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Items: 25

1.

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z.

Nucleic Acids Res. 2019 Nov 7. pii: gkz1054. doi: 10.1093/nar/gkz1054. [Epub ahead of print]

PMID:
31696234
2.

A systems approach to clinical oncology uses deep phenotyping to deliver personalized care.

Yurkovich JT, Tian Q, Price ND, Hood L.

Nat Rev Clin Oncol. 2019 Oct 16. doi: 10.1038/s41571-019-0273-6. [Epub ahead of print] Review.

PMID:
31619755
3.

Genome-scale metabolic model of the rat liver predicts effects of diet restriction.

Baloni P, Sangar V, Yurkovich JT, Robinson M, Taylor S, Karbowski CM, Hamadeh HK, He YD, Price ND.

Sci Rep. 2019 Jul 8;9(1):9807. doi: 10.1038/s41598-019-46245-1.

4.

Cellular responses to reactive oxygen species are predicted from molecular mechanisms.

Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, Chen K, Heckmann D, Szubin R, Hefner Y, Feist AM, Palsson BO.

Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14368-14373. doi: 10.1073/pnas.1905039116. Epub 2019 Jul 3.

PMID:
31270234
5.

Blood Is a Window into Health and Disease.

Yurkovich JT, Hood L.

Clin Chem. 2019 Oct;65(10):1204-1206. doi: 10.1373/clinchem.2018.299065. Epub 2019 Jun 6. No abstract available.

PMID:
31171530
6.

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT.

Nat Protoc. 2019 Mar;14(3):639-702. doi: 10.1038/s41596-018-0098-2.

PMID:
30787451
7.

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.

8.

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.

Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE.

Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):11096-11101. doi: 10.1073/pnas.1811971115. Epub 2018 Oct 9.

9.

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.

10.

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.

Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO.

Nucleic Acids Res. 2018 Nov 16;46(20):10682-10696. doi: 10.1093/nar/gky752.

11.

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.

Yurkovich JT, Alcantar MA, Haiman ZB, Palsson BO.

PLoS Comput Biol. 2018 Aug 7;14(8):e1006356. doi: 10.1371/journal.pcbi.1006356. eCollection 2018 Aug.

12.

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures.

Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO.

Front Microbiol. 2018 May 25;9:1082. doi: 10.3389/fmicb.2018.01082. eCollection 2018.

13.

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC.

Biophys J. 2018 Jun 5;114(11):2691-2702. doi: 10.1016/j.bpj.2018.04.030.

14.

Systems biology as an emerging paradigm in transfusion medicine.

Yurkovich JT, Bordbar A, Sigurjónsson ÓE, Palsson BO.

BMC Syst Biol. 2018 Mar 7;12(1):31. doi: 10.1186/s12918-018-0558-x. Review.

15.

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.

16.

Quantitative -omic data empowers bottom-up systems biology.

Yurkovich JT, Palsson BO.

Curr Opin Biotechnol. 2018 Jun;51:130-136. doi: 10.1016/j.copbio.2018.01.009. Epub 2018 Feb 3. Review.

PMID:
29414439
17.

Modeling the multi-scale mechanisms of macromolecular resource allocation.

Yang L, Yurkovich JT, King ZA, Palsson BO.

Curr Opin Microbiol. 2018 Oct;45:8-15. doi: 10.1016/j.mib.2018.01.002. Epub 2018 Jan 24. Review.

18.

Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks.

Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO.

J Biol Chem. 2017 Dec 1;292(48):19556-19564. doi: 10.1074/jbc.M117.804914. Epub 2017 Oct 13.

19.

A Padawan Programmer's Guide to Developing Software Libraries.

Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA.

Cell Syst. 2017 Nov 22;5(5):431-437. doi: 10.1016/j.cels.2017.08.003. Epub 2017 Oct 4.

20.

Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.

Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10286-10291. doi: 10.1073/pnas.1702581114. Epub 2017 Sep 5.

21.

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics.

Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson BO.

Sci Rep. 2017 Apr 7;7:46249. doi: 10.1038/srep46249.

22.

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.

Yurkovich JT, Yang L, Palsson BO.

PLoS Comput Biol. 2017 Mar 6;13(3):e1005424. doi: 10.1371/journal.pcbi.1005424. eCollection 2017 Mar.

23.

Principles of proteome allocation are revealed using proteomic data and genome-scale models.

Yang L, Yurkovich JT, Lloyd CJ, Ebrahim A, Saunders MA, Palsson BO.

Sci Rep. 2016 Nov 18;6:36734. doi: 10.1038/srep36734.

24.

Toward Community Standards and Software for Whole-Cell Modeling.

Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F.

IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10.

25.

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.

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