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GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism
Dany JV Beste, Tracy Hooper, Graham Stewart, Bhushan Bonde, Claudio Avignone-Rossa, Michael E Bushell, Paul Wheeler, Steffen Klamt, Andrzej M Kierzek, Johnjoe McFadden
Genome Biol. 2007; 8(5): R89. Published online 2007 May 23. doi: 10.1186/gb-2007-8-5-r89
PMCID:
PMC1929162
Abstract Full Text PDF–1.0M Supplementary Material
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 Is Cited by the Following 31 Articles in this Archive:
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
Aarash Bordbar, Adam M Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O Palsson, Iman Famili
BMC Syst Biol. 2011; 5: 180. Published online 2011 October 31. doi: 10.1186/1752-0509-5-180
PMCID:
PMC3219569
Abstract Full Text PDF–4.3M Supplementary Material
Fumarate Reductase Activity Maintains an Energized Membrane in Anaerobic Mycobacterium tuberculosis
Shinya Watanabe, Michael Zimmermann, Michael B. Goodwin, Uwe Sauer, Clifton E. Barry, 3rd, Helena I. Boshoff
PLoS Pathog. 2011 October; 7(10): e1002287. Published online 2011 October 6. doi: 10.1371/journal.ppat.1002287
PMCID:
PMC3188519
Abstract Full Text PDF–1.0M Supplementary Material
13C Metabolic Flux Analysis Identifies an Unusual Route for Pyruvate Dissimilation in Mycobacteria which Requires Isocitrate Lyase and Carbon Dioxide Fixation
Dany J. V. Beste, Bhushan Bonde, Nathaniel Hawkins, Jane L. Ward, Michael H. Beale, Stephan Noack, Katharina Nöh, Nicholas J. Kruger, R. George Ratcliffe, Johnjoe McFadden
PLoS Pathog. 2011 July; 7(7): e1002091. Published online 2011 July 21. doi: 10.1371/journal.ppat.1002091
PMCID:
PMC3141028
Abstract Full Text PDF–2.7M Supplementary Material
Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis
Bhushan K. Bonde, Dany J. V. Beste, Emma Laing, Andrzej M. Kierzek, Johnjoe McFadden
PLoS Comput Biol. 2011 June; 7(6): e1002060. Published online 2011 June 30. doi: 10.1371/journal.pcbi.1002060
PMCID:
PMC3127818
Abstract Full Text PDF–1.0M Supplementary Material
Analysis of complex metabolic behavior through pathway decomposition
Kuhn Ip, Caroline Colijn, Desmond S Lun
BMC Syst Biol. 2011; 5: 91. Published online 2011 June 3. doi: 10.1186/1752-0509-5-91
PMCID:
PMC3135541
Abstract Full Text PDF–356K Supplementary Material
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
Ines Thiele, Daniel R Hyduke, Benjamin Steeb, Guy Fankam, Douglas K Allen, Susanna Bazzani, Pep Charusanti, Feng-Chi Chen, Ronan MT Fleming, Chao A Hsiung, Sigrid CJ De Keersmaecker, Yu-Chieh Liao, Kathleen Marchal, Monica L Mo, Emre Özdemir, Anu Raghunathan, Jennifer L Reed, Sook-Il Shin, Sara Sigurbjörnsdóttir, Jonas Steinmann, Suresh Sudarsan, Neil Swainston, Inge M Thijs, Karsten Zengler, Bernhard O Palsson, Joshua N Adkins, Dirk Bumann
BMC Syst Biol. 2011; 5: 8. Published online 2011 January 18. doi: 10.1186/1752-0509-5-8
PMCID:
PMC3032673
Abstract Full Text PDF–1.2M Supplementary Material
Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery
Sean Ekins, Joel S. Freundlich, Inhee Choi, Malabika Sarker, Carolyn Talcott
Trends Microbiol. Author manuscript; available in PMC 2012 February 1.
Published in final edited form as: Trends Microbiol. 2011 February; 19(2): 65–74. Published online 2010 December 2. doi: 10.1016/j.tim.2010.10.005
PMCID:
PMC3034835
Abstract Full Text PDF–420K
Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
Xin Fang, Anders Wallqvist, Jaques Reifman
BMC Syst Biol. 2010; 4: 160. Published online 2010 November 23. doi: 10.1186/1752-0509-4-160
PMCID:
PMC3225870
Abstract Full Text PDF–1.1M Supplementary Material
The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications
Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne
PLoS Comput Biol. 2010 November; 6(11): e1000976. Published online 2010 November 4. doi: 10.1371/journal.pcbi.1000976
PMCID:
PMC2973814
Abstract Full Text PDF–766K Supplementary Material
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
Aarash Bordbar, Nathan E Lewis, Jan Schellenberger, Bernhard Ø Palsson, Neema Jamshidi
Mol Syst Biol. 2010; 6: 422. Published online 2010 October 19. doi: 10.1038/msb.2010.68
PMCID:
PMC2990636
Abstract Full Text PDF–1.4M Supplementary Material
System-level strategies for studying the metabolism of Mycobacterium tuberculosis
Dany J. V. Beste, Johnjoe McFadden
Mol Biosyst. 2010 December 8; 6 ( 12 ): 2363–2372. Published online 2010 October 11. doi: 10.1039/c003757p
PMCID:
PMC3172586
Abstract Full Text
Carbon flux rerouting during Mycobacterium tuberculosis growth arrest
Lanbo Shi, Charles D. Sohaskey, Carmen Pfeiffer, Pratik Datta, Michael Parks, Johnjoe McFadden, Robert J. North, Maria L. Gennaro
Mol Microbiol. Author manuscript; available in PMC 2011 December 1.
Published in final edited form as: Mol Microbiol. 2010 December; 78(5): 1199–1215. Published online 2010 October 6. doi: 10.1111/j.1365-2958.2010.07399.x
PMCID:
PMC3072047
Abstract Full Text PDF–2.1M Supplementary Material
Tuberculosis: Global Approaches to a Global Disease
Denise E. Kirschner, Douglas Young, JoAnne L. Flynn
Curr Opin Biotechnol. Author manuscript; available in PMC 2011 August 1.
Published in final edited form as: Curr Opin Biotechnol. 2010 August; 21(4): 524–531. Published online 2010 July 14. doi: 10.1016/j.copbio.2010.06.002
PMCID:
PMC2943033
Abstract Full Text PDF–624K
Systems biology approaches to understanding mycobacterial survival mechanisms
Helena I.M. Boshoff, Desmond S. Lun
Drug Discov Today Dis Mech. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Drug Discov Today Dis Mech. 2010 SPRING; 7(1): e75–e82. doi: 10.1016/j.ddmec.2010.09.008
PMCID:
PMC2975547
Abstract Full Text PDF–110K
Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology
Caroline B. Milne, Pan-Jun Kim, James A. Eddy, Nathan D. Price
Biotechnol J. Author manuscript; available in PMC 2011 August 24.
Published in final edited form as: Biotechnol J. 2009 December; 4(12): 1653–1670. doi: 10.1002/biot.200900234
PMCID:
PMC3160784
Abstract Full Text PDF–2.3M
An Anaerobic-Type α-Ketoglutarate Ferredoxin Oxidoreductase Completes the Oxidative Tricarboxylic Acid Cycle of Mycobacterium tuberculosis
Anthony D. Baughn, Scott J. Garforth, Catherine Vilchèze, William R. Jacobs, Jr.
PLoS Pathog. 2009 November; 5(11): e1000662. Published online 2009 November 20. doi: 10.1371/journal.ppat.1000662
PMCID:
PMC2773412
Abstract Full Text PDF–682K
Applications of genome-scale metabolic reconstructions
Matthew A Oberhardt, Bernhard Ø Palsson, Jason A Papin
Mol Syst Biol. 2009; 5: 320. Published online 2009 November 3. doi: 10.1038/msb.2009.77
PMCID:
PMC2795471
Abstract Full Text PDF–2.6M
Global Effects of Inactivation of the Pyruvate Kinase Gene in the Mycobacterium tuberculosis Complex
Sivagamisundaram Chavadi, Esen Wooff, Nicholas G. Coldham, Manjula Sritharan, R. Glyn Hewinson, Stephen V. Gordon, Paul R. Wheeler
J Bacteriol. 2009 December; 191(24): 7545–7553. Published online 2009 October 9. doi: 10.1128/JB.00619-09
PMCID:
PMC2786599
Abstract Full Text PDF–494K Supplementary Material
A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis
Xin Fang, Anders Wallqvist, Jaques Reifman
BMC Syst Biol. 2009; 3: 92. Published online 2009 September 15. doi: 10.1186/1752-0509-3-92
PMCID:
PMC2759933
Abstract Full Text PDF–1.2M Supplementary Material
Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production
Caroline Colijn, Aaron Brandes, Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. Branch Moody, Megan Murray, James E. Galagan
PLoS Comput Biol. 2009 August; 5(8): e1000489. Published online 2009 August 28. doi: 10.1371/journal.pcbi.1000489
PMCID:
PMC2726785
Abstract Full Text PDF–1.1M Supplementary Material
Low early-life social class leaves a biological residue manifested by decreased glucocorticoid and increased proinflammatory signaling
Gregory E. Miller, Edith Chen, Alexandra K. Fok, Hope Walker, Alvin Lim, Erin F. Nicholls, Steve Cole, Michael S. Kobor
Proc Natl Acad Sci U S A. 2009 August 25; 106(34): 14716–14721. Published online 2009 July 14. doi: 10.1073/pnas.0902971106
PMCID:
PMC2732821
Abstract Full Text PDF–660K Supplementary Material
CycSim—an online tool for exploring and experimenting with genome-scale metabolic models
F. Le Fèvre, S. Smidtas, C. Combe, M. Durot, Florence d'Alché-Buc, V. Schachter
Bioinformatics. 2009 August 1; 25(15): 1987–1988. Published online 2009 May 6. doi: 10.1093/bioinformatics/btp268
PMCID:
PMC2712333
Abstract Full Text PDF–174K
The Genetic Requirements for Fast and Slow Growth in Mycobacteria
Dany J. V. Beste, Mateus Espasa, Bhushan Bonde, Andrzej M. Kierzek, Graham R. Stewart, Johnjoe McFadden
PLoS ONE. 2009; 4(4): e5349. Published online 2009 April 28. doi: 10.1371/journal.pone.0005349
PMCID:
PMC2685279
Abstract Full Text PDF–298K Supplementary Material
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis
Karthik Raman, Kalidas Yeturu, Nagasuma Chandra
BMC Syst Biol. 2008; 2: 109. Published online 2008 December 19. doi: 10.1186/1752-0509-2-109
PMCID:
PMC2651862
Abstract Full Text PDF–1.6M Supplementary Material
Chronic Interpersonal Stress Predicts Activation of Pro- and Anti- Inflammatory Signaling Pathways Six Months Later
Gregory Miller, Nicolas Rohleder, Steve W. Cole
Psychosom Med. Author manuscript; available in PMC 2010 January 1.
Published in final edited form as: Psychosom Med. 2009 January; 71(1): 57–62. Published online 2008 December 10. doi: 10.1097/PSY.0b013e318190d7de
PMCID:
PMC2720615
Abstract Full Text PDF–154K
Genome-scale models of bacterial metabolism: reconstruction and applications
Maxime Durot, Pierre-Yves Bourguignon, Vincent Schachter
FEMS Microbiol Rev. 2009 January; 33(1): 164–190. Published online 2008 December. doi: 10.1111/j.1574-6976.2008.00146.x
PMCID:
PMC2704943
Abstract Full Text PDF–520K
In Silico and in Vitro Modeling of Hepatocyte Drug Transport Processes: Importance of ABCC2 Expression Levels in the Disposition of Carboxydichlorofluroscein
Katharine Howe, G. Gordon Gibson, Tanya Coleman, Nick Plant
Drug Metab Dispos. 2009 February; 37(2): 391–399. Published online 2008 November 20. doi: 10.1124/dmd.108.022921
PMCID:
PMC2680525
Abstract Full Text PDF–383K Supplementary Material
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
Maxime Durot, François Le Fèvre, Véronique de Berardinis, Annett Kreimeyer, David Vallenet, Cyril Combe, Serge Smidtas, Marcel Salanoubat, Jean Weissenbach, Vincent Schachter
BMC Syst Biol. 2008; 2: 85. Published online 2008 October 7. doi: 10.1186/1752-0509-2-85
PMCID:
PMC2606687
Abstract Full Text PDF–1.0M Supplementary Material
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
Juan Nogales, Bernhard Ø Palsson, Ines Thiele
BMC Syst Biol. 2008; 2: 79. Published online 2008 September 16. doi: 10.1186/1752-0509-2-79
PMCID:
PMC2569920
Abstract Full Text PDF–2.0M Supplementary Material
A Functional Genomic Fingerprint of Chronic Stress in Humans: Blunted Glucocorticoid and Increased NF-κB Signaling
Gregory E. Miller, Edith Chen, Jasmen Sze, Teresa Marin, Jesusa M. G. Arevalo, Richard Doll, Roy Ma, Steve W. Cole
Biol Psychiatry. Author manuscript; available in PMC 2009 August 15.
Published in final edited form as: Biol Psychiatry. 2008 August 15; 64(4): 266–272. Published online 2008 April 28. doi: 10.1016/j.biopsych.2008.03.017
PMCID:
PMC2581622
Abstract Full Text PDF–460K Supplementary Material
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