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Items: 1 to 50 of 161

1.

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

Zomorrodi AR, Segrè D.

Nat Commun. 2017 Nov 16;8(1):1563. doi: 10.1038/s41467-017-01407-5.

2.

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity.

Reznik E, Christodoulou D, Goldford JE, Briars E, Sauer U, Segrè D, Noor E.

Cell Rep. 2017 Sep 12;20(11):2666-2677. doi: 10.1016/j.celrep.2017.08.066.

3.

Remnants of an Ancient Metabolism without Phosphate.

Goldford JE, Hartman H, Smith TF, Segrè D.

Cell. 2017 Mar 9;168(6):1126-1134.e9. doi: 10.1016/j.cell.2017.02.001. Epub 2017 Mar 2.

4.

Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates.

Jacobs C, Lambourne L, Xia Y, Segrè D.

PLoS One. 2017 Jan 20;12(1):e0170164. doi: 10.1371/journal.pone.0170164. eCollection 2017.

5.

Mapping the landscape of metabolic goals of a cell.

Zhao Q, Stettner AI, Reznik E, Paschalidis ICh, Segrè D.

Genome Biol. 2016 May 23;17(1):109. doi: 10.1186/s13059-016-0968-2.

6.

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

Granger BR, Chang YC, Wang Y, DeLisi C, Segrè D, Hu Z.

PLoS Comput Biol. 2016 Apr 15;12(4):e1004875. doi: 10.1371/journal.pcbi.1004875. eCollection 2016 Apr.

7.

Author's reply to the letter of Doll et al.

Segre D, Pozzo M, Perinotti R, Roche B.

Tech Coloproctol. 2016 Apr;20(4):265-6. doi: 10.1007/s10151-016-1431-9. Epub 2016 Feb 5. No abstract available.

PMID:
26850763
8.

Synthetic Ecology of Microbes: Mathematical Models and Applications.

Zomorrodi AR, Segrè D.

J Mol Biol. 2016 Feb 27;428(5 Pt B):837-61. doi: 10.1016/j.jmb.2015.10.019. Epub 2015 Nov 11. Review.

9.

The treatment of pilonidal disease: guidelines of the Italian Society of Colorectal Surgery (SICCR).

Segre D, Pozzo M, Perinotti R, Roche B; Italian Society of Colorectal Surgery.

Tech Coloproctol. 2015 Oct;19(10):607-13. doi: 10.1007/s10151-015-1369-3. Epub 2015 Sep 16.

PMID:
26377583
10.

Species interactions differ in their genetic robustness.

Chubiz LM, Granger BR, Segrè D, Harcombe WR.

Front Microbiol. 2015 Apr 14;6:271. doi: 10.3389/fmicb.2015.00271. eCollection 2015.

11.

Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli.

Sridhara V, Meyer AG, Rai P, Barrick JE, Ravikumar P, Segrè D, Wilke CO.

PLoS One. 2014 Dec 12;9(12):e114608. doi: 10.1371/journal.pone.0114608. eCollection 2014.

12.

Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY.

Brinsmade SR, Alexander EL, Livny J, Stettner AI, Segrè D, Rhee KY, Sonenshein AL.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8227-32. doi: 10.1073/pnas.1321308111. Epub 2014 May 19.

13.

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics.

Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, Bonilla G, Kar A, Leiby N, Mehta P, Marx CJ, Segrè D.

Cell Rep. 2014 May 22;7(4):1104-15. doi: 10.1016/j.celrep.2014.03.070. Epub 2014 May 1.

14.

Resource competition may lead to effective treatment of antibiotic resistant infections.

Gomes AL, Galagan JE, Segrè D.

PLoS One. 2013 Dec 13;8(12):e80775. doi: 10.1371/journal.pone.0080775. eCollection 2013.

15.

Metabolic proximity in the order of colonization of a microbial community.

Mazumdar V, Amar S, Segrè D.

PLoS One. 2013 Oct 30;8(10):e77617. doi: 10.1371/journal.pone.0077617. eCollection 2013.

16.

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.

17.

Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools.

Reznik E, Mehta P, Segrè D.

PLoS Comput Biol. 2013;9(8):e1003195. doi: 10.1371/journal.pcbi.1003195. Epub 2013 Aug 29.

18.

The average enzyme principle.

Reznik E, Chaudhary O, Segrè D.

FEBS Lett. 2013 Sep 2;587(17):2891-4. doi: 10.1016/j.febslet.2013.07.032. Epub 2013 Jul 23.

19.

The cost of efficiency in energy metabolism.

Stettner AI, Segrè D.

Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9629-30. doi: 10.1073/pnas.1307485110. Epub 2013 May 31. No abstract available.

20.

The dynamics of hybrid metabolic-genetic oscillators.

Reznik E, Kaper TJ, Segrè D.

Chaos. 2013 Mar;23(1):013132. doi: 10.1063/1.4793573.

PMID:
23556969
21.

Intelligence and psychopathy: a correlational study on insane female offenders.

Spironelli C, Segrè D, Stegagno L, Angrilli A.

Psychol Med. 2014 Jan;44(1):111-6. doi: 10.1017/S0033291713000615. Epub 2013 Apr 3.

PMID:
23551975
22.

Invariance and optimality in the regulation of an enzyme.

Reznik E, Yohe S, Segrè D.

Biol Direct. 2013 Mar 22;8:7. doi: 10.1186/1745-6150-8-7.

23.

Temporal expression-based analysis of metabolism.

Collins SB, Reznik E, Segrè D.

PLoS Comput Biol. 2012;8(11):e1002781. doi: 10.1371/journal.pcbi.1002781. Epub 2012 Nov 29.

24.

Comparative multi-goal tradeoffs in systems engineering of microbial metabolism.

Byrne D, Dumitriu A, Segrè D.

BMC Syst Biol. 2012 Sep 26;6:127. doi: 10.1186/1752-0509-6-127.

25.

Epistasis from functional dependence of fitness on underlying traits.

Chiu HC, Marx CJ, Segrè D.

Proc Biol Sci. 2012 Oct 22;279(1745):4156-64. doi: 10.1098/rspb.2012.1449. Epub 2012 Aug 15.

26.

Organization principles in genetic interaction networks.

Jacobs C, Segrè D.

Adv Exp Med Biol. 2012;751:53-78. doi: 10.1007/978-1-4614-3567-9_3. Review.

PMID:
22821453
27.

Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S.

PLoS One. 2012;7(6):e37919. doi: 10.1371/journal.pone.0037919. Epub 2012 Jun 4.

28.

Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis.

Beg QK, Zampieri M, Klitgord N, Collins SB, Altafini C, Serres MH, Segrè D.

Nucleic Acids Res. 2012 Aug;40(15):7132-49. doi: 10.1093/nar/gks467. Epub 2012 May 25.

29.

Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor.

Rosenbaum MA, Bar HY, Beg QK, Segrè D, Booth J, Cotta MA, Angenent LT.

PLoS One. 2012;7(2):e30827. doi: 10.1371/journal.pone.0030827. Epub 2012 Feb 1.

30.

A system-level approach for deciphering the transcriptional response to prion infection.

Zampieri M, Legname G, Segrè D, Altafini C.

Bioinformatics. 2011 Dec 15;27(24):3407-14. doi: 10.1093/bioinformatics/btr580. Epub 2011 Oct 20.

PMID:
22016408
31.

Diminishing returns epistasis among beneficial mutations decelerates adaptation.

Chou HH, Chiu HC, Delaney NF, Segrè D, Marx CJ.

Science. 2011 Jun 3;332(6034):1190-2. doi: 10.1126/science.1203799.

32.

Ecosystems biology of microbial metabolism.

Klitgord N, Segrè D.

Curr Opin Biotechnol. 2011 Aug;22(4):541-6. doi: 10.1016/j.copbio.2011.04.018. Epub 2011 May 16. Review.

PMID:
21592777
33.

Epistatic interaction maps relative to multiple metabolic phenotypes.

Snitkin ES, Segrè D.

PLoS Genet. 2011 Feb 10;7(2):e1001294. doi: 10.1371/journal.pgen.1001294.

34.

Modeling the complex dynamics of enzyme-pathway coevolution.

Schütte M, Skupin A, Segrè D, Ebenhöh O.

Chaos. 2010 Dec;20(4):045115. doi: 10.1063/1.3530440.

PMID:
21198127
35.

Environments that induce synthetic microbial ecosystems.

Klitgord N, Segrè D.

PLoS Comput Biol. 2010 Nov 18;6(11):e1001002. doi: 10.1371/journal.pcbi.1001002.

36.

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.

Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S.

Nucleic Acids Res. 2011 Jan;39(Database issue):D11-4. doi: 10.1093/nar/gkq1168. Epub 2010 Nov 21.

37.

Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor.

Rosenbaum MA, Bar HY, Beg QK, Segrè D, Booth J, Cotta MA, Angenent LT.

Bioresour Technol. 2011 Feb;102(3):2623-8. doi: 10.1016/j.biortech.2010.10.033. Epub 2010 Oct 12.

PMID:
21036604
38.

On the stability of metabolic cycles.

Reznik E, Segrè D.

J Theor Biol. 2010 Oct 21;266(4):536-49. doi: 10.1016/j.jtbi.2010.07.023. Epub 2010 Jul 29.

39.

Introduction to focus issue: genetic interactions.

Segrè D, Marx CJ.

Chaos. 2010 Jun;20(2):026101. doi: 10.1063/1.3456057.

40.

Signatures of arithmetic simplicity in metabolic network architecture.

Riehl WJ, Krapivsky PL, Redner S, Segrè D.

PLoS Comput Biol. 2010 Apr 1;6(4):e1000725. doi: 10.1371/journal.pcbi.1000725.

41.

Co-evolution of metabolism and protein sequences.

Schütte M, Klitgord N, Segrè D, Ebenhöh O.

Genome Inform. 2010 Jan;22:156-66.

42.
43.

Metabolic network model of a human oral pathogen.

Mazumdar V, Snitkin ES, Amar S, Segrè D.

J Bacteriol. 2009 Jan;191(1):74-90. doi: 10.1128/JB.01123-08. Epub 2008 Oct 17.

44.

Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions.

Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segrè D.

Genome Biol. 2008;9(9):R140. doi: 10.1186/gb-2008-9-9-r140. Epub 2008 Sep 22.

45.
46.

Categorization and evaluation of emotional faces in psychopathic women.

Eisenbarth H, Alpers GW, Segrè D, Calogero A, Angrilli A.

Psychiatry Res. 2008 May 30;159(1-2):189-95. doi: 10.1016/j.psychres.2007.09.001. Epub 2008 Apr 18.

PMID:
18423614
47.

Ligasure Precise vs. conventional diathermy for Milligan-Morgan hemorrhoidectomy: a prospective, randomized, multicenter trial.

Altomare DF, Milito G, Andreoli R, Arcanà F, Tricomi N, Salafia C, Segre D, Pecorella G, Pulvirenti d'Urso A, Cracco N, Giovanardi G, Romano G; Ligasure for Hemorrhoids Study Group.

Dis Colon Rectum. 2008 May;51(5):514-9. doi: 10.1007/s10350-007-9171-6. Epub 2008 Jan 30.

PMID:
18231834
48.
49.

Optimal metabolic regulation using a constraint-based model.

Riehl WJ, Segrè D.

Genome Inform. 2008;20:159-70.

50.

Optimality criteria for the prediction of metabolic fluxes in yeast mutants.

Snitkin ES, Segrè D.

Genome Inform. 2008;20:123-34.

PMID:
19425128

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