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  1. Endocrine disrupting chemicals (e.g., estrogens, androgens and their mimics) are known to affect reproduction in fish. 17α-ethynylestradiol is a synthetic estrogen used in birth control pills. 17β-trenbolone i...

    Authors: Zhenhong Li, Kevin J Kroll, Kathleen M Jensen, Daniel L Villeneuve, Gerald T Ankley, Jayne V Brian, María S Sepúlveda, Edward F Orlando, James M Lazorchak, Mitchell Kostich, Brandon Armstrong, Nancy D Denslow and Karen H Watanabe
    Citation: BMC Systems Biology 2011 5:63
    Content type: Research article Published on:

  4. Progressive remodeling of the left ventricle (LV) following myocardial infarction (MI) can lead to congestive heart failure, but the underlying initiation factors remain poorly defined. The objective of this s...

    Authors: Yu-Fang Jin, Hai-Chao Han, Jamie Berger, Qiuxia Dai and Merry L Lindsey
    Citation: BMC Systems Biology 2011 5:60
    Content type: Research article Published on:

  5. The spatial distribution of vascular endothelial growth factor A (VEGF) is an important mediator of vascular patterning. Previous experimental studies in the mouse hindbrain and retina have suggested that VEGF...

    Authors: Prakash Vempati, Aleksander S Popel and Feilim Mac Gabhann
    Citation: BMC Systems Biology 2011 5:59
    Content type: Research article Published on:

  6. Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental ...

    Authors: Taewoo Ryu, Charalampos Harris Mavromatis, Till Bayer, Christian R Voolstra and Timothy Ravasi
    Citation: BMC Systems Biology 2011 5:58
    Content type: Research article Published on:

  7. Comparing metabolic profiles under different biological perturbations has become a powerful approach to investigating the functioning of cells. The profiles can be taken as single snapshots of a system, but mo...

    Authors: Juliet Ndukum, Luís L Fonseca, Helena Santos, Eberhard O Voit and Susmita Datta
    Citation: BMC Systems Biology 2011 5:57
    Content type: Methodology article Published on:

  8. Autosomal dominant polycystic kidney disease (ADPKD) is characterized by cyst formation throughout the kidney parenchyma. It is caused by mutations in either of two genes, PKD1 and PKD2. Mice that lack functional...

    Authors: Priyanka Pandey, Shan Qin, Jacqueline Ho, Jing Zhou and Jordan A Kreidberg
    Citation: BMC Systems Biology 2011 5:56
    Content type: Research article Published on:

  9. Domains are basic units of proteins, and thus exploring associations between protein domains and human inherited diseases will greatly improve our understanding of the pathogenesis of human complex diseases an...

    Authors: Wangshu Zhang, Yong Chen, Fengzhu Sun and Rui Jiang
    Citation: BMC Systems Biology 2011 5:55
    Content type: Research article Published on:

  10. Genetically identical cells often show significant variation in gene expression profile and behaviour even in the same physiological condition. Notably, embryonic cells destined to the same tissue maintain a u...

    Authors: Yasushi Saka, Cédric Lhoussaine, Celine Kuttler, Ekkehard Ullner and Marco Thiel
    Citation: BMC Systems Biology 2011 5:54
    Content type: Research article Published on:

  11. Identifying the key transcription factors (TFs) controlling a biological process is the first step toward a better understanding of underpinning regulatory mechanisms. However, due to the involvement of a larg...

    Authors: Jeff Nie, Ron Stewart, Hang Zhang, James A Thomson, Fang Ruan, Xiaoqi Cui and Hairong Wei
    Citation: BMC Systems Biology 2011 5:53
    Content type: Methodology article Published on:

  12. Reverse engineering in systems biology entails inference of gene regulatory networks from observational data. This data typically include gene expression measurements of wild type and mutant cells in response ...

    Authors: Rita Gupta, Anna Stincone, Philipp Antczak, Sarah Durant, Roy Bicknell, Andreas Bikfalvi and Francesco Falciani
    Citation: BMC Systems Biology 2011 5:52
    Content type: Methodology article Published on:

  13. In aerobically grown cells, iron homeostasis and oxidative stress are tightly linked processes implicated in a growing number of diseases. The deregulation of iron homeostasis due to gene defects or environmen...

    Authors: Fiona Achcar, Jean-Michel Camadro and Denis Mestivier
    Citation: BMC Systems Biology 2011 5:51
    Content type: Research article Published on:

  15. Many complex systems can be represented and analysed as networks. The recent availability of large-scale datasets, has made it possible to elucidate some of the organisational principles and rules that govern ...

    Authors: Antonio Gómez, Juan Cedano, Isaac Amela, Antoni Planas, Jaume Piñol and Enrique Querol
    Citation: BMC Systems Biology 2011 5:49
    Content type: Research article Published on:

  16. Cellular response to changes in the concentration of different chemical species in the extracellular medium is induced by ligand binding to dedicated transmembrane receptors. Receptor density, distribution, an...

    Authors: Bertrand R Caré and Hédi A Soula
    Citation: BMC Systems Biology 2011 5:48
    Content type: Research article Published on:

  17. The signalling cascades involved in many biological processes require the coordination of different subcellular districts. It is the case of the pathways involved in spermatozoa acquisition of fertilizing abil...

    Authors: Nicola Bernabò, Paolo Berardinelli, Annunziata Mauro, Valentina Russo, Pia Lucidi, Mauro Mattioli and Barbara Barboni
    Citation: BMC Systems Biology 2011 5:47
    Content type: Research article Published on:

  18. Endothelial progenitor cells (EPCs) have been implicated in different processes crucial to vasculature repair, which may offer the basis for new therapeutic strategies in cardiovascular disease. Despite advanc...

    Authors: Francisco J Azuaje, Haiying Wang, Huiru Zheng, Frédérique Léonard, Magali Rolland-Turner, Lu Zhang, Yvan Devaux and Daniel R Wagner
    Citation: BMC Systems Biology 2011 5:46
    Content type: Research article Published on:

  19. High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into ...

    Authors: Rolf O Lindén, Ville-Pekka Eronen and Tero Aittokallio
    Citation: BMC Systems Biology 2011 5:45
    Content type: Research article Published on:

  21. Our understanding of the genetic basis of learning and memory remains shrouded in mystery. To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to anal...

    Authors: Christopher C Park, Greg D Gale, Simone de Jong, Anatole Ghazalpour, Brian J Bennett, Charles R Farber, Peter Langfelder, Andy Lin, Arshad H Khan, Eleazar Eskin, Steve Horvath, Aldons J Lusis, Roel A Ophoff and Desmond J Smith
    Citation: BMC Systems Biology 2011 5:43
    Content type: Research article Published on:

  22. Surprisal analysis is a thermodynamic-like molecular level approach that identifies biological constraints that prevents the entropy from reaching its maximum. To examine the significance of altered gene expre...

    Authors: Nataly Kravchenko-Balasha, F Remacle, Ayelet Gross, Varda Rotter, Alexander Levitzki and RD Levine
    Citation: BMC Systems Biology 2011 5:42
    Content type: Research article Published on:

  24. The 3D structure of the chromosome of the model organism Escherichia coli is one key component of its gene regulatory machinery. This type of regulation mediated by topological transitions of the chromosomal DNA ...

    Authors: Nikolaus Sonnenschein, Marcel Geertz, Georgi Muskhelishvili and Marc-Thorsten Hütt
    Citation: BMC Systems Biology 2011 5:40
    Content type: Research article Published on:

  26. To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypothe...

    Authors: Dieter Maier, Wenzel Kalus, Martin Wolff, Susana G Kalko, Josep Roca, Igor Marin de Mas, Nil Turan, Marta Cascante, Francesco Falciani, Miguel Hernandez, Jordi Villà-Freixa and Sascha Losko
    Citation: BMC Systems Biology 2011 5:38
    Content type: Software Published on:

  27. With the rapid development of high-throughput experiments, detecting functional modules has become increasingly important in analyzing biological networks. However, the growing size and complexity of these net...

    Authors: Yueheng Lan and Igor Mezić
    Citation: BMC Systems Biology 2011 5:37
    Content type: Research article Published on:

  28. The storage of photosynthetic carbohydrate products such as starch is subject to complex regulation, effected at both transcriptional and post-translational levels. The relevant genes in plants show pronounced...

    Authors: Oksana Sorokina, Florence Corellou, David Dauvillée, Anatoly Sorokin, Igor Goryanin, Steven Ball, François-Yves Bouget and Andrew J Millar
    Citation: BMC Systems Biology 2011 5:36
    Content type: Research article Published on:

  29. Cancer has remarkable complexity at the molecular level, with multiple genes, proteins, pathways and regulatory interconnections being affected. We introduce a systems biology approach to study cancer that for...

    Authors: Shivashankar H Nagaraj and Antonio Reverter
    Citation: BMC Systems Biology 2011 5:35
    Content type: Research article Published on:

  30. Stoichiometric models constitute the basic framework for fluxome quantification in the realm of metabolic engineering. A recurrent bottleneck, however, is the establishment of consistent stoichiometric models ...

    Authors: Nuno Carinhas, Vicente Bernal, Ana P Teixeira, Manuel JT Carrondo, Paula M Alves and Rui Oliveira
    Citation: BMC Systems Biology 2011 5:34
    Content type: Methodology article Published on:

  31. The availability of high throughput experimental methods has made possible to observe the relationships between proteome and transcirptome. The protein abundances show a positive but weak correlation with the ...

    Authors: Roberto Olivares-Hernández, Sergio Bordel and Jens Nielsen
    Citation: BMC Systems Biology 2011 5:33
    Content type: Research article Published on:

  32. The similarity property principle has been used extensively in drug discovery to identify small compounds that interact with specific drug targets. Here we show it can be applied to identify the interactions o...

    Authors: Yogendra Patel, Catherine A Heyward, Michael RH White and Douglas B Kell
    Citation: BMC Systems Biology 2011 5:32
    Content type: Methodology article Published on:

  33. The inheritance of cellular material between parent and daughter cells during mitosis is highly influential in defining the properties of the cell and therefore the population lineage. This is of particular re...

    Authors: Paul Rees, M Rowan Brown, Huw D Summers, Mark D Holton, Rachel J Errington, Sally C Chappell and Paul J Smith
    Citation: BMC Systems Biology 2011 5:31
    Content type: Methodology article Published on:

  34. Modeling of biological pathways is a key issue in systems biology. When constructing a model, it is tempting to incorporate all known interactions of pathway species, which results in models with a large numbe...

    Authors: Tom Quaiser, Anna Dittrich, Fred Schaper and Martin Mönnigmann
    Citation: BMC Systems Biology 2011 5:30
    Content type: Research article Published on:

  35. Epidermal growth factor receptor (EGFR) signaling plays an important role in the regulation of cell proliferation, survival, metastasis, and invasion in various tumors. Earlier studies showed that the EGFR is ...

    Authors: Yoshimi Naruo, Takeshi Nagashima, Ryoko Ushikoshi-Nakayama, Yuko Saeki, Takashi Nakakuki, Takashi Naka, Hiroshi Tanaka, Shih-Feng Tsai and Mariko Okada-Hatakeyama
    Citation: BMC Systems Biology 2011 5:29
    Content type: Research article Published on:

  38. Sphingolipids play important roles in cell structure and function as well as in the pathophysiology of many diseases. Many of the intermediates of sphingolipid biosynthesis are highly bioactive and sometimes h...

    Authors: Shakti Gupta, Mano R Maurya, Alfred H Merrill Jr, Christopher K Glass and Shankar Subramaniam
    Citation: BMC Systems Biology 2011 5:26
    Content type: Research article Published on:

  40. The regulatory network underlying the yeast galactose-use pathway has emerged as a model system for the study of regulatory network evolution. Evidence has recently been provided for adaptive evolution in this...

    Authors: Christos Josephides and Alan M Moses
    Citation: BMC Systems Biology 2011 5:24
    Content type: Research article Published on:

  41. Sustained stimulation with tumour necrosis factor alpha (TNF-alpha) induces substantial oscillations—observed at both the single cell and population levels—in the nuclear factor kappa B (NF-kappa B) system. Al...

    Authors: Yunjiao Wang, Pawel Paszek, Caroline A Horton, Douglas B Kell, Michael RH White, David S Broomhead and Mark R Muldoon
    Citation: BMC Systems Biology 2011 5:23
    Content type: Research article Published on:

  43. With the advent of high-throughput targeted metabolic profiling techniques, the question of how to interpret and analyze the resulting vast amount of data becomes more and more important. In this work we addre...

    Authors: Jan Krumsiek, Karsten Suhre, Thomas Illig, Jerzy Adamski and Fabian J Theis
    Citation: BMC Systems Biology 2011 5:21
    Content type: Research article Published on:

  44. Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in orde...

    Authors: Stephan Pabinger, Robert Rader, Rasmus Agren, Jens Nielsen and Zlatko Trajanoski
    Citation: BMC Systems Biology 2011 5:20
    Content type: Software Published on:

  45. RNA interference (RNAi) is a regulatory cellular process that controls post-transcriptional gene silencing. During RNAi double-stranded RNA (dsRNA) induces sequence-specific degradation of homologous mRNA via ...

    Authors: Giulia Cuccato, Athanasios Polynikis, Velia Siciliano, Mafalda Graziano, Mario di Bernardo and Diego di Bernardo
    Citation: BMC Systems Biology 2011 5:19
    Content type: Research article Published on:

  46. A common survival strategy of microorganisms subjected to stress involves the generation of phenotypic heterogeneity in the isogenic microbial population enabling a subset of the population to survive under st...

    Authors: Sayantari Ghosh, Kamakshi Sureka, Bhaswar Ghosh, Indrani Bose, Joyoti Basu and Manikuntala Kundu
    Citation: BMC Systems Biology 2011 5:18
    Content type: Research article Published on:

  47. On the basis of large proteomics datasets measured from seven human cell lines we consider their intersection as an approximation of the human central proteome, which is the set of proteins ubiquitously expres...

    Authors: Thomas R Burkard, Melanie Planyavsky, Ines Kaupe, Florian P Breitwieser, Tilmann Bürckstümmer, Keiryn L Bennett, Giulio Superti-Furga and Jacques Colinge
    Citation: BMC Systems Biology 2011 5:17
    Content type: Research article Published on:

  48. Arsenic is an environmental pollutant, potent human toxicant, and oxidative stress agent with a multiplicity of health effects associated with both acute and chronic exposures. A semi-mechanistic cellular-leve...

    Authors: Spyros K Stamatelos, Christopher J Brinkerhoff, Sastry S Isukapalli and Panos G Georgopoulos
    Citation: BMC Systems Biology 2011 5:16
    Content type: Research article Published on:

  49. The thioredoxin system consisting of NADP(H), thioredoxin reductase and thioredoxin provides reducing equivalents to a large and diverse array of cellular processes. Despite a great deal of information on the ...

    Authors: Ché S Pillay, Jan-Hendrik S Hofmeyr and Johann M Rohwer
    Citation: BMC Systems Biology 2011 5:15
    Content type: Research article Published on:

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