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  1. Content type: Research Article

    Large sets of protein-protein interaction data coming either from biological experiments or predictive methods are available and can be combined to construct networks from which information about various cell ...

    Authors: Annie Glatigny, Philippe Gambette, Alexa Bourand-Plantefol, Geneviève Dujardin and Marie-Hélène Mucchielli-Giorgi

    Citation: BMC Systems Biology 2017 11:67

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  2. Content type: Research Article

    Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga which has become a biotechnological target because of its high capacity to produce polyunsaturated fatty acids and tr...

    Authors: Nicolás Loira, Sebastian Mendoza, María Paz Cortés, Natalia Rojas, Dante Travisany, Alex Di Genova, Natalia Gajardo, Nicole Ehrenfeld and Alejandro Maass

    Citation: BMC Systems Biology 2017 11:66

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  3. Content type: Research Article

    α2-adrenoceptors are important regulators of vascular tone and blood pressure. Regulation of cell proliferation is a less well investigated consequence of α2-adrenoceptor activation. We have previously shown that...

    Authors: Anna Huhtinen, Vesa Hongisto, Asta Laiho, Eliisa Löyttyniemi, Dirk Pijnenburg and Mika Scheinin

    Citation: BMC Systems Biology 2017 11:65

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  4. Content type: Research article

    Obesity is frequently linked to insulin resistance, high insulin levels, chronic inflammation, and alterations in the behaviour of CD4+ T cells. Despite the biomedical importance of this condition, the system-...

    Authors: Mariana E. Martinez-Sanchez, Marcia Hiriart and Elena R. Alvarez-Buylla

    Citation: BMC Systems Biology 2017 11:64

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  5. Content type: Research Article

    In quantitative biology, mathematical models are used to describe and analyze biological processes. The parameters of these models are usually unknown and need to be estimated from experimental data using stat...

    Authors: Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer and Fabian J. Theis

    Citation: BMC Systems Biology 2017 11:63

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  6. Content type: Methodology Article

    Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis metho...

    Authors: Wenbin Guo, Cristiane P. G. Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W. S. Brown and Runxuan Zhang

    Citation: BMC Systems Biology 2017 11:62

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  7. Content type: Software

    Finding gene-disease and disease-disease associations play important roles in the biomedical area and many prioritization methods have been proposed for this goal. Among them, approaches based on a heterogeneo...

    Authors: Duc-Hau Le and Van-Huy Pham

    Citation: BMC Systems Biology 2017 11:61

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  8. Content type: Research article

    Type 2 diabetes is one of the leading non-infectious diseases worldwide and closely relates to excess adipose tissue accumulation as seen in obesity. Specifically, hypertrophic expansion of adipose tissues is ...

    Authors: Thierry Chénard, Frédéric Guénard, Marie-Claude Vohl, André Carpentier, André Tchernof and Rafael J. Najmanovich

    Citation: BMC Systems Biology 2017 11:60

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  9. Content type: Research article

    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

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  10. Content type: Research Article

    The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clost...

    Authors: Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas and Dolly Montoya

    Citation: BMC Systems Biology 2017 11:58

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  11. Content type: Research Article

    Iron is an essential element of most living organisms but is a dangerous substance when poorly liganded in solution. The hormone hepcidin regulates the export of iron from tissues to the plasma contributing to...

    Authors: Jignesh H. Parmar, Grey Davis, Hope Shevchuk and Pedro Mendes

    Citation: BMC Systems Biology 2017 11:57

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  12. Content type: Research Article

    The human gut contains approximately 1014 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestiv...

    Authors: Milan J. A. van Hoek and Roeland M. H. Merks

    Citation: BMC Systems Biology 2017 11:56

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  13. Content type: Research Article

    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

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  14. Content type: Methodology Article

    Kinetic models of biochemical systems usually consist of ordinary differential equations that have many unknown parameters. Some of these parameters are often practically unidentifiable, that is, their values ...

    Authors: Attila Gábor, Alejandro F. Villaverde and Julio R. Banga

    Citation: BMC Systems Biology 2017 11:54

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  15. Content type: Methodology Article

    With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods sui...

    Authors: Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner and Mustafa Khammash

    Citation: BMC Systems Biology 2017 11:52

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  16. Content type: Research Article

    The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens...

    Authors: Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula and Anu Raghunathan

    Citation: BMC Systems Biology 2017 11:51

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  17. Content type: Database

    Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction i...

    Authors: Abraham A. Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang and Feng-Biao Guo

    Citation: BMC Systems Biology 2017 11:50

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  18. Content type: Research article

    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

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  19. Content type: Research Article

    Transforming growth factor β (TGF-β) signalling regulates the development of embryos and tissue homeostasis in adults. In conjunction with other oncogenic changes, long-term perturbation of TGF-β signalling is as...

    Authors: Shabnam Khatibi, Hong-Jian Zhu, John Wagner, Chin Wee Tan, Jonathan H. Manton and Antony W. Burgess

    Citation: BMC Systems Biology 2017 11:48

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  20. Content type: Software

    Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of cluste...

    Authors: Juan A. Botía, Jana Vandrovcova, Paola Forabosco, Sebastian Guelfi, Karishma D’Sa, John Hardy, Cathryn M. Lewis, Mina Ryten and Michael E. Weale

    Citation: BMC Systems Biology 2017 11:47

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  21. Content type: Research Article

    Cancer reversion, converting the phenotypes of a cancer cell into those of a normal cell, has been sporadically observed throughout history. However, no systematic analysis has been attempted so far.

    Authors: Yunseong Kim, Sea Choi, Dongkwan Shin and Kwang-Hyun Cho

    Citation: BMC Systems Biology 2017 11:45

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  22. Content type: Research Article

    Early afterdepolarizations (EADs) are pathological voltage oscillations during the repolarization phase of cardiac action potentials (APs). EADs are caused by drugs, oxidative stress or ion channel disease, an...

    Authors: Philipp Kügler, M.A.K. Bulelzai and André H. Erhardt

    Citation: BMC Systems Biology 2017 11:42

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  23. Content type: Methodology article

    Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited ...

    Authors: Athanasios D. Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P. Tampakaki, Konstantinos P. Koutsoumanis and Elias S. Manolakos

    Citation: BMC Systems Biology 2017 11:43

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  24. Content type: Research Article

    Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis o...

    Authors: Eleftherios Avramidis and Ozgur E. Akman

    Citation: BMC Systems Biology 2017 11:40

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  25. Content type: Research Article

    Directed cell migration can be driven by a range of external stimuli, such as spatial gradients of: chemical signals (chemotaxis); adhesion sites (haptotaxis); or temperature (thermotaxis). Continuum models of...

    Authors: Matthew J. Simpson, Kai-Yin Lo and Yung-Shin Sun

    Citation: BMC Systems Biology 2017 11:39

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  26. Content type: Research article

    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

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  27. Content type: Research article

    Protein secretion is one of the most important processes in eukaryotes. It is based on a highly complex machinery involving numerous proteins in several cellular compartments. The elucidation of the cell biolo...

    Authors: Anne Mathilde Lund, Christian Schrøder Kaas, Julian Brandl, Lasse Ebdrup Pedersen, Helene Faustrup Kildegaard, Claus Kristensen and Mikael Rørdam Andersen

    Citation: BMC Systems Biology 2017 11:37

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  28. Content type: Research

    Identifying perturbed pathways in a given condition is crucial in understanding biological phenomena. In addition to identifying perturbed pathways individually, pathway analysis should consider interactions a...

    Authors: Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo and Sun Kim

    Citation: BMC Systems Biology 2017 11(Suppl 2):15

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    This article is part of a Supplement: Volume 11 Supplement 2

  29. Content type: Research

    Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular comp...

    Authors: Hyundoo Jeong and Byung-Jun Yoon

    Citation: BMC Systems Biology 2017 11(Suppl 3):20

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    This article is part of a Supplement: Volume 11 Supplement 3

  30. Content type: Research

    Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion sy...

    Authors: Minghan Chen, Fei Li, Shuo Wang and Young Cao

    Citation: BMC Systems Biology 2017 11(Suppl 3):21

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    This article is part of a Supplement: Volume 11 Supplement 3

  31. Content type: Research

    Motivated by the increased amount of data on protein-RNA interactions and the availability of complete genome sequences of several organisms, many computational methods have been proposed to predict binding si...

    Authors: Daesik Choi, Byungkyu Park, Hanju Chae, Wook Lee and Kyungsook Han

    Citation: BMC Systems Biology 2017 11(Suppl 2):16

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    This article is part of a Supplement: Volume 11 Supplement 2

  32. Content type: Research

    The identification of Protein-RNA Interactions (PRIs) is important to understanding cell activities. Recently, several machine learning-based methods have been developed for identifying PRIs. However, the perf...

    Authors: Zhanzhan Cheng, Kai Huang, Yang Wang, Hui Liu, Jihong Guan and Shuigeng Zhou

    Citation: BMC Systems Biology 2017 11(Suppl 2):9

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    This article is part of a Supplement: Volume 11 Supplement 2

  33. Content type: Research

    Alcoholism has a strong genetic component. Twin studies have demonstrated the heritability of a large proportion of phenotypic variance of alcoholism ranging from 50–80%. The search for genetic variants associ...

    Authors: Amin Zollanvari and Gil Alterovitz

    Citation: BMC Systems Biology 2017 11(Suppl 3):19

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    This article is part of a Supplement: Volume 11 Supplement 3

  34. Content type: Research

    Active module, defined as an area in biological network that shows striking changes in molecular activity or phenotypic signatures, is important to reveal dynamic and process-specific information that is corre...

    Authors: Weiqi Chen, Jing Liu and Shan He

    Citation: BMC Systems Biology 2017 11(Suppl 2):8

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    This article is part of a Supplement: Volume 11 Supplement 2

  35. Content type: Research

    Intuitively, proteins in the same protein complexes should highly interact with each other but rarely interact with the other proteins in protein-protein interaction (PPI) networks. Surprisingly, many existing...

    Authors: Yijie Wang and Xiaoning Qian

    Citation: BMC Systems Biology 2017 11(Suppl 3):22

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    This article is part of a Supplement: Volume 11 Supplement 3

  36. Content type: Research

    Bruton tyrosine kinase (Btk) plays an important role in B-cell development, differentiation, and signaling. It is also found be in involved in male immunodeficiency disease such as X-linked agammaglobulinemia ...

    Authors: Pavithra K. Balasubramanian, Anand Balupuri, Hee-Young Kang and Seung Joo Cho

    Citation: BMC Systems Biology 2017 11(Suppl 2):6

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    This article is part of a Supplement: Volume 11 Supplement 2

  37. Content type: Research

    An orphan disease is any disease that affects a small percentage of the population. Orphan diseases are a great burden to patients and society, and most of them are genetic in origin. Unfortunately, our curren...

    Authors: Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons and Zhiyong Lu

    Citation: BMC Systems Biology 2017 11(Suppl 3):23

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    This article is part of a Supplement: Volume 11 Supplement 3

  38. Content type: Research

    Most disease-associated variants identified by genome-wide association studies (GWAS) exist in noncoding regions. In spite of the common agreement that such variants may disrupt biological functions of their h...

    Authors: Qiao Liu, Mingxin Gan and Rui Jiang

    Citation: BMC Systems Biology 2017 11(Suppl 2):7

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    This article is part of a Supplement: Volume 11 Supplement 2

  39. Content type: Research article

    Physiologically-based toxicokinetic (PBTK) models are often developed to facilitate in vitro to in vivo extrapolation (IVIVE) using a top-down, compartmental approach, favoring architectural simplicity over ph...

    Authors: Michael A. Rowland, Edward J. Perkins and Michael L. Mayo

    Citation: BMC Systems Biology 2017 11:35

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  40. Content type: Research article

    Dengue causes considerable morbidity and mortality in Sri Lanka. Inflammatory mediators such as cytokines, contribute to its evolution from an asymptotic infection to severe forms of dengue. The majority of pr...

    Authors: S. D. Pavithra Jayasundara, S. S. N. Perera, Gathsaurie Neelika Malavige and Saroj Jayasinghe

    Citation: BMC Systems Biology 2017 11:34

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  41. Content type: Research article

    Drugs often kill some cancer cells while others survive. This stochastic outcome is seen even in clonal cells grown under the same conditions. Understanding the molecular reasons for this stochastic outcome is...

    Authors: Anat Zimmer, Shlomit Amar-Farkash, Tamar Danon and Uri Alon

    Citation: BMC Systems Biology 2017 11:33

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  42. Content type: Methodology Article

    Biological networks contribute effectively to unveil the complex structure of molecular interactions and to discover driver genes especially in cancer context. It can happen that due to gene mutations, as for ...

    Authors: Raghvendra Mall, Luigi Cerulo, Halima Bensmail, Antonio Iavarone and Michele Ceccarelli

    Citation: BMC Systems Biology 2017 11:32

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  43. Content type: Research article

    Although renal fibrosis and inflammation have shown to be involved in the pathophysiology of obstructive nephropathies, molecular mechanisms underlying evolution of these processes remain undetermined. In an a...

    Authors: Theofilos Papadopoulos, Audrey Casemayou, Eric Neau, Benjamin Breuil, Cécile Caubet, Denis Calise, Barbara A. Thornhill, Magdalena Bachvarova, Julie Belliere, Robert L. Chevalier, Panagiotis Moulos, Dimcho Bachvarov, Benedicte Buffin-Meyer, Stéphane Decramer, Françoise Conte Auriol, Jean-Loup Bascands…

    Citation: BMC Systems Biology 2017 11:31

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  44. Content type: Research Article

    Parameter estimation in systems biology is typically done by enforcing experimental observations through an objective function as the parameter space of a model is explored by numerical simulations. Past studi...

    Authors: Cihan Oguz, Layne T. Watson, William T. Baumann and John J. Tyson

    Citation: BMC Systems Biology 2017 11:30

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  45. Content type: Research article

    Gain-of-function mutations in SCN9A gene that encodes the voltage-gated sodium channel NaV1.7 have been associated with a wide spectrum of painful syndromes in humans including inherited erythromelalgia, paroxysm...

    Authors: Dimos Kapetis, Jenny Sassone, Yang Yang, Barbara Galbardi, Markos N. Xenakis, Ronald L. Westra, Radek Szklarczyk, Patrick Lindsey, Catharina G. Faber, Monique Gerrits, Ingemar S. J. Merkies, Sulayman D. Dib-Hajj, Massimo Mantegazza, Stephen G. Waxman and Giuseppe Lauria

    Citation: BMC Systems Biology 2017 11:28

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2017 Journal Metrics

  • Citation Impact
    2.05 - 2-year Impact Factor
    2.505 - 5-year Impact Factor
    0.689 - Source Normalized Impact per Paper (SNIP)
    1.109 - SCImago Journal Rank (SJR)


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