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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.


BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.

King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.

Nucleic Acids Res. 2015 Oct 17. pii: gkv1049. [Epub ahead of print]


Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.

Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A.

BMC Syst Biol. 2015 Oct 9;9:68. doi: 10.1186/s12918-015-0212-9.


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.


Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.

King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO.

PLoS Comput Biol. 2015 Aug 27;11(8):e1004321. doi: 10.1371/journal.pcbi.1004321. eCollection 2015 Aug.


Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.

Seo SW, Kim D, Szubin R, Palsson BO.

Cell Rep. 2015 Aug 25;12(8):1289-99. doi: 10.1016/j.celrep.2015.07.043. Epub 2015 Aug 13.


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.


Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.

Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson BO.

Nat Commun. 2015 Aug 10;6:7970. doi: 10.1038/ncomms8970.


JSBML 1.0: providing a smorgasbord of options to encode systems biology models.

Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A.

Bioinformatics. 2015 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16.


Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis.

Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO.

Nat Commun. 2015 Jun 9;6:7101. doi: 10.1038/ncomms8101.


Using Genome-scale Models to Predict Biological Capabilities.

O'Brien EJ, Monk JM, Palsson BO.

Cell. 2015 May 21;161(5):971-87. doi: 10.1016/j.cell.2015.05.019. Review.


Prediction of intracellular metabolic states from extracellular metabolomic data.

Aurich MK, Paglia G, Rolfsson Ó, Hrafnsdóttir S, Magnúsdóttir M, Stefaniak MM, Palsson BØ, Fleming RM, Thiele I.

Metabolomics. 2015;11(3):603-619. Epub 2014 Aug 14.


Decoding the jargon of bottom-up metabolic systems biology.

Rolfsson Ó, Palsson BO.

Bioessays. 2015 Jun;37(6):588-91. doi: 10.1002/bies.201400187. Epub 2015 Mar 11. No abstract available.


Multidimensional analytical approach based on UHPLC-UV-ion mobility-MS for the screening of natural pigments.

Pacini T, Fu W, Gudmundsson S, Chiaravalle AE, Brynjolfson S, Palsson BO, Astarita G, Paglia G.

Anal Chem. 2015 Mar 3;87(5):2593-9. doi: 10.1021/ac504707n. Epub 2015 Feb 13.


Computing the functional proteome: recent progress and future prospects for genome-scale models.

O'Brien EJ, Palsson BO.

Curr Opin Biotechnol. 2015 Aug;34:125-34. doi: 10.1016/j.copbio.2014.12.017. Epub 2015 Jan 8. Review.


Next-generation genome-scale models for metabolic engineering.

King ZA, Lloyd CJ, Feist AM, Palsson BO.

Curr Opin Biotechnol. 2015 Dec;35:23-9. doi: 10.1016/j.copbio.2014.12.016. Epub 2015 Jan 7. Review.


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.


Improving collaboration by standardization efforts in systems biology.

Dräger A, Palsson BØ.

Front Bioeng Biotechnol. 2014 Dec 8;2:61. doi: 10.3389/fbioe.2014.00061. eCollection 2014. Review.


Ion mobility-derived collision cross section as an additional measure for lipid fingerprinting and identification.

Paglia G, Angel P, Williams JP, Richardson K, Olivos HJ, Thompson JW, Menikarachchi L, Lai S, Walsh C, Moseley A, Plumb RS, Grant DF, Palsson BO, Langridge J, Geromanos S, Astarita G.

Anal Chem. 2015 Jan 20;87(2):1137-44. doi: 10.1021/ac503715v. Epub 2014 Dec 29.

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