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Empirical systems biology

Section edited by Matteo Pellegrini

This section covers the conduct of experiments or use of empirical data to improve the understanding of the structure and function of biological systems.

Page 1 of 3

  1. Movement of populations on fitness landscapes has been a problem of interest for a long time. While the subject has been extensively developed theoretically, reconciliation of the theoretical work with recent ...

    Authors: Nishant Gerald, Dibyendu Dutta, R. G. Brajesh and Supreet Saini
    Citation: BMC Systems Biology 2019 13:25
    Content type: Research article Published on:

  3. There is little published regarding metabolism of Salinispora species. In continuation with efforts performed towards this goal, this study is focused on new insights into the metabolism of the three-identified s...

    Authors: Carolina A. Contador, Vida Rodríguez, Barbara A. Andrews and Juan A. Asenjo
    Citation: BMC Systems Biology 2019 13:11
    Content type: Research article Published on:

  4. The lack of a continuous long-term in vitro culture system for Plasmodium vivax severely limits our knowledge of pathophysiology of the most widespread malaria parasite. To gain direct understanding of P. vivax h...

    Authors: Swamy Rakesh Adapa, Rachel A. Taylor, Chengqi Wang, Richard Thomson-Luque, Leah R. Johnson and Rays H. Y. Jiang
    Citation: BMC Systems Biology 2019 13:5
    Content type: Research article Published on:

  5. The formation of acetate by fast-growing Escherichia coli (E. coli) is a commonly observed phenomenon, often referred to as overflow metabolism. Among various studies that have been carried over decades, a recent...

    Authors: Hong Zeng and Aidong Yang
    Citation: BMC Systems Biology 2019 13:3
    Content type: Research article Published on:

  6. Gut microbiota interacts with the human gut in multiple ways. Microbiota composition is altered in inflamed gut conditions. Likewise, certain microbial fermentation products as well as the lipopolysaccharides ...

    Authors: Gunter Neumann, Rebecca Wall, Ignacio Rangel, Tatiana M. Marques and Dirk Repsilber
    Citation: BMC Systems Biology 2018 12:144
    Content type: Research article Published on:

  7. Essentiality assays are important tools commonly utilized for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are also often utilized to test the predictive...

    Authors: Gabriela I. Guzmán, Connor A. Olson, Ying Hefner, Patrick V. Phaneuf, Edward Catoiu, Lais B. Crepaldi, Lucas Goldschmidt Micas, Bernhard O. Palsson and Adam M. Feist
    Citation: BMC Systems Biology 2018 12:143
    Content type: Research article Published on:

  9. The effort to characterize intrinsically disordered regions of signaling proteins is rapidly expanding. An important class of disordered interaction modules are ubiquitous and functionally diverse elements kno...

    Authors: Bob Strome, Ian Shenyen Hsu, Mitchell Li Cheong Man, Taraneh Zarin, Alex Nguyen Ba and Alan M. Moses
    Citation: BMC Systems Biology 2018 12:75
    Content type: Research article Published on:

  10. Existing experimental data have shown hypoxia to be an important factor affecting the proliferation of mesenchymal stromal cells (MSCs), but the contrasting observations made at various hypoxic levels raise th...

    Authors: Bo Zhang, Hua Ye and Aidong Yang
    Citation: BMC Systems Biology 2018 12:35
    Content type: Research article Published on:

  11. Photosynthetic (PS) gene expression in Rhodobacter sphaeroides is regulated in response to changes in light and redox conditions mainly by PrrB/A, FnrL and AppA/PpsR systems. The PrrB/A and FnrL systems activate ...

    Authors: Rakesh Pandey, Judith P. Armitage and George H. Wadhams
    Citation: BMC Systems Biology 2017 11:146
    Content type: Research Article Published on:

  12. Models that incorporate specific chemical mechanisms have been successful in describing the activity of Drosophila developmental enhancers as a function of underlying transcription factor binding motifs. Despite ...

    Authors: Kenneth A. Barr, Carlos Martinez, Jennifer R. Moran, Ah-Ram Kim, Alexandre F. Ramos and John Reinitz
    Citation: BMC Systems Biology 2017 11:116
    Content type: Research Article Published on:

  13. The pursuit of standardization and reliability in synthetic biology has achieved, in recent years, a number of advances in the design of more predictable genetic parts for biological circuits. However, even wi...

    Authors: S. Cardinale and G. Cambray
    Citation: BMC Systems Biology 2017 11:112
    Content type: Research Article Published on:

  14. A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to th...

    Authors: Anna Doloman, Honey Varghese, Charles D. Miller and Nicholas S. Flann
    Citation: BMC Systems Biology 2017 11:69
    Content type: Research Article Published on:

  15. The yeast AMPK/SNF1 pathway is best known for its role in glucose de/repression. When glucose becomes limited, the Snf1 kinase is activated and phosphorylates the transcriptional repressor Mig1, which is then ...

    Authors: Niek Welkenhuysen, Johannes Borgqvist, Mattias Backman, Loubna Bendrioua, Mattias Goksör, Caroline B Adiels, Marija Cvijovic and Stefan Hohmann
    Citation: BMC Systems Biology 2017 11:59
    Content type: Research article Published on:

  16. Mechanical and biophysical properties of the cellular microenvironment regulate cell fate decisions. Mesenchymal stem cell (MSC) fate is influenced by past mechanical dosing (memory), but the mechanisms underl...

    Authors: Tao Peng, Linan Liu, Adam L MacLean, Chi Wut Wong, Weian Zhao and Qing Nie
    Citation: BMC Systems Biology 2017 11:55
    Content type: Research Article Published on:

  17. Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences...

    Authors: Hugo F. Cueto-Rojas, Nicholas Milne, Ward van Helmond, Mervin M. Pieterse, Antonius J. A. van Maris, Jean-Marc Daran and S. Aljoscha Wahl
    Citation: BMC Systems Biology 2017 11:49
    Content type: Research article Published on:

  19. Cellular senescence irreversibly arrests growth of human diploid cells. In addition, recent studies have indicated that senescence is a multi-step evolving process related to important complex biological proce...

    Authors: Chihyun Park, So Jeong Yun, Sung Jin Ryu, Soyoung Lee, Young-Sam Lee, Youngmi Yoon and Sang Chul Park
    Citation: BMC Systems Biology 2017 11:36
    Content type: Research article Published on:

  20. Pichia pastoris shows physiological advantages in producing recombinant proteins, compared to other commonly used cell factories. This yeast is mostly grown in dynamic cultivation syst...

    Authors: Francisco Saitua, Paulina Torres, José Ricardo Pérez-Correa and Eduardo Agosin
    Citation: BMC Systems Biology 2017 11:27
    Content type: Research article Published on:

  21. Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remo...

    Authors: Patricia Aquino, Brent Honda, Suma Jaini, Anna Lyubetskaya, Krutika Hosur, Joanna G. Chiu, Iriny Ekladious, Dongjian Hu, Lin Jin, Marianna K. Sayeg, Arion I. Stettner, Julia Wang, Brandon G. Wong, Winnie S. Wong, Stephen L. Alexander, Cong Ba…
    Citation: BMC Systems Biology 2017 11:1
    Content type: Research article Published on:

  22. Macrophages are essential to innate immunity against many pathogens, but some pathogens also target macrophages as routes to infection. The Porcine Reproductive and Respiratory Syndrome virus (PRRSV) is an RNA...

    Authors: Andrea Doeschl-Wilson, Alison Wilson, Jens Nielsen, Hans Nauwynck, Alan Archibald and Tahar Ait-Ali
    Citation: BMC Systems Biology 2016 10:101
    Content type: Research article Published on:

  23. The malarial parasite Plasmodium falciparum undergoes a complex life cycle, including an intraerythrocytic developmental cycle, during which it is metabolically dependent on the infected human red blood cell (RBC...

    Authors: Anders Wallqvist, Xin Fang, Shivendra G. Tewari, Ping Ye and Jaques Reifman
    Citation: BMC Systems Biology 2016 10:58
    Content type: Research article Published on:

  24. The fungal pathogen Candida albicans colonizes the gastrointestinal (GI) tract of mammalian hosts as a benign commensal. However, in an immunocompromised host, the fungus is capable of causing life-threatening in...

    Authors: Katarzyna M. Tyc, Sanna E. Herwald, Jennifer A. Hogan, Jessica V. Pierce, Edda Klipp and Carol A. Kumamoto
    Citation: BMC Systems Biology 2016 10:20
    Content type: Research article Published on:

  25. Epigenetics has been investigated in cancer initiation, and development, especially, since the appearance of epigenomics. Epigenetics may be defined as the mechanisms that lead to heritable changes in gene fun...

    Authors: Bor-Sen Chen and Cheng-Wei Li
    Citation: BMC Systems Biology 2016 10:18
    Content type: Research article Published on:

  26. The enhanceosome is an enhancer located upstream of the human interferon β gene, bound by transcription factor (TF) complex of extremely rigid structure. Within these rigid constraints, even a slight change of di...

    Authors: Aleksander Jankowski, Paulina Obara, Utsav Mathur and Jerzy Tiuryn
    Citation: BMC Systems Biology 2016 10:14
    Content type: Research Article Published on:

  27. Transcription of genes coding for xylanolytic and cellulolytic enzymes in Aspergillus niger is controlled by the transactivator XlnR. In this work we analyse and model the transcription dynamics in the XlnR regul...

    Authors: Jimmy Omony, Astrid R. Mach-Aigner, Gerrit van Straten and Anton J.B. van Boxtel
    Citation: BMC Systems Biology 2016 10:13
    Content type: Research article Published on:

  29. The Drosophila sex determination hierarchy is a classic example of a transcriptional regulatory hierarchy, with sex-specific isoforms regulating morphology and behavior. We use a structural equation modeling appr...

    Authors: Justin M. Fear, Michelle N. Arbeitman, Matthew P. Salomon, Justin E. Dalton, John Tower, Sergey V. Nuzhdin and Lauren M. McIntyre
    Citation: BMC Systems Biology 2015 9:53
    Content type: Research article Published on:

  30. Constraint-based metabolic models and flux balance analysis (FBA) have been extensively used in the last years to investigate the behavior of cells and also as basis for different industrial applications. In this...

    Authors: Yeimy Morales, Marta Tortajada, Jesús Picó, Josep Vehí and Francisco Llaneras
    Citation: BMC Systems Biology 2014 8:142
    Content type: Research article Published on:

  31. Metabolomic responses to extreme thermal stress have recently been investigated in Drosophila melanogaster. However, a network level understanding of metabolomic responses to longer and less drastic temperature c...

    Authors: Ramkumar Hariharan, Jessica M Hoffman, Ariel S Thomas, Quinlyn A Soltow, Dean P Jones and Daniel EL Promislow
    Citation: BMC Systems Biology 2014 8:139
    Content type: Research article Published on:

  32. Cancer metabolism is emerging as an important focus area in cancer research. However, the in vitro cell culture conditions under which much cellular metabolism research is performed differ drastically from in viv...

    Authors: Kathleen A Vermeersch, Lijuan Wang, John F McDonald and Mark P Styczynski
    Citation: BMC Systems Biology 2014 8:134
    Content type: Research article Published on:

  33. Although much is understood about the enzymatic cascades that underlie cellular biosynthesis, comparatively little is known about the rules that determine their cellular organization. We performed a detailed a...

    Authors: Pablo Meyer, Guillermo Cecchi and Gustavo Stolovitzky
    Citation: BMC Systems Biology 2014 8:131
    Content type: Research article Published on:

  34. Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how ...

    Authors: Christopher L Plaisier, Fang-Yin Lo, Justin Ashworth, Aaron N Brooks, Karlyn D Beer, Amardeep Kaur, Min Pan, David J Reiss, Marc T Facciotti and Nitin S Baliga
    Citation: BMC Systems Biology 2014 8:122
    Content type: Research article Published on:

  35. Bacterial spores are important contaminants in food, and the spore forming bacteria are often implicated in food safety and food quality considerations. Spore formation is a complex developmental process invol...

    Authors: Adaoha EC Ihekwaba, Ivan Mura and Gary C Barker
    Citation: BMC Systems Biology 2014 8:119
    Content type: Research article Published on:

  36. Multifactorial diseases such as type 2 diabetes mellitus (T2DM), are driven by a complex network of interconnected mechanisms that translate to a diverse range of complications at the physiological level. To o...

    Authors: Thomas Kelder, Lars Verschuren, Ben van Ommen, Alain J van Gool and Marijana Radonjic
    Citation: BMC Systems Biology 2014 8:108
    Content type: Research article Published on:

  37. Adaptation to stress is critical for survival. The adrenal medulla, the major source of epinephrine, plays an important role in the development of the hyperadenergic state and increased risk for stress associa...

    Authors: Nikolaos A Papanikolaou, Andrej Tillinger, Xiaoping Liu, Athanasios G Papavassiliou and Esther L Sabban
    Citation: BMC Systems Biology 2014 8:100
    Content type: Research article Published on:

  38. Intra-cellular processes of cells at the interface to an implant surface are influenced significantly by their extra-cellular surrounding. Specifically, when growing osteoblasts on titanium surfaces with regul...

    Authors: Arne T Bittig, Claudia Matschegewski, J Barbara Nebe, Susanne Stählke and Adelinde M Uhrmacher
    Citation: BMC Systems Biology 2014 8:106
    Content type: Research article Published on:

  39. The insulin-like growth factor (IGF) system impacts cell proliferation and is highly activated in ovarian cancer. While an attractive therapeutic target, the IGF system is complex with two receptors (IGF1R, IG...

    Authors: Dan Tian and Pamela K Kreeger
    Citation: BMC Systems Biology 2014 8:98
    Content type: Research article Published on:

  40. Saccharomyces cerevisiae has been widely used for bio-ethanol production and development of rational genetic engineering strategies leading both to the improvement of productivity and ethanol tolerance is very i...

    Authors: Ceyda Kasavi, Serpil Eraslan, Kazim Yalcin Arga, Ebru Toksoy Oner and Betul Kirdar
    Citation: BMC Systems Biology 2014 8:90
    Content type: Research article Published on:

  42. Incorporation of omic data streams for building improved systems biology models has great potential for improving their predictions of biological outcomes. We have recently shown that cyclosporine A (CsA) stro...

    Authors: Jérémy Hamon, Paul Jennings and Frederic Y Bois
    Citation: BMC Systems Biology 2014 8:76
    Content type: Research article Published on:

  43. During osteoclastogenesis, the maturation of osteoclast (OC) progenitors is stimulated by the receptor activator of nuclear factor-κB ligand (RANKL). Excess OC production plays a critical role in the pathogene...

    Authors: Feng-Jen Tseng, Wei-Tso Chia, Jia-Fwu Shyu, Guo-Hau Gou, Huey-Kang Sytwu, Ching-Wu Hsia, Min-Jen Tseng and Ru-Yu Pan
    Citation: BMC Systems Biology 2014 8:57
    Content type: Research article Published on:

  44. The TGF-β signaling pathway is a fundamental pathway in the living cell, which plays a key role in many central cellular processes. The complex and sometimes contradicting mechanisms by which TGF-β yields phen...

    Authors: Khalid Abnaof, Nikhil Mallela, Gudrun Walenda, Steffen K Meurer, Kristin Seré, Qiong Lin, Bert Smeets, Kurt Hoffmann, Wolfgang Wagner, Martin Zenke, Ralf Weiskirchen and Holger Fröhlich
    Citation: BMC Systems Biology 2014 8:55
    Content type: Research article Published on:

  45. Mapping the intracellular fluxes for established mammalian cell lines becomes increasingly important for scientific and economic reasons. However, this is being hampered by the high complexity of metabolic net...

    Authors: Averina Nicolae, Judith Wahrheit, Janina Bahnemann, An-Ping Zeng and Elmar Heinzle
    Citation: BMC Systems Biology 2014 8:50
    Content type: Research article Published on:

  46. Wnt/β-catenin signaling is involved in different stages of mammalian development and implicated in various cancers (e.g. colorectal cancer). Recent experimental and computational studies have revealed characte...

    Authors: Chin Wee Tan, Bruce S Gardiner, Yumiko Hirokawa, David W Smith and Antony W Burgess
    Citation: BMC Systems Biology 2014 8:44
    Content type: Research article Published on:

  47. The protein-protein interaction network (PIN) is an effective information tool for understanding the complex biological processes inside the cell and solving many biological problems such as signaling pathway ...

    Authors: Tong Hao, Zheng Zeng, Bin Wang, Yichen Zhang, Yichen Liu, Xuyun Geng and Jinsheng Sun
    Citation: BMC Systems Biology 2014 8:39
    Content type: Research article Published on:

  48. The evolution of reproductive self-sacrifice is well understood from kin theory, yet our understanding of how actual genes influence the expression of reproductive altruism is only beginning to take shape. As ...

    Authors: Emma Kate Mullen, Mark Daley, Alanna Gabrielle Backx and Graham James Thompson
    Citation: BMC Systems Biology 2014 8:38
    Content type: Research article Published on:

  49. Documented changes in levels of microRNAs (miRNA) in a variety of diseases including cancer are leading to their development as early indicators of disease, and as a potential new class of therapeutic agents. ...

    Authors: Christopher G Hill, Lilya V Matyunina, DeEtte Walker, Benedict B Benigno and John F McDonald
    Citation: BMC Systems Biology 2014 8:36
    Content type: Research article Published on:

  50. Mesenchymal to Epithelial Transition (MET) plasticity is critical to cancer progression, and we recently showed that the OVOL transcription factors (TFs) are critical regulators of MET. Results of that work al...

    Authors: Hernan Roca, Manjusha Pande, Jeffrey S Huo, James Hernandez, James D Cavalcoli, Kenneth J Pienta and Richard C McEachin
    Citation: BMC Systems Biology 2014 8:29
    Content type: Research article Published on:

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