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  1. During gene expression analysis by Serial Analysis of Gene Expression (SAGE), duplicate ditags are routinely removed from the data analysis, because they are suspected to stem from artifacts during SAGE librar...

    Authors: Jeppe Emmersen, Anna M Heidenblut, Annabeth Laursen Høgh, Stephan A Hahn, Karen G Welinder and Kåre L Nielsen
    Citation: BMC Bioinformatics 2007 8:92
  2. With the advance of microarray technology, several methods for gene classification and prognosis have been already designed. However, under various denominations, some of these methods have similar approaches....

    Authors: Caroline Truntzer, Catherine Mercier, Jacques Estève, Christian Gautier and Pascal Roy
    Citation: BMC Bioinformatics 2007 8:90
  3. Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise dista...

    Authors: Isaac Elias and Jens Lagergren
    Citation: BMC Bioinformatics 2007 8:89
  4. The ability to regulate metabolism is a fundamental process in living systems. We present an analysis of one of the mechanisms by which metabolic regulation occurs: enzyme inhibition and activation by small mo...

    Authors: Alex Gutteridge, Minoru Kanehisa and Susumu Goto
    Citation: BMC Bioinformatics 2007 8:88
  5. Reverse transcription followed by real-time PCR is widely used for quantification of specific mRNA, and with the use of double-stranded DNA binding dyes it is becoming a standard for microarray data validation...

    Authors: Mariano J Alvarez, Guillermo J Vila-Ortiz, Mariano C Salibe, Osvaldo L Podhajcer and Fernando J Pitossi
    Citation: BMC Bioinformatics 2007 8:85
  6. Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functi...

    Authors: Stéphane Robin, Sophie Schbath and Vincent Vandewalle
    Citation: BMC Bioinformatics 2007 8:84
  7. Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species ge...

    Authors: René TJM van der Heijden, Berend Snel, Vera van Noort and Martijn A Huynen
    Citation: BMC Bioinformatics 2007 8:83
  8. We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples of convergent evolution, we selected only ...

    Authors: Gabriele Ausiello, Daniele Peluso, Allegra Via and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S24

    This article is part of a Supplement: Volume 8 Supplement 1

  9. Vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens.

    Authors: Nicola Vitulo, Alessandro Vezzi, Chiara Romualdi, Stefano Campanaro and Giorgio Valle
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S23

    This article is part of a Supplement: Volume 8 Supplement 1

  10. New high throughput pyrosequencers such as the 454 Life Sciences GS 20 are capable of massively parallelizing DNA sequencing providing an unprecedented rate of output data as well as potentially reducing costs...

    Authors: Gabriele A Trombetti, Raoul JP Bonnal, Ermanno Rizzi, Gianluca De Bellis and Luciano Milanesi
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S22

    This article is part of a Supplement: Volume 8 Supplement 1

  11. Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood.

    Authors: Andrea Splendiani, Marco Brandizi, Gael Even, Ottavio Beretta, Norman Pavelka, Mattia Pelizzola, Manuel Mayhaus, Maria Foti, Giancarlo Mauri and Paola Ricciardi-Castagnoli
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S21

    This article is part of a Supplement: Volume 8 Supplement 1

  12. The p53 gene family consists of the three genes p53, p63 and p73, which have polyhedral non-overlapping functions in pivotal cellular processes such as DNA synthesis and repair, growth arrest, apoptosis, genom...

    Authors: Elisabetta Sbisà, Domenico Catalano, Giorgio Grillo, Flavio Licciulli, Antonio Turi, Sabino Liuni, Graziano Pesole, Anna De Grassi, Mariano Francesco Caratozzolo, Anna Maria D'Erchia, Beatriz Navarro, Apollonia Tullo, Cecilia Saccone and Andreas Gisel
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S20

    This article is part of a Supplement: Volume 8 Supplement 1

  13. The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity...

    Authors: Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Flavio De Paoli, Domenico Marra, Giancarlo Mauri, Emanuela Merelli and Luciano Milanesi
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S19

    This article is part of a Supplement: Volume 8 Supplement 1

  14. The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical informatics" domain to impro...

    Authors: Dietrich Rebholz-Schuhman, Graham Cameron, Dominic Clark, Erik van Mulligen, Jean-Louis Coatrieux, Eva Del Hoyo Barbolla, Fernando Martin-Sanchez, Luciano Milanesi, Ivan Porro, Francesco Beltrame, Ioannis Tollis and Johan Van der Lei
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S18

    This article is part of a Supplement: Volume 8 Supplement 1

  15. The Affymetrixâ„¢ technology is nowadays a well-established method for the analysis of gene expression profiles in cancer research studies. However, changes in gene expression levels are not the only way to link...

    Authors: Davide Rambaldi, Barbara Felice, Viviane Praz, Philip Bucher, Davide Cittaro and Alessandro Guffanti
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S17

    This article is part of a Supplement: Volume 8 Supplement 1

  16. Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynami...

    Authors: Nicola Neretti, Daniel Remondini, Marc Tatar, John M Sedivy, Michela Pierini, Dawn Mazzatti, Jonathan Powell, Claudio Franceschi and Gastrone C Castellani
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S16

    This article is part of a Supplement: Volume 8 Supplement 1

  17. Thermophilic organisms are able to live at high temperatures ranging from 50 to > 100°C. Their proteins must be sufficiently stable to function under these extreme conditions; however, the basis for thermostab...

    Authors: K Mizuguchi, M Sele and MV Cubellis
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S15

    This article is part of a Supplement: Volume 8 Supplement 1

  18. The increasing protein family and domain based annotations constitute important information to understand protein functions and gain insight into relations among their codifying genes. To allow analyzing of ge...

    Authors: Marco Masseroli, Elisa Bellistri, Andrea Franceschini and Francesco Pinciroli
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S14

    This article is part of a Supplement: Volume 8 Supplement 1

  19. The ESTuber database (http://​www.​itb.​cnr.​it/​estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequence...

    Authors: Barbara Lazzari, Andrea Caprera, Cristian Cosentino, Alessandra Stella, Luciano Milanesi and Angelo Viotti
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S13

    This article is part of a Supplement: Volume 8 Supplement 1

  20. The lysine, threonine, and methionine biosynthetic pathways share the three initial enzymatic steps, which are referred to as the Common Pathway (CP). In Escherichia coli three different aspartokinases (AKI, AKII...

    Authors: Marco Fondi, Matteo Brilli and Renato Fani
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S12

    This article is part of a Supplement: Volume 8 Supplement 1

  21. Activated Protein C (ProC) is an anticoagulant plasma serine protease which also plays an important role in controlling inflammation and cell proliferation. Several mutations of the gene are associated with ph...

    Authors: Pasqualina D'Ursi, Francesca Marino, Andrea Caprera, Luciano Milanesi, Elena M Faioni and Ermanna Rovida
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S11

    This article is part of a Supplement: Volume 8 Supplement 1

  22. Microarray time series studies are essential to understand the dynamics of molecular events. In order to limit the analysis to those genes that change expression over time, a first necessary step is to select ...

    Authors: Barbara Di Camillo, Gianna Toffolo, Sreekumaran K Nair, Laura J Greenlund and Claudio Cobelli
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S10

    This article is part of a Supplement: Volume 8 Supplement 1

  23. The structure annotation of a genome is based either on ab initio methodologies or on similaritiy searches versus molecules that have been already annotated. Ab initio gene predictions in a genome are based on a ...

    Authors: Nunzio D'Agostino, Alessandra Traini, Luigi Frusciante and Maria Luisa Chiusano
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S9

    This article is part of a Supplement: Volume 8 Supplement 1

  24. High-throughput molecular biology provides new data at an incredible rate, so that the increase in the size of biological databanks is enormous and very rapid. This scenario generates severe problems not only ...

    Authors: Claudio Corsi, Paolo Ferragina and Roberto Marangoni
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S8

    This article is part of a Supplement: Volume 8 Supplement 1

  25. Several systems have been presented in the last years in order to manage the complexity of large microarray experiments. Although good results have been achieved, most systems tend to lack in one or more field...

    Authors: Ivan Porro, Livia Torterolo, Luca Corradi, Marco Fato, Adam Papadimitropoulos, Silvia Scaglione, Andrea Schenone and Federica Viti
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S7

    This article is part of a Supplement: Volume 8 Supplement 1

  26. One of the most interesting problems in molecular immunology is epitope mapping, i.e. the identification of the regions of interaction between an antigen and an antibody. The solution to this problem, even if ...

    Authors: Tiziana Castrignanò, Paolo D'Onorio De Meo, Danilo Carrabino, Massimilano Orsini, Matteo Floris and Anna Tramontano
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S6

    This article is part of a Supplement: Volume 8 Supplement 1

  27. Microarrays have been widely used for the analysis of gene expression and several commercial platforms are available. The combined use of multiple platforms can overcome the inherent biases of each approach, a...

    Authors: Roberta Bosotti, Giuseppe Locatelli, Sandra Healy, Emanuela Scacheri, Luca Sartori, Ciro Mercurio, Raffaele Calogero and Antonella Isacchi
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S5

    This article is part of a Supplement: Volume 8 Supplement 1

  28. Protein interactions support cell organization and mediate its response to any specific stimulus. Recent technological advances have produced large data-sets that aim at describing the cell interactome. These ...

    Authors: Massimo Bernaschi, Filippo Castiglione, Alessandra Ferranti, Caius Gavrila, Michele Tinti and Gianni Cesareni
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S4

    This article is part of a Supplement: Volume 8 Supplement 1

  29. Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2–5% of the genes encode for peptidases, irrespectively of the organism source. The basic p...

    Authors: Lisa Bartoli, Remo Calabrese, Piero Fariselli, Damiano G Mita and Rita Casadio
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S3

    This article is part of a Supplement: Volume 8 Supplement 1

  30. An in-silico experiment can be naturally specified as a workflow of activities implementing, in a standardized environment, the process of data and control analysis. A workflow has the advantage to be reproduc...

    Authors: Ezio Bartocci, Flavio Corradini, Emanuela Merelli and Lorenzo Scortichini
    Citation: BMC Bioinformatics 2007 8(Suppl 1):S2

    This article is part of a Supplement: Volume 8 Supplement 1

  31. With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level...

    Authors: Gerhard G Thallinger, Kerstin Baumgartner, Martin Pirklbauer, Martina Uray, Elke Pauritsch, Gabor Mehes, Charles R Buck, Kurt Zatloukal and Zlatko Trajanoski
    Citation: BMC Bioinformatics 2007 8:81
  32. Predicting intrinsically disordered proteins is important in structural biology because they are thought to carry out various cellular functions even though they have no stable three-dimensional structure. We ...

    Authors: Kana Shimizu, Yoichi Muraoka, Shuichi Hirose, Kentaro Tomii and Tamotsu Noguchi
    Citation: BMC Bioinformatics 2007 8:78
  33. Design of protein structure comparison algorithm is an important research issue, having far reaching implications. In this article, we describe a protein structure comparison scheme, which is capable of detect...

    Authors: Sourangshu Bhattacharya, Chiranjib Bhattacharyya and Nagasuma R Chandra
    Citation: BMC Bioinformatics 2007 8:77
  34. Clearly visualized biopathways provide a great help in understanding biological systems. However, manual drawing of large-scale biopathways is time consuming. We proposed a grid layout algorithm that can handl...

    Authors: Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato and Satoru Miyano
    Citation: BMC Bioinformatics 2007 8:76
  35. There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage...

    Authors: Ari B Kahn, Michael C Ryan, Hongfang Liu, Barry R Zeeberg, D Curtis Jamison and John N Weinstein
    Citation: BMC Bioinformatics 2007 8:75
  36. A microarray study may select different differentially expressed gene sets because of different selection criteria. For example, the fold-change and p-value are two commonly known criteria to select differenti...

    Authors: James J Chen, Chen-An Tsai, ShengLi Tzeng and Chun-Houh Chen
    Citation: BMC Bioinformatics 2007 8:74
  37. SPOUT methyltransferases (MTases) are a large class of S-adenosyl-L-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. In 2001, when no crystal structures w...

    Authors: Karolina L Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta and Janusz M Bujnicki
    Citation: BMC Bioinformatics 2007 8:73
  38. Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological sciences. However, the current color-codings limi...

    Authors: Richard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga and Masaru Tomita
    Citation: BMC Bioinformatics 2007 8:72
  39. S/MARs are regions of the DNA that are attached to the nuclear matrix. These regions are known to affect substantially the expression of genes. The computer prediction of S/MARs is a highly significant task wh...

    Authors: Kenneth Evans, Sascha Ott, Annika Hansen, Georgy Koentges and Lorenz Wernisch
    Citation: BMC Bioinformatics 2007 8:71
  40. The question of how a circle or line segment becomes covered when random arcs are marked off has arisen repeatedly in bioinformatics. The number of uncovered gaps is of particular interest. Approximate distrib...

    Authors: John Moriarty, Julian R Marchesi and Anthony Metcalfe
    Citation: BMC Bioinformatics 2007 8:70
  41. MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast, functional annotations are ava...

    Authors: Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser and Mihaela Zavolan
    Citation: BMC Bioinformatics 2007 8:69

    The Erratum to this article has been published in BMC Bioinformatics 2007 8:248

  42. False occurrences of functional motifs in protein sequences can be considered as random events due solely to the sequence composition of a proteome. Here we use a numerical approach to investigate the random a...

    Authors: Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2007 8:68
  43. The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cel...

    Authors: Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen, Gen-Cher Lee, DT Lee, Yow-Ling Shiue, Chang-Wei Yeh…
    Citation: BMC Bioinformatics 2007 8:66

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