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Items: 1 to 50 of 117

1.

A sparse covarying unit that describes healthy and impaired human gut microbiota development.

Raman AS, Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Subramanian S, Kang G, Bessong PO, Lima AAM, Kosek MN, Petri WA Jr, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Huq S, Mostafa I, Islam M, Mahfuz M, Haque R, Ahmed T, Barratt MJ, Gordon JI.

Science. 2019 Jul 12;365(6449). pii: eaau4735. doi: 10.1126/science.aau4735.

PMID:
31296739
2.

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children.

Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Kung VL, Cheng J, Chen RY, Subramanian S, Cowardin CA, Meier MF, O'Donnell D, Talcott M, Spears LD, Semenkovich CF, Henrissat B, Giannone RJ, Hettich RL, Ilkayeva O, Muehlbauer M, Newgard CB, Sawyer C, Head RD, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Hossain MI, Islam M, Choudhury N, Sarker SA, Huq S, Mahmud I, Mostafa I, Mahfuz M, Barratt MJ, Ahmed T, Gordon JI.

Science. 2019 Jul 12;365(6449). pii: eaau4732. doi: 10.1126/science.aau4732.

PMID:
31296738
3.

Prebiotic Potential of Culinary Spices Used to Support Digestion and Bioabsorption.

Peterson CT, Rodionov DA, Iablokov SN, Pung MA, Chopra D, Mills PJ, Peterson SN.

Evid Based Complement Alternat Med. 2019 Jun 2;2019:8973704. doi: 10.1155/2019/8973704. eCollection 2019.

4.

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.

Rodionov DA, Arzamasov AA, Khoroshkin MS, Iablokov SN, Leyn SA, Peterson SN, Novichkov PS, Osterman AL.

Front Microbiol. 2019 Jun 12;10:1316. doi: 10.3389/fmicb.2019.01316. eCollection 2019.

5.

16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics.

Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN.

PLoS One. 2019 Mar 19;14(3):e0213869. doi: 10.1371/journal.pone.0213869. eCollection 2019.

6.

Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria.

Bouvier JT, Sernova NV, Ghasempur S, Rodionova IA, Vetting MW, Al-Obaidi NF, Almo SC, Gerlt JA, Rodionov DA.

J Bacteriol. 2018 Dec 20;201(2). pii: e00431-18. doi: 10.1128/JB.00431-18. Print 2019 Jan 15.

7.

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization.

Arzamasov AA, van Sinderen D, Rodionov DA.

Front Microbiol. 2018 Apr 24;9:776. doi: 10.3389/fmicb.2018.00776. eCollection 2018.

8.

Prediction of enzymatic pathways by integrative pathway mapping.

Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A.

Elife. 2018 Jan 29;7. pii: e31097. doi: 10.7554/eLife.31097.

9.

Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived Consortia.

Leyn SA, Maezato Y, Romine MF, Rodionov DA.

Front Microbiol. 2017 Jul 13;8:1304. doi: 10.3389/fmicb.2017.01304. eCollection 2017.

10.

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.

Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, Barratt MJ, Giannone RJ, Hettich RL, Osterman AL, Gordon JI.

Sci Transl Med. 2017 May 17;9(390). pii: eaal4069. doi: 10.1126/scitranslmed.aal4069.

11.

Comparative genomics and evolution of transcriptional regulons in Proteobacteria.

Leyn SA, Suvorova IA, Kazakov AE, Ravcheev DA, Stepanova VV, Novichkov PS, Rodionov DA.

Microb Genom. 2016 Jul 11;2(7):e000061. doi: 10.1099/mgen.0.000061. eCollection 2016 Jul.

12.

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities.

Romine MF, Rodionov DA, Maezato Y, Osterman AL, Nelson WC.

ISME J. 2017 Jun;11(6):1434-1446. doi: 10.1038/ismej.2017.2. Epub 2017 Feb 10.

13.

Elucidation of roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism.

Romine MF, Rodionov DA, Maezato Y, Anderson LN, Nandhikonda P, Rodionova IA, Carre A, Li X, Xu C, Clauss TR, Kim YM, Metz TO, Wright AT.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1205-E1214. doi: 10.1073/pnas.1612360114. Epub 2017 Jan 30.

14.

A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea.

Rodionova IA, Vetting MW, Li X, Almo SC, Osterman AL, Rodionov DA.

Nucleic Acids Res. 2017 Apr 20;45(7):3785-3799. doi: 10.1093/nar/gkw1331.

15.

A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea.

Rodionov DA, Leyn SA, Li X, Rodionova IA.

J Bacteriol. 2017 Jan 30;199(4). pii: e00743-16. doi: 10.1128/JB.00743-16. Print 2017 Feb 15.

16.

Identification and Regulation of Genes for Cobalamin Transport in the Cyanobacterium Synechococcus sp. Strain PCC 7002.

Pérez AA, Rodionov DA, Bryant DA.

J Bacteriol. 2016 Sep 9;198(19):2753-61. doi: 10.1128/JB.00476-16. Print 2016 Oct 1.

17.

Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin Riboswitch In Vivo.

Pérez AA, Liu Z, Rodionov DA, Li Z, Bryant DA.

J Bacteriol. 2016 Sep 9;198(19):2743-52. doi: 10.1128/JB.00475-16. Print 2016 Oct 1.

18.

Cpe1786/IscR of Clostridium perfringens represses expression of genes involved in Fe-S cluster biogenesis.

André G, Haudecoeur E, Courtois E, Monot M, Dupuy B, Rodionov DA, Martin-Verstraete I.

Res Microbiol. 2017 May;168(4):345-355. doi: 10.1016/j.resmic.2016.03.002. Epub 2016 Mar 26.

19.

Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children.

Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkaveya O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM, Fan YM, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Maleta KM, Newgard CB, Ashorn P, Dewey KG, Gordon JI.

Science. 2016 Feb 19;351(6275). pii: aad3311. doi: 10.1126/science.aad3311.

20.

Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus.

Khoroshkin MS, Leyn SA, Van Sinderen D, Rodionov DA.

Front Microbiol. 2016 Feb 9;7:120. doi: 10.3389/fmicb.2016.00120. eCollection 2016.

21.

Comparative genomics of pyridoxal 5'-phosphate-dependent transcription factor regulons in Bacteria.

Suvorova IA, Rodionov DA.

Microb Genom. 2016 Jan 18;2(1):e000047. doi: 10.1099/mgen.0.000047. eCollection 2016 Jan.

22.

Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections.

Zhang H, Ravcheev DA, Hu D, Zhang F, Gong X, Hao L, Cao M, Rodionov DA, Wang C, Feng Y.

Microbiologyopen. 2015 Dec;4(6):983-1000. doi: 10.1002/mbo3.307. Epub 2015 Nov 5.

23.

A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.

Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A.

Nucleic Acids Res. 2015 Dec 2;43(21):10546-59. doi: 10.1093/nar/gkv1005. Epub 2015 Oct 4.

24.

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides.

Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N, Henrissat B, Osterman AL, Gordon JI.

Science. 2015 Oct 2;350(6256):aac5992. doi: 10.1126/science.aac5992.

25.

Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota.

Leyn SA, Rodionova IA, Li X, Rodionov DA.

J Bacteriol. 2015 Jul;197(14):2383-91. doi: 10.1128/JB.00249-15. Epub 2015 May 4.

26.

Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC.

Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16.

27.

Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria.

Leyn SA, Suvorova IA, Kholina TD, Sherstneva SS, Novichkov PS, Gelfand MS, Rodionov DA.

PLoS One. 2014 Nov 20;9(11):e113714. doi: 10.1371/journal.pone.0113714. eCollection 2014.

28.

Comparative genomics of DtxR family regulons for metal homeostasis in Archaea.

Leyn SA, Rodionov DA.

J Bacteriol. 2015 Feb;197(3):451-8. doi: 10.1128/JB.02386-14. Epub 2014 Nov 17.

29.

Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum.

Rodionova IA, Li X, Plymale AE, Motamedchaboki K, Konopka AE, Romine MF, Fredrickson JK, Osterman AL, Rodionov DA.

Environ Microbiol Rep. 2015 Apr;7(2):204-10. doi: 10.1111/1758-2229.12227. Epub 2014 Dec 17.

PMID:
25345570
30.

Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH.

Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin AP, Wall JD.

J Bacteriol. 2015 Jan 1;197(1):29-39. doi: 10.1128/JB.02083-14. Epub 2014 Oct 13.

31.

Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum.

Zhang L, Nie X, Ravcheev DA, Rodionov DA, Sheng J, Gu Y, Yang S, Jiang W, Yang C.

J Bacteriol. 2014 Nov;196(22):3949-63. doi: 10.1128/JB.02037-14. Epub 2014 Sep 2.

32.

Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe.

Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJ, Thiele I.

J Bacteriol. 2014 Sep;196(18):3289-302. doi: 10.1128/JB.01780-14. Epub 2014 Jul 7.

33.

Transport of magnesium by a bacterial Nramp-related gene.

Shin JH, Wakeman CA, Goodson JR, Rodionov DA, Freedman BG, Senger RS, Winkler WC.

PLoS Genet. 2014 Jun 26;10(6):e1004429. doi: 10.1371/journal.pgen.1004429. eCollection 2014 Jun.

34.

Comparative genomics and evolution of regulons of the LacI-family transcription factors.

Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA.

Front Microbiol. 2014 Jun 11;5:294. doi: 10.3389/fmicb.2014.00294. eCollection 2014.

35.

Computational analysis of riboswitch-based regulation.

Sun EI, Rodionov DA.

Biochim Biophys Acta. 2014 Oct;1839(10):900-907. doi: 10.1016/j.bbagrm.2014.02.011. Epub 2014 Feb 28. Review.

36.

Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria.

Rodionova IA, Li X, Thiel V, Stolyar S, Stanton K, Fredrickson JK, Bryant DA, Osterman AL, Best AA, Rodionov DA.

Front Microbiol. 2013 Dec 23;4:407. doi: 10.3389/fmicb.2013.00407. eCollection 2013.

37.

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks.

Ravcheev DA, Godzik A, Osterman AL, Rodionov DA.

BMC Genomics. 2013 Dec 12;14:873. doi: 10.1186/1471-2164-14-873.

38.

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA.

BMC Genomics. 2013 Nov 1;14:745. doi: 10.1186/1471-2164-14-745.

39.

Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria.

Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin AP, Price MN, Rodionov DA.

Environ Microbiol. 2014 Jan;16(1):1-8. doi: 10.1111/1462-2920.12273. Epub 2013 Oct 9.

PMID:
24118949
40.

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.

Sun EI, Leyn SA, Kazanov MD, Saier MH Jr, Novichkov PS, Rodionov DA.

BMC Genomics. 2013 Sep 2;14:597. doi: 10.1186/1471-2164-14-597.

41.

The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

42.

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.

Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL.

Front Microbiol. 2013 Aug 23;4:244. doi: 10.3389/fmicb.2013.00244. eCollection 2013.

43.

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.

Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS.

J Bacteriol. 2013 Oct;195(19):4466-75. doi: 10.1128/JB.00679-13. Epub 2013 Aug 2.

44.

RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.

Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I.

BMC Genomics. 2013 Apr 2;14:213. doi: 10.1186/1471-2164-14-213.

45.

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.

Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov PS, Rodionov DA.

J Bacteriol. 2013 Jun;195(11):2463-73. doi: 10.1128/JB.00140-13. Epub 2013 Mar 15.

46.

Novel inositol catabolic pathway in Thermotoga maritima.

Rodionova IA, Leyn SA, Burkart MD, Boucher N, Noll KM, Osterman AL, Rodionov DA.

Environ Microbiol. 2013 Aug;15(8):2254-66. doi: 10.1111/1462-2920.12096. Epub 2013 Feb 27.

PMID:
23441918
47.

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria.

Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov PS, Rodionov DA.

BMC Genomics. 2013 Feb 12;14:94. doi: 10.1186/1471-2164-14-94.

48.

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.

Kazanov MD, Li X, Gelfand MS, Osterman AL, Rodionov DA.

Nucleic Acids Res. 2013 Jan;41(2):790-803. doi: 10.1093/nar/gks1184. Epub 2012 Dec 2.

49.

Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.

Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS.

J Bacteriol. 2013 Jan;195(1):29-38. doi: 10.1128/JB.01977-12. Epub 2012 Oct 19.

50.

Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile.

Antunes A, Camiade E, Monot M, Courtois E, Barbut F, Sernova NV, Rodionov DA, Martin-Verstraete I, Dupuy B.

Nucleic Acids Res. 2012 Nov;40(21):10701-18. doi: 10.1093/nar/gks864. Epub 2012 Sep 18.

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