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  1. SpectraClassifier (SC) is a Java solution for designing and implementing Magnetic Resonance Spectroscopy (MRS)-based classifiers. The main goal of SC is to allow users with minimum background knowledge of multiva...

    Authors: Sandra Ortega-Martorell, Iván Olier, Margarida Julià-Sapé and Carles Arús
    Citation: BMC Bioinformatics 2010 11:106
    Content type: Software Published on:

  2. Estimation of DNA duplex hybridization free energy is widely used for predicting cross-hybridizations in DNA computing and microarray experiments. A number of software programs based on different methods and p...

    Authors: Dan Tulpan, Mirela Andronescu and Serge Leger
    Citation: BMC Bioinformatics 2010 11:105
    Content type: Research article Published on:

  3. Affymetrix GeneChip microarrays are popular platforms for expression profiling in two types of studies: detection of differential expression computed by p-values of t-test and estimation of fold change between an...

    Authors: Jakub Mieczkowski, Magdalena E Tyburczy, Michal Dabrowski and Piotr Pokarowski
    Citation: BMC Bioinformatics 2010 11:104
    Content type: Methodology article Published on:

  4. Overlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, they are ubiquitous in microbial genomes and more conserved between species than non-overlap...

    Authors: Chih-Hsien Cheng, Chung-Han Yang, Hsien-Tai Chiu and Chin Lung Lu
    Citation: BMC Bioinformatics 2010 11:102
    Content type: Research article Published on:

  5. In HIV treatment it is critical to have up-to-date resistance data of applicable drugs since HIV has a very high rate of mutation. These data are made available through scientific publications and must be extr...

    Authors: Quoc-Chinh Bui, Breanndán Ó Nualláin, Charles A Boucher and Peter MA Sloot
    Citation: BMC Bioinformatics 2010 11:101
    Content type: Research article Published on:

  6. New "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arise...

    Authors: Stacy Duncan, Ruchita Sirkanungo, Leslie Miller and Gregory J Phillips
    Citation: BMC Bioinformatics 2010 11:100
    Content type: Software Published on:

  7. Predicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher the protein function, and useful in drug design. A classical assumption in structural b...

    Authors: Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe Vert and Véronique Stoven
    Citation: BMC Bioinformatics 2010 11:99
    Content type: Research article Published on:

  8. The recognition of functional binding sites in genomic DNA remains one of the fundamental challenges of genome research. During the last decades, a plethora of different and well-adapted models has been develo...

    Authors: Jens Keilwagen, Jan Grau, Stefan Posch, Marc Strickert and Ivo Grosse
    Citation: BMC Bioinformatics 2010 11:98
    Content type: Methodology article Published on:

  9. The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for ...

    Authors: Alessandro Pandini, Arianna Fornili and Jens Kleinjung
    Citation: BMC Bioinformatics 2010 11:97
    Content type: Research article Published on:

  10. Finding the subgraphs of a graph database that are isomorphic to a given query graph has practical applications in several fields, from cheminformatics to image understanding. Since subgraph isomorphism is a c...

    Authors: Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti and Dennis Shasha
    Citation: BMC Bioinformatics 2010 11:96
    Content type: Methodology article Published on:

  12. High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods a...

    Authors: James H Bullard, Elizabeth Purdom, Kasper D Hansen and Sandrine Dudoit
    Citation: BMC Bioinformatics 2010 11:94
    Content type: Research article Published on:

  14. Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. Howev...

    Authors: Yaping Feng, Andrzej Kloczkowski and Robert L Jernigan
    Citation: BMC Bioinformatics 2010 11:92
    Content type: Software Published on:

  15. The increasing availability and diversity of omics data in the post-genomic era offers new perspectives in most areas of biomedical research. Graph-based biological networks models capture the topology of the ...

    Authors: Alexander Martin, Maria E Ochagavia, Laya C Rabasa, Jamilet Miranda, Jorge Fernandez-de-Cossio and Ricardo Bringas
    Citation: BMC Bioinformatics 2010 11:91
    Content type: Software Published on:

  16. Experimental screening of large sets of peptides with respect to their MHC binding capabilities is still very demanding due to the large number of possible peptide sequences and the extensive polymorphism of t...

    Authors: Kirsten Roomp, Iris Antes and Thomas Lengauer
    Citation: BMC Bioinformatics 2010 11:90
    Content type: Research article Published on:

  17. Detection of common evolutionary origin (homology) is a primary means of inferring protein structure and function. At present, comparison of protein families represented as sequence profiles is arguably the mo...

    Authors: Mindaugas Margelevičius and Česlovas Venclovas
    Citation: BMC Bioinformatics 2010 11:89
    Content type: Research article Published on:

  19. Systems biologists are faced with the difficultly of analyzing results from large-scale studies that profile the activity of many genes, RNAs and proteins, applied in different experiments, under different con...

    Authors: Alexander Lachmann and Avi Ma'ayan
    Citation: BMC Bioinformatics 2010 11:87
    Content type: Software Published on:

  22. Image analysis is an essential component in many biological experiments that study gene expression, cell cycle progression, and protein localization. A protocol for tracking the expression of individual C. elegan...

    Authors: Zafer Aydin, John I Murray, Robert H Waterston and William S Noble
    Citation: BMC Bioinformatics 2010 11:84
    Content type: Research article Published on:

  25. ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of protein-DNA interactions in vivo in the genome. H...

    Authors: Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A Wilson and Dabing Zhang
    Citation: BMC Bioinformatics 2010 11:81
    Content type: Research article Published on:

  26. Genome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and which score parameters to use. Surprisingly, there ...

    Authors: Martin C Frith, Michiaki Hamada and Paul Horton
    Citation: BMC Bioinformatics 2010 11:80
    Content type: Research article Published on:

  27. All polypeptide backbones have the potential to form amyloid fibrils, which are associated with a number of degenerative disorders. However, the likelihood that amyloidosis would actually occur under physiolog...

    Authors: Maria Pamela C David, Gisela P Concepcion and Eduardo A Padlan
    Citation: BMC Bioinformatics 2010 11:79
    Content type: Research article Published on:

  30. Hundreds of genes that are causally implicated in oncogenesis have been found and collected in various databases. For efficient application of these abundant but diverse data sources, it is of fundamental impo...

    Authors: Xue Gong, Ruihong Wu, Yuannv Zhang, Wenyuan Zhao, Lixin Cheng, Yunyan Gu, Lin Zhang, Jing Wang, Jing Zhu and Zheng Guo
    Citation: BMC Bioinformatics 2010 11:76
    Content type: Research article Published on:

  32. Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasin...

    Authors: Xiaowu Gai, Juan C Perin, Kevin Murphy, Ryan O'Hara, Monica D'arcy, Adam Wenocur, Hongbo M Xie, Eric F Rappaport, Tamim H Shaikh and Peter S White
    Citation: BMC Bioinformatics 2010 11:74
    Content type: Software Published on:

  33. The development of DNA microarrays has facilitated the generation of hundreds of thousands of transcriptomic datasets. The use of a common reference microarray design allows existing transcriptomic data to be ...

    Authors: Mark J Alston, John Seers, Jay CD Hinton and Sacha Lucchini
    Citation: BMC Bioinformatics 2010 11:73
    Content type: Software Published on:

  34. Tag-based techniques, such as SAGE, are commonly used to sample the mRNA pool of an organism's transcriptome. Incomplete digestion during the tag formation process may allow for multiple tags to be generated f...

    Authors: Russell L Zaretzki, Michael A Gilchrist, William M Briggs and Artin Armagan
    Citation: BMC Bioinformatics 2010 11:72
    Content type: Methodology article Published on:

  36. Biological knowledge is represented in scientific literature that often describes the function of genes/proteins (bioentities) in terms of their interactions (biointeractions). Such bioentities are often relat...

    Authors: Adriano Barbosa-Silva, Theodoros G Soldatos, Ivan LF Magalhães, Georgios A Pavlopoulos, Jean-Fred Fontaine, Miguel A Andrade-Navarro, Reinhard Schneider and J Miguel Ortega
    Citation: BMC Bioinformatics 2010 11:70
    Content type: Software Published on:

  37. Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacter...

    Authors: Bram Slabbinck, Willem Waegeman, Peter Dawyndt, Paul De Vos and Bernard De Baets
    Citation: BMC Bioinformatics 2010 11:69
    Content type: Research article Published on:

  39. Multiplex Ligation-Dependent Probe Amplification (MLPA) is an application that can be used for the detection of multiple chromosomal aberrations in a single experiment. In one reaction, up to 50 different geno...

    Authors: Ronald van Eijk, Paul HC Eilers, Remco Natté, Anne-Marie Cleton-Jansen, Hans Morreau, Tom van Wezel and Jan Oosting
    Citation: BMC Bioinformatics 2010 11:67
    Content type: Software Published on:

  41. Natural selection eliminates detrimental and favors advantageous phenotypes. This process leaves characteristic signatures in underlying genomic segments that can be recognized through deviations in allelic or...

    Authors: Julie Hussin, Philippe Nadeau, Jean-François Lefebvre and Damian Labuda
    Citation: BMC Bioinformatics 2010 11:65
    Content type: Methodology article Published on:

  43. Sustained research on the problem of determining which genes are differentially expressed on the basis of microarray data has yielded a plethora of statistical algorithms, each justified by theory, simulation,...

    Authors: Corey M Yanofsky and David R Bickel
    Citation: BMC Bioinformatics 2010 11:63
    Content type: Methodology article Published on:

  44. The ability to design thermostable proteins is theoretically important and practically useful. Robust and accurate algorithms, however, remain elusive. One critical problem is the lack of reliable methods to e...

    Authors: Yunqi Li, C Russell Middaugh and Jianwen Fang
    Citation: BMC Bioinformatics 2010 11:62
    Content type: Research article Published on:

  45. Codon bias is believed to play an important role in the control of gene expression. In Escherichia coli, some rare codons, which can limit the expression level of exogenous protein, have been defined by gene engi...

    Authors: Xianming Wu, Songfeng Wu, Dong Li, Jiyang Zhang, Lin Hou, Jie Ma, Wanlin Liu, Daming Ren, Yunping Zhu and Fuchu He
    Citation: BMC Bioinformatics 2010 11:61
    Content type: Research article Published on:

  46. Microarray experiments examine the change in transcript levels of tens of thousands of genes simultaneously. To derive meaningful data, biologists investigate the response of genes within specific pathways. Pa...

    Authors: Mayer Alvo, Zhongzhu Liu, Andrew Williams and Carole Yauk
    Citation: BMC Bioinformatics 2010 11:60
    Content type: Methodology article Published on:

  48. The success achieved by genome-wide association (GWA) studies in the identification of candidate loci for complex diseases has been accompanied by an inability to explain the bulk of heritability. Here, we des...

    Authors: Benjamin A Logsdon, Gabriel E Hoffman and Jason G Mezey
    Citation: BMC Bioinformatics 2010 11:58
    Content type: Methodology article Published on:

  49. Enzymes belonging to acyl:CoA synthetase (ACS) superfamily activate wide variety of substrates and play major role in increasing the structural and functional diversity of various secondary metabolites in micr...

    Authors: Pankaj Khurana, Rajesh S Gokhale and Debasisa Mohanty
    Citation: BMC Bioinformatics 2010 11:57
    Content type: Research article Published on:

  50. The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, ...

    Authors: Javier Garcia-Garcia, Emre Guney, Ramon Aragues, Joan Planas-Iglesias and Baldo Oliva
    Citation: BMC Bioinformatics 2010 11:56
    Content type: Software Published on:

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