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Hot Papers

2006

The Transcriptional Landscape of the Mammalian Genome, The FANTOM3 Consortium, Science, 2 September 2006

The FANTOM3 Consortium
The Transcriptional Landscape of the Mammalian Genome
Science, Vol 309, Issue 5740, 1559-1563 , 2 September 2005
DOI: 10.1126/science.1112014

posted 2006.09.02

Systems-Level Dissection of the Cell-Cycle Oscillator: Bypassing Positive Feedback Produces Damped Oscillations, Pomerening, et al., Cell, 26 August 2006

Joseph R. Pomerening, Sun Young Kim and James E. Ferrell, Jr.
Systems-Level Dissection of the Cell-Cycle Oscillator: Bypassing Positive Feedback Produces Damped Oscillations, Cell, 122(4), 565-578, 2006.

A review paper on this paper is: Cross, FR. and Siggia, ED.., Shake it, don't break it: positive feedback and the evolution of oscillator design, Dev Cell. 2005 Sep;9(3):309-10

posted 2006.08.26

Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments, Molecular Systems Biology, July 2006

Yoav Soen, Akiko Mori, Theo D Palmer and Patrick O Brown,
Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironmentsMolecular Systems Biology, 4 July 2006

posted 2006.07.04

Evolutionary and Physiological Importance of Hub Proteins, PLoS Computational Biology

Nizar N. Batada, Laurence D. Hurst, Mike Tyers,

Evolutionary and Physiological Importance of Hub Proteins

PLoS Computational Biology, 2(7) July 2006

posted 2006.07.02

In vivo Robustness Analysis of Cell Division Cycle Genes in S. cerevisiae, Moriya, Shimizu-Yoshida, and Kitano

Moriya, H. Shimizu-Yoshida, Y., and Kitano, H.,

In vivo Robustness Analysis of Cell Division Cycle Genes in S. cerevisiae
, PLoS Genetics, Advanced On-line Release, Provisional Version, 5, June, 2006

posted 2006.06.05

Why Do Hubs Tend to Be Essential in Protein Networks?, He and Zhang, PLoS Genetics, June 2006

Xionglei He, Jianzhi Zhang,

Why Do Hubs Tend to Be Essential in Protein Networks?

PLoS Genetics, 2(6) 2006

posted 2006.06.02

Proteome analysis of yeast response to various nutrient limitations, Kolkman, et al., Molecular Systems Biology, 16 May, 2006

Annemieke Kolkman, Pascale Daran-Lapujade, Asier Fullaondo, Maurien M A Olsthoorn, Jack T Pronk, Monique Slijper and Albert J R Heck,
Proteome analysis of yeast response to various nutrient limitations,
Molecular Systems Biology, 16 May, 2006

posted 2006.05.16

Reverse Engineering the Gap Gene Network of Drosophila melanogaster , Perkins, et al., PLoS Computational Biology, 2(5) 2006

Theodore J. Perkins, Johannes Jaeger, John Reinitz, Leon Glass,
Reverse Engineering the Gap Gene Network of Drosophila melanogasterPLoS Computational Biology 2(5) 2006

posted 2006.05.02

Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach, Barrett and Palsson, PLoS Computational Biology 2(5) 2006

Christian L. Barrett, Bernhard O. Palsson,
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach, PLoS Computational Biology, 2(5) 2006

posted 2006.05.02

Spatial Regulation and the Rate of Signal Transduction Activation, Batada, et al., PLoS Computational Biology, 2(5) 2006

Nizar N. Batada, Larry A. Shepp, David O. Siegmund, Michael Levitt,
Spatial Regulation and the Rate of Signal Transduction Activation, PLoS Computational Biology, 2(5) 2006

posted 2006.05.02

Residues crucial for maintaining short paths in network communication mediate signaling in proteins, del Sol, et al., Molecular Systems Biology, 2 May 2006

Antonio del Sol, Hirotomo Fujihashi, Dolors Amoros and Ruth Nussinov,
Residues crucial for maintaining short paths in network communication mediate signaling in proteins,
Molecular Systems Biology, 2 May 2006.

posted 2006.05.02

A comprehensive map of the toll-like receptor signaling network, Oda and Kitano, Molecular Systems Biology

Oda, K. and Kitano, H.,
A comprehensive map of the toll-like receptor signaling network Molecular Systems Biology, doi:10.1038/msb4100057
Published online: 18 April 2006

posted 2006.04.18

Deciphering principles of transcription regulation in eukaryotic genomes, Nguyen, DH and D'haeseleer, P. Molecular Systems Biology

Dat H Nguyen and Patrik D'haeseleer,
Deciphering principles of transcription regulation in eukaryotic genomesMolecular Systems Biology, doi:10.1038/msb4100054
Published online: 18 April 2006

posted 2006.04.18

Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System, Kurata, et al., PLoS Computational Biology

Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash,
Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System
PLoS Computational Biology, early on-line release. (april 13, 2006)

posted 2006.04.13

Iterative Reconstruction of Transcriptional Regulatory Networks: an Algorithmic Approach, Barrett and Palsson, PLoS Computational Biology

Christian Barrett and Bernhard O. Palsson,

Iterative Reconstruction of Transcriptional Regulatory Networks: an Algorithmic Approach

PLoS Computational Biology, Early On-line release, 5 April, 2006

posted 2006.04.05

Nature Reviews Molecular Cell Biology: Focus Issue on Modelling Cell Systems

Nature Reviews Molecular Cell Biology featuring a focus issue on Modelling Cell Systems in its March 2006 issue.

High-throughput technologies now enable the study of cell biology at a systems level â€" from subcellular systems such as signalling networks, multiprotein complexes and organelles, to cells, tissues and even entire organisms. The diverse systems can be modelled through a combination of high-throughput experimental data and mathematical and computational approaches. This special Focus issue of Nature Reviews Molecular Cell Biology illustrates several cellular systems and describes the different approaches that can be used to model them. The articles of this Focus are freely available for a period of three months.

posted 2006.03.30

Feedback repression is required for mammalian circadian clock function, Sato, et al., Nature Genetics, 12 Feb. 2006 (Advanced On-line)

Sato, T., et al.,
Feedback repression is required for mammalian circadian clock function
Nature Genetics, Advanced Online Publishing, 12 Feb., 2006.
doi:10.1038/ng1745

posted 2006.02.12

Critical nodes in signalling pathways: insights into insulin action, Nature Reviews Molecular Cell Biology

Cullen M. Taniguchi, Brice Emanuelli and C. Ronald Kahn

Critical nodes in signalling pathways: insights into insulin action

Nature Reviews Molecular Cell Biology 7, 85-96 (February 2006)

posted 2006.02.10

Gene Regulatory Networks and the Evolution of Animal Body Plans, Davidson and Erwin, Science, 10 Feb., 2006

Eric H. Davidson and Douglas H. Erwin
Gene Regulatory Networks and the Evolution of Animal Body Plans
Science 10 February 2006: 796-800

posted 2006.02.10

The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour, Andrew J Pocklington, et al., Molecular Systems Biology

Andrew J Pocklington, Mark Cumiskey, J Douglas Armstrong, and Seth G N Grant,
The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour,
Molecular Systems Biology

posted 2006.01.17

Robustness trade-offs and host-microbial symbiosis in the immune system, Kitano and Oda, Molecular Systems Biology

Systems-level analyses identify extensive coupling among gene expression machine

Karolina Maciag, Steven J Altschuler, Michael D Slack, Nevan J Krogan,Andrew Emili, Jack F Greenblatt, Tom Maniatis and Lani F Wu
Systems-level analyses identify extensive coupling among gene expression machine
doi:10.1038/msb4100045
Published online: 17 January 2006

posted 2006.01.17

The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour

Andrew J Pocklington, Mark Cumiskey, J Douglas Armstrong and Seth G N Grant
The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour
doi:10.1038/msb4100041
Published online: 17 January 2006

posted 2006.01.17