Dynamic simulation of the human red blood cell metabolic network. - Neema Jamshidi; Jeremy S. Edwards; Tom Fahland; George M. Church; Bernhard O. Palsson (Bioinform., 2001)

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. - Neema Jamshidi; Bernhard Ø. Palsson (BMC Syst. Biol., 2007)

Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks. - Neema Jamshidi; Bernhard Ø. Palsson (PLoS Comput. Biol., 2008)

Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. - Neema Jamshidi; Bernhard O. Palsson (BMC Syst. Biol., 2009)

Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology. - Albert A. de Graaf; Andreas P. Freidig; Baukje De Roos; Neema Jamshidi; Matthias Heinemann; Johan A. C. Rullmann; Kevin D. Hall; Martin Adiels; Ben van Ommen (PLoS Comput. Biol., 2009)

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling. - Fan Li 002; Ines Thiele; Neema Jamshidi; Bernhard O. Palsson (PLoS Comput. Biol., 2009)

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. - Ines Thiele; Neema Jamshidi; Ronan M. T. Fleming; Bernhard O. Palsson (PLoS Comput. Biol., 2009)

Metabolic Systems Biology. - Nathan E. Lewis; Neema Jamshidi; Ines Thiele; Bernhard O. Palsson (Encyclopedia of Complexity and Systems Science, 2009)

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. - Martin I. Sigurdsson; Neema Jamshidi; Eiríkur Steingrímsson; Ines Thiele; Bernhard Ø. Palsson (BMC Syst. Biol., 2010)

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. - Aarash Bordbar; Neema Jamshidi; Bernhard O. Palsson (BMC Syst. Biol., 2011)

Individualized therapy of HHT driven by network analysis of metabolomic profiles. - Neema Jamshidi; Franklin J. Miller; Jess Mandel; Timothy Evans; Michael D. Kuo (BMC Syst. Biol., 2011)

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. - Alyaa M. Abdel-Haleem; Hooman Hefzi; Katsuhiko Mineta; Xin Gao 001; Takashi Gojobori; Bernhard O. Palsson; Nathan E. Lewis; Neema Jamshidi (PLoS Comput. Biol., 2018)