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  1. Content type: Software

    Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results ...

    Authors: Jordi Martorell-Marugan, Daniel Toro-Dominguez, Marta E. Alarcon-Riquelme and Pedro Carmona-Saez

    Citation: BMC Bioinformatics 2017 18:563

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  2. Content type: Methodology Article

    The spatial Principal Component Analysis (sPCA, Jombart (Heredity 101:92-103, 2008) is designed to investigate non-random spatial distributions of genetic variation. Unfortunately, the associated tests used fo...

    Authors: V. Montano and T. Jombart

    Citation: BMC Bioinformatics 2017 18:562

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  3. Content type: Software

    High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number ...

    Authors: Kenneth D. Doig, Jason Ellul, Andrew Fellowes, Ella R. Thompson, Georgina Ryland, Piers Blombery, Anthony T. Papenfuss and Stephen B. Fox

    Citation: BMC Bioinformatics 2017 18:555

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  4. Content type: Software

    Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in...

    Authors: Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck and Geert Vandeweyer

    Citation: BMC Bioinformatics 2017 18:554

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  5. Content type: Research Article

    As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model ...

    Authors: Yuangen Yao, Rong Gui, Quan Liu, Ming Yi and Haiyou Deng

    Citation: BMC Bioinformatics 2017 18:542

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  6. Content type: Methodology Article

    One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, fu...

    Authors: Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol and Gregory Bonito

    Citation: BMC Bioinformatics 2017 18:538

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  7. Content type: Research

    An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implement...

    Authors: Chunchun Zhao and Sartaj Sahni

    Citation: BMC Bioinformatics 2017 18(Suppl 15):518

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  8. Content type: Research

    Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino a...

    Authors: Jan Jelínek, Petr Škoda and David Hoksza

    Citation: BMC Bioinformatics 2017 18(Suppl 15):492

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  9. Content type: Research

    Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds)...

    Authors: Sergey S. Aganezov and Max A. Alekseyev

    Citation: BMC Bioinformatics 2017 18(Suppl 15):496

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  10. Content type: Research Article

    Chromosome structure is a very limited model of the genome including the information about its chromosomes such as their linear or circular organization, the order of genes on them, and the DNA strand encoding...

    Authors: Vassily Lyubetsky, Roman Gershgorin and Konstantin Gorbunov

    Citation: BMC Bioinformatics 2017 18:537

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  11. Content type: Research

    The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet...

    Authors: Ralph W. Crosby and Tiffani L. Williams

    Citation: BMC Bioinformatics 2017 18(Suppl 15):514

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  12. Content type: Research

    In recent years, protein-protein interaction (PPI) networks have been well recognized as important resources to elucidate various biological processes and cellular mechanisms. In this paper, we address the pro...

    Authors: Osamu Maruyama and Yuki Kuwahara

    Citation: BMC Bioinformatics 2017 18(Suppl 15):491

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  13. Content type: Research

    Understanding protein structure and dynamics is essential for understanding their function. This is a challenging task due to the high complexity of the conformational landscapes of proteins and their rugged e...

    Authors: Nurit Haspel, Dong Luo and Eduardo González

    Citation: BMC Bioinformatics 2017 18(Suppl 15):502

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  14. Content type: Research

    RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolu...

    Authors: Ning Yu, Zeng Yu and Yi Pan

    Citation: BMC Bioinformatics 2017 18(Suppl 15):511

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  15. Content type: Methodology Article

    qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the st...

    Authors: Michael T. Ganger, Geoffrey D. Dietz and Sarah J. Ewing

    Citation: BMC Bioinformatics 2017 18:534

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  16. Content type: Research

    With the rapid development of deep sequencing techniques in the recent years, enhancers have been systematically identified in such projects as FANTOM and ENCODE, forming genome-wide landscapes in a series of ...

    Authors: Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen and Rui Jiang

    Citation: BMC Bioinformatics 2017 18(Suppl 13):478

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  17. Content type: Research

    Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identifi...

    Authors: Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji and Zhiping Weng

    Citation: BMC Bioinformatics 2017 18(Suppl 13):464

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  18. Content type: Methodology Article

    In the search for novel causal mutations, public and/or private variant databases are nearly always used to facilitate the search as they result in a massive reduction of putative variants in one step. Practic...

    Authors: Bart J. G. Broeckx, Luc Peelman, Jimmy H. Saunders, Dieter Deforce and Lieven Clement

    Citation: BMC Bioinformatics 2017 18:535

    Published on:

  19. Content type: Research

    The accurate identification of protein complexes is important for the understanding of cellular organization. Up to now, computational methods for protein complex detection are mostly focus on mining clusters ...

    Authors: Le Ou-Yang, Hong Yan and Xiao-Fei Zhang

    Citation: BMC Bioinformatics 2017 18(Suppl 13):463

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  20. Content type: Research

    RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and...

    Authors: Yongjun Tang, Diwei Liu, Zixiang Wang, Ting Wen and Lei Deng

    Citation: BMC Bioinformatics 2017 18(Suppl 13):465

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  21. Content type: Methodology Article

    High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Cur...

    Authors: Janna L. Fierst and Duncan A. Murdock

    Citation: BMC Bioinformatics 2017 18:533

    Published on:

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