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  1. Content type: Research Article

    The Boolean network paradigm is a simple and effective way to interpret genomic systems, but discovering the structure of these networks remains a difficult task. The minimum description length (MDL) principle...

    Authors: John Dougherty, Ioan Tabus and Jaakko Astola

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:482090

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  2. Content type: Research Article

    Typical problems in bioinformatics involve large discrete datasets. Therefore, in order to apply statistical methods in such domains, it is important to develop efficient algorithms suitable for discrete data....

    Authors: Petri Kontkanen, Hannes Wettig and Petri Myllymäki

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:90947

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  3. Content type: Research Article

    This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions o...

    Authors: JohnS Conery

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:72936

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  4. Content type: Research Article

    Motif discovery for the identification of functional regulatory elements underlying gene expression is a challenging problem. Sequence inspection often leads to discovery of novel motifs (including transcripti...

    Authors: Arvind Rao, Alfred O Hero III, David J States and James Douglas Engel

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:13853

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  5. Content type: Research Article

    We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sen-sitivities. A Bayesian latent intensity model is introduced for the analysis of such d...

    Authors: Rashi Gupta, Elja Arjas, Sangita Kulathinal, Andrew Thomas and Petri Auvinen

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2008:231950

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  6. Content type: Research Article

    Is it better to design a classifier and estimate its error on the full sample or to design a classifier on a training subset and estimate its error on the holdout test subset? Full-sample design provides the b...

    Authors: Marcel Brun, Qian Xu and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2008:297945

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  7. Content type: Research Article

    Several natural language processing tools, both commercial and freely available, are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic prog...

    Authors: Hena Jose, Thangavel Vadivukarasi and Jyothi Devakumar

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:53096

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  8. Content type: Research Article

    Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances....

    Authors: Hasan Metin Aktulga, Ioannis Kontoyiannis, L Alex Lyznik, Lukasz Szpankowski, Ananth Y Grama and Wojciech Szpankowski

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:14741

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  9. Content type: Research Article

    The exponential growth in the volume of publications in the biomedical domain has made it impossible for an individual to keep pace with the advances. Even though evidence-based medicine has gained wide accept...

    Authors: Parikshit Sondhi, Purushottam Raj, V Vinod Kumar and Ankush Mittal

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:28576

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  10. Content type: Research Article

    The aim of many microarray experiments is to build discriminatory diagnosis and prognosis models. Given the huge number of features and the small number of examples, model validity which refers to the precisio...

    Authors: Blaise Hanczar, Jianping Hua and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:38473

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  11. Content type: Research Article

    We describe initial results of miRNA sequence analysis with the optimal symbol compression ratio (OSCR) algorithm and recast this grammar inference algorithm as an improved minimum description length (MDL) lea...

    Authors: Scott C Evans, Antonis Kourtidis, T Stephen Markham, Jonathan Miller, Douglas S Conklin and Andrew S Torres

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:43670

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  12. Content type: Research Article

    We study the nonrandomness of proteome sequences by analysing the correlations that arise between amino acids at a short and medium range, more specifically, between amino acids located 10 or 100 residues apar...

    Authors: Dario Benedetto, Emanuele Caglioti and Claudia Chica

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:60723

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  13. Content type: Research Article

    Sequencing the complete genome of Mycobacterium tuberculosis H37Rv is a major milestone in the genome project and it sheds new light in our fight with tuberculosis. The genome contains around 4000 genes (protein-...

    Authors: Li M Fu and Thomas M Shinnick

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:23054

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  14. Content type: Research Article

    We investigate methods of estimating residue correlation within protein sequences. We begin by using mutual information (MI) of adjacent residues, and improve our methodology by defining the mutual information ve...

    Authors: Chris Hemmerich and Sun Kim

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:87356

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  15. Content type: Research Article

    Two computational methods for estimating the cell cycle phase distribution of a budding yeast (Saccharomyces cerevisiae) cell population are presented. The first one is a nonparametric method that is based on the...

    Authors: Antti Niemistö, Matti Nykter, Tommi Aho, Henna Jalovaara, Kalle Marjanen, Miika Ahdesmäki, Pekka Ruusuvuori, Mikko Tiainen, Marja-Leena Linne and Olli Yli-Harja

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:46150

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  16. Content type: Editorial

    Authors: Edward R Dougherty, Tatsuya Akutsu, Paul Dan Cristea and Ahmed H Tewfik

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:17321

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  17. Content type: Research Article

    Hepatocellular carcinoma (HCC) in a liver with advanced-stage chronic hepatitis C (CHC) is induced by hepatitis C virus, which chronically infects about 170 million people worldwide. To elucidate the associati...

    Authors: Sachiyo Aburatani, Fuyan Sun, Shigeru Saito, Masao Honda, Shu-ichi Kaneko and Katsuhisa Horimoto

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:47214

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  18. Content type: Research Article

    G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlatio...

    Authors: Haruo Suzuki, Rintaro Saito and Masaru Tomita

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:61374

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  19. Content type: Research Article

    Gene expression profiling has been widely used to study molecular signatures of many diseases and to develop molecular diagnostics for disease prediction. Gene selection, as an important step for improved diag...

    Authors: Jianhua Xuan, Yue Wang, Yibin Dong, Yuanjian Feng, Bin Wang, Javed Khan, Maria Bakay, Zuyi Wang, Lauren Pachman, Sara Winokur, Yi-Wen Chen, Robert Clarke and Eric Hoffman

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:64628

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  20. Content type: Research Article

    We investigate in this paper reverse engineering of gene regulatory networks from time-series microarray data. We apply dynamic Bayesian networks (DBNs) for modeling cell cycle regulations. In developing a net...

    Authors: Isabel Tienda Luna, Yufei Huang, Yufang Yin, Diego P Ruiz Padillo and M Carmen Carrion Perez

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:71312

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  21. Content type: Research Article

    The paper presents MRNET, an original method for inferring genetic networks from microarray data. The method is based on maximum relevance/minimum redundancy (MRMR), an effective information-theoretic techniqu...

    Authors: Patrick E Meyer, Kevin Kontos, Frederic Lafitte and Gianluca Bontempi

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:79879

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  22. Content type: Research Article

    Microarray data acquired during time-course experiments allow the temporal variations in gene expression to be monitored. An original postprandial fasting experiment was conducted in the mouse and the expressi...

    Authors: S Déjean, PGP Martin, A Baccini and P Besse

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:70561

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  23. Content type: Research Article

    Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum)...

    Authors: Francesco Fabris, Andrea Sgarro and Alessandro Tossi

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:31450

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  24. Content type: Research Article

    The modeling of genetic regulatory networks is becoming increasingly widespread in the study of biological systems. In the abstract, one would prefer quantitatively comprehensive models, such as a differential...

    Authors: Marcel Brun, Seungchan Kim, Woonjung Choi and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:82702

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  25. Content type: Research Article

    The cell division cycle comprises a sequence of phenomena controlled by a stable and robust genetic network. We applied a probabilistic genetic network (PGN) to construct a hypothetical model with a dynamical ...

    Authors: Nestor Walter Trepode, Hugo Aguirre Armelin, Michael Bittner, Junior Barrera, Marco Dimas Gubitoso and Ronaldo Fumio Hashimoto

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:73109

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  26. Content type: Research Article

    A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be...

    Authors: JZ Song, KM Duan, T Ware and M Surette

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:39382

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  27. Content type: Research Article

    The inference of gene regulatory networks is a key issue for genomic signal processing. This paper addresses the inference of probabilistic Boolean networks (PBNs) from observed temporal sequences of network s...

    Authors: Stephen Marshall, Le Yu, Yufei Xiao and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:32454

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  28. Content type: Research Article

    It is desirable to have efficient mathematical methods to extract information about regulatory iterations between genes from repeated measurements of gene transcript concentrations. One piece of information is...

    Authors: Dorothy Bollman, Omar Colón-Reyes and Edusmildo Orozco

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:97356

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  29. Content type: Research Article

    A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to ...

    Authors: Shu-Qin Zhang, Morihiro Hayashida, Tatsuya Akutsu, Wai-Ki Ching and Michael K Ng

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:20180

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  30. Content type: Research Article

    Most current methods for gene regulatory network identification lead to the inference of steady-state networks, that is, networks prevalent over all times, a hypothesis which has been challenged. There has bee...

    Authors: Arvind Rao, Alfred O Hero III, David J States and James Douglas Engel

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:51947

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  31. Content type: Research Article

    The gene coexpression study has emerged as a novel holistic approach for microarray data analysis. Different indices have been used in exploring coexpression relationship, but each is associated with certain p...

    Authors: Huai Li, Yu Sun and Ming Zhan

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:49478

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  32. Content type: Research Article

    The identification and analysis of repetitive patterns are active areas of biological and computational research. Tandem repeats in telomeres play a role in cancer and hypervariable trinucleotide tandem repeat...

    Authors: Ravi Gupta, Divya Sarthi, Ankush Mittal and Kuldip Singh

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:43596

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  33. Content type: Research Article

    Given the relatively small number of microarrays typically used in gene-expression-based classification, all of the data must be used to train a classifier and therefore the same training data is used for erro...

    Authors: Yufei Xiao, Jianping Hua and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:16354

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  34. Content type: Research Article

    A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportu...

    Authors: Lalit Ponnala, Anne-Marie Stomp, Donald L Bitzer and Mladen A Vouk

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2006 2006:23613

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  35. Content type: Research Article

    The modeling of the dynamics of interaction between ERK and STAT signaling pathways in the cell needs to establish the biochemical diagram of the corresponding proteins interactions as well as the correspondin...

    Authors: Nikola Georgiev, Valko Petrov and Georgi Georgiev

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2006 2006:85759

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  36. Content type: Research Article

    When using cDNA microarrays, normalization to correct labeling bias is a common preliminary step before further data analysis is applied, its objective being to reduce the variation between arrays. To date, as...

    Authors: Jianping Hua, Yoganand Balagurunathan, Yidong Chen, James Lowey, Michael L Bittner, Zixiang Xiong, Edward Suh and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2006 2006:43056

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  37. Content type: Research Article

    Decomposing a biological sequence into its functional regions is an important prerequisite to understand the molecule. Using the multiple alignments of the sequences, we evaluate a segmentation based on the ty...

    Authors: David KY Chiu and Yan Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2006 2006:35809

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