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  2. The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of ge...

    Authors: Doug Hyatt, Gwo-Liang Chen, Philip F LoCascio, Miriam L Land, Frank W Larimer and Loren J Hauser
    Citation: BMC Bioinformatics 2010 11:119
    Content type: Software Published on:

  3. High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables ...

    Authors: Chongle Pan, Byung H Park, William H McDonald, Patricia A Carey, Jillian F Banfield, Nathan C VerBerkmoes, Robert L Hettich and Nagiza F Samatova
    Citation: BMC Bioinformatics 2010 11:118
    Content type: Research article Published on:

  5. The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models,...

    Authors: Daniel Wegmann, Christoph Leuenberger, Samuel Neuenschwander and Laurent Excoffier
    Citation: BMC Bioinformatics 2010 11:116
    Content type: Software Published on:

  8. Efficient dissection of large proteins into their structural domains is critical for high throughput proteome analysis. So far, no study has focused on mathematically modeling a protein dissection protocol in ...

    Authors: Eisuke Chikayama, Atsushi Kurotani, Takanori Tanaka, Takashi Yabuki, Satoshi Miyazaki, Shigeyuki Yokoyama and Yutaka Kuroda
    Citation: BMC Bioinformatics 2010 11:113
    Content type: Research article Published on:

  9. Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors,...

    Authors: Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W Hentze, Thomas Dandekar and Martina U Muckenthaler
    Citation: BMC Bioinformatics 2010 11:112
    Content type: Software Published on:

  11. Random forests (RF) have been increasingly used in applications such as genome-wide association and microarray studies where predictor correlation is frequently observed. Recent works on permutation-based vari...

    Authors: Kristin K Nicodemus, James D Malley, Carolin Strobl and Andreas Ziegler
    Citation: BMC Bioinformatics 2010 11:110
    Content type: Research article Published on:

  13. Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository ha...

    Authors: Timothy J Robinson, Michaela A Dinan, Mark Dewhirst, Mariano A Garcia-Blanco and James L Pearson
    Citation: BMC Bioinformatics 2010 11:108
    Content type: Methodology article Published on:

  15. 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:

  16. 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:

  17. 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:

  18. In the current era of scientific research, efficient communication of information is paramount. As such, the nature of scholarly and scientific communication is changing; cyberinfrastructure is now absolutely ...

    Authors: J Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex Wade, Oscar Naim, Gregory B Quinn and Philip E Bourne
    Citation: BMC Bioinformatics 2010 11:103
    Content type: Software Published on:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  27. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  34. 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:

  37. 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:

  40. 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:

  41. 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:

  42. 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:

  45. 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:

  47. 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:

  48. 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:

  49. 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:

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