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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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

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

  7. 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

  8. 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

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

  9. The application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some model organisms. Until now, however, such ...

    Authors: Maria Persico, Arnaud Ceol, Caius Gavrila, Robert Hoffmann, Arnaldo Florio and Gianni Cesareni
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S21

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

  10. Protein kinases are a well defined family of proteins, characterized by the presence of a common kinase catalytic domain and playing a significant role in many important cellular processes, such as proliferati...

    Authors: Luciano Milanesi, Mauro Petrillo, Leandra Sepe, Angelo Boccia, Nunzio D'Agostino, Myriam Passamano, Salvatore Di Nardo, Gianluca Tasco, Rita Casadio and Giovanni Paolella
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S20

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

  11. 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

  12. 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

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

  13. 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

  14. 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

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

  15. Histones are short proteins involved in chromatin packaging; in eukaryotes, two H2a-H2b and H3-H4 histone dimers form the nucleosomal core, which acts as the fundamental DNA-packaging element. The double histo...

    Authors: Claudio Greco, Piercarlo Fantucci and Luca De Gioia
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S15

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

  16. 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

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

  17. The SH3 domain family is one of the most representative and widely studied cases of so-called Peptide Recognition Modules (PRM). The polyproline II motif PxxP that generally characterizes its ligands does not ...

    Authors: Enrico Ferraro, Allegra Via, Gabriele Ausiello and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S13

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

  18. 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

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

  19. Reconstructing regulatory networks from gene expression profiles is a challenging problem of functional genomics. In microarray studies the number of samples is often very limited compared to the number of gen...

    Authors: Barbara Di Camillo, Fatima Sanchez-Cabo, Gianna Toffolo, Sreekumaran K Nair, Zlatko Trajanoski and Claudio Cobelli
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S11

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

  20. 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

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

  21. 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

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

  22. Secondary structure is used in hierarchical classification of protein structures, identification of protein features, such as helix caps and loops, for fold recognition, and as a precursor to ab initio structu...

    Authors: Maria Vittoria Cubellis, Fabien Cailliez and Simon C Lovell
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S8

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

  23. 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

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

  24. Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used i...

    Authors: Sarah Burgarella, Dario Cattaneo, Francesco Pinciroli and Marco Masseroli
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S6

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

  25. 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

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

  26. 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

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

  27. 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

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

  28. The advent of the technology of DNA microarrays constitutes an epochal change in the classification and discovery of different types of cancer because the information provided by DNA microarrays allows an appr...

    Authors: Nicola Ancona, Rosalia Maglietta, Annarita D'Addabbo, Sabino Liuni and Graziano Pesole
    Citation: BMC Bioinformatics 2005 6(Suppl 4):S2

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

  29. 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

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

  30. Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides, which is called a peak-list. In or...

    Authors: Witold E Wolski, Maciej Lalowski, Peter Martus, Ralf Herwig, Patrick Giavalisco, Johan Gobom, Albert Sickmann, Hans Lehrach and Knut Reinert
    Citation: BMC Bioinformatics 2005 6:285
  31. Families of homologous enzymes evolved from common progenitors. The availability of multiple sequences representing each activity presents an opportunity for extracting information specifying the functionality...

    Authors: Kimberly M Mayer, Sean R McCorkle and John Shanklin
    Citation: BMC Bioinformatics 2005 6:284
  32. Determination and quantification of nucleic acid components in a mixture is usually accomplished by microarray approaches, where the mixtures are hybridized against specific probes. As an alternative, we propo...

    Authors: Alexander Pozhitkov, Kathryn Stemshorn and Diethard Tautz
    Citation: BMC Bioinformatics 2005 6:281
  33. The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBM...

    Authors: Yunlong Liu, Matthew P Vincenti and Hiroki Yokota
    Citation: BMC Bioinformatics 2005 6:276
  34. A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target id...

    Authors: Emmitt R Jolly, Chen-Shan Chin, Ira Herskowitz and Hao Li
    Citation: BMC Bioinformatics 2005 6:275
  35. In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the...

    Authors: Mehrnoush Khojasteh, Wan L Lam, Rabab K Ward and Calum MacAulay
    Citation: BMC Bioinformatics 2005 6:274
  36. Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algor...

    Authors: Alexander K Hudek and Daniel G Brown
    Citation: BMC Bioinformatics 2005 6:273
  37. It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis...

    Authors: Homin K Lee, William Braynen, Kiran Keshav and Paul Pavlidis
    Citation: BMC Bioinformatics 2005 6:269
  38. The generation of large amounts of microarray data presents challenges for data collection, annotation, exchange and analysis. Although there are now widely accepted formats, minimum standards for data content...

    Authors: Mahendra Navarange, Laurence Game, Derek Fowler, Vihar Wadekar, Helen Banks, Nicola Cooley, Fatimah Rahman, Justin Hinshelwood, Peter Broderick and Helen C Causton
    Citation: BMC Bioinformatics 2005 6:268

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