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Items: 1 to 50 of 65

1.

Navy bean supplemented high-fat diet improves intestinal health, epithelial barrier integrity and critical aspects of the obese inflammatory phenotype.

Monk JM, Wu W, Lepp D, Wellings HR, Hutchinson AL, Liddle DM, Graf D, Pauls KP, Robinson LE, Power KA.

J Nutr Biochem. 2019 May 10;70:91-104. doi: 10.1016/j.jnutbio.2019.04.009. [Epub ahead of print]

PMID:
31195365
2.

Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates.

Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM.

Front Cell Infect Microbiol. 2019 May 24;9:161. doi: 10.3389/fcimb.2019.00161. eCollection 2019.

3.

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media.

Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM.

Sci Data. 2019 Apr 26;6(1):43. doi: 10.1038/s41597-019-0051-4.

4.

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.

Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ.

PLoS Comput Biol. 2019 Apr 22;15(4):e1006971. doi: 10.1371/journal.pcbi.1006971. eCollection 2019 Apr.

5.

Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt.

Attia H, Szubin R, Yassin AS, Monk JM, Aziz RK.

Microbiol Resour Announc. 2019 Feb 14;8(7). pii: e01418-18. doi: 10.1128/MRA.01418-18. eCollection 2019 Feb.

6.

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.

Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO.

PLoS Comput Biol. 2019 Jan 9;15(1):e1006644. doi: 10.1371/journal.pcbi.1006644. eCollection 2019 Jan.

7.

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology.

Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM.

Microbiol Resour Announc. 2018 Oct 4;7(13). pii: e00890-18. doi: 10.1128/MRA.00890-18. eCollection 2018 Oct.

8.

Predicting Antimicrobial Resistance and Associated Genomic Features from Whole-Genome Sequencing.

Monk JM.

J Clin Microbiol. 2019 Jan 30;57(2). pii: e01610-18. doi: 10.1128/JCM.01610-18. Print 2019 Feb.

PMID:
30463894
9.

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.

Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L.

Front Microbiol. 2018 Oct 30;9:2559. doi: 10.3389/fmicb.2018.02559. eCollection 2018.

10.

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance.

Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V, Monk JM, Palsson BO.

Nat Commun. 2018 Oct 17;9(1):4306. doi: 10.1038/s41467-018-06634-y.

11.

Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice.

Du B, Zielinski DC, Monk JM, Palsson BO.

Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):11339-11344. doi: 10.1073/pnas.1805367115. Epub 2018 Oct 11.

12.

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.

Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM.

Nat Commun. 2018 Sep 14;9(1):3771. doi: 10.1038/s41467-018-06112-5.

13.

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.

Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO.

BMC Syst Biol. 2018 Jun 11;12(1):66. doi: 10.1186/s12918-018-0587-5.

14.

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.

Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM.

Front Genet. 2018 Apr 10;9:121. doi: 10.3389/fgene.2018.00121. eCollection 2018.

15.

Navy and black bean supplementation attenuates colitis-associated inflammation and colonic epithelial damage.

Monk JM, Wu W, Hutchinson AL, Pauls P, Robinson LE, Power KA.

J Nutr Biochem. 2018 Jun;56:215-223. doi: 10.1016/j.jnutbio.2018.02.013. Epub 2018 Feb 27.

PMID:
29631142
16.

Chickpea supplementation prior to colitis onset reduces inflammation in dextran sodium sulfate-treated C57Bl/6 male mice.

Monk JM, Wu W, McGillis LH, Wellings HR, Hutchinson AL, Liddle DM, Graf D, Robinson LE, Power KA.

Appl Physiol Nutr Metab. 2018 Sep;43(9):893-901. doi: 10.1139/apnm-2017-0689. Epub 2018 Mar 9.

PMID:
29522694
17.

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions.

Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM.

BMC Syst Biol. 2018 Mar 2;12(1):25. doi: 10.1186/s12918-018-0557-y.

18.

ssbio: a Python framework for structural systems biology.

Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO.

Bioinformatics. 2018 Jun 15;34(12):2155-2157. doi: 10.1093/bioinformatics/bty077.

PMID:
29444205
19.

Marine fish oil is more potent than plant-based n-3 polyunsaturated fatty acids in the prevention of mammary tumors.

Liu J, Abdelmagid SA, Pinelli CJ, Monk JM, Liddle DM, Hillyer LM, Hucik B, Silva A, Subedi S, Wood GA, Robinson LE, Muller WJ, Ma DWL.

J Nutr Biochem. 2018 May;55:41-52. doi: 10.1016/j.jnutbio.2017.12.011. Epub 2017 Dec 27.

20.

Integrated Immunomodulatory Mechanisms through which Long-Chain n-3 Polyunsaturated Fatty Acids Attenuate Obese Adipose Tissue Dysfunction.

Liddle DM, Hutchinson AL, Wellings HR, Power KA, Robinson LE, Monk JM.

Nutrients. 2017 Nov 27;9(12). pii: E1289. doi: 10.3390/nu9121289. Review.

21.

iML1515, a knowledgebase that computes Escherichia coli traits.

Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO.

Nat Biotechnol. 2017 Oct 11;35(10):904-908. doi: 10.1038/nbt.3956. No abstract available.

22.

Navy and black bean supplementation primes the colonic mucosal microenvironment to improve gut health.

Monk JM, Lepp D, Wu W, Pauls KP, Robinson LE, Power KA.

J Nutr Biochem. 2017 Nov;49:89-100. doi: 10.1016/j.jnutbio.2017.08.002. Epub 2017 Aug 10.

PMID:
28915390
23.

The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli.

Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson BO, Charusanti P.

Microbiol Res. 2017 Jan;194:47-52. doi: 10.1016/j.micres.2016.10.006. Epub 2016 Nov 4.

24.

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.

Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM.

Cell Syst. 2016 Sep 28;3(3):238-251.e12. doi: 10.1016/j.cels.2016.08.013. Epub 2016 Sep 22.

25.

Purified rutin and rutin-rich asparagus attenuates disease severity and tissue damage following dextran sodium sulfate-induced colitis.

Power KA, Lu JT, Monk JM, Lepp D, Wu W, Zhang C, Liu R, Tsao R, Robinson LE, Wood GA, Wolyn DJ.

Mol Nutr Food Res. 2016 Nov;60(11):2396-2412. doi: 10.1002/mnfr.201500890. Epub 2016 Aug 5.

PMID:
27349947
26.

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.

Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V, Palsson BØ.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):E3801-9. doi: 10.1073/pnas.1523199113. Epub 2016 Jun 10.

27.

Fish-oil-derived n-3 polyunsaturated fatty acids reduce NLRP3 inflammasome activity and obesity-related inflammatory cross-talk between adipocytes and CD11b(+) macrophages.

De Boer AA, Monk JM, Liddle DM, Hutchinson AL, Power KA, Ma DW, Robinson LE.

J Nutr Biochem. 2016 Aug;34:61-72. doi: 10.1016/j.jnutbio.2016.04.004. Epub 2016 Apr 29.

PMID:
27208584
28.

The delta 6 desaturase knock out mouse reveals that immunomodulatory effects of essential n-6 and n-3 polyunsaturated fatty acids are both independent of and dependent upon conversion.

Monk JM, Liddle DM, Cohen DJ, Tsang DH, Hillyer LM, Abdelmagid SA, Nakamura MT, Power KA, Ma DW, Robinson LE.

J Nutr Biochem. 2016 Jun;32:29-38. doi: 10.1016/j.jnutbio.2016.01.004. Epub 2016 Mar 2.

29.

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA Jr, Yang XF, Zhang JJ, Vinetz JM.

PLoS Negl Trop Dis. 2016 Feb 18;10(2):e0004403. doi: 10.1371/journal.pntd.0004403. eCollection 2016 Feb.

30.

Diets enriched with cranberry beans alter the microbiota and mitigate colitis severity and associated inflammation.

Monk JM, Lepp D, Zhang CP, Wu W, Zarepoor L, Lu JT, Pauls KP, Tsao R, Wood GA, Robinson LE, Power KA.

J Nutr Biochem. 2016 Feb;28:129-39. doi: 10.1016/j.jnutbio.2015.10.014. Epub 2015 Nov 4.

PMID:
26878790
31.

Dietary flaxseed modulates the colonic microenvironment in healthy C57Bl/6 male mice which may alter susceptibility to gut-associated diseases.

Power KA, Lepp D, Zarepoor L, Monk JM, Wu W, Tsao R, Liu R.

J Nutr Biochem. 2016 Feb;28:61-9. doi: 10.1016/j.jnutbio.2015.09.028. Epub 2015 Oct 21.

PMID:
26878783
32.

Anti-inflammatory and anti-chemotactic effects of dietary flaxseed oil on CD8(+) T cell/adipocyte-mediated cross-talk.

Monk JM, Liddle DM, Brown MJ, Zarepoor L, De Boer AA, Ma DW, Power KA, Robinson LE.

Mol Nutr Food Res. 2016 Mar;60(3):621-30. doi: 10.1002/mnfr.201500541. Epub 2015 Dec 29.

PMID:
26616354
33.

Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations.

Aziz RK, Monk JM, Lewis RM, In Loh S, Mishra A, Abhay Nagle A, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Fong NL, Li HJ, Palsson BO, Charusanti P.

Sci Rep. 2015 Nov 4;5:16025. doi: 10.1038/srep16025.

34.

Fish Oil-Derived Long-Chain n-3 Polyunsaturated Fatty Acids Reduce Expression of M1-Associated Macrophage Markers in an ex vivo Adipose Tissue Culture Model, in Part through Adiponectin.

De Boer AA, Monk JM, Liddle DM, Power KA, Ma DW, Robinson LE.

Front Nutr. 2015 Oct 13;2:31. doi: 10.3389/fnut.2015.00031. eCollection 2015.

35.

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.

Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P.

Front Microbiol. 2015 Sep 23;6:958. doi: 10.3389/fmicb.2015.00958. eCollection 2015.

36.

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, Palsson BO.

Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10810-5. doi: 10.1073/pnas.1501384112. Epub 2015 Aug 10.

37.

Using Genome-scale Models to Predict Biological Capabilities.

O'Brien EJ, Monk JM, Palsson BO.

Cell. 2015 May 21;161(5):971-987. doi: 10.1016/j.cell.2015.05.019. Review.

38.

The integrative role of leptin, oestrogen and the insulin family in obesity-associated breast cancer: potential effects of exercise.

Schmidt S, Monk JM, Robinson LE, Mourtzakis M.

Obes Rev. 2015 Jun;16(6):473-87. doi: 10.1111/obr.12281. Epub 2015 Apr 15. Review.

39.

White and dark kidney beans reduce colonic mucosal damage and inflammation in response to dextran sodium sulfate.

Monk JM, Zhang CP, Wu W, Zarepoor L, Lu JT, Liu R, Pauls KP, Wood GA, Tsao R, Robinson LE, Power KA.

J Nutr Biochem. 2015 Jul;26(7):752-60. doi: 10.1016/j.jnutbio.2015.02.003. Epub 2015 Mar 21.

PMID:
25841250
40.

Fish-oil-derived n-3 PUFAs reduce inflammatory and chemotactic adipokine-mediated cross-talk between co-cultured murine splenic CD8+ T cells and adipocytes.

Monk JM, Liddle DM, De Boer AA, Brown MJ, Power KA, Ma DW, Robinson LE.

J Nutr. 2015 Apr;145(4):829-38. doi: 10.3945/jn.114.205443. Epub 2015 Feb 4.

PMID:
25833786
41.

Proinflammatory effects of arachidonic acid in a lipopolysaccharide-induced inflammatory microenvironment in 3T3-L1 adipocytes in vitro.

Cranmer-Byng MM, Liddle DM, De Boer AA, Monk JM, Robinson LE.

Appl Physiol Nutr Metab. 2015 Feb;40(2):142-54. doi: 10.1139/apnm-2014-0022. Epub 2014 Oct 16.

PMID:
25641170
42.

Model-driven discovery of underground metabolic functions in Escherichia coli.

Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):929-34. doi: 10.1073/pnas.1414218112. Epub 2015 Jan 6.

43.

n-3 polyunsaturated fatty acids and mechanisms to mitigate inflammatory paracrine signaling in obesity-associated breast cancer.

Monk JM, Turk HF, Liddle DM, De Boer AA, Power KA, Ma DW, Robinson LE.

Nutrients. 2014 Oct 30;6(11):4760-93. doi: 10.3390/nu6114760. Review.

44.

Antagonizing arachidonic acid-derived eicosanoids reduces inflammatory Th17 and Th1 cell-mediated inflammation and colitis severity.

Monk JM, Turk HF, Fan YY, Callaway E, Weeks B, Yang P, McMurray DN, Chapkin RS.

Mediators Inflamm. 2014;2014:917149. doi: 10.1155/2014/917149. Epub 2014 Jul 17.

45.

n-3 PUFAs reduce T-helper 17 cell differentiation by decreasing responsiveness to interleukin-6 in isolated mouse splenic CD4⁺ T cells.

Allen MJ, Fan YY, Monk JM, Hou TY, Barhoumi R, McMurray DN, Chapkin RS.

J Nutr. 2014 Aug;144(8):1306-13. doi: 10.3945/jn.114.194407. Epub 2014 Jun 18.

46.

Cooked navy and black bean diets improve biomarkers of colon health and reduce inflammation during colitis.

Zhang C, Monk JM, Lu JT, Zarepoor L, Wu W, Liu R, Pauls KP, Wood GA, Robinson L, Tsao R, Power KA.

Br J Nutr. 2014 May;111(9):1549-63. doi: 10.1017/S0007114513004352. Epub 2014 Feb 13.

PMID:
24521520
47.

Docosahexaenoic acid decreases pro-inflammatory mediators in an in vitro murine adipocyte macrophage co-culture model.

De Boer AA, Monk JM, Robinson LE.

PLoS One. 2014 Jan 20;9(1):e85037. doi: 10.1371/journal.pone.0085037. eCollection 2014.

48.

Constraint-based models predict metabolic and associated cellular functions.

Bordbar A, Monk JM, King ZA, Palsson BO.

Nat Rev Genet. 2014 Feb;15(2):107-20. doi: 10.1038/nrg3643. Epub 2014 Jan 16. Review.

PMID:
24430943
49.

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.

Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20338-43. doi: 10.1073/pnas.1307797110. Epub 2013 Nov 25.

50.

n3 PUFAs reduce mouse CD4+ T-cell ex vivo polarization into Th17 cells.

Monk JM, Hou TY, Turk HF, McMurray DN, Chapkin RS.

J Nutr. 2013 Sep;143(9):1501-8. doi: 10.3945/jn.113.178178. Epub 2013 Jul 17.

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