Systems Biology of Metabolism

Gene Ontology: tool for the unification of biology

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Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

Vander Heiden, M. G., Cantley, L. C., & Thompson, C. B. (2009) · Science · doi:10.1126/science.1160809 · Cited by 16,197

Tissue-based map of the human proteome

Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624

Diet rapidly and reproducibly alters the human gut microbiome

David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100

A metagenome-wide association study of gut microbiota in type 2 diabetes

Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762

Exploring the metabolic and genetic control of gene expression on a genomic scale.

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Functional interactions between the gut microbiota and host metabolism

Tremaroli, V., & Bäckhed, F. (2012) · Nature · doi:10.1038/nature11552 · Cited by 4,387

Resveratrol improves health and survival of mice on a high-calorie diet

Baur, J. A., Pearson, K. J., Price, N. L., Jamieson, H. A., Lerin, C., Kalra, A., Prabhu, V. V., Allard, J. S., Lopez-Lluch, G., Lewis, K., et al. (2006) · Nature · doi:10.1038/nature05354 · Cited by 4,290

Systems biology: a brief overview

Kitano, H. (2002) · Science · doi:10.1126/science.1069492 · Cited by 4,265

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti–PD-L1 efficacy

Sivan, A., Corrales, L., Hubert, N., Williams, J. B., Aquino-Michaels, K., Earley, Z. M., Benyamin, F. W., Man Lei, Y., Jabri, B., Alegre, M.-L., et al. (2015) · Science · doi:10.1126/science.aac4255 · Cited by 3,888 · cited 1×

Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan

Howitz, K. T., Bitterman, K. J., Cohen, H. Y., Lamming, D. W., Lavu, S., Wood, J. G., Zipkin, R. E., Chung, P., Kisielewski, A., Zhang, L.-L., et al. (2003) · Nature · doi:10.1038/nature01960 · Cited by 3,796

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

Vétizou, M., Pitt, J. M., Daillère, R., Lepage, P., Waldschmitt, N., Flament, C., Rusakiewicz, S., Routy, B., Roberti, M. P., Duong, C. P. M., et al. (2015) · Science · doi:10.1126/science.aad1329 · Cited by 3,488 · cited 1×

AMPK regulates energy expenditure by modulating NAD+ metabolism and SIRT1 activity

Cantó, C., Gerhart-Hines, Z., Feige, J. N., Lagouge, M., Noriega, L., Milne, J. C., Elliott, P. J., Puigserver, P., & Auwerx, J. (2009) · Nature · doi:10.1038/nature07813 · Cited by 3,300

On the Dependency of Cellular Protein Levels on mRNA Abundance

Liu, Y., Beyer, A., & Aebersold, R. (2016) · Cell · doi:10.1016/j.cell.2016.03.014 · Cited by 3,221

Gut metagenome in European women with normal, impaired and diabetic glucose control

Karlsson, F. H., Tremaroli, V., Nookaew, I., Bergström, G., Behre, C. J., Fagerberg, B., Nielsen, J., & Bäckhed, F. (2013) · Nature · doi:10.1038/nature12198 · Cited by 3,115

Production of the antimalarial drug precursor artemisinic acid in engineered yeast

Ro, D.-K., Paradise, E. M., Ouellet, M., Fisher, K. J., Newman, K. L., Ndungu, J. M., Ho, K. A., Eachus, R. A., Ham, T. S., Kirby, J., et al. (2006) · Nature · doi:10.1038/nature04640 · Cited by 2,805

Computational systems biology.

Kitano, H. (2002) · Nature · doi:10.1038/nature01254 · Cited by 2,209

Transcriptional regulatory code of a eukaryotic genome

Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., MacIsaac, K. D., Danford, T., Hannett, N. M., Tagne, J., Reynolds, D. B., Yoo, J. Y., et al. (2004) · Nature · doi:10.1038/nature02800 · Cited by 2,135

Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network

Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., & Hood, L. (2001) · Science · doi:10.1126/science.292.5518.929 · Cited by 2,050

Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia

Metallo, C. M., Gameiro, P. A., Bell, E. L., Mattaini, K. R., Yang, J., Hiller, K., Jewell, C. M., Johnson, Z. R., Irvine, D. J., Guarente, L., et al. (2012) · Nature · doi:10.1038/nature10602 · Cited by 1,791

A N EW A PPROACH TO D ECODING L IFE : Systems Biology

Ideker, T., Galitski, T., & Hood, L. (2001) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.2.1.343 · Cited by 1,664

NAD + /NADH and NADP + /NADPH in Cellular Functions and Cell Death: Regulation and Biological Consequences

Ying, W. (2008) · Antioxidants & Redox Signaling · doi:10.1089/ars.2007.1672 · Cited by 1,494

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

Scott, M., Gunderson, C. W., Mateescu, E. M., Zhang, Z., & Hwa, T. (2010) · Science · doi:10.1126/science.1192588 · Cited by 1,470

A Linear Steady-State Treatment of Enzymatic Chains. General Properties, Control and Effector Strength

Heinrich, R., & Rapoport, T. A. (1974) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1974.tb03318.x · Cited by 1,400

Engineering Cellular Metabolism

Nielsen, J., & Keasling, J. D. (2016) · Cell · doi:10.1016/j.cell.2016.02.004 · Cited by 1,400

Global reconstruction of the human metabolic network based on genomic and bibliomic data

Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., & Palsson, B. Ø. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610772104 · Cited by 1,374

Symptomatic atherosclerosis is associated with an altered gut metagenome

Karlsson, F. H., Fåk, F., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Bäckhed, F., & Nielsen, J. (2012) · Nature Communications · doi:10.1038/ncomms2266 · Cited by 1,371 · cited 1×

Microbial production of fatty-acid-derived fuels and chemicals from plant biomass

Steen, E. J., Kang, Y., Bokinsky, G., Hu, Z., Schirmer, A., McClure, A., del Cardayré, S. B., & Keasling, J. D. (2010) · Nature · doi:10.1038/nature08721 · Cited by 1,338

Calorie Restriction-like Effects of 30 Days of Resveratrol Supplementation on Energy Metabolism and Metabolic Profile in Obese Humans

Timmers, S., Konings, E., Bilet, L., Houtkooper, R. H., van de Weijer, T., Goossens, G. H., Hoeks, J., van der Krieken, S., Ryu, D., Kersten, S., et al. (2011) · Cell Metabolism · doi:10.1016/j.cmet.2011.10.002 · Cited by 1,320

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., Assad-Garcia, N., Glass, J. I., & Covert, M. W. (2012) · Cell · doi:10.1016/j.cell.2012.05.044 · Cited by 1,300 · cited 2×

Discovering regulatory and signalling circuits in molecular interaction networks

Ideker, T., Ozier, O., Schwikowski, B., & Siegel, A. F. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s233 · Cited by 1,197

Toward a Science of Metabolic Engineering

Bailey, J. E. (1991) · Science · doi:10.1126/science.2047876 · Cited by 1,182

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

Yim, H. H., Haselbeck, R. J., Niu, W., Pujol-Baxley, C., Burgard, A. P., Boldt, J., Khandurina, J., Trawick, J. D., Osterhout, R. E., Stephen, R., et al. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.580 · Cited by 1,114

Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network

Förster, J., Famili, I., Fu, P., Palsson, B. Ø., & Nielsen, J. (2003) · Genome Research · doi:10.1101/gr.234503 · Cited by 1,069

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

Bar-Even, A., Noor, E., Savir, Y., Liebermeister, W., Davidi, D., Tawfik, D. S., & Milo, R. (2011) · Biochemistry · doi:10.1021/bi2002289 · Cited by 1,050

A community-driven global reconstruction of human metabolism

Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019

Complete biosynthesis of opioids in yeast

Galanie, S. S., Thodey, K., Trenchard, I. J., Interrante, M. V. F., & Smolke, C. D. (2015) · Science · doi:10.1126/science.aac9373 · Cited by 1,010

A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011

Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A., Nam, H., Feist, A. M., & Palsson, B. Ø. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.65 · Cited by 1,006

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

Edwards, J. S., Ibarra, R. U., & Palsson, B. Ø. (2001) · Nature Biotechnology · doi:10.1038/84379 · Cited by 941

Metabolic dependencies drive species co-occurrence in diverse microbial communities

Zelezniak, A., Andrejev, S., Ponomarova, O., Mende, D. R., Bork, P., & Patil, K. R. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1421834112 · Cited by 930

The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities

Edwards, J. S., & Palsson, B. O. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.10.5528 · Cited by 875

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

Ibarra, R. U., Edwards, J. S., & Palsson, B. O. (2002) · Nature · doi:10.1038/nature01149 · Cited by 857 · cited 2×

A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila , and Humans

Bricker, D. K., Taylor, E. B., Schell, J. C., Orsak, T., Boutron, A., Chen, Y.-C., Cox, J. E., Cardon, C. M., Van Vranken, J. G., Dephoure, N., et al. (2012) · Science · doi:10.1126/science.1218099 · Cited by 843

13C Metabolic Flux Analysis

Wiechert, W. (2001) · Metabolic Engineering · doi:10.1006/mben.2001.0187 · Cited by 817

Metabolic engineering for the microbial production of 1,3-propanediol.

Nakamura, C. E., & Whited, G. (2003) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2003.08.005 · Cited by 801

Overflow metabolism in Escherichia coli results from efficient proteome allocation

Basan, M., Hui, S., Okano, H., Zhang, Z., Shen, Y., Williamson, J. R., & Hwa, T. (2015) · Nature · doi:10.1038/nature15765 · Cited by 785

E-CELL: software environment for whole-cell simulation

Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T. S., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J. C., et al. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.1.72 · Cited by 764

The quantitative and condition-dependent Escherichia coli proteome

Schmidt, A., Kochanowski, K., Vedelaar, S. R., Ahrné, E., Volkmer, B., Callipo, L., Knoops, K., Bauer, M., Aebersold, R. H., & Heinemann, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3418 · Cited by 759

Sirtuin 1 Modulates Cellular Responses to Hypoxia by Deacetylating Hypoxia-Inducible Factor 1α

Lim, J.-H., Lee, Y.-M., Chun, Y.-S., Chen, J., Kim, J.-E., & Park, J.-W. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.023 · Cited by 758

Identification and Functional Expression of the Mitochondrial Pyruvate Carrier

Herzig, S., Raemy, E., Montessuit, S., Veuthey, J.-L., Zamboni, N., Westermann, B., Kunji, E. R. S., & Martinou, J.-C. (2012) · Science · doi:10.1126/science.1218530 · Cited by 747

Using Genome-scale Models to Predict Biological Capabilities

O’Brien, E. J., Monk, J. M., & Palsson, B. Ø. (2015) · Cell · doi:10.1016/j.cell.2015.05.019 · Cited by 732

Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

Schuetz, R. J., Kuepfer, L., & Sauer, U. (2007) · Molecular Systems Biology · doi:10.1038/msb4100162 · Cited by 706

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

Väremo, L., Nielsen, J., & Nookaew, I. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt111 · Cited by 688

Uncovering transcriptional regulation of metabolism by using metabolic network topology

Patil, K. R., & Nielsen, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406811102 · Cited by 644

Network-based prediction of human tissue-specific metabolism

Shlomi, T., Cabili, M. N., Herrgård, M. J., Palsson, B. Ø., & Ruppin, E. (2008) · Nature Biotechnology · doi:10.1038/nbt.1487 · Cited by 637

Network Rigidity and Metabolic Engineering in Metabolite Overproduction

Stephanopoulos, G. N., & Vallino, J. J. (1991) · Science · doi:10.1126/science.1904627 · Cited by 601

From zero to hero—Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production

Becker, J., Zelder, O., Häfner, S., Schröder, H., & Wittmann, C. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.01.003 · Cited by 594

Metabolic engineering of Escherichia coli for the production of l -valine based on transcriptome analysis and in silico gene knockout simulation

Park, J. H., Lee, K. H., Kim, T. Y., & Lee, S. Y. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702609104 · Cited by 592

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1492 · Cited by 588

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

Marguerat, S., Schmidt, A., Codlin, S., Chen, W., Aebersold, R., & Bähler, J. (2012) · Cell · doi:10.1016/j.cell.2012.09.019 · Cited by 571

Dynamic modeling of the central carbon metabolism of Escherichia coli

Chassagnole, C., Noisommit‐Rizzi, N., Schmid, J. W., Mauch, K., & Reuß, M. (2002) · Biotechnology and Bioengineering · doi:10.1002/bit.10288 · Cited by 553

Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis‐driven science in the post‐genomic era

Kell, D. B., & Oliver, S. G. (2004) · BioEssays · doi:10.1002/bies.10385 · Cited by 535

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

Mardinoğlu, A., Ågren, R., Kampf, C., Asplund, A., Uhlén, M., & Nielsen, J. (2014) · Nature Communications · doi:10.1038/ncomms4083 · Cited by 523

Mathematical Models of Protein Kinase Signal Transduction

Heinrich, R., Neel, B. G., & Rapoport, T. A. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00528-2 · Cited by 511

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

Frezza, C., Zheng, L., Folger, O., Rajagopalan, K. N., MacKenzie, E. D., Jerby, L., Micaroni, M., Chaneton, B., Adam, J., Hedley, A., et al. (2011) · Nature · doi:10.1038/nature10363 · Cited by 503

Predicting selective drug targets in cancer through metabolic networks

Folger, O., Jerby‐Arnon, L., Frezza, C., Gottlieb, E., Ruppin, E., & Shlomi, T. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.35 · Cited by 480

Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

O'Brien, E. J., Lerman, J. A., Chang, R. L., Hyduke, D. R., & Palsson, B. Ø. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.52 · Cited by 471

Assessing the Human Gut Microbiota in Metabolic Diseases

Karlsson, F. H., Tremaroli, V., Nielsen, J., & Bäckhed, F. (2013) · Diabetes · doi:10.2337/db13-0844 · Cited by 468

Evolutionary programming as a platform for in silico metabolic engineering

Patil, K. R., Rocha, I., Förster, J., & Nielsen, J. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-308 · Cited by 464

Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries

Hong, K.-K., & Nielsen, J. (2012) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-012-0945-1 · Cited by 451

Integrative model of the response of yeast to osmotic shock

Klipp, E., Nordlander, B., Krüger, R., Gennemark, P., & Hohmann, S. (2005) · Nature Biotechnology · doi:10.1038/nbt1114 · Cited by 447

Microbial production of short-chain alkanes

Choi, Y. J., & Lee, S. Y. (2013) · Nature · doi:10.1038/nature12536 · Cited by 446

Altered sterol composition renders yeast thermotolerant

Caspeta, L., Chen, Y., Ghiaci, P., Feizi, A., Buskov, S., Hallström, B. M., Petranović, D., & Nielsen, J. (2014) · Science · doi:10.1126/science.1258137 · Cited by 441

The Edinburgh human metabolic network reconstruction and its functional analysis

Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O., & Goryanin, I. (2007) · Molecular Systems Biology · doi:10.1038/msb4100177 · Cited by 435

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

Ågren, R., Bordel, S., Mardinoğlu, A., Pornputtapong, N., Nookaew, I., & Nielsen, J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002518 · Cited by 435

Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype

Edwards, J. S., & Palsson, B. Ø. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.25.17410 · Cited by 434

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Ågren, R., Liu, L., Shoaie, S., Vongsangnak, W., Nookaew, I., & Nielsen, J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002980 · Cited by 429

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

Shoaie, S., Ghaffari, P., Kovatcheva‐Datchary, P., Mardinoğlu, A., Sen, P., Pujos‐Guillot, E., de Wouters, T., Juste, C., Rizkalla, S. W., Chilloux, J., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.07.001 · Cited by 428

Resveratrol is not a direct activator of SIRT1 enzyme activity

Beher, D., Wu, J., Cumine, S., Kim, K. W., Lu, S., Atangan, L., & Wang, M. (2009) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2009.00901.x · Cited by 426

Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories

Zhou, Y. J., Buijs, N. A. A., Zhu, Z., Qin, J., Siewers, V., & Nielsen, J. (2016) · Nature Communications · doi:10.1038/ncomms11709 · Cited by 422

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

Machado, D., & Herrgård, M. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003580 · Cited by 415

Global metabolite analysis of yeast: evaluation of sample preparation methods

Villas-Bôas, S. G., Højer‐Pedersen, J., Åkesson, M., Smedsgaard, J., & Nielsen, J. (2005) · Yeast · doi:10.1002/yea.1308 · Cited by 399

Caloric restriction, SIRT1 and longevity

Cantó, C., & Auwerx, J. (2009) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2009.03.008 · Cited by 395

The role of TOR in autophagy regulation from yeast to plants and mammals

Díaz‐Troya, S., Pérez‐Pérez, M. E., Florencio, F. J., & Crespo, J. L. (2008) · Autophagy · doi:10.4161/auto.6555 · Cited by 392

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome‐scale metabolic modeling

Ågren, R., Mardinoğlu, A., Asplund, A., Kampf, C., Uhlén, M., & Nielsen, J. (2014) · Molecular Systems Biology · doi:10.1002/msb.145122 · Cited by 383

Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis

Rabinovich, S., Adler, L., Yizhak, K., Sarver, A., Silberman, A., Agron, S., Stettner, N., Sun, Q., Brandis, A., Helbling, D., et al. (2015) · Nature · doi:10.1038/nature15529 · Cited by 382

Defining the transcriptome and proteome in three functionally different human cell lines

Lundberg, E., Fagerberg, L., Klevebring, D., Matic, I., Geiger, T., Cox, J., Älgenäs, C., Lundeberg, J., Mann, M., & Uhlen, M. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.106 · Cited by 373

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production

Bro, C., Regenberg, B., FORSTER, J., & Nielsen, J. (2005) · Metabolic Engineering · doi:10.1016/j.ymben.2005.09.007 · Cited by 368

The Cost of Protein Production

Kafri, M., Metzl-Raz, E., Jona, G., & Barkai, N. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.12.015 · Cited by 366

In silico design and adaptive evolution of Escherichia coli for production of lactic acid

Fong, S. S., Burgard, A. P., Herring, C. D., Knight, E. M., Blattner, F. R., Maranas, C. D., & Palsson, B. Ø. (2005) · Biotechnology and Bioengineering · doi:10.1002/bit.20542 · Cited by 363

Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network

Famili, I., Förster, J., Nielsen, J., & Palsson, B. O. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2235812100 · Cited by 353

Cardiac Action and Pacemaker Potentials based on the Hodgkin-Huxley Equations

Noble, D. (1960) · Nature · doi:10.1038/188495b0 · Cited by 342

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli

McCloskey, D., Palsson, B. Ø., & Feist, A. M. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.18 · Cited by 327

Metabolic engineering

Nielsen, J. (2001) · Applied Microbiology and Biotechnology · doi:10.1007/s002530000511 · Cited by 327

Genome-Scale Metabolic Model of Helicobacter pylori 26695

Schilling, C. H., Covert, M. W., Famili, I., Church, G. M., Edwards, J. S., & Palsson, B. Ø. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.16.4582-4593.2002 · Cited by 326

Total biosynthesis of hydrocortisone from a simple carbon source in yeast

Szczebara, F. M., Chandelier, C., Villeret, C., Heneman-Masurel, A., Bourot, S., Duport, C., Blanchard, S., Groisillier, A., Testet, E., Costaglioli, P., et al. (2003) · Nature Biotechnology · doi:10.1038/nbt775 · Cited by 326

Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism

Fischer, E., & Sauer, U. (2005) · Nature Genetics · doi:10.1038/ng1555 · Cited by 321

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

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Overproduction of glycolytic enzymes in yeast

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De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae

Li, M., Kildegaard, K. R., Chen, Y., Prado, A. R., Borodina, I., & Nielsen, J. (2015) · Metabolic Engineering · doi:10.1016/j.ymben.2015.08.007 · Cited by 286

Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality

Jerby‐Arnon, L., Pfetzer, N., Waldman, Y. Y., McGarry, L., James, D. T., Shanks, E. J., Seashore-Ludlow, B. A., Weinstock, A., Geiger, T., Clemons, P. A., et al. (2014) · Cell · doi:10.1016/j.cell.2014.07.027 · Cited by 282

Fat synthesis in adipose tissue. An examination of stoichiometric constraints

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Understanding the interactions between bacteria in the human gut through metabolic modeling

Shoaie, S., Karlsson, F. H., Mardinoğlu, A., Nookaew, I., Bordel, S., & Nielsen, J. (2013) · Scientific Reports · doi:10.1038/srep02532 · Cited by 269

Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode

Scalcinati, G., Knuf, C., Partow, S., Chen, Y., Maury, J., Schalk, M., Daviet, L., Nielsen, J., & Siewers, V. (2012) · Metabolic Engineering · doi:10.1016/j.ymben.2012.01.007 · Cited by 255

Real-time metabolome profiling of the metabolic switch between starvation and growth

Link, H., Fuhrer, T., Gerosa, L., Zamboni, N., & Sauer, U. (2015) · Nature Methods · doi:10.1038/nmeth.3584 · Cited by 251

The danger of metabolic pathways with turbo design

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Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

Shlomi, T., Benyamini, T., Gottlieb, E., Sharan, R., & Ruppin, E. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002018 · Cited by 244

The next wave in metabolome analysis

Nielsen, J., & Oliver, S. G. (2005) · Trends in biotechnology · doi:10.1016/j.tibtech.2005.08.005 · Cited by 244

Non-Enzymatic Glycolysis and Pentose Phosphate Pathway-Like Reactions in a Plausible Archean Ocean

Keller, M. A., Turchyn, A. V., & Ralser, M. (2014) · Molecular Systems Biology · doi:10.1002/msb.20145228 · Cited by 242

Integration of clinical data with a genome‐scale metabolic model of the human adipocyte

Mardinoğlu, A., Ågren, R., Kampf, C., Asplund, A., Nookaew, I., Jacobson, P., Walley, A. J., Froguel, P., Carlsson, L. M. S., Uhlén, M., et al. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.5 · Cited by 237

It Is All about MetabolicFluxes

Nielsen, J. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.24.7031-7035.2003 · Cited by 236

Optimization of Ethanol Production in Saccharomyces cerevisiae by Metabolic Engineering of the Ammonium Assimilation

Nissen, T. L., Kielland‐Brandt, M. C., Nielsen, J., & Villadsen, J. (2000) · Metabolic Engineering · doi:10.1006/mben.1999.0140 · Cited by 232

Integration of gene expression data into genome-scale metabolic models

Åkesson, M., Förster, J., & Nielsen, J. (2004) · Metabolic Engineering · doi:10.1016/j.ymben.2003.12.002 · Cited by 204

Recent advances in reconstruction and applications of genome-scale metabolic models

Kim, T. Y., Sohn, S. B., Kim, Y. B., Kim, W. J., & Lee, S. Y. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.10.007 · Cited by 202

Optimizing genome-scale network reconstructions

Monk, J. M., Nogales, J., & Palsson, B. Ø. (2014) · Nature Biotechnology · doi:10.1038/nbt.2870 · Cited by 200

Metabolic flux analysis at ultra short time scale: Isotopically non-stationary 13C labeling experiments

Nöh, K., Grönke, K., Luo, B., Takors, R., Oldiges, M., & Wiechert, W. (2006) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2006.11.015 · Cited by 200

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

Andersen, M. R., Nielsen, M. L., & Nielsen, J. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.12 · Cited by 199

Metformin Decreases Glucose Oxidation and Increases the Dependency of Prostate Cancer Cells on Reductive Glutamine Metabolism

Fendt, S., Bell, E. L., Keibler, M. A., Davidson, S. M., Wirth, G. J., Fiske, B. P., Mayers, J. R., Schwab, M. G., Bellinger, G., Csibi, A., et al. (2013) · Cancer Research · doi:10.1158/0008-5472.can-13-0080 · Cited by 196

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

Zhang, J., Vaga, S., Chumnanpuen, P., Kumar, R., Vemuri, G. N., Aebersold, R. H., & Nielsen, J. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.80 · Cited by 191

Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis

Chubukov, V., Uhr, M., Le Chat, L., Kleijn, R. J., Jules, M., Link, H., Aymerich, S., Stelling, J., & Sauer, U. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.66 · Cited by 191

Modeling cancer metabolism on a genome scale

Yizhak, K., Chaneton, B., Gottlieb, E., & Ruppin, E. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145307 · Cited by 187

Spermidine: A novel autophagy inducer and longevity elixir

Madeo, F., Eisenberg, T., Büttner, S., Ruckenstuhl, C., & Kroemer, G. (2010) · Autophagy · doi:10.4161/auto.6.1.10600 · Cited by 186

Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes

Bordel, S., Agren, R., & Nielsen, J. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000859 · Cited by 185

Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network

Østergaard, S., Lisbeth Olsson, A., Johnston, M., & Nielsen, J. (2000) · Nature Biotechnology · doi:10.1038/82400 · Cited by 184

Longevity, aging and rapamycin

Ehninger, D., Neff, F., & Xie, K. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1677-1 · Cited by 183

Personal model‐assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLD

Mardinoğlu, A., Björnson, E., Zhang, C., Klevstig, M., Söderlund, S., Ståhlman, M., Adiels, M., Hakkarainen, A., Lundbom, N. M. I., Kiliçarslan, M., et al. (2017) · Molecular Systems Biology · doi:10.15252/msb.20167422 · Cited by 180

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

Otero, J. M., Cimini, D., Patil, K. R., Poulsen, S. G., Lisbeth Olsson, A., & Nielsen, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054144 · Cited by 176

Impact of systems biology on metabolic engineering ofSaccharomyces cerevisiae

Nielsen, J., & Jewett, M. C. (2007) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2007.00302.x · Cited by 169

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data

Gerosa, L., van Rijsewijk, B. R. B. H., Christodoulou, D., Kochanowski, K., Schmidt, T., Noor, Ε., & Sauer, U. (2015) · Cell Systems · doi:10.1016/j.cels.2015.09.008 · Cited by 161

Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis

Hong, K.-K., Vongsangnak, W., Vemuri, G. N., & Nielsen, J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1103219108 · Cited by 161

13C metabolic flux analysis in complex systems

Zamboni, N. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.08.009 · Cited by 156

Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism

Aung, H. W., Henry, S. A., & Walker, L. P. (2013) · Industrial Biotechnology · doi:10.1089/ind.2013.0013 · Cited by 156

Transcriptomics resources of human tissues and organs

Uhlén, M., Hallström, B. M., Lindskog, C., Mardinoğlu, A., Pontén, F., & Nielsen, J. (2016) · Molecular Systems Biology · doi:10.15252/msb.20155865 · Cited by 152

Towards kinetic modeling of genome‐scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

Chakrabarti, A., Mišković, L., Soh, K. C., & Vassily Hatzimanikatis, A. (2013) · Biotechnology Journal · doi:10.1002/biot.201300091 · Cited by 149

Computer model for glucose‐limited growth of a single cell of Escherichia coli B/r‐A

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Integration of metabolome data with metabolic networks reveals reporter reactions

Çakır, T., Patil, K. R., Önsan, Z. I., Ülgen, K. Ö., Kırdar, B., & Nielsen, J. (2006) · Molecular Systems Biology · doi:10.1038/msb4100085 · Cited by 140

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

Nilsson, A., & Nielsen, J. (2016) · Scientific Reports · doi:10.1038/srep22264 · Cited by 137

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

Oliveira, A. P., Patil, K. R., & Nielsen, J. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-17 · Cited by 136

Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae

Rossell, S., van der Weijden, C. C., Lindenbergh, A., van Tuijl, A., Francke, C., Bakker, B. M., & Westerhoff, H. V. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509831103 · Cited by 133

Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma

Gatto, F., Nookaew, I., & Nielsen, J. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319196111 · Cited by 132

A unifying view of 21st century systems biology

Vidal, M. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.11.024 · Cited by 130

Improvement of Galactose Uptake in Saccharomyces cerevisiae through Overexpression of Phosphoglucomutase: Example of Transcript Analysis as a Tool in Inverse Metabolic Engineering

Bro, C., Knudsen, S., Regenberg, B., Lisbeth Olsson, A., & Nielsen, J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.11.6465-6472.2005 · Cited by 126

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

Hadadi, N., & Vassily Hatzimanikatis, A. (2015) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2015.06.025 · Cited by 126

Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress

Petelenz, E., Kühn, C., Nordlander, B., Klein, D., Hong, K.-K., Jacobson, T., Dahl, P. J., Schaber, J., Nielsen, J., Hohmann, S., et al. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003084 · Cited by 125

Mathematical Models for Fermentation Processes

Fredrickson, A. G., Megee, R. D., & Tsuchiya, H. M. (1970) · Advances in applied microbiology · doi:10.1016/s0065-2164(08)70413-1 · Cited by 125

Identification of metabolic model: Citrate production from glucose by Candida lipolytica

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Dynamic metabolic flux analysis (DMFA): A framework for determining fluxes at metabolic non-steady state

Leighty, R. W., & Antoniewicz, M. R. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.09.010 · Cited by 118

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes

Väremo, L., Schéele, C., Broholm, C., Mardinoğlu, A., Kampf, C., Asplund, A., Nookaew, I., Uhlén, M., Pedersen, B. K., & Nielsen, J. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.04.010 · Cited by 118

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

Chang, R. L., Andrews, K. A., Kim, D., Li, Z., Godzik, A., & Palsson, B. Ø. (2013) · Science · doi:10.1126/science.1234012 · Cited by 116

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

Canelas, A. B., Harrison, N., Fazio, A., Zhang, J., Pitkänen, J., van den Brink, J., Bakker, B. M., Bogner, L., Bouwman, J., Castrillo, J. I., et al. (2010) · Nature Communications · doi:10.1038/ncomms1150 · Cited by 115

Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

Usaite, R., Jewett, M. C., Oliveira, A. P., Yates, J. R., Lisbeth Olsson, A., & Nielsen, J. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.67 · Cited by 110

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

Thiele, I., Fleming, R. M. T., Que, R. A., Bordbar, A., Diep, D. H., & Palsson, B. Ø. (2012) · PLoS ONE · doi:10.1371/journal.pone.0045635 · Cited by 109

Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions

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Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

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Deciphering the transcriptional regulatory logic of amino acid metabolism

Cho, B., Federowicz, S., Park, Y.-S., Zengler, K., & Palsson, B. Ø. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.710 · Cited by 94

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

Brunk, E., George, K. W., Alonso-Gutiérrez, J., Thompson, M. G., Baidoo, E., Wang, G., Petzold, C. J., McCloskey, D., Monk, J. M., Yang, L., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.04.004 · Cited by 88

Mapping Yeast Transcriptional Networks

Hughes, T. R., & de Boer, C. G. (2013) · Genetics · doi:10.1534/genetics.113.153262 · Cited by 85

New paradigms for metabolic modeling of human cells

Mardinoğlu, A., & Nielsen, J. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.12.013 · Cited by 80

Genome-Scale Modeling of the Protein Secretory Machinery in Yeast

Feizi, A., Österlund, T., Petranović, D., Bordel, S., & Nielsen, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0063284 · Cited by 79

Genome scale models of yeast: towards standardized evaluation and consistent omic integration

Sánchez, B. J., & Nielsen, J. (2015) · Integrative Biology · doi:10.1039/c5ib00083a · Cited by 75

Isolation of a Regulatory Mutant of Fructose-1, 6-diphosphatase in Saccharomyces carlsbergensis

van de Poll, K. W., Kerkenaar, A., & Schamhart, D. H. J. (1974) · Journal of Bacteriology · doi:10.1128/jb.117.3.965-970.1974 · Cited by 73

Yeast cell factories on the horizon

Nielsen, J. (2015) · Science · doi:10.1126/science.aad2081 · Cited by 73

Are we ready for genome-scale modeling in plants?

Collakova, E., Yen, J. Y., & Senger, R. S. (2012) · Plant Science · doi:10.1016/j.plantsci.2012.04.010 · Cited by 68

Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis

Oliveira, A. P., Ludwig, C., Zampieri, M., Weisser, H., Aebersold, R. H., & Sauer, U. (2015) · Science Signaling · doi:10.1126/scisignal.2005768 · Cited by 68

The roles of galactitol, galactose‐1‐phosphate, and phosphoglucomutase in galactose‐induced toxicity in Saccharomyces cerevisiae

de Jongh, W. A., Bro, C., Østergaard, S., Regenberg, B., Lisbeth Olsson, A., & Nielsen, J. (2008) · Biotechnology and Bioengineering · doi:10.1002/bit.21890 · Cited by 67

Unraveling condition‐dependent networks of transcription factors that control metabolic pathway activity in yeast

Fendt, S., Oliveira, A. P., Christen, S., Picotti, P., Dechant, R. C., & Sauer, U. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.91 · Cited by 67

Expression of Genes Encoding F 1 -ATPase Results in Uncoupling of Glycolysis from Biomass Production in Lactococcus lactis

Koebmann, B. J., Solem, C., Pedersen, M. B., Nilsson, D., & Jensen, P. R. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.9.4274-4282.2002 · Cited by 66

Glycosaminoglycan Profiling in Patients’ Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma

Gatto, F., Volpi, N., Nilsson, H., Nookaew, I., Maruzzo, M., Roma, A., Johansson, M., Stierner, U. K., Lundstam, S., Basso, U., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.056 · Cited by 59

Quantification of statin effects on hepatic cholesterol synthesis by transient 13C-flux analysis

Maier, K., Hofmann, U., Bauer, A., Niebel, A., Vacun, G., Reuß, M., & Mauch, K. (2009) · Metabolic Engineering · doi:10.1016/j.ymben.2009.06.001 · Cited by 51

Glucose de‐repression by yeast AMP ‐activated protein kinase SNF 1 is controlled via at least two independent steps

García‐Salcedo, R., Lubitz, T., Beltran, G., Elbing, K., Tian, Y., Frey, S., Wolkenhauer, O., Krantz, M., Klipp, E., & Hohmann, S. (2014) · FEBS Journal · doi:10.1111/febs.12753 · Cited by 49

Specific ATP and specific oxygen uptake rate in immobilized cell aggregates: Experimental results and theoretical analysis using a structured model of immobilized cell growth

Gikas, P., & Livingston, A. G. (1997) · Biotechnology and Bioengineering · doi:10.1002/(sici)1097-0290(19970820)55:4 · Cited by 39

Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae

Liu, G., Bergenholm, D., & Nielsen, J. (2016) · mBio · doi:10.1128/mbio.00559-16 · Cited by 26

Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors

Österlund, T., Bordel, S., & Nielsen, J. (2015) · Integrative Biology · doi:10.1039/c4ib00247d · Cited by 23

Polymerase chain reaction engineering

Hsu, J. T., Das, S., & Mohapatra, S. C. (1997) · Biotechnology and Bioengineering · doi:10.1002/(sici)1097-0290(19970720)55:2 · Cited by 22

Dynamic13C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains

Hong, K.-K., Hou, J., Shoaie, S., Nielsen, J., & Bordel, S. (2012) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2012.00823.x · Cited by 20

Schizosaccharomyces pombegmd3+/alg11+ is a functional homologue ofSaccharomyces cerevisiaeALG11 which is involved inN-linked oligosaccharide synthesis

Umeda, K., Yoko‐o, T., Nakayama, K.-I., Suzuki, T., & Jigami, Y. (2000) · Yeast · doi:10.1002/1097-0061(200010)16:14 · Cited by 12

Trehalose-6-phosphate synthase and stabilization of yeast glycolysis

Fraenkel, D. G., & Nielsen, J. (2015) · FEMS Yeast Research · doi:10.1093/femsyr/fov100 · Cited by 7

2023 international olympic committee's (IOC) consensus statement on relative energy deficiency in sport (REDs)

Mountjoy, M., Ackerman, K. E., Bailey, D. M., Burke, L. M., Constantini, N., Hackney, A. C., Heikura, I. A., Melin, A., Pensgaard, A. M., Stellingwerff, T., et al. (2023) · British Journal of Sports Medicine · doi:10.1136/bjsports-2023-106994 · Cited by 724

Systems biology and multi-omics integration: viewpoints from the metabolomics research community

Pinu, F. R., Beale, D. J., Paten, A. M., Kouremenos, K., Swarup, S., Schirra, H. J., & Wishart, D. (2019) · Metabolites · doi:10.3390/metabo9040076 · Cited by 723

Pseudomonas putida as a functional chassis for industrial biocatalysis: from native biochemistry to trans-metabolism

Nikel, P. I., & de Lorenzo, V. (2018) · Metabolic Engineering · doi:10.1016/j.ymben.2018.05.005 · Cited by 480

Yeast Systems Biology: Model Organism and Cell Factory

Nielsen, J. (2019) · Biotechnology Journal · doi:10.1002/biot.201800421 · Cited by 298

Drosophila as a model for ageing

Piper, M. D. W., & Partridge, L. (2018) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2017.09.016 · Cited by 273

Background

(2015) · BENTHAM SCIENCE PUBLISHERS eBooks · doi:10.2174/9781681080864115010004

Thermodynamics-based Significance Ranking of Candidates for Metabolomics

Kiparissides, A., & Vassily Hatzimanikatis, A. (2013) · Infoscience (Ecole Polytechnique Fédérale de Lausanne)

Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models

Dahal, S., Yurkovich, J. T., Xu, H., Palsson, B. Ø., & Yang, L. (2020) · PROTEOMICS · doi:10.1002/pmic.201900282 · Cited by 55

Quantitative modeling of human metabolism: A call for a community effort

Masid, M., & Vassily Hatzimanikatis, A. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.04.008 · Cited by 7

From Gene Expression to Metabolic Fluxes

Oliveira, A. P., Jewett, M. C., & Nielsen, J. (2008) · Humana Press eBooks · doi:10.1007/978-1-59745-531-2_3 · Cited by 7