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  1. There are currently many different methods for processing and summarizing probe-level data from Affymetrix oligonucleotide arrays. It is of great interest to validate these methods and identify those that are ...

    Authors: Li-Xuan Qin, Richard P Beyer, Francesca N Hudson, Nancy J Linford, Daryl E Morris and Kathleen F Kerr
    Citation: BMC Bioinformatics 2006 7:23
  2. Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the s...

    Authors: Alexei A Adzhubei, Jon K Laerdahl and Anna V Vlasova
    Citation: BMC Bioinformatics 2006 7:22
  3. A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aim...

    Authors: Patrick Durand, Laurent Labarre, Alain Meil, Jean-Louis Divol, Yves Vandenbrouck, Alain Viari and Jérôme Wojcik
    Citation: BMC Bioinformatics 2006 7:21
  4. A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties da...

    Authors: Youfang Cao, Shi Liu, Lida Zhang, Jie Qin, Jiang Wang and Kexuan Tang
    Citation: BMC Bioinformatics 2006 7:20
  5. Several high-throughput searches for ppotential natural antisense transcripts (NATs) have been performed recently, but most of the reports were focused on cis type. A thorough in silico analysis of human transcri...

    Authors: Yuan-Yuan Li, Lei Qin, Zong-Ming Guo, Lei Liu, Hao Xu, Pei Hao, Jiong Su, Yixiang Shi, Wei-Zhong He and Yi-Xue Li
    Citation: BMC Bioinformatics 2006 7:18
  6. Methods for predicting protein function directly from amino acid sequences are useful tools in the study of uncharacterised protein families and in comparative genomics. Until now, this problem has been approa...

    Authors: Markus Brameier, Josien Haan, Andrea Krings and Robert M MacCallum
    Citation: BMC Bioinformatics 2006 7:16
  7. In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen significantly and in fold recognition inc...

    Authors: Oliver Sander, Ingolf Sommer and Thomas Lengauer
    Citation: BMC Bioinformatics 2006 7:14
  8. Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of the...

    Authors: Feng Li, Maoyu Li, Zhiqiang Xiao, Pengfei Zhang, Jianling Li and Zhuchu Chen
    Citation: BMC Bioinformatics 2006 7:13
  9. The choice of probe set algorithms for expression summary in a GeneChip study has a great impact on subsequent gene expression data analysis. Spiked-in cRNAs with known concentration are often used to assess t...

    Authors: Zihua Hu and Gail R Willsky
    Citation: BMC Bioinformatics 2006 7:12
  10. Various experimental techniques yield peptides that are biologically active but have unfavourable pharmacological properties. The design of structurally similar organic compounds, i.e. peptide mimetics, is a c...

    Authors: Andrean Goede, Elke Michalsky, Ulrike Schmidt and Robert Preissner
    Citation: BMC Bioinformatics 2006 7:11
  11. Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural cl...

    Authors: James A Casbon, Gavin E Crooks and Mansoor AS Saqi
    Citation: BMC Bioinformatics 2006 7:10
  12. Single nucleotide polymorphisms (SNPs) are locations at which the genomic sequences of population members differ. Since these differences are known to follow patterns, disease association studies are facilitat...

    Authors: Staal A Vinterbo, Stephan Dreiseitl and Lucila Ohno-Machado
    Citation: BMC Bioinformatics 2006 7:8
  13. Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the d...

    Authors: Jie Zheng, Jan T Svensson, Kavitha Madishetty, Timothy J Close, Tao Jiang and Stefano Lonardi
    Citation: BMC Bioinformatics 2006 7:7
  14. Escherichia coli is the model organism for which our knowledge of its regulatory network is the most extensive. Over the last few years, our project has been collecting and curating the literature concerning E. c...

    Authors: Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D Karp and Julio Collado-Vides
    Citation: BMC Bioinformatics 2006 7:5
  15. Single nucleotide polymorphisms (SNP) constitute more than 90% of the genetic variation, and hence can account for most trait differences among individuals in a given species. Polymorphism detection software P...

    Authors: Lakshmi K Matukumalli, John J Grefenstette, David L Hyten, Ik-Young Choi, Perry B Cregan and Curtis P Van Tassell
    Citation: BMC Bioinformatics 2006 7:4
  16. Protein-protein interactions have traditionally been studied on a small scale, using classical biochemical methods to investigate the proteins of interest. More recently large-scale methods, such as two-hybrid...

    Authors: Pall F Jonsson, Tamara Cavanna, Daniel Zicha and Paul A Bates
    Citation: BMC Bioinformatics 2006 7:2
  17. Type 1 diabetes mellitus (T1DM) is a autoimmune disease caused by a long-term negative balance between immune-mediated beta-cell damage and beta-cell repair/regeneration. Following immune-mediated damage the b...

    Authors: Nils E Magnusson, Alessandra K Cardozo, Mogens Kruhøffer, Decio L Eizirik, Torben F Ørntoft and Jens L Jensen
    Citation: BMC Bioinformatics 2005 6:311
  18. MicroRNAs (miRNAs) are a group of short (~22 nt) non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their hairpin structures. However, a large amount of si...

    Authors: Chenghai Xue, Fei Li, Tao He, Guo-Ping Liu, Yanda Li and Xuegong Zhang
    Citation: BMC Bioinformatics 2005 6:310
  19. The quality of microarray data can seriously affect the accuracy of downstream analyses. In order to reduce variability and enhance signal reproducibility in these data, many normalization methods have been pr...

    Authors: Wei Wu, Nilesh Dave, George C Tseng, Thomas Richards, Eric P Xing and Naftali Kaminski
    Citation: BMC Bioinformatics 2005 6:309
  20. Significant inconsistencies between probe-to-gene annotations between different releases of probe set identifiers by commercial microarray platform solutions have been reported. Such inconsistencies lead to mi...

    Authors: Sebastian Noth and Arndt Benecke
    Citation: BMC Bioinformatics 2005 6:307
  21. Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for impl...

    Authors: Xiaoqin Xia, Michael McClelland and Yipeng Wang
    Citation: BMC Bioinformatics 2005 6:306
  22. Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis an...

    Authors: Robert Kim, Francesca Demichelis, Jeffery Tang, Alberto Riva, Ronglai Shen, Doug F Gibbs, Vasudeva Mahavishno, Arul M Chinnaiyan and Mark A Rubin
    Citation: BMC Bioinformatics 2005 6:304
  23. Different classes of haplotype block algorithms exist and the ideal dataset to assess their performance would be to comprehensively re-sequence a large genomic region in a large population. Such data sets are ...

    Authors: Amit R Indap, Gabor T Marth, Craig A Struble, Peter Tonellato and Michael Olivier
    Citation: BMC Bioinformatics 2005 6:303
  24. One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode of protein function a...

    Authors: Emmanuel D Levy, Christos A Ouzounis, Walter R Gilks and Benjamin Audit
    Citation: BMC Bioinformatics 2005 6:302
  25. Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or nativ...

    Authors: Federico Fogolari, Silvio CE Tosatto and Giorgio Colombo
    Citation: BMC Bioinformatics 2005 6:301
  26. In expressed sequence tag (EST) sequencing, we are often interested in how many genes we can capture in an EST sample of a targeted size. This information provides insights to sequencing efficiency in experime...

    Authors: Ji-Ping Z Wang, Bruce G Lindsay, Liying Cui, P Kerr Wall, Josh Marion, Jiaxuan Zhang and Claude W dePamphilis
    Citation: BMC Bioinformatics 2005 6:300
  27. Elucidating the dynamic behaviour of genetic regulatory networks is one of the most significant challenges in systems biology. However, conventional quantitative predictions have been limited to small networks...

    Authors: Katsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama and Masaru Tomita
    Citation: BMC Bioinformatics 2005 6:299
  28. Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar ar...

    Authors: Mayte Suárez-Fariñas, Maurizio Pellegrino, Knut M Wittkowski and Marcelo O Magnasco
    Citation: BMC Bioinformatics 2005 6:294
  29. Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) a...

    Authors: Nameeta Shah, Michael V Teplitsky, Simon Minovitsky, Len A Pennacchio, Philip Hugenholtz, Bernd Hamann and Inna L Dubchak
    Citation: BMC Bioinformatics 2005 6:292
  30. Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the ...

    Authors: Vito Di Gesú, Raffaele Giancarlo, Giosué Lo Bosco, Alessandra Raimondi and Davide Scaturro
    Citation: BMC Bioinformatics 2005 6:289
  31. Synthetic lethality experiments identify pairs of genes with complementary function. More direct functional associations (for example greater probability of membership in a single protein complex) may be infer...

    Authors: Yan Qi, Ping Ye and Joel S Bader
    Citation: BMC Bioinformatics 2005 6:288
  32. Biological resources are essential tools for biomedical research. Their availability is promoted through on-line catalogues. Common Access to Biological Resources and Information (CABRI) is a service for distr...

    Authors: Paolo Romano, Peter Dawyndt, Francesca Piersigilli and Jean Swings
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S23

    This article is part of a Supplement: Volume 6 Supplement 4

  33. This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the...

    Authors: Ivan Merelli, Giulia Morra, Daniele D'Agostino, Andrea Clematis and Luciano Milanesi
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S19

    This article is part of a Supplement: Volume 6 Supplement 4

  34. In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80–85% of the inhabitants of each village belong to a single huge pedigree with fam...

    Authors: Gianmaria Mancosu, Massimiliano Cosso, Francesca Marras, Cesare Cappio Borlino, Giuseppe Ledda, Teresa Manias, Mauro Adamo, Donatella Serra, Paola Melis and Mario Pirastu
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S17

    This article is part of a Supplement: Volume 6 Supplement 4

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