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  1. Amyloids are proteins capable of forming fibrils. Many of them underlie serious diseases, like Alzheimer disease. The number of amyloid-associated diseases is constantly increasing. Recent studies indicate tha...

    Authors: Jerzy Stanislawski, Malgorzata Kotulska and Olgierd Unold
    Citation: BMC Bioinformatics 2013 14:21
    Content type: Research article Published on:

  2. Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting ...

    Authors: Yasin Bakış, Hasan H Otu, Nivart Taşçı, Cem Meydan, Neş’e Bilgin, Sırrı Yüzbaşıoğlu and O Uğur Sezerman
    Citation: BMC Bioinformatics 2013 14:20
    Content type: Methodology article Published on:

  4. A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it i...

    Authors: Emanuel Gonçalves, Martijn van Iersel and Julio Saez-Rodriguez
    Citation: BMC Bioinformatics 2013 14:17
    Content type: Software Published on:

  5. The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ult...

    Authors: Brad Boyle, Nicole Hopkins, Zhenyuan Lu, Juan Antonio Raygoza Garay, Dmitry Mozzherin, Tony Rees, Naim Matasci, Martha L Narro, William H Piel, Sheldon J Mckay, Sonya Lowry, Chris Freeland, Robert K Peet and Brian J Enquist
    Citation: BMC Bioinformatics 2013 14:16
    Content type: Software Published on:

  6. Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from...

    Authors: Karan Uppal, Quinlyn A Soltow, Frederick H Strobel, W Stephen Pittard, Kim M Gernert, Tianwei Yu and Dean P Jones
    Citation: BMC Bioinformatics 2013 14:15
    Content type: Software Published on:

  7. Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Hi...

    Authors: Raheel Nawaz, Paul Thompson and Sophia Ananiadou
    Citation: BMC Bioinformatics 2013 14:14
    Content type: Research article Published on:

  8. Gene fusions are the result of chromosomal aberrations and encode chimeric RNA (fusion transcripts) that play an important role in cancer genesis. Recent advances in high throughput transcriptome sequencing ha...

    Authors: Andrew E Bruno, Jeffrey C Miecznikowski, Maochun Qin, Jianmin Wang and Song Liu
    Citation: BMC Bioinformatics 2013 14:13
    Content type: Software Published on:

  11. The increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease m...

    Authors: Raphael Cohen, Michael Elhadad and Noémie Elhadad
    Citation: BMC Bioinformatics 2013 14:10
    Content type: Research article Published on:

  13. Today’s biological experiments often involve the collaboration of multidisciplinary researchers utilising several high throughput ‘omics platforms. There is a requirement for the details of the experiment to b...

    Authors: Chris D Tomlinson, Geraint R Barton, Mark Woodbridge and Sarah A Butcher
    Citation: BMC Bioinformatics 2013 14:8
    Content type: Software Published on:

  14. Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis ...

    Authors: Sonja Hänzelmann, Robert Castelo and Justin Guinney
    Citation: BMC Bioinformatics 2013 14:7
    Content type: Software Published on:

  15. One of the fundamental problems in time course gene expression data analysis is to identify genes associated with a biological process or a particular stimulus of interest, like a treatment or virus infection....

    Authors: Shuang Wu and Hulin Wu
    Citation: BMC Bioinformatics 2013 14:6
    Content type: Methodology article Published on:

  18. Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, S...

    Authors: Gabriel Cardona, Arnau Mir, Francesc Rosselló, Lucía Rotger and David Sánchez
    Citation: BMC Bioinformatics 2013 14:3
    Content type: Methodology article Published on:

  19. Biomedical corpora annotated with event-level information represent an important resource for domain-specific information extraction (IE) systems. However, bio-event annotation alone cannot cater for all the n...

    Authors: Claudiu Mihăilă, Tomoko Ohta, Sampo Pyysalo and Sophia Ananiadou
    Citation: BMC Bioinformatics 2013 14:2
    Content type: Research article Published on:

  20. Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecti...

    Authors: Kevin L Neff, David P Argue, Alvin C Ma, Han B Lee, Karl J Clark and Stephen C Ekker
    Citation: BMC Bioinformatics 2013 14:1
    Content type: Software Published on:

  21. We present a novel ab initio predictor of protein enzymatic class. The predictor can classify proteins, solely based on their sequences, into one of six classes extracted from the enzyme commission (EC) classi...

    Authors: Viola Volpato, Alessandro Adelfio and Gianluca Pollastri
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  22. Recently, information derived by correlated mutations in proteins has regained relevance for predicting protein contacts. This is due to new forms of mutual information analysis that have been proven to be mor...

    Authors: Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli and Rita Casadio
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  23. The capability of correlating specific genotypes with human diseases is a complex issue in spite of all advantages arisen from high-throughput technologies, such as Genome Wide Association Studies (GWAS). New ...

    Authors: Ivan Merelli, Andrea Calabria, Paolo Cozzi, Federica Viti, Ettore Mosca and Luciano Milanesi
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  24. K-means clustering is widely used for exploratory data analysis. While its dependence on initialisation is well-known, it is common practice to assume that the partition with lowest sum-of-squares (SSQ) total ...

    Authors: Paulo JG Lisboa, Terence A Etchells, Ian H Jarman and Simon J Chambers
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  25. Despite the importance of osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectan...

    Authors: Ederson A Kido, José RC Ferreira Neto, Roberta LO Silva, Luis C Belarmino, João P Bezerra Neto, Nina M Soares-Cavalcanti, Valesca Pandolfi, Manassés D Silva, Alexandre L Nepomuceno and Ana M Benko-Iseppon
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  26. Clustering is one of the most well known activities in scientific investigation and the object of research in many disciplines, ranging from statistics to computer science. Following Handl et al., it can be summa...

    Authors: Raffaele Giancarlo, Giosué Lo Bosco, Luca Pinello and Filippo Utro
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  27. We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is ab...

    Authors: Antonino Fiannaca, Massimo La Rosa, Alfonso Urso, Riccardo Rizzo and Salvatore Gaglio
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  28. The diagnosis of many diseases can be often formulated as a decision problem; uncertainty affects these problems so that many computerized Diagnostic Decision Support Systems (in the following, DDSSs) have bee...

    Authors: Antonio d'Acierno, Massimo Esposito and Giuseppe De Pietro
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  29. Supervised machine learning approaches have been recently adopted in the inference of transcriptional targets from high throughput trascriptomic and proteomic data showing major improvements from with respect ...

    Authors: Luigi Cerulo, Vincenzo Paduano, Pietro Zoppoli and Michele Ceccarelli
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  30. The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding ap...

    Authors: Luis Carlos Belarmino, Roberta Lane de Oliveira Silva, Nina da Mota Soares Cavalcanti, Nicolas Krezdorn, Ederson Akio Kido, Ralf Horres, Peter Winter, Günter Kahl and Ana Maria Benko-Iseppon
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  31. Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrom...

    Authors: Giuseppe Agapito, Pietro Hiram Guzzi and Mario Cannataro
    Citation: BMC Bioinformatics 2013 14(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 1

  33. RNA interference (RNAi) becomes an increasingly important and effective genetic tool to study the function of target genes by suppressing specific genes of interest. This system approach helps identify signali...

    Authors: Hua Tan, Jing Fan, Jiguang Bao, Jennifer G Dy and Xiaobo Zhou
    Citation: BMC Bioinformatics 2012 13:337
    Content type: Research article Published on:

  34. Copy number variations (CNVs) are genomic structural variants that are found in healthy populations and have been observed to be associated with disease susceptibility. Existing methods for CNV detection are o...

    Authors: Melissa Pronold, Marzieh Vali, Roger Pique-Regi and Shahab Asgharzadeh
    Citation: BMC Bioinformatics 2012 13:336
    Content type: Methodology article Published on:

  35. With an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no...

    Authors: Jonatan Taminau, Stijn Meganck, Cosmin Lazar, David Steenhoff, Alain Coletta, Colin Molter, Robin Duque, Virginie de Schaetzen, David Y Weiss Solís, Hugues Bersini and Ann Nowé
    Citation: BMC Bioinformatics 2012 13:335
    Content type: Software Published on:

  36. Distinguishing biologically relevant interfaces from lattice contacts in protein crystals is a fundamental problem in structural biology. Despite efforts towards the computational prediction of interface chara...

    Authors: Jose M Duarte, Adam Srebniak, Martin A Schärer and Guido Capitani
    Citation: BMC Bioinformatics 2012 13:334
    Content type: Research article Published on:

  37. The structures of biological macromolecules provide a framework for studying their biological functions. Three-dimensional structures of proteins, nucleic acids, or their complexes, are difficult to visualize ...

    Authors: Michal J Pietal, Natalia Szostak, Kristian M Rother and Janusz M Bujnicki
    Citation: BMC Bioinformatics 2012 13:333
    Content type: Software Published on:

  39. Ancestral recombinations graph (ARG) is a topological structure that captures the relationship between the extant genomic sequences in terms of genetic events including recombinations. IRiS is a system that es...

    Authors: Filippo Utro, Omar Eduardo Cornejo, Donald Livingstone, Juan Carlos Motamayor and Laxmi Parida
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  40. Reconciliation is the classical method for inferring a duplication and loss history from a set of extant genes. It is based upon the notion of embedding the gene tree into the species tree, the incongruence be...

    Authors: Krister M Swenson and Nadia El-Mabrouk
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  41. The double-cut-and-join (DCJ) is a model that is able to efficiently sort a genome into another, generalizing the typical mutations (inversions, fusions, fissions, translocations) to which genomes are subject,...

    Authors: Poly H da Silva, Raphael Machado, Simone Dantas and Marília DV Braga
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  42. Computing the edit distance between two genomes under certain operations is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic resea...

    Authors: Mingfu Shao and Yu Lin
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  43. Maximum likelihood has been widely used for over three decades to infer phylogenetic trees from molecular data. When reticulate evolutionary events occur, several genomic regions may have conflicting evolution...

    Authors: Hyun Jung Park and Luay Nakhleh
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  44. Nowadays, metagenomic sample analyses are mainly achieved by comparing them with a priori knowledge stored in data banks. While powerful, such approaches do not allow to exploit unknown and/or "unculturable" spec...

    Authors: Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier and Pierre Peterlongo
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  45. It has recently been shown that fractionation, the random loss of excess gene copies after a whole genome duplication event, is a major cause of gene order disruption. When estimating evolutionary distances be...

    Authors: Katharina Jahn, Chunfang Zheng, Jakub Kováč and David Sankoff
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  46. Mancheron, Uricaru and Rivals (Nucleic Acids Res. 39:e101, 2011) recently introduced a new approach in the context of multiple genome comparison that allows to detect regions of strong overlaps in a set of pairwi...

    Authors: Katharina Jahn, Henner Sudek and Jens Stoye
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  47. Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is k...

    Authors: Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T Huber, Vincent Moulton and Peter F Stadler
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  48. Median construction is at the heart of several approaches to gene-order phylogeny. It has been observed that the solution to a median problem is generally not unique, and that alternate solutions may be quite ...

    Authors: Maryam Haghighi and David Sankoff
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  49. The "small phylogeny" problem consists in inferring ancestral genomes associated with each internal node of a phylogenetic tree of a set of extant species. Existing methods can be grouped into two main categor...

    Authors: Yves Gagnon, Mathieu Blanchette and Nadia El-Mabrouk
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

  50. In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evo...

    Authors: Sergey Aganezov Jr and Max A Alekseyev
    Citation: BMC Bioinformatics 2012 13(Suppl 19):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 19

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