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  1. The assignment of gene function remains a difficult but important task in computational biology. The establishment of the first Critical Assessment of Functional Annotation (CAFA) was aimed at increasing progr...

    Authors: Jesse Gillis and Paul Pavlidis
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  2. Long non-coding RNAs (lncRNA) are a major class of non-coding RNAs. They are involved in diverse intra-cellular mechanisms like molecular scaffolding, splicing and DNA methylation. Through these mechanisms the...

    Authors: Swaraj Basu, Ferenc Müller and Remo Sanges
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  3. Graphs can represent biological networks at the molecular, protein, or species level. An important query is to find all matches of a pattern graph to a target graph. Accomplishing this is inherently difficult ...

    Authors: Vincenzo Bonnici, Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha and Alfredo Ferro
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  4. Neuroblastoma is the most common pediatric solid tumor. About fifty percent of high risk patients die despite treatment making the exploration of new and more effective strategies for improving stratification ...

    Authors: Davide Cangelosi, Fabiola Blengio, Rogier Versteeg, Angelika Eggert, Alberto Garaventa, Claudio Gambini, Massimo Conte, Alessandra Eva, Marco Muselli and Luigi Varesio
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  5. The advent of massively parallel sequencing technologies (Next Generation Sequencing, NGS) profoundly modified the landscape of human genetics.

    Authors: Mattia D'Antonio, Paolo D'Onorio De Meo, Daniele Paoletti, Berardino Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole and Tiziana Castrignanò
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  6. Next-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner. Nevertheless, NGS data analysis requires bioinformatics sk...

    Authors: Ilenia Boria, Lara Boatti, Graziano Pesole and Flavio Mignone
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  7. The interaction between proteins and ligands occurs at pockets that are often lined by conserved amino acids. These pockets can represent the targets for low molecular weight drugs. In order to make the resear...

    Authors: Marco Cammisa, Antonella Correra, Giuseppina Andreotti and Maria Vittoria Cubellis
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  8. microRNAs (miRNAs) are a class of small non-coding RNAs which have been recognized as ubiquitous post-transcriptional regulators. The analysis of interactions between different miRNAs and their target genes is...

    Authors: Gianvito Pio, Michelangelo Ceci, Domenica D'Elia, Corrado Loglisci and Donato Malerba
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  9. The wet-lab synthesis of the simplest forms of life (minimal cells) is a challenging aspect in modern synthetic biology. Quasi-cellular systems able to produce proteins directly from DNA can be obtained by enc...

    Authors: Lorenzo Calviello, Pasquale Stano, Fabio Mavelli, Pier Luigi Luisi and Roberto Marangoni
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  10. In recent years more than 20 assemblers have been proposed to tackle the hard task of assembling NGS data. A common heuristic when assembling a genome is to use several assemblers and then select the best asse...

    Authors: Riccardo Vicedomini, Francesco Vezzi, Simone Scalabrin, Lars Arvestad and Alberto Policriti
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  11. RNA Editing is a type of post-transcriptional modification that takes place in the eukaryotes. It alters the sequence of primary RNA transcripts by deleting, inserting or modifying residues. Several forms of R...

    Authors: Rosario Distefano, Giovanni Nigita, Valentina Macca, Alessandro Laganà, Rosalba Giugno, Alfredo Pulvirenti and Alfredo Ferro
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  12. The key idea of DNA barcode initiative is to identify, for each group of species belonging to different kingdoms of life, a short DNA sequence that can act as a true taxon barcode. DNA barcode represents a val...

    Authors: Massimo La Rosa, Antonino Fiannaca, Riccardo Rizzo and Alfonso Urso
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  13. Intrinsic protein disorder is becoming an increasingly important topic in protein science. During the last few years, intrinsically disordered proteins (IDPs) have been shown to play a role in many important b...

    Authors: Tomás Di Domenico, Ian Walsh and Silvio CE Tosatto
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  14. RNA-seq has the potential to discover genes created by chromosomal rearrangements. Fusion genes, also known as "chimeras", are formed by the breakage and re-joining of two different chromosomes. It is known th...

    Authors: Matteo Carrara, Marco Beccuti, Federica Cavallo, Susanna Donatelli, Fulvio Lazzarato, Francesca Cordero and Raffaele A Calogero
    Citation: BMC Bioinformatics 2013 14(Suppl 7):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 7

  15. The transcriptomes of several cyanobacterial strains have been shown to exhibit diurnal oscillation patterns reflecting the diurnal phototrophic lifestyle of the organisms. The analysis of such genome-wide tra...

    Authors: Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka M Axmann and Ralf Steuer
    Citation: BMC Bioinformatics 2013 14:133
    Content type: Methodology article Published on:

  17. Cancer stem cell theory suggests that cancers are derived by a population of cells named Cancer Stem Cells (CSCs) that are involved in the growth and in the progression of tumors, and lead to a hierarchical st...

    Authors: Francesca Cordero, Marco Beccuti, Chiara Fornari, Stefania Lanzardo, Laura Conti, Federica Cavallo, Gianfranco Balbo and Raffaele Calogero
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  18. The Beauchemin model is a simple particle-based description of stochastic lymphocyte migration in tissue, which has been successfully applied to studying immunological questions. In addition to being easy to i...

    Authors: Johannes Textor, Mathieu Sinn and Rob J de Boer
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  19. Experimental autoimmune encephalomyelitis has been used extensively as an animal model of T cell mediated autoimmunity. A down-regulatory pathway through which encephalitogenic CD4Th1 cells are killed by CD8 r...

    Authors: Richard A Williams, Richard Greaves, Mark Read, Jon Timmis, Paul S Andrews and Vipin Kumar
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  20. The germinal center (GC) reaction leads to antibody affinity maturation and generation of memory B cells, but its underlying mechanisms are poorly understood. To assemble this puzzle, several key pieces of inf...

    Authors: Jose Faro and Michal Or-Guil
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  21. In recent years, there has been an increasing interest in the mathematical and computational modeling of the human immune system (HIS). Computational models of HIS dynamics may contribute to a better understan...

    Authors: Alexandre Bittencourt Pigozzo, Gilson Costa Macedo, Rodrigo Weber dos Santos and Marcelo Lobosco
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  22. Many advances in research regarding immuno-interactions with cancer were developed with the help of ordinary differential equation (ODE) models. These models, however, are not effectively capable of representi...

    Authors: Grazziela P Figueredo, Peer-Olaf Siebers and Uwe Aickelin
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  23. Germinal Centers (GC) are short-lived micro-anatomical structures, within lymphoid organs, where affinity maturation is initiated. Theoretical modeling of the dynamics of the GC reaction including follicular CD4+

    Authors: David N Olivieri, Merly Escalona and Jose Faro
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  24. Allergy is a form of hypersensitivity to normally innocuous substances, such as dust, pollen, foods or drugs. Allergens are small antigens that commonly provoke an IgE antibody response. There are two types of...

    Authors: Ivan Dimitrov, Darren R Flower and Irini Doytchinova
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  25. Vaccine protection investigation includes three processes: vaccination, pathogen challenge, and vaccine protection efficacy assessment. Many variables can affect the results of vaccine protection. Brucella, a gen...

    Authors: Thomas E Todd, Omar Tibi, Yu Lin, Samantha Sayers, Denise N Bronner, Zuoshuang Xiang and Yongqun He
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  26. Many physiological processes within the human body can be perceived and modeled as large systems of interacting particles or swarming agents. The complex processes of the human immune system prove to be challe...

    Authors: Vladimir Sarpe and Christian Jacob
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  27. H1N1 influenza viruses were responsible for the 1918 pandemic that caused millions of deaths worldwide and the 2009 pandemic that caused approximately twenty thousand deaths. The cellular response to such viru...

    Authors: Elena Zaslavsky, German Nudelman, Susanna Marquez, Uri Hershberg, Boris M Hartmann, Juilee Thakar, Stuart C Sealfon and Steven H Kleinstein
    Citation: BMC Bioinformatics 2013 14(Suppl 6):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 6

  29. Human breast cancer resistance protein (BCRP) is an ATP-binding cassette (ABC) efflux transporter that confers multidrug resistance in cancers and also plays an important role in the absorption, distribution a...

    Authors: Eszter Hazai, Istvan Hazai, Isabelle Ragueneau-Majlessi, Sophie P Chung, Zsolt Bikadi and Qingcheng Mao
    Citation: BMC Bioinformatics 2013 14:130
    Content type: Research article Published on:

  31. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new k...

    Authors: Edward Y Chen, Christopher M Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R Clark and Avi Ma’ayan
    Citation: BMC Bioinformatics 2013 14:128
    Content type: Software Published on:

  32. Despite progress in conventional cancer therapies, cancer is still one of the leading causes of death in industrial nations. Therefore, an urgent need of progress in fighting cancer remains. A promising altern...

    Authors: Joachim von Eichborn, Anna Lena Woelke, Filippo Castiglione and Robert Preissner
    Citation: BMC Bioinformatics 2013 14:127
    Content type: Software Published on:

  33. In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biolo...

    Authors: Julien Wollbrett, Pierre Larmande, Frédéric de Lamotte and Manuel Ruiz
    Citation: BMC Bioinformatics 2013 14:126
    Content type: Software Published on:

  37. The editors of BMC Bioinformatics would like to thank all our reviewers who have contributed to the journal in volume 13 (2012).

    Authors: Catherine M Rice
    Citation: BMC Bioinformatics 2013 14:80
    Content type: Reviewer acknowledgement Published on:

  39. Through transcription and alternative splicing, a gene can be transcribed into different RNA sequences (isoforms), depending on the individual, on the tissue the cell is in, or in response to some stimuli. Rec...

    Authors: Alexandru I Tomescu, Anna Kuosmanen, Romeo Rizzi and Veli Mäkinen
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  41. With the remarkable development in inexpensive sequencing technologies and supporting computational tools, we have the promise of medicine being personalized by knowledge of the individual genome. Current tech...

    Authors: Christine Lo, Sangwoo Kim, Shay Zakov and Vineet Bafna
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  42. RNA-seq, a next-generation sequencing based method for transcriptome analysis, is rapidly emerging as the method of choice for comprehensive transcript abundance estimation. The accuracy of RNA-seq can be high...

    Authors: Yi Li and Xiaohui Xie
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  43. DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional...

    Authors: Sheng Li, Francine E Garrett-Bakelman, Altuna Akalin, Paul Zumbo, Ross Levine, Bik L To, Ian D Lewis, Anna L Brown, Richard J D'Andrea, Ari Melnick and Christopher E Mason
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  46. Somatically-acquired translocations may serve as important markers for assessing the cause and nature of diseases like cancer. Algorithms to locate translocations may use next-generation sequencing (NGS) platf...

    Authors: Matthew Hayes and Jing Li
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  47. New biological techniques and technological advances in high-throughput sequencing are paving the way for systematic, comprehensive annotation of many genomes, allowing differences between cell types or betwee...

    Authors: Jacob Biesinger, Yuanfeng Wang and Xiaohui Xie
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  48. The joint sequencing of related genomes has become an important means to discover rare variants. Normal-tumor genome pairs are routinely sequenced together to find somatic mutations and their associations with...

    Authors: Eric Bareke, Virginie Saillour, Jean-François Spinella, Ramon Vidal, Jasmine Healy, Daniel Sinnett and Miklós Csűrös
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  49. Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-g...

    Authors: Christina Ander, Ole B Schulz-Trieglaff, Jens Stoye and Anthony J Cox
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  50. Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS)....

    Authors: Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G Costa, Sven Rahmann and Tobias Marschall
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

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