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  1. Sequencing of bacterial genomes became an essential approach to study pathogen virulence and the phylogenetic relationship among close related strains. Bacterium Enterococcus faecium emerged as an important nosoc...

    Authors: Yajun Wang, Yao Yu, Bohu Pan, Pei Hao, Yixue Li, Zhifeng Shao, Xiaogang Xu and Xuan Li
    Citation: BMC Systems Biology 2012 6(Suppl 3):S21
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  2. One of the primary challenges in translational research data management is breaking down the barriers between the multiple data silos and the integration of 'omics data with clinical information to complete th...

    Authors: Catherine P Jayapandian, Meng Zhao, Rob M Ewing, Guo-Qiang Zhang and Satya S Sahoo
    Citation: BMC Systems Biology 2012 6(Suppl 3):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  3. Central precocious puberty (CPP) is a common pediatric endocrine disease caused by early activation of hypothalamic-putuitary-gonadal (HPG) axis, yet the exact mechanism was poorly understood. Although there w...

    Authors: Linlin Yang, Kailin Tang, Ying Qi, Hao Ye, Wenlian Chen, Yongyu Zhang and Zhiwei Cao
    Citation: BMC Systems Biology 2012 6(Suppl 3):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  4. Animal models are indispensable tools in studying the cause of human diseases and searching for the treatments. The scientific value of an animal model depends on the accurate mimicry of human diseases. The pr...

    Authors: Shuhao Yu, Lulu Zheng, Yun Li, Chunyan Li, Chenchen Ma, Yixue Li, Xuan Li and Pei Hao
    Citation: BMC Systems Biology 2012 6(Suppl 3):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  5. Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. Studies have correlated risk of CRC development with dietary habits and environmental conditions. Gene signatures for any diseas...

    Authors: Meeta P Pradhan, Kshithija Nagulapalli and Mathew J Palakal
    Citation: BMC Systems Biology 2012 6(Suppl 3):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  6. Many genetic studies, including single gene studies and Genome-wide association studies (GWAS), aim to identify risk alleles for genetic diseases such as Type II Diabetes (T2D). However, in T2D studies, there ...

    Authors: Paul J Hale, Alfredo M López-Yunez and Jake Y Chen
    Citation: BMC Systems Biology 2012 6(Suppl 3):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  7. Interactions among genomic loci (also known as epistasis) have been suggested as one of the potential sources of missing heritability in single locus analysis of genome-wide association studies (GWAS). The com...

    Authors: Yu Liu, Sean Maxwell, Tao Feng, Xiaofeng Zhu, Robert C Elston, Mehmet Koyutürk and Mark R Chance
    Citation: BMC Systems Biology 2012 6(Suppl 3):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  8. Detecting epistatic interactions plays a significant role in improving pathogenesis, prevention, diagnosis, and treatment of complex human diseases. Applying machine learning or statistical methods to epistati...

    Authors: Bing Han, Xue-wen Chen, Zohreh Talebizadeh and Hua Xu
    Citation: BMC Systems Biology 2012 6(Suppl 3):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  9. Pathway analysis of large-scale omics data assists us with the examination of the cumulative effects of multiple functionally related genes, which are difficult to detect using the traditional single gene/marker ...

    Authors: Peilin Jia, Yang Liu and Zhongming Zhao
    Citation: BMC Systems Biology 2012 6(Suppl 3):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  10. Bacterial 16S Ribosomal RNAs profiling have been widely used in the classification of microbiota associated diseases. Dimensionality reduction is among the keys in mining high-dimensional 16S rRNAs' expression...

    Authors: Yin Wang, Yuhua Zhou, Yixue Li, Zongxin Ling, Yan Zhu, Xiaokui Guo and Hong Sun
    Citation: BMC Systems Biology 2012 6(Suppl 3):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  11. Dealing with high dimensional markers, such as gene expression data obtained using microarray chip technology or genomics studies, is a key challenge because the numbers of features greatly exceeds the number ...

    Authors: Pei-Fang Su, Xi Chen, Heidi Chen and Yu Shyr
    Citation: BMC Systems Biology 2012 6(Suppl 3):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  12. Cardiac aging is characterized by diastolic dysfunction of the left ventricle (LV), which is due in part to increased LV wall stiffness. In the diastolic phase, myocytes are relaxed and extracellular matrix (E...

    Authors: Tianyi Yang, Ying Ann Chiao, Yunji Wang, Andrew Voorhees, Hai-Chao Han, Merry L Lindsey and Yu-Fang Jin
    Citation: BMC Systems Biology 2012 6(Suppl 3):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  13. Typical analysis of time-series gene expression data such as clustering or graphical models cannot distinguish between early and later drug responsive gene targets in cancer cells. However, these genes would r...

    Authors: Pengyue Zhang, Raphaël Mourad, Yang Xiang, Kun Huang, Tim Huang, Kenneth Nephew, Yunlong Liu and Lang Li
    Citation: BMC Systems Biology 2012 6(Suppl 3):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  14. Contemporary high-throughput analyses often produce lengthy lists of genes or proteins. It is desirable to divide the genes into functionally coherent subsets for further investigation, by integrating heteroge...

    Authors: Adam J Richards, John H Schwacke, Bärbel Rohrer, L Ashley Cowart and Xinghua Lu
    Citation: BMC Systems Biology 2012 6(Suppl 3):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  15. Cells are subject to fluctuating and multiple stimuli in their natural environment. The signaling pathways often crosstalk to each other and give rise to complex nonlinear dynamics. Specifically repetitive exp...

    Authors: Yan Fu, Xiaoshan Jiang, Hang Zhang and Jianhua Xing
    Citation: BMC Systems Biology 2012 6(Suppl 3):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  16. Malaria causes over one million deaths annually, posing an enormous health and economic burden in endemic regions. The completion of genome sequencing of the causative agents, a group of parasites in the genus Pl...

    Authors: Hong Cai, Changjin Hong, Jianying Gu, Timothy G Lilburn, Rui Kuang and Yufeng Wang
    Citation: BMC Systems Biology 2012 6(Suppl 3):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  17. Recent advances in molecular biology have led to the accumulation of large amounts of data on protein-protein interaction networks in different species. An important challenge for the analysis of these data is...

    Authors: Bingjing Cai, Haiying Wang, Huiru Zheng and Hui Wang
    Citation: BMC Systems Biology 2012 6(Suppl 3):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  18. Despite large amounts of available genomic and proteomic data, predicting the structure and response of signaling networks is still a significant challenge. While statistical method such as Bayesian network ha...

    Authors: Tingting Qin, Lam C Tsoi, Kellie J Sims, Xinghua Lu and W Jim Zheng
    Citation: BMC Systems Biology 2012 6(Suppl 3):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  19. Protein-protein interaction (PPI) networks carry vital information about proteins' functions. Analysis of PPI networks associated with specific disease systems including cancer helps us in the understanding of...

    Authors: Ru Shen, Nalin CW Goonesekere and Chittibabu Guda
    Citation: BMC Systems Biology 2012 6(Suppl 3):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  20. The 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) was held on April 22-24, 2012 in Nashville, Tennessee, USA. The conference featured six technical sessions, one tutorial sessi...

    Authors: Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr and Bing Zhang
    Citation: BMC Systems Biology 2012 6(Suppl 3):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 6 Supplement 3

  21. Lineage specific differentiation of human embryonic stem cells (hESCs) is largely mediated by specific growth factors and extracellular matrix molecules. Growth factors initiate a cascade of signals which cont...

    Authors: Shibin Mathew, Maria Jaramillo, Xinan Zhang, Li Ang Zhang, Alejandro Soto-Gutiérrez and Ipsita Banerjee
    Citation: BMC Systems Biology 2012 6:154
    Content type: Research article Published on:

  23. Transcriptional networks of higher eukaryotes are difficult to obtain. Available experimental data from conventional approaches are sporadic, while those generated with modern high-throughput technologies are ...

    Authors: Martin Haubrock, Jie Li and Edgar Wingender
    Citation: BMC Systems Biology 2012 6(Suppl 2):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  24. The expression of microRNA (miRNA) genes undergoes several maturation steps. Recent studies brought new insights into the maturation process, but also raised debates on the maturation mechanism. To understand ...

    Authors: Sung-Chou Li, Kuo-Wang Tsai, Hung-Wei Pan, Yung-Ming Jeng, Meng-Ru Ho and Wen-Hsiung Li
    Citation: BMC Systems Biology 2012 6(Suppl 2):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  25. Protein complexes participate in many important cellular functions, so finding the set of existent complexes is essential for understanding the organization and regulation of processes in the cell. With the av...

    Authors: Chern Han Yong, Guimei Liu, Hon Nian Chua and Limsoon Wong
    Citation: BMC Systems Biology 2012 6(Suppl 2):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  26. TNF (Tumor Necrosis Factor-α) induces HUVEC (Human Umbilical Vein Endothelial Cells) to proliferate and form new blood vessels. This TNF-induced angiogenesis plays a key role in cancer and rheumatic disease. H...

    Authors: Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin Print and Satoru Miyano
    Citation: BMC Systems Biology 2012 6(Suppl 2):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  27. A great success of the genome wide association study enabled us to give more attention on the personal genome and clinical application such as diagnosis and disease risk prediction. However, previous predictio...

    Authors: Dankyu Yoon, Young Jin Kim and Taesung Park
    Citation: BMC Systems Biology 2012 6(Suppl 2):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  28. Current next-generation sequencing (NGS) platforms adopt two types of sequencing mechanisms: by synthesis or by ligation. The former is employed by 454 and Solexa systems, while the latter by SOLiD system. Alt...

    Authors: Yu-Feng Huang, Sheng-Chung Chen, Yih-Shien Chiang, Tzu-Han Chen and Kuo-Ping Chiu
    Citation: BMC Systems Biology 2012 6(Suppl 2):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  29. The C4 photosynthetic cycle supercharges photosynthesis by concentrating CO2 around ribulose-1,5-bisphosphate carboxylase and significantly reduces the oxygenation reaction. Therefore engineering C4 feature into ...

    Authors: Chuanli Wang, Longyun Guo, Yixue Li and Zhuo Wang
    Citation: BMC Systems Biology 2012 6(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  30. Due to the difficulty in separating two (paternal and maternal) copies of a chromosome, most published human genome sequences only provide genotype information, i.e., the mixed information of the underlying two h...

    Authors: Minzhu Xie, Jianxin Wang and Tao Jiang
    Citation: BMC Systems Biology 2012 6(Suppl 2):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  31. Proteins interact with other proteins or biomolecules in complexes to perform cellular functions. Existing protein-protein interaction (PPI) databases and protein complex databases for human proteins are not o...

    Authors: Shingo Kikugawa, Kensaku Nishikata, Katsuhiko Murakami, Yoshiharu Sato, Mami Suzuki, Md Altaf-Ul-Amin, Shigehiko Kanaya and Tadashi Imanishi
    Citation: BMC Systems Biology 2012 6(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  32. Hot spots are residues contributing the most of binding free energy yet accounting for a small portion of a protein interface. Experimental approaches to identify hot spots such as alanine scanning mutagenesis...

    Authors: Bin Xu, Xiaoming Wei, Lei Deng, Jihong Guan and Shuigeng Zhou
    Citation: BMC Systems Biology 2012 6(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  33. The discovery of single-nucleotide polymorphisms (SNPs) has important implications in a variety of genetic studies on human diseases and biological functions. One valuable approach proposed for SNP discovery i...

    Authors: Xin Chen, Qiong Wu, Ruimin Sun and Louxin Zhang
    Citation: BMC Systems Biology 2012 6(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  34. Computational approaches for finding DNA regulatory motifs in promoter sequences are useful to biologists in terms of reducing the experimental costs and speeding up the discovery process of de novo binding sites...

    Authors: Dianhui Wang and Sarwar Tapan
    Citation: BMC Systems Biology 2012 6(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  35. One important application of microarray in clinical settings is for constructing a diagnosis or prognosis model. Batch effects are a well-known obstacle in this type of applications. Recently, a prominent stud...

    Authors: Chuan Hock Koh and Limsoon Wong
    Citation: BMC Systems Biology 2012 6(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  36. Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, ...

    Authors: Hufeng Zhou, Jingjing Jin, Haojun Zhang, Bo Yi, Michal Wozniak and Limsoon Wong
    Citation: BMC Systems Biology 2012 6(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  37. Mouse E11.5 embryonic heart enhancers were found to exhibit exceptionally weak sequence conservation during vertebrate evolution compared to enhancers of other developing organs. However, it is unknown whether...

    Authors: Ben-Yang Liao and Meng-Pin Weng
    Citation: BMC Systems Biology 2012 6(Suppl 2):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  38. Torcetrapib, a cholesteryl ester transfer protein (CETP) inhibitor which raises high-density lipoprotein (HDL) cholesterol and reduces low-density lipoprotein (LDL) cholesterol level, has been documented to in...

    Authors: Shengjun Fan, Qiang Geng, Zhenyu Pan, Xin Li, Lu Tie, Yan Pan and Xuejun Li
    Citation: BMC Systems Biology 2012 6:152
    Content type: Research article Published on:

  39. Temperature strongly affects microbial growth, and many microorganisms have to deal with temperature fluctuations in their natural environment. To understand regulation strategies that underlie microbial tempe...

    Authors: AnaLuisa B Cruz, Marit Hebly, Giang-Huong Duong, Sebastian A Wahl, Jack T Pronk, Joseph J Heijnen, Pascale Daran-Lapujade and Walter M van Gulik
    Citation: BMC Systems Biology 2012 6:151
    Content type: Research article Published on:

  41. Signal transduction plays a fundamental role in the understanding of cellular physiology. The bacterial phosphotransferase system (PTS) together with the PEP/pyruvate node in central metabolism represents a si...

    Authors: Andreas Kremling, Katharina Pflüger-Grau, Max Chavarría, Jacek Puchalka, VitorMartins dos Santos and Víctorde Lorenzo
    Citation: BMC Systems Biology 2012 6:149
    Content type: Research article Published on:

  42. Changes in environmental conditions require temporal effectuation of different metabolic pathways in order to maintain the organisms’ viability but also to enable the settling into newly arising conditions. Wh...

    Authors: Nadine Töpfer, Szymon Jozefczuk and Zoran Nikoloski
    Citation: BMC Systems Biology 2012 6:148
    Content type: Research article Published on:

  43. Network inference is an important tool to reveal the underlying interactions of biological systems. In the liver, a complex system of transcription factors is active to distribute signals and induce the cellul...

    Authors: Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja, Eugenia Marbach, Jörg Linde, Anke Meyer-Baese, Sebastian Zellmer, Reinhard Guthke and Rolf Gebhardt
    Citation: BMC Systems Biology 2012 6:147
    Content type: Methodology article Published on:

  44. Stomata are tiny pores in plant leaves that regulate gas and water exchange between the plant and its environment. Abscisic acid and ethylene are two well-known elicitors of stomatal closure when acting indepe...

    Authors: Mariano Beguerisse-Dıaz, MercedesC Hernández-Gómez, AlessandroM Lizzul, Mauricio Barahona and Radhika Desikan
    Citation: BMC Systems Biology 2012 6:146
    Content type: Research article Published on:

  45. Inferring the structure of gene regulatory networks (GRN) from a collection of gene expression data has many potential applications, from the elucidation of complex biological processes to the identification o...

    Authors: Anne-Claire Haury, Fantine Mordelet, Paola Vera-Licona and Jean-Philippe Vert
    Citation: BMC Systems Biology 2012 6:145
    Content type: Methodology article Published on:

  46. With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks.

    Authors: Michal Kolář, Jörn Meier, Ville Mustonen, Michael Lässig and Johannes Berg
    Citation: BMC Systems Biology 2012 6:144
    Content type: Software Published on:

  48. An efficient and reliable parameter estimation method is essential for the creation of biological models using ordinary differential equation (ODE). Most of the existing estimation methods involve finding the ...

    Authors: Gengjie Jia, Gregory Stephanopoulos and Rudiyanto Gunawan
    Citation: BMC Systems Biology 2012 6:142
    Content type: Methodology article Published on:

  49. 5-lipoxygenase (5-LO) is a key enzyme in the synthesis of leukotrienes and 5-Oxo-6E,8Z,11Z,14Z-eicosatetraenoic acid (oxoETE). These inflammatory signaling molecules play a role in the pathology of asthma and ...

    Authors: Tatiana A Karelina, Kirill V Zhudenkov, Oleg O Demin, Dmitry V Svetlichny, Balaji Agoram, David Fairman and Oleg V Demin
    Citation: BMC Systems Biology 2012 6:141
    Content type: Research article Published on:

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