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  1. Software

    StrAuto: automation and parallelization of STRUCTURE analysis

    Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data...

    Vikram E. Chhatre and Kevin J. Emerson

    BMC Bioinformatics 2017 18:192

    Published on: 24 March 2017

  2. Research article

    Genomic prediction using subsampling

    Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fittin...

    Alencar Xavier, Shizhong Xu, William Muir and Katy Martin Rainey

    BMC Bioinformatics 2017 18:191

    Published on: 24 March 2017

  3. Research article

    DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins

    Insecticide resistance is a major challenge for the control program of insect pests in the fields of crop protection, human and animal health etc. Resistance to different insecticides is conferred by the prote...

    Prabina Kumar Meher, Tanmaya Kumar Sahu, Anjali Banchariya and Atmakuri Ramakrishna Rao

    BMC Bioinformatics 2017 18:190

    Published on: 24 March 2017

  4. Methodology Article

    Enhanced construction of gene regulatory networks using hub gene information

    Gene regulatory networks reveal how genes work together to carry out their biological functions. Reconstructions of gene networks from gene expression data greatly facilitate our understanding of underlying bi...

    Donghyeon Yu, Johan Lim, Xinlei Wang, Faming Liang and Guanghua Xiao

    BMC Bioinformatics 2017 18:186

    Published on: 23 March 2017

  5. Research article

    Generalizing cell segmentation and quantification

    In recent years, the microscopy technology for imaging cells has developed greatly and rapidly. The accompanying requirements for automatic segmentation and quantification of the imaged cells are becoming more...

    Zhenzhou Wang and Haixing Li

    BMC Bioinformatics 2017 18:189

    Published on: 23 March 2017

  6. Research Article

    Identification of long non-coding transcripts with feature selection: a comparative study

    The unveiling of long non-coding RNAs as important gene regulators in many biological contexts has increased the demand for efficient and robust computational methods to identify novel long non-coding RNAs fro...

    Giovanna M. M. Ventola, Teresa M. R. Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli and Luigi Cerulo

    BMC Bioinformatics 2017 18:187

    Published on: 23 March 2017

  7. Research

    Interpretive time-frequency analysis of genomic sequences

    Time-Frequency (TF) analysis has been extensively used for the analysis of non-stationary numeric signals in the past decade. At the same time, recent studies have statistically confirmed the non-stationarity ...

    Hamed Hassani Saadi, Reza Sameni and Amin Zollanvari

    BMC Bioinformatics 2017 18(Suppl 4):154

    Published on: 22 March 2017

    This article is part of a Supplement: Volume 18 Supplement 4

  8. Research

    Combination therapy design for maximizing sensitivity and minimizing toxicity

    Design of personalized targeted therapies involve modeling of patient sensitivity to various drugs and drug combinations. Majority of studies evaluate the sensitivity of tumor cells to targeted drugs without m...

    Kevin Matlock, Noah Berlow, Charles Keller and Ranadip Pal

    BMC Bioinformatics 2017 18(Suppl 4):116

    Published on: 22 March 2017

    This article is part of a Supplement: Volume 18 Supplement 4

  9. Research

    Towards targeted combinatorial therapy design for the treatment of castration-resistant prostate cancer

    Prostate cancer is one of the most prevalent cancers in males in the United States and amongst the leading causes of cancer related deaths. A particularly virulent form of this disease is castration-resistant ...

    Osama Ali Arshad and Aniruddha Datta

    BMC Bioinformatics 2017 18(Suppl 4):134

    Published on: 22 March 2017

    This article is part of a Supplement: Volume 18 Supplement 4

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

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