A portal site for systems biology.

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

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

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

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

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

Xionglei He, Jianzhi Zhang,

Why Do Hubs Tend to Be Essential in Protein Networks?
PLoS Genetics, 2(6) 2006

posted 2006.06.02

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

posted 2006.01.17

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

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

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

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

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

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

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

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

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 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

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: 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

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

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

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

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

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

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

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

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

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

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

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

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

Kitano, H., Oda, K., Kimura, T., Matsuoka, Y., Csete, M., Doyle, J., Muramatsu, M.. Metabolic Syndrome and Robustness Tradeoffs, Diabetes 53, S6-S15, 2004
PFD file

posted 2004.04.01

Kitano, H.. Biological Robustness. Nature Review Genetics. 5, 826-837, 2004
PDF file

posted 2004.04.01

Oda, K.; Kimura, T, Matsuoka, Y.; Funahashi, A.; Muramatsu, M.; Kitano, H. Molecular Interaction Map of Macrophage. AfCS Report. 2004.
PDF file

posted 2004.04.01

M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project.
IEE Systems Biology. 1:41-53, 2004

posted 2004.04.01

Kitano, H. Cancer as a robust system: implications for anticancer therapy. Nature Reviews Cancer 4:227-235, 2004.
Abstract..

posted 2004.04.01

Kitano, H. Cancer as a robust system: implications for anticancer therapy. Nature Reviews Cancer 4:227-235, 2004.
Abstract..

posted 2004.04.01

Kitano, H.
Systems Biology: A Brief Overview.
Science. 295, 1662-1664, 2002.
Abstract...

posted 2002.04.01

Kitano, H.
Computational Systems Biology.
Nature. 420, 206-210, 2002.
Abstract...

posted 2002.04.01

Kitano, H.
Standards for modeling.
Nat. Biotech. 20, 337, 2002.
Abstract...

posted 2002.04.01

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H.
The ERATO Systems Biology Workbench: enabling interaction and exchange
between software tools for computational biology.
Proc. Pac Symp Biocomput. 2002, 450-61, 2002.
Abstract...

posted 2002.04.01

Kitano, H.
Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology.
Curr Genet. 41, 1-10, 2002.
Abstract...

posted 2002.04.01

Morohashi, M., Winn, A. E., Borisuk, M. T., Bolouri, H., Doyle, J.,
and Kitano, H.
Robustness as a measure of plausibility in models of biochemical networks.
J. Theor. Biol. 216, 19-30, 2002.
Abstract...

posted 2002.04.01

Kyoda, K. M., Morohashi, M., Onami, S., and Kitano, H.
A gene network inference method from continuous-value gene expression data of wild-type and mutants.
Genome Informatics. 11, 196-204, 2000.
Abstract...

posted 2000.04.01

• Conference:
• Natural Genetic Engineering and Natural Genome Editing, July 3-6, 2008
• Salzburg. 6th Pathways, Networks and Systems Medicine Conference, 16-21 June 2008; Chania, Crete.
• Jobs:
• PhD Positions: Mathematical Modelling and Analysis of Cell Death. For details, check Jobs section.

posted 2007.12.04

• Courses:
• Molecular Evolution and Comparative Genetics, 3-7 December 2007. 1 Week Course at the University of Oxford,UK, http://bioinfomsc.stats.ox.ac.uk/subjects/MECG.html
• Conference: Call for Papers
• World Congress on Computational Intelligence, June 1-6, 2008, Hong Kong Special Session on Evolving Gene Regulatory Networks http://www.soft-computing.de/EC20.html

posted 2007.11.13

- Courses: Computational and Systems Biology Course at CoSBi, March 10-14, 2008, The Microsoft Research - University of Trento Centre for
Computational and Systems Biology, Trento, Italy
http://www.cosbi.eu/events/course08.php
- Jobs: POST DOCTORAL POSITION IN SYSTEMS BIOLOGY AT CSIRO AUSTRALIA. For details, check Jobs section.

posted 2007.10.31

- Courses: Systems Biology 1 week course at the Oxford Bioinformatics Programme: http://bioinfomsc.stats.ox.ac.uk/subjects/SysBio.html

posted 2007.10.17

- Jobs: Systems Biology Modeller, Research assistant or postdoc researchers on computational systems biology projects in the Alzheimer's disease. For details, check Jobs  section.
- Conference:The 7th Annual ORFeome Meeting: ORFeomes and Systems, Oct 24-26 Boston, MA, ttp://www.orfeomemeeting.org/

posted 2007.09.21

- Jobs: Faculty Position in Plant Biology. For details, check Jobs  section.
-Conference: 2008 Calendar updated.

posted 2007.08.31

- Jobs:Post-doc in Systems Biology of Cancer. For details, check Jobs  section.
-New link to The Netherlands Institute for Systems Biology (NISB).
- Conference Update: RECOMB (2007.6.5)
- Jobs: (2007.6.5)

posted 2007.06.30

- Call for Abstract: ICSB-2007 (2007.5.31)
- Jobs: (2007.5.11)
- Jobs: Postdoctoral position (2007.5.10)

posted 2007.05.30

# Jobs Postdoc in systems biology
# Links New systems biology unit in biotech R&D park in Portugal.
# ConferenceCFP: Multiscale Modeling and Simulation: from Molecules to Cells to Organisms,Pacific Symposium on Biocomputing, Jan 4-8, 2008, the big island of Hawaii- Jobs:Post-doc in Systems Biology of Cancer. For details, check Jobs  section.
-New link to The Netherlands Institute for Systems Biology (NISB).
- Conference Update: RECOMB (2007.6.5)
- Jobs: (2007.6.5)

posted 2007.04.30

- Conferences Update (2007.3.26)
--5th Pathways, Networks and Systems Conference, June 25-29, Porto Heli, Greece
--Summit on Systems Biology, June 5-7, 2007, Richmond, Virginia
Check also Up-coming Conference Calendar 2007.

- Jobs: Senior Research Scientist (2007.3.22)
ADIT Postdoctorial position at Siena Biotech. For details, check Jobs section.

- Conference: Metabolomics Society 3rd Annual Conference (2007.3.22)
Metabolomics Society 3rd Annual Conference
June 11-14,2007 Manchester, UK
http://www.metabolomics2007.org.uk.
Check also Up-coming Conference Calendar 2007.

- Jobs: Senior Research Scientist (2007.3.13)
Plant Systems Biology and more. For details, check Jobs section.

- Jobs: Post-Doc Position (2007.3.8)
Post-doctoral positions at the Bioinformatics and Computational Systems Biology Unit, Institut Curie, Paris, and more...For details, check Jobs section.

- Conference Calendar 2007 (2007.3.8)
Check Up-coming Conference Calendar 2007

- Call for Participation on Pathway Curation (2007.3.2)
PANTHER Pathway is a community effort to build up the pathway database with curation. Please contact pathcuration at pantherdb.org for any questions.
http://curation.pantherdb.org/

- Jobs: Post-Doc Fellow (2007.2.6)
new position in computational methods for systems genetics, and in computational platform development. For details, check Jobs section.

posted 2007.02.27

- CellDesigner 3.5.1 Released (2007.1.10)
Download CellDesigner3.5.1
- Jobs: BioPharmaceutical Applications Engineer (2007.1.5)
new positions are posted in Jobs section.
- BioPharmaceutical Applications Engineer for The MathWorks (MATLAB)

posted 2007.01.30

Strasbourg, October 12th

HFSP Publishing is proud to announce the launch of the HFSP Journal, Frontiers of Interdisciplinary Research in the Life Sciences.

The HFSP Journal aims to foster communication between scientists publishing high quality, innovative interdisciplinary research at the interface between biology and the physical sciences.

Scientists working in fields at the interface between the life sciences and physics, chemistry, mathematics, engineering, or informatics tend to publish in a wide variety of often specialized, discipline-specific journals and as a result their work may not be read by the professional audience for whom it is most relevant. The HFSP Journal will establish a forum that unites and engages researchers from a wide range of backgrounds. By also publishing Commentaries and Perspectives, which provide context to the basic research articles, the HFSP Journal will encourage broader understanding and synthesis of the exciting work being done across different scientific fields of research.

'The HFSP Journal is unique in that the peer-review process of articles submitted for consideration by the HFSP Journal will be truly interdisciplinary', says Editor-in-Chief, Arturo Falaschi 'This is because every member of the Editorial Board is actively involved in interdisciplinary research, and will consult with colleagues on the Board to take advantage of their distinct scientific backgrounds in making editorial decisions. This is in contrast to other journals where the editorial decision-making is often divided between disciplines.'

The Editorial Board of the HFSP Journal represents 5 distinguished scientists from different disciplines but each with a strong focus on living systems:-
* Arturo Falaschi (International Centre for Genetic Engineering and Biotechnology, Trieste and Scuola Normale of Pisa).
* Marcelo Magnasco (Department of Physics, Rockefeller University),
* Peter Seeberger (Department of Chemistry, ETH Zurich),
* Dan Kiehart (Department of Biology, Duke University) and
* Mitsuo Kawato (ATR Computational Neuroscience Laboratories, Kyoto University)

The HFSP Journal offers its authors the option to pay a fee to make their research articles Open Access immediately upon publication. For other articles, access is limited to subscribers for the first 6 months after publication, and access will be free thereafter. The HFSP Journal will be published online and in print.

HFSPO Secretary General and Nobel laureate Torsten Wiesel comments, "Due to its reputation for excellence in interdisciplinary research in biology, HFSPO is well placed to endorse the establishment of a high-level journal that shares its scientific values and will increase the visibility of the Program. This is the main reason I had no hesitation to agree to chair the Editorial Advisory Council of the HFSP Journal. "

The first articles will appear online in December 2006 and the first issue will be published in March 2007.

The HFSP Journal is operated by HFSP Publishing the not-for-profit publisher of the leading international funding agency the Human Frontier Science Program Organization (HFSPO). This international funding agency has been supporting innovative research at the frontier of biology since its establishment in 1989.

Contact:
Dr. Valerie Ferrier
Managing Editor
Tel + 33 (0) 3 88 21 52 83
info @ hfsp-publishing.org
HFSP Journal homepage http://hfspj.aip.org

posted 2006.10.12

Strasbourg, October 12th

HFSP Publishing is proud to announce the launch of the HFSP Journal, Frontiers of Interdisciplinary Research in the Life Sciences.

The HFSP Journal aims to foster communication between scientists publishing high quality, innovative interdisciplinary research at the interface between biology and the physical sciences.

Contact:
Dr. Valerie Ferrier
Managing Editor
Tel + 33 (0) 3 88 21 52 83
info @ hfsp-publishing.org
HFSP Journal homepage http://hfspj.aip.org

posted 2006.10.12

www.ariadnegenomics.com/company/news/09262006.php?cmp=PR_09262006

posted 2006.09.26

For details, see Jobs  section.

posted 2006.07.22

For details, see Jobs  section.

posted 2006.07.05

CellDesigner3.2 now support libSBML, a standard SBML library. You can handle files smoothly from modelling to simulation. It also supports Java 5 and Intel Mac.
Download CellDesigner3.2

posted 2006.07.05

"An introduction to Systems Biology: Design Principles of Biological Circuits" by Uri Alon to be published in June adn more books in Resources / Books section

posted 2006.05.25

Announcing the approaching abstract deadline for the 2nd Cold Spring Harbor/Wellcome Trust meeting on Interactome Networks, June 7, 2006. For details, check http://meetings.cshl.edu/meetings/interuk06.shtml

posted 2006.05.25

International Conference on Computational Methods in Systems Biology (CMSB)
Oct 18 - 19 2006, Trento, Italy
http://www.msr-unitn.unitn.it/events/cmsb06.php

posted 2006.04.24

Standardization is an important issue in biological research and in computational modeling of cellular processes. In order to foster this process, it is necessary to get an overview on modeling and representation tools and techniques that are used by the scientific community. The presented questionnaire shall also give the user the opportunity to express needs and demands for standardization and new developments in the area of systems biology. The aim is to support the exchange of experience and of models between researchers from different fields and regions.
This questionnaire is supported by the EU-funded project Yeast Systems Biology Network. Collected data will be published on the YSBN web site (ysbn.org) and used for a report in an anonymous way. No personal data will be given to third party or used for any other purpose. Data submission is voluntary. It is not necessary to answer all questions. Even partial information is welcome.

The questionnaire can be found at
http://www.molgen.mpg.de/~ag_klipp/questionnaire/

posted 2006.04.07

3rd Integrative Bioinformatics Workshop
September 4-6, 2006
Rothamsted Research, Harpenden, Hertfordshire, United Kingdom http://www.rothamsted.bbsrc.ac.uk/bab/conf/ibiof/
Accepted papers will also appear in the Journal of Integrative Bioinformatics http://journal.imbio.de/

posted 2006.04.03

CellDesigner3.1 speeds up its performance and and some bug fixes...

posted 2006.03.24

Systems Biology is chosen as one of the nine Runners-Up of Science magazine's Breakthrough of the Year 2005. Details

posted 2005.12.27

posted 2005.12.01

posted 2005.11.30

posted 2005.11.20

posted 2005.11.10

Location: California Institute of Technology, Pasadena, CA
Job description: We seek a Scientific Database Curator to contribute to the maintenance and extension of BioModels Database.
Closing date: 30 November 2005
Web page: http://www.biomodels.net/

posted 2005.11.01

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.
The mission is headed by Dr. Marvin Cassman, a former director of NIGMS/NIH.

posted 2005.10.30

BBSRC announed a call for research proposals on systems biology in microorganisms (SysMO). Along with recent series of calls such as Complexity in Biomolecular systems (COMBIOSYS) and Centres for Integrative Systems Biology grant, BBSRC announed a new program that focus on microorganisms. Deadline for expression of interest is Nov. 1 2005

posted 2005.10.20

CellDesigner 3.0 now supports a new notation that enhanced previous process diagram into gene and RNA, as well as protein complex structure. It also supports simulation and parameter scan by an integration with SBML ODE Solver.
By using CellDesigner3.0, you can browse and modify existing SBML models, simulate and view the dynamics through an intuitive graphical interface.

posted 2005.10.15

CellDesigner2.5 now supports simulation and parameter scan by an integration with SBML ODE Solver.

posted 2005.09.01

Preview version for new graphical notation.

posted 2005.08.04

More than 5000 copies of CellDesigner has been downloaded in a year since its release in June 2003.

posted 2005.06.09

Connection to the databases such as PubMed and DBGET is now supported.

posted 2005.05.24

The 5th International Conference on Systems Biology (ICSB2004) will take place in Heidelberg, Germany, from Oct. 9-13.

posted 2004.10.09

A molecular interaction map that describes most nteractions involved in the metabolic syndrome is added to our Model Repository.

posted 2004.10.01

Check also an example of CellDesigner usage:
"Molecular Interaction Map of Macrophage" published in AfCS Report.

posted 2004.09.30

http://ysbn.org

posted 2004.09.01

CellDesigner ver.2.0 will be released in near future.

posted 2004.08.26

More than 2500 copies of CellDesigner has been downloaded in a year since its release in June 2003. More than 1000 registrants are using CellDesigner today.

posted 2004.07.12

SBML.org has fully renewed! The site provides information about SBML (Systems Biology Markup Language) and related tools.

posted 2003.09.12

The 1st International Workshop on Systems Biology of Yeast will take place in St. Louis, USA, on Nov. 9, in conjunction with ICSB2003 (The 4th International Conference on Systems Biology).

posted 2003.09.01