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  1. Handling genotype data typed at hundreds of thousands of loci is very time-consuming and it is no exception for population structure inference. Therefore, we propose to apply PCA to the genotype data of a popu...

    Authors: Chih Lee, Ali Abdool and Chun-Hsi Huang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S73
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  2. Recent studies have shown genetic variation is the basis of the genome-wide disease association research. However, due to the high cost on genotyping large number of single nucleotide polymorphisms (SNPs), it ...

    Authors: Jun Wang, Mao-zu Guo and Chun-yu Wang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S71
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  3. Automated candidate gene prediction systems allow geneticists to hone in on disease genes more rapidly by identifying the most probable candidate genes linked to the disease phenotypes under investigation. Her...

    Authors: Erdahl T Teber, Jason Y Liu, Sara Ballouz, Diane Fatkin and Merridee A Wouters
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S69
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  4. Regions with copy number variations (in germline cells) or copy number alteration (in somatic cells) are of great interest for human disease gene mapping and cancer studies. They represent a new type of mutati...

    Authors: Wentian Li, Annette Lee and Peter K Gregersen
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S67
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  5. The key roles of epistatic interactions between multiple genetic variants in the pathogenesis of complex diseases notwithstanding, the detection of such interactions remains a great challenge in genome-wide as...

    Authors: Rui Jiang, Wanwan Tang, Xuebing Wu and Wenhui Fu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S65
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  6. The syndrome is the basic pathological unit and the key concept in traditional Chinese medicine (TCM) and the herbal remedy is prescribed according to the syndrome a patient catches. Nevertheless, few studies ...

    Authors: Jing Chen and Guangcheng Xi
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S63
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  8. MicroRNAs (miRNAs) are small and noncoding RNAs that play important roles in various biological processes. They regulate target mRNAs post-transcriptionally through complementary base pairing. Since the change...

    Authors: Je-Gun Joung and Zhangjun Fei
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S34
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  9. The detection of cis-regulatory modules (CRMs) that mediate transcriptional responses in eukaryotes remains a key challenge in the postgenomic era. A CRM is characterized by a set of co-occurring transcription fa...

    Authors: Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor and Kathleen Marchal
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S30
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  10. Posttranslational modifications of histones influence the structure of chromatine and in such a way take part in the regulation of gene expression. Certain histone modification patterns, distributed over the g...

    Authors: Corinna Kolářik, Roman Klinger and Martin Hofmann-Apitius
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S28
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  11. Gene expression microarray technologies are widely used across most areas of biological and medical research. Comparing and integrating microarray data from different experiments would be very useful, but is c...

    Authors: Reija Autio, Sami Kilpinen, Matti Saarela, Olli Kallioniemi, Sampsa Hautaniemi and Jaakko Astola
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S24
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  12. There is much interest in developing fast and accurate supertree methods to infer the tree of life. Supertree methods combine smaller input trees with overlapping sets of taxa to make a comprehensive phylogene...

    Authors: Harris T Lin, J Gordon Burleigh and Oliver Eulenstein
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  13. Given three signed permutations, an inversion median is a fourth permutation that minimizes the sum of the pairwise inversion distances between it and the three others. This problem is NP-hard as well as hard ...

    Authors: Krister M Swenson, Yokuki To, Jijun Tang and Bernard ME Moret
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  14. Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have...

    Authors: Sarah K Kummerfeld and Sarah A Teichmann
    Citation: BMC Bioinformatics 2009 10:39
    Content type: Research article Published on:

  15. Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight i...

    Authors: Roland Nilsson, Johan Björkegren and Jesper Tegnér
    Citation: BMC Bioinformatics 2009 10:38
    Content type: Research article Published on:

  16. Expression profiling assays done by using DNA microarray technology generate enormous data sets that are not amenable to simple analysis. The greatest challenge in maximizing the use of this huge amount of dat...

    Authors: Daniel Glez-Peña, Rodrigo Álvarez, Fernando Díaz and Florentino Fdez-Riverola
    Citation: BMC Bioinformatics 2009 10:37
    Content type: Software Published on:

  17. Protein-protein interactions (PPI) can be classified according to their characteristics into, for example obligate or transient interactions. The identification and characterization of these PPI types may help...

    Authors: Sung Hee Park, José A Reyes, David R Gilbert, Ji Woong Kim and Sangsoo Kim
    Citation: BMC Bioinformatics 2009 10:36
    Content type: Research article Published on:

  18. As sequencing costs have decreased, whole genome sequencing has become a viable and integral part of biological laboratory research. However, the tools with which genes can be found and functionally characteri...

    Authors: Andrew S Warren and João Carlos Setubal
    Citation: BMC Bioinformatics 2009 10:35
    Content type: Software Published on:

  19. 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:

  20. Since the transfer and application of modern sequencing technologies to the analysis of amplified fragment-length polymorphisms (AFLP), evolutionary biologists have included an increasing number of samples and...

    Authors: Nils Arrigo, Jarek W Tuszynski, Dorothee Ehrich, Tommy Gerdes and Nadir Alvarez
    Citation: BMC Bioinformatics 2009 10:33
    Content type: Research article Published on:

  21. 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:

  22. 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:

  25. 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:

  26. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  37. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  47. 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:

  49. 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:

  50. 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:

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