| | Other Issues: previous | next | latest | archiveArticles Modeling the electron transport chain of purple non-sulfur bacteria Steffen Klamt, Hartmut Grammel, Ronny Straube, Robin Ghosh, and Ernst Dieter Gilles PMCID: PMC2238716 Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model Francois-Pierre J Martin, Yulan Wang, Norbert Sprenger, Ivan K S Yap, Torbjörn Lundstedt, Per Lek, Serge Rezzi, Ziad Ramadan, Peter van Bladeren, Laurent B Fay, Sunil Kochhar, John C Lindon, Elaine Holmes, and Jeremy K Nicholson PMCID: PMC2238715 On the relation between promoter divergence and gene expression evolution Itay Tirosh, Adina Weinberger, Dana Bezalel, Mark Kaganovich, and Naama Barkai PMCID: PMC2238714 Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, and Hiroyuki Kurata PMCID: PMC2238713 Modular cell biology: retroactivity and insulation Domitilla Del Vecchio, Alexander J Ninfa, and Eduardo D Sontag PMCID: PMC2267736 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, and Craig P Hunter PMCID: PMC2267734 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, and David A Rand PMCID: PMC2267733 Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method Lukas Burger and Erik van Nimwegen PMCID: PMC2267735 1H NMR metabonomics approach to the disease continuum of diabetic complications and premature death Ville-Petteri Mäkinen, Pasi Soininen, Carol Forsblom, Maija Parkkonen, Petri Ingman, Kimmo Kaski, Per-Henrik Groop, and Mika Ala-Korpela PMCID: PMC2267737 Predicting synthetic rescues in metabolic networks Adilson E Motter, Natali Gulbahce, Eivind Almaas, and Albert-László Barabási PMCID: PMC2267730 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, and Jean Weissenbach PMCID: PMC2290942 The liver pharmacological and xenobiotic gene response repertoire Georges Natsoulis, Cecelia I Pearson, Jeremy Gollub, Barrett P Eynon, Joe Ferng, Ramesh Nair, Radha Idury, May D Lee, Mark R Fielden, Richard J Brennan, Alan H Roter, and Kurt Jarnagin PMCID: PMC2290941 Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major Arvind K Chavali, Jeffrey D Whittemore, James A Eddy, Kyle T Williams, and Jason A Papin PMCID: PMC2290936 Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger Mikael Rørdam Andersen, Michael Lynge Nielsen, and Jens Nielsen PMCID: PMC2290933 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, and Edward M Marcotte PMCID: PMC2387231 Mathematical modeling of pathogenicity of Cryptococcus neoformans Jacqueline Garcia, John Shea, Fernando Alvarez-Vasquez, Asfia Qureshi, Chiara Luberto, Eberhard O Voit, and Maurizio Del Poeta PMCID: PMC2387229 Transient heterogeneity in extracellular protease production by Bacillus subtilis Jan-Willem Veening, Oleg A Igoshin, Robyn T Eijlander, Reindert Nijland, Leendert W Hamoen, and Oscar P Kuipers PMCID: PMC2387230 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, and Kevin P White PMCID: PMC2394496 Network-based global inference of human disease genes Xuebing Wu, Rui Jiang, Michael Q Zhang, and Shao Li PMCID: PMC2424293 Reverse engineering of force integration during mitosis in the Drosophila embryo Roy Wollman, Gul Civelekoglu-Scholey, Jonathan M Scholey, and Alex Mogilner PMCID: PMC2424291 Colored extrinsic fluctuations and stochastic gene expression Vahid Shahrezaei, Julien F Ollivier, and Peter S Swain PMCID: PMC2424296 Gene network dynamics controlling keratinocyte migration Hauke Busch, David Camacho-Trullio, Zbigniew Rogon, Kai Breuhahn, Peter Angel, Roland Eils, and Axel Szabowski PMCID: PMC2516358 Parasites lead to evolution of robustness against gene loss in host signaling networks Marcel Salathé and Orkun S Soyer PMCID: PMC2516366 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, and Jeremy K Nicholson PMCID: PMC2516362 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, and Andreas Deutsch PMCID: PMC2516367 From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions Igor Ulitsky, Tomer Shlomi, Martin Kupiec, and Ron Shamir PMCID: PMC2516364 Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size Jingshan Zhang, Sergei Maslov, and Eugene I Shakhnovich PMCID: PMC2538908 Variable sizes of Escherichia coli chemoreceptor signaling teams Robert G Endres, Olga Oleksiuk, Clinton H Hansen, Yigal Meir, Victor Sourjik, and Ned S Wingreen PMCID: PMC2538909 Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity Oded Shaham, Ru Wei, Thomas J Wang, Catherine Ricciardi, Gregory D Lewis, Ramachandran S Vasan, Steven A Carr, Ravi Thadhani, Robert E Gerszten, and Vamsi K Mootha PMCID: PMC2538910 A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves Simona Digiuni, Swen Schellmann, Florian Geier, Bettina Greese, Martina Pesch, Katja Wester, Burcu Dartan, Valerie Mach, Bhylahalli Purushottam Srinivas, Jens Timmer, Christian Fleck, and Martin Hulskamp PMCID: PMC2564731 InnateDB: facilitating systems-level analyses of the mammalian innate immune response David J Lynn, Geoffrey L Winsor, Calvin Chan, Nicolas Richard, Matthew R Laird, Aaron Barsky, Jennifer L Gardy, Fiona M Roche, Timothy H W Chan, Naisha Shah, Raymond Lo, Misbah Naseer, Jaimmie Que, Melissa Yau, Michael Acab, Dan Tulpan, Matthew D Whiteside, Avinash Chikatamarla, Bernadette Mah, Tamara Munzner, Karsten Hokamp, Robert E W Hancock, and Fiona S L Brinkman PMCID: PMC2564732 Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes Sandrine P Claus, Tsz M Tsang, Yulan Wang, Olivier Cloarec, Eleni Skordi, François-Pierre Martin, Serge Rezzi, Alastair Ross, Sunil Kochhar, Elaine Holmes, and Jeremy K Nicholson PMCID: PMC2583082 An integrated cell-free metabolic platform for protein production and synthetic biology Michael C Jewett, Kara A Calhoun, Alexei Voloshin, Jessica J Wuu, and James R Swartz PMCID: PMC2583083 A quantitative comparison of sRNA-based and protein-based gene regulation Pankaj Mehta, Sidhartha Goyal, and Ned S Wingreen PMCID: PMC2583084 Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation Ophir Shalem, Orna Dahan, Michal Levo, Maria Rodriguez Martinez, Itay Furman, Eran Segal, and Yitzhak Pilpel PMCID: PMC2583085 Model-guided design of ligand-regulated RNAi for programmable control of gene expression Chase L Beisel, Travis S Bayer, Kevin G Hoff, and Christina D Smolke PMCID: PMC2583087 p53-repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation Ran Brosh, Reut Shalgi, Atar Liran, Gilad Landan, Katya Korotayev, Giang Huong Nguyen, Espen Enerly, Hilde Johnsen, Yosef Buganim, Hilla Solomon, Ido Goldstein, Shalom Madar, Naomi Goldfinger, Anne-Lise Børresen-Dale, Doron Ginsberg, Curtis C Harris, Yitzhak Pilpel, Moshe Oren, and Varda Rotter PMCID: PMC2600669 Hepatitis C virus infection protein network B de Chassey, V Navratil, L Tafforeau, M S Hiet, A Aublin-Gex, S Agaugué, G Meiffren, F Pradezynski, B F Faria, T Chantier, M Le Breton, J Pellet, N Davoust, P E Mangeot, A Chaboud, F Penin, Y Jacob, P O Vidalain, M Vidal, P André, C Rabourdin-Combe, and V Lotteau PMCID: PMC2600670 Analysis of pairwise cell interactions using an integrated dielectrophoretic-microfluidic system Zhizhong Yin, David Noren, C Joanne Wang, Rob Hang, and Andre Levchenko PMCID: PMC2615303 Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue Laurence Coquin, Jacob D Feala, Andrew D McCulloch, and Giovanni Paternostro PMCID: PMC2615305 Robust and sensitive control of a quorum-sensing circuit by two interlocked feedback loops Joshua W Williams, Xiaohui Cui, Andre Levchenko, and Ann M Stevens PMCID: PMC2615304 News and Views Modularity defined Herbert M Sauro PMCID: PMC2267732 Systems engineering to systems biology Muhammed A Yıldırım and Marc Vidal PMCID: PMC2387234 A theoretical model of mitotic spindle elongation under experimental constraints Thomas Surrey PMCID: PMC2424298 When microarrays Met epidermal-cell migration Kevin A Janes PMCID: PMC2516363 Comment on ‘Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions' Daniel A Beard PMCID: PMC2516359 In reply: ‘Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions' Ruo-Yu Luo, Yi-Xue Li, and Qingming Luo PMCID: PMC2516360 Developmental regulatory bits Eric D Siggia PMCID: PMC2600668 Small hairpin RNA as a small molecule sensor Yaakov Benenson PMCID: PMC2583088 ‘Junk' DNA meets the p53 network Christine Blattner PMCID: PMC2600671 Perspectives Formulating genome-scale kinetic models in the post-genome era Neema Jamshidi and Bernhard Ø Palsson PMCID: PMC2290940 Understanding NF-κB signaling via mathematical modeling Raymond Cheong, Alexander Hoffmann, and Andre Levchenko PMCID: PMC2424295 Life Sciences and the web: a new era for collaboration Jonathan A Sagotsky, Le Zhang, Zhihui Wang, Sean Martin, and Thomas S Deisboeck PMCID: PMC2516361 High-order combination effects and biological robustness Joseph Lehár, Andrew Krueger, Grant Zimmermann, and Alexis Borisy PMCID: PMC2538911 Reports eQED: an efficient method for interpreting eQTL associations using protein networks Silpa Suthram, Andreas Beyer, Richard M Karp, Yonina Eldar, and Trey Ideker PMCID: PMC2290938 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, and Andrea Califano PMCID: PMC2267731 Selection to minimise noise in living systems and its implications for the evolution of gene expression Ben Lehner PMCID: PMC2290932 A systems-level approach to mapping the telomere length maintenance gene circuitry Rafi Shachar, Lior Ungar, Martin Kupiec, Eytan Ruppin, and Roded Sharan PMCID: PMC2290934 The role of disorder in interaction networks: a structural analysis Philip M Kim, Andrea Sboner, Yu Xia, and Mark Gerstein PMCID: PMC2290937 Synthetic gene brushes: a structure–function relationship Amnon Buxboim, Shirley S Daube, and Roy Bar-Ziv PMCID: PMC2387232 Ultrasensitive gene regulation by positive feedback loops in nucleosome modification Kim Sneppen, Mille A Micheelsen, and Ian B Dodd PMCID: PMC2387233 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, and Lingchong You PMCID: PMC2387235 Recurrent design patterns in the feedback regulation of the mammalian signalling network Stefan Legewie, Hanspeter Herzel, Hans V Westerhoff, and Nils Blüthgen PMCID: PMC2424294 Recursive construction of perfect DNA molecules from imperfect oligonucleotides Gregory Linshiz, Tuval Ben Yehezkel, Shai Kaplan, Ilan Gronau, Sivan Ravid, Rivka Adar, and Ehud Shapiro PMCID: PMC2424292 Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis Naoyuki Sugiyama, Hirofumi Nakagami, Keiichi Mochida, Arsalan Daudi, Masaru Tomita, Ken Shirasu, and Yasushi Ishihama PMCID: PMC2424297 Gender-dependent progression of systemic metabolic states in early childhood Janne Nikkilä, Marko Sysi-Aho, Andrey Ermolov, Tuulikki Seppänen-Laakso, Olli Simell, Samuel Kaski, and Matej Orešič PMCID: PMC2483410 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, and Philip Hugenholtz PMCID: PMC2483411 The incoherent feed-forward loop can generate non-monotonic input functions for genes Shai Kaplan, Anat Bren, Erez Dekel, and Uri Alon PMCID: PMC2516365 Fus3-triggered Tec1 degradation modulates mating transcriptional output during the pheromone response Song Chou, Su Zhao, You Song, Haoping Liu, and Qing Nie PMCID: PMC2538907 Survival of the sparsest: robust gene networks are parsimonious Robert D Leclerc PMCID: PMC2538912 Models from experiments: combinatorial drug perturbations of cancer cells Sven Nelander, Weiqing Wang, Björn Nilsson, Qing-Bai She, Christine Pratilas, Neal Rosen, Peter Gennemark, and Chris Sander PMCID: PMC2564730 The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest Gábor Balázsi, Allison P Heath, Lanbo Shi, and Maria L Gennaro PMCID: PMC2600667 Review Articles A comprehensive modular map of molecular interactions in RB/E2F pathway Laurence Calzone, Amélie Gelay, Andrei Zinovyev, François Radvanyi, and Emmanuel Barillot PMCID: PMC2290939 Theoretical and experimental approaches to understand morphogen gradients Marta Ibañes and Juan Carlos Izpisúa Belmonte PMCID: PMC2290935 Selected reaction monitoring for quantitative proteomics: a tutorial Vinzenz Lange, Paola Picotti, Bruno Domon, and Ruedi Aebersold PMCID: PMC2583086 Corrigenda Isoform switching facilitates period control in the Neurospora crassa circadian clock Ozgur E Akman, James CW Locke, Sanyi Tang, Isabelle Carré, Andrew J Millar, and David A Rand PMCID: PMC2387236 Corrects:Ozgur E Akman, et al. Isoform switching facilitates period control in the Neurospora crassa circadian clock. Mol Syst Biol. 2008; 4: 164. Increased glycolytic flux as an outcome of whole-genome duplication in yeast Gavin C Conant and Kenneth H Wolfe PMCID: PMC2516368 Corrects:Gavin C Conant, et al. Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol Syst Biol. 2007; 3: 129. |
