Predicting synthetic rescues in metabolic networks
Adilson E Motter, Natali Gulbahce, Eivind Almaas & Albert-László Barabási
doi:10.1038/msb.2008.1
Published online:
12 February 2008
Synopsis | Full Text | PDF (366K) | Supplementary information
Subject archive
Computational methods
2008
A systems-level approach to mapping the telomere length maintenance gene circuitry
Rafi Shachar, Lior Ungar, Martin Kupiec, Eytan Ruppin & Roded Sharan
doi:10.1038/msb.2008.13
Published online:
04 March 2008
Reverse engineering of force integration during mitosis in the Drosophila embryo
Roy Wollman, Gul Civelekoglu-Scholey, Jonathan M Scholey & Alex Mogilner
doi:10.1038/msb.2008.23
Published online:
06 May 2008
Synopsis | Full Text | PDF (1,309K) | Supplementary information
Recursive construction of perfect DNA molecules from imperfect oligonucleotides
Gregory Linshiz, Tuval Ben Yehezkel, Shai Kaplan, Ilan Gronau, Sivan Ravid, Rivka Adar & Ehud Shapiro
doi:10.1038/msb.2008.26
Published online:
06 May 2008
Network-based global inference of human disease genes
Xuebing Wu, Rui Jiang, Michael Q Zhang & Shao Li
doi:10.1038/msb.2008.27
Published online:
06 May 2008
Synopsis | Full Text | PDF (3,282K) | Supplementary information
Colored extrinsic fluctuations and stochastic gene expression
Vahid Shahrezaei, Julien F Ollivier & Peter S Swain
doi:10.1038/msb.2008.31
Published online:
06 May 2008
Synopsis | Full Text | PDF (3,577K) | Supplementary information
Gender-dependent progression of systemic metabolic states in early childhood
Janne Nikkilä,
Marko Sysi-Aho,
Andrey Ermolov,
Tuulikki Seppänen-Laakso,
Olli Simell,
Samuel Kaski
&
Matej Ore
i
doi:10.1038/msb.2008.34
Published online:
03 June 2008
eQED: an efficient method for interpreting eQTL associations using protein networks
Silpa Suthram, Andreas Beyer, Richard M Karp, Yonina Eldar & Trey Ideker
doi:10.1038/msb.2008.4
Published online:
04 March 2008
Models from experiments: combinatorial drug perturbations of cancer cells
Sven Nelander, Weiqing Wang, Björn Nilsson, Qing-Bai She, Christine Pratilas, Neal Rosen, Peter Gennemark & Chris Sander
doi:10.1038/msb.2008.53
Published online:
02 September 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
Formulating genome-scale kinetic models in the post-genome era
Neema Jamshidi & Bernhard Ø Palsson
doi:10.1038/msb.2008.8
Published online:
04 March 2008
Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method
Lukas Burger & Erik van Nimwegen
doi:10.1038/msb4100203
Published online:
12 February 2008
Synopsis | Full Text | PDF (409K) | Supplementary information
Modular cell biology: retroactivity and insulation
Domitilla Del Vecchio, Alexander J Ninfa & Eduardo D Sontag
doi:10.1038/msb4100204
Published online:
12 February 2008
Synopsis | Full Text | PDF (755K) | Supplementary information
2007
Tissue-specific regulatory elements in mammalian promoters
Andrew D Smith, Pavel Sumazin & Michael Q Zhang
doi:10.1038/msb4100114
Published online:
16 January 2007
Reconstructing dynamic regulatory maps
Jason Ernst, Oded Vainas, Christopher T Harbison, Itamar Simon & Ziv Bar-Joseph
doi:10.1038/msb4100115
Published online:
16 January 2007
Synopsis | Full Text | PDF (402K) | Supplementary information
Network-based prediction of protein function
Roded Sharan, Igor Ulitsky & Ron Shamir
doi:10.1038/msb4100129
Published online:
13 March 2007
Inferring condition-specific transcription factor function from DNA binding and gene expression data
Rachel Patton McCord, Michael F Berger, Anthony A Philippakis & Martha L Bulyk
doi:10.1038/msb4100140
Published online:
17 April 2007
A genome-scale computational study of the interplay between transcriptional regulation and metabolism
Tomer Shlomi, Yariv Eisenberg, Roded Sharan & Eytan Ruppin
doi:10.1038/msb4100141
Published online:
17 April 2007
Novel peptide identification from tandem mass spectra using ESTs and sequence database compression
Nathan J Edwards
doi:10.1038/msb4100142
Published online:
17 April 2007
UV-B responsive microRNA genes in Arabidopsis thaliana
Xuefeng Zhou, Guandong Wang & Weixiong Zhang
doi:10.1038/msb4100143
Published online:
17 April 2007
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
Igor Ulitsky & Ron Shamir
doi:10.1038/msb4100144
Published online:
17 April 2007
An integrated approach to prognosis using protein microarrays and nonparametric methods
Tanya Knickerbocker, Jiunn R Chen, Ravi Thadhani & Gavin MacBeath
doi:10.1038/msb4100167
Published online:
26 June 2007
The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks
Sergio Grimbs, Joachim Selbig, Sascha Bulik, Hermann-Georg Holzhütter & Ralf Steuer
doi:10.1038/msb4100186
Published online:
13 November 2007
Synopsis | Full Text | PDF (1,156K) | Supplementary information
2006
Systems-level analyses identify extensive coupling among gene expression machines
Karolina Maciag, Steven J Altschuler, Michael D Slack, Nevan J Krogan, Andrew Emili, Jack F Greenblatt, Tom Maniatis & Lani F Wu
doi:10.1038/msb4100045
Published online:
17 January 2006
Synopsis | Full Text | PDF (825K) | Supplementary information
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
Synopsis | Full Text | PDF (2,246K) | Supplementary information
Deciphering principles of transcription regulation in eukaryotic genomes
Dat H Nguyen & Patrik D'haeseleer
doi:10.1038/msb4100054
Published online:
18 April 2006
Synopsis | Full Text | PDF (418K) | Supplementary information
Stochastic dynamics of macromolecular-assembly networks
Leonor Saiz & Jose MG Vilar
doi:10.1038/msb4100061
Published online:
16 May 2006
Adaptively inferring human transcriptional subnetworks
Debopriya Das, Zaher Nahlé & Michael Q Zhang
doi:10.1038/msb4100067
Published online:
06 June 2006
Synopsis | Full Text | PDF (255K) | Supplementary information
2005
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium
Amos Tanay, Israel Steinfeld, Martin Kupiec & Ron Shamir
doi:10.1038/msb4100005
Published online:
29 March 2005
Synopsis | Full Text | PDF (447K) | Supplementary information
A comprehensive pathway map of epidermal growth factor receptor signaling
Kanae Oda, Yukiko Matsuoka, Akira Funahashi & Hiroaki Kitano
doi:10.1038/msb4100014
Published online:
25 May 2005
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
Andrew Keller, Jimmy Eng, Ning Zhang, Xiao-jun Li & Ruedi Aebersold
doi:10.1038/msb4100024
Published online:
02 August 2005
A theoretical framework for specificity in cell signaling
Natalia L Komarova, Xiufen Zou, Qing Nie & Lee Bardwell
doi:10.1038/msb4100031
Published online:
18 October 2005
