, Feng J, Shi Z, Li Z, Feng B, Gao Q, Wu L, Shi W, Zhou A, Fu Y, Wu L, ... ... Tiedje JM, et al. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity. Nature Ecology & Evolution. PMID 30911147 DOI: 10.1038/s41559-019-0848-8  0.4
2019 Yoo K, Han I, Ko KS, Lee TK, Yoo H, Khan MI, Tiedje JM, Park J. Bacillus-Dominant Airborne Bacterial Communities Identified During Asian Dust Events. Microbial Ecology. PMID 30904989 DOI: 10.1007/s00248-019-01348-0  0.6
2019 Feng J, Penton CR, He Z, Van Nostrand JD, Yuan MM, Wu L, Wang C, Qin Y, Shi ZJ, Guo X, Schuur EAG, Luo Y, Bracho R, Konstantinidis KT, Cole JR, ... Tiedje JM, et al. Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils. Mbio. 10. PMID 30808694 DOI: 10.1128/mBio.02521-18  0.96
2019 Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, ... ... Tiedje JM, et al. Toward unrestricted use of public genomic data. Science (New York, N.Y.). 363: 350-352. PMID 30679363 DOI: 10.1126/science.aaw1280  0.96
2018 Khan MAW, Bohannan BJM, Nüsslein K, Tiedje JM, Tringe SG, Parlade E, Barberán A, Rodrigues JLM. Deforestation Impacts Network Co-occurrence Patterns of Microbial Communities in Amazon Soils. Fems Microbiology Ecology. PMID 30481288 DOI: 10.1093/femsec/fiy230  0.36
2018 Wang F, Xu M, Stedtfeld RD, Sheng H, Fan J, Liu M, Chai B, de Carvalho TS, Li H, Li Z, Hashsham SA, Tiedje JM. Long-term Effect of Different Fertilization and Cropping Systems on the Soil Antibiotic Resistome. Environmental Science & Technology. PMID 30375866 DOI: 10.1021/acs.est.8b04330  0.72
2018 Vital M, Howe A, Bergeron N, Krauss RM, Jansson JK, Tiedje JM. Metagenomic insights into resistant starch degradation by human gut microbiota. Applied and Environmental Microbiology. PMID 30266729 DOI: 10.1128/AEM.01562-18  0.64
2018 Mackelprang R, Grube AM, Lamendella R, Jesus EDC, Copeland A, Liang C, Jackson RD, Rice CW, Kapucija S, Parsa B, Tringe SG, Tiedje JM, Jansson JK. Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States. Frontiers in Microbiology. 9: 1775. PMID 30158906 DOI: 10.3389/fmicb.2018.01775  0.64
2018 Liang J, Zhou Z, Huo C, Shi Z, Cole JR, Huang L, Konstantinidis KT, Li X, Liu B, Luo Z, Penton CR, Schuur EAG, Tiedje JM, Wang YP, Wu L, et al. More replenishment than priming loss of soil organic carbon with additional carbon input. Nature Communications. 9: 3175. PMID 30093611 DOI: 10.1038/s41467-018-05667-7  0.96
2018 Kroeger ME, Delmont TO, Eren AM, Meyer KM, Guo J, Khan K, Rodrigues JLM, Bohannan BJM, Tringe SG, Borges CD, Tiedje JM, Tsai SM, Nüsslein K. New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. Frontiers in Microbiology. 9: 1635. PMID 30083144 DOI: 10.3389/fmicb.2018.01635  0.36
2018 Stedtfeld RD, Guo X, Stedtfeld TM, Sheng H, Williams MR, Hauschild K, Gunturu S, Tift L, Wang F, Howe A, Chai B, Yin D, Cole JR, Tiedje JM, Hashsham SA. Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements. Fems Microbiology Ecology. 94. PMID 30052926 DOI: 10.1093/femsec/fiy130  0.72
2018 Zhang AN, Li LG, Ma L, Gillings MR, Tiedje JM, Zhang T. Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection. Microbiome. 6: 130. PMID 30031405 DOI: 10.1186/s40168-018-0516-2  0.4
2018 Guo X, Stedtfeld RD, Hedman H, Eisenberg JNS, Truebac G, Yin D, Tiedje JM, Zhang L. Antibiotic Resistome Associated with Small-scale Poultry Production in Rural Ecuador. Environmental Science & Technology. PMID 29944836 DOI: 10.1021/acs.est.8b01667  0.32
2018 Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, Konstantinidis KT. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Research. PMID 29905870 DOI: 10.1093/nar/gky467  0.96
2018 Guo X, Zhou X, Hale L, Yuan M, Feng J, Ning D, Shi Z, Qin Y, Liu F, Wu L, He Z, Van Nostrand JD, Liu X, Luo Y, Tiedje JM, et al. Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass. Frontiers in Microbiology. 9: 954. PMID 29904372 DOI: 10.3389/fmicb.2018.00954  0.32
2018 Liang J, Xia J, Shi Z, Jiang L, Ma S, Lu X, Mauritz M, Natali SM, Pegoraro E, Penton CR, Plaza C, Salmon VG, Celis G, Cole JR, Konstantinidis KT, ... Tiedje JM, et al. Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra. Global Change Biology. PMID 29802797 DOI: 10.1111/gcb.14325  0.96
2018 Rodriguez-R LM, Gunturu S, Tiedje JM, Cole JR, Konstantinidis KT. Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity. Msystems. 3. PMID 29657970 DOI: 10.1128/mSystems.00039-18  0.96
2018 Xiao J, Yu F, Zhu W, Xu C, Zhang K, Luo Y, Tiedje JM, Zhou J, Cheng L. Comment on "The whole-soil carbon flux in response to warming". Science (New York, N.Y.). 359. PMID 29472453 DOI: 10.1126/science.aao0218  0.32
2018 Li B, Wu WM, Watson DB, Cardenas E, Chao Y, Phillips DH, Mehlhorn T, Lowe K, Kelly SD, Li P, Tao H, Tiedje JM, Criddle CS, Zhang T. Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation. Applied and Environmental Microbiology. PMID 29453264 DOI: 10.1128/AEM.02885-17  0.44
2018 Yin X, Jiang XT, Chai B, Li L, Yang Y, Cole JR, Tiedje JM, Zhang T. ARGs-OAP v2.0 with an Expanded SARG Database and Hidden Markov Models for Enhancement Characterization and Quantification of Antibiotic Resistance Genes in Environmental Metagenomes. Bioinformatics (Oxford, England). PMID 29408954 DOI: 10.1093/bioinformatics/bty053  0.56
2018 Rodriguez-R LM, Castro JC, Kyrpides NC, Cole JR, Tiedje JM, Konstantinidis KT. How much do rRNA gene surveys underestimate extant bacterial diversity? Applied and Environmental Microbiology. PMID 29305502 DOI: 10.1128/AEM.00014-18  0.96
2017 Etchebarne BE, Li Z, Stedtfeld RD, Nicholas MC, Williams MR, Johnson TA, Stedtfeld TM, Kostic T, Khalife WT, Tiedje JM, Hashsham SA, Hughes MJ. Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection. Frontiers in Microbiology. 8: 2211. PMID 29312154 DOI: 10.3389/fmicb.2017.02211  0.72
2017 Deng J, Auchtung J, Konstantinidis KT, Caro-Quintero A, Brettar I, Höfle M, Tiedje JM. Divergence in gene regulation contributes to sympatric speciation of Shewanella baltica strains. Applied and Environmental Microbiology. PMID 29222101 DOI: 10.1128/AEM.02015-17  0.96
2017 Šket R, Treichel N, Kublik S, Debevec T, Eiken O, Mekjavić I, Schloter M, Vital M, Chandler J, Tiedje JM, Murovec B, Prevoršek Z, Likar M, Stres B. Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study. Plos One. 12: e0188556. PMID 29211803 DOI: 10.1371/journal.pone.0188556  0.68
2017 Do TT, Tamames J, Stedtfeld RD, Guo X, Murphy S, Tiedje JM, Walsh F. Antibiotic Resistance Gene Detection in the Microbiome Context. Microbial Drug Resistance (Larchmont, N.Y.). PMID 29185915 DOI: 10.1089/mdr.2017.0199  0.32
2017 Williams MR, Stedtfeld RD, Tiedje JM, Hashsham SA. MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome. Frontiers in Microbiology. 8: 1896. PMID 29021788 DOI: 10.3389/fmicb.2017.01896  0.72
2017 Stedtfeld RD, Chai B, Crawford RB, Stedtfeld TM, Williams MR, Xiangwen S, Kuwahara T, Cole JR, Kaminski NE, Tiedje JM, Hashsham SA. Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD. Frontiers in Microbiology. 8: 1708. PMID 28936204 DOI: 10.3389/fmicb.2017.01708  0.72
2017 Stedtfeld RD, Brett Sallach J, Crawford RB, Stedtfeld TM, Williams MR, Waseem H, Johnston CT, Li H, Teppen BJ, Kaminski NE, Boyd SA, Tiedje JM, Hashsham SA. TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal. Applied Microbiology and Biotechnology. PMID 28812142 DOI: 10.1007/s00253-017-8460-9  0.72
2017 Muziasari WI, Pitkänen LK, Sørum H, Stedtfeld RD, Tiedje JM, Virta M. Corrigendum: The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms. Frontiers in Microbiology. 8: 1491. PMID 28785257 DOI: 10.3389/fmicb.2017.01491  0.32
2017 Yuan MM, Zhang J, Xue K, Wu L, Deng Y, Deng J, Hale L, Zhou X, He Z, Yang Y, Van Nostrand JD, Schuur EAG, Konstantinidis KT, Penton CR, Cole JR, ... Tiedje JM, et al. Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil. Global Change Biology. PMID 28715138 DOI: 10.1111/gcb.13820  0.96
2017 Munir A, Waseem H, Williams MR, Stedtfeld RD, Gulari E, Tiedje JM, Hashsham SA. Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB. Microarrays (Basel, Switzerland). 6. PMID 28555058 DOI: 10.3390/microarrays6020009  0.72
2017 Williams MR, Stedtfeld RD, Stedtfeld TM, Tiedje JM, Hashsham SA. Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device. Biomedical Microdevices. 19: 45. PMID 28536858 DOI: 10.1007/s10544-017-0191-2  0.72
2017 Šket R, Treichel N, Debevec T, Eiken O, Mekjavic I, Schloter M, Vital M, Chandler J, Tiedje JM, Murovec B, Prevoršek Z, Stres B. Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study. Frontiers in Physiology. 8: 250. PMID 28522975 DOI: 10.3389/fphys.2017.00250  0.68
2017 Stedtfeld RD, Stedtfeld TM, Fader KA, Williams MR, Bhaduri P, Quensen J, Zacharewski TR, Tiedje JM, Hashsham SA. TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome. Fems Microbiology Ecology. PMID 28475713 DOI: 10.1093/femsec/fix058  0.72
2017 Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae JC, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, ... Tiedje JM, et al. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. Journal of Environmental Management. 198: 213-220. PMID 28460328 DOI: 10.1016/j.jenvman.2017.04.079  0.72
2017 Muurinen J, Stedtfeld RD, Karkman A, Pärnänen K, Tiedje JM, Virta MPJ. Influence of Manure Application on the Environmental Resistome Under Finnish Agricultural Practice with Restricted Antibiotic Use. Environmental Science & Technology. PMID 28453251 DOI: 10.1021/acs.est.7b00551  0.32
2017 Srinivasan V, Stedtfeld RD, Tourlousse DM, Baushke SW, Xin Y, Miller SM, Pham T, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA. Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner. Journal of Microbiological Methods. PMID 28438642 DOI: 10.1016/j.mimet.2017.04.009  0.72
2017 Cheng L, Zhang N, Yuan M, Xiao J, Qin Y, Deng Y, Tu Q, Xue K, Van Nostrand JD, Wu L, He Z, Zhou X, Leigh MB, Konstantinidis KT, Schuur EA, ... ... Tiedje JM, et al. Warming enhances old organic carbon decomposition through altering functional microbial communities. The Isme Journal. PMID 28430189 DOI: 10.1038/ismej.2017.48  0.96
2017 Waseem H, Williams MR, Stedtfeld T, Chai B, Stedtfeld RD, Cole JR, Tiedje JM, Hashsham SA. Virulence factor activity relationships (VFARs): a bioinformatics perspective. Environmental Science. Processes & Impacts. PMID 28261716 DOI: 10.1039/c6em00689b  0.72
2017 Meyer KM, Klein AM, Rodrigues JL, Nüsslein K, Tringe SG, Mirza BS, Tiedje JM, Bohannan BJ. Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms. Molecular Ecology. PMID 28100018 DOI: 10.1111/mec.14011  0.64
2016 Muziasari WI, Pitkänen LK, Sørum H, Stedtfeld RD, Tiedje JM, Virta M. The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms. Frontiers in Microbiology. 7: 2137. PMID 28111573 DOI: 10.3389/fmicb.2016.02137  0.32
2016 Ahmad F, Stedtfeld RD, Waseem H, Williams MR, Cupples AM, Tiedje JM, Hashsham SA. Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min. Journal of Microbiological Methods. 132: 27-33. PMID 27856278 DOI: 10.1016/j.mimet.2016.11.010  0.72
2016 Wang F, Stedtfeld RD, Kim OS, Chai B, Yang L, Stedtfeld TM, Hong SG, Kim D, Lim HS, Hashsham SA, Tiedje JM, Sul WJ. Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils. Environmental Science & Technology. PMID 27797533 DOI: 10.1021/acs.est.6b02863  0.72
2016 Hambright WS, Deng J, Tiedje JM, Brettar I, Rodrigues JL. Shewanella baltica Ecotypes Have Wide Transcriptional Variation under the Same Growth Conditions. Msphere. 1. PMID 27777983 DOI: 10.1128/mSphere.00158-16  0.64
2016 Xue K, Yuan MM, Xie J, Li D, Qin Y, Hale LE, Wu L, Deng Y, He Z, Van Nostrand JD, Luo Y, Tiedje JM, Zhou J. Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming. Mbio. 7. PMID 27677789 DOI: 10.1128/mBio.00976-16  0.32
2016 Penton CR, Gupta VV, Yu J, Tiedje JM. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons. Frontiers in Microbiology. 7: 824. PMID 27313569 DOI: 10.3389/fmicb.2016.00824  0.36
2016 Chai B, Tsoi TV, Iwai S, Liu C, Fish JA, Gu C, Johnson TA, Zylstra G, Teppen BJ, Li H, Hashsham SA, Boyd SA, Cole JR, Tiedje JM. Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay. Plos One. 11: e0157008. PMID 27309357 DOI: 10.1371/journal.pone.0157008  1
2016 Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, Schuur EA, Luo Y, Tiedje JM, Zhou J, Konstantinidis KT. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. Frontiers in Microbiology. 7: 579. PMID 27199914 DOI: 10.3389/fmicb.2016.00579  0.96
2016 Yang Y, Jiang X, Chai B, Ma L, Li B, Zhang A, Cole JR, Tiedje JM, Zhang T. ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. Bioinformatics (Oxford, England). PMID 27153579 DOI: 10.1093/bioinformatics/btw136  0.56
2016 Johnson TA, Stedtfeld RD, Wang Q, Cole JR, Hashsham SA, Looft T, Zhu YG, Tiedje JM. Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture. Mbio. 7. PMID 27073098 DOI: 10.1128/mBio.02214-15  1
2016 Wei H, Dai J, Xia M, Romine MF, Shi L, Beliav A, Tiedje JM, Nealson KH, Fredrickson JK, Zhou J, Qiu D. Functional Roles of CymA and NapC in Reduction of Nitrate and Nitrite by Shewanella putrefaciens W3-18-1. Microbiology (Reading, England). PMID 27010745 DOI: 10.1099/mic.0.000285  0.32
2016 Muziasari WI, Pärnänen K, Johnson TA, Lyra C, Karkman A, Stedtfeld RD, Tamminen M, Tiedje JM, Virta M. Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments. Fems Microbiology Ecology. PMID 26976842 DOI: 10.1093/femsec/fiw052  0.44
2016 Stedtfeld RD, Williams M, Fakher U, Johnson TA, Stedtfeld TM, Wang F, Khalife WT, Hughes M, Etchebarne B, Tiedje JM, Hashsham SA. Antimicrobial Resistance (AR) Dashboard Application for Mapping Environmental Occurrence and Resistant Pathogens. Fems Microbiology Ecology. PMID 26850162 DOI: 10.1093/femsec/fiw020  0.32
2016 Karkman A, Johnson TA, Lyra C, Stedtfeld RD, Tamminen M, Tiedje JM, Virta M. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. Fems Microbiology Ecology. PMID 26832203 DOI: 10.1093/femsec/fiw014  0.32
2016 Xue C, Penton CR, Zhang B, Zhao M, Rothstein DE, Mladenoff DJ, Forrester JA, Shen Q, Tiedje JM. Soil fungal and bacterial responses to conversion of open land to short-rotation woody biomass crops Gcb Bioenergy. DOI: 10.1111/gcbb.12303  1
2016 Liang C, Jesus EdC, Duncan DS, Quensen JF, Jackson RD, Balser TC, Tiedje JM. Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA Soil Biology and Biochemistry. 94: 173-180. DOI: 10.1016/j.soilbio.2015.11.020  0.32
2015 Navarrete AA, Venturini AM, Meyer KM, Klein AM, Tiedje JM, Bohannan BJ, Nüsslein K, Tsai SM, Rodrigues JL. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. Frontiers in Microbiology. 6: 1443. PMID 26733981 DOI: 10.3389/fmicb.2015.01443  0.32
2015 Ma L, Xia Y, Li B, Yang Y, Li LG, Tiedje JM, Zhang T. Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken and Human Feces. Environmental Science & Technology. PMID 26650334 DOI: 10.1021/acs.est.5b03522  1
2015 Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, et al. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in Microbiology. 6: 1205. PMID 26583008 DOI: 10.3389/fmicb.2015.01205  0.32
2015 Seyrig G, Stedtfeld RD, Tourlousse DM, Ahmad F, Towery K, Cupples AM, Tiedje JM, Hashsham SA. Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. Journal of Microbiological Methods. PMID 26554941 DOI: 10.1016/j.mimet.2015.11.004  0.32
2015 Guo J, Cole JR, Zhang Q, Brown CT, Tiedje JM. Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. Applied and Environmental Microbiology. PMID 26475107 DOI: 10.1128/AEM.02772-15  1
2015 Singh P, Teal TK, Marsh TL, Tiedje JM, Mosci R, Jernigan K, Zell A, Newton DW, Salimnia H, Lephart P, Sundin D, Khalife W, Britton RA, Rudrik JT, Manning SD. Intestinal microbial communities associated with acute enteric infections and disease recovery. Microbiome. 3: 45. PMID 26395244 DOI: 10.1186/s40168-015-0109-2  0.56
2015 Penton CR, St Louis D, Pham A, Cole JR, Wu L, Luo Y, Schuur EA, Zhou J, Tiedje JM. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. Frontiers in Microbiology. 6: 746. PMID 26284038 DOI: 10.3389/fmicb.2015.00746  0.56
2015 Stedtfeld RD, Liu YC, Stedtfeld TM, Kostic T, Kronlein M, Srivannavit O, Khalife WT, Tiedje JM, Gulari E, Hughes M, Etchebarne B, Hashsham SA. Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens. Biomedical Microdevices. 17: 9994. PMID 26260693 DOI: 10.1007/s10544-015-9994-1  0.32
2015 Wang Q, Fish JA, Gilman M, Sun Y, Brown CT, Tiedje JM, Cole JR. Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome. 3: 32. PMID 26246894 DOI: 10.1186/s40168-015-0093-6  0.56
2015 Li B, Yang Y, Ma L, Ju F, Guo F, Tiedje JM, Zhang T. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. The Isme Journal. PMID 25918831 DOI: 10.1038/ismej.2015.59  1
2015 Zhang B, Penton CR, Xue C, Wang Q, Zheng T, Tiedje JM. Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH. Applied and Environmental Microbiology. 81: 4536-45. PMID 25911484 DOI: 10.1128/AEM.00111-15  1
2015 Zhang P, Wu WM, Van Nostrand JD, Deng Y, He Z, Gihring T, Zhang G, Schadt CW, Watson D, Jardine P, Criddle CS, Brooks S, Marsh TL, Tiedje JM, Arkin AP, et al. Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction. Applied and Environmental Microbiology. 81: 4164-72. PMID 25862231 DOI: 10.1128/AEM.00043-15  1
2015 Rachid CT, Balieiro FC, Fonseca ES, Peixoto RS, Chaer GM, Tiedje JM, Rosado AS. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations. Plos One. 10: e0118515. PMID 25706388 DOI: 10.1371/journal.pone.0118515  1
2015 He R, Wooller MJ, Pohlman JW, Tiedje JM, Leigh MB. Methane-derived carbon flow through microbial communities in arctic lake sediments. Environmental Microbiology. PMID 25581131 DOI: 10.1111/1462-2920.12773  1
2015 Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM, Zhu YG. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. The Isme Journal. 9: 1269-79. PMID 25500508 DOI: 10.1038/ismej.2014.226  1
2015 Deng J, Gu Y, Zhang J, Xue K, Qin Y, Yuan M, Yin H, He Z, Wu L, Schuur EA, Tiedje JM, Zhou J. Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska. Molecular Ecology. 24: 222-34. PMID 25424441 DOI: 10.1111/mec.13015  1
2015 Su JQ, Ding LJ, Xue K, Yao HY, Quensen J, Bai SJ, Wei WX, Wu JS, Zhou J, Tiedje JM, Zhu YG. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Molecular Ecology. 24: 136-50. PMID 25410123 DOI: 10.1111/mec.13010  1
2015 Vital M, Gao J, Rizzo M, Harrison T, Tiedje JM. Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia. The Isme Journal. 9: 832-43. PMID 25343515 DOI: 10.1038/ismej.2014.179  1
2015 Vital M, Chai B, Østman B, Cole J, Konstantinidis KT, Tiedje JM. Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. The Isme Journal. 9: 1130-40. PMID 25343512 DOI: 10.1038/ismej.2014.204  1
2015 Penton CR, St. Louis D, Pham A, Cole JR, Wu L, Luo Y, Schuur EAG, Zhou J, Tiedje JM. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils Frontiers in Microbiology. 6. DOI: 10.3389/fmicb.2015.00746  0.32
2015 Vital M, Harkema JR, Rizzo M, Tiedje J, Brandenberger C. Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease Journal of Immunology Research. 2015. DOI: 10.1155/2015/892568  1
2015 Jesus EdC, Liang C, Quensen JF, Susilawati E, Jackson RD, Balser TC, Tiedje JM. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States Gcb Bioenergy. DOI: 10.1111/gcbb.12289  1
2015 Liang J, Li D, Shi Z, Tiedje JM, Zhou J, Schuur EAG, Konstantinidis KT, Luo Y. Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation Soil Biology and Biochemistry. 80: 127-135. DOI: 10.1016/j.soilbio.2014.10.005  1
2014 Zaborin A, Smith D, Garfield K, Quensen J, Shakhsheer B, Kade M, Tirrell M, Tiedje J, Gilbert JA, Zaborina O, Alverdy JC. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. Mbio. 5: e01361-14. PMID 25249279 DOI: 10.1128/mBio.01361-14  1
2014 Zhang Y, Boyd SA, Teppen BJ, Tiedje JM, Li H. Organic acids enhance bioavailability of tetracycline in water to Escherichia coli for uptake and expression of antibiotic resistance. Water Research. 65: 98-106. PMID 25100186 DOI: 10.1016/j.watres.2014.07.021  1
2014 Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, ... ... Tiedje JM, et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. Plos Biology. 12: e1001920. PMID 25093819 DOI: 10.1371/journal.pbio.1001920  1
2014 Siles JA, Rachid CT, Sampedro I, García-Romera I, Tiedje JM. Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment. Plos One. 9: e103035. PMID 25058610 DOI: 10.1371/journal.pone.0103035  1
2014 Smalla K, Tiedje JM. Editorial overview: Ecology and industrial microbiology. Current Opinion in Microbiology. 19: v-vii. PMID 25012965 DOI: 10.1016/j.mib.2014.06.011  1
2014 Paula FS, Rodrigues JL, Zhou J, Wu L, Mueller RC, Mirza BS, Bohannan BJ, Nüsslein K, Deng Y, Tiedje JM, Pellizari VH. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities. Molecular Ecology. 23: 2988-99. PMID 24806276 DOI: 10.1111/mec.12786  1
2014 Vital M, Howe AC, Tiedje JM. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. Mbio. 5: e00889. PMID 24757212 DOI: 10.1128/mBio.00889-14  1
2014 Zhang Y, Boyd SA, Teppen BJ, Tiedje JM, Li H. Role of tetracycline speciation in the bioavailability to Escherichia coli for uptake and expression of antibiotic resistance. Environmental Science & Technology. 48: 4893-900. PMID 24717018 DOI: 10.1021/es5003428  1
2014 Penton CR, Gupta VV, Tiedje JM, Neate SM, Ophel-Keller K, Gillings M, Harvey P, Pham A, Roget DK. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing. Plos One. 9: e93893. PMID 24699870 DOI: 10.1371/journal.pone.0093893  1
2014 Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT. Tackling soil diversity with the assembly of large, complex metagenomes. Proceedings of the National Academy of Sciences of the United States of America. 111: 4904-9. PMID 24632729 DOI: 10.1073/pnas.1402564111  1
2014 Cole JR, Tiedje JM. History and impact of RDP: a legacy from Carl Woese to microbiology. Rna Biology. 11: 239-43. PMID 24607969 DOI: 10.4161/rna.28306  1
2014 Zhou J, Deng Y, Zhang P, Xue K, Liang Y, Van Nostrand JD, Yang Y, He Z, Wu L, Stahl DA, Hazen TC, Tiedje JM, Arkin AP. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences of the United States of America. 111: E836-45. PMID 24550501 DOI: 10.1073/pnas.1324044111  1
2014 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, ... ... Tiedje JM, et al. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Applied and Environmental Microbiology. 80: 1777-86. PMID 24375144 DOI: 10.1128/AEM.03712-13  1
2014 Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research. 42: D633-42. PMID 24288368 DOI: 10.1093/nar/gkt1244  1
2014 Deng J, Brettar I, Luo C, Auchtung J, Konstantinidis KT, Rodrigues JL, Höfle M, Tiedje JM. Stability, genotypic and phenotypic diversity of Shewanella baltica in the redox transition zone of the Baltic Sea. Environmental Microbiology. 16: 1854-66. PMID 24286373 DOI: 10.1111/1462-2920.12344  1
2014 Yang Y, Quensen J, Mathieu J, Wang Q, Wang J, Li M, Tiedje JM, Alvarez PJ. Pyrosequencing reveals higher impact of silver nanoparticles than Ag+ on the microbial community structure of activated sludge. Water Research. 48: 317-25. PMID 24120408 DOI: 10.1016/j.watres.2013.09.046  1
2014 Stres B, Sul WJ, Murovec B, Tiedje JM. Correction: Recently deglaciated high-altitude soils of the himalaya: Diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere (PLoS ONE) Plos One. 9. DOI: 10.1371/annotation/1406824c-f082-400b-8fc7-4995c97a6249  1
2014 Penton CR, Deenik JL, Popp BN, Bruland GL, Engstrom P, Mueller J, Worden A, Tiedje JM. Assessing nitrogen transformations in a flooded agroecosystem using the isotope pairing technique and nitrogen functional gene abundances Soil Science. 179: 2-10. DOI: 10.1097/SS.0000000000000038  1
2014 Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT. Tackling soil diversity with the assembly of large, complex metagenomes (Proceedings of the National Academy of Sciences of the United States of America (2014) 111, 13, (4904-4909) doi:10.1073/pnas.1402564111) Proceedings of the National Academy of Sciences of the United States of America. 111: 6115. DOI: 10.1073/pnas.1405719111  1
2014 Leigh MB, Wu WM, Cardenas E, Uhlik O, Carroll S, Gentry T, Marsh TL, Zhou J, Jardine P, Criddle CS, Tiedje JM. Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing Frontiers of Environmental Science & Engineering. DOI: 10.1007/s11783-014-0721-6  1
2013 Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, ... ... Tiedje JM, et al. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 1: 9. PMID 24451366 DOI: 10.1186/2049-2618-1-9  1
2013 Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML, Morrison HG, Raffals L, Chang EB, Huffnagle GB, Schmidt TM, Cole JR, Tiedje JM. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome. 1: 8. PMID 24451334 DOI: 10.1186/2049-2618-1-8  1
2013 Van Doan T, Lee TK, Shukla SK, Tiedje JM, Park J. Increased nitrous oxide accumulation by bioelectrochemical denitrification under autotrophic conditions: kinetics and expression of denitrification pathway genes. Water Research. 47: 7087-97. PMID 24210359 DOI: 10.1016/j.watres.2013.08.041  1
2013 Fish JA, Chai B, Wang Q, Sun Y, Brown CT, Tiedje JM, Cole JR. FunGene: the functional gene pipeline and repository. Frontiers in Microbiology. 4: 291. PMID 24101916 DOI: 10.3389/fmicb.2013.00291  1
2013 Stres B, Sul WJ, Murovec B, Tiedje JM. Recently deglaciated high-altitude soils of the Himalaya: diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere. Plos One. 8: e76440. PMID 24086740 DOI: 10.1371/journal.pone.0076440  1
2013 Penton CR, Johnson TA, Quensen JF, Iwai S, Cole JR, Tiedje JM. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. Frontiers in Microbiology. 4: 279. PMID 24062736 DOI: 10.3389/fmicb.2013.00279  1
2013 Wang Q, Quensen JF, Fish JA, Lee TK, Sun Y, Tiedje JM, Cole JR. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. Mbio. 4: e00592-13. PMID 24045641 DOI: 10.1128/mBio.00592-13  1
2013 Penton CR, St Louis D, Cole JR, Luo Y, Wu L, Schuur EA, Zhou J, Tiedje JM. Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions. Applied and Environmental Microbiology. 79: 7063-72. PMID 24014534 DOI: 10.1128/AEM.01702-13  1
2013 Jin M, Bothfeld W, Austin S, Sato TK, La Reau A, Li H, Foston M, Gunawan C, LeDuc RD, Quensen JF, McGee M, Uppugundla N, Higbee A, Ranatunga R, Donald CW, ... ... Tiedje JM, et al. Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate. Bioresource Technology. 147: 212-20. PMID 23999256 DOI: 10.1016/j.biortech.2013.08.018  1
2013 Rhodes AN, Fulthorpe RR, Tiedje JM. Probing the functional diversity of global pristine soil communities with 3-chlorobenzoate reveals that communities of generalists dominate catabolic transformation. Applied and Environmental Microbiology. 79: 6932-40. PMID 23995940 DOI: 10.1128/AEM.01905-13  1
2013 Taketani RG, Lima AB, da Conceição Jesus E, Teixeira WG, Tiedje JM, Tsai SM. Bacterial community composition of anthropogenic biochar and Amazonian anthrosols assessed by 16S rRNA gene 454 pyrosequencing. Antonie Van Leeuwenhoek. 104: 233-42. PMID 23743632 DOI: 10.1007/s10482-013-9942-0  1
2013 Hinsa-Leasure SM, Koid C, Tiedje JM, Schultzhaus JN. Biofilm formation by Psychrobacter arcticus and the role of a large adhesin in attachment to surfaces. Applied and Environmental Microbiology. 79: 3967-73. PMID 23603675 DOI: 10.1128/AEM.00867-13  1
2013 Rachid CT, Santos AL, Piccolo MC, Balieiro FC, Coutinho HL, Peixoto RS, Tiedje JM, Rosado AS. Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure. Plos One. 8: e59342. PMID 23533619 DOI: 10.1371/journal.pone.0059342  1
2013 Zhu YG, Johnson TA, Su JQ, Qiao M, Guo GX, Stedtfeld RD, Hashsham SA, Tiedje JM. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proceedings of the National Academy of Sciences of the United States of America. 110: 3435-40. PMID 23401528 DOI: 10.1073/pnas.1222743110  1
2013 Rodrigues JL, Pellizari VH, Mueller R, Baek K, Jesus Eda C, Paula FS, Mirza B, Hamaoui GS, Tsai SM, Feigl B, Tiedje JM, Bohannan BJ, Nüsslein K. Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America. 110: 988-93. PMID 23271810 DOI: 10.1073/pnas.1220608110  1
2013 Sul WJ, Asuming-Brempong S, Wang Q, Tourlousse DM, Penton CR, Deng Y, Rodrigues JLM, Adiku SGK, Jones JW, Zhou J, Cole JR, Tiedje JM. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon Soil Biology and Biochemistry. 65: 33-38. DOI: 10.1016/j.soilbio.2013.05.007  1
2013 Penton CR, Deenik JL, Popp BN, Bruland GL, Engstrom P, St. Louis D, Tiedje J. Importance of sub-surface rhizosphere-mediated coupled nitrification-denitrification in a flooded agroecosystem in Hawaii Soil Biology and Biochemistry. 57: 362-373. DOI: 10.1016/j.soilbio.2012.10.018  1
2013 Liang C, Duncan DS, Balser TC, Tiedje JM, Jackson RD. Soil microbial residue storage linked to soil legacy under biofuel cropping systems in southern Wisconsin, USA Soil Biology and Biochemistry. 57: 939-942. DOI: 10.1016/j.soilbio.2012.09.006  1
2012 Rosenzweig N, Tiedje JM, Quensen JF, Meng Q, Hao JJ. Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses. Plant Disease. 96: 718-725. PMID 30727523 DOI: 10.1094/PDIS-07-11-0571  0.36
2012 Ormeño-Orrillo E, Rogel MA, Chueire LM, Tiedje JM, Martínez-Romero E, Hungria M. Genome sequences of Burkholderia sp. strains CCGE1002 and H160, isolated from legume nodules in Mexico and Brazil. Journal of Bacteriology. 194: 6927. PMID 23209196 DOI: 10.1128/JB.01756-12  1
2012 Oh S, Buddenborg S, Yoder-Himes DR, Tiedje JM, Konstantinidis KT. Genomic diversity of Escherichia isolates from diverse habitats. Plos One. 7: e47005. PMID 23056556 DOI: 10.1371/journal.pone.0047005  1
2012 Katharios-Lanwermeyer S, Rakic-Martinez M, Elhanafi D, Ratani S, Tiedje JM, Kathariou S. Coselection of cadmium and benzalkonium chloride resistance in conjugative transfers from nonpathogenic Listeria spp. to other Listeriae. Applied and Environmental Microbiology. 78: 7549-56. PMID 22904051 DOI: 10.1128/AEM.02245-12  1
2012 Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Brown CT. Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proceedings of the National Academy of Sciences of the United States of America. 109: 13272-7. PMID 22847406 DOI: 10.1073/pnas.1121464109  1
2012 He R, Wooller MJ, Pohlman JW, Quensen J, Tiedje JM, Leigh MB. Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments. The Isme Journal. 6: 1937-48. PMID 22592821 DOI: 10.1038/ismej.2012.34  1
2012 Tourlousse DM, Ahmad F, Stedtfeld RD, Seyrig G, Tiedje JM, Hashsham SA. A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomedical Microdevices. 14: 769-78. PMID 22566273 DOI: 10.1007/s10544-012-9658-3  1
2012 Baushke SW, Stedtfeld RD, Tourlousse DM, Ahmad F, Wick LM, Gulari E, Tiedje JM, Hashsham SA. Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves. Journal of Microbiological Methods. 90: 29-35. PMID 22537822 DOI: 10.1016/j.mimet.2012.04.003  1
2012 He R, Wooller MJ, Pohlman JW, Quensen J, Tiedje JM, Leigh MB. Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes. Applied and Environmental Microbiology. 78: 4715-23. PMID 22522690 DOI: 10.1128/AEM.00853-12  1
2012 He R, Wooller MJ, Pohlman JW, Catranis C, Quensen J, Tiedje JM, Leigh MB. Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing. Environmental Microbiology. 14: 1403-19. PMID 22429394 DOI: 10.1111/j.1462-2920.2012.02725.x  1
2012 Stedtfeld RD, Tourlousse DM, Seyrig G, Stedtfeld TM, Kronlein M, Price S, Ahmad F, Gulari E, Tiedje JM, Hashsham SA. Gene-Z: a device for point of care genetic testing using a smartphone. Lab On a Chip. 12: 1454-62. PMID 22374412 DOI: 10.1039/c2lc21226a  1
2012 Caro-Quintero A, Auchtung J, Deng J, Brettar I, Höfle M, Tiedje JM, Konstantinidis KT. Genome sequencing of five Shewanella baltica strains recovered from the oxic-anoxic interface of the Baltic Sea. Journal of Bacteriology. 194: 1236. PMID 22328742 DOI: 10.1128/JB.06468-11  1
2012 Li R, Tiedje JM, Chiu C, Worden RM. Soluble electron shuttles can mediate energy taxis toward insoluble electron acceptors. Environmental Science & Technology. 46: 2813-20. PMID 22324484 DOI: 10.1021/es204302w  1
2012 Kim SH, Harzman C, Davis JK, Hutcheson R, Broderick JB, Marsh TL, Tiedje JM. Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction. Bmc Microbiology. 12: 21. PMID 22316246 DOI: 10.1186/1471-2180-12-21  1
2012 Looft T, Johnson TA, Allen HK, Bayles DO, Alt DP, Stedtfeld RD, Sul WJ, Stedtfeld TM, Chai B, Cole JR, Hashsham SA, Tiedje JM, Stanton TB. In-feed antibiotic effects on the swine intestinal microbiome. Proceedings of the National Academy of Sciences of the United States of America. 109: 1691-6. PMID 22307632 DOI: 10.1073/pnas.1120238109  1
2012 Green SJ, Prakash O, Jasrotia P, Overholt WA, Cardenas E, Hubbard D, Tiedje JM, Watson DB, Schadt CW, Brooks SC, Kostka JE. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Applied and Environmental Microbiology. 78: 1039-47. PMID 22179233 DOI: 10.1128/AEM.06435-11  1
2012 Rosenzweig N, Tiedje JM, Quensen JF, Meng Q, Hao JJ. Microbial communities associated with potato common Scab-Suppressive soil determined by pyrosequencing analyses Plant Disease. 96: 718-725. DOI: org/10.1094/PDIS-07-11-0571  1
2012 Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Titus Brown C. Workshop: Graph compression approaches in assembly 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182675  1
2012 Liang C, Jesus EdC, Duncan DS, Jackson RD, Tiedje JM, Balser TC. Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: Impact of crop species and soil properties Applied Soil Ecology. 54: 24-31. DOI: 10.1016/j.apsoil.2011.11.015  1
2011 Santos AL, Siqueira JF, Rôças IN, Jesus EC, Rosado AS, Tiedje JM. Comparing the bacterial diversity of acute and chronic dental root canal infections. Plos One. 6: e28088. PMID 22132218 DOI: 10.1371/journal.pone.0028088  1
2011 Sul WJ, Cole JR, Jesus Eda C, Wang Q, Farris RJ, Fish JA, Tiedje JM. Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering. Proceedings of the National Academy of Sciences of the United States of America. 108: 14637-42. PMID 21873204 DOI: 10.1073/pnas.1111435108  1
2011 Ahmad F, Seyrig G, Tourlousse DM, Stedtfeld RD, Tiedje JM, Hashsham SA. A CCD-based fluorescence imaging system for real-time loop-mediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips. Biomedical Microdevices. 13: 929-37. PMID 21720851 DOI: 10.1007/s10544-011-9562-2  1
2011 Rodrigues JL, Serres MH, Tiedje JM. Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level. Applied and Environmental Microbiology. 77: 5352-60. PMID 21642407 DOI: 10.1128/AEM.00097-11  1
2011 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Tiedje JM, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29: 415-20. PMID 21552244 DOI: 10.1038/nbt.1823  0.6
2011 Patrauchan MA, Parnell JJ, McLeod MP, Florizone C, Tiedje JM, Eltis LD. Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400. Archives of Microbiology. 193: 641-50. PMID 21519854 DOI: 10.1007/s00203-011-0705-x  1
2011 Van Nostrand JD, Wu L, Wu WM, Huang Z, Gentry TJ, Deng Y, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle CS, Watson DB, Jardine PM, Marsh TL, ... Tiedje JM, et al. Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer. Applied and Environmental Microbiology. 77: 3860-9. PMID 21498771 DOI: 10.1128/AEM.01981-10  1
2011 Iwai S, Johnson TA, Chai B, Hashsham SA, Tiedje JM. Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. Applied and Environmental Microbiology. 77: 3551-7. PMID 21498766 DOI: 10.1128/AEM.00331-11  1
2011 Lee TK, Lee J, Sul WJ, Iwai S, Chai B, Tiedje JM, Park J. Novel biphenyl-oxidizing bacteria and dioxygenase genes from a korean tidal mudflat. Applied and Environmental Microbiology. 77: 3888-91. PMID 21498748 DOI: 10.1128/AEM.00023-11  1
2011 Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proceedings of the National Academy of Sciences of the United States of America. 108: 7200-5. PMID 21482770 DOI: 10.1073/pnas.1015622108  1
2011 Vishnivetskaya TA, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Dalin E, Tice H, Bruce DC, Goodwin LA, Pitluck S, Saunders E, Brettin T, Detter C, Han C, Larimer F, ... ... Tiedje JM, et al. Complete genome sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b. Journal of Bacteriology. 193: 2880-1. PMID 21460088 DOI: 10.1128/JB.00303-11  1
2011 Cruz-García C, Murray AE, Rodrigues JL, Gralnick JA, McCue LA, Romine MF, Löffler FE, Tiedje JM. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1. Bmc Microbiology. 11: 64. PMID 21450087 DOI: 10.1186/1471-2180-11-64  1
2011 dos Santos HF, Cury JC, do Carmo FL, dos Santos AL, Tiedje J, van Elsas JD, Rosado AS, Peixoto RS. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. Plos One. 6: e16943. PMID 21399677 DOI: 10.1371/journal.pone.0016943  1
2011 Li R, Auchtung JM, Tiedje JM, Worden RM. Shewanella oneidensis MR-1 chemotaxis in a diffusion gradient chamber. Environmental Science & Technology. 45: 1014-20. PMID 21174460 DOI: 10.1021/es102425p  1
2011 Brown CT, Tiedje JM. Metagenomics: The Paths Forward Handbook of Molecular Microbial Ecology Ii: Metagenomics in Different Habitats. 579-588. DOI: 10.1002/9781118010549.ch54  1
2011 Cole JR, Wang Q, Chai B, Tiedje JM. The Ribosomal Database Project: Sequences and Software for High-Throughput rRNA Analysis Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. 313-324. DOI: 10.1002/9781118010518.ch36  1
2011 Iwai S, Chai B, Jesus EdC, Penton CR, Lee TK, Cole JR, Tiedje JM. Gene-Targeted Metagenomics (GT Metagenomics) to Explore the Extensive Diversity of Genes of Interest in Microbial Communities Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. 235-243. DOI: 10.1002/9781118010518.ch28  1
2011 Cardenas E, Cole JR, Tiedje JM, Park J. Microbial community analysis using RDP II (ribosomal database project II): Methods, tools and new advances Environmental Engineering Research. 16: 3-9.  1
2011 Wu W, Carley J, Watson D, Gu B, Brooks S, Kelly SD, Kemner K, van Nostrand JD, Wu L, Xu M, Zhou J, Luo J, Cardenas E, Hwang C, Fields MW, ... ... Tiedje JM, et al. Bioreduction and immobilization of uranium in situ: A case study at a USA Department of Energy radioactive waste site, Oak Ridge, Tennessee Huanjing Kexue Xuebao/Acta Scientiae Circumstantiae. 31: 449-459.  1
2010 Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glöckner FO, Klenk HP, Wommack KE, Glass E, Docherty K, et al. The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Standards in Genomic Sciences. 3: 249-53. PMID 21304728 DOI: 10.4056/aigs.1443528  1
2010 Gao H, Barua S, Liang Y, Wu L, Dong Y, Reed S, Chen J, Culley D, Kennedy D, Yang Y, He Z, Nealson KH, Fredrickson JK, Tiedje JM, Romine M, et al. Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration. Microbial Biotechnology. 3: 455-66. PMID 21255343 DOI: 10.1111/j.1751-7915.2010.00181.x  1
2010 Stres B, Philippot L, Faganeli J, Tiedje JM. Frequent freeze-thaw cycles yield diminished yet resistant and responsive microbial communities in two temperate soils: a laboratory experiment. Fems Microbiology Ecology. 74: 323-35. PMID 20735477 DOI: 10.1111/j.1574-6941.2010.00951.x  1
2010 Cardenas E, Wu WM, Leigh MB, Carley J, Carroll S, Gentry T, Luo J, Watson D, Gu B, Ginder-Vogel M, Kitanidis PK, Jardine PM, Zhou J, Criddle CS, Marsh TL, ... Tiedje JM, et al. Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach. Applied and Environmental Microbiology. 76: 6778-86. PMID 20729318 DOI: 10.1128/AEM.01097-10  1
2010 Hinsa-Leasure SM, Bhavaraju L, Rodrigues JL, Bakermans C, Gilichinsky DA, Tiedje JM. Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample. Fems Microbiology Ecology. 74: 103-13. PMID 20695892 DOI: 10.1111/j.1574-6941.2010.00945.x  1
2010 Murovec B, Tiedje JM, Stres B. DNA encoding for an efficient 'Omics processing. Computer Methods and Programs in Biomedicine. 100: 175-90. PMID 20444519 DOI: 10.1016/j.cmpb.2010.03.014  1
2010 Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. The Isme Journal. 4: 989-1001. PMID 20357834 DOI: 10.1038/ismej.2010.35  1
2010 Xu M, Wu WM, Wu L, He Z, Van Nostrand JD, Deng Y, Luo J, Carley J, Ginder-Vogel M, Gentry TJ, Gu B, Watson D, Jardine PM, Marsh TL, Tiedje JM, et al. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. The Isme Journal. 4: 1060-70. PMID 20237512 DOI: 10.1038/ismej.2010.31  1
2010 Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L, Barua S, Barry K, Tringe SG, Watson DB, He Z, Hazen TC, Tiedje JM, Rubin EM, Zhou J. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. The Isme Journal. 4: 660-72. PMID 20182523 DOI: 10.1038/ismej.2009.154  1
2010 Ayala-del-Río HL, Chain PS, Grzymski JJ, Ponder MA, Ivanova N, Bergholz PW, Di Bartolo G, Hauser L, Land M, Bakermans C, Rodrigues D, Klappenbach J, Zarka D, Larimer F, Richardson P, ... ... Tiedje JM, et al. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Applied and Environmental Microbiology. 76: 2304-12. PMID 20154119 DOI: 10.1128/AEM.02101-09  1
2010 Yoder-Himes DR, Konstantinidis KT, Tiedje JM. Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. Plos One. 5: e8724. PMID 20090946 DOI: 10.1371/journal.pone.0008724  1
2010 Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. The Isme Journal. 4: 279-85. PMID 19776767 DOI: 10.1038/ismej.2009.104  1
2010 Parnell JJ, Denef VJ, Park J, Tsoi T, Tiedje JM. Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400. Biodegradation. 21: 147-56. PMID 19672561 DOI: 10.1007/s10532-009-9289-4  1
2010 da Jesus EC, Susilawati E, Smith SL, Wang Q, Chai B, Farris R, Rodrigues JLM, Thelen KD, Tiedje JM. Bacterial communities in the rhizosphere of biofuel crops grown on marginal lands as evaluated by 16S rRNA gene pyrosequences Bioenergy Research. 3: 20-27. DOI: 10.1007/s12155-009-9073-7  1
2009 Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, ... ... Tiedje JM, et al. Genomics. Genome project standards in a new era of sequencing. Science (New York, N.Y.). 326: 236-7. PMID 19815760 DOI: 10.1126/science.1180614  1
2009 Konstantinidis KT, Serres MH, Romine MF, Rodrigues JL, Auchtung J, McCue LA, Lipton MS, Obraztsova A, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM. Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proceedings of the National Academy of Sciences of the United States of America. 106: 15909-14. PMID 19805231 DOI: 10.1073/pnas.0902000106  1
2009 Walk ST, Alm EW, Gordon DM, Ram JL, Toranzos GA, Tiedje JM, Whittam TS. Cryptic lineages of the genus Escherichia. Applied and Environmental Microbiology. 75: 6534-44. PMID 19700542 DOI: 10.1128/AEM.01262-09  1
2009 Sul WJ, Park J, Quensen JF, Rodrigues JL, Seliger L, Tsoi TV, Zylstra GJ, Tiedje JM. DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Applied and Environmental Microbiology. 75: 5501-6. PMID 19648381 DOI: 10.1128/AEM.00121-09  1
2009 Van Nostrand JD, Wu WM, Wu L, Deng Y, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle CS, Watson DB, Jardine PM, Marsh TL, Tiedje JM, Hazen TC, et al. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environmental Microbiology. 11: 2611-26. PMID 19624708 DOI: 10.1111/j.1462-2920.2009.01986.x  1
2009 Rodríguez-Minguela CM, Apajalahti JH, Chai B, Cole JR, Tiedje JM. Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact. Applied and Environmental Microbiology. 75: 5100-10. PMID 19502434 DOI: 10.1128/AEM.00133-09  1
2009 da C Jesus E, Marsh TL, Tiedje JM, de S Moreira FM. Changes in land use alter the structure of bacterial communities in Western Amazon soils. The Isme Journal. 3: 1004-11. PMID 19440233 DOI: 10.1038/ismej.2009.47  1
2009 Gao H, Yang ZK, Barua S, Reed SB, Romine MF, Nealson KH, Fredrickson JK, Tiedje JM, Zhou J. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA. The Isme Journal. 3: 966-76. PMID 19387485 DOI: 10.1038/ismej.2009.40  1
2009 Vishnivetskaya TA, Kathariou S, Tiedje JM. The Exiguobacterium genus: biodiversity and biogeography. Extremophiles : Life Under Extreme Conditions. 13: 541-55. PMID 19381755 DOI: 10.1007/s00792-009-0243-5  1
2009 Stres B, Tiedje JM, Murovec B. BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases. Bioinformatics (Oxford, England). 25: 1556-8. PMID 19369501 DOI: 10.1093/bioinformatics/btp254  1
2009 Rodrigues DF, da C Jesus E, Ayala-Del-Río HL, Pellizari VH, Gilichinsky D, Sepulveda-Torres L, Tiedje JM. Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium. The Isme Journal. 3: 658-65. PMID 19322243 DOI: 10.1038/ismej.2009.25  1
2009 Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America. 106: 3976-81. PMID 19234113 DOI: 10.1073/pnas.0813403106  1
2009 Ramette A, Tiedje JM, Boetius A. Impact of space, time and complex environments on microbial communities. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. 15: 60-2. PMID 19220358 DOI: 10.1111/j.1469-0691.2008.02692.x  1
2009 Bergholz PW, Bakermans C, Tiedje JM. Psychrobacter arcticus 273-4 uses resource efficiency and molecular motion adaptations for subzero temperature growth. Journal of Bacteriology. 191: 2340-52. PMID 19168616 DOI: 10.1128/JB.01377-08  1
2009 Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research. 37: D141-5. PMID 19004872 DOI: 10.1093/nar/gkn879  1
2009 Bakermans C, Sloup RE, Zarka DG, Tiedje JM, Thomashow MF. Development and use of genetic system to identify genes required for efficient low-temperature growth of Psychrobacter arcticus 273-4. Extremophiles : Life Under Extreme Conditions. 13: 21-30. PMID 18818866 DOI: 10.1007/s00792-008-0193-3  1
2009 Vogel TM, Simonet P, Hirsch PR, Jansson JK, Tiedje JM, van Elsas JD, Nalin R, Philippot L, Bailey MJ. Advantages of the metagenomic approach for soil exploration: Reply from Vogel et al. Nature Reviews Microbiology. 7: 756-757. DOI: 10.1038/nrmicro2119-c3  1
2009 Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, van Elsas JD, Bailey MJ, Nalin R, Philippot L. TerraGenome: A consortium for the sequencing of a soil metagenome Nature Reviews Microbiology. 7: 252. DOI: 10.1038/nrmicro2119  1
2008 Rodrigues DF, Ivanova N, He Z, Huebner M, Zhou J, Tiedje JM. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach. Bmc Genomics. 9: 547. PMID 19019206 DOI: 10.1186/1471-2164-9-547  1
2008 Cardenas E, Tiedje JM. New tools for discovering and characterizing microbial diversity. Current Opinion in Biotechnology. 19: 544-9. PMID 18984052 DOI: 10.1016/j.copbio.2008.10.010  1
2008 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, ... ... Tiedje JM, et al. Towards environmental systems biology of Shewanella. Nature Reviews. Microbiology. 6: 592-603. PMID 18604222 DOI: 10.1038/nrmicro1947  1
2008 Wu L, Kellogg L, Devol AH, Tiedje JM, Zhou J. Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Applied and Environmental Microbiology. 74: 4516-29. PMID 18515485 DOI: 10.1128/AEM.02751-07  1
2008 Cardenas E, Wu WM, Leigh MB, Carley J, Carroll S, Gentry T, Luo J, Watson D, Gu B, Ginder-Vogel M, Kitanidis PK, Jardine PM, Zhou J, Criddle CS, Marsh TL, ... Tiedje JM, et al. Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels. Applied and Environmental Microbiology. 74: 3718-29. PMID 18456853 DOI: 10.1128/AEM.02308-07  1
2008 Stedtfeld RD, Baushke SW, Tourlousse DM, Miller SM, Stedtfeld TM, Gulari E, Tiedje JM, Hashsham SA. Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform. Applied and Environmental Microbiology. 74: 3831-8. PMID 18424532 DOI: 10.1128/AEM.02743-07  1
2008 Ponder MA, Thomashow MF, Tiedje JM. Metabolic activity of Siberian permafrost isolates, Psychrobacter arcticus and Exiguobacterium sibiricum, at low water activities. Extremophiles : Life Under Extreme Conditions. 12: 481-90. PMID 18335164 DOI: 10.1007/s00792-008-0151-0  1
2008 Wu L, Liu X, Fields MW, Thompson DK, Bagwell CE, Tiedje JM, Hazen TC, Zhou J. Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness. The Isme Journal. 2: 642-55. PMID 18309358 DOI: 10.1038/ismej.2008.23  1
2008 Miller SM, Tourlousse DM, Stedtfeld RD, Baushke SW, Herzog AB, Wick LM, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA. In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water. Applied and Environmental Microbiology. 74: 2200-9. PMID 18245235 DOI: 10.1128/AEM.01962-07  1
2008 Rodrigues DF, Tiedje JM. Coping with our cold planet. Applied and Environmental Microbiology. 74: 1677-86. PMID 18203855 DOI: 10.1128/AEM.02000-07  1
2008 Asuming-Brempong S, Gantner S, Adiku SGK, Archer G, Edusei V, Tiedje JM. Changes in the biodiversity of microbial populations in tropical soils under different fallow treatments Soil Biology and Biochemistry. 40: 2811-2818. DOI: 10.1016/j.soilbio.2008.08.010  1
2007 Leigh MB, Pellizari VH, Uhlík O, Sutka R, Rodrigues J, Ostrom NE, Zhou J, Tiedje JM. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs) Isme Journal. 1: 134-148. PMID 18043623 DOI: 10.1038/ismej.2007.26  1
2007 Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Current Opinion in Microbiology. 10: 504-9. PMID 17923431 DOI: 10.1016/j.mib.2007.08.006  1
2007 Hansen AA, Herbert RA, Mikkelsen K, Jensen LL, Kristoffersen T, Tiedje JM, Lomstein BA, Finster KW. Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway. Environmental Microbiology. 9: 2870-84. PMID 17922769 DOI: 10.1111/j.1462-2920.2007.01403.x  1
2007 Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology. 73: 5261-7. PMID 17586664 DOI: 10.1128/AEM.00062-07  1
2007 Smith DJ, Park J, Tiedje JM, Mohn WW. A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism. Journal of Bacteriology. 189: 6195-204. PMID 17586638 DOI: 10.1128/JB.00179-07  1
2007 Gilichinsky DA, Wilson GS, Friedmann EI, McKay CP, Sletten RS, Rivkina EM, Vishnivetskaya TA, Erokhina LG, Ivanushkina NE, Kochkina GA, Shcherbakova VA, Soina VS, Spirina EV, Vorobyova EA, Fyodorov-Davydov DG, ... ... Tiedje JM, et al. Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology. Astrobiology. 7: 275-311. PMID 17480161 DOI: 10.1089/ast.2006.0012  1
2007 Vishnivetskaya TA, Siletzky R, Jefferies N, Tiedje JM, Kathariou S. Effect of low temperature and culture media on the growth and freeze-thawing tolerance of Exiguobacterium strains. Cryobiology. 54: 234-40. PMID 17382311 DOI: 10.1016/j.cryobiol.2007.01.008  1
2007 O'Sullivan LA, Weightman AJ, Jones TH, Marchbank AM, Tiedje JM, Mahenthiralingam E. Identifying the genetic basis of ecologically and biotechnologically useful functions of the bacterium Burkholderia vietnamiensis. Environmental Microbiology. 9: 1017-34. PMID 17359273 DOI: 10.1111/j.1462-2920.2006.01228.x  1
2007 Ramette A, Tiedje JM. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proceedings of the National Academy of Sciences of the United States of America. 104: 2761-6. PMID 17296935 DOI: 10.1073/pnas.0610671104  1
2007 Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology. 57: 81-91. PMID 17220447 DOI: 10.1099/ijs.0.64483-0  1
2007 Zheng S, Ponder MA, Shih JY, Tiedje JM, Thomashow MF, Lubman DM. A proteomic analysis of Psychrobacter articus 273-4 adaptation to low temperature and salinity using a 2-D liquid mapping approach. Electrophoresis. 28: 467-88. PMID 17177241 DOI: 10.1002/elps.200600173  1
2007 Rodrigues DF, Tiedje JM. Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost. Fems Microbiology Ecology. 59: 489-99. PMID 17156079 DOI: 10.1111/j.1574-6941.2006.00233.x  1
2007 Bakermans C, Tollaksen SL, Giometti CS, Wilkerson C, Tiedje JM, Thomashow MF. Proteomic analysis of Psychrobacter cryohalolentis K5 during growth at subzero temperatures. Extremophiles : Life Under Extreme Conditions. 11: 343-54. PMID 17123128 DOI: 10.1007/s00792-006-0042-1  1
2007 Stedtfeld RD, Wick LM, Baushke SW, Tourlousse DM, Herzog AB, Xia Y, Rouillard JM, Klappenbach JA, Cole JR, Gulari E, Tiedje JM, Hashsham SA. Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays. Applied and Environmental Microbiology. 73: 380-9. PMID 17114322 DOI: 10.1128/AEM.01785-06  1
2007 Ramette A, Tiedje JM. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microbial Ecology. 53: 197-207. PMID 17106806 DOI: 10.1007/s00248-005-5010-2  1
2007 Cruz-García C, Murray AE, Klappenbach JA, Stewart V, Tiedje JM. Respiratory nitrate ammonification by Shewanella oneidensis MR-1. Journal of Bacteriology. 189: 656-62. PMID 17098906 DOI: 10.1128/JB.01194-06  1
2007 Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Research. 35: D169-72. PMID 17090583 DOI: 10.1093/nar/gkl889  1
2007 Griffin BM, Tiedje JM. Microbial reductive dehalogenation in Antarctic melt pond sediments Antarctic Science. 19: 411-416. DOI: 10.1017/S0954102007000570  1
2007 Hashsham SA, Gulari E, Tiedje JM. Microfluidic systems being adapted for microbial, molecular biological analyses Microbe. 2: 531-536.  1
2006 Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 1929-40. PMID 17062412 DOI: 10.1098/rstb.2006.1920  1
2006 Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, ... ... Tiedje JM, et al. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proceedings of the National Academy of Sciences of the United States of America. 103: 15280-7. PMID 17030797 DOI: 10.1073/pnas.0606924103  1
2006 Penton CR, Devol AH, Tiedje JM. Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments. Applied and Environmental Microbiology. 72: 6829-32. PMID 17021238 DOI: 10.1128/AEM.01254-06  1
2006 Parnell JJ, Park J, Denef V, Tsoi T, Hashsham S, Quensen J, Tiedje JM. Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Applied and Environmental Microbiology. 72: 6607-14. PMID 17021212 DOI: 10.1128/AEM.01129-06  1
2006 Konstantinidis KT, Ramette A, Tiedje JM. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Applied and Environmental Microbiology. 72: 7286-93. PMID 16980418 DOI: 10.1128/AEM.01398-06  1
2006 Gao H, Obraztova A, Stewart N, Popa R, Fredrickson JK, Tiedje JM, Nealson KH, Zhou J. Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean. International Journal of Systematic and Evolutionary Microbiology. 56: 1911-6. PMID 16902030 DOI: 10.1099/ijs.0.64354-0  1
2006 Vishnivetskaya TA, Petrova MA, Urbance J, Ponder M, Moyer CL, Gilichinsky DA, Tiedje JM. Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods. Astrobiology. 6: 400-14. PMID 16805696 DOI: 10.1089/ast.2006.6.400  1
2006 Bakermans C, Ayala-del-Río HL, Ponder MA, Vishnivetskaya T, Gilichinsky D, Thomashow MF, Tiedje JM. Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost. International Journal of Systematic and Evolutionary Microbiology. 56: 1285-91. PMID 16738105 DOI: 10.1099/ijs.0.64043-0  1
2006 Payne GW, Ramette A, Rose HL, Weightman AJ, Jones TH, Tiedje JM, Mahenthiralingam E. Application of a recA gene-based identification approach to the maize rhizosphere reveals novel diversity in Burkholderia species. Fems Microbiology Letters. 259: 126-32. PMID 16684112 DOI: 10.1111/j.1574-6968.2006.00257.x  1
2006 Rodrigues JL, Kachel CA, Aiello MR, Quensen JF, Maltseva OV, Tsoi TV, Tiedje JM. Degradation of aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. strain RHA1(fcb). Applied and Environmental Microbiology. 72: 2476-82. PMID 16597946 DOI: 10.1128/AEM.72.4.2476-2482.2006  1
2006 Rodrigues DF, Goris J, Vishnivetskaya T, Gilichinsky D, Thomashow MF, Tiedje JM. Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov. Extremophiles : Life Under Extreme Conditions. 10: 285-94. PMID 16489412 DOI: 10.1007/s00792-005-0497-5  1
2006 Wick LM, Rouillard JM, Whittam TS, Gulari E, Tiedje JM, Hashsham SA. On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Research. 34: e26. PMID 16478712 DOI: 10.1093/nar/gnj024  1
2006 Qiu X, Daly MJ, Vasilenko A, Omelchenko MV, Gaidamakova EK, Wu L, Zhou J, Sundin GW, Tiedje JM. Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation. Journal of Bacteriology. 188: 1199-204. PMID 16428429 DOI: 10.1128/JB.188.3.1199-1204.2006  1
2006 Denef VJ, Klappenbach JA, Patrauchan MA, Florizone C, Rodrigues JL, Tsoi TV, Verstraete W, Eltis LD, Tiedje JM. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Applied and Environmental Microbiology. 72: 585-95. PMID 16391095 DOI: 10.1128/AEM.72.1.585-595.2006  1
2005 Gilichinsky D, Rivkina E, Bakermans C, Shcherbakova V, Petrovskaya L, Ozerskaya S, Ivanushkina N, Kochkina G, Laurinavichuis K, Pecheritsina S, Fattakhova R, Tiedje JM. Biodiversity of cryopegs in permafrost. Fems Microbiology Ecology. 53: 117-28. PMID 16329934 DOI: 10.1016/j.femsec.2005.02.003  1
2005 Ponder MA, Gilmour SJ, Bergholz PW, Mindock CA, Hollingsworth R, Thomashow MF, Tiedje JM. Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria. Fems Microbiology Ecology. 53: 103-15. PMID 16329933 DOI: 10.1016/j.femsec.2004.12.003  1
2005 Denef VJ, Patrauchan MA, Florizone C, Park J, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD. Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400. Journal of Bacteriology. 187: 7996-8005. PMID 16291673 DOI: 10.1128/JB.187.23.7996-8005.2005  1
2005 Beliaev AS, Klingeman DM, Klappenbach JA, Wu L, Romine MF, Tiedje JM, Nealson KH, Fredrickson JK, Zhou J. Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. Journal of Bacteriology. 187: 7138-45. PMID 16199584 DOI: 10.1128/JB.187.20.7138-7145.2005  1
2005 Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. Journal of Bacteriology. 187: 6258-64. PMID 16159757 DOI: 10.1128/JB.187.18.6258-6264.2005  1
2005 Qiu X, Tiedje JM, Sundin GW. Genome-wide examination of the natural solar radiation response in Shewanella oneidensis MR-1. Photochemistry and Photobiology. 81: 1559-68. PMID 16022560 DOI: 10.1562/2005-04-15-RA-490  1
2005 Qiu X, Sundin GW, Wu L, Zhou J, Tiedje JM. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation. Journal of Bacteriology. 187: 3556-64. PMID 15866945 DOI: 10.1128/JB.187.10.3556-3564.2005  1
2005 Ramette A, LiPuma JJ, Tiedje JM. Species abundance and diversity of Burkholderia cepacia complex in the environment. Applied and Environmental Microbiology. 71: 1193-201. PMID 15746318 DOI: 10.1128/AEM.71.3.1193-1201.2005  1
2005 Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proceedings of the National Academy of Sciences of the United States of America. 102: 2567-72. PMID 15701695 DOI: 10.1073/pnas.0409727102  1
2005 Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, ... ... Tiedje JM, et al. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proceedings of the National Academy of Sciences of the United States of America. 102: 2099-104. PMID 15684069 DOI: 10.1073/pnas.0409111102  1
2005 Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Research. 33: D294-6. PMID 15608200 DOI: 10.1093/nar/gki038  1
2005 Snow AA, Andow DA, Gepts P, Hallerman EM, Power A, Tiedje JM, Wolfenbarger LL. Genetically engineered organisms and the environment: Current status and recommendations Ecological Applications. 15: 377-404.  1
2004 Wu L, Thompson DK, Liu X, Fields MW, Bagwell CE, Tiedje JM, Zhou J. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environmental Science & Technology. 38: 6775-82. PMID 15669338 DOI: 10.1021/es049508i  1
2004 Qiu X, Sundin GW, Chai B, Tiedje JM. Survival of Shewanella oneidensis MR-1 after UV radiation exposure. Applied and Environmental Microbiology. 70: 6435-43. PMID 15528503 DOI: 10.1128/AEM.70.11.6435-6443.2004  1
2004 Hashsham SA, Wick LM, Rouillard JM, Gulari E, Tiedje JM. Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. Biosensors & Bioelectronics. 20: 668-83. PMID 15522582 DOI: 10.1016/j.bios.2004.06.032  1
2004 Goris J, De Vos P, Caballero-Mellado J, Park J, Falsen E, Quensen JF, Tiedje JM, Vandamme P. Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov. International Journal of Systematic and Evolutionary Microbiology. 54: 1677-81. PMID 15388727 DOI: 10.1099/ijs.0.63101-0  1
2004 Griffin BM, Tiedje JM, Löffler FE. Anaerobic microbial reductive dechlorination of tetrachloroethene to predominately trans-1,2-dichloroethene. Environmental Science & Technology. 38: 4300-3. PMID 15382856 DOI: 10.1021/es035439g  1
2004 Qiu XY, Hurt RA, Wu LY, Chen CH, Tiedje JM, Zhou JZ. Detection and quantification of copper-denitrifying bacteria by quantitative competitive PCR. Journal of Microbiological Methods. 59: 199-210. PMID 15369856 DOI: 10.1016/j.mimet.2004.07.008  1
2004 Denef VJ, Park J, Tsoi TV, Rouillard JM, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM. Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Applied and Environmental Microbiology. 70: 4961-70. PMID 15294836 DOI: 10.1128/AEM.70.8.4961-4970.2004  1
2004 Ayala-Del-Río HL, Callister SJ, Criddle CS, Tiedje JM. Correspondence between community structure and function during succession in phenol- and phenol-plus-trichloroethene-fed sequencing batch reactors. Applied and Environmental Microbiology. 70: 4950-60. PMID 15294835 DOI: 10.1128/AEM.70.8.4950-4960.2004  1
2004 Zhou J, Xia B, Huang H, Palumbo AV, Tiedje JM. Microbial diversity and heterogeneity in sandy subsurface soils. Applied and Environmental Microbiology. 70: 1723-34. PMID 15006798 DOI: 10.1128/AEM.70.3.1723-1734.2004  1
2004 Konstantinidis KT, Tiedje JM. Trends between gene content and genome size in prokaryotic species with larger genomes. Proceedings of the National Academy of Sciences of the United States of America. 101: 3160-5. PMID 14973198 DOI: 10.1073/pnas.0308653100  1
2004 Stres B, Mahne I, Avgustin G, Tiedje JM. Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils. Applied and Environmental Microbiology. 70: 301-9. PMID 14711656 DOI: 10.1128/AEM.70.1.301-309.2004  1
2003 Dollhopf SL, Pariseau ML, Hashsham SA, Tiedje JM. Competitive and interactions affecting a fermentative spirochete in anaerobic chemostats. Microbial Ecology. 46: 1-11. PMID 14582492  0.72
2003 Denef VJ, Park J, Rodrigues JL, Tsoi TV, Hashsham SA, Tiedje JM. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environmental Microbiology. 5: 933-43. PMID 14510847 DOI: 10.1046/j.1462-2920.2003.00490.x  1
2003 Dorofeeva LV, Krausova VI, Evtushenko LI, Tiedje JM. Agromyces albus sp. nov., isolated from a plant (Androsace sp.). International Journal of Systematic and Evolutionary Microbiology. 53: 1435-8. PMID 13130029 DOI: 10.1099/ijs.0.02428-0  1
2003 Liu X, Tiquia SM, Holguin G, Wu L, Nold SC, Devol AH, Luo K, Palumbo AV, Tiedje JM, Zhou J. Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico. Applied and Environmental Microbiology. 69: 3549-60. PMID 12788762  1
2003 Braker G, Tiedje JM. Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Applied and Environmental Microbiology. 69: 3476-83. PMID 12788753  1
2003 Sung Y, Ritalahti KM, Sanford RA, Urbance JW, Flynn SJ, Tiedje JM, Löffler FE. Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov. Applied and Environmental Microbiology. 69: 2964-74. PMID 12732573 DOI: 10.1128/AEM.69.5.2964-2974.2003  1
2003 Yan T, Fields MW, Wu L, Zu Y, Tiedje JM, Zhou J. Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environmental Microbiology. 5: 13-24. PMID 12542709  0.32
2003 Urbance JW, Cole J, Saxman P, Tiedje JM. BSD: the Biodegradative Strain Database. Nucleic Acids Research. 31: 152-5. PMID 12519970  0.32
2003 Treves DS, Xia B, Zhou J, Tiedje JM. A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil Microbial Ecology. 45: 20-28. PMID 12415419 DOI: 10.1007/s00248-002-1044-x  1
2003 Zhou J, Xia B, Huang H, Treves DS, Hauser LJ, Mural RJ, Palumbo AV, Tiedje JM. Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils Soil Biology and Biochemistry. 35: 915-924. DOI: 10.1016/S0038-0717(03)00124-X  1
2002 Sun B, Griffin BM, Ayala-del-Río HL, Hashsham SA, Tiedje JM. Microbial dehalorespiration with 1,1,1-trichloroethane. Science (New York, N.Y.). 298: 1023-5. PMID 12411705 DOI: 10.1126/science.1074675  1
2002 He J, Sung Y, Dollhopf ME, Fathepure BZ, Tiedje JM, Löffler FE. Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites. Environmental Science & Technology. 36: 3945-52. PMID 12269747 DOI: 10.1021/es025528d  1
2002 Rodrigues JL, Aiello MR, Urbance JW, Tsoi TV, Tiedje JM. Use of both 16S rRNA and engineered functional genes with real-time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil. Journal of Microbiological Methods. 51: 181-9. PMID 12133610  0.64
2002 Itoh K, Kanda R, Sumita Y, Kim H, Kamagata Y, Suyama K, Yamamoto H, Hausinger RP, Tiedje JM. tfdA-like genes in 2,4-dichlorophenoxyacetic acid-degrading bacteria belonging to the Bradyrhizobium-Agromonas-Nitrobacter-Afipia cluster in alpha-Proteobacteria. Applied and Environmental Microbiology. 68: 3449-54. PMID 12089027 DOI: 10.1128/AEM.68.7.3449-3454.2002  1
2002 Beliaev AS, Thompson DK, Khare T, Lim H, Brandt CC, Li G, Murray AE, Heidelberg JF, Giometti CS, Yates J, Nealson KH, Tiedje JM, Zhoui J. Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors. Omics : a Journal of Integrative Biology. 6: 39-60. PMID 11881834  1
2002 Cho JC, Tiedje JM. Quantitative detection of microbial genes by using DNA microarrays. Applied and Environmental Microbiology. 68: 1425-30. PMID 11872496 DOI: 10.1128/AEM.68.3.1425-1430.2002  1
2002 Dedysh SN, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Liesack W, Tiedje JM. Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. International Journal of Systematic and Evolutionary Microbiology. 52: 251-61. PMID 11837310 DOI: 10.1099/00207713-52-1-251  1
2002 Sanford RA, Cole JR, Tiedje JM. Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Applied and Environmental Microbiology. 68: 893-900. PMID 11823233 DOI: 10.1128/AEM.68.2.893-900.2002  1
2001 Dollhopf SL, Hashsham SA, Tiedje JM. Interpreting 16S rDNA T-RFLP Data: Application of Self-Organizing Maps and Principal Component Analysis to Describe Community Dynamics and Convergence. Microbial Ecology. 42: 495-505. PMID 12024232 DOI: 10.1007/s00248-001-0027-7  1
2001 Hurt RA, Qiu X, Wu L, Roh Y, Palumbo AV, Tiedje JM, Zhou J. Simultaneous recovery of RNA and DNA from soils and sediments. Applied and Environmental Microbiology. 67: 4495-503. PMID 11571148 DOI: 10.1128/AEM.67.10.4495-4503.2001  1
2001 Dollhopf SL, Hashsham SA, Dazzo FB, Hickey RF, Criddle CS, Tiedje JM. The impact of fermentative organisms on carbon flow in methanogenic systems under constant low-substrate conditions. Applied Microbiology and Biotechnology. 56: 531-8. PMID 11549033 DOI: 10.1007/s002530100612  1
2001 Rodrigues JL, Maltseva OV, Tsoi TV, Helton RR, Quensen JF, Fukuda M, Tiedje JM. Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of PCBs. Environmental Science & Technology. 35: 663-8. PMID 11349275 DOI: 10.1021/es001308t  1
2001 Braker G, Ayala-del-Río HL, Devol AH, Fesefeldt A, Tiedje JM. Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Applied and Environmental Microbiology. 67: 1893-901. PMID 11282647 DOI: 10.1128/AEM.67.4.1893-1901.2001  1
2001 Qiu X, Wu L, Huang H, McDonel PE, Palumbo AV, Tiedje JM, Zhou J. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Applied and Environmental Microbiology. 67: 880-7. PMID 11157258 DOI: 10.1128/AEM.67.2.880-887.2001  1
2001 Grüntzig V, Nold SC, Zhou J, Tiedje JM. Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR. Applied and Environmental Microbiology. 67: 760-8. PMID 11157241 DOI: 10.1128/AEM.67.2.760-768.2001  0.32
2000 Fernandez AS, Hashsham SA, Dollhopf SL, Raskin L, Glagoleva O, Dazzo FB, Hickey RF, Criddle CS, Tiedje JM. Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Applied and Environmental Microbiology. 66: 4058-67. PMID 10966429 DOI: 10.1128/AEM.66.9.4058-4067.2000  1
2000 Hashsham SA, Fernandez AS, Dollhopf SL, Dazzo FB, Hickey RF, Tiedje JM, Criddle CS. Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose. Applied and Environmental Microbiology. 66: 4050-7. PMID 10966428 DOI: 10.1128/AEM.66.9.4050-4057.2000  1
1989 Jansson JK, Holben WE, Tiedje JM. Detection in soil of a deletion in an engineered DNA sequence by using DNA probes. Applied and Environmental Microbiology. 55: 3022-5. PMID 2624468  1
1988 Holben WE, Jansson JK, Chelm BK, Tiedje JM. DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community. Applied and Environmental Microbiology. 54: 703-711. PMID 16347582  1
1980 Firestone MK, Firestone RB, Tiedje JM. Nitrous oxide from soil denitrification: factors controlling its biological production. Science (New York, N.Y.). 208: 749-51. PMID 17771133 DOI: 10.1126/science.208.4445.749  0.96
1979 Firestone MK, Tiedje JM. Temporal change in nitrous oxide and dinitrogen from denitrification following onset of anaerobiosis. Applied and Environmental Microbiology. 38: 673-9. PMID 16345447  0.96
1979 Firestone MK, Firestone RB, Tiedje JM. Nitric oxide as an intermediate in denitrification: evidence from nitrogen-13 isotope exchange. Biochemical and Biophysical Research Communications. 91: 10-6. PMID 518609 DOI: 10.1016/0006-291X(79)90575-8  1
1978 Firestone MK, Tiedje JM. Pathway of degradation of nitrilotriacetate by a Pseudomonas species. Applied and Environmental Microbiology. 35: 955-61. PMID 655711  1
1978 Firestone MK, Aust SD, Tiedje JM. A nitrilotriacetic acid monooxygenase with conditional NADH-oxidase activity. Archives of Biochemistry and Biophysics. 190: 617-23. PMID 31137 DOI: 10.1016/0003-9861(78)90318-1  1
1975 Firestone MK, Tiedje JM. Biodegradation of metal-nitrilotriacetate complexes by a Pseudomonas species: mechanism of reaction. Applied Microbiology. 29: 758-64. PMID 1155932  1
1970 Duxbury JM, Tiedje JM, Alexander M, Dawson JE. 2,4-D metabolism: Enzymatic conversion of chloromaleylacetic acid to succinic acid Journal of Agricultural and Food Chemistry. 18: 199-201. PMID 4400316  1
1969 Tiedje JM, Alexander M. Enzymic cleavage of the ether bond of 2,4-dichlorophenoxyacetate. Journal of Agricultural and Food Chemistry. 17: 1080-4. PMID 21428356 DOI: 10.1021/jf60165a012  1
1969 Tiedje JM, Duxbury JM, Alexander M, Dawson JE. 2,4-D metabolism: pathway of degradation of chlorocatechols by Arthrobacter sp. Journal of Agricultural and Food Chemistry. 17: 1021-6. PMID 21428341 DOI: 10.1021/jf60165a037  1
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