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  1. Protein identification using mass spectrometry is an important tool in many areas of the life sciences, and in proteomics research in particular. Increasing the number of proteins correctly identified is depen...

    Authors: Leo C McHugh and Jonathan W Arthur
    Citation: BMC Bioinformatics 2010 11:448
    Content type: Software Published on:

  2. Data generated using 'omics' technologies are characterized by high dimensionality, where the number of features measured per subject vastly exceeds the number of subjects in the study. In this paper, we consi...

    Authors: Yu Guo, Armin Graber, Robert N McBurney and Raji Balasubramanian
    Citation: BMC Bioinformatics 2010 11:447
    Content type: Research article Published on:

  4. Determining beforehand specific positions to align (anchor points) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This feature can be used manually to include biolog...

    Authors: Florian Pitschi, Claudine Devauchelle and Eduardo Corel
    Citation: BMC Bioinformatics 2010 11:445
    Content type: Research article Published on:

  5. New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and i...

    Authors: Thomas M Asbury, Matt Mitman, Jijun Tang and W Jim Zheng
    Citation: BMC Bioinformatics 2010 11:444
    Content type: Software Published on:

  8. Most biomedical ontologies are represented in the OBO Flatfile Format, which is an easy-to-use graph-based ontology language. The semantics of the OBO Flatfile Format 1.2 enforces a strict predetermined interp...

    Authors: Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann and Heinrich Herre
    Citation: BMC Bioinformatics 2010 11:441
    Content type: Methodology article Published on:

  10. The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challeng...

    Authors: Gong-Hua Li and Jing-Fei Huang
    Citation: BMC Bioinformatics 2010 11:439
    Content type: Methodology article Published on:

  11. Modern biology uses experimental systems that involve the exploration of phenotypic variation as a result of the recombination of several genomes. Such systems are useful to investigate the functional evolutio...

    Authors: Diego H Milone, Georgina S Stegmayer, Laura Kamenetzky, Mariana López, Je Min Lee, James J Giovannoni and Fernando Carrari
    Citation: BMC Bioinformatics 2010 11:438
    Content type: Software Published on:

  12. Robust biomarkers are needed to improve microbial identification and diagnostics. Proteomics methods based on mass spectrometry can be used for the discovery of novel biomarkers through their high sensitivity ...

    Authors: Ali Al-Shahib, Raju Misra, Nadia Ahmod, Min Fang, Haroun Shah and Saheer Gharbia
    Citation: BMC Bioinformatics 2010 11:437
    Content type: Research article Published on:

  14. Transcription Factors (TFs) and microRNAs (miRNAs) are key players for gene expression regulation in higher eukaryotes. In the last years, a large amount of bioinformatic studies were devoted to the elucidatio...

    Authors: Olivier Friard, Angela Re, Daniela Taverna, Michele De Bortoli and Davide Corá
    Citation: BMC Bioinformatics 2010 11:435
    Content type: Database Published on:

  15. Accurate classification into genotypes is critical in understanding evolution of divergent viruses. Here we report a new approach, MuLDAS, which classifies a query sequence based on the statistical genotype mo...

    Authors: Jiwoong Kim, Yongju Ahn, Kichan Lee, Sung Hee Park and Sangsoo Kim
    Citation: BMC Bioinformatics 2010 11:434
    Content type: Methodology article Published on:

  16. In the last decade, a large amount of microarray gene expression data has been accumulated in public repositories. Integrating and analyzing high-throughput gene expression data have become key activities for ...

    Authors: Ming Zhang, Yudong Zhang, Li Liu, Lijuan Yu, Shirley Tsang, Jing Tan, Wenhua Yao, Manjit S Kang, Yongqiang An and Xingming Fan
    Citation: BMC Bioinformatics 2010 11:433
    Content type: Software Published on:

  19. We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. ...

    Authors: Steven N Evans, Valerie Hower and Lior Pachter
    Citation: BMC Bioinformatics 2010 11:430
    Content type: Research article Published on:

  20. Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that t...

    Authors: Kasper Stovgaard, Christian Andreetta, Jesper Ferkinghoff-Borg and Thomas Hamelryck
    Citation: BMC Bioinformatics 2010 11:429
    Content type: Research article Published on:

  21. Phylogenetic analysis can be used to divide a protein family into subfamilies in the absence of experimental information. Most phylogenetic analysis methods utilize multiple alignment of sequences and are base...

    Authors: Aydin Albayrak, Hasan H Otu and Ugur O Sezerman
    Citation: BMC Bioinformatics 2010 11:428
    Content type: Methodology article Published on:

  22. Generally speaking, different classifiers tend to work well for certain types of data and conversely, it is usually not known a priori which algorithm will be optimal in any given classification application. I...

    Authors: Susmita Datta, Vasyl Pihur and Somnath Datta
    Citation: BMC Bioinformatics 2010 11:427
    Content type: Methodology article Published on:

  23. Many protein structures determined in high-throughput structural genomics centers, despite their significant novelty and importance, are available only as PDB depositions and are not accompanied by a peer-revi...

    Authors: Dana Weekes, S Sri Krishna, Constantina Bakolitsa, Ian A Wilson, Adam Godzik and John Wooley
    Citation: BMC Bioinformatics 2010 11:426
    Content type: Methodology article Published on:

  24. Identification of transcription factors (TFs) involved in a biological process is the first step towards a better understanding of the underlying regulatory mechanisms. However, due to the involvement of a lar...

    Authors: Xiaoqi Cui, Tong Wang, Huann-Sheng Chen, Victor Busov and Hairong Wei
    Citation: BMC Bioinformatics 2010 11:425
    Content type: Methodology article Published on:

  25. Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. ...

    Authors: Ernst Althaus, Stefan Canzar, Carsten Ehrler, Mark R Emmett, Andreas Karrenbauer, Alan G Marshall, Anke Meyer-Bäse, Jeremiah D Tipton and Hui-Min Zhang
    Citation: BMC Bioinformatics 2010 11:424
    Content type: Methodology article Published on:

  26. The study of biological systems demands computational support. If targeting a biological problem, the reuse of existing computational models can save time and effort. Deciding for potentially suitable models, ...

    Authors: Ron Henkel, Lukas Endler, Andre Peters, Nicolas Le Novère and Dagmar Waltemath
    Citation: BMC Bioinformatics 2010 11:423
    Content type: Methodology article Published on:

  28. Over the past decade, gene expression microarray studies have greatly expanded our knowledge of genetic mechanisms of human diseases. Meta-analysis of substantial amounts of accumulated data, by integrating va...

    Authors: Wei-Chung Cheng, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen, Wun-Yi Shu, Yun-Shien Lee, Tzu-Hao Wang, Ji-Hong Hong, Chia-Yang Li and Ian C Hsu
    Citation: BMC Bioinformatics 2010 11:421
    Content type: Database Published on:

  30. MicroRNAs (miRNAs) are a class of important gene regulators. The number of identified miRNAs has been increasing dramatically in recent years. An emerging major challenge is the interpretation of the genome-sc...

    Authors: Ming Lu, Bing Shi, Juan Wang, Qun Cao and Qinghua Cui
    Citation: BMC Bioinformatics 2010 11:419
    Content type: Methodology article Published on:

  31. With the biomedical literature continually expanding, searching PubMed for information about specific genes becomes increasingly difficult. Not only can thousands of results be returned, but gene name ambiguit...

    Authors: Catalina O Tudor, Carl J Schmidt and K Vijay-Shanker
    Citation: BMC Bioinformatics 2010 11:418
    Content type: Software Published on:

  33. Epistasis is recognized as a fundamental part of the genetic architecture of individuals. Several computational approaches have been developed to model gene-gene interactions in case-control studies, however, ...

    Authors: Lorenzo Beretta, Alessandro Santaniello, Piet LCM van Riel, Marieke JH Coenen and Raffaella Scorza
    Citation: BMC Bioinformatics 2010 11:416
    Content type: Research article Published on:

  36. The correlation between the expression levels of transcription factors and their target genes can be used to infer interactions within animal regulatory networks, but current methods are limited in their abili...

    Authors: Anil Aswani, Soile VE Keränen, James Brown, Charless C Fowlkes, David W Knowles, Mark D Biggin, Peter Bickel and Claire J Tomlin
    Citation: BMC Bioinformatics 2010 11:413
    Content type: Research article Published on:

  37. To further understand the implementation of hyperparameters re-estimation technique in Bayesian hierarchical model, we added two more prior assumptions over the weight in BayesPI, namely Laplace prior and Cauc...

    Authors: Junbai Wang
    Citation: BMC Bioinformatics 2010 11:412
    Content type: Research article Published on:

  38. At present, the organization of system modules is typically limited to either a multilevel hierarchy that describes the "vertical" relationships between modules at different levels (e.g., module A at level two...

    Authors: Chia-Ying Cheng and Yuh-Jyh Hu
    Citation: BMC Bioinformatics 2010 11:411
    Content type: Research article Published on:

  39. Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious d...

    Authors: Miguel García-Remesal, Alejandro Cuevas, Victoria López-Alonso, Guillermo López-Campos, Guillermo de la Calle, Diana de la Iglesia, David Pérez-Rey, José Crespo, Fernando Martín-Sánchez and Víctor Maojo
    Citation: BMC Bioinformatics 2010 11:410
    Content type: Methodology article Published on:

  40. Failure on Highly Active Anti-Retroviral Treatment is often accompanied with development of antiviral resistance to one or more drugs included in the treatment. In general, the virus is more likely to develop ...

    Authors: Kristof Theys, Koen Deforche, Gertjan Beheydt, Yves Moreau, Kristel van Laethem, Philippe Lemey, Ricardo J Camacho, Soo-Yon Rhee, Robert W Shafer, Eric Van Wijngaerden and Anne-Mieke Vandamme
    Citation: BMC Bioinformatics 2010 11:409
    Content type: Research article Published on:

  41. Meta-analysis methods exist for combining multiple microarray datasets. However, there are a wide range of issues associated with microarray meta-analysis and a limited ability to compare the performance of di...

    Authors: Anna Campain and Yee Hwa Yang
    Citation: BMC Bioinformatics 2010 11:408
    Content type: Research article Published on:

  43. While multiple alignment is the first step of usual classification schemes for biological sequences, alignment-free methods are being increasingly used as alternatives when multiple alignments fail. Subword-ba...

    Authors: Eduardo Corel, Florian Pitschi, Ivan Laprevotte, Gilles Grasseau, Gilles Didier and Claudine Devauchelle
    Citation: BMC Bioinformatics 2010 11:406
    Content type: Research article Published on:

  45. The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification langu...

    Authors: Joshua Colvin, Michael I Monine, Ryan N Gutenkunst, William S Hlavacek, Daniel D Von Hoff and Richard G Posner
    Citation: BMC Bioinformatics 2010 11:404
    Content type: Software Published on:

  48. Approximate Bayesian computation (ABC) is a recent flexible class of Monte-Carlo algorithms increasingly used to make model-based inference on complex evolutionary scenarios that have acted on natural populati...

    Authors: Jean-Marie Cornuet, Virgine Ravigné and Arnaud Estoup
    Citation: BMC Bioinformatics 2010 11:401
    Content type: Research article Published on:

  50. Immunoglobulin (IG or antibody) and the T-cell receptor (TR) are pivotal proteins in the immune system of higher organisms. In cancer immunotherapy, the immune responses mediated by tumor-epitope-binding IG or...

    Authors: Yoji Nakamura, Tomoyoshi Komiyama, Motoki Furue, Takashi Gojobori and Yasuto Akiyama
    Citation: BMC Bioinformatics 2010 11:398
    Content type: Database Published on:

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