BMC Systems Biology

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Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

Neema Jamshidi and Bernhard Ø Palsson*

BMC Systems Biology 2007, 1:26 doi:10.1186/1752-0509-1-26

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BioMed Central: 15 citations

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Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease

Arvind K Chavali, Anna S Blazier, Jose L Tlaxca, Paul A Jensen, Richard D Pearson, Jason A Papin BMC Systems Biology 2012, 6:27 (27 April 2012)

Database   Open Access Highly Accessed

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

Akhil Kumar, Patrick F Suthers, Costas D Maranas BMC Bioinformatics 2012, 13:6 (10 January 2012)

Research article   Open Access Highly Accessed

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 Systems Biology 2011, 5:180 (31 October 2011)

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Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

Kechi Fang, Hansheng Zhao, Changyue Sun, Carolyn M C Lam, Suhua Chang, Kunlin Zhang, Gurudutta Panda, Miguel Godinho, Vítor A P Martins dos Santos, Jing Wang BMC Systems Biology 2011, 5:83 (25 May 2011)

Method   Open Access

Flux balance analysis accounting for metabolite dilution

Tomer Benyamini, Ori Folger, Eytan Ruppin, Tomer Shlomi Genome Biology 2010, 11:R43 (16 April 2010)

A flux balance analysis method for gene essentiality prediction, which takes into account variation in biomass composition under different growth conditions.

Research article   Open Access

Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli

Rishi Jain, Ranjan Srivastava BMC Systems Biology 2009, 3:121 (30 December 2009)

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A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis

Xin Fang, Anders Wallqvist, Jaques Reifman BMC Systems Biology 2009, 3:92 (15 September 2009)

Research   Open Access

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens Genome Biology 2009, 10:R69 (25 June 2009)

A new and validated genome-scale metabolic model of Bacillus subtilis 168, iBsu1103, is presented that has significantly improved completeness and accuracy.

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The conservation and evolutionary modularity of metabolism

José M Peregrín-Alvarez, Chris Sanford, John Parkinson Genome Biology 2009, 10:R63 (12 June 2009)

A novel evolutionary analysis of metabolic networks across 26 taxa reveals a highly-conserved but flexible core of metabolic enzymes.

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Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

Anu Raghunathan, Jennifer Reed, Sookil Shin, Bernhard Palsson, Simon Daefler BMC Systems Biology 2009, 3:38 (8 April 2009)

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targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

Karthik Raman, Kalidas Yeturu, Nagasuma Chandra BMC Systems Biology 2008, 2:109 (19 December 2008)

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A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

Juan Nogales, Bernhard Ø Palsson, Ines Thiele BMC Systems Biology 2008, 2:79 (16 September 2008)

Methodology article   Open Access

Machine learning based analyses on metabolic networks supports high-throughput knockout screens

Kitiporn Plaimas, Jan-Phillip Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, Rainer König BMC Systems Biology 2008, 2:67 (24 July 2008)

Research   Open Access

Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks

Ádám Kun, Balázs Papp, Eörs Szathmáry Genome Biology 2008, 9:R51 (10 March 2008)

Small-molecular metabolic autocatalytic regulators, which are crucial to metabolic pathways, are identified in a novel systems-wide study in different organisms, revealing that in the enzymatic reactions of conserved autocatalytic cycles, the autocatalytic behavior of replicators varies.

Research article   Open Access

Three factors underlying incorrect in silico predictions of essential metabolic genes

Scott A Becker, Bernhard O Palsson BMC Systems Biology 2008, 2:14 (4 February 2008)