A genome-scale database and reconstruction of Caenorhabditis elegans metabolism

R: A Language and Environment for Statistical Computing

R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., & Mello, C. C. (1998) · Nature · doi:10.1038/35888 · Cited by 15,429 · see citing works

Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology

Berg, J. (1998) · Science · doi:10.1126/science.282.5396.2012 · Cited by 4,458 · see citing works

The embryonic cell lineage of the nematode Caenorhabditis elegans

Sulston, J. E., Schierenberg, E., White, J. G., & Thomson, J. N. (1983) · Developmental Biology · doi:10.1016/0012-1606(83)90201-4 · Cited by 4,199 · see citing works

WoLF PSORT: protein localization predictor

Horton, P., Park, K., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm259 · Cited by 4,154 · see citing works

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395 · see citing works

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060 · see citing works

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835 · see citing works

A protocol for generating a high-quality genome-scale metabolic reconstruction

Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789 · see citing works

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 · see citing works

Biochemical, physiological and medical aspects of ubiquinone function

Ernster, L., & Dallner, G. (1995) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/0925-4439(95)00028-3 · Cited by 1,232 · see citing works

Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans

Herndon, L. A., Schmeissner, P. J., Dudaronek, J. M., Brown, P. A., Listner, K. M., Sakano, Y., Paupard, M. C., Hall, D. H., & Driscoll, M. (2002) · Nature · doi:10.1038/nature01135 · Cited by 1,214 · see citing works

Glucose restriction extends Caenorhabditis elegans life span by inducing mitochondrial respiration and increasing oxidative stress

Schulz, T. J., Zarse, K., Voigt, A., Urban, N., Birringer, M., & Ristow, M. (2007) · Cell Metabolism · doi:10.1016/j.cmet.2007.08.011 · Cited by 1,209 · see citing works

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1103 · Cited by 1,204 · see citing works

Finding function in novel targets: C. elegans as a model organism

Kaletta, T., & Hengartner, M. O. (2006) · Nature Reviews Drug Discovery · doi:10.1038/nrd2031 · Cited by 1,091 · see citing works

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 · see citing works

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 · see citing works

The genetics of caloric restriction in Caenorhabditis elegans

Lakowski, B., & Hekimi, S. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.22.13091 · Cited by 967 · see citing works

Neuropharmacology of quinolinic and kynurenic acids.

Stone, T. W. (1993) · Pharmacological Reviews · doi:10.1016/s0031-6997(25)00441-7 · Cited by 949 · see citing works

The postembryonic cell lineages of the hermaphrodite and male gonads in Caenorhabditis elegans

Kimble, J. E., & Hirsh, D. (1979) · Developmental Biology · doi:10.1016/0012-1606(79)90035-6 · Cited by 886 · see citing works

Applications of genome‐scale metabolic reconstructions

Oberhardt, M., Palsson, B. Ø., & Papin, J. A. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.77 · Cited by 820 · see citing works

Physiology of the bacterial cell : a molecular approach

Neidhardt, F. C., Ingraham, J. L., & Schaechter, M. (1990) · Cited by 808 · see citing works

Calorie Restriction Increases Muscle Mitochondrial Biogenesis in Healthy Humans

Civitarese, A. E., Carling, S., Heilbronn, L. K., Hulver, M. H., Ukropcova, B., Deutsch, W. A., Smith, S. R., & Ravussin, E. (2007) · PLoS Medicine · doi:10.1371/journal.pmed.0040076 · Cited by 790 · see citing works

How increased oxidative stress promotes longevity and metabolic health: The concept of mitochondrial hormesis (mitohormesis)

Ristow, M., & Zarse, K. (2010) · Experimental Gerontology · doi:10.1016/j.exger.2010.03.014 · Cited by 789 · see citing works

Physiology of the bacterial cell — A molecular approach

Murrell, J. C. (1991) · Trends in Genetics · doi:10.1016/0168-9525(91)90427-r · Cited by 784 · see citing works

Biological stress response terminology: Integrating the concepts of adaptive response and preconditioning stress within a hormetic dose–response framework

Calabrese, E. J., Bachmann, K. A., Bailer, A. J., Bolger, P. M., Borak, J. B., Cai, L., Nina Cedergreen, G., Cherian, M. G., Chiueh, C. C., Clarkson, T. W., et al. (2007) · Toxicology and Applied Pharmacology · doi:10.1016/j.taap.2007.02.015 · Cited by 751 · see citing works

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694 · see citing works

Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering

Schuster, S. (1999) · Trends in biotechnology · doi:10.1016/s0167-7799(98)01290-6 · Cited by 665 · see citing works

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 · see citing works

SUBSTRATE SPECIFICITY OF BRAIN HEXOKINASE

Sols, A., & Crane, R. K. (1954) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)65384-0 · Cited by 599 · see citing works

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

Schellenberger, J., Park, J. O., Conrad, T. M., & Palsson, B. Ø. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-213 · Cited by 585 · see citing works

GenBank

Benson, D. A., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1079 · Cited by 552 · see citing works

EcoCyc: fusing model organism databases with systems biology

Keseler, I. M., Mackie, A. M., Peralta-Gil, M., Santos-Zavaleta, A., Gama‐Castro, S., Bonavides-Martínez, C., Fulcher, C. A., Huerta, A. M., Kothari, A., Krummenacker, M., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1027 · Cited by 542 · see citing works

Determination of Life-Span in Caenorhabditis elegans by Four Clock Genes

Lakowski, B., & Hekimi, S. (1996) · Science · doi:10.1126/science.272.5264.1010 · Cited by 539 · see citing works

New Genes Tied to Endocrine, Metabolic, and Dietary Regulation of Lifespan from a Caenorhabditis elegans Genomic RNAi Screen

Hansen, M., Hsu, A., Dillin, A. G., & Kenyon, C. J. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010017 · Cited by 533 · see citing works

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 507 · see citing works

Lifespan Regulation by Evolutionarily Conserved Genes Essential for Viability

Curran, S. P., & Ruvkun, G. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030056 · Cited by 479 · see citing works

OrthoList: A Compendium of C. elegans Genes with Human Orthologs

Shaye, D. D., & Greenwald, I. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020085 · Cited by 469 · see citing works

A method for the isolation of longevity mutants in the nematode Caenorhabditis elegans and initial results

Klass, M. R. (1983) · Mechanisms of Ageing and Development · doi:10.1016/0047-6374(83)90082-9 · Cited by 449 · see citing works

Impaired insulin/IGF1 signaling extends life span by promoting mitochondrial L-proline catabolism to induce a transient ROS signal

Zarse, K., Schmeisser, S., Groth, M., Priebe, S., Beuster, G., Kuhlow, D., Guthke, R., Platzer, M., Kahn, C. R., & Ristow, M. (2012) · Cell Metabolism · doi:10.1016/j.cmet.2012.02.013 · Cited by 430 · see citing works

Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice

Cao, S. X., Dhahbi, J. M., Mote, P. L., & Spindler, S. R. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.191313598 · Cited by 413 · see citing works

Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys

Kayo, T., Allison, D. B., Weindruch, R., & Prolla, T. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.081061898 · Cited by 384 · see citing works

iMAT: an integrative metabolic analysis tool

Zur, H., Ruppin, E., & Shlomi, T. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq602 · Cited by 357 · see citing works

Transcriptional profiles associated with aging and middle age-onset caloric restriction in mouse hearts

Lee, C.-K., Allison, D. B., Brand, J., Weindruch, R., & Prolla, T. A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.232308999 · Cited by 314 · see citing works

Global analysis of dauer gene expression inCaenorhabditis elegans

Wang, J., & Kim, S. K. (2003) · Development · doi:10.1242/dev.00363 · Cited by 313 · see citing works

Genomic Analysis of Gene Expression in C. elegans

Hill, A. A. V., Hunter, C. P., Tsung, B. T., Tucker‐Kellogg, G., & Brown, E. L. (2000) · Science · doi:10.1126/science.290.5492.809 · Cited by 299 · see citing works

A role for Caenorhabditis elegans in understanding the function and interactions of human disease genes

Culetto, E. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.6.869 · Cited by 288 · see citing works

Reconstructing eukaryotic NAD metabolism.

Rongvaux, A., Andris, F., Gool, F. V., & Leo, O. (2003) · Bioessays · doi:10.1002/bies.10297 · Cited by 284 · see citing works

Membrane Fatty Acid Unsaturation, Protection against Oxidative Stress, and Maximum Life Span

Pamplona, R., Barja, G., & Portero‐Otín, M. (2002) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2002.tb02118.x · Cited by 264 · see citing works

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

GREEN, M. L., & Karp, P. D. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-76 · Cited by 259 · see citing works

Extension of Life-Span in Caenorhabditis elegans by a Diet Lacking Coenzyme Q

Larsen, P. L., & Clarke, C. F. (2002) · Science · doi:10.1126/science.1064653 · Cited by 249 · see citing works

Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide

Schmeisser, K., Mansfeld, J., Kuhlow, D., Weimer, S., Priebe, S., Heiland, I., Birringer, M., Groth, M., Segref, A., Kanfi, Y., et al. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1352 · Cited by 236 · see citing works

Functional integration of a metabolic network model and expression data without arbitrary thresholding

Jensen, P. A., & Papin, J. A. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq702 · Cited by 226 · see citing works

Mechanisms of amino acid-mediated lifespan extension in Caenorhabditis elegans

Edwards, C., Canfield, J., Copes, N., Brito, A. G., Rehan, M. A. Y., Lipps, D., Brunquell, J., Westerheide, S. D., & Bradshaw, P. C. (2015) · BMC Genetics · doi:10.1186/s12863-015-0167-2 · Cited by 218 · see citing works

On the importance of fatty acid composition of membranes for aging

Hulbert, A. J. (2005) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2004.11.024 · Cited by 208 · see citing works

Altered Quinone Biosynthesis in the Long-lived clk-1Mutants of Caenorhabditis elegans

Miyadera, H., Amino, H., Hiraishi, A., Taka, H., Murayama, K., Miyoshi, H., Sakamoto, K., Ishii, N., Hekimi, S., & Kita, K. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.c000889200 · Cited by 199 · see citing works

Delaying aging and the aging-associated decline in protein homeostasis by inhibition of tryptophan degradation

van der Goot, A. T., Zhu, W., Vázquez‐Manrique, R. P., Seinstra, R. I., Dettmer, K., Michels, H., Farina, F., Krijnen, J., Melki, R., Buijsman, R. C., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203083109 · Cited by 192 · see citing works

Machine learning methods for metabolic pathway prediction

Dale, J. M., Popescu, L., & Karp, P. D. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-15 · Cited by 168 · see citing works

WormBase 2014: new views of curated biology

Harris, T. W., Baran, J., Bieri, T. A., Mayes, A. C., Chan, J., Chen, W. J., Davis, P., Done, J., Grove, C. A., Howe, K., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1063 · Cited by 164 · see citing works

Arresting development arrests aging in the nematode Caenorhabditis elegans

Johnson, T. E., Mitchell, D., Kline, S., Kemal, R., & Foy, J. (1984) · Mechanisms of Ageing and Development · doi:10.1016/0047-6374(84)90150-7 · Cited by 162 · see citing works

Serum profiling of healthy aging identifies phospho- and sphingolipid species as markers of human longevity

Montoliu, I., Scherer, M., Beguelin, F., Silva, L. D., Mari, D., Salvioli, S., Martin, F., Capri, M., Bucci, L., Ostan, R., et al. (2014) · Aging · doi:10.18632/aging.100630 · Cited by 151 · see citing works

Branched-chain amino acid catabolism is a conserved regulator of physiological ageing

Mansfeld, J., Urban, N., Priebe, S., Groth, M., Frahm, C., Hartmann, N., Gebauer, J., Ravichandran, M., Dommaschk, A., Schmeisser, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms10043 · Cited by 149 · see citing works

A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration

Yizhak, K., Dévédec, S. E. L., Rogkoti, V.-M., Baenke, F., de Boer, V. C. J., Frezza, C., Schulze, A., van de Water, B., & Ruppin, E. (2014) · Molecular Systems Biology · doi:10.15252/msb.20134993 · Cited by 147 · see citing works

Longitudinal RNA-Seq Analysis of Vertebrate Aging Identifies Mitochondrial Complex I as a Small-Molecule-Sensitive Modifier of Lifespan

Baumgart, M., Priebe, S., Groth, M., Hartmann, N., Menzel, U., Pandolfini, L., Koch, P., Felder, M., Ristow, M., Englert, C., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.01.014 · Cited by 147 · see citing works

Neuronal ROS signaling rather than AMPK/sirtuin-mediated energy sensing links dietary restriction to lifespan extension

Schmeisser, S., Priebe, S., Groth, M., Monajembashi, S., Hemmerich, P. H., Guthke, R., Platzer, M., & Ristow, M. (2013) · Molecular Metabolism · doi:10.1016/j.molmet.2013.02.002 · Cited by 145 · see citing works

Chemically defined medium and Caenorhabditis elegans

Szewczyk, N. J., Kozak, E. M., & Conley, C. A. (2003) · BMC Biotechnology · doi:10.1186/1472-6750-3-19 · Cited by 137 · see citing works

Induction of Cytoprotective Pathways Is Central to the Extension of Lifespan Conferred by Multiple Longevity Pathways

Shore, D. E., Carr, C. E., & Ruvkun, G. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002792 · Cited by 125 · see citing works

Tissue coenzyme Q (ubiquinone) and protein concentrations over the life span of the laboratory rat

Beyer, R. E., Burnett, B.-A., Cartwright, K. J., Edington, D. W., Falzon, M. J., Kreitman, K. R., Kuhn, T. W., Ramp, B. J., Rhee, S. Y. S., Rosenwasser, M. J., et al. (1985) · Mechanisms of Ageing and Development · doi:10.1016/0047-6374(85)90085-5 · Cited by 119 · see citing works

Rate of aerobic metabolism and superoxide production rate potential in the nematodeCaenorhabditis elegans

Vanfleteren, J. R., & Vreese, A. D. (1996) · Journal of Experimental Zoology · doi:10.1002/(sici)1097-010x(19960201)274:2 · Cited by 117 · see citing works

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

Ganter, M., Bernard, T., Moretti, S., Stelling, J., & Pagni, M. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt036 · Cited by 113 · see citing works

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

Sahoo, S., Aurich, M. K., Jónsson, J. J., & Thiele, I. (2014) · Frontiers in Physiology · doi:10.3389/fphys.2014.00091 · Cited by 103 · see citing works

Systems biology of host–microbe metabolomics

Heinken, A., & Thiele, I. (2015) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1301 · Cited by 96 · see citing works

Dietary restriction attenuates age‐associated muscle atrophy by lowering oxidative stress in mice even in complete absence of CuZnSOD

Jang, Y. C., Liu, Y., Hayworth, C. R., Bhattacharya, A., Lustgarten, M. S., Müller, F. L., Chaudhuri, A. R., Qi, W., Li, Y., Huang, J., et al. (2012) · Aging Cell · doi:10.1111/j.1474-9726.2012.00843.x · Cited by 94 · see citing works

Isolation and Functional Expression of Human COQ3, a Gene Encoding a Methyltransferase Required for Ubiquinone Biosynthesis

Jonassen, T., & Clarke, C. F. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.17.12381 · Cited by 89 · see citing works

Development and Fertility in Caenorhabditis elegans clk-1 Mutants Depend upon Transport of Dietary Coenzyme Q8 to Mitochondria

Jonassen, T., Marbois, B. N., Faull, K. F., Clarke, C. F., & Larsen, P. L. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m204758200 · Cited by 87 · see citing works

Ageing is reversed, and metabolism is reset to young levels in recovering dauer larvae of C. elegans

Houthoofd, K., Braeckman, B. P., Lenaerts, I., Brys, K., Vreese, A. D., Eygen, S. V., & Vanfleteren, J. R. (2002) · Experimental Gerontology · doi:10.1016/s0531-5565(02)00063-3 · Cited by 87 · see citing works

Can sugars be produced from fatty acids? A test case for pathway analysis tools

de Figueiredo, L. F., Schuster, S., Kaleta, C., & Fell, D. A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn500 · Cited by 85 · see citing works

Bifunctional Glyoxylate Cycle Protein of Caenorhabditis elegans: A Developmentally Regulated Protein of Intestine and Muscle

Liu, F., Thatcher, J. D., Barral, J. M., & Epstein, H. F. (1995) · Developmental Biology · doi:10.1006/dbio.1995.1156 · Cited by 81 · see citing works

Caloric restriction reveals a metabolomic and lipidomic signature in liver of male mice

Jové, M., Naudí, A., Ramírez‐Núñez, O., Portero‐Otín, M., Selman, C., Withers, D. J., & Pamplona, R. (2014) · Aging Cell · doi:10.1111/acel.12241 · Cited by 76 · see citing works

A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration

Yizhak, K., Dévédec, S. E. L., Rogkoti, V.-M., Baenke, F., de Boer, V. C. J., Frezza, C., Schulze, A., van de Water, B., & Ruppin, E. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145746 · Cited by 76 · see citing works

Programmed aging or error catastrophe? An exmination by two-dimensional polyacrylamide gel electrophoresis

Johnson, T. E., & McCaffrey, G. (1985) · Mechanisms of Ageing and Development · doi:10.1016/0047-6374(85)90118-6 · Cited by 67 · see citing works

NAD+ biosynthesis and salvage – a phylogenetic perspective

Gossmann, T. I., Ziegler, M., Puntervoll, P., de Figueiredo, L. F., Schuster, S., & Heiland, I. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08559.x · Cited by 52 · see citing works

Quinones in long‐lived clk‐1 mutants of Caenorhabditis elegans

Miyadera, H., Kano, K., Miyoshi, H., Ishii, N., Hekimi, S., & Kita, K. (2002) · FEBS Letters · doi:10.1016/s0014-5793(02)02282-2 · Cited by 46 · see citing works

EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks

Kaleta, C., de Figueiredo, L. F., Behre, J., & Schuster, S. (2009) · Cited by 43 · see citing works

Can sugars be produced from fatty acids? A test case for pathway analysis tools

de Figueiredo, L. F., Schuster, S., Kaleta, C., & Fell, D. A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn621 · Cited by 39 · see citing works

Nematode biochemistry-III. Excretion products

Rothstein, M. (1963) · Comparative Biochemistry and Physiology · doi:10.1016/0010-406x(63)90028-8 · Cited by 35 · see citing works

Developmental effect of polyamine depletion in Caenorhabditis elegans

Macrae, M., Kramer, D. L., & Coffino, P. (1998) · Biochemical Journal · doi:10.1042/bj3330309 · Cited by 31 · see citing works

Increased longevity of some C. elegans mitochondrial mutants explained by activation of an alternative energy-producing pathway

Gallo, M., Park, D., & Riddle, D. L. (2011) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2011.08.004 · Cited by 28 · see citing works

Development of a liquid chromatography–mass spectrometry method for the determination of the neurotoxic quinolinic acid in human serum

Meinitzer, A., Tomaschitz, A., Pilz, S., Truber, M., Zechner, G., Gaksch, M., Prietl, B., Treiber, G. M., Schwarz, M., & Baranyi, A. (2014) · Clinica Chimica Acta · doi:10.1016/j.cca.2014.06.010 · Cited by 27 · see citing works

Complementation of a polyamine-deficient Escherichia coli mutant by expression of mouse ornithine decarboxylase.

Macrae, M., & Coffino, P. (1987) · Molecular and Cellular Biology · doi:10.1128/mcb.7.1.564 · Cited by 27 · see citing works

Restoring de novo coenzyme Q biosynthesis in Caenorhabditis elegans coq-3 mutants yields profound rescue compared to exogenous coenzyme Q supplementation

Gómez, F., Saiki, R., Chin, R., Srinivasan, C., & Clarke, C. F. (2012) · Gene · doi:10.1016/j.gene.2012.06.023 · Cited by 26 · see citing works

Detecting and investigating substrate cycles in a genome‐scale human metabolic network

Gebauer, J., Schuster, S., de Figueiredo, L. F., & Kaleta, C. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08700.x · Cited by 23 · see citing works

Influence of age and genetic background on in vivo fatty acid synthesis in obese (ob/ob) mice

Rath, E. A., & Thenen, S. W. (1980) · Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism · doi:10.1016/0005-2760(80)90049-1 · Cited by 22 · see citing works

Extension of Life Span by Impaired Glucose Metabolism in Caenorhabditis elegans Is Accompanied by Structural Rearrangements of the Transcriptomic Network

Priebe, S., Menzel, U., Zarse, K., Groth, M., Platzer, M., Ristow, M., & Guthke, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077776 · Cited by 20 · see citing works

Molecular and biochemical characterization of S-adenosylmethionine decarboxylase from the free-living nematode Caenorhabditis elegans

Da’dara, A. A., & Walter, R. D. (1998) · Biochemical Journal · doi:10.1042/bj3360545 · Cited by 14 · see citing works

Fluorometric Determination of Quinolinic Acid Using the Catalytic Activity of Horseradish Peroxidase

Odō, J., Inoguchi, M., & Hirai, A. (2009) · Eisei kagaku · doi:10.1248/jhs.55.242 · Cited by 10 · see citing works

Functional GATA- and initiator-like-elements exhibit a similar arrangement in the promoters of Caenorhabditis elegans polyamine synthesis enzymes

Lüersen, K., Eschbach, M.-L., Liebau, E., & Walter, R. D. (2004) · Biological Chemistry · doi:10.1515/bc.2004.087 · Cited by 7 · see citing works

Kultivierung von Caenorhabditis elegans über Flüssigmedium zur Untersuchung des molekularen Folsäuremetabolismus

Langer, S. K. (2009) · University of Vienna · doi:10.25365/thesis.5703 · Cited by 1 · see citing works

Current status and applications of genome-scale metabolic models

Gu, C., Kim, G. B., Kim, W. J., Kim, H. U., & Lee, S. Y. (2019) · Genome biology · doi:10.1186/s13059-019-1730-3 · Cited by 765 · see citing works

Metabolic Flexibility as an Adaptation to Energy Resources and Requirements in Health and Disease

Smith, R. L., Soeters, M. R., Wüst, R. C. I., & Houtkooper, R. H. (2018) · Endocrine Reviews · doi:10.1210/er.2017-00211 · Cited by 787 · see citing works

De novo NAD+ synthesis enhances mitochondrial function and improves health

Katsyuba, E., Mottis, A., Ziętak, M., Franco, F., van der Velpen, V., Gariani, K., Ryu, D., Cialabrini, L., Matilainen, O., Liscio, P., et al. (2018) · Nature · doi:10.1038/s41586-018-0645-6 · Cited by 436 · see citing works

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Bernardes, J. P., Mishra, N., Tran, F., Bahmer, T., Best, L., Blase, J. I., Bordoni, D., Franzenburg, J., Geisen, U. M., Josephs‐Spaulding, J., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.11.017 · Cited by 353 · see citing works

Lipid and Carbohydrate Metabolism in Caenorhabditis elegans

Watts, J. L., & Ristow, M. (2017) · Genetics · doi:10.1534/genetics.117.300106 · Cited by 263 · see citing works

The genome of Onchocerca volvulus, agent of river blindness

Cotton, J. A., Bennuru, S., Grote, A., Harsha, B., Tracey, A., Beech, R. N., Doyle, S. R., Dunn, M., Hotopp, J. C. D., Holroyd, N. E., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.216 · Cited by 126 · see citing works

Targeting metabolic pathways for extension of lifespan and healthspan across multiple species

Parkhitko, A. A., Filine, E., Mohr, S. E., Moskalev, A., & Perrimon, N. (2020) · Ageing Research Reviews · doi:10.1016/j.arr.2020.101188 · Cited by 90 · see citing works

The C. elegans intestine: organogenesis, digestion, and physiology

Dimov, I. B., & Maduro, M. (2019) · Cell and Tissue Research · doi:10.1007/s00441-019-03036-4 · Cited by 83 · see citing works

Non-enzymatic molecular damage as a prototypic driver of aging

Golubev, A. G., Hanson, A. D., & Gladyshev, V. N. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.r116.751164 · Cited by 69 · see citing works

Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging

Hastings, J., Mains, A., Virk, B., Rodríguez, N., Murdoch, S., Pearce, J., Bergmann, S., Novère, N. G. L., & Casanueva, O. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00002 · Cited by 62 · see citing works

Metabolic network modeling with model organisms

Yilmaz, L. S., & Walhout, A. J. M. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2016.12.025 · Cited by 59 · see citing works

Metabolomics and lipidomics in Caenorhabditis elegans using a single-sample preparation

Molenaars, M., Schomakers, B. V., Elfrink, H. L., Gao, A. W., Vervaart, M. A. T., Pras‐Raves, M. L., Luyf, A. C. M., Smith, R. L., Sterken, M. G., Kammenga, J. E., et al. (2021) · Disease Models & Mechanisms · doi:10.1242/dmm.047746 · Cited by 58 · see citing works

Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels

Yilmaz, L. S., Li, X., Nanda, S., Fox, B. W., Schroeder, F. C., & Walhout, A. J. M. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209649 · Cited by 47 · see citing works

Beyond Proteostasis: Lipid Metabolism as a New Player in ER Homeostasis

Xu, J., & Taubert, S. (2021) · Metabolites · doi:10.3390/metabo11010052 · Cited by 47 · see citing works

Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans

Witting, M. A., Hastings, J., Rodríguez, N., Joshi, C. J., Hattwell, J. P. N., Ebert, P. R., van Weeghel, M., Gao, A. W., Wakelam, M. J. O., Houtkooper, R. H., et al. (2018) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2018.00096 · Cited by 36 · see citing works

The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life

Yang, W., Petersen, C., Pees, B., Zimmermann, J., Waschina, S., Dirksen, P., Rosenstiel, P. C., Tholey, A., Leippe, M., Dierking, K., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01793 · Cited by 32 · see citing works

Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the Nematode

Salzer, L., & Witting, M. A. (2021) · Metabolites · doi:10.3390/metabo11050284 · Cited by 28 · see citing works

Is C. elegans a suitable model for nutritional science?

Gottschling, D.-C., & Döring, F. (2019) · Genes & Nutrition · doi:10.1186/s12263-018-0625-3 · Cited by 18 · see citing works

Stressful development: integrating endoderm development, stress, and longevity

Ewe, C. K., Alok, G., & Rothman, J. H. (2020) · Developmental Biology · doi:10.1016/j.ydbio.2020.12.002 · Cited by 13 · see citing works

WormJam: A consensusC. elegansMetabolic Reconstruction and Metabolomics Community and Workshop Series

Hastings, J., Mains, A., Artal‐Sanz, M., Bergmann, S., Braeckman, B. P., Bundy, J. G., Cabreiro, F., Dobson, P. D., Ebert, P. R., Hattwell, J. P. N., et al. (2017) · Worm · doi:10.1080/21624054.2017.1373939 · Cited by 13 · see citing works

Systems biology of Haemonchus contortus – Advancing biotechnology for parasitic nematode control

Zheng, Y., Young, N. D., Wang, T., Chang, B. C. H., Song, J., & Gasser, R. B. (2025) · Biotechnology Advances · doi:10.1016/j.biotechadv.2025.108567 · Cited by 13 · see citing works

Systems biology analysis using a genome-scale metabolic model shows that phosphine triggers global metabolic suppression in a resistant strain of C. elegansPreprint

Ma, L., Chan, A., Hattwell, J. P. N., Ebert, P. R., & Schirra, H. J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/144386 · Cited by 10 · see citing works

A genome-scale metabolic model of parasitic whipworm

Bay, Ö. F., Hayes, K. S., Schwartz, J., Grencis, R. K., & Roberts, I. S. (2023) · Nature Communications · doi:10.1038/s41467-023-42552-4 · Cited by 9 · see citing works

Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model

Witting, M. A. (2020) · Metabolites · doi:10.3390/metabo10040130 · Cited by 6 · see citing works

An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics

Shaver, A. O., Garcia, B. M., Gouveia, G., Morse, A. M., Liu, Z.-H., Asef, C. K., Borges, R. M., Leach, F. E., Andersen, E. C., Amster, I., et al. (2022) · bioRxiv · doi:10.3389/fmolb.2022.930204 · Cited by 3 · see citing works

A metabolic constraint in the kynurenine pathway drives mucosal inflammation in IBDPreprint

Welz, L., Harris, D. M. M., Kim, N., Alsaadi, A. I., Wu, Q., Oumari, M., Taubenheim, J., Volk, V., Credido, G., Koncina, E., et al. (2024) · medRxiv · doi:10.1101/2024.08.08.24311598 · Cited by 6 · see citing works

Resolving tissue and cellular functions of parasitic nematodes

Airs, P. M., & Correa, M. A. D. (2025) · Trends in Parasitology · doi:10.1016/j.pt.2025.09.012 · Cited by 5 · see citing works

Why and How Do We Age? A Single Answer to Two Questions

Golubev, A. G. (2019) · Advances in Gerontology · doi:10.1134/s2079057019010065 · Cited by 5 · see citing works

Comparative Metabolic Network Flux Analysis to Identify Differences in Cellular Metabolism

McGarrity, S., Karvelsson, S. T., Sigurjónsson, Ó. E., & Rolfsson, Ó. (2019) · Methods in molecular biology · doi:10.1007/978-1-0716-0159-4_11 · Cited by 3 · see citing works

Caenorhabditis elegans Gets Metabolic Network Models

Taubert, S. (2016) · Cell Systems · doi:10.1016/j.cels.2016.05.003 · Cited by 2 · see citing works

Using Genome-Scale Metabolic Networks for Analysis, Visualization, and Integration of Targeted Metabolomics Data

Hattwell, J. P. N., Hastings, J., Casanueva, O., Schirra, H. J., & Witting, M. A. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0239-3_18 · Cited by 2 · see citing works

Flow with the flux: Systems biology tools predict metabolic drivers of ageing in C. elegans

Hastings, J., Suriyalaksh, M., & Casanueva, O. (2018) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2018.11.005 · Cited by 1 · see citing works

Low-dimensional representations of genome-scale metabolismPreprint

Cain, S., Merzbacher, C., & Oyarzún, D. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.31.596808 · Cited by 1 · see citing works

Metabolic influences on ageing in Caenorhabditis elegans: A time series multi-omics and metabolic modelling study

Hastings, J. (2019) · Apollo (University of Cambridge) · doi:10.17863/cam.43232

Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging

Hastings, J., Mains, A., Virk, B., Rodríguez, N., Murdoch, S., Pearce, J., Bergmann, S., Novère, N. G. L., & Casanueva, O. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00002 · Cited by 62 · see citing works

The effects of supplemented metabolites on lifespan and stress response pathways in Caenorhabditis elegans

Edwards, C. (2015) · Digital Commons - University of South Florida (University of South Florida)

Using local gene network approach to functionally link lifespan genes and nutrient metabolism modules in C. elegans

Tan, X., Xuan, D., Wang, J., & Zhang, Z. (2011) · International Conference on Remote Sensing, Environment and Transportation Engineering · doi:10.1109/rsete.2011.5966308 · Cited by 2 · see citing works

A Caenorhabditis elegans genome-scale metabolic network model

Yilmaz, L. S., & Walhout, A. J. M. (2016) · Cell Systems · doi:10.1016/j.cels.2016.04.012 · Cited by 88 · see citing works