NPG Library
Below is a selection of recent Research Articles, Research Highlights, Reviews and Perspectives that have been published by Nature Publishing group journals on the topic of modelling cellular systems.
Research highlights
Systems biology: Spotting interactions
Ekat Kritikou
doi:10.1038/nrm1845
Nature Reviews Molecular Cell Biology 7, 5 (2005)
Network biology: A protein network of one's own proteins
Magdalena Skipper
doi:10.1038/nrg1731
Nature Reviews Genetics 6, 800
Systems biology: The variable cell
Arianne Heinrichs
doi:10.1038/nrm1768
Nature Reviews Molecular Cell Biology 6, 800 (2005)
Molecular networks: The power of prediction
Ekat Kritikou
doi:10.1038/nrm1748
Nature Reviews Molecular Cell Biology 6, 752-753 (2005)
Gene networks: Testing the network
Louisa Flintoft
doi:10.1038/nrg1694
Nature Reviews Genetics 6, 668 (2005)
Network analysis: Profiling epistasis
Orli Bahcall
doi:10.1038/nrg1626
Nature Reviews Genetics 6, 349 (2005)
Gene networks: The flexible network
Louisa Flintoft
doi:10.1038/nrg1585
Nature Reviews Genetics 6, 252 (2005)
Systems biology: The dynamics of the cycle
Katrin Bussell
doi:10.1038/nrm1612
Nature Reviews Molecular Cell Biology 6, 190 (2005)
Reviews
Towards multidimensional genome annotation
Jennifer L. Reed, Iman Famili, Ines Thiele and Bernhard O. Palsson
doi:10.1038/nrg1769
Nature Reviews Genetics 7, 130-141 (2006)
Critical nodes in signalling pathways: insights into insulin action
Cullen M. Taniguchi, Brice Emanuelli and C. Ronald Kahn
doi:10.1038/nrm1837
Nature Reviews Molecular Cell Biology 7, 85-96 (2006)
Modelling strategies for the industrial exploitation of lactic acid bacteria
Bas Teusink and Eddy J. Smid
doi:10.1038/nrmicro1319
Nature Reviews Microbiology 4, 46-56 (2006)
The Cbl interactome and its functions
Mirko H.H. Schmidt and Ivan Dikic
doi:10.1038/nrm1762
Nature Reviews Molecular Cell Biology 6, 907-918 (2006)
Discovering novel biology by in silico archaeology
Thijs J. G. Ettema, Willem M. de Vos and John van der Oost
doi:10.1038/nrmicro1268
Nature Reviews Microbiology 3, 859-869 (2005)
Regulatory networks in embryo-derived pluripotent stem cells
Michele Boiani and Hans R. Schöler
doi:10.1038/nrm1744
Nature Reviews Molecular Cell Biology 6, 872-881 (2005)
Metabolic footprinting and systems biology: the medium is the message
Douglas B. Kell, Marie Brown, Hazel M. Davey, Warwick B. Dunn, Irena Spasic and Stephen G. Oliver
doi:10.1038/nrmicro1177
Nature Reviews Microbiology 3, 557-565 (2005)
Miniaturization in functional genomics and proteomics
Sascha Sauer, Bodo M. H. Lange, Johan Gobom, Lajos Nyarsik, Harald Seitz and Hans Lehrach
doi:10.1038/nrg1618
Nature Reviews Genetics 6, 465-476 (2005)
Viral hijacking of G-protein-coupled-receptor signalling networks
Akrit Sodhi, Silvia Montaner and J. Silvio Gutkind
doi:10.1038/nrm1529
Nature Reviews Molecular Cell Biology 5, 998-1012 (2004)
Biological robustness
Hiroaki Kitano
doi:10.1038/nrg1471
Nature Reviews Genetics 5, 826-837 (2004)
Genome-scale models of microbial cells: evaluating the consequences of constraints
Nathan D. Price, Jennifer L. Reed and Bernhard Ø. Palsson
doi:10.1038/nrmicro1023
Nature Reviews Microbiology 2, 886-897 (2004)
Mathematical and computational models of immune-receptor signalling
Byron Goldstein, James R. Faeder and William S. Hlavacek
doi:10.1038/nri1374
Nature Reviews Immunology 4, 445-456 (2004)
Network biology: understanding the cell's functional organization
Albert-László Barabási and Zoltán N. Oltvai
doi:10.1038/nrg1272
Nature Reviews Genetics 5, 101-113 (2004)
Perspectives
Mapping normal and cancer cell signalling networks: towards single-cell proteomics
Jonathan M. Irish, Nikesh Kotecha and Garry P. Nolan
doi:10.1038/nrc1804
Nature Reviews Cancer 6, 146-155 (2006)
Minimum information requested in the annotation of biochemical models (MIRIAM)
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 and Barry L Wanner
doi:10.1038/nbt1156
Nature Biotechnology 23, 1509-1515 (2004)
Probabilistic model of the human protein-protein interaction network
Daniel R Rhodes, Scott A Tomlins, Sooryanarayana Varambally, Vasudeva Mahavisno, Terrence Barrette, Shanker Kalyana-Sundaram, Debashis Ghosh, Akhilesh Pandey and Arul M Chinnaiyan
doi:10.1038/nbt1103
Nature Biotechnology 23, 951-959 (2005)
Engineering vascularized skeletal muscle tissue
Shulamit Levenberg, Jeroen Rouwkema, Mara Macdonald, Evan S Garfein, Daniel S Kohane, Diane C Darland, Robert Marini, Clemens A van Blitterswijk, Richard C Mulligan, Patricia A D'Amore and Robert Langer
doi:10.1038/nbt1109
Nature Biotechnology 23, 879-884 (2005)
Scoring proteomes with proteotypic peptide probes
Bernhard Kuster, Markus Schirle, Parag Mallick and Ruedi Aebersold
doi:10.1038/nrm1683
Nature Reviews Molecular Cell Biology 6, 577-583 (2005)
Systematic interpretation of genetic interactions using protein networks
Ryan Kelley and Trey Ideker
doi:10.1038/nbt1096
Nature Biotechnology 23, 561-566 (2005)
Crosstalk between RNA metabolic pathways: an RNOMICS approach
Jean D. Beggs and David Tollervey
doi:10.1038/nrm1648
Nature Reviews Molecular Cell Biology 6, 423-429 (2005)
Automatic generation of cellular reaction networks with Moleculizer 1.0
Larry Lok and Roger Brent
doi:10.1038/nbt1054
Nature Biotechnology 23, 131-136 (2005)
Metabolite profiling: from diagnostics to systems biology
Alisdair R. Fernie, Richard N. Trethewey, Arno J. Krotzky and Lothar Willmitzer
doi:10.1038/nrm1451
Nature Reviews Molecular Cell Biology 5, 763-769 (2004)
Opinion: Comparative biology of mouse versus human cells: modelling human cancer in mice
Annapoorni Rangarajan and Robert A. Weinberg
doi:10.1038/nrc1235
Nature Reviews Cancer 3, 952-959 (2003)
Opinion: Lateral phosphorylation propagation: an aspect of feedback signalling?
Christian Tischer and Philippe I. H. Bastiaens
doi:10.1038/nrm1258
Nature Reviews Molecular Cell Biology 4, 971-975 (2003)
Research articles
Microarrays of lentiviruses for gene function screens in immortalized and primary cells
Steve N Bailey, Siraj M Ali, Anne E Carpenter, Caitlin O Higgins and David M Sabatini
doi:10.1038/nmeth848
Nature Methods 3, 117-122 (2006)
Proteome survey reveals modularity of the yeast cell machinery
Anne-Claude Gavin, Patrick Aloy, Paola Grandi, Roland Krause, Markus Boesche, Martina Marzioch, Christina Rau, Lars Juhl Jensen, Sonja Bastuck, Birgit Dümpelfeld, Angela Edelmann, Marie-Anne Heurtier, Verena Hoffman, Christian Hoefert, Karin Klein, Manuela Hudak, Anne-Marie Michon, Malgorzata Schelder, Markus Schirle, Marita Remor, Tatjana Rudi, Sean Hooper, Andreas Bauer, Tewis Bouwmeester, Georg Casari, Gerard Drewes, Gitte Neubauer, Jens M. Rick, Bernhard Kuster, Peer Bork, Robert B. Russell and Giulio Superti-Furga
doi:10.1038/nature04532
Nature (2006)
Wnt–Ryk signalling mediates medial–lateral retinotectal topographic mapping
Adam M. Schmitt, Jun Shi, Alex M. Wolf, Chin-Chun Lu, Leslie A. King and Yimin Zou
doi:10.1038/nature04334
Nature 439, 31-37 (2006)
A protein interaction network of the malaria parasite Plasmodium falciparum
Douglas J. LaCount, Marissa Vignali, Rakesh Chettier, Amit Phansalkar, Russell Bell, Jay R. Hesselberth, Lori W. Schoenfeld, Irene Ota, Sudhir Sahasrabudhe, Cornelia Kurschner, Stanley Fields and Robert E. Hughes
doi:10.1038/nature04104
Nature 438, 103-107 (2005)
Towards a proteome-scale map of the human protein–protein interaction network
Jean-François Rual, Kavitha Venkatesan, Tong Hao, Tomoko Hirozane-Kishikawa, Amélie Dricot, Ning Li, Gabriel F. Berriz, Francis D. Gibbons, Matija Dreze, Nono Ayivi-Guedehoussou, Niels Klitgord, Christophe Simon, Mike Boxem, Stuart Milstein, Jennifer Rosenberg, Debra S. Goldberg, Lan V. Zhang, Sharyl L. Wong, Giovanni Franklin, Siming Li, Joanna S. Albala, Janghoo Lim, Carlene Fraughton, Estelle Llamosas, Sebiha Cevik, Camille Bex, Philippe Lamesch, Robert S. Sikorski, Jean Vandenhaute, Huda Y. Zoghbi, Alex Smolyar, Stephanie Bosak, Reynaldo Sequerra, Lynn Doucette-Stamm, Michael E. Cusick, David E. Hill, Frederick P. Roth and Marc Vidal
doi:10.1038/nature04209
Nature 437, 1173-1178 (2005)
Integrative model of the response of yeast to osmotic shock
Edda Klipp, Bodil Nordlander, Roland Krüger, Peter Gennemark and Stefan Hohmann
doi:10.1038/nbt1114
Nature Biotechnology 23, 975-982 (2005)
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry
W Andy Tao, Bernd Wollscheid, Robert O'Brien, Jimmy K Eng, Xiao-jun Li, Bernd Bodenmiller, Julian D Watts, Leroy Hood and Ruedi Aebersold
doi:10.1038/nmeth776
Nature Methods 2, 591-598 (2005)
Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis
Lucas Pelkmans, Eugenio Fava, Hannes Grabner, Michael Hannus, Bianca Habermann, Eberhard Krausz and Marino Zerial
doi:10.1038/nature03571
Nature 436, 78-86 (2005)
Engineering vascularized skeletal muscle tissue
Shulamit Levenberg, Jeroen Rouwkema, Mara Macdonald, Evan S Garfein, Daniel S Kohane, Diane C Darland, Robert Marini, Clemens A van Blitterswijk, Richard C Mulligan, Patricia A D'Amore and Robert Langer
doi:10.1038/nbt1109
Nature Biotechnology 23, 879-884 (2005)
Ultrahigh density microarrays of solid samples
Matthew J LeBaron, Heidi R Crismon, Fransiscus E Utama, Lynn M Neilson, Ahmed S Sultan, Kevin J Johnson, Eva C Andersson and Hallgeir Rui
doi:10.1038/nmeth772
Nature Methods 2, 511-513 (2005)
Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism
Eliane Fischer and Uwe Sauer
doi:10.1038/ng1555
Nature Genetics 37, 636-640 (2005)
Reverse MAPPIT: screening for protein-protein interaction modifiers in mammalian cells
Sven Eyckerman, Irma Lemmens, Dominiek Catteeuw, Annick Verhee, Joel Vandekerckhove, Sam Lievens and Jan Tavernier
doi:10.1038/nmeth760
Nature Methods 2, 427-433 (2005)
Epistasis analysis with global transcriptional phenotypes
Nancy Van Driessche, Janez Demsar, Ezgi O Booth, Paul Hill, Peter Juvan, Blaz Zupan, Adam Kuspa and Gad Shaulsky
doi:10.1038/ng1545
Nature Genetics 37, 471-477 (2005)
Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia
Paola Sebastiani, Marco F Ramoni, Vikki Nolan, Clinton T Baldwin and Martin H Steinberg
doi:10.1038/ng1533
Nature Genetics 37, 435-440 (2005)
Prediction and validation of the distinct dynamics of transient and sustained ERK activation
Satoru Sasagawa, Yu-ichi Ozaki, Kazuhiro Fujita and Shinya Kuroda
doi:10.1038/ncb1233
Nature Cell Biology 7, 365-373 (2005)
Interaction network containing conserved and essential protein complexes in Escherichia coli
Gareth Butland, José Manuel Peregrín-Alvarez, Joyce Li, Wehong Yang, Xiaochun Yang, Veronica Canadien, Andrei Starostine, Dawn Richards, Bryan Beattie, Nevan Krogan, Michael Davey, John Parkinson, Jack Greenblatt and Andrew Emili
doi:10.1038/nature03239
Nature 433, 531-537 (2005)
System-level identification of transcriptional circuits underlying mammalian circadian clocks
Hiroki R Ueda, Satoko Hayashi, Wenbin Chen, Motoaki Sano, Masayuki Machida, Yasufumi Shigeyoshi, Masamitsu Iino and Seiichi Hashimoto
doi:10.1038/ng1504
Nature Genetics 37, 187-192 (2005)
Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae
Fernando Alvarez-Vasquez, Kellie J. Sims, L. Ashley Cowart, Yasuo Okamoto, Eberhard O. Voit and Yusuf A. Hannun
doi:10.1038/nature03232
Nature 433, 425-430 (2004)
Epistasis analysis with global transcriptional phenotypes
Nancy Van Driessche, Janez Demsar, Ezgi O Booth, Paul Hill, Peter Juvan, Blaz Zupan, Adam Kuspa and Gad Shaulsky
doi:10.1038/ng1545
Nature Genetics 37, 471-477 (2004)
A physical and functional map of the human TNF-
/NF-
B signal transduction pathway
Tewis Bouwmeester, Angela Bauch, Heinz Ruffner, Pierre-Olivier Angrand, Giovanna Bergamini, Karen Croughton, Cristina Cruciat, Dirk Eberhard, Julien Gagneur, Sonja Ghidelli, Carsten Hopf, Bettina Huhse, Raffaella Mangano, Anne-Marie Michon, Markus Schirle, Judith Schlegl, Markus Schwab, Martin A. Stein, Andreas Bauer, Georg Casari, Gerard Drewes, Anne-Claude Gavin, David B. Jackson, Gerard Joberty, Gitte Neubauer, Jens Rick, Bernhard Kuster and Giulio Superti-Furga
doi:10.1038/ncb1086
Nature Cell Biology 6, 97-105 (2004)
Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2
Joseph R. Pomerening, Eduardo D. Sontag and James E. Ferrell, Jr
doi:10.1038/ncb954
Nature Cell Biology 5, 346-351 (2003)
