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Hot Papers

2005

Origins of extrinsic variability in eukaryotic gene expression, Nature (On-line), 21 Dec. 2005

Dmitri Volfson, Jennifer Marciniak, William J. Blake, Natalie Ostroff, Lev S. Tsimring, and Jeff Hasty
Origins of extrinsic variability in eukaryotic gene expression

posted 2005.12.21

Threshold responses to morphogen gradients by zero-order ultrasensitivity

Gustavo J Melen, Sagi Levy, Naama Barkai and Ben-Zion Shilo
Threshold responses to morphogen gradients by zero-order ultrasensitivity
doi:10.1038/msb4100036
Published online: 13 December 2005

posted 2005.12.13

A Systems Model of Signaling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis, Science, 9 Dec. 2005

Kevin A. Janes, John G. Albeck, Suzanne Gaudet, Peter K. Sorger, Douglas A. Lauffenburger, Michael B. Yaffe
A Systems Model of Signaling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis
Science 9 December 2005:
Vol. 310. no. 5754, pp. 1646 - 1653
DOI: 10.1126/science.1116598

posted 2005.12.09

Minimum information requested in the annotation of biochemical models (MIRIAM), Nature Biotechnology, Dec. 2005

Nicolas Le Novère, Andrew Finney, Michael Hucka, Upinder S Bhalla, Fabien Campagne, Julio Collado-Vides, Edmund J Crampin, Matt Halstead, Edda Klipp, Pedro Mendes, Poul Nielsen, Herbert Sauro, Bruce Shapiro, Jacky L Snoep, Hugh D Spence & Barry L Wanner,

Minimum information requested in the annotation of biochemical models (MIRIAM)
,
Nature Biotechnology 23, 1509 - 1515 (2005)
Published online: 6 December 2005; | doi:10.1038/nbt1156

posted 2005.12.06

Global analysis of protein phosphorylation in yeast, Nature

Jason Ptacek, Geeta Devgan, Gregory Michaud, Heng Zhu, Xiaowei Zhu, Joseph Fasolo, Hong Guo, Ghil Jona, Ashton Breitkreutz, Richelle Sopko, Rhonda R. McCartney, Martin C. Schmidt, Najma Rachidi, Soo-Jung Lee, Angie S. Mah, Lihao Meng, Michael J. R. Stark, David F. Stern, Claudio De Virgilio, Mike Tyers, Brenda Andrews, Mark Gerstein, Barry Schweitzer, Paul F. Predki and Michael Snyder
Global analysis of protein phosphorylation in yeast
Nature 438, 679-684 (1 December 2005) | doi:10.1038/nature04187

posted 2005.12.01

A data integration methodology for systems biology, PNAS, 29 Nov. 2005

Daehee Hwang, Alistair G. Rust, Stephen Ramsey, Jennifer J. Smith, Deena M. Leslie, Andrea D. Weston, Pedro de Atauri, John D. Aitchison, Leroy Hood, Andrew F. Siegel and Hamid Bolouri,
A data integration methodology for systems biology
PNAS | November 29, 2005 | vol. 102 | no. 48 | 17296-17301

posted 2005.11.29

A data integration methodology for systems biology: Experimental verification, PNAS, 29 Nov. 2005

Daehee Hwang, Jennifer J. Smith, Deena M. Leslie, Andrea D. Weston, Alistair G. Rust, Stephen Ramsey, Pedro de Atauri, Andrew F. Siegel, Hamid Bolouri, John D. Aitchison, and Leroy Hood
A data integration methodology for systems biology: Experimental verification
PNAS | November 29, 2005 | vol. 102 | no. 48 | 17302-17301

posted 2005.11.29

Nature featured Synthetic Biology

Nature featured Synthetic Biology in their Nov. 24 2005 issue
Two reviews, Reconstruction of genetic circuits by Sprizakand and Elowitz, and Foundtions for engineering biology by Drew Endy are featured.

posted 2005.11.24

Monitoring dynamics of single-cell gene expression over multiple cell cycles, Molecular Systems Biology, Nov. 2005

Scott Cookson, Natalie Ostroff, Wyming Lee Pang, Dmitri Volfson, and Jeff Hasty
Monitoring dynamics of single-cell gene expression over multiple cell cycles, Molecular Systems Biology, Nov. 22 2005.

posted 2005.11.22

Logic of the Yeast Metabolic Cycle

Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes
by Benjamin P. Tu, Andrzej Kudlicki, Maga Rowicka, and Steven L. McKnight
Science, 19 November, 2005

posted 2005.11.19

Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome, PNAS

Mitsuhiro Itaya, Kenji Tsuge, Maki Koizumi and Kyoko Fujita
Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome Proceedings of National Academy of Science, November 1, 2005 vol. 102 no. 44, 15971-15976

posted 2005.11.01

A network-based analysis of systemic inflammation in humans, Calvano, et al., Nature, 13 Oct. 2005

Steve E. Calvano, et al.,
A network-based analysis of systemic inflammation in humans
Nature 437, 1032-1037 (13 October 2005) | doi: 10.1038/nature03985

posted 2005.10.13

Towards a proteome-scale map of the human protein-protein interaction network, Rual, JF., et al., Nature, 2005

Jean-Francois Rual, et al.,
Towards a proteome-scale map of the human protein-protein interaction network,
Nature, Advanced On-line Publication, doi: 10.1038/nature04209

posted 2005.10.13

WTEC Report: Assessment of International Research and Development in Systems Biology

W-TEC report that represents US view on current state of systems biology and assessment of competitive strength of each coutry they have investigated is now on-line.

According to the web site, "The goal of this study is to gather information on the worldwide status and trends in systems biology: “Network Behavior in Biological Systems” and to disseminate it to government decision makers and the research community

The study panelists will gather information on systems biology abroad useful to the U.S. government in its own R&D programs, and will critically analyze and compare the research in the United States with that being pursued in Japan, Europe, or other major industrialized countries. This information will serve the following purposes:
(1) Identify good ideas overseas worth exploring in U.S. R&D programs, (2) Clarify research opportunities and needs for promoting progress in the field generally, (3)Identify opportunities for international collaboration, and (4) Evaluate the position of foreign research programs relative to those in the U.S."

posted 2005.10.13

News Feature, Drug Discovery: Playing Dirty, Nature 13, Oct. 2005

A news feature article Drug discovery: Playing dirty by Simon Frantz focuses on complex relationship between genes and diseases. Some "dirty" drugs under development interacts with multiple kinases at the same time.

posted 2005.10.13

Regulated cell-to-cell variation in a cell-fate decision system, Alejandro Colman-Lerner, et al., Nature (29 Sept. 2005)

Alejandro Colman-Lerner, Andrew Gordon, Eduard Serra1, Tina Chin, Orna Resnekov, Drew Endy, C. Gustavo Pesce1 and Roger Brent
Regulated cell-to-cell variation in a cell-fate decision system
Nature 437, 699-706 (29 September 2005)
doi:10.1038/nature03998

posted 2005.09.29

Using process diagrams for the graphical representation of biological networks, Kitano et al., Nature Biotechnology, August 2005

Hiroaki Kitano, Akira Funahashi, Yukiko Matsuoka, Kanae Oda
Using process diagrams for the graphical representation of biological networks
Nature Biotechnology 23, 961 - 966 (2005)
Published online: 4 August 2005; | doi:10.1038/nbt1111

posted 2005.08.04

Integrative model of the response of yeast to osmotic shock, Klipp, et al., Nature Biotechnology, August 2006

Edda Klipp, Bodil Nordlander, Roland Krüger, Peter Gennemark & Stefan Hohmann
Integrative model of the response of yeast to osmotic shock
Nature Biotechnology 23, 975 - 982 (2005)
Published online: 17 July 2005; | doi:10.1038/nbt1114

posted 2005.07.17

Comparative studies of suppression of malignant cancer cell phenotype by

Hiroi, N.; Funahashi, A.; Kitano, H.;
Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA
Cancer Gene Therapy advance online publication 05 August 2005

posted 2005.04.01

Using process diagrams for the graphical representation of biological networks

Kitano, H.; Funahashi, A.; Matsuoka, Y.; Oda, K.;
Using process diagrams for the graphical representation of biological networks
Nature Biotechnology 23(8), 961 - 966 (2005)

posted 2005.04.01

A comprehensive pathway map of epidermal growth factor receptor signaling

Oda, K.; Matsuoka, Y.; Funahashi, A.; Kitano, H.;
A comprehensive pathway map of epidermal growth factor receptor signaling
Molecular Systems Biology

*Download the structured data (supplementary SBML file) to view the PubMed reference using the new function of CellDesigner 2.2 - Database connection.

posted 2005.04.01

The PANTHER database of protein families, subfamilies, functions and pathways

Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano and Paul D. Thomas. 2005.
The PANTHER database of protein families, subfamilies, functions and pathways.
Nucl. Acids. Res., 31:334-341.

posted 2005.04.01