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  1. In contemporary biology, complex biological processes are increasingly studied by collecting and analyzing measurements of the same entities that are collected with different analytical platforms. Such data co...

    Authors: Robert A van den Berg, Iven Van Mechelen, Tom F Wilderjans, Katrijn Van Deun, Henk AL Kiers and Age K Smilde
    Citation: BMC Bioinformatics 2009 10:340
    Content type: Research article Published on:

  3. Classification using microarray datasets is usually based on a small number of samples for which tens of thousands of gene expression measurements have been obtained. The selection of the genes most significan...

    Authors: Malik Yousef, Mohamed Ketany, Larry Manevitz, Louise C Showe and Michael K Showe
    Citation: BMC Bioinformatics 2009 10:337
    Content type: Methodology article Published on:

  4. Time-course microarray experiments are widely used to study the temporal profiles of gene expression. Storey et al. (2005) developed a method for analyzing time-course microarray studies that can be applied to di...

    Authors: Insuk Sohn, Kouros Owzar, Stephen L George, Sujong Kim and Sin-Ho Jung
    Citation: BMC Bioinformatics 2009 10:336
    Content type: Methodology article Published on:

  5. The number of protein family members defined by DNA sequencing is usually much larger than those characterised experimentally. This paper describes a method to divide protein families into subtypes purely on s...

    Authors: Pavle Goldstein, Jurica Zucko, Dušica Vujaklija, Anita Kriško, Daslav Hranueli, Paul F Long, Catherine Etchebest, Bojan Basrak and John Cullum
    Citation: BMC Bioinformatics 2009 10:335
    Content type: Research article Published on:

  7. Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools ar...

    Authors: Alejandro Real-Chicharro, Iván Ruiz-Mostazo, Ismael Navas-Delgado, Amine Kerzazi, Othmane Chniber, Francisca Sánchez-Jiménez, Miguel Ángel Medina and José F Aldana-Montes
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  8. The cell cycle is a complex process that allows eukaryotic cells to replicate chromosomal DNA and partition it into two daughter cells. A relevant regulatory step is in the G0/G1 phase, a point called the restric...

    Authors: Roberta Alfieri, Matteo Barberis, Ferdinando Chiaradonna, Daniela Gaglio, Luciano Milanesi, Marco Vanoni, Edda Klipp and Lilia Alberghina
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  9. Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structur...

    Authors: Matteo D'Antonio and Marco Masseroli
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  10. Due to the huge amount of information at genomic level made recently available by high-throughput experimental technologies, networks of regulatory interactions between genes and gene products, the so-called gene...

    Authors: Liliana Ironi and Luigi Panzeri
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  11. The associations existing among different biomarkers are important in clinical settings because they contribute to the characterisation of specific pathways related to the natural history of the disease, genet...

    Authors: Federico M Stefanini, Danila Coradini and Elia Biganzoli
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  12. Cell motility plays a central role in development, wound-healing and tumour invasion. Cultures of eucariotic cells are a complex system where most cells move according to 'random' patterns, but may also be ind...

    Authors: Concita Cantarella, Leandra Sepe, Francesca Fioretti, Maria Carla Ferrari and Giovanni Paolella
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  13. One of the topics of major interest in proteomics is protein identification. Protein identification can be achieved by analyzing the mass spectrum of a protein sample through different approaches. One of them,...

    Authors: Alessandra Tiengo, Nicola Barbarini, Sonia Troiani, Luisa Rusconi and Paolo Magni
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  14. Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presen...

    Authors: Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano and Ulrich Pfeffer
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  15. Mass spectrometry spectra, widely used in proteomics studies as a screening tool for protein profiling and to detect discriminatory signals, are high dimensional data. A large number of local maxima (a.k.a. peaks

    Authors: Michele Ceccarelli, Antonio d'Acierno and Angelo Facchiano
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  16. The identification of the organisation and dynamics of molecular pathways is crucial for the understanding of cell function. In order to reconstruct the molecular pathways in which a gene of interest is involv...

    Authors: Ettore Mosca, Gloria Bertoli, Eleonora Piscitelli, Laura Vilardo, Rolland A Reinbold, Ileana Zucchi and Luciano Milanesi
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  17. The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising ...

    Authors: Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini and David Manset
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  18. In the diagnosis of complex diseases such as neurological pathologies, a wealth of clinical and molecular information is often available to help the interpretation. Yet, the pieces of information are usually c...

    Authors: Emanuel Schwarz, F Markus Leweke, Sabine Bahn and Pietro Liò
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  19. Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in p...

    Authors: Angelo Nuzzo, Alberto Riva and Riccardo Bellazzi
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  20. Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortuna...

    Authors: Filippo Menolascina, Domenico Bellomo, Thomas Maiwald, Vitoantonio Bevilacqua, Caterina Ciminelli, Angelo Paradiso and Stefania Tommasi
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  21. The design of mutants in protein functional regions, such as the ligand binding sites, is a powerful approach to recognize the determinants of specific protein activities in cellular pathways. For an exhaustiv...

    Authors: Federica Chiappori, Pasqualina D'Ursi, Ivan Merelli, Luciano Milanesi and Ermanna Rovida
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  22. The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene expression studies, provided it can ...

    Authors: Ivan Merelli, Andrea Caprera, Alessandra Stella, Marcello Del Corvo, Luciano Milanesi and Barbara Lazzari
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  23. The integration of data from multiple genome-wide assays is essential for understanding dynamic spatio-temporal interactions within cells. Such integration, which leads to a more complete view of cellular proc...

    Authors: Chiara Balestrieri, Lilia Alberghina, Marco Vanoni and Ferdinando Chiaradonna
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  24. In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools a...

    Authors: Luciano Milanesi, Paolo Romano, Gastone Castellani, Daniel Remondini and Pietro Liò
    Citation: BMC Bioinformatics 2009 10(Suppl 12):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  25. In systems biology, comparative analyses of molecular interactions across diverse species indicate that conservation and divergence of networks can be used to understand functional evolution from a systems per...

    Authors: Sinan Erten, Xin Li, Gurkan Bebek, Jing Li and Mehmet Koyutürk
    Citation: BMC Bioinformatics 2009 10:333
    Content type: Methodology article Published on:

  26. Although expression microarrays have become a standard tool used by biologists, analysis of data produced by microarray experiments may still present challenges. Comparison of data from different platforms, or...

    Authors: Daniel Jupiter, Hailin Chen and Vincent VanBuren
    Citation: BMC Bioinformatics 2009 10:332
    Content type: Software Published on:

  27. In some genomic applications it is necessary to design large numbers of PCR primers in exons flanking one or several introns on the basis of orthologous gene sequences in related species. The primer pairs desi...

    Authors: Frank M You, Naxin Huo, Yong Q Gu, Gerard R Lazo, Jan Dvorak and Olin D Anderson
    Citation: BMC Bioinformatics 2009 10:331
    Content type: Software Published on:

  30. MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and ro...

    Authors: Wei-Chi Wang, Feng-Mao Lin, Wen-Chi Chang, Kuan-Yu Lin, Hsien-Da Huang and Na-Sheng Lin
    Citation: BMC Bioinformatics 2009 10:328
    Content type: Software Published on:

  32. The Comparative Toxicogenomics Database (CTD) is a publicly available resource that promotes understanding about the etiology of environmental diseases. It provides manually curated chemical-gene/protein inter...

    Authors: Thomas C Wiegers, Allan Peter Davis, K Bretonnel Cohen, Lynette Hirschman and Carolyn J Mattingly
    Citation: BMC Bioinformatics 2009 10:326
    Content type: Research article Published on:

  33. The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, reg...

    Authors: Konstantinos Moutselos, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis and Fragiskos N Kolisis
    Citation: BMC Bioinformatics 2009 10:324
    Content type: Software Published on:

  34. Modern gene perturbation techniques, like RNA interference (RNAi), enable us to study effects of targeted interventions in cells efficiently. In combination with mRNA or protein expression data this allows to ...

    Authors: Holger Fröhlich, Özgür Sahin, Dorit Arlt, Christian Bender and Tim Beißbarth
    Citation: BMC Bioinformatics 2009 10:322
    Content type: Research article Published on:

  35. Microarray technology has made it possible to simultaneously monitor the expression levels of thousands of genes in a single experiment. However, the large number of genes greatly increases the challenges of a...

    Authors: Cuilan Gao, Xin Dang, Yixin Chen and Dawn Wilkins
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  36. Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate huge datasets which need to be i...

    Authors: Ken Pendarvis, Ranjit Kumar, Shane C Burgess and Bindu Nanduri
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  37. Next-generation sequencing techniques enable several novel transcriptome profiling approaches. Recent studies indicated that digital gene expression profiling based on short sequence tags has superior performa...

    Authors: Xin Zhou, Zhen Su, R Douglas Sammons, Yanhui Peng, Patrick J Tranel, C Neal Stewart Jr and Joshua S Yuan
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  38. Understanding the relationship between the protein sequence and the 3D structure is a major research area in bioinformatics. The prediction of complete protein tertiary structure based only on sequence informa...

    Authors: Bernard Chen and Matthew Johnson
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  39. There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as ...

    Authors: Shweta S Chavan, Michael A Bauer, Marco Scutari and Radhakrishnan Nagarajan
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  40. To grow beyond certain size and reach oxygen and other essential nutrients, solid tumors trigger angiogenesis (neovascularization) by secreting various growth factors. Based on this fact, several researches pr...

    Authors: Mutlu Mete, Leah Hennings, Horace J Spencer and Umit Topaloglu
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  41. Several different microarray platforms are available for measuring gene expression. There are disagreements within the microarray scientific community for intra- and inter-platform consistency of these platfor...

    Authors: Zhiguang Li, Zhenqiang Su, Zhining Wen, Leming Shi and Tao Chen
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  42. Environmental monitoring for pharmaceuticals and endocrine disruptors in the aquatic environment traditionally employs a variety of methods including analytical chemistry, as well as a variety of histological ...

    Authors: Natàlia Garcia-Reyero, Ira R Adelman, Dalma Martinović, Li Liu and Nancy D Denslow
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  43. Nanomaterials are being manufactured on a commercial scale for use in medical, diagnostic, energy, component and communications industries. However, concerns over the safety of engineered nanomaterials have su...

    Authors: Amin Zollanvari, Mary Jane Cunningham, Ulisses Braga-Neto and Edward R Dougherty
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  44. The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression and proteomics. However, for ...

    Authors: Lauren A Bright, Shane C Burgess, Bhanu Chowdhary, Cyprianna E Swiderski and Fiona M McCarthy
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  45. Multiple alignment of protein sequences can provide insight into sequence conservation across many species and thus allow identification of those sections of the sequence most critical to protein function. Thi...

    Authors: TJ Jankun-Kelly, Andrew D Lindeman and Susan M Bridges
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  46. Prostate carcinoma is among the most common types of cancer affecting hundreds of thousands people every year. Once the metastatic form of prostate carcinoma is documented, the majority of patients die from th...

    Authors: Andrey Ptitsyn
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  47. Gene co-expression networks are often constructed by computing some measure of similarity between expression levels of gene transcripts and subsequently applying a high-pass filter to remove all but the most l...

    Authors: Andy D Perkins and Michael A Langston
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  48. As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modificati...

    Authors: Zhanyou Xu, Dandan Zhang, Jun Hu, Xin Zhou, Xia Ye, Kristen L Reichel, Nathan R Stewart, Ryan D Syrenne, Xiaohan Yang, Peng Gao, Weibing Shi, Crissa Doeppke, Robert W Sykes, Jason N Burris, Joseph J Bozell, Max Zong-Ming Cheng…
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  49. Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest...

    Authors: Teresia J Buza, Ranjit Kumar, Cathy R Gresham, Shane C Burgess and Fiona M McCarthy
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

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