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  1. A standard procedure in many areas of bioinformatics is to use a single multiple sequence alignment (MSA) as the basis for various types of analysis. However, downstream results may be highly sensitive to the ...

    Authors: Joseph L Herman, Ádám Novák, Rune Lyngsø, Adrienn Szabó, István Miklós and Jotun Hein
    Citation: BMC Bioinformatics 2015 16:108
    Content type: Methodology Article Published on:

  2. Relation extraction is a fundamental technology in biomedical text mining. Most of the previous studies on relation extraction from biomedical literature have focused on specific or predefined types of relatio...

    Authors: Nhung TH Nguyen, Makoto Miwa, Yoshimasa Tsuruoka, Takashi Chikayama and Satoshi Tojo
    Citation: BMC Bioinformatics 2015 16:107
    Content type: Research Article Published on:

  3. Construction and validation of a prognostic model for survival data in the clinical domain is still an active field of research. Nevertheless there is no consensus on how to develop routine prognostic tests ba...

    Authors: Maud Tournoud, Audrey Larue, Marie-Angelique Cazalis, Fabienne Venet, Alexandre Pachot, Guillaume Monneret, Alain Lepape and Jean-Baptiste Veyrieras
    Citation: BMC Bioinformatics 2015 16:106
    Content type: Methodology Article Published on:

  6. Epidermal growth factor receptor (EGFR) signalling plays a major role in biological processes, including cell proliferation, differentiation and survival. Since the over-expression of EGFR causes human cancers...

    Authors: Ninnutt Moonrin, Napat Songtawee, Siriluk Rattanabunyong, Surasuk Chunsrivirot, Wanwimon Mokmak, Sissades Tongsima and Kiattawee Choowongkomon
    Citation: BMC Bioinformatics 2015 16:103
    Content type: Research article Published on:

  7. Recent techniques for tagging and visualizing single molecules in fixed or living organisms and cell lines have been revolutionizing our understanding of the spatial and temporal dynamics of fundamental biolog...

    Authors: Allison Chia-Yi Wu and Scott A Rifkin
    Citation: BMC Bioinformatics 2015 16:102
    Content type: Software Published on:

  9. Emergence of multiple drug resistant strains of M. tuberculosis (MDR-TB) threatens to derail global efforts aimed at reigning in the pathogen. Co-infections of M. tuberculosis with HIV are difficult to treat. To ...

    Authors: Tong Huo, Wei Liu, Yu Guo, Cheng Yang, Jianping Lin and Zihe Rao
    Citation: BMC Bioinformatics 2015 16:100
    Content type: Research article Published on:

  10. Invasive monitoring of brain activity by means of intracerebral electrodes is widely practiced to improve pre-surgical seizure onset zone localization in patients with medically refractory seizures. Stereo-Ele...

    Authors: Gabriele Arnulfo, Massimo Narizzano, Francesco Cardinale, Marco Massimo Fato and Jaakko Matias Palva
    Citation: BMC Bioinformatics 2015 16:99
    Content type: Research Article Published on:

  11. Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome ...

    Authors: Julie M Allen, Daisie I Huang, Quentin C Cronk and Kevin P Johnson
    Citation: BMC Bioinformatics 2015 16:98
    Content type: Software Published on:

  12. Genes that regulate stem cell function are suspected to exert adverse effects on prognosis in malignancy. However, diverse cancer stem cell signatures are difficult for physicians to interpret and apply clinic...

    Authors: Xinan Holly Yang, Meiyi Li, Bin Wang, Wanqi Zhu, Aurelie Desgardin, Kenan Onel, Jill de Jong, Jianjun Chen, Luonan Chen and John M Cunningham
    Citation: BMC Bioinformatics 2015 16:97
    Content type: Research article Published on:

  13. Computational predictions of catalytic function are vital for in-depth understanding of enzymes. Because several novel approaches performing better than the common BLAST tool are rarely applied in research, we...

    Authors: Tianmin Wang, Hiroshi Mori, Chong Zhang, Ken Kurokawa, Xin-Hui Xing and Takuji Yamada
    Citation: BMC Bioinformatics 2015 16:96
    Content type: Research article Published on:

  14. The impact of cell-composition effects in analysis of DNA methylation data is now widely appreciated. With the availability of a reference data set consisting of DNA methylation measurements on isolated cell t...

    Authors: E Andres Houseman, Karl T Kelsey, John K Wiencke and Carmen J Marsit
    Citation: BMC Bioinformatics 2015 16:95
    Content type: Methodology article Published on:

  15. In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are l...

    Authors: Juyong Lee, Kiho Lee, InSuk Joung, Keehyoung Joo, Bernard R Brooks and Jooyoung Lee
    Citation: BMC Bioinformatics 2015 16:94
    Content type: Methodology Article Published on:

  16. Identifying druggable cavities on a protein surface is a crucial step in structure based drug design. The cavities have to present suitable size and shape, as well as appropriate chemical complementarity with ...

    Authors: Emna Harigua-Souiai, Isidro Cortes-Ciriano, Nathan Desdouits, Thérèse E Malliavin, Ikram Guizani, Michael Nilges, Arnaud Blondel and Guillaume Bouvier
    Citation: BMC Bioinformatics 2015 16:93
    Content type: Methodology article Published on:

  17. Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the r...

    Authors: Xindong Zhang, Lin Gao, Zhi-Ping Liu and Luonan Chen
    Citation: BMC Bioinformatics 2015 16:92
    Content type: Research article Published on:

  18. When studying the genetics of a human trait, we typically have to manage both genome-wide and targeted genotype data. There can be overlap of both people and markers from different genotyping experiments; the ...

    Authors: Robert V Baron, Yvette P Conley, Michael B Gorin and Daniel E Weeks
    Citation: BMC Bioinformatics 2015 16:91
    Content type: Software Published on:

  19. Spatial frameworks are used to capture organ or whole organism image data in biomedical research. The registration of large biomedical volumetric images is a complex and challenging task, but one that is requi...

    Authors: Bill Hill and Richard A Baldock
    Citation: BMC Bioinformatics 2015 16:90
    Content type: Research Article Published on:

  20. Metabolomics is the study of small molecules, called metabolites, of a cell, tissue or organism. It is of particular interest as endogenous metabolites represent the phenotype resulting from gene expression. A...

    Authors: Mai A Hamdalla, Reda A Ammar and Sanguthevar Rajasekaran
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  21. Epigenetic alterations are known to correlate with changes in gene expression among various diseases including cancers. However, quantitative models that accurately predict the up or down regulation of gene ex...

    Authors: Jeffery Li, Travers Ching, Sijia Huang and Lana X Garmire
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  22. Identifying segments in the genome of different individuals that are identical-by-descent (IBD) is a fundamental element of genetics. IBD data is used for numerous applications including demographic inference,...

    Authors: Danny S Park, Yael Baran, Farhad Hormozdiari, Celeste Eng, Dara G Torgerson, Esteban G Burchard and Noah Zaitlen
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  23. Based on the next generation genome sequencing technologies, a variety of biological applications are developed, while alignment is the first step once the sequencing reads are obtained. In recent years, many ...

    Authors: Xiaoqing Peng, Jianxin Wang, Zhen Zhang, Qianghua Xiao, Min Li and Yi Pan
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  24. We consider the emerging problem of comparing the similarity between (unlabeled) pedigrees. More specifically, we focus on the simplest pedigrees, namely, the 2-generation pedigrees. We show that the isomorphi...

    Authors: Haitao Jiang, Guohui Lin, Weitian Tong, Daming Zhu and Binhai Zhu
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  25. Systems approaches to studying drug-side-effect (drug-SE) associations are emerging as an active research area for both drug target discovery and drug repositioning. However, a comprehensive drug-SE associatio...

    Authors: Rong Xu and QuanQiu Wang
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  26. Ovarian cancer is a deadly female reproductive cancer. Understanding the biological mechanisms underlying ovarian cancer could help lead to quicker and more accurate diagnosis and more effective treatments. Bo...

    Authors: Andrew Quitadamo, Lu Tian, Benika Hall and Xinghua Shi
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  27. Progressive sequence alignment is one of the most commonly used method for multiple sequence alignment. Roughly speaking, the method first builds a guide tree, and then aligns the sequences progressively accor...

    Authors: Qing Zhan, Yongtao Ye, Tak-Wah Lam, Siu-Ming Yiu, Yadong Wang and Hing-Fung Ting
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  28. Large-scale cancer genomic projects are providing lots of data on genomic, epigenomic and gene expression aberrations in many cancer types. One key challenge is to detect functional driver pathways and to filt...

    Authors: Hao Wu, Lin Gao, Feng Li, Fei Song, Xiaofei Yang and Nikola Kasabov
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  29. With the rapid development of high-throughput technologies, researchers can sequence the whole metagenome of a microbial community sampled directly from the environment. The assignment of these metagenomic rea...

    Authors: Ruichang Zhang, Zhanzhan Cheng, Jihong Guan and Shuigeng Zhou
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  30. Disease genes cause or contribute genetically to the development of the most complex diseases. Drugs are the major approaches to treat the complex disease through interacting with their targets. Thus, drug tar...

    Authors: Jingchun Sun, Kevin Zhu, W Jim Zheng and Hua Xu
    Citation: BMC Bioinformatics 2015 16(Suppl 5):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 5

  31. Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences...

    Authors: Scott Schuette, Brian Piatkowski, Aaron Corley, Daniel Lang and Matt Geisler
    Citation: BMC Bioinformatics 2015 16:89
    Content type: Research article Published on:

  34. Despite several recent advances in the automated generation of draft metabolic reconstructions, the manual curation of these networks to produce high quality genome-scale metabolic models remains a labour-inte...

    Authors: Rodrigo Liberal, Beata K Lisowska, David J Leak and John W Pinney
    Citation: BMC Bioinformatics 2015 16:86
    Content type: Software Published on:

  35. Epidermal growth factor receptor (EGFR) mutation-induced drug resistance has caused great difficulties in the treatment of non-small-cell lung cancer (NSCLC). However, structural information is available for j...

    Authors: Lichun Ma, Debby D Wang, Yiqing Huang, Hong Yan, Maria P Wong and Victor HF Lee
    Citation: BMC Bioinformatics 2015 16:85
    Content type: Research article Published on:

  36. A usually confronted problem in association studies is the occurrence of population stratification. In this work, we propose a novel framework to consider population matchings in the contexts of genome-wide an...

    Authors: André Lacour, Vitalia Schüller, Dmitriy Drichel, Christine Herold, Frank Jessen, Markus Leber, Wolfgang Maier, Markus M Noethen, Alfredo Ramirez, Tatsiana Vaitsiakhovich and Tim Becker
    Citation: BMC Bioinformatics 2015 16:84
    Content type: Research Article Published on:

  37. Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new en...

    Authors: Nicolas Fiorini, Sylvie Ranwez, Jacky Montmain and Vincent Ranwez
    Citation: BMC Bioinformatics 2015 16:83
    Content type: Research Article Published on:

  39. There are recent experimental reports on the cross-regulation between molecules involved in the control of the cell cycle and the differentiation of the vulval precursor cells (VPCs) of Caenorhabditis elegans. Su...

    Authors: Nathan Weinstein, Elizabeth Ortiz-Gutiérrez, Stalin Muñoz, David A Rosenblueth, Elena R Álvarez-Buylla and Luis Mendoza
    Citation: BMC Bioinformatics 2015 16:81
    Content type: Research Article Published on:

  41. A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species. Due to the extensive within-species diversity in the microbial world, the pan-genome is oft...

    Authors: Lars Snipen and Kristian Hovde Liland
    Citation: BMC Bioinformatics 2015 16:79
    Content type: Software Published on:

  44. Obesity-induced chronic inflammation plays a fundamental role in the pathogenesis of metabolic syndrome (MS). Recently, a growing body of evidence supports that miRNAs are largely dysregulated in obesity and t...

    Authors: Xi-Mei Zhang, Lin Guo, Mei-Hua Chi, Hong-Mei Sun and Xiao-Wen Chen
    Citation: BMC Bioinformatics 2015 16:76
    Content type: Research article Published on:

  45. Sequencing studies of exonic regions aim to identify rare variants contributing to complex traits. With high coverage and large sample size, these studies tend to apply simple variant calling algorithms. Howev...

    Authors: Yancy Lo, Hyun M Kang, Matthew R Nelson, Mohammad I Othman, Stephanie L Chissoe, Margaret G Ehm, Gonçalo R Abecasis and Sebastian Zöllner
    Citation: BMC Bioinformatics 2015 16:75
    Content type: Research article Published on:

  46. Decoding the temporal control of gene expression patterns is key to the understanding of the complex mechanisms that govern developmental decisions during heart development. High-throughput methods have been e...

    Authors: Wuming Gong, Naoko Koyano-Nakagawa, Tongbin Li and Daniel J Garry
    Citation: BMC Bioinformatics 2015 16:74
    Content type: Methodology article Published on:

  47. Massive parallel sequencing is a powerful tool for variant discovery and genotyping. To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized. This technology is...

    Authors: Koen Herten, Matthew S Hestand, Joris R Vermeesch and Jeroen KJ Van Houdt
    Citation: BMC Bioinformatics 2015 16:73
    Content type: Software Published on:

  48. Transposable elements constitute an important part of the genome and are essential in adaptive mechanisms. Transposition events associated with phenotypic changes occur naturally or are induced in insertional ...

    Authors: Chuan Jiang, Chao Chen, Ziyue Huang, Renyi Liu and Jerome Verdier
    Citation: BMC Bioinformatics 2015 16:72
    Content type: Methodology article Published on:

  49. Human Papillomavirus (HPV) genotyping is an important approach to fight cervical cancer due to the relevant information regarding risk stratification for diagnosis and the better understanding of the relations...

    Authors: Watcharaporn Tanchotsrinon, Chidchanok Lursinsap and Yong Poovorawan
    Citation: BMC Bioinformatics 2015 16:71
    Content type: Methodology Article Published on:

  50. Workflows, or computational pipelines, consisting of collections of multiple linked tasks are becoming more and more popular in many scientific fields, including computational biology. For example, simulation ...

    Authors: Etienne Lord, Abdoulaye Baniré Diallo and Vladimir Makarenkov
    Citation: BMC Bioinformatics 2015 16:68
    Content type: Research article Published on:

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