Subject archive

Cellular Metabolism

2009

High heritability of metabolomic profiles in families burdened with premature cardiovascular disease

Svati H Shah, Elizabeth R Hauser, James R Bain, Michael J Muehlbauer, Carol Haynes, Robert D Stevens, Brett R Wenner, Z Elaine Dowdy, Christopher B Granger, Geoffrey S Ginsburg, Christopher B Newgard & William E Kraus

doi:10.1038/msb.2009.11
Published online: 07 April 2009

Full Text | PDF (337K) | Supplementary information

Metabolomics of the interaction between PPAR-alpha and age in the PPAR-alpha-null mouse

Helen J Atherton, Melanie K Gulston, Nigel J Bailey, Kian-Kai Cheng, Wen Zhang, Kieran Clarke & Julian L Griffin

doi:10.1038/msb.2009.18
Published online: 07 April 2009

Synopsis | Full Text | PDF (1,039K) | Supplementary information

Glucose regulates transcription in yeast through a network of signaling pathways

Shadia Zaman, Soyeon I Lippman, Lisa Schneper, Noam Slonim & James R Broach

doi:10.1038/msb.2009.2
Published online: 17 February 2009

Synopsis | Full Text | PDF (1,947K) | Supplementary information

Predicting metabolic biomarkers of human inborn errors of metabolism

Tomer Shlomi, Moran N Cabili & Eytan Ruppin

doi:10.1038/msb.2009.22
Published online: 28 April 2009

Full Text | PDF (287K) | Supplementary information

Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters

Gilles Curien, Olivier Bastien, Mylène Robert-Genthon, Athel Cornish-Bowden, María Luz Cárdenas & Renaud Dumas

doi:10.1038/msb.2009.29
Published online: 19 May 2009

Synopsis | Full Text | PDF (448K) | Supplementary information

Genome-scale gene/reaction essentiality and synthetic lethality analysis

Patrick F Suthers, Alireza Zomorrodi & Costas D Maranas

doi:10.1038/msb.2009.56
Published online: 18 August 2009

Synopsis | Full Text | PDF (3,714K) | Supplementary information

Large-scale identification of genetic design strategies using local search

Desmond S Lun, Graham Rockwell, Nicholas J Guido, Michael Baym, Jonathan A Kelner, Bonnie Berger, James E Galagan & George M Church

doi:10.1038/msb.2009.57
Published online: 18 August 2009

Full Text | PDF (732K) | Supplementary information

Shifts in growth strategies reflect tradeoffs in cellular economics

Douwe Molenaar, Rogier van Berlo, Dick de Ridder & Bas Teusink

doi:10.1038/msb.2009.82
Published online: 03 November 2009

Full Text | PDF (403K) | Supplementary information

2008

Predicting synthetic rescues in metabolic networks

Adilson E Motter, Natali Gulbahce, Eivind Almaas & Albert-László Barabási

doi:10.1038/msb.2008.1
Published online: 12 February 2008

Synopsis | Full Text | PDF (366K) | Supplementary information

A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

Véronique de Berardinis, David Vallenet, Vanina Castelli, Marielle Besnard, Agnès Pinet, Corinne Cruaud, Sumitta Samair, Christophe Lechaplais, Gabor Gyapay, Céline Richez, Maxime Durot, Annett Kreimeyer, François Le Fèvre, Vincent Schächter, Valérie Pezo, Volker Döring, Claude Scarpelli, Claudine Médigue, Georges N Cohen, Philippe Marlière, Marcel Salanoubat & Jean Weissenbach

doi:10.1038/msb.2008.10
Published online: 04 March 2008

Synopsis | Full Text | PDF (579K) | Supplementary information

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

Mikael Rørdam Andersen, Michael Lynge Nielsen & Jens Nielsen

doi:10.1038/msb.2008.12
Published online: 25 March 2008

Synopsis | Full Text | PDF (494K) | Supplementary information

Mathematical modeling of pathogenicity of Cryptococcus neoformans

Jacqueline Garcia, John Shea, Fernando Alvarez-Vasquez, Asfia Qureshi, Chiara Luberto, Eberhard O Voit & Maurizio Del Poeta

doi:10.1038/msb.2008.17
Published online: 15 April 2008

Synopsis | Full Text | PDF (384K) | Supplementary information

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Victor Kunin, Jeroen Raes, J Kirk Harris, John R Spear, Jeffrey J Walker, Natalia Ivanova, Christian von Mering, Brad M Bebout, Norman R Pace, Peer Bork & Philip Hugenholtz

doi:10.1038/msb.2008.35
Published online: 03 June 2008

Full Text | PDF (341K) | Supplementary information

Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity

Oded Shaham, Ru Wei, Thomas J Wang, Catherine Ricciardi, Gregory D Lewis, Ramachandran S Vasan, Steven A Carr, Ravi Thadhani, Robert E Gerszten & Vamsi K Mootha

doi:10.1038/msb.2008.50
Published online: 05 August 2008

Synopsis | Full Text | PDF (318K) | Supplementary information

An integrated cell-free metabolic platform for protein production and synthetic biology

Michael C Jewett, Kara A Calhoun, Alexei Voloshin, Jessica J Wuu & James R Swartz

doi:10.1038/msb.2008.57
Published online: 14 October 2008

Synopsis | Full Text | PDF (377K) | Supplementary information

Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue

Laurence Coquin, Jacob D Feala, Andrew D McCulloch & Giovanni Paternostro

doi:10.1038/msb.2008.71
Published online: 16 December 2008

Synopsis | Full Text | PDF (341K) | Supplementary information

Modeling the electron transport chain of purple non-sulfur bacteria

Steffen Klamt, Hartmut Grammel, Ronny Straube, Robin Ghosh & Ernst Dieter Gilles

doi:10.1038/msb4100191
Published online: 15 January 2008

Synopsis | Full Text | PDF (351K) | Supplementary information

2007

Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli

Daniel J Dwyer, Michael A Kohanski, Boris Hayete & James J Collins

doi:10.1038/msb4100135
Published online: 13 March 2007

Synopsis | Full Text | PDF (429K) | Supplementary information

Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis

Jacob D Feala, Laurence Coquin, Andrew D McCulloch & Giovanni Paternostro

doi:10.1038/msb4100139
Published online: 17 April 2007

Full Text | PDF (292K) | Supplementary information

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

Adam M Feist, Christopher S Henry, Jennifer L Reed, Markus Krummenacker, Andrew R Joyce, Peter D Karp, Linda J Broadbelt, Vassily Hatzimanikatis & Bernhard Ø Palsson

doi:10.1038/msb4100155
Published online: 26 June 2007

Synopsis | Full Text | PDF (953K) | Supplementary information

The Edinburgh human metabolic network reconstruction and its functional analysis

Hongwu Ma, Anatoly Sorokin, Alexander Mazein, Alex Selkov, Evgeni Selkov, Oleg Demin & Igor Goryanin

doi:10.1038/msb4100177
Published online: 18 September 2007

Full Text | PDF (258K) | Supplementary information

2006

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

Adam M Feist, Johannes C M Scholten, Bernhard Ø Palsson, Fred J Brockman & Trey Ideker

doi:10.1038/msb4100046
Published online: 31 January 2006

Synopsis | Full Text | PDF (571K) | Supplementary information

Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism

Jennifer J Smith, Yaroslav Sydorskyy, Marcello Marelli, Daehee Hwang, Hamid Bolouri, Richard A Rachubinski & John D Aitchison

doi:10.1038/msb4100051
Published online: 21 February 2006

Full Text | PDF (367K) | Supplementary information

Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions

Ruo-Yu Luo, Sha Liao, Guan-Yang Tao, Yuan-Yuan Li, Shaoqun Zeng, Yi-Xue Li & Qingming Luo

doi:10.1038/msb4100071
Published online: 06 June 2006

Full Text | PDF (156K) | Supplementary information

Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

Anne Kümmel, Sven Panke & Matthias Heinemann

doi:10.1038/msb4100074
Published online: 20 June 2006

Synopsis | Full Text | PDF (182K) | Supplementary information

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