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  2. Machine learning techniques are known to be a powerful way of distinguishing microRNA hairpins from pseudo hairpins and have been applied in a number of recognised miRNA search tools. However, many current met...

    Authors: Adam Gudyś, Michał Wojciech Szcześniak, Marek Sikora and Izabela Makałowska
    Citation: BMC Bioinformatics 2013 14:83
    Content type: Methodology article Published on:

  4. Culture-independent phylogenetic analysis of 16S ribosomal RNA (rRNA) gene sequences has emerged as an incisive method of profiling bacteria present in a specimen. Currently, multiple techniques are available ...

    Authors: Xiao Wu, Kathryn Berkow, Daniel N Frank, Ellen Li, Ajay S Gulati and Wei Zhu
    Citation: BMC Bioinformatics 2013 14:79
    Content type: Research article Published on:

  5. All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must h...

    Authors: Björn Hammesfahr, Florian Odronitz, Stefanie Mühlhausen, Stephan Waack and Martin Kollmar
    Citation: BMC Bioinformatics 2013 14:77
    Content type: Software Published on:

  6. Genome-wide tiling array experiments are increasingly used for the analysis of DNA methylation. Because DNA methylation patterns are tissue and cell type specific, the detection of differentially methylated re...

    Authors: Jerry Guintivano, Michal Arad, Kellie LK Tamashiro, Todd D Gould and Zachary A Kaminsky
    Citation: BMC Bioinformatics 2013 14:76
    Content type: Software Published on:

  8. In methylome-wide association studies (MWAS) there are many possible differences between cases and controls (e.g. related to life style, diet, and medication use) that may affect the methylome and produce fals...

    Authors: Wenan Chen, Guimin Gao, Srilaxmi Nerella, Christina M Hultman, Patrik KE Magnusson, Patrick F Sullivan, Karolina A Aberg and Edwin JCG van den Oord
    Citation: BMC Bioinformatics 2013 14:74
    Content type: Software Published on:

  9. Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one plac...

    Authors: Dariusz Mrozek, Bożena Małysiak-Mrozek and Artur Siążnik
    Citation: BMC Bioinformatics 2013 14:73
    Content type: Software Published on:

  10. Advances in sequencing technology over the past decade have resulted in an abundance of sequenced proteins whose function is yet unknown. As such, computational systems that can automatically predict and annot...

    Authors: Andrew Wong and Hagit Shatkay
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  11. The prediction of biochemical function from the 3D structure of a protein has proved to be much more difficult than was originally foreseen. A reliable method to test the likelihood of putative annotations and...

    Authors: Zhouxi Wang, Pengcheng Yin, Joslynn S Lee, Ramya Parasuram, Srinivas Somarowthu and Mary Jo Ondrechen
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  12. Predicting the function of newly sequenced proteins is crucial due to the pace at which these raw sequences are being obtained. Almost all resources for predicting protein function assign functional terms to w...

    Authors: Daniel Lopez and Florencio Pazos
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  13. Daphnia pulex (Water flea) is the first fully sequenced crustacean genome. The crustaceans and insects have diverged from a common ancestor. It is a model organism for studying the molecular makeup for coping ...

    Authors: Nadav Rappoport and Michal Linial
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  14. Combining heterogeneous sources of data is essential for accurate prediction of protein function. The task is complicated by the fact that while sequence-based features can be readily compared across species, ...

    Authors: Artem Sokolov, Christopher Funk, Kiley Graim, Karin Verspoor and Asa Ben-Hur
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  15. Computational/manual annotations of protein functions are one of the first routes to making sense of a newly sequenced genome. Protein domain predictions form an essential part of this annotation process. This...

    Authors: Hai Fang and Julian Gough
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  16. Protein function determination is a key challenge in the post-genomic era. Experimental determination of protein functions is accurate, but time-consuming and resource-intensive. A cost-effective alternative i...

    Authors: Liang Lan, Nemanja Djuric, Yuhong Guo and Slobodan Vucetic
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  17. Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference.

    Authors: Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass…
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  18. Annotating protein function with both high accuracy and sensitivity remains a major challenge in structural genomics. One proven computational strategy has been to group a few key functional amino acids into t...

    Authors: Serkan Erdin, Eric Venner, Andreas Martin Lisewski and Olivier Lichtarge
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  19. Here we assessed the use of domain families for predicting the functions of whole proteins. These 'functional families' (FunFams) were derived using a protocol that combines sequence clustering with supervised...

    Authors: Robert Rentzsch and Christine A Orengo
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  20. In the genomic era a key issue is protein annotation, namely how to endow protein sequences, upon translation from the corresponding genes, with structural and functional features. Routinely this operation is ...

    Authors: Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Andrea Zauli, Ivan Rossi and Rita Casadio
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  21. Predicting protein function from sequence is useful for biochemical experiment design, mutagenesis analysis, protein engineering, protein design, biological pathway analysis, drug design, disease diagnosis, an...

    Authors: Zheng Wang, Renzhi Cao and Jianlin Cheng
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  22. Many Automatic Function Prediction (AFP) methods were developed to cope with an increasing growth of the number of gene sequences that are available from high throughput sequencing experiments. To support the ...

    Authors: Meghana Chitale, Ishita K Khan and Daisuke Kihara
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  23. Accurate protein function annotation is a severe bottleneck when utilizing the deluge of high-throughput, next generation sequencing data. Keeping database annotations up-to-date has become a major scientific ...

    Authors: Domenico Cozzetto, Daniel WA Buchan, Kevin Bryson and David T Jones
    Citation: BMC Bioinformatics 2013 14(Suppl 3):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 14 Supplement 3

  25. The position of a sentence in a document has been traditionally considered an indicator of the relevance of the sentence, and therefore it is frequently used by automatic summarization systems as an attribute ...

    Authors: Laura Plaza and Jorge Carrillo-de-Albornoz
    Citation: BMC Bioinformatics 2013 14:71
    Content type: Research article Published on:

  26. Analysis of gene expression from different species is a powerful way to identify evolutionarily conserved transcriptional responses. However, due to evolutionary events such as gene duplication, there is no on...

    Authors: Erik Kristiansson, Tobias Österlund, Lina Gunnarsson, Gabriella Arne, D G Joakim Larsson and Olle Nerman
    Citation: BMC Bioinformatics 2013 14:70
    Content type: Methodology article Published on:

  27. DNA microarrays have become ubiquitous in biological and medical research. The most difficult problem that needs to be solved is the design of DNA oligonucleotides that (i) are highly specific, that is, bind o...

    Authors: Lucian Ilie, Hamid Mohamadi, Geoffrey Brian Golding and William F Smyth
    Citation: BMC Bioinformatics 2013 14:69
    Content type: Research article Published on:

  28. Proteins are the key elements on the path from genetic information to the development of life. The roles played by the different proteins are difficult to uncover experimentally as this process involves comple...

    Authors: Jorge Alberto Jaramillo-Garzón, Joan Josep Gallardo-Chacón, César Germán Castellanos-Domínguez and Alexandre Perera-Lluna
    Citation: BMC Bioinformatics 2013 14:68
    Content type: Research article Published on:

  29. The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing t...

    Authors: Yupeng Chen, Bertil Schmidt and Douglas L Maskell
    Citation: BMC Bioinformatics 2013 14:67
    Content type: Methodology article Published on:

  30. A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relatio...

    Authors: Andrés Varón and Ward C Wheeler
    Citation: BMC Bioinformatics 2013 14:66
    Content type: Methodology article Published on:

  31. Characterising genetic diversity through the analysis of massively parallel sequencing (MPS) data offers enormous potential to significantly improve our understanding of the genetic basis for observed phenotyp...

    Authors: Bernard J Pope, Tú Nguyen-Dumont, Fabrice Odefrey, Fleur Hammet, Russell Bell, Kayoko Tao, Sean V Tavtigian, David E Goldgar, Andrew Lonie, Melissa C Southey and Daniel J Park
    Citation: BMC Bioinformatics 2013 14:65
    Content type: Methodology article Published on:

  33. Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation.

    Authors: J Eduardo Fajardo and Andras Fiser
    Citation: BMC Bioinformatics 2013 14:63
    Content type: Methodology article Published on:

  34. The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native struc...

    Authors: Michal Jamroz and Andrzej Kolinski
    Citation: BMC Bioinformatics 2013 14:62
    Content type: Software Published on:

  35. Population stratification is a systematic difference in allele frequencies between subpopulations. This can lead to spurious association findings in the case-control genome wide association studies (GWASs) use...

    Authors: Mohsen Hajiloo, Yadav Sapkota, John R Mackey, Paula Robson, Russell Greiner and Sambasivarao Damaraju
    Citation: BMC Bioinformatics 2013 14:61
    Content type: Research article Published on:

  36. For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its pur...

    Authors: Jan P Meier-Kolthoff, Alexander F Auch, Hans-Peter Klenk and Markus Göker
    Citation: BMC Bioinformatics 2013 14:60
    Content type: Methodology article Published on:

  37. The learning active subnetworks problem involves finding subnetworks of a bio-molecular network that are active in a particular condition. Many approaches integrate observation data (e.g., gene expression) wit...

    Authors: Ilana Lichtenstein, Michael A Charleston, Tiberio S Caetano, Jennifer R Gamble and Mathew A Vadas
    Citation: BMC Bioinformatics 2013 14:59
    Content type: Methodology article Published on:

  38. A popular objective of many high-throughput genome projects is to discover various genomic markers associated with traits and develop statistical models to predict traits of future patients based on marker val...

    Authors: Jinseog Kim, Insuk Sohn, Dae-Soon Son, Dong Hwan Kim, Taejin Ahn and Sin-Ho Jung
    Citation: BMC Bioinformatics 2013 14:58
    Content type: Methodology article Published on:

  40. Liquid chromatography mass spectrometry (LC-MS) maps in shotgun proteomics are often too complex to select every detected peptide signal for fragmentation by tandem mass spectrometry (MS/MS). Standard methods ...

    Authors: Alexandra Zerck, Eckhard Nordhoff, Hans Lehrach and Knut Reinert
    Citation: BMC Bioinformatics 2013 14:56
    Content type: Methodology article Published on:

  42. Automatic recognition of biomedical names is an essential task in biomedical information extraction, presenting several complex and unsolved challenges. In recent years, various solutions have been implemented...

    Authors: David Campos, Sérgio Matos and José Luís Oliveira
    Citation: BMC Bioinformatics 2013 14:54
    Content type: Software Published on:

  43. Gene Ontology (GO) enrichment analysis remains one of the most common methods for hypothesis generation from high throughput datasets. However, we believe that researchers strive to test other hypotheses that ...

    Authors: Tobias Wittkop, Emily TerAvest, Uday S Evani, K Mathew Fleisch, Ari E Berman, Corey Powell, Nigam H Shah and Sean D Mooney
    Citation: BMC Bioinformatics 2013 14:53
    Content type: Methodology article Published on:

  44. CD4+ T-cell epitopes play a crucial role in eliciting vigorous protective immune responses during peptide (epitope)-based vaccination. The prediction of these epitopes focuses on the peptide binding process by...

    Authors: Patricio Oyarzún, Jonathan J Ellis, Mikael Bodén and Boštjan Kobe
    Citation: BMC Bioinformatics 2013 14:52
    Content type: Research article Published on:

  45. Biomarkers and target-specific phenotypes are important to targeted drug design and individualized medicine, thus constituting an important aspect of modern pharmaceutical research and development. More and mo...

    Authors: Carlo A Trugenberger, Christoph Wälti, David Peregrim, Mark E Sharp and Svetlana Bureeva
    Citation: BMC Bioinformatics 2013 14:51
    Content type: Research article Published on:

  46. Methylation studies are a promising complement to genetic studies of DNA sequence. However, detailed prior biological knowledge is typically lacking, so methylome-wide association studies (MWAS) will be critic...

    Authors: Edwin JCG van den Oord, Jozsef Bukszar, Gábor Rudolf, Srilaxmi Nerella, Joseph L McClay, Lin Y Xie and Karolina A Aberg
    Citation: BMC Bioinformatics 2013 14:50
    Content type: Methodology article Published on:

  47. MultiAlign is a free software tool that aligns multiple liquid chromatography-mass spectrometry datasets to one another by clustering mass and chromatographic elution features across datasets. Applicable to bo...

    Authors: Brian L LaMarche, Kevin L Crowell, Navdeep Jaitly, Vladislav A Petyuk, Anuj R Shah, Ashoka D Polpitiya, John D Sandoval, Gary R Kiebel, Matthew E Monroe, Stephen J Callister, Thomas O Metz, Gordon A Anderson and Richard D Smith
    Citation: BMC Bioinformatics 2013 14:49
    Content type: Software Published on:

  48. Digitised monogenean images are usually stored in file system directories in an unstructured manner. In this paper we propose a semantic representation of these images in the form of a Monogenean Haptoral Bar ...

    Authors: Arpah Abu, Lim Lee Hong Susan, Amandeep Singh Sidhu and Sarinder Kaur Dhillon
    Citation: BMC Bioinformatics 2013 14:48
    Content type: Research article Published on:

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