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  1. Feature extraction (FE) is difficult, particularly if there are more features than samples, as small sample numbers often result in biased outcomes or overfitting. Furthermore, multiple sample classes often co...

    Authors: Y-h Taguchi, Mitsuo Iwadate and Hideaki Umeyama
    Citation: BMC Bioinformatics 2015 16:139
    Content type: Research Article Published on:

  2. This article provides an overview of the first BioASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BioASQ as...

    Authors: George Tsatsaronis, Georgios Balikas, Prodromos Malakasiotis, Ioannis Partalas, Matthias Zschunke, Michael R Alvers, Dirk Weissenborn, Anastasia Krithara, Sergios Petridis, Dimitris Polychronopoulos, Yannis Almirantis, John Pavlopoulos, Nicolas Baskiotis, Patrick Gallinari, Thierry Artiéres, Axel-Cyrille Ngonga Ngomo…
    Citation: BMC Bioinformatics 2015 16:138
    Content type: Research Article Published on:

  6. This report summarizes the scientific content and activities of the first edition of the Latin American Symposium organized by the Student Council of the International Society for Computational Biology (ISCB),...

    Authors: R Gonzalo Parra, Franco L Simonetti, Marcia A Hasenahuer, Gabriel J Olguin-Orellana and Avinash K Shanmugam
    Citation: BMC Bioinformatics 2015 16(Suppl 8):A1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 16 Supplement 8

  9. The interpretation of the results from genome-scale experiments is a challenging and important problem in contemporary biomedical research. Biological networks that integrate experimental results with existing...

    Authors: Corinna Vehlow, David P Kao, Michael R Bristow, Lawrence E Hunter, Daniel Weiskopf and Carsten Görg
    Citation: BMC Bioinformatics 2015 16:135
    Content type: Research Article Published on:

  10. Characterization of respiratory phenotypes can enhance complex trait and genomic studies involving allergic/autoimmune and infectious diseases. Many aspects of respiration can be measured using devices known a...

    Authors: Daniel Bottomly, Beth Wilmot and Shannon K McWeeney
    Citation: BMC Bioinformatics 2015 16:134
    Content type: Software Published on:

  12. Permutation-based gene set tests are standard approaches for testing relationships between collections of related genes and an outcome of interest in high throughput expression analyses. Using M random permutatio...

    Authors: Jessica L Larson and Art B Owen
    Citation: BMC Bioinformatics 2015 16:132
    Content type: Methodology Article Published on:

  13. Epigenome-wide association scans (EWAS) are an increasingly powerful and widely-used approach to assess the role of epigenetic variation in human complex traits. However, this rapidly emerging field lacks dedi...

    Authors: Tiphaine C Martin, Idil Yet, Pei-Chien Tsai and Jordana T Bell
    Citation: BMC Bioinformatics 2015 16:131
    Content type: Software Published on:

  14. Metagenomics, the sequencing of DNA collected from an entire microbial community, enables the study of natural microbial consortia in their native habitats. Metagenomics studies produce huge volumes of data, i...

    Authors: Michael Cantor, Henrik Nordberg, Tatyana Smirnova, Matthias Hess, Susannah Tringe and Inna Dubchak
    Citation: BMC Bioinformatics 2015 16:130
    Content type: Software Published on:

  16. Many tree structures are found in nature and organisms. Such trees are believed to be constructed on the basis of certain rules. We have previously developed grammar-based compression methods for ordered and u...

    Authors: Yang Zhao, Morihiro Hayashida, Yue Cao, Jaewook Hwang and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2015 16:128
    Content type: Research Article Published on:

  17. Proteins interact with a variety of other molecules such as nucleic acids, small molecules and other proteins inside the cell. Structure-determination of protein-protein complexes is challenging due to several...

    Authors: Sony Malhotra, Oommen K Mathew and Ramanathan Sowdhamini
    Citation: BMC Bioinformatics 2015 16:127
    Content type: Software Published on:

  18. The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing r...

    Authors: Kevin M Livingston, Michael Bada, William A Baumgartner Jr and Lawrence E Hunter
    Citation: BMC Bioinformatics 2015 16:126
    Content type: Research article Published on:

  19. With the advances in high throughput technologies, increasing amounts of cancer somatic mutation data are being generated and made available. Only a small number of (driver) mutations occur in driver genes and...

    Authors: Jimmy Van den Eynden, Ana Carolina Fierro, Lieven PC Verbeke and Kathleen Marchal
    Citation: BMC Bioinformatics 2015 16:125
    Content type: Methodology article Published on:

  21. Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built...

    Authors: Ruibang Luo, Jeanno Cheung, Edward Wu, Heng Wang, Sze-Hang Chan, Wai-Chun Law, Guangzhu He, Chang Yu, Chi-Man Liu, Dazong Zhou, Yingrui Li, Ruiqiang Li, Jun Wang, Xiaoqian Zhu, Shaoliang Peng and Tak-Wah Lam
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  22. The lives of half a million children in the United States are severely affected due to the alterations in their functional and mental abilities which epilepsy causes. This study aims to introduce a novel decis...

    Authors: Saman Sargolzaei, Mercedes Cabrerizo, Arman Sargolzaei, Shirin Noei, Anas Salah Eddin, Hoda Rajaei, Alberto Pinzon-Ardila, Sergio M Gonzalez-Arias, Prasanna Jayakar and Malek Adjouadi
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  23. Intracranial volume (ICV) is an important normalization measure used in morphometric analyses to correct for head size in studies of Alzheimer Disease (AD). Inaccurate ICV estimation could introduce bias in th...

    Authors: Saman Sargolzaei, Arman Sargolzaei, Mercedes Cabrerizo, Gang Chen, Mohammed Goryawala, Shirin Noei, Qi Zhou, Ranjan Duara, Warren Barker and Malek Adjouadi
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  24. The reconstruction of gene regulatory network from time course microarray data can help us comprehensively understand the biological system and discover the pathogenesis of cancer and other diseases. But how t...

    Authors: Haijun Gong, Jakob Klinger, Kevin Damazyn, Xiangrui Li and Shiyang Huang
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  25. Pairwise relationships extracted from biomedical literature are insufficient in formulating biomolecular interactions. Extraction of complex relations (namely, biomedical events) has become the main focus of t...

    Authors: Tsendsuren Munkhdalai, Oyun-Erdene Namsrai and Keun Ho Ryu
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  26. Genome assemblers to date have predominantly targeted haploid reference reconstruction from homozygous data. When applied to diploid genome assembly, these assemblers perform poorly, owing to the violation of ...

    Authors: Paul M Bodily, M Stanley Fujimoto, Cameron Ortega, Nozomu Okuda, Jared C Price, Mark J Clement and Quinn Snell
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  27. In recent years, with advances in techniques for protein structure analysis, the knowledge about protein structure and function has been published in a vast number of articles. A method to search for specific ...

    Authors: Azusa Ito and Takenao Ohkawa
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  28. Most cases of idiopathic autism spectrum disorder (ASD) likely result from unknown environmental triggers in genetically susceptible individuals. These triggers may include maternal exposure of a fetus to minu...

    Authors: Gaurav Kaushik, Michael A Thomas and Ken A Aho
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  29. The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most...

    Authors: Rob Smith, Ryan M Taylor and John T Prince
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  30. Liquid chromatography-mass spectrometry is a popular technique for high-throughput protein, lipid, and metabolite comparative analysis. Such statistical comparison of millions of data points requires the gener...

    Authors: Rob Smith, John T Prince and Dan Ventura
    Citation: BMC Bioinformatics 2015 16(Suppl 7):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 7

  32. Mapping of short sequencing reads is a crucial step in the analysis of RNA sequencing (RNA-seq) data. ContextMap is an RNA-seq mapping algorithm that uses a context-based approach to identify the best alignmen...

    Authors: Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer and Caroline C Friedel
    Citation: BMC Bioinformatics 2015 16:122
    Content type: Software Published on:

  33. Comparative proteomics in bacteria are often hampered by the differential nature of dataset quality and/or inherent biological deviations. Although common practice compensates by reproducing and normalizing da...

    Authors: Sa Rang Kim, Tuong Vi Nguyen, Na Ri Seo, Seunghup Jung, Hyun Joo An, David A Mills and Jae Han Kim
    Citation: BMC Bioinformatics 2015 16:121
    Content type: Research article Published on:

  34. Dynamic gene-regulatory networks are complex since the interaction patterns between their components mean that it is impossible to study parts of the network in separation. This holistic character of gene-regu...

    Authors: Ernst C Wit and Antonino Abbruzzo
    Citation: BMC Bioinformatics 2015 16(Suppl 6):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 6

  35. Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these anno...

    Authors: Pietro Pinoli, Davide Chicco and Marco Masseroli
    Citation: BMC Bioinformatics 2015 16(Suppl 6):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 6

  36. Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable bindin...

    Authors: Hossam M Ashtawy and Nihar R Mahapatra
    Citation: BMC Bioinformatics 2015 16(Suppl 6):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 6

  37. Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode...

    Authors: Massimo La Rosa, Antonino Fiannaca, Riccardo Rizzo and Alfonso Urso
    Citation: BMC Bioinformatics 2015 16(Suppl 6):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 6

  38. This paper considers the problem of estimation and variable selection for large high-dimensional data (high number of predictors p and large sample size N, without excluding the possibility that N < p) resulting ...

    Authors: Marta Avalos, Hélène Pouyes, Yves Grandvalet, Ludivine Orriols and Emmanuel Lagarde
    Citation: BMC Bioinformatics 2015 16(Suppl 6):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 6

  39. Sterol glycosyltransferases (SGTs) are ubiquitous but one of the most diverse group of enzymes of glycosyltransferases family. Members of this family modulate physical and chemical properties of secondary plan...

    Authors: Vibha Pandey, Yogeshwar Vikram Dhar, Parul Gupta, Sumit K Bag, Neelam Atri, Mehar Hasan Asif, Prabodh Kumar Trivedi and Pratibha Misra
    Citation: BMC Bioinformatics 2015 16:120
    Content type: Research article Published on:

  40. Understanding channel structures that lead to active sites or traverse the molecule is important in the study of molecular functions such as ion, ligand, and small molecule transport. Efficient methods for ext...

    Authors: Talha Bin Masood, Sankaran Sandhya, Nagasuma Chandra and Vijay Natarajan
    Citation: BMC Bioinformatics 2015 16:119
    Content type: Methodology Article Published on:

  41. Untargeted metabolomics generates a huge amount of data. Software packages for automated data processing are crucial to successfully process these data. A variety of such software packages exist, but the outco...

    Authors: Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes
    Citation: BMC Bioinformatics 2015 16:118
    Content type: Software Published on:

  43. Point mutations can have a strong impact on protein stability. A change in stability may subsequently lead to dysfunction and finally cause diseases. Moreover, protein engineering approaches aim to deliberatel...

    Authors: Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl and Peter Lackner
    Citation: BMC Bioinformatics 2015 16:116
    Content type: Methodology Article Published on:

  44. We recently identified two robust ovarian cancer subtypes, defined by the expression of genes involved in angiogenesis, with significant differences in clinical outcome. To identify potential regulatory mechan...

    Authors: Kimberly Glass, John Quackenbush, Dimitrios Spentzos, Benjamin Haibe-Kains and Guo-Cheng Yuan
    Citation: BMC Bioinformatics 2015 16:115
    Content type: Research article Published on:

  46. Research in biomedical text categorization has mostly used the bag-of-words representation. Other more sophisticated representations of text based on syntactic, semantic and argumentative properties have been les...

    Authors: Antonio Jose Jimeno Yepes, Laura Plaza, Jorge Carrillo-de-Albornoz, James G Mork and Alan R Aronson
    Citation: BMC Bioinformatics 2015 16:113
    Content type: Research article Published on:

  47. Recent depression research has revealed a growing awareness of how to best classify depression into depressive subtypes. Appropriately subtyping depression can lead to identification of subtypes that are more ...

    Authors: Fan Xu, Jing Yang, Jin Chen, Qingyuan Wu, Wei Gong, Jianguo Zhang, Weihua Shao, Jun Mu, Deyu Yang, Yongtao Yang, Zhiwei Li and Peng Xie
    Citation: BMC Bioinformatics 2015 16:112
    Content type: Research article Published on:

  48. Comparing and aligning genomes is a key step in analyzing closely related genomes. Despite the development of many genome aligners in the last 15 years, the problem is not yet fully resolved, even when alignin...

    Authors: Raluca Uricaru, Célia Michotey, Hélène Chiapello and Eric Rivals
    Citation: BMC Bioinformatics 2015 16:111
    Content type: Methodology article Published on:

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