Molecular Systems Biology Molecular Systems Biology is a peer-reviewed author-pays online journal that publishes full-length papers and accompanying synopses describing original research in the field of molecular systems biology and which focuses on the analysis, integration and modeling of molecular and cellular phenomena. The journal will make full use of the online environment to allow reader interaction with data and models presented in the published articles. http://www.nature.com/msb/current_issue/ Nature Publishing Group en © 2008 Nature Publishing Group Molecular Systems Biology 1744-4292 © 2008 Nature Publishing Group permissions@nature.com Molecular Systems Biology http://www.nature.com/includes/rj_globnavimages/msb_logo.gif http://www.nature.com/msb/ Predicting synthetic rescues in metabolic networks http://dx.doi.org/10.1038/msb.2008.1 Predicting synthetic rescues in metabolic networks

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.1

Authors: Adilson E Motter, Natali Gulbahce, Eivind Almaas & Albert-László Barabási

]]> Predicting synthetic rescues in metabolic networks Adilson E Motter Natali Gulbahce Eivind Almaas Albert-László Barabási doi:10.1038/msb.2008.1 Molecular Systems Biology 4, (2008) 2008-02-12 Molecular Systems Biology 2008-02-12 4 Article A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1 http://dx.doi.org/10.1038/msb.2008.10 A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.10

Authors: Véronique de Berardinis, David Vallenet, Vanina Castelli, Marielle Besnard, Agnès Pinet, Corinne Cruaud, Sumitta Samair, Christophe Lechaplais, Gabor Gyapay, Céline Richez, Maxime Durot, Annett Kreimeyer, François Le Fèvre, Vincent Schächter, Valérie Pezo, Volker Döring, Claude Scarpelli, Claudine Médigue, Georges N Cohen, Philippe Marlière, Marcel Salanoubat & Jean Weissenbach

]]> A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1 Véronique de Berardinis David Vallenet Vanina Castelli Marielle Besnard Agnès Pinet Corinne Cruaud Sumitta Samair Christophe Lechaplais Gabor Gyapay Céline Richez Maxime Durot Annett Kreimeyer François Le Fèvre Vincent Schächter Valérie Pezo Volker Döring Claude Scarpelli Claudine Médigue Georges N Cohen Philippe Marlière Marcel Salanoubat Jean Weissenbach doi:10.1038/msb.2008.10 Molecular Systems Biology 4, (2008) 2008-03-04 Molecular Systems Biology 2008-03-04 4 Article Selection to minimise noise in living systems and its implications for the evolution of gene expression http://dx.doi.org/10.1038/msb.2008.11 Selection to minimise noise in living systems and its implications for the evolution of gene expression

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.11

Author: Ben Lehner

]]> Selection to minimise noise in living systems and its implications for the evolution of gene expression Ben Lehner doi:10.1038/msb.2008.11 Molecular Systems Biology 4, (2008) 2008-03-04 Molecular Systems Biology 2008-03-04 4 Report Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger http://dx.doi.org/10.1038/msb.2008.12 Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.12

Authors: Mikael Rørdam Andersen, Michael Lynge Nielsen & Jens Nielsen

]]> Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger Mikael Rørdam Andersen Michael Lynge Nielsen Jens Nielsen doi:10.1038/msb.2008.12 Molecular Systems Biology 4, (2008) 2008-03-25 Molecular Systems Biology 2008-03-25 4 Article A systems-level approach to mapping the telomere length maintenance gene circuitry http://dx.doi.org/10.1038/msb.2008.13 A systems-level approach to mapping the telomere length maintenance gene circuitry

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.13

Authors: Rafi Shachar, Lior Ungar, Martin Kupiec, Eytan Ruppin & Roded Sharan

]]> 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 Molecular Systems Biology 4, (2008) 2008-03-04 Molecular Systems Biology 2008-03-04 4 Report Theoretical and experimental approaches to understand morphogen gradients http://dx.doi.org/10.1038/msb.2008.14 Theoretical and experimental approaches to understand morphogen gradients

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.14

Authors: Marta Ibañes & Juan Carlos Izpisúa Belmonte

]]> Theoretical and experimental approaches to understand morphogen gradients Marta Ibañes Juan Carlos Izpisúa Belmonte doi:10.1038/msb.2008.14 Molecular Systems Biology 4, (2008) 2008-03-25 Molecular Systems Biology 2008-03-25 4 Review Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major http://dx.doi.org/10.1038/msb.2008.15 Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.15

Authors: Arvind K Chavali, Jeffrey D Whittemore, James A Eddy, Kyle T Williams & Jason A Papin

]]> Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major Arvind K Chavali Jeffrey D Whittemore James A Eddy Kyle T Williams Jason A Papin doi:10.1038/msb.2008.15 Molecular Systems Biology 4, (2008) 2008-03-25 Molecular Systems Biology 2008-03-25 4 Article The role of disorder in interaction networks: a structural analysis http://dx.doi.org/10.1038/msb.2008.16 The role of disorder in interaction networks: a structural analysis

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.16

Authors: Philip M Kim, Andrea Sboner, Yu Xia & Mark Gerstein

]]> The role of disorder in interaction networks: a structural analysis Philip M Kim Andrea Sboner Yu Xia Mark Gerstein doi:10.1038/msb.2008.16 Molecular Systems Biology 4, (2008) 2008-03-25 Molecular Systems Biology 2008-03-25 4 Report Mathematical modeling of pathogenicity of Cryptococcus neoformans http://dx.doi.org/10.1038/msb.2008.17 Mathematical modeling of pathogenicity of Cryptococcus neoformans

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.17

Authors: Jacqueline Garcia, John Shea, Fernando Alvarez-Vasquez, Asfia Qureshi, Chiara Luberto, Eberhard O Voit & Maurizio Del Poeta

]]> Mathematical modeling of pathogenicity of Cryptococcus neoformans Jacqueline Garcia John Shea Fernando Alvarez-Vasquez Asfia Qureshi Chiara Luberto Eberhard O Voit Maurizio Del Poeta doi:10.1038/msb.2008.17 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 Article Transient heterogeneity in extracellular protease production by Bacillus subtilis http://dx.doi.org/10.1038/msb.2008.18 Transient heterogeneity in extracellular protease production by Bacillus subtilis

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.18

Authors: Jan-Willem Veening, Oleg A Igoshin, Robyn T Eijlander, Reindert Nijland, Leendert W Hamoen & Oscar P Kuipers

]]> Transient heterogeneity in extracellular protease production by Bacillus subtilis Jan-Willem Veening Oleg A Igoshin Robyn T Eijlander Reindert Nijland Leendert W Hamoen Oscar P Kuipers doi:10.1038/msb.2008.18 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 Article A map of human protein interactions derived from co-expression of human mRNAs and their orthologs http://dx.doi.org/10.1038/msb.2008.19 A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.19

Authors: Arun K Ramani, Zhihua Li, G Traver Hart, Mark W Carlson, Daniel R Boutz & Edward M Marcotte

]]> A map of human protein interactions derived from co-expression of human mRNAs and their orthologs Arun K Ramani Zhihua Li G Traver Hart Mark W Carlson Daniel R Boutz Edward M Marcotte doi:10.1038/msb.2008.19 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 Article A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas http://dx.doi.org/10.1038/msb.2008.2 A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.2

Authors: Kartik M Mani, Celine Lefebvre, Kai Wang, Wei Keat Lim, Katia Basso, Riccardo Dalla-Favera & Andrea Califano

]]> A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas Kartik M Mani Celine Lefebvre Kai Wang Wei Keat Lim Katia Basso Riccardo Dalla-Favera Andrea Califano doi:10.1038/msb.2008.2 Molecular Systems Biology 4, (2008) 2008-02-12 Molecular Systems Biology 2008-02-12 4 Report Synthetic gene brushes: a structure–function relationship http://dx.doi.org/10.1038/msb.2008.20 Synthetic gene brushes: a structure–function relationship

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.20

Authors: Amnon Buxboim, Shirley S Daube & Roy Bar-Ziv

]]> Synthetic gene brushes: a structure–function relationship Amnon Buxboim Shirley S Daube Roy Bar-Ziv doi:10.1038/msb.2008.20 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 Report Ultrasensitive gene regulation by positive feedback loops in nucleosome modification http://dx.doi.org/10.1038/msb.2008.21 Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.21

Authors: Kim Sneppen, Mille A Micheelsen & Ian B Dodd

]]> Ultrasensitive gene regulation by positive feedback loops in nucleosome modification Kim Sneppen Mille A Micheelsen Ian B Dodd doi:10.1038/msb.2008.21 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 Report Systems engineering to systems biology http://dx.doi.org/10.1038/msb.2008.22 Systems engineering to systems biology

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.22

Authors: Muhammed A Yıldırım & Marc Vidal

]]> Systems engineering to systems biology Muhammed A Yıldırım Marc Vidal doi:10.1038/msb.2008.22 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 News and Views Reverse engineering of force integration during mitosis in the Drosophila embryo http://dx.doi.org/10.1038/msb.2008.23 Reverse engineering of force integration during mitosis in the Drosophila embryo

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.23

Authors: Roy Wollman, Gul Civelekoglu-Scholey, Jonathan M Scholey & Alex Mogilner

]]> 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 Molecular Systems Biology 4, (2008) 2008-05-06 Molecular Systems Biology 2008-05-06 4 Article A synthetic Escherichia coli predator–prey ecosystem http://dx.doi.org/10.1038/msb.2008.24 A synthetic Escherichia coli predator–prey ecosystem

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.24

Authors: Frederick K Balagaddé, Hao Song, Jun Ozaki, Cynthia H Collins, Matthew Barnet, Frances H Arnold, Stephen R Quake & Lingchong You

]]> A synthetic Escherichia coli predator–prey ecosystem Frederick K Balagaddé Hao Song Jun Ozaki Cynthia H Collins Matthew Barnet Frances H Arnold Stephen R Quake Lingchong You doi:10.1038/msb.2008.24 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 Report Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression http://dx.doi.org/10.1038/msb.2008.25 Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.25

Authors: Sujun Hua, Caleb B Kallen, Ruby Dhar, Maria T Baquero, Christopher E Mason, Beth A Russell, Parantu K Shah, Jiang Liu, Andrey Khramtsov, Maria S Tretiakova, Thomas N Krausz, Olufunmilayo I Olopade, David L Rimm & Kevin P White

]]> Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression Sujun Hua Caleb B Kallen Ruby Dhar Maria T Baquero Christopher E Mason Beth A Russell Parantu K Shah Jiang Liu Andrey Khramtsov Maria S Tretiakova Thomas N Krausz Olufunmilayo I Olopade David L Rimm Kevin P White doi:10.1038/msb.2008.25 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 Article Recursive construction of perfect DNA molecules from imperfect oligonucleotides http://dx.doi.org/10.1038/msb.2008.26 Recursive construction of perfect DNA molecules from imperfect oligonucleotides

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.26

Authors: Gregory Linshiz, Tuval Ben Yehezkel, Shai Kaplan, Ilan Gronau, Sivan Ravid, Rivka Adar & Ehud Shapiro

]]> 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 Molecular Systems Biology 4, (2008) 2008-05-06 Molecular Systems Biology 2008-05-06 4 Report Network-based global inference of human disease genes http://dx.doi.org/10.1038/msb.2008.27 Network-based global inference of human disease genes

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.27

Authors: Xuebing Wu, Rui Jiang, Michael Q Zhang & Shao Li

]]> Network-based global inference of human disease genes Xuebing Wu Rui Jiang Michael Q Zhang Shao Li doi:10.1038/msb.2008.27 Molecular Systems Biology 4, (2008) 2008-05-06 Molecular Systems Biology 2008-05-06 4 Article Isoform switching facilitates period control in the Neurospora crassa circadian clock http://dx.doi.org/10.1038/msb.2008.28 Isoform switching facilitates period control in the Neurospora crassa circadian clock

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.28

Author: Ozgur E Akman, James CW Locke, Sanyi Tang, Isabelle Carré, Andrew J Millar & David A Rand

]]> Isoform switching facilitates period control in the Neurospora crassa circadian clock Ozgur E Akman James CW Locke Sanyi Tang Isabelle Carré Andrew J Millar David A Rand doi:10.1038/msb.2008.28 Molecular Systems Biology 4, (2008) 2008-04-15 Molecular Systems Biology 2008-04-15 4 Corrigendum Recurrent design patterns in the feedback regulation of the mammalian signalling network http://dx.doi.org/10.1038/msb.2008.29 Recurrent design patterns in the feedback regulation of the mammalian signalling network

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.29

Authors: Stefan Legewie, Hanspeter Herzel, Hans V Westerhoff & Nils Blüthgen

]]> Recurrent design patterns in the feedback regulation of the mammalian signalling network Stefan Legewie Hanspeter Herzel Hans V Westerhoff Nils Blüthgen doi:10.1038/msb.2008.29 Molecular Systems Biology 4, (2008) 2008-05-06 Molecular Systems Biology 2008-05-06 4 Report Modularity defined http://dx.doi.org/10.1038/msb.2008.3 Modularity defined

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.3

Author: Herbert M Sauro

]]> Modularity defined Herbert M Sauro doi:10.1038/msb.2008.3 Molecular Systems Biology 4, (2008) 2008-02-12 Molecular Systems Biology 2008-02-12 4 News and Views Understanding NF-κB signaling via mathematical modeling http://dx.doi.org/10.1038/msb.2008.30 Understanding NF-κB signaling via mathematical modeling

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.30

Authors: Raymond Cheong, Alexander Hoffmann & Andre Levchenko

]]> Understanding NF-κB signaling via mathematical modeling Raymond Cheong Alexander Hoffmann Andre Levchenko doi:10.1038/msb.2008.30 Molecular Systems Biology 4, (2008) 2008-05-06 Molecular Systems Biology 2008-05-06 4 Perspective Colored extrinsic fluctuations and stochastic gene expression http://dx.doi.org/10.1038/msb.2008.31 Colored extrinsic fluctuations and stochastic gene expression

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.31

Authors: Vahid Shahrezaei, Julien F Ollivier & Peter S Swain

]]> Colored extrinsic fluctuations and stochastic gene expression Vahid Shahrezaei Julien F Ollivier Peter S Swain doi:10.1038/msb.2008.31 Molecular Systems Biology 4, (2008) 2008-05-06 Molecular Systems Biology 2008-05-06 4 Article Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis http://dx.doi.org/10.1038/msb.2008.32 Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.32

Authors: Naoyuki Sugiyama, Hirofumi Nakagami, Keiichi Mochida, Arsalan Daudi, Masaru Tomita, Ken Shirasu & Yasushi Ishihama

]]> Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis Naoyuki Sugiyama Hirofumi Nakagami Keiichi Mochida Arsalan Daudi Masaru Tomita Ken Shirasu Yasushi Ishihama doi:10.1038/msb.2008.32 Molecular Systems Biology 4, (2008) 2008-05-06 Molecular Systems Biology 2008-05-06 4 Report A theoretical model of mitotic spindle elongation under experimental constraints http://dx.doi.org/10.1038/msb.2008.33 A theoretical model of mitotic spindle elongation under experimental constraints

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.33

Author: Thomas Surrey

]]> A theoretical model of mitotic spindle elongation under experimental constraints Thomas Surrey doi:10.1038/msb.2008.33 Molecular Systems Biology 4, (2008) 2008-05-06 Molecular Systems Biology 2008-05-06 4 News and Views Gender-dependent progression of systemic metabolic states in early childhood http://dx.doi.org/10.1038/msb.2008.34 Gender-dependent progression of systemic metabolic states in early childhood

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.34

Authors: Janne Nikkilä, Marko Sysi-Aho, Andrey Ermolov, Tuulikki Seppänen-Laakso, Olli Simell, Samuel Kaski & Matej Orešič

]]> 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 Orešič doi:10.1038/msb.2008.34 Molecular Systems Biology 4, (2008) 2008-06-03 Molecular Systems Biology 2008-06-03 4 Report Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat http://dx.doi.org/10.1038/msb.2008.35 Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.35

Authors: Victor Kunin, Jeroen Raes, J Kirk Harris, John R Spear, Jeffrey J Walker, Natalia Ivanova, Christian von Mering, Brad M Bebout, Norman R Pace, Peer Bork & Philip Hugenholtz

]]> Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat Victor Kunin Jeroen Raes J Kirk Harris John R Spear Jeffrey J Walker Natalia Ivanova Christian von Mering Brad M Bebout Norman R Pace Peer Bork Philip Hugenholtz doi:10.1038/msb.2008.35 Molecular Systems Biology 4, (2008) 2008-06-03 Molecular Systems Biology 2008-06-03 4 Report Gene network dynamics controlling keratinocyte migration http://dx.doi.org/10.1038/msb.2008.36 Gene network dynamics controlling keratinocyte migration

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.36

Authors: Hauke Busch, David Camacho-Trullio, Zbigniew Rogon, Kai Breuhahn, Peter Angel, Roland Eils & Axel Szabowski

]]> Gene network dynamics controlling keratinocyte migration Hauke Busch David Camacho-Trullio Zbigniew Rogon Kai Breuhahn Peter Angel Roland Eils Axel Szabowski doi:10.1038/msb.2008.36 Molecular Systems Biology 4, (2008) 2008-07-01 Molecular Systems Biology 2008-07-01 4 Article Comment on ‘Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions’ http://dx.doi.org/10.1038/msb.2008.37 Comment on ‘Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions’

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.37

Author: Daniel A Beard

]]> Comment on ‘Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions’ Daniel A Beard doi:10.1038/msb.2008.37 Molecular Systems Biology 4, (2008) 2008-07-15 Molecular Systems Biology 2008-07-15 4 News and Views In reply: ‘Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions’ http://dx.doi.org/10.1038/msb.2008.38 In reply: ‘Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions’

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.38

Authors: Ruo-Yu Luo, Yi-Xue Li & Qingming Luo

]]> In reply: ‘Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions’ Ruo-Yu Luo Yi-Xue Li Qingming Luo doi:10.1038/msb.2008.38 Molecular Systems Biology 4, (2008) 2008-07-15 Molecular Systems Biology 2008-07-15 4 News and Views Life Sciences and the web: a new era for collaboration http://dx.doi.org/10.1038/msb.2008.39 Life Sciences and the web: a new era for collaboration

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.39

Authors: Jonathan A Sagotsky, Le Zhang, Zhihui Wang, Sean Martin & Thomas S Deisboeck

]]> Life Sciences and the web: a new era for collaboration Jonathan A Sagotsky Le Zhang Zhihui Wang Sean Martin Thomas S Deisboeck doi:10.1038/msb.2008.39 Molecular Systems Biology 4, (2008) 2008-07-01 Molecular Systems Biology 2008-07-01 4 Perspective eQED: an efficient method for interpreting eQTL associations using protein networks http://dx.doi.org/10.1038/msb.2008.4 eQED: an efficient method for interpreting eQTL associations using protein networks

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.4

Authors: Silpa Suthram, Andreas Beyer, Richard M Karp, Yonina Eldar & Trey Ideker

]]> 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 Molecular Systems Biology 4, (2008) 2008-03-04 Molecular Systems Biology 2008-03-04 4 Report Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model http://dx.doi.org/10.1038/msb.2008.40 Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.40

Authors: Francois-Pierre J Martin, Yulan Wang, Norbert Sprenger, Ivan K S Yap, Serge Rezzi, Ziad Ramadan, Emma Peré-Trepat, Florence Rochat, Christine Cherbut, Peter van Bladeren, Laurent B Fay, Sunil Kochhar, John C Lindon, Elaine Holmes & Jeremy K Nicholson

]]> Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model Francois-Pierre J Martin Yulan Wang Norbert Sprenger Ivan K S Yap Serge Rezzi Ziad Ramadan Emma Peré-Trepat Florence Rochat Christine Cherbut Peter van Bladeren Laurent B Fay Sunil Kochhar John C Lindon Elaine Holmes Jeremy K Nicholson doi:10.1038/msb.2008.40 Molecular Systems Biology 4, (2008) 2008-07-15 Molecular Systems Biology 2008-07-15 4 Article When microarrays Met epidermal-cell migration http://dx.doi.org/10.1038/msb.2008.41 When microarrays Met epidermal-cell migration

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.41

Author: Kevin A Janes

]]> When microarrays Met epidermal-cell migration Kevin A Janes doi:10.1038/msb.2008.41 Molecular Systems Biology 4, (2008) 2008-07-01 Molecular Systems Biology 2008-07-01 4 News and Views From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions http://dx.doi.org/10.1038/msb.2008.42 From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.42

Authors: Igor Ulitsky, Tomer Shlomi, Martin Kupiec & Ron Shamir

]]> From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions Igor Ulitsky Tomer Shlomi Martin Kupiec Ron Shamir doi:10.1038/msb.2008.42 Molecular Systems Biology 4, (2008) 2008-07-15 Molecular Systems Biology 2008-07-15 4 Article The incoherent feed-forward loop can generate non-monotonic input functions for genes http://dx.doi.org/10.1038/msb.2008.43 The incoherent feed-forward loop can generate non-monotonic input functions for genes

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.43

Authors: Shai Kaplan, Anat Bren, Erez Dekel & Uri Alon

]]> The incoherent feed-forward loop can generate non-monotonic input functions for genes Shai Kaplan Anat Bren Erez Dekel Uri Alon doi:10.1038/msb.2008.43 Molecular Systems Biology 4, (2008) 2008-07-15 Molecular Systems Biology 2008-07-15 4 Report Parasites lead to evolution of robustness against gene loss in host signaling networks http://dx.doi.org/10.1038/msb.2008.44 Parasites lead to evolution of robustness against gene loss in host signaling networks

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.44

Authors: Marcel Salathé & Orkun S Soyer

]]> Parasites lead to evolution of robustness against gene loss in host signaling networks Marcel Salathé Orkun S Soyer doi:10.1038/msb.2008.44 Molecular Systems Biology 4, (2008) 2008-07-15 Molecular Systems Biology 2008-07-15 4 Article Membrane identity and GTPase cascades regulated by toggle and cut-out switches http://dx.doi.org/10.1038/msb.2008.45 Membrane identity and GTPase cascades regulated by toggle and cut-out switches

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.45

Authors: Perla Del Conte-Zerial, Lutz Brusch, Jochen C Rink, Claudio Collinet, Yannis Kalaidzidis, Marino Zerial & Andreas Deutsch

]]> Membrane identity and GTPase cascades regulated by toggle and cut-out switches Perla Del Conte-Zerial Lutz Brusch Jochen C Rink Claudio Collinet Yannis Kalaidzidis Marino Zerial Andreas Deutsch doi:10.1038/msb.2008.45 Molecular Systems Biology 4, (2008) 2008-07-15 Molecular Systems Biology 2008-07-15 4 Article Increased glycolytic flux as an outcome of whole-genome duplication in yeast http://dx.doi.org/10.1038/msb.2008.46 Increased glycolytic flux as an outcome of whole-genome duplication in yeast

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.46

Author: Gavin C Conant & Kenneth H Wolfe

]]> Increased glycolytic flux as an outcome of whole-genome duplication in yeast Gavin C Conant Kenneth H Wolfe doi:10.1038/msb.2008.46 Molecular Systems Biology 4, (2008) 2008-07-01 Molecular Systems Biology 2008-07-01 4 Corrigendum Isoform switching facilitates period control in the Neurospora crassa circadian clock http://dx.doi.org/10.1038/msb.2008.5 Isoform switching facilitates period control in the Neurospora crassa circadian clock

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.5

Authors: Ozgur E Akman, James C W Locke, Sanyi Tang, Isabelle Carré, Andrew J Millar & David A Rand

]]> Isoform switching facilitates period control in the Neurospora crassa circadian clock Ozgur E Akman James C W Locke Sanyi Tang Isabelle Carré Andrew J Millar David A Rand doi:10.1038/msb.2008.5 Molecular Systems Biology 4, (2008) 2008-02-12 Molecular Systems Biology 2008-02-12 4 Article Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression http://dx.doi.org/10.1038/msb.2008.6 Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.6

Authors: Itai Yanai, L Ryan Baugh, Jessica J Smith, Casey Roehrig, Shai S Shen-Orr, Julia M Claggett, Andrew A Hill, Donna K Slonim & Craig P Hunter

]]> Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression Itai Yanai L Ryan Baugh Jessica J Smith Casey Roehrig Shai S Shen-Orr Julia M Claggett Andrew A Hill Donna K Slonim Craig P Hunter doi:10.1038/msb.2008.6 Molecular Systems Biology 4, (2008) 2008-02-12 Molecular Systems Biology 2008-02-12 4 Article A comprehensive modular map of molecular interactions in RB/E2F pathway http://dx.doi.org/10.1038/msb.2008.7 A comprehensive modular map of molecular interactions in RB/E2F pathway

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.7

Authors: Laurence Calzone, Amélie Gelay, Andrei Zinovyev, François Radvanyi & Emmanuel Barillot

]]> A comprehensive modular map of molecular interactions in RB/E2F pathway Laurence Calzone Amélie Gelay Andrei Zinovyev François Radvanyi Emmanuel Barillot doi:10.1038/msb.2008.7 Molecular Systems Biology 4, (2008) 2008-03-04 Molecular Systems Biology 2008-03-04 4 Review Formulating genome-scale kinetic models in the post-genome era http://dx.doi.org/10.1038/msb.2008.8 Formulating genome-scale kinetic models in the post-genome era

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.8

Authors: Neema Jamshidi & Bernhard Ø Palsson

]]> Formulating genome-scale kinetic models in the post-genome era Neema Jamshidi Bernhard Ø Palsson doi:10.1038/msb.2008.8 Molecular Systems Biology 4, (2008) 2008-03-04 Molecular Systems Biology 2008-03-04 4 Perspective The liver pharmacological and xenobiotic gene response repertoire http://dx.doi.org/10.1038/msb.2008.9 The liver pharmacological and xenobiotic gene response repertoire

Molecular Systems Biology 4, (2008). doi:10.1038/msb.2008.9

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Molecular Systems Biology 4, (2008). doi:10.1038/msb4100198

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Molecular Systems Biology 4, (2008). doi:10.1038/msb4100203

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