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  1. Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-ca...

    Authors: Filip Bielejec, Philippe Lemey, Luiz Max Carvalho, Guy Baele, Andrew Rambaut and Marc A Suchard
    Citation: BMC Bioinformatics 2014 15:133
    Content type: Software Published on:

  3. Current-generation sequencing technologies are able to produce low-cost, high-throughput reads. However, the produced reads are imperfect and may contain various sequencing errors. Although many error correcti...

    Authors: Adrianto Wirawan, Robert S Harris, Yongchao Liu, Bertil Schmidt and Jan Schröder
    Citation: BMC Bioinformatics 2014 15:131
    Content type: Methodology article Published on:

  4. Biclustering is a critical task for biomedical applications. Order-preserving biclusters, submatrices where the values of rows induce the same linear ordering across columns, capture local regularities with co...

    Authors: Rui Henriques and Sara C Madeira
    Citation: BMC Bioinformatics 2014 15:130
    Content type: Research article Published on:

  5. Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism’s processes...

    Authors: Gustavo A Salazar, Ayton Meintjes, Gaston K Mazandu, Holifidy A Rapanoël, Richard O Akinola and Nicola J Mulder
    Citation: BMC Bioinformatics 2014 15:129
    Content type: Software Published on:

  6. Cancer patient's outcome is written, in part, in the gene expression profile of the tumor. We previously identified a 62-probe sets signature (NB-hypo) to identify tissue hypoxia in neuroblastoma tumors and sh...

    Authors: Davide Cangelosi, Marco Muselli, Stefano Parodi, Fabiola Blengio, Pamela Becherini, Rogier Versteeg, Massimo Conte and Luigi Varesio
    Citation: BMC Bioinformatics 2014 15(Suppl 5):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 5

  7. Time-course gene expression experiments are useful tools for exploring biological processes. In this type of experiments, gene expression changes are monitored along time. Unfortunately, replication of time se...

    Authors: Paolo Martini, Gabriele Sales, Enrica Calura, Stefano Cagnin, Monica Chiogna and Chiara Romualdi
    Citation: BMC Bioinformatics 2014 15(Suppl 5):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 5

  8. The huge quantity of data produced in Biomedical research needs sophisticated algorithmic methodologies for its storage, analysis, and processing. High Performance Computing (HPC) appears as a magic bullet in ...

    Authors: Gianni D'Angelo and Salvatore Rampone
    Citation: BMC Bioinformatics 2014 15(Suppl 5):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 5

  9. Molecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measure...

    Authors: Safwat Abdel-Azeim, Edrisse Chermak, Anna Vangone, Romina Oliva and Luigi Cavallo
    Citation: BMC Bioinformatics 2014 15(Suppl 5):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 5

  10. Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for ...

    Authors: Ralf Stefan Neumann, Surendra Kumar, Thomas Hendricus Augustus Haverkamp and Kamran Shalchian-Tabrizi
    Citation: BMC Bioinformatics 2014 15:128
    Content type: Software Published on:

  11. Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard co...

    Authors: Leo van Iersel, Steven Kelk, Nela Lekić and Celine Scornavacca
    Citation: BMC Bioinformatics 2014 15:127
    Content type: Research article Published on:

  12. The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to ...

    Authors: Sergey Koren, Todd J Treangen, Christopher M Hill, Mihai Pop and Adam M Phillippy
    Citation: BMC Bioinformatics 2014 15:126
    Content type: Software Published on:

  13. Genotypes generated in next generation sequencing studies contain errors which can significantly impact the power to detect signals in common and rare variant association tests. These genotyping errors are not...

    Authors: Andrew R Carson, Erin N Smith, Hiroko Matsui, Sigrid K Brækkan, Kristen Jepsen, John-Bjarne Hansen and Kelly A Frazer
    Citation: BMC Bioinformatics 2014 15:125
    Content type: Methodology article Published on:

  14. Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-m...

    Authors: Ivani de ON Lopes, Alexander Schliep and André CP de LF de Carvalho
    Citation: BMC Bioinformatics 2014 15:124
    Content type: Research article Published on:

  16. RNA-seq and its variant differential RNA-seq (dRNA-seq) are today routine methods for transcriptome analysis in bacteria. While expression profiling and transcriptional start site prediction are standard tasks...

    Authors: Thorsten Bischler, Matthias Kopf and Björn Voß
    Citation: BMC Bioinformatics 2014 15:122
    Content type: Software Published on:

  18. It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein mode...

    Authors: Renzhi Cao, Zheng Wang, Yiheng Wang and Jianlin Cheng
    Citation: BMC Bioinformatics 2014 15:120
    Content type: Software Published on:

  20. The identification of functionally important residue positions is an important task of computational biology. Methods of correlation analysis allow for the identification of pairs of residue positions, whose o...

    Authors: Jan-Oliver Janda, Ajmal Popal, Jochen Bauer, Markus Busch, Michael Klocke, Wolfgang Spitzer, Jörg Keller and Rainer Merkl
    Citation: BMC Bioinformatics 2014 15:118
    Content type: Methodology article Published on:

  21. A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a d...

    Authors: Barbara Mirel and Carsten Görg
    Citation: BMC Bioinformatics 2014 15:117
    Content type: Commentary Published on:

  22. Complex designs are common in (observational) clinical studies. Sequencing data for such studies are produced more and more often, implying challenges for the analysis, such as excess of zeros, presence of ran...

    Authors: Mark A van de Wiel, Maarten Neerincx, Tineke E Buffart, Daoud Sie and Henk MW Verheul
    Citation: BMC Bioinformatics 2014 15:116
    Content type: Software Published on:

  23. It is of great importance to identify molecular processes and pathways that are involved in disease etiology. Although there has been an extensive use of various high-throughput methods for this task, pathogen...

    Authors: Ståle Nygård, Trond Reitan, Trevor Clancy, Vegard Nygaard, Johannes Bjørnstad, Biljana Skrbic, Theis Tønnessen, Geir Christensen and Eivind Hovig
    Citation: BMC Bioinformatics 2014 15:115
    Content type: Methodology article Published on:

  24. Studies involving the analysis of structural variation including Copy Number Variation (CNV) have recently exploded in the literature. Furthermore, CNVs have been associated with a number of complex diseases a...

    Authors: Christina A Castellani, Melkaye G Melka, Andrea E Wishart, M Elizabeth O Locke, Zain Awamleh, Richard L O’Reilly and Shiva M Singh
    Citation: BMC Bioinformatics 2014 15:114
    Content type: Research article Published on:

  25. The aim of connectivity mapping is to match drugs using drug-treatment gene expression profiles from multiple cell lines. This can be viewed as an information retrieval task, with the goal of finding the most ...

    Authors: Juuso A Parkkinen and Samuel Kaski
    Citation: BMC Bioinformatics 2014 15:113
    Content type: Methodology article Published on:

  26. Bacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the archetypal Bacteroides thetaiotaomicron genome identi...

    Authors: Anna Sheydina, Ruth Y Eberhardt, Daniel J Rigden, Yuanyuan Chang, Zhanwen Li, Christian C Zmasek, Herbert L Axelrod and Adam Godzik
    Citation: BMC Bioinformatics 2014 15:112
    Content type: Research article Published on:

  27. Small insertion and deletion polymorphisms (Indels) are the second most common mutations in the human genome, after Single Nucleotide Polymorphisms (SNPs). Recent studies have shown that they have significant ...

    Authors: Carlos Bermejo-Das-Neves, Hoan-Ngoc Nguyen, Olivier Poch and Julie D Thompson
    Citation: BMC Bioinformatics 2014 15:111
    Content type: Research article Published on:

  28. Integrating and analyzing heterogeneous genome-scale data is a huge algorithmic challenge for modern systems biology. Bipartite graphs can be useful for representing relationships across pairs of disparate dat...

    Authors: Yun Zhang, Charles A Phillips, Gary L Rogers, Erich J Baker, Elissa J Chesler and Michael A Langston
    Citation: BMC Bioinformatics 2014 15:110
    Content type: Methodology article Published on:

  31. Tuberculosis is an infectious bacterial disease caused by Mycobacterium tuberculosis. It remains a major health threat, killing over one million people every year worldwide. An early antibiotic therapy is the bas...

    Authors: Jean-Pierre Flandrois, Gérard Lina and Oana Dumitrescu
    Citation: BMC Bioinformatics 2014 15:107
    Content type: Database Published on:

  32. Artificial neural networks (ANNs) have been used to classify eye diseases, such as diabetic retinopathy (DR) and glaucoma. DR is the leading cause of blindness in working-age adults in the developed world. The...

    Authors: Gábor Márk Somfai, Erika Tátrai, Lenke Laurik, Boglárka Varga, Veronika Ölvedy, Hong Jiang, Jianhua Wang, William E Smiddy, Anikó Somogyi and Delia Cabrera DeBuc
    Citation: BMC Bioinformatics 2014 15:106
    Content type: Research article Published on:

  34. Accurate genomic variant detection is an essential step in gleaning medically useful information from genome data. However, low concordance among variant-calling methods reduces confidence in the clinical vali...

    Authors: Brandi L Cantarel, Daniel Weaver, Nathan McNeill, Jianhua Zhang, Aaron J Mackey and Justin Reese
    Citation: BMC Bioinformatics 2014 15:104
    Content type: Software Published on:

  35. Protein–protein interactions can be seen as a hierarchical process occurring at three related levels: proteins bind by means of specific domains, which in turn form interfaces through patches of residues. Detaile...

    Authors: Claudio Saccà, Stefano Teso, Michelangelo Diligenti and Andrea Passerini
    Citation: BMC Bioinformatics 2014 15:103
    Content type: Methodology article Published on:

  37. It is a common practice in bioinformatics to validate each group returned by a clustering algorithm through manual analysis, according to a-priori biological knowledge. This procedure helps finding functionally r...

    Authors: Diego H Milone, Georgina Stegmayer, Mariana López, Laura Kamenetzky and Fernando Carrari
    Citation: BMC Bioinformatics 2014 15:101
    Content type: Research article Published on:

  39. Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily r...

    Authors: Birte Kehr, Kathrin Trappe, Manuel Holtgrewe and Knut Reinert
    Citation: BMC Bioinformatics 2014 15:99
    Content type: Research article Published on:

  40. Measuring the impact of combinations of genetic or chemical perturbations on cellular fitness, sometimes referred to as synthetic lethal screening, is a powerful method for obtaining novel insights into gene f...

    Authors: Markus K Muellner, Gerhard Duernberger, Florian Ganglberger, Claudia Kerzendorfer, Iris Z Uras, Andreas Schoenegger, Klaudia Bagienski, Jacques Colinge and Sebastian MB Nijman
    Citation: BMC Bioinformatics 2014 15:98
    Content type: Software Published on:

  41. Over the last decade, metabolomics has evolved into a mainstream enterprise utilized by many laboratories globally. Like other “omics” data, metabolomics data has the characteristics of a smaller sample size c...

    Authors: Suyan Tian, Howard H Chang, Chi Wang, Jing Jiang, Xiaomei Wang and Junqi Niu
    Citation: BMC Bioinformatics 2014 15:97
    Content type: Research article Published on:

  42. The identification of functionally or structurally important non-conserved residue sites in protein MSAs is an important challenge for understanding the structural basis and molecular mechanism of protein func...

    Authors: Mehmet Gültas, Güncel Düzgün, Sebastian Herzog, Sven Joachim Jäger, Cornelia Meckbach, Edgar Wingender and Stephan Waack
    Citation: BMC Bioinformatics 2014 15:96
    Content type: Methodology article Published on:

  44. In this study we consider DNA sequences as mathematical strings. Total and reduced alignments between two DNA sequences have been considered in the literature to measure their similarity. Results for explicit ...

    Authors: Helena Andrade, Iván Area, Juan J Nieto and Ángela Torres
    Citation: BMC Bioinformatics 2014 15:94
    Content type: Research article Published on:

  45. Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software...

    Authors: Bastiaan A van den Berg, Marcel JT Reinders, Johannes A Roubos and Dick de Ridder
    Citation: BMC Bioinformatics 2014 15:93
    Content type: Software Published on:

  47. High-throughput sequencing is now regularly used for studies of the transcriptome (RNA-seq), particularly for comparisons among experimental conditions. For the time being, a limited number of biological repli...

    Authors: Andrea Rau, Guillemette Marot and Florence Jaffrézic
    Citation: BMC Bioinformatics 2014 15:91
    Content type: Methodology article Published on:

  49. Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (TSS) ...

    Authors: Fabian Amman, Michael T Wolfinger, Ronny Lorenz, Ivo L Hofacker, Peter F Stadler and Sven Findeiß
    Citation: BMC Bioinformatics 2014 15:89
    Content type: Software Published on:

  50. The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. T...

    Authors: Brett Hanson, Charles Westin, Mario Rosa, Alexander Grier, Mikhail Osipovitch, Madolyn L MacDonald, Greg Dodge, Paule M Boli, Cyprian W Corwin, Haeja Kessler, Talia McKay, Herbert J Bernstein and Paul A Craig
    Citation: BMC Bioinformatics 2014 15:87
    Content type: Software Published on:

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