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  1. 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

  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. 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

  4. 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

  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. Classification using aCGH data is an important and insufficiently investigated problem in bioinformatics. In this paper we propose a new classification method of DNA copy number data based on the concept of li...

    Authors: Tomasz Gambin and Krzysztof Walczak
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S64
    Content type: Research Published on:

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

  7. 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. Genome-scale models of metabolism have only been analyzed with the constraint-based modelling philosophy. Some gene deletion studies on in silico organism models at genome-scale have been made, but most of them w...

    Authors: Zixiang Xu, Xiao Sun and Shihai Yu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S62
    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

  10. Protein-Protein Interactions (PPIs) play important roles in many biological functions. Protein domains, which are defined as independently folding structural blocks of proteins, physically interact with each o...

    Authors: Kelvin X Zhang and BF Francis Ouellette
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S60
    Content type: Research Published on:

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

  12. Constraint-based modeling of reconstructed genome-scale metabolic networks has been successfully applied on several microorganisms. In constraint-based modeling, in order to characterize all allowable phenotyp...

    Authors: Yanping Xi, Yi-Ping Phoebe Chen, Ming Cao, Weirong Wang and Fei Wang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S58
    Content type: Research Published on:

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

  13. 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

  14. The gene shaving algorithm and many other clustering algorithms identify gene clusters showing high variation across samples. However, gene expression in many signaling pathways show only modest and concordant...

    Authors: Dongxiao Zhu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S54
    Content type: Research Published on:

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

  15. Although microarray gene expression analysis has become popular, it remains difficult to interpret the biological changes caused by stimuli or variation of conditions. Clustering of genes and associating each ...

    Authors: Taiji Suzuki, Masashi Sugiyama, Takafumi Kanamori and Jun Sese
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S52
    Content type: Research Published on:

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

  16. Peptide identification via tandem mass spectrometry is the basic task of current proteomics research. Due to the complexity of mass spectra, the majority of mass spectra cannot be interpreted at present. The e...

    Authors: Yan Fu, Wei Jia, Zhuang Lu, Haipeng Wang, Zuofei Yuan, Hao Chi, You Li, Liyun Xiu, Wenping Wang, Chao Liu, Leheng Wang, Ruixiang Sun, Wen Gao, Xiaohong Qian and Si-Min He
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S50
    Content type: Research Published on:

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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generat...

    Authors: Chun-Chi Liu, Jianjun Hu, Mrinal Kalakrishnan, Haiyan Huang and Xianghong Jasmine Zhou
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S25
    Content type: Research Published on:

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

  32. 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

  33. Different microarray data sets can be collected for studying the same or similar diseases. We expect to achieve a more efficient analysis of differential expression if an efficient statistical method can be de...

    Authors: Yinglei Lai, Sarah E Eckenrode and Jin-Xiong She
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S23
    Content type: Research Published on:

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

  34. 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

  35. The importance of network-based approach to identifying biological markers for diagnostic classification and prognostic assessment in the context of microarray data has been increasingly recognized. To our kno...

    Authors: Yanni Zhu, Xiaotong Shen and Wei Pan
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S21
    Content type: Research Published on:

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

  36. 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

  37. Microarray gene expression profiling has provided extensive datasets that can describe characteristics of cancer patients. An important challenge for this type of data is the discovery of gene sets which can b...

    Authors: Md Rafiul Hassan, M Maruf Hossain, James Bailey, Geoff Macintyre, Joshua WK Ho and Kotagiri Ramamohanarao
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S19
    Content type: Research Published on:

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

  38. 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

  39. The emerging next-generation sequencing method based on PCR technology boosts genome sequencing speed considerably, the expense is also get decreased. It has been utilized to address a broad range of bioinform...

    Authors: Wendi Wang, Peiheng Zhang and Xinchun Liu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S17
    Content type: Research Published on:

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

  40. 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

  41. DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DN...

    Authors: Francis YL Chin, Henry CM Leung, Wei-Lin Li and Siu-Ming Yiu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S15
    Content type: Research Published on:

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

  42. 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

  44. 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

  46. 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

  47. Reconstructing complete ancestral genomes (at least in terms of their gene inventory and arrangement) is attracting much interest due to the rapidly increasing availability of whole genome sequences. While mod...

    Authors: Krister M Swenson and Bernard ME Moret
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S7
    Content type: Research Published on:

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

  48. 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

  49. With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite...

    Authors: Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty and Dong Xu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S5
    Content type: Research Published on:

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

  50. 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

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