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Items: 1 to 50 of 72

1.

Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains.

Rashid S, Long Z, Singh S, Kohram M, Vashistha H, Navlakha S, Salman H, Oltvai ZN, Bar-Joseph Z.

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11770-11775. doi: 10.1073/pnas.1816315116. Epub 2019 May 24.

PMID:
31127043
2.

Statin drugs to reduce breast cancer recurrence and mortality.

Beckwitt CH, Brufsky A, Oltvai ZN, Wells A.

Breast Cancer Res. 2018 Nov 20;20(1):144. doi: 10.1186/s13058-018-1066-z. Review.

3.

Statins attenuate outgrowth of breast cancer metastases.

Beckwitt CH, Clark AM, Ma B, Whaley D, Oltvai ZN, Wells A.

Br J Cancer. 2018 Oct;119(9):1094-1105. doi: 10.1038/s41416-018-0267-7. Epub 2018 Nov 7.

4.

Concomitant attenuation of HMG-CoA reductase expression potentiates the cancer cell growth-inhibitory effect of statins and expands their efficacy in tumor cells with epithelial characteristics.

Ishikawa T, Hosaka YZ, Beckwitt C, Wells A, Oltvai ZN, Warita K.

Oncotarget. 2018 Jun 29;9(50):29304-29315. doi: 10.18632/oncotarget.25448. eCollection 2018 Jun 29.

5.

Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors.

Singh M, Warita K, Warita T, Faeder JR, Lee REC, Sant S, Oltvai ZN.

Sci Rep. 2018 Jun 20;8(1):9388. doi: 10.1038/s41598-018-27266-8.

6.

Quantitative assessment of cell fate decision between autophagy and apoptosis.

Liu B, Oltvai ZN, Bayır H, Silverman GA, Pak SC, Perlmutter DH, Bahar I.

Sci Rep. 2017 Dec 14;7(1):17605. doi: 10.1038/s41598-017-18001-w.

7.

Biomarker identification for statin sensitivity of cancer cell lines.

Raghu VK, Beckwitt CH, Warita K, Wells A, Benos PV, Oltvai ZN.

Biochem Biophys Res Commun. 2018 Jan 1;495(1):659-665. doi: 10.1016/j.bbrc.2017.11.065. Epub 2017 Nov 14.

8.

Cell-cell communication enhances bacterial chemotaxis toward external attractants.

Long Z, Quaife B, Salman H, Oltvai ZN.

Sci Rep. 2017 Oct 9;7(1):12855. doi: 10.1038/s41598-017-13183-9.

9.

Macromolecular crowding explains overflow metabolism in cells.

Vazquez A, Oltvai ZN.

Sci Rep. 2016 Aug 3;6:31007. doi: 10.1038/srep31007.

10.

Statin-induced mevalonate pathway inhibition attenuates the growth of mesenchymal-like cancer cells that lack functional E-cadherin mediated cell cohesion.

Warita K, Warita T, Beckwitt CH, Schurdak ME, Vazquez A, Wells A, Oltvai ZN.

Sci Rep. 2014 Dec 23;4:7593. doi: 10.1038/srep07593.

11.

BalestraWeb: efficient online evaluation of drug-target interactions.

Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I.

Bioinformatics. 2015 Jan 1;31(1):131-3. doi: 10.1093/bioinformatics/btu599. Epub 2014 Sep 5.

12.

Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies.

Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I.

Sci Rep. 2014 Sep 1;4:6245. doi: 10.1038/srep06245.

13.

Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells.

Zhou Y, Vazquez A, Wise A, Warita T, Warita K, Bar-Joseph Z, Oltvai ZN.

BMC Syst Biol. 2013 Dec 12;7:138. doi: 10.1186/1752-0509-7-138.

14.

Predicting drug-target interactions using probabilistic matrix factorization.

Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I.

J Chem Inf Model. 2013 Dec 23;53(12):3399-409. doi: 10.1021/ci400219z. Epub 2013 Dec 10.

15.

The metabolic demands of cancer cells are coupled to their size and protein synthesis rates.

Dolfi SC, Chan LL, Qiu J, Tedeschi PM, Bertino JR, Hirshfield KM, Oltvai ZN, Vazquez A.

Cancer Metab. 2013 Nov 7;1(1):20. doi: 10.1186/2049-3002-1-20.

16.

Contribution of serine, folate and glycine metabolism to the ATP, NADPH and purine requirements of cancer cells.

Tedeschi PM, Markert EK, Gounder M, Lin H, Dvorzhinski D, Dolfi SC, Chan LL, Qiu J, DiPaola RS, Hirshfield KM, Boros LG, Bertino JR, Oltvai ZN, Vazquez A.

Cell Death Dis. 2013 Oct 24;4:e877. doi: 10.1038/cddis.2013.393.

17.

Identifying ligand binding conformations of the β2-adrenergic receptor by using its agonists as computational probes.

Isin B, Estiu G, Wiest O, Oltvai ZN.

PLoS One. 2012;7(12):e50186. doi: 10.1371/journal.pone.0050186. Epub 2012 Dec 31.

18.

Ongoing technological revolution. Preface.

Wells A, Oltvai ZN.

Clin Lab Med. 2012 Dec;32(4):ix-x. doi: 10.1016/j.cll.2012.07.007. No abstract available.

PMID:
23078666
19.

Workflow organization in pathology.

Park S, Pantanowitz L, Parwani AV, Wells A, Oltvai ZN.

Clin Lab Med. 2012 Dec;32(4):601-22. doi: 10.1016/j.cll.2012.07.008. Review.

PMID:
23078662
20.

Identification of motions in membrane proteins by elastic network models and their experimental validation.

Isin B, Tirupula KC, Oltvai ZN, Klein-Seetharaman J, Bahar I.

Methods Mol Biol. 2012;914:285-317. doi: 10.1007/978-1-62703-023-6_17.

21.

Matching experiments across species using expression values and textual information.

Wise A, Oltvai ZN, Bar-Joseph Z.

Bioinformatics. 2012 Jun 15;28(12):i258-64. doi: 10.1093/bioinformatics/bts205.

22.

Serine biosynthesis with one carbon catabolism and the glycine cleavage system represents a novel pathway for ATP generation.

Vazquez A, Markert EK, Oltvai ZN.

PLoS One. 2011;6(11):e25881. doi: 10.1371/journal.pone.0025881. Epub 2011 Nov 2.

23.
24.

Cross-species queries of large gene expression databases.

Le HS, Oltvai ZN, Bar-Joseph Z.

Bioinformatics. 2010 Oct 1;26(19):2416-23. doi: 10.1093/bioinformatics/btq451. Epub 2010 Aug 11.

25.

Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays.

Henriksen ST, Liu J, Estiu G, Oltvai ZN, Wiest O.

Bioorg Med Chem. 2010 Jul 15;18(14):5148-56. doi: 10.1016/j.bmc.2010.05.060. Epub 2010 Jun 1.

26.

Catabolic efficiency of aerobic glycolysis: the Warburg effect revisited.

Vazquez A, Liu J, Zhou Y, Oltvai ZN.

BMC Syst Biol. 2010 May 6;4:58. doi: 10.1186/1752-0509-4-58.

27.

Blueprint for antimicrobial hit discovery targeting metabolic networks.

Shen Y, Liu J, Estiu G, Isin B, Ahn YY, Lee DS, Barabási AL, Kapatral V, Wiest O, Oltvai ZN.

Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1082-7. doi: 10.1073/pnas.0909181107. Epub 2010 Jan 5.

28.

Computational disease modeling - fact or fiction?

Tegnér JN, Compte A, Auffray C, An G, Cedersund G, Clermont G, Gutkin B, Oltvai ZN, Stephan KE, Thomas R, Villoslada P.

BMC Syst Biol. 2009 Jun 4;3:56. doi: 10.1186/1752-0509-3-56.

29.

Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets.

Lee DS, Burd H, Liu J, Almaas E, Wiest O, Barabási AL, Oltvai ZN, Kapatral V.

J Bacteriol. 2009 Jun;191(12):4015-24. doi: 10.1128/JB.01743-08. Epub 2009 Apr 17.

30.

Impact of limited solvent capacity on metabolic rate, enzyme activities, and metabolite concentrations of S. cerevisiae glycolysis.

Vazquez A, de Menezes MA, Barabási AL, Oltvai ZN.

PLoS Comput Biol. 2008 Oct;4(10):e1000195. doi: 10.1371/journal.pcbi.1000195. Epub 2008 Oct 10.

31.

The implications of human metabolic network topology for disease comorbidity.

Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabási AL.

Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9880-5. doi: 10.1073/pnas.0802208105. Epub 2008 Jul 3. Review.

32.

A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli.

Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z.

PLoS Comput Biol. 2008 Mar 28;4(3):e1000044. doi: 10.1371/journal.pcbi.1000044.

33.

Impact of the solvent capacity constraint on E. coli metabolism.

Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, Barabási AL, Boros LG, Oltvai ZN.

BMC Syst Biol. 2008 Jan 23;2:7. doi: 10.1186/1752-0509-2-7.

34.

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity.

Beg QK, Vazquez A, Ernst J, de Menezes MA, Bar-Joseph Z, Barabási AL, Oltvai ZN.

Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12663-8. Epub 2007 Jul 24.

35.
36.

Shaping specificity in signaling networks.

Albert R, Oltvai ZN.

Nat Genet. 2007 Mar;39(3):286-7. No abstract available.

PMID:
17325675
37.

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae.

Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN.

BMC Bioinformatics. 2006 Oct 28;7:478.

38.

Exploring transcriptional regulatory networks in the worm.

Farkas IJ, Beg QK, Oltvai ZN.

Cell. 2006 Jun 16;125(6):1032-4.

39.

The activity reaction core and plasticity of metabolic networks.

Almaas E, Oltvai ZN, Barabási AL.

PLoS Comput Biol. 2005 Dec;1(7):e68. Epub 2005 Dec 16.

40.

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli.

Balázsi G, Barabási AL, Oltvai ZN.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7841-6. Epub 2005 May 20.

41.

Sensing your surroundings: how transcription-regulatory networks of the cell discern environmental signals.

Balázsi G, Oltvai ZN.

Sci STKE. 2005 May 3;2005(282):pe20. Review.

PMID:
15870424
42.

The topological relationship between the large-scale attributes and local interaction patterns of complex networks.

Vázquez A, Dobrin R, Sergi D, Eckmann JP, Oltvai ZN, Barabási AL.

Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):17940-5. Epub 2004 Dec 14.

43.

Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays.

Tong X, Campbell JW, Balázsi G, Kay KA, Wanner BL, Gerdes SY, Oltvai ZN.

Biochem Biophys Res Commun. 2004 Sep 10;322(1):347-54.

PMID:
15313213
44.

Functional and topological characterization of protein interaction networks.

Yook SH, Oltvai ZN, Barabási AL.

Proteomics. 2004 Apr;4(4):928-42.

PMID:
15048975
45.

Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network.

Dobrin R, Beg QK, Barabási AL, Oltvai ZN.

BMC Bioinformatics. 2004 Jan 30;5:10.

46.

Global organization of metabolic fluxes in the bacterium Escherichia coli.

Almaas E, Kovács B, Vicsek T, Oltvai ZN, Barabási AL.

Nature. 2004 Feb 26;427(6977):839-43.

PMID:
14985762
47.

Network biology: understanding the cell's functional organization.

Barabási AL, Oltvai ZN.

Nat Rev Genet. 2004 Feb;5(2):101-13. Review. No abstract available.

PMID:
14735121
48.

Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae.

Dezso Z, Oltvai ZN, Barabási AL.

Genome Res. 2003 Nov;13(11):2450-4. Epub 2003 Oct 14.

49.

Experimental determination and system level analysis of essential genes in Escherichia coli MG1655.

Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabási AL, Oltvai ZN, Osterman AL.

J Bacteriol. 2003 Oct;185(19):5673-84.

50.

Evolutionary conservation of motif constituents in the yeast protein interaction network.

Wuchty S, Oltvai ZN, Barabási AL.

Nat Genet. 2003 Oct;35(2):176-9. Epub 2003 Sep 14.

PMID:
12973352

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