Molecular Systems Biology

Computational methods

2009

Toward accurate reconstruction of functional protein networks

Nir Yosef, Lior Ungar, Einat Zalckvar, Adi Kimchi, Martin Kupiec, Eytan Ruppin & Roded Sharan

doi:10.1038/msb.2009.3
Published online: 17 March 2009

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Genome-wide allele- and strand-specific expression profiling

Julien Gagneur, Himanshu Sinha, Fabiana Perocchi, Richard Bourgon, Wolfgang Huber & Lars M Steinmetz

doi:10.1038/msb.2009.31
Published online: 16 June 2009

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A simple and efficient algorithm for genome-wide homozygosity analysis in disease

Wei Liu, Jinhui Ding, Jesse Raphael Gibbs, Sue Jane Wang, John Hardy & Andrew Singleton

doi:10.1038/msb.2009.53
Published online: 15 September 2009

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Network-assisted protein identification and data interpretation in shotgun proteomics

Jing Li, Lisa J Zimmerman, Byung-Hoon Park, David L Tabb, Daniel C Liebler & Bing Zhang

doi:10.1038/msb.2009.54
Published online: 18 August 2009

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Large-scale identification of genetic design strategies using local search

Desmond S Lun, Graham Rockwell, Nicholas J Guido, Michael Baym, Jonathan A Kelner, Bonnie Berger, James E Galagan & George M Church

doi:10.1038/msb.2009.57
Published online: 18 August 2009

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Listening to the noise: random fluctuations reveal gene network parameters

Brian Munsky, Brooke Trinh & Mustafa Khammash

doi:10.1038/msb.2009.75
Published online: 13 October 2009

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2008

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

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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

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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

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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

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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

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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

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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 s caron i c caron

doi:10.1038/msb.2008.34
Published online: 03 June 2008

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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

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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

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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

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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

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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

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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

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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

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Network-based prediction of protein function

Roded Sharan, Igor Ulitsky & Ron Shamir

doi:10.1038/msb4100129
Published online: 13 March 2007

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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

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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

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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

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UV-B responsive microRNA genes in Arabidopsis thaliana

Xuefeng Zhou, Guandong Wang & Weixiong Zhang

doi:10.1038/msb4100143
Published online: 17 April 2007

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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

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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

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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

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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

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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

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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

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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

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