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Increased microbiota diversity associated with higher FEV0.5 in infants.

Kloepfer KM, Ross SE, Hemmerich CM, Slaven JE, Rusch DB, Davis SD.

Pediatr Pulmonol. 2020 Jan;55(1):27-29. doi: 10.1002/ppul.24559. Epub 2019 Nov 5. No abstract available.


Diversity in Natural Transformation Frequencies and Regulation across Vibrio Species.

Simpson CA, Podicheti R, Rusch DB, Dalia AB, van Kessel JC.

mBio. 2019 Dec 17;10(6). pii: e02788-19. doi: 10.1128/mBio.02788-19.


Global H-NS counter-silencing by LuxR activates quorum sensing gene expression.

Chaparian RR, Tran MLN, Miller Conrad LC, Rusch DB, van Kessel JC.

Nucleic Acids Res. 2020 Jan 10;48(1):171-183. doi: 10.1093/nar/gkz1089.


The neurogenomic transition from territory establishment to parenting in a territorial female songbird.

Bentz AB, Rusch DB, Buechlein A, Rosvall KA.

BMC Genomics. 2019 Nov 7;20(1):819. doi: 10.1186/s12864-019-6202-3.


Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly.

Bentz AB, Thomas GWC, Rusch DB, Rosvall KA.

Sci Rep. 2019 Nov 1;9(1):15849. doi: 10.1038/s41598-019-52312-4.


Transcriptome Profiling Reveals Matrisome Alteration as a Key Feature of Ovarian Cancer Progression.

Mitra S, Tiwari K, Podicheti R, Pandhiri T, Rusch DB, Bonetto A, Zhang C, Mitra AK.

Cancers (Basel). 2019 Oct 9;11(10). pii: E1513. doi: 10.3390/cancers11101513.


DNA methyltransferase inhibition reduces inflammation-induced colon tumorigenesis.

Maiuri AR, Savant SS, Podicheti R, Rusch DB, O'Hagan HM.

Epigenetics. 2019 Dec;14(12):1209-1223. doi: 10.1080/15592294.2019.1634986. Epub 2019 Jun 26.


Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota.

McKay LJ, Dlakić M, Fields MW, Delmont TO, Eren AM, Jay ZJ, Klingelsmith KB, Rusch DB, Inskeep WP.

Nat Microbiol. 2019 Apr;4(4):614-622. doi: 10.1038/s41564-019-0362-4. Epub 2019 Mar 4.


Flagellar Mutants Have Reduced Pilus Synthesis in Caulobacter crescentus.

Ellison CK, Rusch DB, Brun YV.

J Bacteriol. 2019 Aug 22;201(18). pii: e00031-19. doi: 10.1128/JB.00031-19. Print 2019 Sep 15.


Redefining the Small Regulatory RNA Transcriptome in Streptococcus pneumoniae Serotype 2 Strain D39.

Sinha D, Zimmer K, Cameron TA, Rusch DB, Winkler ME, De Lay NR.

J Bacteriol. 2019 Jun 21;201(14). pii: e00764-18. doi: 10.1128/JB.00764-18. Print 2019 Jul 15.


Microbial mechanisms and ecosystem flux estimation for aerobic NOy emissions from deciduous forest soils.

Mushinski RM, Phillips RP, Payne ZC, Abney RB, Jo I, Fei S, Pusede SE, White JR, Rusch DB, Raff JD.

Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2138-2145. doi: 10.1073/pnas.1814632116. Epub 2019 Jan 18.


Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats.

Jay ZJ, Beam JP, Dlakić M, Rusch DB, Kozubal MA, Inskeep WP.

Nat Microbiol. 2018 Jun;3(6):732-740. doi: 10.1038/s41564-018-0163-1. Epub 2018 May 14.


Promoter Boundaries for the luxCDABE and betIBA-proXWV Operons in Vibrio harveyi Defined by the Method Rapid Arbitrary PCR Insertion Libraries (RAIL).

Hustmyer CM, Simpson CA, Olney SG, Rusch DB, Bochman ML, van Kessel JC.

J Bacteriol. 2018 May 9;200(11). pii: e00724-17. doi: 10.1128/JB.00724-17. Print 2018 Jun 1.


In children, the microbiota of the nasopharynx and bronchoalveolar lavage fluid are both similar and different.

Kloepfer KM, Deschamp AR, Ross SE, Peterson-Carmichael SL, Hemmerich CM, Rusch DB, Davis SD.

Pediatr Pulmonol. 2018 Apr;53(4):475-482. doi: 10.1002/ppul.23953. Epub 2018 Feb 6.


RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis.

McKinlay A, Podicheti R, Wendte JM, Cocklin R, Rusch DB.

RNA Biol. 2018 Feb 1;15(2):269-279. doi: 10.1080/15476286.2017.1409930. Epub 2017 Dec 21.


Genes linked to species diversity in a sexually dimorphic communication signal in electric fish.

Smith GT, Proffitt MR, Smith AR, Rusch DB.

J Comp Physiol A Neuroethol Sens Neural Behav Physiol. 2018 Jan;204(1):93-112. doi: 10.1007/s00359-017-1223-3. Epub 2017 Oct 20.


Complete Genome Sequence of the Pathogenic Vibrio vulnificus Type Strain ATCC 27562.

Rusch DB, Rowe-Magnus DA.

Genome Announc. 2017 Aug 31;5(35). pii: e00907-17. doi: 10.1128/genomeA.00907-17.


Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.

Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, Stoiber MH, Spanier KI, Gilbert D, Jansen M, Rusch DB, Pfrender ME, Colbourne JK, Frilander MJ, Kvist J, Decaestecker E, De Schamphelaere KAC, De Meester L.

Mol Ecol. 2018 Feb;27(4):886-897. doi: 10.1111/mec.14261. Epub 2017 Aug 19.


Mismatch Repair Proteins Initiate Epigenetic Alterations during Inflammation-Driven Tumorigenesis.

Maiuri AR, Peng M, Podicheti R, Sriramkumar S, Kamplain CM, Rusch DB, DeStefano Shields CE, Sears CL, O'Hagan HM.

Cancer Res. 2017 Jul 1;77(13):3467-3478. doi: 10.1158/0008-5472.CAN-17-0056. Epub 2017 May 18. Erratum in: Cancer Res. 2018 Jan 15;78(2):584.


Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rusch DB, Decaestecker E, Asselman J, De Schamphelaere KA, Ebert D, Haag CR, Kvist J, Laforsch C, Petrusek A, Beckerman AP, Little TJ, Chaturvedi A, Pfrender ME, De Meester L, Frilander MJ.

Sci Data. 2017 Jan 31;4:170006. doi: 10.1038/sdata.2017.6. No abstract available.


MicroRNA-335-5p and -3p synergize to inhibit estrogen receptor alpha expression and promote tamoxifen resistance.

Martin EC, Conger AK, Yan TJ, Hoang VT, Miller DF, Buechlein A, Rusch DB, Nephew KP, Collins-Burow BM, Burow ME.

FEBS Lett. 2017 Jan;591(2):382-392. doi: 10.1002/1873-3468.12538. Epub 2017 Jan 12.


Complete Transcriptome RNA-Seq.

Miller DF, Yan P, Fang F, Buechlein A, Kroll K, Frankhouser D, Stump C, Stump P, Ford JB, Tang H, Michaels S, Matei D, Huang TH, Chien J, Liu Y, Rusch DB, Nephew KP.

Methods Mol Biol. 2017;1513:141-162.


Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.

Llorens-Marès T, Liu Z, Allen LZ, Rusch DB, Craig MT, Dupont CL, Bryant DA, Casamayor EO.

ISME J. 2017 Jan;11(1):201-211. doi: 10.1038/ismej.2016.93. Epub 2016 Jul 8.


Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

Díez B, Nylander JA, Ininbergs K, Dupont CL, Allen AE, Yooseph S, Rusch DB, Bergman B.

PLoS One. 2016 May 19;11(5):e0155757. doi: 10.1371/journal.pone.0155757. eCollection 2016.


Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rusch DB, Decaestecker E, Asselman J, De Schamphelaere KA, Ebert D, Haag CR, Kvist J, Laforsch C, Petrusek A, Beckerman AP, Little TJ, Chaturvedi A, Pfrender ME, De Meester L, Frilander MJ.

Sci Data. 2016 May 10;3:160030. doi: 10.1038/sdata.2016.30. Erratum in: Sci Data. 2017 Jan 31;4:170006. Rush, Douglas [corrected to Rusch, Douglas B].


The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park.

Jay ZJ, Beam JP, Kozubal MA, Jennings RD, Rusch DB, Inskeep WP.

Environ Microbiol. 2016 Dec;18(12):4755-4769. doi: 10.1111/1462-2920.13366. Epub 2016 May 30.


Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes.

Colman DR, Jay ZJ, Inskeep WP, Jennings Rd, Maas KR, Rusch DB, Takacs-Vesbach CD.

Front Microbiol. 2016 Mar 15;7:304. doi: 10.3389/fmicb.2016.00304. eCollection 2016.


Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat.

Melendrez MC, Becraft ED, Wood JM, Olsen MT, Bryant DA, Heidelberg JF, Rusch DB, Cohan FM, Ward DM.

Front Microbiol. 2016 Jan 14;6:1540. doi: 10.3389/fmicb.2015.01540. eCollection 2015.


DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila.

Liu J, Zimmer K, Rusch DB, Paranjape N, Podicheti R, Tang H, Calvi BR.

Nucleic Acids Res. 2015 Oct 15;43(18):8746-61. doi: 10.1093/nar/gkv766. Epub 2015 Jul 30.


The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat.

Olsen MT, Nowack S, Wood JM, Becraft ED, LaButti K, Lipzen A, Martin J, Schackwitz WS, Rusch DB, Cohan FM, Bryant DA, Ward DM.

Front Microbiol. 2015 Jun 23;6:604. doi: 10.3389/fmicb.2015.00604. eCollection 2015.


The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park.

Becraft ED, Wood JM, Rusch DB, Kühl M, Jensen SI, Bryant DA, Roberts DW, Cohan FM, Ward DM.

Front Microbiol. 2015 Jun 22;6:590. doi: 10.3389/fmicb.2015.00590. eCollection 2015.


Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community.

Beam JP, Jay ZJ, Schmid MC, Rusch DB, Romine MF, Jennings Rde M, Kozubal MA, Tringe SG, Wagner M, Inskeep WP.

ISME J. 2016 Jan;10(1):210-24. doi: 10.1038/ismej.2015.83. Epub 2015 Jul 3.


Dual regulation by microRNA-200b-3p and microRNA-200b-5p in the inhibition of epithelial-to-mesenchymal transition in triple-negative breast cancer.

Rhodes LV, Martin EC, Segar HC, Miller DF, Buechlein A, Rusch DB, Nephew KP, Burow ME, Collins-Burow BM.

Oncotarget. 2015 Jun 30;6(18):16638-52.


Concordance of bacterial communities of two tick species and blood of their shared rodent host.

Rynkiewicz EC, Hemmerich C, Rusch DB, Fuqua C, Clay K.

Mol Ecol. 2015 May;24(10):2566-79. doi: 10.1111/mec.13187. Epub 2015 Apr 22.


Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript.

Wheeler EC, Washburn MC, Major F, Rusch DB, Hundley HA.

RNA Biol. 2015;12(2):162-74. doi: 10.1080/15476286.2015.1017220.


Stranded Whole Transcriptome RNA-Seq for All RNA Types.

Miller DFB, Yan PX, Fang F, Buechlein A, Ford JB, Tang H, Huang TH, Burow ME, Liu Y, Rusch DB, Nephew KP.

Curr Protoc Hum Genet. 2015 Jan 20;84:11.14.1-11.14.23. doi: 10.1002/0471142905.hg1114s84.


Mapping RNA Sequences that Contact Viral Capsid Proteins in Virions.

Kao CC, Chuang E, Ford J, Huang J, Podicheti R, Rusch DB.

Bio Protoc. 2014 Jul 20;7(14). pii: e2398. doi: 10.21769/BioProtoc.2398.


Effects of the endocrine-disrupting chemical DDT on self-renewal and differentiation of human mesenchymal stem cells.

Strong AL, Shi Z, Strong MJ, Miller DF, Rusch DB, Buechlein AM, Flemington EK, McLachlan JA, Nephew KP, Burow ME, Bunnell BA.

Environ Health Perspect. 2015 Jan;123(1):42-8. doi: 10.1289/ehp.1408188. Epub 2014 Jul 11.


Saccharide breakdown and fermentation by the honey bee gut microbiome.

Lee FJ, Rusch DB, Stewart FJ, Mattila HR, Newton IL.

Environ Microbiol. 2015 Mar;17(3):796-815. doi: 10.1111/1462-2920.12526. Epub 2014 Jul 8.


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

Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B.

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


Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities.

Jay ZJ, Rusch DB, Tringe SG, Bailey C, Jennings RM, Inskeep WP.

Appl Environ Microbiol. 2014 Jan;80(1):294-305. doi: 10.1128/AEM.02860-13. Epub 2013 Oct 25.


Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments.

Klatt CG, Inskeep WP, Herrgard MJ, Jay ZJ, Rusch DB, Tringe SG, Niki Parenteau M, Ward DM, Boomer SM, Bryant DA, Miller SR.

Front Microbiol. 2013 Jun 3;4:106. doi: 10.3389/fmicb.2013.00106. eCollection 2013.


Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages.

Takacs-Vesbach C, Inskeep WP, Jay ZJ, Herrgard MJ, Rusch DB, Tringe SG, Kozubal MA, Hamamura N, Macur RE, Fouke BW, Reysenbach AL, McDermott TR, Jennings Rd, Hengartner NW, Xie G.

Front Microbiol. 2013 May 29;4:84. doi: 10.3389/fmicb.2013.00084. eCollection 2013.


Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.

Inskeep WP, Jay ZJ, Herrgard MJ, Kozubal MA, Rusch DB, Tringe SG, Macur RE, Jennings Rd, Boyd ES, Spear JR, Roberto FF.

Front Microbiol. 2013 May 15;4:95. doi: 10.3389/fmicb.2013.00095. eCollection 2013.


The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem.

Inskeep WP, Jay ZJ, Tringe SG, Herrgård MJ, Rusch DB; YNP Metagenome Project Steering Committee and Working Group Members.

Front Microbiol. 2013 May 6;4:67. doi: 10.3389/fmicb.2013.00067. eCollection 2013.


A new method for stranded whole transcriptome RNA-seq.

Miller DF, Yan PS, Buechlein A, Rodriguez BA, Yilmaz AS, Goel S, Lin H, Collins-Burow B, Rhodes LV, Braun C, Pradeep S, Rupaimoole R, Dalkilic M, Sood AK, Burow ME, Tang H, Huang TH, Liu Y, Rusch DB, Nephew KP.

Methods. 2013 Sep 15;63(2):126-34. doi: 10.1016/j.ymeth.2013.03.023. Epub 2013 Apr 1.


Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa.

Rusch DB, Lombardo MJ, Yee-Greenbaum J, Novotny M, Brinkac LM, Lasken RS, Dupont CL.

Genome Announc. 2013 Jan;1(1). pii: e00030-12. doi: 10.1128/genomeA.00030-12. Epub 2013 Jan 15.


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. 2013 Mar;7(3):622-34. doi: 10.1038/ismej.2012.132. Epub 2012 Nov 15.


'Candidatus Thermochlorobacter aerophilum:' an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics.

Liu Z, Klatt CG, Ludwig M, Rusch DB, Jensen SI, Kühl M, Ward DM, Bryant DA.

ISME J. 2012 Oct;6(10):1869-82. doi: 10.1038/ismej.2012.24. Epub 2012 Mar 29.

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