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  1. Several diseases, many of which nowadays pandemic, consist of multifactorial pathologies. Paradigmatic examples come from the immune response to pathogens, in which cases the effects of different infections co...

    Authors: Anil Sorathiya, Andrea Bracciali and Pietro Liò
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S67
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  2. Use of alternative gene promoters that drive widespread cell-type, tissue-type or developmental gene regulation in mammalian genomes is a common phenomenon. Chromatin immunoprecipitation methods coupled with D...

    Authors: Ravi Gupta, Priyankara Wikramasinghe, Anirban Bhattacharyya, Francisco A Perez, Sharmistha Pal and Ramana V Davuluri
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S65
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  3. Complex human diseases are often caused by multiple mutations, each of which contributes only a minor effect to the disease phenotype. To study the basis for these complex phenotypes, we developed a network-ba...

    Authors: Michael R Mehan, Juan Nunez-Iglesias, Chao Dai, Michael S Waterman and Xianghong Jasmine Zhou
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S62
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  4. Coevolutionary systems like hosts and their parasites are commonly used model systems for evolutionary studies. Inferring the coevolutionary history based on given phylogenies of both groups is often done by e...

    Authors: Daniel Merkle, Martin Middendorf and Nicolas Wieseke
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S60
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  5. About 30% of genes code for membrane proteins, which are involved in a wide variety of crucial biological functions. Despite their importance, experimentally determined structures correspond to only about 1.7%...

    Authors: Hatice U Osmanbeyoglu, Jessica A Wehner, Jaime G Carbonell and Madhavi K Ganapathiraju
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S58
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  6. Biological processes in cells are carried out by means of protein-protein interactions. Determining whether a pair of proteins interacts by wet-lab experiments is resource-intensive; only about 38,000 interact...

    Authors: Thahir P Mohamed, Jaime G Carbonell and Madhavi K Ganapathiraju
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S57
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  7. Gene regulatory network is an abstract mapping of gene regulations in living cells that can help to predict the system behavior of living organisms. Such prediction capability can potentially lead to the devel...

    Authors: Mitra Kabir, Nasimul Noman and Hitoshi Iba
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S56
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  8. Type III secretion system (T3SS) is a specialized protein delivery system in gram-negative bacteria that injects proteins (called effectors) directly into the eukaryotic host cytosol and facilitates bacterial ...

    Authors: Yang Yang, Jiayuan Zhao, Robyn L Morgan, Wenbo Ma and Tao Jiang
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S47
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  9. Haplotype-based approaches have been extensively studied for case-control association mapping in recent years. It has been shown that haplotype methods can provide more consistent results comparing to single-l...

    Authors: Yixuan Chen, Xin Li and Jing Li
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S45
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  10. Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for proc...

    Authors: Mukul S Bansal, J Gordon Burleigh and Oliver Eulenstein
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S42
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  11. One important goal of structural bioinformatics is to recognize and predict the interactions between protein binding sites and RNA. Recently, a comprehensive analysis of ribosomal proteins and their interactio...

    Authors: Giovanni Ciriello, Claudio Gallina and Concettina Guerra
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S41
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  13. The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the comput...

    Authors: Abu Dayem Ullah and Kathleen Steinhöfel
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S39
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  14. Pathways provide topical descriptions of cellular circuitry. Comparing analogous pathways reveals intricate insights into individual functional differences among species. While previous works in the field perf...

    Authors: Adi Mano, Tamir Tuller, Oded Béjà and Ron Y Pinter
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S38
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  16. RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly uses highly coupled Dynamic Programming (D...

    Authors: SPT Krishnan, Sim Sze Liang and Bharadwaj Veeravalli
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S36
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  17. Analyzing interaction networks for functional characterization poses significant challenges arising from the noisy, incomplete, and generic nature of both the interaction data as well as functional annotation ...

    Authors: Jayesh Pandey, Mehmet Koyutürk and Ananth Grama
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S35
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  18. Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore protein structure alignment algorithms are...

    Authors: Zaixin Lu, Zhiyu Zhao and Bin Fu
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S34
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  19. The study of genome rearrangements has become a mainstay of phylogenetics and comparative genomics. Fundamental in such a study is the median problem: given three genomes find a fourth that minimizes the sum o...

    Authors: Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M Swenson and Bernard ME Moret
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S30
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  20. Finding sequences of evolutionary operations that transform one genome into another is a classical problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactl...

    Authors: Martin Bader
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S27
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  21. Many research results show that the biological systems are composed of functional modules. Members in the same module usually have common functions. This is useful information to understand how biological syst...

    Authors: Chia-Hao Chin, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat Ko and Chung-Yen Lin
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S25
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  22. Recombinant protein production is a useful biotechnology to produce a large quantity of highly soluble proteins. Currently, the most widely used production system is to fuse a target protein into different vec...

    Authors: Wen-Ching Chan, Po-Huang Liang, Yan-Ping Shih, Ueng-Cheng Yang, Wen-chang Lin and Chun-Nan Hsu
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S21
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  23. Single nucleotide polymorphism (SNP) based association studies aim at identifying SNPs associated with phenotypes, for example, complex diseases. The associated SNPs may influence the disease risk individually...

    Authors: Can Yang, Xiang Wan, Qiang Yang, Hong Xue and Weichuan Yu
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  24. MapReduce is a parallel framework that has been used effectively to design large-scale parallel applications for large computing clusters. In this paper, we evaluate the viability of the MapReduce framework fo...

    Authors: Suzanne J Matthews and Tiffani L Williams
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  25. Metagenomics is the study of environmental samples using sequencing. Rapid advances in sequencing technology are fueling a vast increase in the number and scope of metagenomics projects. Most metagenome sequen...

    Authors: Suparna Mitra, Max Schubach and Daniel H Huson
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  26. Improving the accuracy and efficiency of motif recognition is an important computational challenge that has application to detecting transcription factor binding sites in genomic data. Closely related to motif...

    Authors: Christina Boucher and James King
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  27. Post-translational modifications (PTMs) have a key role in regulating cell functions. Consequently, identification of PTM sites has a significant impact on understanding protein function and revealing cellular...

    Authors: Inkyung Jung, Akihisa Matsuyama, Minoru Yoshida and Dongsup Kim
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  28. Prediction of protein structural classes (α, β, α + β and α/β) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. Many methods have been ...

    Authors: Jian-Yi Yang, Zhen-Ling Peng and Xin Chen
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  29. Feature selection techniques are critical to the analysis of high dimensional datasets. This is especially true in gene selection from microarray data which are commonly with extremely high feature-to-sample r...

    Authors: Pengyi Yang, Bing B Zhou, Zili Zhang and Albert Y Zomaya
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  30. Many biological functions involve various protein-protein interactions (PPIs). Elucidating such interactions is crucial for understanding general principles of cellular systems. Previous studies have shown the...

    Authors: Darby Tien-Hao Chang, Yu-Tang Syu and Po-Chang Lin
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  31. MicroRNAs (miRNAs) play an essential task in gene regulatory networks by inhibiting the expression of target mRNAs. As their mRNA targets are genes involved in important cell functions, there is a growing inte...

    Authors: Vinod Chandra, Reshmi Girijadevi, Achuthsankar S Nair, Sreenadhan S Pillai and Radhakrishna M Pillai
    Citation: BMC Bioinformatics 2010 11(Suppl 1):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 11 Supplement 1

  32. With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of informati...

    Authors: Harald Barsnes, Richard G Côté, Ingvar Eidhammer and Lennart Martens
    Citation: BMC Bioinformatics 2010 11:34
    Content type: Software Published on:

  33. With the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and apply it to de novo sequencing of new organisms. ...

    Authors: Lance E Palmer, Mathaeus Dejori, Randall Bolanos and Daniel Fasulo
    Citation: BMC Bioinformatics 2010 11:33
    Content type: Research article Published on:

  36. Light microscopy is of central importance in cell biology. The recent introduction of automated high content screening has expanded this technology towards automation of experiments and performing large scale ...

    Authors: Benjamin Misselwitz, Gerhard Strittmatter, Balamurugan Periaswamy, Markus C Schlumberger, Samuel Rout, Peter Horvath, Karol Kozak and Wolf-Dietrich Hardt
    Citation: BMC Bioinformatics 2010 11:30
    Content type: Software Published on:

  37. MicroRNAs (miRNAs) are endogenous small RNAs that play a key role in post-transcriptional regulation of gene expression in animals and plants. The number of known miRNAs has increased rapidly over the years. T...

    Authors: Anders Jacobsen, Anders Krogh, Sakari Kauppinen and Morten Lindow
    Citation: BMC Bioinformatics 2010 11:29
    Content type: Software Published on:

  38. Text mining has become a useful tool for biologists trying to understand the genetics of diseases. In particular, it can help identify the most interesting candidate genes for a disease for further experimenta...

    Authors: Shi Yu, Leon-Charles Tranchevent, Bart De Moor and Yves Moreau
    Citation: BMC Bioinformatics 2010 11:28
    Content type: Methodology article Published on:

  39. For heterogeneous tissues, such as blood, measurements of gene expression are confounded by relative proportions of cell types involved. Conclusions have to rely on estimation of gene expression signals for ho...

    Authors: Dirk Repsilber, Sabine Kern, Anna Telaar, Gerhard Walzl, Gillian F Black, Joachim Selbig, Shreemanta K Parida, Stefan HE Kaufmann and Marc Jacobsen
    Citation: BMC Bioinformatics 2010 11:27
    Content type: Research article Published on:

  40. The accumulation of high-throughput data greatly promotes computational investigation of gene function in the context of complex biological systems. However, a biological function is not simply controlled by a...

    Authors: Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang and Luonan Chen
    Citation: BMC Bioinformatics 2010 11:26
    Content type: Research article Published on:

  42. Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, ...

    Authors: Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón
    Citation: BMC Bioinformatics 2010 11:24
    Content type: Software Published on:

  44. Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelia...

    Authors: Alexander Churbanov, Igor Vořechovský and Chindo Hicks
    Citation: BMC Bioinformatics 2010 11:22
    Content type: Methodology article Published on:

  45. De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to analyze the ...

    Authors: Carl Kingsford, Michael C Schatz and Mihai Pop
    Citation: BMC Bioinformatics 2010 11:21
    Content type: Research article Published on:

  47. Theme-driven cancer survival studies address whether the expression signature of genes related to a biological process can predict patient survival time. Although this should ideally be achieved by testing two...

    Authors: Esteban Czwan, Benedikt Brors and David Kipling
    Citation: BMC Bioinformatics 2010 11:19
    Content type: Methodology article Published on:

  49. Recent reanalysis of spike-in datasets underscored the need for new and more accurate benchmark datasets for statistical microarray analysis. We present here a fresh method using biologically-relevant data to ...

    Authors: Benoît De Hertogh, Bertrand De Meulder, Fabrice Berger, Michael Pierre, Eric Bareke, Anthoula Gaigneaux and Eric Depiereux
    Citation: BMC Bioinformatics 2010 11:17
    Content type: Methodology article Published on:

  50. Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the ...

    Authors: Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk and Armita Sheari
    Citation: BMC Bioinformatics 2010 11:16
    Content type: Research article Published on:

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