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  1. Recent methods have been developed to perform high-throughput sequencing of DNA by Single Molecule Sequencing (SMS). While Next-Generation sequencing methods may produce reads up to several hundred bases long,...

    Authors: Mark J Chaisson and Glenn Tesler
    Citation: BMC Bioinformatics 2012 13:238
    Content type: Methodology article Published on:

  2. Yeasts are a model system for exploring eukaryotic genome evolution. Next-generation sequencing technologies are poised to vastly increase the number of yeast genome sequences, both from resequencing projects ...

    Authors: Estelle Proux-Wéra, David Armisén, Kevin P Byrne and Kenneth H Wolfe
    Citation: BMC Bioinformatics 2012 13:237
    Content type: Research article Published on:

  3. Protein interactions play a key role in life processes. Characterization of conformational properties of protein-protein interactions is important for understanding the mechanisms of protein association. The r...

    Authors: Tatsiana Kirys, Anatoly M Ruvinsky, Alexander V Tuzikov and Ilya A Vakser
    Citation: BMC Bioinformatics 2012 13:236
    Content type: Research article Published on:

  4. A large panel of methods exists that aim to identify residues with critical impact on protein function based on evolutionary signals, sequence and structure information. However, it is not clear to what extent...

    Authors: Elin Teppa, Angela D Wilkins, Morten Nielsen and Cristina Marino Buslje
    Citation: BMC Bioinformatics 2012 13:235
    Content type: Research article Published on:

  5. Existing statistical methods for tiling array transcriptome data either focus on transcript discovery in one biological or experimental condition or on the detection of differential expression between two cond...

    Authors: Kristof De Beuf, Peter Pipelers, Megan Andriankaja, Olivier Thas, Dirk Inzé, Ciprian Crainiceanu and Lieven Clement
    Citation: BMC Bioinformatics 2012 13:234
    Content type: Software Published on:

  7. Correct segmentation is critical to many applications within automated microscopy image analysis. Despite the availability of advanced segmentation algorithms, variations in cell morphology, sample preparation...

    Authors: William J Cukierski, Kaustav Nandy, Prabhakar Gudla, Karen J Meaburn, Tom Misteli, David J Foran and Stephen J Lockett
    Citation: BMC Bioinformatics 2012 13:232
    Content type: Research article Published on:

  8. Meta-analysis (MA) is widely used to pool genome-wide association studies (GWASes) in order to a) increase the power to detect strong or weak genotype effects or b) as a result verification method. As a conseq...

    Authors: Christian Meesters, Markus Leber, Christine Herold, Marina Angisch, Manuel Mattheisen, Dmitriy Drichel, André Lacour and Tim Becker
    Citation: BMC Bioinformatics 2012 13:231
    Content type: Methodology article Published on:

  10. High-throughput molecular biology techniques yield vast amounts of data, often by detecting small portions of ribonucleotides corresponding to specific identifiers. Existing bioinformatic methodologies categor...

    Authors: Fahim Mohammad, Robert M Flight, Benjamin J Harrison, Jeffrey C Petruska and Eric C Rouchka
    Citation: BMC Bioinformatics 2012 13:229
    Content type: Methodology article Published on:

  11. Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the ...

    Authors: Piotr Setny, Ranjit Prasad Bahadur and Martin Zacharias
    Citation: BMC Bioinformatics 2012 13:228
    Content type: Methodology article Published on:

  12. Relative expression algorithms such as the top-scoring pair (TSP) and the top-scoring triplet (TST) have several strengths that distinguish them from other classification methods, including resistance to overf...

    Authors: Andrew T Magis and Nathan D Price
    Citation: BMC Bioinformatics 2012 13:227
    Content type: Methodology article Published on:

  13. Gene-set enrichment analyses (GEA or GSEA) are commonly used for biological characterization of an experimental gene-set. This is done by finding known functional categories, such as pathways or Gene Ontology ...

    Authors: Andrey Alexeyenko, Woojoo Lee, Maria Pernemalm, Justin Guegan, Philippe Dessen, Vladimir Lazar, Janne Lehtiö and Yudi Pawitan
    Citation: BMC Bioinformatics 2012 13:226
    Content type: Methodology article Published on:

  14. The detection of significant compensatory mutation signals in multiple sequence alignments (MSAs) is often complicated by noise. A challenging problem in bioinformatics is remains the separation of significant...

    Authors: Mehmet Gültas, Martin Haubrock, Nesrin Tüysüz and Stephan Waack
    Citation: BMC Bioinformatics 2012 13:225
    Content type: Methodology article Published on:

  15. In this work, we empirically evaluate the capability of various scoring functions of Bayesian networks for recovering true underlying structures. Similar investigations have been carried out before, but they t...

    Authors: Zhifa Liu, Brandon Malone and Changhe Yuan
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  16. Currently, the tandem mass spectrometry (MSMS) of peptides is a dominant technique used to identify peptides and consequently proteins. The peptide fragmentation inside the mass analyzer typically offers a spe...

    Authors: Tibor Pechan and Steven R Gwaltney
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  17. Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as protei...

    Authors: Gaihua Zhang and Zhen Su
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  18. Analyzing global experimental data can be tedious and time-consuming. Thus, helping biologists see results as quickly and easily as possible can facilitate biological research, and is the purpose of the softwa...

    Authors: Lifeng Zhang, Daniel Berleant, Yi Wang, Ling Li, Diane Cook and Eve Syrkin Wurtele
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  19. NAC domain transcription factors are important transcriptional regulators involved in plant growth, development and stress responses. Recent studies have revealed several classes of NAC transcriptional factors...

    Authors: Dongxia Yao, Qiang Wei, Wenying Xu, Ryan D Syrenne, Joshua S Yuan and Zhen Su
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  20. Members of the phylum Proteobacteria are most prominent among bacteria causing plant diseases that result in a diminution of the quantity and quality of food produced by agriculture. To ameliorate these losses...

    Authors: Ruchi Verma and Ulrich Melcher
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  21. Multidimensional protein identification technology (MudPIT)-based shot-gun proteomics has been proven to be an effective platform for functional proteomics. In particular, the various sample preparation method...

    Authors: Yixiang Zhang, Sanmin Liu, Susie Y Dai and Joshua S Yuan
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  22. Next-Generation Sequencing (NGS) technologies and Genome-Wide Association Studies (GWAS) generate millions of reads and hundreds of datasets, and there is an urgent need for a better way to accurately interpre...

    Authors: Fan Zhang and Renee Drabier
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  23. Drug repositioning offers an opportunity to revitalize the slowing drug discovery pipeline by finding new uses for currently existing drugs. Our hypothesis is that drugs sharing similar side effect profiles ar...

    Authors: Halil Bisgin, Zhichao Liu, Reagan Kelly, Hong Fang, Xiaowei Xu and Weida Tong
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  24. Early evolution of animals led to profound changes in body plan organization, symmetry and the rise of tissue complexity including formation of muscular and nervous systems. This process was associated with ma...

    Authors: Andrey Ptitsyn and Leonid L Moroz
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  25. Computational methods for structural gene annotation have propelled gene discovery but face certain drawbacks with regards to prokaryotic genome annotation. Identification of transcriptional start sites, demar...

    Authors: Joseph S Reddy, Ranjit Kumar, James M Watt, Mark L Lawrence, Shane C Burgess and Bindu Nanduri
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  26. In the context of drug discovery and development, much effort has been exerted to determine which conformers of a given molecule are responsible for the observed biological activity. In this work we aimed to p...

    Authors: Gang Fu, Xiaofei Nan, Haining Liu, Ronak Y Patel, Pankaj R Daga, Yixin Chen, Dawn E Wilkins and Robert J Doerksen
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  27. Over the past decade, pathway and gene-set enrichment analysis has evolved into the study of high-throughput functional genomics. Owing to poorly annotated and incomplete pathway data, researchers have begun t...

    Authors: Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N Mandape, Ragini Pandey, Karl F MacDorman, Ping Wan and Jake Y Chen
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  29. Employing methods to assess the quality of modeled protein structures is now standard practice in bioinformatics. In a broad sense, the techniques can be divided into methods relying on consensus prediction on...

    Authors: Arjun Ray, Erik Lindahl and Björn Wallner
    Citation: BMC Bioinformatics 2012 13:224
    Content type: Methodology article Published on:

  30. The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database ex...

    Authors: Arno Meiler, Claudia Klinger and Michael Kaufmann
    Citation: BMC Bioinformatics 2012 13:223
    Content type: Software Published on:

  31. Reaction-diffusion based models have been widely used in the literature for modeling the growth of solid tumors. Many of the current models treat both diffusion/consumption of nutrients and cell proliferation....

    Authors: Paola Lecca and Daniele Morpurgo
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  32. Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, usually derived from the ...

    Authors: Irene Sánchez-Linares, Horacio Pérez-Sánchez, José M Cecilia and José M García
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  33. This work focuses on the computational modelling of osteomyelitis, a bone pathology caused by bacteria infection (mostly Staphylococcus aureus). The infection alters the RANK/RANKL/OPG signalling dynamics that re...

    Authors: Pietro Liò, Nicola Paoletti, Mohammad Ali Moni, Kathryn Atwell, Emanuela Merelli and Marco Viceconti
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  34. The Internet is a major source of health information but most seekers are not familiar with medical vocabularies. Hence, their searches fail due to bad query formulation. Several methods have been proposed to ...

    Authors: Lina F Soualmia, Elise Prieur-Gaston, Zied Moalla, Thierry Lecroq and Stéfan J Darmoni
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  35. Magnesium research is increasing in molecular medicine due to the relevance of this ion in several important biological processes and associated molecular pathogeneses. It is still difficult to predict from th...

    Authors: Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli and Rita Casadio
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  36. Whole exome sequencing (WES) has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting bot...

    Authors: Sophie Coutant, Chloé Cabot, Arnaud Lefebvre, Martine Léonard, Elise Prieur-Gaston, Dominique Campion, Thierry Lecroq and Hélène Dauchel
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  37. Next Generation Sequencing technologies are able to provide high genome coverages at a relatively low cost. However, due to limited reads' length (from 30 bp up to 200 bp), specific bioinformatics problems hav...

    Authors: Francesca Nadalin, Francesco Vezzi and Alberto Policriti
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  38. Imputation is a statistical process used to predict genotypes of loci not directly assayed in a sample of individuals. Our goal is to measure the performance of imputation in predicting the genotype of the bes...

    Authors: Vladan Mijatovic, Ilaria Iacobucci, Marco Sazzini, Luciano Xumerle, Antonio Mori, Pier Franco Pignatti, Giovanni Martinelli and Giovanni Malerba
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  39. Genome Wide Association Studies represent powerful approaches that aim at disentangling the genetic and molecular mechanisms underlying complex traits. The usual "one-SNP-at-the-time" testing strategy cannot c...

    Authors: Alberto Malovini, Nicola Barbarini, Riccardo Bellazzi and Francesca De Michelis
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  40. Inflammatory bowel diseases (IBD) refer to a group of inflammatory conditions concerning colon and small intestine, which cause socially uncomfortable symptoms and often are associated with an increased risk o...

    Authors: I Merelli, F Viti and L Milanesi
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  41. Hospitals nowadays have to serve numerous patients with limited medical staff and equipment while maintaining healthcare quality. Clinical pathway informatics is regarded as an efficient way to solve a series ...

    Authors: Xian Yang, Rui Han, Yike Guo, Jeremy Bradley, Benita Cox, Robert Dickinson and Richard Kitney
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  42. Co-expression based Cancer Modules (CMs) are sets of genes that act in concert to carry out specific functions in different cancer types, and are constructed by exploiting gene expression profiles related to s...

    Authors: Matteo Re and Giorgio Valentini
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  43. Multifactorial diseases arise from complex patterns of interaction between a set of genetic traits and the environment. To fully capture the genetic biomarkers that jointly explain the heritability component o...

    Authors: Francesco Sambo, Emanuele Trifoglio, Barbara Di Camillo, Gianna M Toffolo and Claudio Cobelli
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  44. Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop,...

    Authors: Riccardo Bellazzi, Marco Masseroli, Shawn Murphy, Amnon Shabo and Paolo Romano
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  45. High-density oligonucleotide microarray is an appropriate technology for genomic analysis, and is particulary useful in the generation of transcriptional maps, ChIP-on-chip studies and re-sequencing of the gen...

    Authors: Víctor Segura, Alejandro Toledo-Arana, Maite Uzqueda, Iñigo Lasa and Arrate Muñoz-Barrutia
    Citation: BMC Bioinformatics 2012 13:222
    Content type: Research article Published on:

  46. Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores a...

    Authors: Christopher R Cabanski, Keary Cavin, Chris Bizon, Matthew D Wilkerson, Joel S Parker, Kirk C Wilhelmsen, Charles M Perou, JS Marron and D Neil Hayes
    Citation: BMC Bioinformatics 2012 13:221
    Content type: Software Published on:

  47. One of the crucial steps in regulation of gene expression is the binding of transcription factor(s) to specific DNA sequences. Knowledge of the binding affinity and specificity at a structural level between tr...

    Authors: Daniel Turner, RyangGuk Kim and Jun-tao Guo
    Citation: BMC Bioinformatics 2012 13:220
    Content type: Database Published on:

  48. Food security is an issue that has come under renewed scrutiny amidst concerns that substantial yield increases in cereal crops are required to feed the world’s booming population. Wheat is of fundamental impo...

    Authors: Paul A Wilkinson, Mark O Winfield, Gary LA Barker, Alexandra M Allen, Amanda Burridge, Jane A Coghill and Keith J Edwards
    Citation: BMC Bioinformatics 2012 13:219
    Content type: Database Published on:

  49. The epidermal growth factor receptor (EGFR) signaling pathway and angiogenesis in brain cancer act as an engine for tumor initiation, expansion and response to therapy. Since the existing literature does not h...

    Authors: Xiaoqiang Sun, Le Zhang, Hua Tan, Jiguang Bao, Costas Strouthos and Xiaobo Zhou
    Citation: BMC Bioinformatics 2012 13:218
    Content type: Software Published on:

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