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  1. 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
    Content type: Methodology article Published on:

  2. 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
    Content type: Methodology article Published on:

  3. 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
    Content type: Software Published on:

  5. 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
    Content type: Commentary Published on:

  6. 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
    Content type: Methodology article Published on:

  8. 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
    Content type: Methodology article Published on:

  10. 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
    Content type: Methodology article Published on:

  11. 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
    Content type: Methodology article Published on:

  12. 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
    Content type: Research article Published on:

  14. 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
    Content type: Research article Published on:

  15. 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
    Content type: Software Published on:

  17. 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
    Content type: Research article Published on:

  18. 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
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  20. 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
    Content type: Research article Published on:

  21. 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
    Content type: Methodology article Published on:

  22. 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
    Content type: Research article Published on:

  27. 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
    Content type: Software Published on:

  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
    Content type: Software Published on:

  32. 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
    Content type: Software Published on:

  33. 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
    Content type: Methodology article Published on:

  34. Numerous microarray analysis programs have been created through the efforts of Open Source software development projects. Providing browser-based interfaces that allow these programs to be executed over the In...

    Authors: Gary L Argraves, Saurin Jani, Jeremy L Barth and W Scott Argraves
    Citation: BMC Bioinformatics 2005 6:287
    Content type: Software Published on:

  35. The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for a system that is able to auto...

    Authors: Paolo Romano, Domenico Marra and Luciano Milanesi
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S24
    Content type: Research article Published on:

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

  36. 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
    Content type: Research article Published on:

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

  37. NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and...

    Authors: Davide Rambaldi, Alessandro Guffanti, Paolo Morandi and Giuseppe Cassata
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S22
    Content type: Research article Published on:

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

  38. 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
    Content type: Research article Published on:

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

  39. Analysis of inherited diseases and their associated phenotypes is of great importance to gain knowledge of underlying genetic interactions and could ultimately give clinically useful insights into disease proc...

    Authors: Marco Masseroli, Osvaldo Galati, Mauro Manzotti, Karina Gibert and Francesco Pinciroli
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S18
    Content type: Research article Published on:

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

  40. 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
    Content type: Research article Published on:

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

  41. The ESTree db http://​www.​itb.​cnr.​it/​estree/​ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach...

    Authors: Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Alessandra Stella, Luciano Milanesi and Carlo Pozzi
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S16
    Content type: Research article Published on:

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

  42. Routine application of gene expression microarray technology is rapidly producing large amounts of data that necessitate new approaches of analysis. The analysis of a specific microarray experiment profits eno...

    Authors: Giacomo Finocchiaro, Francesco Mancuso and Heiko Muller
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S14
    Content type: Research article Published on:

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

  43. Structure prediction of membrane proteins is still a challenging computational problem. Hidden Markov models (HMM) have been successfully applied to the problem of predicting membrane protein topology. In a pr...

    Authors: Piero Fariselli, Pier Luigi Martelli and Rita Casadio
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S12
    Content type: Research article Published on:

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

  44. The organic polychlorinated compounds like dichlorodiphenyltrichloroethane with its metabolites and polychlorinated biphenyls are a class of highly persistent environmental contaminants. They have been recogni...

    Authors: Pasqualina D'Ursi, Erika Salvi, Paola Fossa, Luciano Milanesi and Ermanna Rovida
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S10
    Content type: Research article Published on:

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

  45. Expressed Sequence Tags (ESTs) are short and error-prone DNA sequences generated from the 5' and 3' ends of randomly selected cDNA clones. They provide an important resource for comparative and functional geno...

    Authors: Nunzio D'Agostino, Mario Aversano and Maria Luisa Chiusano
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S9
    Content type: Research article Published on:

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

  46. Neoplastic transformation is a multistep process in which distinct gene products of specific cell regulatory pathways are involved at each stage. Identification of overexpressed genes provides an unprecedented...

    Authors: Federica Cavallo, Annalisa Astolfi, Manuela Iezzi, Francesca Cordero, Pier-Luigi Lollini, Guido Forni and Raffaele Calogero
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S7
    Content type: Research article Published on:

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

  47. The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known s...

    Authors: Gabriele Ausiello, Allegra Via and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S5
    Content type: Research article Published on:

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

  48. Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distribu...

    Authors: Marcella Attimonelli, Matteo Accetturo, Monica Santamaria, Daniela Lascaro, Gaetano Scioscia, Graziano Pappadà, Luigi Russo, Luigi Zanchetta and Mila Tommaseo-Ponzetta
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S4
    Content type: Research article Published on:

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

  49. Due to the strict relation between protein function and structure, the prediction of protein 3D-structure has become one of the most important tasks in bioinformatics and proteomics. In fact, notwithstanding t...

    Authors: Giuliano Armano, Gianmaria Mancosu, Luciano Milanesi, Alessandro Orro, Massimiliano Saba and Eloisa Vargiu
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S3
    Content type: Research article Published on:

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

  50. The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan. This Editor...

    Authors: Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle and Cecilia Saccone
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S1
    Content type: Introduction Published on:

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

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