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  1. Identifying the genetic components of common diseases has long been an important area of research. Recently, genotyping technology has reached the level where it is cost effective to genotype single nucleotide...

    Authors: Søren Besenbacher, Christian NS Pedersen and Thomas Mailund
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S74

    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

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

  3. Genome-wide association studies prove to be a powerful approach to identify the genetic basis of different human diseases. We studied the relationship between seven diseases characterized in a previous genome-...

    Authors: Wenhui Huang, Pengyuan Wang, Zhen Liu and Liqing Zhang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S68

    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

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

  5. 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

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

  6. 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

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

  7. 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

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

  8. 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

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

  9. Supervised learning and many stochastic methods for predicting protein-protein interactions require both negative and positive interactions in the training data set. Unlike positive interactions, negative inte...

    Authors: Jisu Kim, De-Shuang Huang and Kyungsook Han
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S57

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

  10. 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

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

  11. The Janus kinase-signal transducer and activator of transcription (JAK/STAT) pathway is one of the most important targets for myeloproliferative disorder (MPD). Although several efforts toward modeling the pat...

    Authors: Hong-Hee Won, Inho Park, Eunjung Lee, Jong-Won Kim and Doheon Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S53

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

  12. 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

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

  13. Spectra resulting from Surface-Enhanced Laser Desorption/Ionisation (SELDI) mass spectrometry measurements are constructed by combining sub-spectra, each of which are the result of a single firing of the laser...

    Authors: Wouter Meuleman, Judith YMN Engwegen, Marie-Christine W Gast, Lodewyk FA Wessels and Marcel JT Reinders
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S51

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

  14. 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

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

  15. 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

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

  16. 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

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

  17. Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midn...

    Authors: Yi Jia, Jun Huan, Vincent Buhr, Jintao Zhang and Leonidas N Carayannopoulos
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S46

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

  18. 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

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

  19. 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

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

  20. Intrinsically unstructured or disordered proteins are common and functionally important. Prediction of disordered regions in proteins can provide useful information for understanding protein function and for h...

    Authors: Pengfei Han, Xiuzhen Zhang and Zhi-Ping Feng
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S42

    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

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

  22. Electron cryomicroscopy is a fast developing technique aiming at the determination of the 3-dimensional structures of large protein complexes. Using this technique, protein density maps can be generated with 6...

    Authors: Weitao Sun and Jing He
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S40

    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

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

  24. RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Pseudoknot is one of the typical substructures appearing in several RNAs, an...

    Authors: Unyanee Poolsap, Yuki Kato and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S38

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

  25. 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

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

  26. Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using til...

    Authors: Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen and Tao Jiang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S36

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

  27. 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

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

  28. MicroRNA (miRNA) target prediction is an important component in understanding gene regulation. One approach is computational: searching nucleotide sequences for miRNA complementary base pairing. An alternative...

    Authors: Brian J Parker and Jiayu Wen
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S32

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

  29. 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

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

  30. 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

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

  31. 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

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

  32. Clustering analysis is a common statistical tool for knowledge discovery. It is mainly conducted when a project still is in the exploratory phase without any priori hypotheses. However, the statistical signifi...

    Authors: Wensheng Zhang, Hong-Bin Fang and Jiuzhou Song
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S26

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

  33. 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

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

  34. 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

    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

    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

    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

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

  38. 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

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

  39. 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

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

  40. 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

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

  41. 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

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

  42. Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as ...

    Authors: Daniel H Huson, Daniel C Richter, Suparna Mitra, Alexander F Auch and Stephan C Schuster
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S12

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

  43. A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstr...

    Authors: Feng Yue, Jian Shi and Jijun Tang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S11

    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

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

  45. 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

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

  46. 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

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

  47. Generating sequence alignments from superimposed structures is an important part of many structure comparison programs. The accuracy of the alignment affects structure recognition, classification and possibly ...

    Authors: Chin-Hsien Tai, James J Vincent, Changhoon Kim and Byungkook Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S4

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

  48. 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

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

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