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  1. Content type: Research

    Restricted Boolean networks are simplified Boolean networks that are required for either negative or positive regulations between genes. Higa et al. (BMC Proc 5:S5, 2011) proposed a three-rule algorithm to inf...

    Authors: Hongjia Ouyang, Jie Fang, Liangzhong Shen, Edward R Dougherty and Wenbin Liu

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:10

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  2. Content type: Research

    The inference of gene regulatory networks is a core problem in systems biology. Many inference algorithms have been proposed and all suffer from false positives. In this paper, we use the minimum description l...

    Authors: Jie Fang, Hongjia Ouyang, Liangzhong Shen, Edward R Dougherty and Wenbin Liu

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:13

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  3. Content type: Research

    Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for...

    Authors: Brian R King, Maurice Aburdene, Alex Thompson and Zach Warres

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:8

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  4. Content type: Research

    Copy number variations (CNVs) are abundant in the human genome. They have been associated with complex traits in genome-wide association studies (GWAS) and expected to continue playing an important role in ide...

    Authors: Alexandros Iliadis, Dimitris Anastassiou and Xiaodong Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:7

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  5. Content type: Research

    Perfect knowledge of the underlying state transition probabilities is necessary for designing an optimal intervention strategy for a given Markovian genetic regulatory network. However, in many practical situa...

    Authors: Mohammadmahdi R Yousefi and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:6

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  6. Content type: Research

    Parameter estimation in dynamic systems finds applications in various disciplines, including system biology. The well-known expectation-maximization (EM) algorithm is a popular method and has been widely used ...

    Authors: Bin Jia and Xiaodong Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:5

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  7. Content type: Research

    It is widely accepted that cellular requirements and environmental conditions dictate the architecture of genetic regulatory networks. Nonetheless, the status quo in regulatory network modeling and analysis as...

    Authors: Jehandad Khan, Nidhal Bouaynaya and Hassan M Fathallah-Shaykh

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:3

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  8. Content type: Research

    Linear algebraic concept of subspace plays a significant role in the recent techniques of spectrum estimation. In this article, the authors have utilized the noise subspace concept for finding hidden periodici...

    Authors: Manidipa Roy and Soma Barman

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:2

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  9. Content type: Research

    In this paper, we first present a new concept of ‘weight’ for 64 triplets and define a different weight for each kind of triplet. Then, we give a novel 2D graphical representation for DNA sequences, which can ...

    Authors: Sai Zou, Lei Wang and Junfeng Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:1

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  10. Content type: Research

    The extended Kalman filter (EKF) has been applied to inferring gene regulatory networks. However, it is well known that the EKF becomes less accurate when the system exhibits high nonlinearity. In addition, ce...

    Authors: Bin Jia and Xiaodong Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:16

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  11. Content type: Review

    Hannah Arendt, one of the foremost political philosophers of the twentieth century, has argued that it is the responsibility of educators not to leave children in their own world but instead to bring them into...

    Authors: Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:15

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  12. Content type: Research

    Copy number alterations (CNAs) can be observed in most of cancer patients. Several oncogenes and tumor suppressor genes with CNAs have been identified in different kinds of tumor. However, the systematic surve...

    Authors: Tzu-Hung Hsiao, Hung-I Harry Chen, Stephanie Roessler, Xin Wei Wang and Yidong Chen

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:14

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  13. Content type: Research

    We propose methods to integrate data across several genomic platforms using a hierarchical Bayesian analysis framework that incorporates the biological relationships among the platforms to identify genes whose...

    Authors: Elizabeth M Jennings, Jeffrey S Morris, Raymond J Carroll, Ganiraju C Manyam and Veerabhadran Baladandayuthapani

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:13

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  14. Content type: Research

    Interaction among different risk factors plays an important role in the development and progress of complex disease, such as diabetes. However, traditional epidemiological methods often focus on analyzing indi...

    Authors: Amin Ahmadi Adl, Xiaoning Qian, Ping Xu, Kendra Vehik and Jeffrey P Krischer

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:12

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  15. Content type: Research

    Networks of molecular interactions regulate key processes in living cells. Therefore, understanding their functionality is a high priority in advancing biological knowledge. Boolean networks are often used to ...

    Authors: Guy Karlebach

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:11

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  16. Content type: Review

    A typical small-sample biomarker classification paper discriminates between types of pathology based on, say, 30,000 genes and a small labeled sample of less than 100 points. Some classification rule is used t...

    Authors: Edward R Dougherty and Lori A Dalton

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:10

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  17. Content type: Research

    Recent advances in genome technologies and the subsequent collection of genomic information at various molecular resolutions hold promise to accelerate the discovery of new therapeutic targets. A critical step...

    Authors: Sanvesh Srivastava, Wenyi Wang, Ganiraju Manyam, Carlos Ordonez and Veerabhadran Baladandayuthapani

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:9

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  18. Content type: Research

    DNA methylation plays an important role in many biological processes by regulating gene expression. It is commonly accepted that turning on the DNA methylation leads to silencing of the expression of the corre...

    Authors: Yihua Liu, Yuan Ji and Peng Qiu

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:8

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  19. Content type: Editorial

    Paul Dan Cristea, professor of Electrical Engineering and Computer Science at ‘Politehnica’ University of Bucharest died on 17 April 2013, following several years of bravely battling a perfidious illness.

    Authors: Ioan Tabus, Erchin Serpedin and Jaakko Astola

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:7

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  20. Content type: Research

    Clustering is an important data processing tool for interpreting microarray data and genomic network inference. In this article, we propose a clustering algorithm based on the hierarchical Dirichlet processes ...

    Authors: Liming Wang and Xiaodong Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:5

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  21. Content type: Research

    One of the major challenges in complex systems biology is that of providing a general theoretical framework to describe the phenomena involved in cell differentiation, i.e., the process whereby stem cells, whi...

    Authors: Marco Villani and Roberto Serra

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:4

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  22. Content type: Research

    There is a growing body of evidence associating microRNAs (miRNAs) with human diseases. MiRNAs are new key players in the disease paradigm demonstrating roles in several human diseases. The functional associat...

    Authors: Ala Qabaja, Mohammed Alshalalfa, Tarek A Bismar and Reda Alhajj

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:3

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  23. Content type: Research

    In the clinical practice, many diseases such as glioblastoma, leukemia, diabetes, and prostates have multiple subtypes. Classifying subtypes accurately using genomic data will provide individualized treatments to...

    Authors: Wenlong Tang, Junbo Duan, Ji-Gang Zhang and Yu-Ping Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:2

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  24. Content type: Research

    Transcriptional regulation networks are often modeled as Boolean networks. We discuss certain properties of Boolean functions (BFs), which are considered as important in such networks, namely, membership to th...

    Authors: Johannes Georg Klotz, Ronny Feuer, Oliver Sawodny, Martin Bossert, Michael Ederer and Steffen Schober

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:1

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  25. Content type: Research

    Drug discovery today is a complex, expensive, and time-consuming process with high attrition rate. A more systematic approach is needed to combine innovative approaches in order to lead to more effective and e...

    Authors: Xiangfang Li, Lijun Qian and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:19

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  26. Content type: Research

    Reference assisted assembly requires the use of a reference sequence, as a model, to assist in the assembly of the novel genome. The standard method for identifying the best reference sequence for the assembly...

    Authors: Bilal Wajid, Erchin Serpedin, Mohamed Nounou and Hazem Nounou

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:18

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  27. Content type: Research

    Performing quantitative, highly sensitive measurements at a single molecule level is often necessary to address specific issues related to complex molecular and biochemical systems. For that purpose, we presen...

    Authors: Martin Gerald Puchinger, Clemens Alexander Zarzer, Philipp Kügler, Erwin Gaubitzer and Gottfried Köhler

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:17

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  28. Content type: Research

    Genomic studies are now being undertaken on thousands of samples requiring new computational tools that can rapidly analyze data to identify clinically important features. Inferring structural variations in ca...

    Authors: Ryan Bressler, Jake Lin, Andrea Eakin, Thomas Robinson, Richard Kreisberg, Hector Rovira, Theo Knijnenburg, John Boyle and Ilya Shmulevich

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:15

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  29. Content type: Research

    Bacterial strains that were genetically blocked in important metabolic pathways and grown under selective conditions underwent a process of adaptive evolution: certain pathways may have been deregulated and th...

    Authors: Ronny Feuer, Katrin Gottlieb, Gero Viertel, Johannes Klotz, Steffen Schober, Martin Bossert, Oliver Sawodny, Georg Sprenger and Michael Ederer

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:14

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  30. Content type: Research

    We describe some new conceptual tools for the rigorous, mathematical description of the “set-complexity” of graphs. This set-complexity has been shown previously to be a useful measure for analyzing some biolo...

    Authors: Tomasz M Ignac, Nikita A Sakhanenko and David J Galas

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:13

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  31. Content type: Research

    CpG dinucleotide clusters also referred to as CpG islands (CGIs) are usually located in the promoter regions of genes in a deoxyribonucleic acid (DNA) sequence. CGIs play a crucial role in gene expression and ...

    Authors: Rajasekhar Kakumani, Omair Ahmad and Vijay Devabhaktuni

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:12

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  32. Content type: Research

    The kinetic models of metabolic pathways represent a system of biochemical reactions in terms of metabolic fluxes and enzyme kinetics. Therefore, the apparent differences of metabolic fluxes might reflect dist...

    Authors: Peteris Zikmanis and Inara Kampenusa

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:11

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  33. Content type: Research

    In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway is involved in the regulation of cell growth and proliferation in response to nutritional sensing and stress conditions. The pathway is tightly regu...

    Authors: Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Sonia Colombo and Enzo Martegani

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:10

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  34. Content type: Research

    Recent experimental imaging techniques are able to tag and count molecular populations in a living cell. From these data mathematical models are inferred and calibrated. If small populations are present, discr...

    Authors: Aleksandr Andreychenko, Linar Mikeev, David Spieler and Verena Wolf

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:9

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  35. Content type: Research

    Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal wh...

    Authors: Kirk K Durston, David KY Chiu, Andrew KC Wong and Gary CL Li

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:8

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  36. Content type: Research

    In our previous study, we introduced a combination methodology of Fluorescence Correlation Spectroscopy (FCS) and Transmission Electron Microscopy (TEM), which is powerful to investigate the effect of intracel...

    Authors: Noriko Hiroi, Michael Klann, Keisuke Iba, Pablo de Heras Ciechomski, Shuji Yamashita, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Yasunori Okada, Kotaro Oka, Robin Mange, Michael Unger, Akira Funahashi and Heinz Koeppl

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:7

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  37. Content type: Research

    Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm ha...

    Authors: David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Seda Arat and Reinhard Laubenbacher

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:5

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  38. Content type: Research

    In recent years, cell population models have become increasingly common. In contrast to classic single cell models, population models allow for the study of cell-to-cell variability, a crucial phenomenon in mo...

    Authors: Jan Hasenauer, Julian Heinrich, Malgorzata Doszczak, Peter Scheurich, Daniel Weiskopf and Frank Allgöwer

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:4

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  39. Content type: Research

    The identification of molecular target and mechanism of action of compounds is a key hurdle in drug discovery. Multiplexed techniques for bead-based expression profiling allow the measurement of transcriptiona...

    Authors: Florian Nigsch, Janna Hutz, Ben Cornett, Douglas W Selinger, Gregory McAllister, Somnath Bandyopadhyay, Joseph Loureiro and Jeremy L Jenkins

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:2

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  40. Content type: Research

    Advancements in sequencing technologies have witnessed an exponential rise in the number of newly found enzymes. Enzymes are proteins that catalyze bio-chemical reactions and play an important role in metaboli...

    Authors: Chetan Kumar and Alok Choudhary

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:1

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  41. Content type: Research

    Boolean models of regulatory networks are assumed to be tolerant to perturbations. That qualitatively implies that each function can only depend on a few nodes. Biologically motivated constraints further show ...

    Authors: Steffen Schober, David Kracht, Reinhard Heckel and Martin Bossert

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:6

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  42. Content type: Research

    In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to...

    Authors: Syed Murtuza Baker, C Hart Poskar and Björn H Junker

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:7

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  43. Content type: Research

    Proteins and their interactions are essential for the survival of each human cell. Knowledge of their tissue occurrence is important for understanding biological processes. Therefore, we analyzed microarray an...

    Authors: Dorothea Emig, Tim Kacprowski and Mario Albrecht

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:5

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  44. Content type: Research

    The weighted stochastic simulation algorithm (wSSA) recently developed by Kuwahara and Mura and the refined wSSA proposed by Gillespie et al. based on the importance sampling technique open the door for effici...

    Authors: Zhouyi Xu and Xiaodong Cai

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:4

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  45. Content type: Research

    Stimulation of human epithelial cells with IL-1 (10 ng/ml) + UVB radiation results in sustained NFκB activation caused by continuous IKKβ phosphorylation. We have recently published a strictly reduced ordinary...

    Authors: Johannes Witt, Sandra Barisic, Oliver Sawodny, Michael Ederer, Dagmar Kulms and Thomas Sauter

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:3

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