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  1. It is commonly believed that including domain knowledge in a prediction model is desirable. However, representing and incorporating domain information in the learning process is, in general, a challenging prob...

    Authors: Xiaofei Nan, Gang Fu, Zhengdong Zhao, Sheng Liu, Ronak Y Patel, Haining Liu, Pankaj R Daga, Robert J Doerksen, Xin Dang, Yixin Chen and Dawn Wilkins
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  2. Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequ...

    Authors: Stephen Winters-Hilt, Evenie Horton-Chao and Eric Morales
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  3. Gene Regulatory Networks (GRNs) provide integrated views of gene interactions that control biological processes. Many public databases contain biological interactions extracted from experimentally validated li...

    Authors: Ying Li, Ping Gong, Edward J Perkins, Chaoyang Zhang and Nan Wang
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  4. Identification of transcription factors (TFs) responsible for modulation of differentially expressed genes is a key step in deducing gene regulatory pathways. Most current methods identify TFs by searching for...

    Authors: Sujoy Roy, Kevin Heinrich, Vinhthuy Phan, Michael W Berry and Ramin Homayouni
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  5. Proteins search along the DNA for targets, such as transcription initiation sequences, according to one-dimensional diffusion, which is interrupted by micro- and macro-hopping events and intersegmental transfe...

    Authors: Michael L Mayo, Edward J Perkins and Preetam Ghosh
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  6. Biology is rapidly becoming a data intensive, data-driven science. It is essential that data is represented and connected in ways that best represent its full conceptual content and allows both automated integ...

    Authors: Shelton D Griffith, Daniel J Quest, Thomas S Brettin and Robert W Cottingham
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  7. Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic tre...

    Authors: Suzanne J Matthews and Tiffani L Williams
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  8. Hypertension may increase tortuosity or twistedness of arteries. We applied a centerline extraction algorithm and tortuosity metric to magnetic resonance angiography (MRA) brain images to quantitatively measur...

    Authors: Karl T Diedrich, John A Roberts, Richard H Schmidt, Chang-Ki Kang, Zang-Hee Cho and Dennis L Parker
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  9. In all amyloid diseases, protein aggregates have been implicated fully or partly, in the etiology of the disease. Due to their significance in human pathologies, there have been unprecedented efforts towards p...

    Authors: Srisairam Achuthan, Bong Jae Chung, Preetam Ghosh, Vijayaraghavan Rangachari and Ashwin Vaidya
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  10. Dermoscopy is one of the major imaging modalities used in the diagnosis of melanoma and other pigmented skin lesions. In current practice, dermatologists determine lesion area by manually drawing lesion border...

    Authors: Sait Suer, Sinan Kockara and Mutlu Mete
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  11. The Food and Drug Administration (FDA) approved drug labels contain a broad array of information, ranging from adverse drug reactions (ADRs) to drug efficacy, risk-benefit consideration, and more. However, the...

    Authors: Halil Bisgin, Zhichao Liu, Hong Fang, Xiaowei Xu and Weida Tong
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  12. One of the most important goals of the mathematical modeling of gene regulatory networks is to alter their behavior toward desirable phenotypes. Therapeutic techniques are derived for intervention in terms of ...

    Authors: Noushin Ghaffari, Ivan Ivanov, Xiaoning Qian and Edward R Dougherty
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  13. Accumulation of gene mutations in cells is known to be responsible for tumor progression, driving it from benign states to malignant states. However, previous studies have shown that the detailed sequence of g...

    Authors: Mohammad Shahrokh Esfahani, Byung-Jun Yoon and Edward R Dougherty
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  14. Recent advances in genomics and proteomics have allowed us to study the nuances of the Warburg effect – a long-standing puzzle in cancer energy metabolism – at an unprecedented level of detail. While modern ne...

    Authors: Aleksandra A Markovets and Damir Herman
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  15. Comparative network analysis aims to identify common subnetworks in biological networks. It can facilitate the prediction of conserved functional modules across different species and provide deep insights into...

    Authors: Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  16. Each organ has a specific function in the body. “Organ-specificity” refers to differential expressions of the same gene across different organs. An organ-specific gene/protein is defined as a gene/protein whos...

    Authors: Fan Zhang and Jake Y Chen
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  17. Genomic biomarkers play an increasing role in both preclinical and clinical application. Development of genomic biomarkers with microarrays is an area of intensive investigation. However, despite sustained and...

    Authors: Minjun Chen, Leming Shi, Reagan Kelly, Roger Perkins, Hong Fang and Weida Tong
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  18. Microarray experiments are becoming increasingly common in biomedical research, as is their deposition in publicly accessible repositories, such as Gene Expression Omnibus (GEO). As such, there has been a surg...

    Authors: Mikhail G Dozmorov and Jonathan D Wren
    Citation: BMC Bioinformatics 2011 12(Suppl 10):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 10

  20. How to compare studies on the basis of their biological significance is a problem of central importance in high-throughput genomics. Many methods for performing such comparisons are based on the information in...

    Authors: Miquel Salicrú, Jordi Ocaña and Alex Sánchez-Pla
    Citation: BMC Bioinformatics 2011 12:401
    Content type: Research article Published on:

  21. One-dimensional 1H-NMR spectroscopy is widely used for high-throughput characterization of metabolites in complex biological mixtures. However, the accurate identification of individual compounds is still a chall...

    Authors: Dan Tulpan, Serge Léger, Luc Belliveau, Adrian Culf and Miroslava Čuperlović-Culf
    Citation: BMC Bioinformatics 2011 12:400
    Content type: Research article Published on:

  22. Post-genomic molecular biology has resulted in an explosion of data, providing measurements for large numbers of genes, proteins and metabolites. Time series experiments have become increasingly common, necess...

    Authors: Emma J Cooke, Richard S Savage, Paul DW Kirk, Robert Darkins and David L Wild
    Citation: BMC Bioinformatics 2011 12:399
    Content type: Methodology article Published on:

  23. Protein interactions are essential for coordinating cellular functions. Proteomic studies have already elucidated a huge amount of protein-protein interactions that require detailed functional analysis. Unders...

    Authors: Joan Teyra, Sergey A Samsonov, Sven Schreiber and M Teresa Pisabarro
    Citation: BMC Bioinformatics 2011 12:398
    Content type: Database Published on:

  24. Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for ...

    Authors: Paul Thompson, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, Valeria Quochi, CJ Rupp, Yutaka Sasaki, Giulia Venturi, Dietrich Rebholz-Schuhmann and Sophia Ananiadou
    Citation: BMC Bioinformatics 2011 12:397
    Content type: Research article Published on:

  25. To investigate how patterns of cell differentiation are related to underlying intra- and inter-cellular signalling pathways, we use a stochastic individual-based model to simulate pattern formation when stem c...

    Authors: John A Fozard, Glen R Kirkham, Lee DK Buttery, John R King, Oliver E Jensen and Helen M Byrne
    Citation: BMC Bioinformatics 2011 12:396
    Content type: Research article Published on:

  26. Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.

    Authors: Steven G Cresawn, Matt Bogel, Nathan Day, Deborah Jacobs-Sera, Roger W Hendrix and Graham F Hatfull
    Citation: BMC Bioinformatics 2011 12:395
    Content type: Research article Published on:

  27. Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algo...

    Authors: Paul M Ruegger, Gianluca Della Vedova, Tao Jiang and James Borneman
    Citation: BMC Bioinformatics 2011 12:394
    Content type: Methodology article Published on:

  28. Biomedical papers contain rich information about entities, facts and events of biological relevance. To discover these automatically, we use text mining techniques, which rely on annotated corpora for training...

    Authors: Paul Thompson, Raheel Nawaz, John McNaught and Sophia Ananiadou
    Citation: BMC Bioinformatics 2011 12:393
    Content type: Research article Published on:

  29. Mass spectrometry (MS) based metabolite profiling has been increasingly popular for scientific and biomedical studies, primarily due to recent technological development such as comprehensive two-dimensional ga...

    Authors: Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim and Changyu Shen
    Citation: BMC Bioinformatics 2011 12:392
    Content type: Research article Published on:

  30. Although numerous methods of using microarray data analysis for cancer classification have been proposed, most utilize many genes to achieve accurate classification. This can hamper interpretability of the mod...

    Authors: Xiaosheng Wang and Richard Simon
    Citation: BMC Bioinformatics 2011 12:391
    Content type: Research article Published on:

  31. Machine learning is a powerful approach for describing and predicting classes in microarray data. Although several comparative studies have investigated the relative performance of various machine learning met...

    Authors: Jenny Önskog, Eva Freyhult, Mattias Landfors, Patrik Rydén and Torgeir R Hvidsten
    Citation: BMC Bioinformatics 2011 12:390
    Content type: Research article Published on:

  33. Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this anal...

    Authors: Anabel Usié, Hiren Karathia, Ivan Teixidó, Joan Valls, Xavier Faus, Rui Alves and Francesc Solsona
    Citation: BMC Bioinformatics 2011 12:387
    Content type: Software Published on:

  34. Structural variations in human genomes, such as insertions, deletion, or rearrangements, play an important role in cancer development. Next-Generation Sequencing technologies have been central in providing way...

    Authors: Roland Wittler and Cedric Chauve
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S21
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  35. Segmental duplications in genomes have been studied for many years. Recently, several studies have highlighted a biological phenomenon called breakpoint-duplication that apparently associates a significant propor...

    Authors: Antoine Thomas, Jean-Stéphane Varré and Aïda Ouangraoua
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  36. Changes in transcriptional orientation (“CTOs”) occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication an...

    Authors: Chieh-Hua Lin, Chun-Yi Lian, Chao Agnes Hsiung and Feng-Chi Chen
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  37. In this paper we study the problem of sorting unsigned genomes by double-cut-and-join operations, where genomes allow a mix of linear and circular chromosomes to be present. First, we formulate an equivalent o...

    Authors: Xin Chen, Ruimin Sun and Jiadong Yu
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  38. We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcriptio...

    Authors: Cathal Seoighe and Paul K Korir
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  39. Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches.

    Authors: Birte Kehr, David Weese and Knut Reinert
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  40. Comparison of complete genomes of Bacteria and Archaea shows that gene content varies considerably and that genomes evolve quite rapidly via gene duplication and deletion and horizontal gene transfer. We analy...

    Authors: R Eric Collins, Hugh Merz and Paul G Higgs
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  41. Classical approaches to compute the genomic distance are usually limited to genomes with the same content, without duplicated markers. However, differences in the gene content are frequently observed and can r...

    Authors: Marília D V Braga, Raphael Machado, Leonardo C Ribeiro and Jens Stoye
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  42. In a previous study we demonstrated that co-evolutionary information can be utilized for improving the accuracy of ancestral gene content reconstruction. To this end, we defined a new computational problem, th...

    Authors: Hadas Birin and Tamir Tuller
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  43. Many metazoan genomes conserve chromosome-scale gene linkage relationships (“macro-synteny”) from the common ancestor of multicellular animal life [1–4], but the biological explanation for this conservation is st...

    Authors: Jie Lv, Paul Havlak and Nicholas H Putnam
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  44. A large family of viruses that infect bacteria, called phages, is characterized by long tails used to inject DNA into their victims' cells. The tape measure protein got its name because the length of the correspo...

    Authors: Mahdi Belcaid, Anne Bergeron and Guylaine Poisson
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  45. The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of su...

    Authors: Marília D V Braga, Raphael Machado, Leonardo C Ribeiro and Jens Stoye
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  46. Changes in the order of mitochondrial genes are a good source of information for phylogenetic investigations. Phylogenetic hypotheses are often supported by parsimonious mitochondrial gene order rearrangement ...

    Authors: Matthias Bernt and Martin Middendorf
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  48. The lengths of 5’UTRs of multicellular eukaryotes have been suggested to be subject to stochastic changes, with upstream start codons (uAUGs) as the major constraint to suppress 5’UTR elongation. However, this...

    Authors: Chun-Hsi Chen, Hsuan-Yu Lin, Chia-Lin Pan and Feng-Chi Chen
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  49. Tandemly Arrayed Gene (TAG) clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication eve...

    Authors: Olivier Tremblay Savard, Denis Bertrand and Nadia El-Mabrouk
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  50. During evolution, large-scale genome rearrangements of chromosomes shuffle the order of homologous genome sequences ("synteny blocks") across species. Some years ago, a controversy erupted in genome rearrangem...

    Authors: Oliver Attie, Aaron E Darling and Sophia Yancopoulos
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

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