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  1. In the context of systems biology, few sparse approaches have been proposed so far to integrate several data sets. It is however an important and fundamental issue that will be widely encountered in post genom...

    Authors: Kim-Anh Lê Cao, Pascal GP Martin, Christèle Robert-Granié and Philippe Besse
    Citation: BMC Bioinformatics 2009 10:34
    Content type: Research article Published on:

  2. Structural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in livin...

    Authors: Georg Steinkellner, Robert Rader, Gerhard G Thallinger, Christoph Kratky and Karl Gruber
    Citation: BMC Bioinformatics 2009 10:32
    Content type: Software Published on:

  3. Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, prote...

    Authors: Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa and Masaru Tomita
    Citation: BMC Bioinformatics 2009 10:31
    Content type: Software Published on:

  6. Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approache...

    Authors: Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder and Thomas Wächter
    Citation: BMC Bioinformatics 2009 10:28
    Content type: Research article Published on:

  7. The landscape of biological and biomedical research is being changed rapidly with the invention of microarrays which enables simultaneous view on the transcription levels of a huge number of genes across diffe...

    Authors: Ujjwal Maulik, Anirban Mukhopadhyay and Sanghamitra Bandyopadhyay
    Citation: BMC Bioinformatics 2009 10:27
    Content type: Methodology article Published on:

  11. ChIP-chip data are routinely used to identify transcription factor binding targets. However, the presence of false positives and false negatives in ChIP-chip data complicates and hinders analyses, especially w...

    Authors: Debayan Datta and Hongyu Zhao
    Citation: BMC Bioinformatics 2009 10:23
    Content type: Methodology article Published on:

  12. The nucleus, a highly organized organelle, plays important role in cellular homeostasis. The nuclear proteins are crucial for chromosomal maintenance/segregation, gene expression, RNA processing/export, and ma...

    Authors: Manish Kumar and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2009 10:22
    Content type: Research article Published on:

  13. Protein-protein interaction (PPI) data sets generated by high-throughput experiments are contaminated by large numbers of erroneous PPIs. Therefore, computational methods for PPI validation are necessary to im...

    Authors: Christian Frech, Michael Kommenda, Viktoria Dorfer, Thomas Kern, Helmut Hintner, Johann W Bauer and Kamil Önder
    Citation: BMC Bioinformatics 2009 10:21
    Content type: Methodology article Published on:

  14. Microarray technology is commonly used as a simple screening tool with a focus on selecting genes that exhibit extremely large differential expressions between different phenotypes. It lacks the ability to sel...

    Authors: Rui Hu, Xing Qiu, Galina Glazko, Lev Klebanov and Andrei Yakovlev
    Citation: BMC Bioinformatics 2009 10:20
    Content type: Research article Published on:

  15. Network visualization would serve as a useful first step for analysis. However, current graph layout algorithms for biological pathways are insensitive to biologically important information, e.g. subcellular l...

    Authors: Tatsunori B Hashimoto, Masao Nagasaki, Kaname Kojima and Satoru Miyano
    Citation: BMC Bioinformatics 2009 10:19
    Content type: Research article Published on:

  18. Nowadays, microarray gene expression analysis is a widely used technology that scientists handle but whose final interpretation usually requires the participation of a specialist. The need for this participati...

    Authors: Victoria Martin-Requena, Antonio Muñoz-Merida, M Gonzalo Claros and Oswaldo Trelles
    Citation: BMC Bioinformatics 2009 10:16
    Content type: Software Published on:

  21. The interactions of multiple single nucleotide polymorphisms (SNPs) are highly hypothesized to affect an individual's susceptibility to complex diseases. Although many works have been done to identify and quan...

    Authors: Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson LS Tang and Weichuan Yu
    Citation: BMC Bioinformatics 2009 10:13
    Content type: Methodology article Published on:

  22. Array-based comparative genomic hybridization (CGH) is a commonly-used approach to detect DNA copy number variation in whole genome-wide screens. Several statistical methods have been proposed to define genomi...

    Authors: Kai Wang, Jian Li, Shengting Li, Lars Bolund and Carsten Wiuf
    Citation: BMC Bioinformatics 2009 10:12
    Content type: Methodology article Published on:

  23. Due to the large number of hypothesis tests performed during the process of routine analysis of microarray data, a multiple testing adjustment is certainly warranted. However, when the number of tests is very ...

    Authors: Amber J Hackstadt and Ann M Hess
    Citation: BMC Bioinformatics 2009 10:11
    Content type: Research article Published on:

  24. Some diseases, like tumors, can be related to chromosomal aberrations, leading to changes of DNA copy number. The copy number of an aberrant genome can be represented as a piecewise constant function, since it...

    Authors: Paola MV Rancoita, Marcus Hutter, Francesco Bertoni and Ivo Kwee
    Citation: BMC Bioinformatics 2009 10:10
    Content type: Research article Published on:

  28. We investigate automated and generic alphabet reduction techniques for protein structure prediction datasets. Reducing alphabet cardinality without losing key biochemical information opens the door to potentia...

    Authors: Jaume Bacardit, Michael Stout, Jonathan D Hirst, Alfonso Valencia, Robert E Smith and Natalio Krasnogor
    Citation: BMC Bioinformatics 2009 10:6
    Content type: Research article Published on:

  29. In high throughput screening, such as differential gene expression screening, drug sensitivity screening, and genome-wide RNAi screening, tens of thousands of tests need to be conducted simultaneously. However...

    Authors: Jing Cao, Xian-Jin Xie, Song Zhang, Angelique Whitehurst and Michael A White
    Citation: BMC Bioinformatics 2009 10:5
    Content type: Methodology article Published on:

  31. Affymetrix Genechips are characterized by probe pairs, a perfect match (PM) and a mismatch (MM) probe differing by a single nucleotide. Most of the data preprocessing algorithms neglect MM signals, as it was s...

    Authors: Alessandro Ferrantini, Joke Allemeersch, Paul Van Hummelen and Enrico Carlon
    Citation: BMC Bioinformatics 2009 10:3
    Content type: Methodology article Published on:

  32. Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile ...

    Authors: Steffen Durinck, James Bullard, Paul T Spellman and Sandrine Dudoit
    Citation: BMC Bioinformatics 2009 10:2
    Content type: Software Published on:

  33. In cancer studies, it is common that multiple microarray experiments are conducted to measure the same clinical outcome and expressions of the same set of genes. An important goal of such experiments is to ide...

    Authors: Shuangge Ma and Jian Huang
    Citation: BMC Bioinformatics 2009 10:1
    Content type: Methodology article Published on:

  34. Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns am...

    Authors: Peter Langfelder and Steve Horvath
    Citation: BMC Bioinformatics 2008 9:559
    Content type: Software Published on:

  35. Microarray analysis allows the simultaneous measurement of thousands to millions of genes or sequences across tens to thousands of different samples. The analysis of the resulting data tests the limits of exis...

    Authors: Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence M Sloan, Florian Scharinger, Arthur Trew and Peter Ghazal
    Citation: BMC Bioinformatics 2008 9:558
    Content type: Software Published on:

  37. Protein structural alignment provides a fundamental basis for deriving principles of functional and evolutionary relationships. It is routinely used for structural classification and functional characterizatio...

    Authors: Walter Pirovano, K Anton Feenstra and Jaap Heringa
    Citation: BMC Bioinformatics 2008 9:556
    Content type: Research article Published on:

  38. Reverse Phase Protein Arrays (RPPA) are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies, substantial amounts of analytical dat...

    Authors: Romesh Stanislaus, Mark Carey, Helena F Deus, Kevin Coombes, Bryan T Hennessy, Gordon B Mills and Jonas S Almeida
    Citation: BMC Bioinformatics 2008 9:555
    Content type: Research article Published on:

  39. Multiple sequence alignments are a fundamental tool for the comparative analysis of proteins and nucleic acids. However, large data sets are no longer manageable for visualization and investigation using the t...

    Authors: Alberto I Roca, Albert E Almada and Aaron C Abajian
    Citation: BMC Bioinformatics 2008 9:554
    Content type: Software Published on:

  41. High-throughput methods that allow for measuring the expression of thousands of genes or proteins simultaneously have opened new avenues for studying biochemical processes. While the noisiness of the data nece...

    Authors: Andreas Keller, Christina Backes, Maher Al-Awadhi, Andreas Gerasch, Jan Küntzer, Oliver Kohlbacher, Michael Kaufmann and Hans-Peter Lenhof
    Citation: BMC Bioinformatics 2008 9:552
    Content type: Software Published on:

  42. Phylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. However, the evolutionary profile...

    Authors: Matteo Brilli, Alessio Mengoni, Marco Fondi, Marco Bazzicalupo, Pietro Liò and Renato Fani
    Citation: BMC Bioinformatics 2008 9:551
    Content type: Research article Published on:

  43. Continuous-time Markov models allow flexible, parametrically succinct descriptions of sequence divergence. Non-reversible forms of these models are more biologically realistic but are challenging to develop. T...

    Authors: Harold W Schranz, Von Bing Yap, Simon Easteal, Rob Knight and Gavin A Huttley
    Citation: BMC Bioinformatics 2008 9:550
    Content type: Research article Published on:

  44. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objecti...

    Authors: Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar and Lincoln D Stein
    Citation: BMC Bioinformatics 2008 9:549
    Content type: Research article Published on:

  45. The amount of gene expression data in the public repositories, such as NCBI Gene Expression Omnibus (GEO) has grown exponentially, and provides a gold mine for bioinformaticians, but has not been easily access...

    Authors: Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam and Atul J Butte
    Citation: BMC Bioinformatics 2008 9:548
    Content type: Software Published on:

  47. Each genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of ...

    Authors: Fengfeng Zhou, Victor Olman and Ying Xu
    Citation: BMC Bioinformatics 2008 9:546
    Content type: Research article Published on:

  48. Experimental examinations of biofluids to measure concentrations of proteins or their fragments or metabolites are being explored as a means of early disease detection, distinguishing diseases with similar sym...

    Authors: Brian T Luke and Jack R Collins
    Citation: BMC Bioinformatics 2008 9:545
    Content type: Research article Published on:

  49. Enzymes are responsible for the catalysis of the biochemical reactions in metabolic pathways. Analogous enzymes are able to catalyze the same reactions, but they present no significant sequence similarity at t...

    Authors: Thomas D Otto, Ana Carolina R Guimarães, Wim M Degrave and Antonio B de Miranda
    Citation: BMC Bioinformatics 2008 9:544
    Content type: Software Published on:

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