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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. We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G1 and G2, with both mutation ...

    Authors: Laxmi Parida, Asif Javed, Marta Melé, Francesc Calafell and Jaume Bertranpetit
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S72
    Content type: Research Published on:

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

  3. 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

  4. 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

  5. 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

  6. Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is im...

    Authors: Jan Freudenberg, Mingyi Wang, Yaning Yang and Wentian Li
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S66
    Content type: Research Published on:

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

  7. 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

  8. 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

  9. The COMPARABILITY EDITING problem appears in the context of hierarchical disease classification based on noisy data. We are given a directed graph G representing hierarchical relationships between patient subgrou...

    Authors: Sebastian Böcker, Sebastian Briesemeister and Gunnar W Klau
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S61
    Content type: Research Published on:

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

  11. Considerable efforts have been made to extract protein-protein interactions from the biological literature, but little work has been done on the extraction of interaction detection methods. It is crucial to an...

    Authors: Hongning Wang, Minlie Huang and Xiaoyan Zhu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S55
    Content type: Research Published on:

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

  12. Tandem mass spectrometry has become particularly useful for the rapid identification and characterization of protein components of complex biological mixtures. Powerful database search methods have been develo...

    Authors: An-Min Zou, Fang-Xiang Wu, Jia-Rui Ding and Guy G Poirier
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S49
    Content type: Research Published on:

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

  13. Protein subcellular localization is concerned with predicting the location of a protein within a cell using computational method. The location information can indicate key functionalities of proteins. Accurate...

    Authors: Qian Xu, Derek Hao Hu, Hong Xue, Weichuan Yu and Qiang Yang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S47
    Content type: Research Published on:

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

  14. Amyloid fibrillar aggregates of proteins or polypeptides are known to be associated with many human diseases. Recent studies suggest that short protein regions trigger this aggregation. Thus, identifying these...

    Authors: Jian Tian, Ningfeng Wu, Jun Guo and Yunliu Fan
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S45
    Content type: Research Published on:

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

  15. Protein subcellular localization is crucial information to elucidate protein functions. Owing to the need for large-scale genome analysis, computational method for efficiently predicting protein subcellular lo...

    Authors: Thai Quang Tung and Doheon Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S43
    Content type: Research Published on:

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

  16. In pandemic and epidemic forms, avian and human influenza viruses often cause significant damage to human society and economics. Gradually accumulated mutations on hemagglutinin (HA) cause immunologically dist...

    Authors: Jhang-Wei Huang, Chwan-Chuen King and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S41
    Content type: Research Published on:

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

  18. The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-...

    Authors: Fenix WD Huang, Linda YM Li and Christian M Reidys
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S39
    Content type: Research Published on:

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

  19. In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers o...

    Authors: Fei Xia, Yong Dou, Xingming Zhou, Xuejun Yang, Jiaqing Xu and Yang Zhang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S37
    Content type: Research Published on:

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

  20. MicroRNA s (miRNAs) are small non-coding single-stranded RNAs (20–23 nts) that are known to act as post-transcriptional and translational regulators of gene expression. Although, they were initially overlooked, t...

    Authors: Sabah Kadri, Veronica Hinman and Panayiotis V Benos
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S35
    Content type: Research Published on:

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

  21. 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

  22. Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucle...

    Authors: Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Yangyang Deng, Jiang Wang and Caisheng He
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S31
    Content type: Research Published on:

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

  23. 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

  24. A "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region bet...

    Authors: Quan Wang, Lin Wan, Dayong Li, Lihuang Zhu, Minping Qian and Minghua Deng
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S29
    Content type: Research Published on:

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

  25. 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

  26. Biclustering algorithms belong to a distinct class of clustering algorithms that perform simultaneous clustering of both rows and columns of the gene expression matrix and can be a very useful analysis tool wh...

    Authors: Smitha Dharan and Achuthsankar S Nair
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S27
    Content type: Research Published on:

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

  27. 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

  28. Most machine-learning classifiers output label predictions for new instances without indicating how reliable the predictions are. The applicability of these classifiers is limited in critical domains where inc...

    Authors: Fan Yang, Hua-zhen Wang, Hong Mi, Cheng-de Lin and Wei-wen Cai
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S22
    Content type: Research Published on:

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

  29. Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods h...

    Authors: Martin H van Vliet, Lodewyk FA Wessels and Marcel JT Reinders
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S20
    Content type: Research Published on:

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

  30. Alternative splicing (AS) is an important regulatory mechanism for gene expression and protein diversity in eukaryotes. Previous studies have demonstrated that it can be causative for, or specific to splicing-...

    Authors: Hao Zheng, Xingyi Hang, Ji Zhu, Minping Qian, Wubin Qu, Chenggang Zhang and Minghua Deng
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S18
    Content type: Research Published on:

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

  31. New short-read sequencing technologies produce enormous volumes of 25–30 base paired-end reads. The resulting reads have vastly different characteristics than produced by Sanger sequencing, and require differe...

    Authors: Mohammad Sajjad Hossain, Navid Azimi and Steven Skiena
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S16
    Content type: Research Published on:

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

  32. The de novo assembly of genomes and transcriptomes from short sequences is a challenging problem. Because of the high coverage needed to assemble short sequences as well as the overhead of modeling the assembly p...

    Authors: Benjamin G Jackson, Patrick S Schnable and Srinivas Aluru
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S14
    Content type: Research Published on:

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

  33. The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorith...

    Authors: Dimitris Papamichail and Georgios Papamichail
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S10
    Content type: Research Published on:

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

  35. 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

  36. 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

  37. The genome aliquoting probem is, given an observed genome A with n copies of each gene, presumed to descend from an n-way polyploidization event from an ordinary diploid genome B, followed by a history of chromos...

    Authors: Robert Warren and David Sankoff
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S2
    Content type: Research Published on:

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

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  49. 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:

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