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  1. Software

    TreeToReads - a pipeline for simulating raw reads from phylogenies

    Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several...

    Emily Jane McTavish, James Pettengill, Steven Davis, Hugh Rand, Errol Strain, Marc Allard and Ruth E. Timme

    BMC Bioinformatics 2017 18:178

    Published on: 20 March 2017

  2. Software

    LW-FQZip 2: a parallelized reference-based compression of FASTQ files

    The rapid progress of high-throughput DNA sequencing techniques has dramatically reduced the costs of whole genome sequencing, which leads to revolutionary advances in gene industry. The explosively increasing...

    Zhi-An Huang, Zhenkun Wen, Qingjin Deng, Ying Chu, Yiwen Sun and Zexuan Zhu

    BMC Bioinformatics 2017 18:179

    Published on: 20 March 2017

  3. Methodology Article

    Preservation affinity in consensus modules among stages of HIV-1 progression

    Analysis of gene expression data provides valuable insights into disease mechanism. Investigating relationship among co-expression modules of different stages is a meaningful tool to understand the way in whic...

    Sk Md Mosaddek Hossain, Sumanta Ray and Anirban Mukhopadhyay

    BMC Bioinformatics 2017 18:181

    Published on: 20 March 2017

  4. Methodology article

    EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples

    Characterization of mature protein N-termini by large scale proteomics is challenging. This is especially true for proteins undergoing cleavage of transit peptides when they are targeted to specific organelles...

    Willy Vincent Bienvenut, Jean-Pierre Scarpelli, Johan Dumestier, Thierry Meinnel and Carmela Giglione

    BMC Bioinformatics 2017 18:182

    Published on: 20 March 2017

  5. Software

    QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing

    Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate m...

    Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent and Baohong Zhang

    BMC Bioinformatics 2017 18:180

    Published on: 20 March 2017

  6. Research Article

    Using simulated fluorescence cell micrographs for the evaluation of cell image segmentation algorithms

    Manual assessment and evaluation of fluorescent micrograph cell experiments is time-consuming and tedious. Automated segmentation pipelines can ensure efficient and reproducible evaluation and analysis with co...

    Veit Wiesmann, Matthias Bergler, Ralf Palmisano, Martin Prinzen, Daniela Franz and Thomas Wittenberg

    BMC Bioinformatics 2017 18:176

    Published on: 18 March 2017

  7. Software

    microclass: an R-package for 16S taxonomy classification

    Taxonomic classification based on the 16S rRNA gene sequence is important for the profiling of microbial communities. In addition to giving the best possible accuracy, it is also important to quantify uncertai...

    Kristian Hovde Liland, Hilde Vinje and Lars Snipen

    BMC Bioinformatics 2017 18:172

    Published on: 16 March 2017

  8. Methodology Article

    Subgroup detection in genotype data using invariant coordinate selection

    The current gold standard in dimension reduction methods for high-throughput genotype data is the Principle Component Analysis (PCA). The presence of PCA is so dominant, that other methods usually cannot be fo...

    Daniel Fischer, Mervi Honkatukia, Maria Tuiskula-Haavisto, Klaus Nordhausen, David Cavero, Rudolf Preisinger and Johanna Vilkki

    BMC Bioinformatics 2017 18:173

    Published on: 16 March 2017

  9. Research

    Improving prediction of burial state of residues by exploiting correlation among residues

    Residues in a protein might be buried inside or exposed to the solvent surrounding the protein. The buried residues usually form hydrophobic cores to maintain the structural integrity of proteins while the exp...

    Hai’e Gong, Haicang Zhang, Jianwei Zhu, Chao Wang, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu

    BMC Bioinformatics 2017 18(Suppl 3):70

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 3

  10. Research

    AfterQC: automatic filtering, trimming, error removing and quality control for fastq data

    Some applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed...

    Shifu Chen, Tanxiao Huang, Yanqing Zhou, Yue Han, Mingyan Xu and Jia Gu

    BMC Bioinformatics 2017 18(Suppl 3):80

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 3

  11. Research

    Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features

    Protein carbonylation, an irreversible and non-enzymatic post-translational modification (PTM), is often used as a marker of oxidative stress. When reactive oxygen species (ROS) oxidized the amino acid side ch...

    Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Chien-Hsun Huang, Hui-Ju Kao, Tzu-Hao Chang, Hsin-Yao Wang, Jang-Jih Lu and Tzong-Yi Lee

    BMC Bioinformatics 2017 18(Suppl 3):66

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 3

  12. Research

    DTL reconciliation repair

    Maximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs. Since the p...

    Weiyun Ma, Dmitriy Smirnov and Ran Libeskind-Hadas

    BMC Bioinformatics 2017 18(Suppl 3):76

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 3

  13. Research

    Comparative network stratification analysis for identifying functional interpretable network biomarkers

    A major challenge of bioinformatics in the era of precision medicine is to identify the molecular biomarkers for complex diseases. It is a general expectation that these biomarkers or signatures have not only ...

    Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng and Luonan Chen

    BMC Bioinformatics 2017 18(Suppl 3):48

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 3

  14. Research

    A framework for space-efficient read clustering in metagenomic samples

    A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning ...

    Jarno Alanko, Fabio Cunial, Djamal Belazzougui and Veli Mäkinen

    BMC Bioinformatics 2017 18(Suppl 3):59

    Published on: 14 March 2017

    This article is part of a Supplement: Volume 18 Supplement 3

  15. Research article

    MicroRNA categorization using sequence motifs and k-mers

    Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and...

    Malik Yousef, Waleed Khalifa, İlhan Erkin Acar and Jens Allmer

    BMC Bioinformatics 2017 18:170

    Published on: 14 March 2017

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