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BMC Bioinformatics

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  1. Content type: Methodology Article

    Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accum...

    Authors: Yahya Bokhari and Tomasz Arodz

    Citation: BMC Bioinformatics 2017 18:458

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  2. Content type: Methodology Article

    Detection of important functional and/or structural elements and identification of their positions in a large eukaryotic genomic sequence are an active research area. Gene is an important functional and struct...

    Authors: Biswanath Chowdhury, Arnav Garai and Gautam Garai

    Citation: BMC Bioinformatics 2017 18:460

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  3. Content type: Research Article

    An organism’s protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally...

    Authors: R. Greg Stacey, Michael A. Skinnider, Nichollas E. Scott and Leonard J. Foster

    Citation: BMC Bioinformatics 2017 18:457

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  4. Content type: Research Article

    In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the bas...

    Authors: Jakub Wiedemann, Tomasz Zok, Maciej Milostan and Marta Szachniuk

    Citation: BMC Bioinformatics 2017 18:456

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  5. Content type: Methodology Article

    DNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variatio...

    Authors: Chaitanya R. Acharya, Kouros Owzar and Andrew S. Allen

    Citation: BMC Bioinformatics 2017 18:455

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  6. Content type: Research

    Predicting protein complexes from protein-protein interaction (PPI) networks has been studied for decade. Various methods have been proposed to address some challenging issues of this problem, including overla...

    Authors: Bin Xu, Yang Wang, Zewei Wang, Jiaogen Zhou, Shuigeng Zhou and Jihong Guan

    Citation: BMC Bioinformatics 2017 18(Suppl 12):419

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  7. Content type: Software

    The recent release of the gene-targeted metagenomics assembler Xander has demonstrated that using the trained Hidden Markov Model (HMM) to guide the traversal of de Bruijn graph gives obvious advantage over other...

    Authors: Dinghua Li, Yukun Huang, Chi-Ming Leung, Ruibang Luo, Hing-Fung Ting and Tak-Wah Lam

    Citation: BMC Bioinformatics 2017 18(Suppl 12):408

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  8. Content type: Research

    Drug Combination is one of the effective approaches for treating complex diseases. However, determining combinative drug pairs in clinical trials is still costly. Thus, computational approaches are used to ide...

    Authors: Jian-Yu Shi, Jia-Xin Li, Ke Gao, Peng Lei and Siu-Ming Yiu

    Citation: BMC Bioinformatics 2017 18(Suppl 12):409

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  9. Content type: Research

    The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning ab...

    Authors: Michał Piotr Startek, Jakub Nogły, Agnieszka Gromadka, Dariusz Grzebelus and Anna Gambin

    Citation: BMC Bioinformatics 2017 18(Suppl 12):422

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    This article is part of a Supplement: Volume 18 Supplement 12

  10. Content type: Research

    Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species....

    Authors: Prapaporn Techa-Angkoon, Yanni Sun and Jikai Lei

    Citation: BMC Bioinformatics 2017 18(Suppl 12):414

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  11. Content type: Research

    Genome rearrangements are essential processes for evolution and are responsible for existing varieties of genome architectures. Many studies have been conducted to obtain an algorithm that identifies the minim...

    Authors: Ghada H. Badr and Haifa A. Al-aqel

    Citation: BMC Bioinformatics 2017 18(Suppl 12):427

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  12. Content type: Research

    The binding of small ligands to RNA elements can cause substantial changes in the RNA structure. This constitutes an important, fast-acting mechanism of ligand-controlled transcriptional and translational gene...

    Authors: Felix Kühnl, Peter F. Stadler and Sebastian Will

    Citation: BMC Bioinformatics 2017 18(Suppl 12):424

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  13. Content type: Research

    Studies have shown that enhancers are significant regulatory elements to play crucial roles in gene expression regulation. Since enhancers are unrelated to the orientation and distance to their target genes, i...

    Authors: Hongda Bu, Yanglan Gan, Yang Wang, Shuigeng Zhou and Jihong Guan

    Citation: BMC Bioinformatics 2017 18(Suppl 12):418

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  14. Content type: Research

    A network motif is defined as a statistically significant and recurring subgraph pattern within a network. Most existing instance collection methods are not feasible due to high memory usage issues and provisi...

    Authors: Wooyoung Kim and Lynnette Haukap

    Citation: BMC Bioinformatics 2017 18(Suppl 12):423

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  15. Content type: Research

    Methylation is a common modification of DNA. It has been a very important and hot topic to study the correlation between methylation and diseases in medical science. Because of the special process with bisulfi...

    Authors: Min Li, Ping Huang, Xiaodong Yan, Jianxin Wang, Yi Pan and Fang-Xiang Wu

    Citation: BMC Bioinformatics 2017 18(Suppl 12):410

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  16. Content type: Research

    Genomic structural variants (SV) play a significant role in the onset and progression of cancer. Genomic deletions can create oncogenic fusion genes or cause the loss of tumor suppressing gene function which c...

    Authors: Matthew Hayes and Jeremy S. Pearson

    Citation: BMC Bioinformatics 2017 18(Suppl 12):413

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    This article is part of a Supplement: Volume 18 Supplement 12

  17. Content type: Research

    Chromosomal deletions represent an important class of human genetic variation. Various methods have been developed to mine “next-generation” sequencing (NGS) data to detect deletions and quantify their clonal ...

    Authors: Colleen M. Bosworth, Sneha Grandhi, Meetha P. Gould and Thomas LaFramboise

    Citation: BMC Bioinformatics 2017 18(Suppl 12):407

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  18. Content type: Research

    Long non-coding RNA (lncRNA) plays important roles in many biological and pathological processes, including transcriptional regulation and gene regulation. As lncRNA interacts with multiple proteins, predicting l...

    Authors: Xiaoxiong Zheng, Yang Wang, Kai Tian, Jiaogen Zhou, Jihong Guan, Libo Luo and Shuigeng Zhou

    Citation: BMC Bioinformatics 2017 18(Suppl 12):420

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 12

  19. Content type: Software

    Threshold regression models are a diverse set of non-regular regression models that all depend on change points or thresholds. They provide a simple but elegant and interpretable way to model certain kinds of ...

    Authors: Youyi Fong, Ying Huang, Peter B. Gilbert and Sallie R. Permar

    Citation: BMC Bioinformatics 2017 18:454

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  20. Content type: Methodology Article

    Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biol...

    Authors: Chenggang Yu, Hyung Jun Woo, Xueping Yu, Tatsuya Oyama, Anders Wallqvist and Jaques Reifman

    Citation: BMC Bioinformatics 2017 18:453

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  21. Content type: Meeting abstracts

    Authors: Eric C. Rouchka, Julia H. Chariker, David A. Tieri, Juw Won Park, Shreedharkumar Rajurkar, Vikas Singh, Nishchal K. Verma, Yan Cui, Mark Farman, Bradford Condon, Neil Moore, Jerzy Jaromczyk, Jolanta Jaromczyk, Daniel Harris, Patrick Calie, Eun Kyong Shin…

    Citation: BMC Bioinformatics 2017 18(Suppl 9):377

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    This article is part of a Supplement: Volume 18 Supplement 9

  22. Content type: Database

    Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. Howe...

    Authors: Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao and Yunping Zhu

    Citation: BMC Bioinformatics 2017 18:452

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  23. Content type: Research Article

    The prediction of human gene–abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with ...

    Authors: Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini

    Citation: BMC Bioinformatics 2017 18:449

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