Subject archive

Microbiology & Pathogens

2008

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

Arvind K Chavali, Jeffrey D Whittemore, James A Eddy, Kyle T Williams & Jason A Papin

doi:10.1038/msb.2008.15
Published online: 25 March 2008

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

Transient heterogeneity in extracellular protease production by Bacillus subtilis

Jan-Willem Veening, Oleg A Igoshin, Robyn T Eijlander, Reindert Nijland, Leendert W Hamoen & Oscar P Kuipers

doi:10.1038/msb.2008.18
Published online: 15 April 2008

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

Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model

Francois-Pierre J Martin, Yulan Wang, Norbert Sprenger, Ivan K S Yap, Serge Rezzi, Ziad Ramadan, Emma Peré-Trepat, Florence Rochat, Christine Cherbut, Peter van Bladeren, Laurent B Fay, Sunil Kochhar, John C Lindon, Elaine Holmes & Jeremy K Nicholson

doi:10.1038/msb.2008.40
Published online: 15 July 2008

Parasites lead to evolution of robustness against gene loss in host signaling networks

Marcel Salathé & Orkun S Soyer

doi:10.1038/msb.2008.44
Published online: 15 July 2008

Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes

Sandrine P Claus, Tsz M Tsang, Yulan Wang, Olivier Cloarec, Eleni Skordi, François-Pierre Martin, Serge Rezzi, Alastair Ross, Sunil Kochhar, Elaine Holmes & Jeremy K Nicholson

doi:10.1038/msb.2008.56
Published online: 14 October 2008

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest

Gábor Balázsi, Allison P Heath, Lanbo Shi & Maria L Gennaro

doi:10.1038/msb.2008.63
Published online: 04 November 2008

Hepatitis C virus infection protein network

B de Chassey, V Navratil, L Tafforeau, M S Hiet, A Aublin-Gex, S Agaugué, G Meiffren, F Pradezynski, B F Faria, T Chantier, M Le Breton, J Pellet, N Davoust, P E Mangeot, A Chaboud, F Penin, Y Jacob, P O Vidalain, M Vidal, P André, C Rabourdin-Combe & V Lotteau

doi:10.1038/msb.2008.66
Published online: 04 November 2008

Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model

Francois-Pierre J Martin, Yulan Wang, Norbert Sprenger, Ivan K S Yap, Torbjörn Lundstedt, Per Lek, Serge Rezzi, Ziad Ramadan, Peter van Bladeren, Laurent B Fay, Sunil Kochhar, John C Lindon, Elaine Holmes & Jeremy K Nicholson

doi:10.1038/msb4100190
Published online: 15 January 2008

2007

Noise in timing and precision of gene activities in a genetic cascade

Amnon Amir, Oren Kobiler, Assaf Rokney, Amos B Oppenheim & Joel Stavans

doi:10.1038/msb4100113
Published online: 13 February 2007

Metabolic modeling of a mutualistic microbial community

Sergey Stolyar, Steve Van Dien, Kristina Linnea Hillesland, Nicolas Pinel, Thomas J Lie, John A Leigh & David A Stahl

doi:10.1038/msb4100131
Published online: 13 March 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

The environmental fate of organic pollutants through the global microbial metabolism

Manuel J Gómez, Florencio Pazos, Francisco J Guijarro, Víctor de Lorenzo & Alfonso Valencia

doi:10.1038/msb4100156
Published online: 05 June 2007

2006

Ab initio genotype–phenotype association reveals intrinsic modularity in genetic networks

Noam Slonim, Olivier Elemento & Saeed Tavazoie

doi:10.1038/msb4100047
Published online: 31 January 2006

Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability

Andrew C Tolonen, John Aach, Debbie Lindell, Zackary I Johnson, Trent Rector, Robert Steen, George M Church & Sallie W Chisholm

doi:10.1038/msb4100087
Published online: 03 October 2006

An integrated systems approach for understanding cellular responses to gamma radiation

Kenia Whitehead, Adrienne Kish, Min Pan, Amardeep Kaur, David J Reiss, Nichole King, Laura Hohmann, Jocelyne DiRuggiero & Nitin S Baliga

doi:10.1038/msb4100091
Published online: 12 September 2006

A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways

Jun Li, Liang Wang, Yoshifumi Hashimoto, Chen-Yu Tsao, Thomas K Wood, James J Valdes, Evanghelos Zafiriou & William E Bentley

doi:10.1038/msb4100107
Published online: 12 December 2006

2005

A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli

Shiraz Kalir, Shmoolik Mangan & Uri Alon

doi:10.1038/msb4100010
Published online: 29 March 2005

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