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  1. Methodology Article

    Mapping eQTL by leveraging multiple tissues and DNA methylation

    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...

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

    BMC Bioinformatics 2017 18:455

    Published on: 18 October 2017

  2. Research

    DCJ-RNA - double cut and join for RNA secondary structures

    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...

    Ghada H. Badr and Haifa A. Al-aqel

    BMC Bioinformatics 2017 18(Suppl 12):427

    Published on: 16 October 2017

  3. Research

    Tractable RNA–ligand interaction kinetics

    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...

    Felix Kühnl, Peter F. Stadler and Sebastian Will

    BMC Bioinformatics 2017 18(Suppl 12):424

    Published on: 16 October 2017

  4. Research

    A new method for enhancer prediction based on deep belief network

    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...

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

    BMC Bioinformatics 2017 18(Suppl 12):418

    Published on: 16 October 2017

  5. Research

    VAliBS: a visual aligner for bisulfite sequences

    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...

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

    BMC Bioinformatics 2017 18(Suppl 12):410

    Published on: 16 October 2017

  6. Research

    Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions

    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...

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

    BMC Bioinformatics 2017 18(Suppl 12):420

    Published on: 16 October 2017

  7. Software

    chngpt: threshold regression model estimation and inference

    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 ...

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

    BMC Bioinformatics 2017 18:454

    Published on: 16 October 2017

  8. Methodology Article

    A strategy for evaluating pathway analysis methods

    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...

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

    BMC Bioinformatics 2017 18:453

    Published on: 13 October 2017

  9. Meeting abstracts

    Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics

    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…

    BMC Bioinformatics 2017 18(Suppl 9):377

    Published on: 13 October 2017

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

  10. Database

    LiverWiki: a wiki-based database for human liver

    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...

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

    BMC Bioinformatics 2017 18:452

    Published on: 13 October 2017

  11. Software

    VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data

    Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perfor...

    Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy L. Monson, William H. Rounds, Florian Rubelt, Walter Scarborough, Richard H. Scheuermann and Lindsay G. Cowell

    BMC Bioinformatics 2017 18:448

    Published on: 11 October 2017

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