Skip to main content

Articles

Page 7 of 42

  1. 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
    Content type: Research Published on:

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

  2. 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
    Content type: Research Published on:

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

  3. 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
    Content type: Research Published on:

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

  4. 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
    Content type: Research Published on:

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

  5. 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
    Content type: Research Published on:

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

  6. 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
    Content type: Research Published on:

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

  7. 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
    Content type: Research Published on:

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

  8. 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
    Content type: Research Published on:

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

  9. 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
    Content type: Research article Published on:

  10. 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
    Content type: Research article Published on:

  11. 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
    Content type: Research article Published on:

  12. 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
    Content type: Methodology Article Published on:

  13. 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
    Content type: Research article Published on:

  14. 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
    Content type: Research Article Published on:

  15. This review summarizes various mathematical models of cell-autonomous mammalian circadian clock. We present the basics necessary for understanding of the cell-autonomous mammalian circadian oscillator, modern ...

    Authors: Olga A. Podkolodnaya, Natalya N. Tverdokhleb and Nikolay L. Podkolodnyy
    Citation: BMC Systems Biology 2017 11(Suppl 1):379
    Content type: Review Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  16. Spindle FRAP curves depend on the kinetic parameters of microtubule polymerization and depolymerization. The empirical FRAP curve proposed earlier permits determination of only one such dynamic parameter, comm...

    Authors: Leonid V. Omelyanchuk and Alina F. Munzarova
    Citation: BMC Systems Biology 2017 11(Suppl 1):378
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  17. Restriction-modification (R-M) systems are rudimentary bacterial immune systems. The main components include restriction enzyme (R), which cuts specific unmethylated DNA sequences, and the methyltransferase (M...

    Authors: Andjela Rodic, Bojana Blagojevic, Evgeny Zdobnov, Magdalena Djordjevic and Marko Djordjevic
    Citation: BMC Systems Biology 2017 11(Suppl 1):377
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  18. We contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis...

    Authors: Walter Bottje, Byung-Whi Kong, Antonio Reverter, Ashley J. Waardenberg, Kentu Lassiter and Nicholas J. Hudson
    Citation: BMC Systems Biology 2017 11:29
    Content type: Research article Published on:

  19. 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
    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. Mathematical models are used to gain an integrative understanding of biochemical processes and networks. Commonly the models are based on deterministic ordinary differential equations. When molecular counts ar...

    Authors: Luis U. Aguilera, Christoph Zimmer and Ursula Kummer
    Citation: BMC Systems Biology 2017 11:26
    Content type: Research Article Published on:

  22. Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better under...

    Authors: Sara Saheb Kashaf, Claudio Angione and Pietro Lió
    Citation: BMC Systems Biology 2017 11:25
    Content type: Research Article Published on:

  23. Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell–state tran...

    Authors: Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García and Elena R. Alvarez-Buylla
    Citation: BMC Systems Biology 2017 11:24
    Content type: Research Published on:

  24. Systems Biology continues to produce increasingly large models of complex biochemical reaction networks. In applications requiring, for example, parameter estimation, the use of agent-based modelling approache...

    Authors: Thomas J. Snowden, Piet H. van der Graaf and Marcus J. Tindall
    Citation: BMC Systems Biology 2017 11:17
    Content type: Methodology Article Published on:

  25. Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understan...

    Authors: Brian K. Chu, Margaret J. Tse, Royce R. Sato and Elizabeth L. Read
    Citation: BMC Systems Biology 2017 11:14
    Content type: Research article Published on:

  27. Physical and functional interplays between genes or proteins have important biological meaning for cellular functions. Some efforts have been made to construct weighted gene association meta-networks by integr...

    Authors: Jian Yang, Tinghong Yang, Duzhi Wu, Limei Lin, Fan Yang and Jing Zhao
    Citation: BMC Systems Biology 2017 11:12
    Content type: Research article Published on:

  28. Positive and negative feedback loops are ubiquitous motifs in biochemical signaling pathways. The mitogen-activated protein kinase (MAPK) pathway module is part of many distinct signaling networks and comprise...

    Authors: Antje Jensch, Caterina Thomaseth and Nicole E. Radde
    Citation: BMC Systems Biology 2017 11:11
    Content type: Research Article Published on:

  29. Ensemble modeling is a promising approach for obtaining robust predictions and coarse grained population behavior in deterministic mathematical models. Ensemble approaches address model uncertainty by using pa...

    Authors: David M. Bassen, Michael Vilkhovoy, Mason Minot, Jonathan T. Butcher and Jeffrey D. Varner
    Citation: BMC Systems Biology 2017 11:10
    Content type: Software Published on:

  31. Computational, genome based predictions of organism phenotypes has enhanced the ability to investigate the biological phenomena that help organisms survive and respond to their environments. In this study, we ...

    Authors: Joseph J. Gardner and Nanette R. Boyle
    Citation: BMC Systems Biology 2017 11:4
    Content type: Research article Published on:

  32. 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:

  33. Aging is a complex process relating multi-scale omics data. Finding key age markers in normal tissues could help to provide reliable aging predictions in human. However, predicting age based on multi-omics dat...

    Authors: Yin Wang, Tao Huang, Lu Xie and Lei Liu
    Citation: BMC Systems Biology 2016 10(Suppl 4):132
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  34. One of the most challenging tasks in the exploration of anti-aging is to discover drugs that can promote longevity and delay the incidence of age-associated diseases of human. Up to date, a number of drugs, in...

    Authors: Hui Liu, Mengmeng Guo, Ting Xue, Jihong Guan, Libo Luo and Ziheng Zhuang
    Citation: BMC Systems Biology 2016 10(Suppl 4):131
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  35. Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. In this work, we present Sig2GRN, a ...

    Authors: Fan Zhang, Runsheng Liu and Jie Zheng
    Citation: BMC Systems Biology 2016 10(Suppl 4):123
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  36. Although there have been many studies revealing that dynamic robustness of a biological network is related to its modularity characteristics, no proper tool exists to investigate the relation between network d...

    Authors: Cong-Doan Truong, Tien-Dzung Tran and Yung-Keun Kwon
    Citation: BMC Systems Biology 2016 10(Suppl 4):122
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  37. Gene Ontology (GO) is a collaborative project that maintains and develops controlled vocabulary (or terms) to describe the molecular function, biological roles and cellular location of gene products in a hiera...

    Authors: Guoxian Yu, Wei Luo, Guangyuan Fu and Jun Wang
    Citation: BMC Systems Biology 2016 10(Suppl 4):121
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  38. Protein-protein interactions (PPIs) are essential to most biological processes. Since bioscience has entered into the era of genome and proteome, there is a growing demand for the knowledge about PPI network. ...

    Authors: Yu-An Huang, Zhu-Hong You, Xing Chen and Gui-Ying Yan
    Citation: BMC Systems Biology 2016 10(Suppl 4):120
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  39. Measures of gene functional similarity are essential tools for gene clustering, gene function prediction, evaluation of protein-protein interaction, disease gene prioritization and other applications. In recen...

    Authors: Zhen Tian, Chunyu Wang, Maozu Guo, Xiaoyan Liu and Zhixia Teng
    Citation: BMC Systems Biology 2016 10(Suppl 4):119
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  40. High-throughput technology could generate thousands to millions biomarker measurements in one experiment. However, results from high throughput analysis are often barely reproducible due to small sample size. ...

    Authors: Cong Liu, Jianping Jiang, Jianlei Gu, Zhangsheng Yu, Tao Wang and Hui Lu
    Citation: BMC Systems Biology 2016 10(Suppl 4):118
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  41. MicroRNAs (miRNAs) are involved in many biological processes by regulating post-transcriptional gene expression. The alterations of the regulatory pathways can cause different diseases including cancer. Althou...

    Authors: Shuqin Zhang and Michael K. Ng
    Citation: BMC Systems Biology 2016 10(Suppl 4):117
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  42. Aberrant epigenetic modifications, including DNA methylation, are key regulators of gene activity in tumorigenesis. Breast cancer is a heterogeneous disease, and large-scale analyses indicate that tumor from n...

    Authors: Heejoon Chae, Sangseon Lee, Kenneth P. Nephew and Sun Kim
    Citation: BMC Systems Biology 2016 10(Suppl 4):116
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  43. Drought tolerance is an important trait related to growth and yield in crop. Until now, drought related research has focused on coding genes. However, non-coding RNAs also respond significantly to environmenta...

    Authors: Inuk Jung, Hongryul Ahn, Seon-Ju Shin, Jukon Kim, Hawk-Bin Kwon, Woosuk Jung and Sun Kim
    Citation: BMC Systems Biology 2016 10(Suppl 4):115
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  44. It is necessary and essential to discovery protein function from the novel primary sequences. Wet lab experimental procedures are not only time-consuming, but also costly, so predicting protein structure and f...

    Authors: Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang and Xiangxiang Zeng
    Citation: BMC Systems Biology 2016 10(Suppl 4):114
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  45. With the rapid development of high-throughput sequencing technology, the proteomics research becomes a trendy field in the post genomics era. It is necessary to identify all the native-encoding protein sequenc...

    Authors: Qiwen Dong, Kai Wang and Xuan Liu
    Citation: BMC Systems Biology 2016 10(Suppl 4):113
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  46. Protein-protein interface holds important information of protein-protein interactions which play key roles in most biological processes. In the past few years, a lot of efforts have been made to improve interf...

    Authors: Wentao Dai, Aiping Wu, Liangxiao Ma, Yi-Xue Li, Taijiao Jiang and Yuan-Yuan Li
    Citation: BMC Systems Biology 2016 10(Suppl 4):112
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  47. Extracting drug-disease correlations is crucial in unveiling disease mechanisms, as well as discovering new indications of available drugs, or drug repositioning. Both the interactome and the knowledge of dise...

    Authors: Liang Yu, Bingbo Wang, Xiaoke Ma and Lin Gao
    Citation: BMC Systems Biology 2016 10(Suppl 4):111
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  48. Genetic switches exhibit multistability, form the basis of epigenetic memory, and are found in natural decision making systems, such as cell fate determination in developmental pathways. Synthetic genetic swit...

    Authors: Miriam Leon, Mae L. Woods, Alex J. H. Fedorec and Chris P. Barnes
    Citation: BMC Systems Biology 2016 10:130
    Content type: Research Article Published on:

  49. Drug repositioning can reduce the time, costs and risks of drug development by identifying new therapeutic effects for known drugs. It is challenging to reposition drugs as pharmacological data is large and co...

    Authors: Yahui Sun, Pathima Nusrath Hameed, Karin Verspoor and Saman Halgamuge
    Citation: BMC Systems Biology 2016 10(Suppl 5):128
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 5

  50. Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulatio...

    Authors: Yun Zheng, Vandana Hivrale, Xiaotuo Zhang, Babu Valliyodan, Christine Lelandais-Brière, Andrew D. Farmer, Gregory D. May, Martin Crespi, Henry T. Nguyen and Ramanjulu Sunkar
    Citation: BMC Systems Biology 2016 10(Suppl 5):126
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 5

BMC Systems Biology

ISSN: 1752-0509

Contact us