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High-level dCas9 expression induces abnormal cell morphology in Escherichia coli.

Cho S, Choe D, Lee E, Kim SC, Palsson BØ, Cho BK.

ACS Synth Biol. 2018 Mar 15. doi: 10.1021/acssynbio.7b00462. [Epub ahead of print]


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.


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.


Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO.

Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19.


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, Valencia A.

Bioinformatics. 2018 Feb 12. doi: 10.1093/bioinformatics/bty077. [Epub ahead of print]


Quantitative -omic data empowers bottom-up systems biology.

Yurkovich JT, Palsson BO.

Curr Opin Biotechnol. 2018 Feb 3;51:130-136. doi: 10.1016/j.copbio.2018.01.009. [Epub ahead of print] Review.


Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance.

Choe D, Szubin R, Dahesh S, Cho S, Nizet V, Palsson B, Cho BK.

Sci Rep. 2018 Feb 2;8(1):2215. doi: 10.1038/s41598-018-20661-1.


Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.

Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK, Palsson BO.

Nucleic Acids Res. 2018 Jan 31. doi: 10.1093/nar/gky069. [Epub ahead of print]


Modeling the multi-scale mechanisms of macromolecular resource allocation.

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

Curr Opin Microbiol. 2018 Jan 20;45:8-15. doi: 10.1016/j.mib.2018.01.002. [Epub ahead of print] Review.


Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N.

PLoS Comput Biol. 2018 Jan 4;14(1):e1005895. doi: 10.1371/journal.pcbi.1005895. eCollection 2018 Jan.


Metabolic Models of Protein Allocation Call for the Kinetome.

Nilsson A, Nielsen J, Palsson BO.

Cell Syst. 2017 Dec 27;5(6):538-541. doi: 10.1016/j.cels.2017.11.013.


Topological and kinetic determinants of the modal matrices of dynamic models of metabolism.

Du B, Zielinski DC, Palsson BO.

PLoS One. 2017 Dec 21;12(12):e0189880. doi: 10.1371/journal.pone.0189880. eCollection 2017.


Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli.

Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.

Proc Natl Acad Sci U S A. 2018 Jan 2;115(1):222-227. doi: 10.1073/pnas.1716056115. Epub 2017 Dec 18.


Proceedings of the Food and Drug Administration's public workshop on new red blood cell product regulatory science 2016.

Vostal JG, Buehler PW, Gelderman MP, Alayash AI, Doctor A, Zimring JC, Glynn SA, Hess JR, Klein H, Acker JP, Spinella PC, D'Alessandro A, Palsson B, Raife TJ, Busch MP, McMahon TJ, Intaglietta M, Swartz HM, Dubick MA, Cardin S, Patel RP, Natanson C, Weisel JW, Muszynski JA, Norris PJ, Ness PM.

Transfusion. 2018 Jan;58(1):255-266. doi: 10.1111/trf.14435. Epub 2017 Dec 15.


Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function.

Yang JH, Bhargava P, McCloskey D, Mao N, Palsson BO, Collins JJ.

Cell Host Microbe. 2017 Dec 13;22(6):757-765.e3. doi: 10.1016/j.chom.2017.10.020. Epub 2017 Nov 30.


Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation.

Chen K, Gao Y, Mih N, O'Brien EJ, Yang L, Palsson BO.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11548-11553. doi: 10.1073/pnas.1705524114. Epub 2017 Oct 10.


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.


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.


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.


Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring.

Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.

Metab Eng. 2017 Nov;44:100-107. doi: 10.1016/j.ymben.2017.09.012. Epub 2017 Sep 23.


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.


Mannose and fructose metabolism in red blood cells during cold storage in SAGM.

Rolfsson Ó, Johannsson F, Magnusdottir M, Paglia G, Sigurjonsson ÓE, Bordbar A, Palsson S, Brynjólfsson S, Guðmundsson S, Palsson B.

Transfusion. 2017 Nov;57(11):2665-2676. doi: 10.1111/trf.14266. Epub 2017 Aug 21.


Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655.

Seo SW, Gao Y, Kim D, Szubin R, Yang J, Cho BK, Palsson BO.

Sci Rep. 2017 May 19;7(1):2181. doi: 10.1038/s41598-017-02110-7.


Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies.

Sandberg TE, Lloyd CJ, Palsson BO, Feist AM.

Appl Environ Microbiol. 2017 Jun 16;83(13). pii: e00410-17. doi: 10.1128/AEM.00410-17. Print 2017 Jul 1.


Machine learning in computational biology to accelerate high-throughput protein expression.

Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, Rockberg J, Brunk E.

Bioinformatics. 2017 Aug 15;33(16):2487-2495. doi: 10.1093/bioinformatics/btx207.


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.


Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism.

Rolfsson Ó, Sigurjonsson ÓE, Magnusdottir M, Johannsson F, Paglia G, Guðmundsson S, Bordbar A, Palsson S, Brynjólfsson S, Guðmundsson S, Palsson B.

Vox Sang. 2017 May;112(4):326-335. doi: 10.1111/vox.12506. Epub 2017 Mar 31.


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.


Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels.

Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K.

mSystems. 2017 Feb 14;2(1). pii: e00142-16. doi: 10.1128/mSystems.00142-16. eCollection 2017 Jan-Feb.


A Model for Designing Adaptive Laboratory Evolution Experiments.

LaCroix RA, Palsson BO, Feist AM.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03115-16. doi: 10.1128/AEM.03115-16. Print 2017 Apr 15.


Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.

Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO.

Sci Rep. 2017 Jan 25;7:41241. doi: 10.1038/srep41241.


Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression.

Ma D, Yang L, Fleming RM, Thiele I, Palsson BO, Saunders MA.

Sci Rep. 2017 Jan 18;7:40863. doi: 10.1038/srep40863.


Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion.

van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson BO, Lewis NE, Nizet V, Esko JD.

MBio. 2017 Jan 10;8(1). pii: e02128-16. doi: 10.1128/mBio.02128-16.


Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion.

King ZA, O'Brien EJ, Feist AM, Palsson BO.

Metab Eng. 2017 Jan;39:220-227. doi: 10.1016/j.ymben.2016.12.004. Epub 2016 Dec 13.


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.


Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis.

Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson BO.

Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):E8344-E8353. doi: 10.1073/pnas.1613446113. Epub 2016 Dec 1.


A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE.

Cell Syst. 2016 Nov 23;3(5):434-443.e8. doi: 10.1016/j.cels.2016.10.020.


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.


Citrate metabolism in red blood cells stored in additive solution-3.

D'Alessandro A, Nemkov T, Yoshida T, Bordbar A, Palsson BO, Hansen KC.

Transfusion. 2017 Feb;57(2):325-336. doi: 10.1111/trf.13892. Epub 2016 Nov 4.


Multi-omic data integration enables discovery of hidden biological regularities.

Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO.

Nat Commun. 2016 Oct 26;7:13091. doi: 10.1038/ncomms13091.


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.


solveME: fast and reliable solution of nonlinear ME models.

Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO.

BMC Bioinformatics. 2016 Sep 22;17(1):391.


Biomarkers defining the metabolic age of red blood cells during cold storage.

Paglia G, D'Alessandro A, Rolfsson Ó, Sigurjónsson ÓE, Bordbar A, Palsson S, Nemkov T, Hansen KC, Gudmundsson S, Palsson BO.

Blood. 2016 Sep 29;128(13):e43-50. doi: 10.1182/blood-2016-06-721688. Epub 2016 Aug 23.


Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N.

Nat Biotechnol. 2016 Aug 9;34(8):828-837. doi: 10.1038/nbt.3597.


Metabolic fate of adenine in red blood cells during storage in SAGM solution.

Paglia G, Sigurjónsson ÓE, Bordbar A, Rolfsson Ó, Magnusdottir M, Palsson S, Wichuk K, Gudmundsson S, Palsson BO.

Transfusion. 2016 Oct;56(10):2538-2547. doi: 10.1111/trf.13740. Epub 2016 Aug 5.


A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.

Mih N, Brunk E, Bordbar A, Palsson BO.

PLoS Comput Biol. 2016 Jul 28;12(7):e1005039. doi: 10.1371/journal.pcbi.1005039. eCollection 2016 Jul.


An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network.

Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SY, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO, Nigam SK.

J Biol Chem. 2016 Sep 9;291(37):19474-86. doi: 10.1074/jbc.M116.745216. Epub 2016 Jul 20.


Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.

O'Brien EJ, Utrilla J, Palsson BO.

PLoS Comput Biol. 2016 Jun 28;12(6):e1004998. doi: 10.1371/journal.pcbi.1004998. eCollection 2016 Jun.


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.


Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO.

BMC Syst Biol. 2016 Jun 6;10(1):40. doi: 10.1186/s12918-016-0283-2.

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