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  1. Since peak alignment in metabolomics has a huge effect on the subsequent statistical analysis, it is considered a key preprocessing step and many peak alignment methods have been developed. However, existing p...

    Authors: Jaesik Jeong, Xiang Zhang, Xue Shi, Seongho Kim and Changyu Shen
    Citation: BMC Bioinformatics 2013 14:123
    Content type: Research article Published on:

  2. RNA-Seq has become a key technology in transcriptome studies because it can quantify overall expression levels and the degree of alternative splicing for each gene simultaneously. To interpret high-throughout ...

    Authors: Xi Wang and Murray J Cairns
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  3. Metagenomic sequencing is becoming a powerful technology for exploring micro-ogranisms from various environments, such as human body, without isolation and cultivation. Accurately identifying genes from metage...

    Authors: Yongchu Liu, Jiangtao Guo, Gangqing Hu and Huaiqiu Zhu
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  4. The techniques of next generation sequencing allow an increasing number of draft genomes to be produced rapidly in a decreasing cost. However, these draft genomes usually are just partially sequenced as collec...

    Authors: Chi-Long Li, Kun-Tze Chen and Chin Lung Lu
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  5. Identification of gene-phenotype relationships is a fundamental challenge in human health clinic. Based on the observation that genes causing the same or similar phenotypes tend to correlate with each other in...

    Authors: Jie Zhu, Yufang Qin, Taigang Liu, Jun Wang and Xiaoqi Zheng
    Citation: BMC Bioinformatics 2013 14(Suppl 5):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 5

  7. Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics. The performance of clustering approaches in delineating biolog...

    Authors: Cheong Xin Chan, Maisarah Mahbob and Mark A Ragan
    Citation: BMC Bioinformatics 2013 14:120
    Content type: Methodology article Published on:

  9. Pyrrolysine (the 22nd amino acid) is in certain organisms and under certain circumstances encoded by the amber stop codon, UAG. The circumstances driving pyrrolysine translation are not well understood. The in...

    Authors: Christian Theil Have, Sine Zambach and Henning Christiansen
    Citation: BMC Bioinformatics 2013 14:118
    Content type: Research article Published on:

  10. The maximal sensitivity for local alignments makes the Smith-Waterman algorithm a popular choice for protein sequence database search based on pairwise alignment. However, the algorithm is compute-intensive du...

    Authors: Yongchao Liu, Adrianto Wirawan and Bertil Schmidt
    Citation: BMC Bioinformatics 2013 14:117
    Content type: Methodology article Published on:

  12. Phytoplankton communities are often used as a marker for the determination of fresh water quality. The routine analysis, however, is very time consuming and expensive as it is carried out manually by trained p...

    Authors: Katja Schulze, Ulrich M Tillich, Thomas Dandekar and Marcus Frohme
    Citation: BMC Bioinformatics 2013 14:115
    Content type: Methodology article Published on:

  13. As more complete genome sequences become available, bioinformatics challenges arise in how to exploit genome sequences to make phenotypic predictions. One type of phenotypic prediction is to determine sets of ...

    Authors: Steven Eker, Markus Krummenacker, Alexander G Shearer, Ashish Tiwari, Ingrid M Keseler, Carolyn Talcott and Peter D Karp
    Citation: BMC Bioinformatics 2013 14:114
    Content type: Research article Published on:

  14. A popular query from scientists reading a biomedical abstract is to search for topic-related documents in bibliographic databases. Such a query is challenging because the amount of information attached to a si...

    Authors: Francisco M Ortuño, Ignacio Rojas, Miguel A Andrade-Navarro and Jean-Fred Fontaine
    Citation: BMC Bioinformatics 2013 14:113
    Content type: Methodology article Published on:

  15. The MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. We present a comparison of the co...

    Authors: Tomer Altman, Michael Travers, Anamika Kothari, Ron Caspi and Peter D Karp
    Citation: BMC Bioinformatics 2013 14:112
    Content type: Research article Published on:

  16. Helical membrane proteins are vital for the interaction of cells with their environment. Predicting the location of membrane helices in protein amino acid sequences provides substantial understanding of their ...

    Authors: Emma M Rath, Dominique Tessier, Alexander A Campbell, Hong Ching Lee, Tim Werner, Noeris K Salam, Lawrence K Lee and W Bret Church
    Citation: BMC Bioinformatics 2013 14:111
    Content type: Database Published on:

  17. RNA-Seq technology measures the transcript abundance by generating sequence reads and counting their frequencies across different biological conditions. To identify differentially expressed genes between two c...

    Authors: Lisa M Chung, John P Ferguson, Wei Zheng, Feng Qian, Vincent Bruno, Ruth R Montgomery and Hongyu Zhao
    Citation: BMC Bioinformatics 2013 14:110
    Content type: Methodology article Published on:

  18. The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to r...

    Authors: Thomas Bigot, Vincent Daubin, Florent Lassalle and Guy Perrière
    Citation: BMC Bioinformatics 2013 14:109
    Content type: Software Published on:

  21. Classification using class-imbalanced data is biased in favor of the majority class. The bias is even larger for high-dimensional data, where the number of variables greatly exceeds the number of samples. The ...

    Authors: Rok Blagus and Lara Lusa
    Citation: BMC Bioinformatics 2013 14:106
    Content type: Research article Published on:

  23. The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles ar...

    Authors: Anne-Lise Veuthey, Alan Bridge, Julien Gobeill, Patrick Ruch, Johanna R McEntyre, Lydie Bougueleret and Ioannis Xenarios
    Citation: BMC Bioinformatics 2013 14:104
    Content type: Methodology article Published on:

  24. User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software appl...

    Authors: Paula de Matos, Jennifer A Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez and Christoph Steinbeck
    Citation: BMC Bioinformatics 2013 14:103
    Content type: Correspondence Published on:

  25. Mobile Genetic Elements (MGEs) are selfish DNA integrated in the genomes. Their detection is mainly based on consensus-like searches by scanning the investigated genome against the sequence of an already ident...

    Authors: Giulia Menconi, Giovanni Battaglia, Roberto Grossi, Nadia Pisanti and Roberto Marangoni
    Citation: BMC Bioinformatics 2013 14:102
    Content type: Research article Published on:

  26. DNA microarrays are used for discovery of genes expressed differentially between various biological conditions. In microarray experiments the number of analyzed samples is often much lower than the number of g...

    Authors: Michal Marczyk, Roman Jaksik, Andrzej Polanski and Joanna Polanska
    Citation: BMC Bioinformatics 2013 14:101
    Content type: Methodology article Published on:

  27. Microarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of t...

    Authors: Hsiu-Ling Chou, Chung-Tay Yao, Sui-Lun Su, Chia-Yi Lee, Kuang-Yu Hu, Harn-Jing Terng, Yun-Wen Shih, Yu-Tien Chang, Yu-Fen Lu, Chi-Wen Chang, Mark L Wahlqvist, Thomas Wetter and Chi-Ming Chu
    Citation: BMC Bioinformatics 2013 14:100
    Content type: Research article Published on:

  28. This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expr...

    Authors: Cécile Bazot, Nicolas Dobigeon, Jean-Yves Tourneret, Aimee K Zaas, Geoffrey S Ginsburg and Alfred O Hero III
    Citation: BMC Bioinformatics 2013 14:99
    Content type: Research article Published on:

  29. NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can pro...

    Authors: Anna Katharina Dehof, Simon Loew, Hans-Peter Lenhof and Andreas Hildebrandt
    Citation: BMC Bioinformatics 2013 14:98
    Content type: Research article Published on:

  30. For the representation of RNA interference (RNAi) dynamics, several mathematical models based on systems of ordinary differential equations (ODEs) have been proposed. These models consist of equations for each...

    Authors: Takanori Ueda, Daisuke Tominaga, Noriko Araki and Tomohiro Yoshikawa
    Citation: BMC Bioinformatics 2013 14:97
    Content type: Methodology article Published on:

  31. In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A num...

    Authors: Satish M Srinivasan, Suleyman Vural, Brian R King and Chittibabu Guda
    Citation: BMC Bioinformatics 2013 14:96
    Content type: Methodology article Published on:

  33. Networks are ubiquitous in modern cell biology and physiology. A large literature exists for inferring/proposing biological pathways/networks using statistical or machine learning algorithms. Despite these adv...

    Authors: Phillip D Yates and Nitai D Mukhopadhyay
    Citation: BMC Bioinformatics 2013 14:94
    Content type: Methodology article Published on:

  34. Automatic 3D digital reconstruction (tracing) of neurons embedded in noisy microscopic images is challenging, especially when the cell morphology is complex.

    Authors: Jinzhu Yang, Paloma T Gonzalez-Bellido and Hanchuan Peng
    Citation: BMC Bioinformatics 2013 14:93
    Content type: Research article Published on:

  35. Transcription factors (TFs) and microRNAs (miRNAs) are primary metazoan gene regulators. Regulatory mechanisms of the two main regulators are of great interest to biologists and may provide insights into the c...

    Authors: Thuc D Le, Lin Liu, Bing Liu, Anna Tsykin, Gregory J Goodall, Kenji Satou and Jiuyong Li
    Citation: BMC Bioinformatics 2013 14:92
    Content type: Methodology article Published on:

  37. DNA-binding proteins (DNA-BPs) play a pivotal role in both eukaryotic and prokaryotic proteomes. There have been several computational methods proposed in the literature to deal with the DNA-BPs, many informat...

    Authors: Chuanxin Zou, Jiayu Gong and Honglin Li
    Citation: BMC Bioinformatics 2013 14:90
    Content type: Methodology article Published on:

  38. Norovirus is the major cause of nonbacterial epidemic gastroenteritis, being highly prevalent in both developing and developed countries. Despite of the available monoclonal antibodies (MAbs) for different sub...

    Authors: Liping Chen, Di Wu, Lei Ji, Xiaofang Wu, Deshun Xu, Zhiwei Cao and Jiankang Han
    Citation: BMC Bioinformatics 2013 14(Suppl 4):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  39. Protein-ligand interactions are key processes in triggering and controlling biological functions within cells. Prediction of protein binding regions on the protein surface assists in understanding the mechanis...

    Authors: Ying-Tsang Lo, Hsin-Wei Wang, Tun-Wen Pai, Wen-Shoung Tzou, Hui-Huang Hsu and Hao-Teng Chang
    Citation: BMC Bioinformatics 2013 14(Suppl 4):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  40. A conformational epitope (CE) in an antigentic protein is composed of amino acid residues that are spatially near each other on the antigen's surface but are separated in sequence; CEs bind their complementary...

    Authors: Ying-Tsang Lo, Tun-Wen Pai, Wei-Kuo Wu and Hao-Teng Chang
    Citation: BMC Bioinformatics 2013 14(Suppl 4):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  41. Herpes simplex virus (HSV) types 1 and 2 (HSV-1 and HSV-2) are the most common infectious agents of humans. No safe and effective HSV vaccines have been licensed. Reverse vaccinology is an emerging and revolut...

    Authors: Zuoshuang Xiang and Yongqun He
    Citation: BMC Bioinformatics 2013 14(Suppl 4):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  42. Computational vaccinology or vaccine informatics is an interdisciplinary field that addresses scientific and clinical questions in vaccinology using computational and informatics approaches. Computational vacc...

    Authors: Yongqun He, Zhiwei Cao, Anne S De Groot, Vladimir Brusic, Christian Schönbach and Nikolai Petrovsky
    Citation: BMC Bioinformatics 2013 14(Suppl 4):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  43. Allergy involves a series of complex reactions and factors that contribute to the development of the disease and triggering of the symptoms, including rhinitis, asthma, atopic eczema, skin sensitivity, even ac...

    Authors: Jing Wang, Yabin Yu, Yunan Zhao, Dabing Zhang and Jing Li
    Citation: BMC Bioinformatics 2013 14(Suppl 4):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 4

  44. Cellular heterogeneity is present in almost all gene expression profiles. However, transcriptome analysis of tissue specimens often ignores the cellular heterogeneity present in these samples. Standard deconvo...

    Authors: Yi Zhong, Ying-Wooi Wan, Kaifang Pang, Lionel ML Chow and Zhandong Liu
    Citation: BMC Bioinformatics 2013 14:89
    Content type: Methodology article Published on:

  46. In investigating differentially expressed genes or other selected features, researchers conduct hypothesis tests to determine which biological categories, such as those of the Gene Ontology (GO), are enriched ...

    Authors: Zhenyu Yang, Zuojing Li and David R Bickel
    Citation: BMC Bioinformatics 2013 14:87
    Content type: Methodology article Published on:

  48. Accurate model comparison requires extensive computation times, especially for parameter-rich models of sequence evolution. In the Bayesian framework, model selection is typically performed through the evaluat...

    Authors: Guy Baele, Philippe Lemey and Stijn Vansteelandt
    Citation: BMC Bioinformatics 2013 14:85
    Content type: Methodology article Published on:

  49. The cellular function of a vast majority of proteins is performed through physical interactions with other biomolecules, which, most of the time, are other proteins. Peptides represent templates of choice for ...

    Authors: Sébastien Giguère, Mario Marchand, François Laviolette, Alexandre Drouin and Jacques Corbeil
    Citation: BMC Bioinformatics 2013 14:82
    Content type: Research article Published on:

  50. Public databases such as the NCBI Gene Expression Omnibus contain extensive and exponentially increasing amounts of high-throughput data that can be applied to molecular phenotype characterization. Collectivel...

    Authors: John C Earls, James A Eddy, Cory C Funk, Younhee Ko, Andrew T Magis and Nathan D Price
    Citation: BMC Bioinformatics 2013 14:78
    Content type: Software Published on:

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