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Items: 1 to 20 of 420

1.

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 1. pii: 201613446. [Epub ahead of print]

PMID:
27911809
2.

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.

PMID:
27883890
3.

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.

4.

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. 2016 Nov 4. doi: 10.1111/trf.13892. [Epub ahead of print]

PMID:
27813142
5.

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.

6.

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.

PMID:
27667363
7.

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.

8.

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.

PMID:
27554084
9.

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, Boya P CA, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJ, 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 AM, 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 BØ, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N.

Nat Biotechnol. 2016 Aug 9;34(8):828-37. doi: 10.1038/nbt.3597.

PMID:
27504778
10.

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.

PMID:
27491795
11.

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.

12.

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.

PMID:
27440044
13.

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.

14.

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.

15.

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.

16.

What do cells actually want?

Feist AM, Palsson BO.

Genome Biol. 2016 May 23;17(1):110. doi: 10.1186/s13059-016-0983-3.

17.

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, Keasling JD, Palsson BO, Lee TS.

Cell Syst. 2016 May 25;2(5):335-46. doi: 10.1016/j.cels.2016.04.004.

PMID:
27211860
18.

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.

Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K.

PLoS One. 2016 May 6;11(5):e0155038. doi: 10.1371/journal.pone.0155038.

19.

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics.

Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO.

Cell Syst. 2015 Oct 28;1(4):283-92. doi: 10.1016/j.cels.2015.10.003.

20.

Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.

Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO.

Cell Syst. 2016 Apr 27;2(4):260-71. doi: 10.1016/j.cels.2016.04.003.

PMID:
27135538
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