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  1. Methodology Article

    Significance evaluation in factor graphs

    Factor graphs provide a flexible and general framework for specifying probability distributions. They can capture a range of popular and recent models for analysis of both genomics data as well as data from ot...

    Tobias Madsen, Asger Hobolth, Jens Ledet Jensen and Jakob Skou Pedersen

    BMC Bioinformatics 2017 18:199

    Published on: 31 March 2017

  2. Research Article

    The autophagy interaction network of the aging model Podospora anserina

    Autophagy is a conserved molecular pathway involved in the degradation and recycling of cellular components. It is active either as response to starvation or molecular damage. Evidence is emerging that autopha...

    Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz and Ina Koch

    BMC Bioinformatics 2017 18:196

    Published on: 27 March 2017

  3. 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

  4. 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

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:222

  5. 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

  6. Introduction

    The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes

    The 15th International NETTAB workshop and the 11th Integrative Bioinformatics Symposium were held together in Bari, on October 14–16, 2016, as Joint NETTAB/IB 2015 Meeting. A special topic for the meeting was “B...

    Paolo Romano, Ralf Hofestädt, Matthias Lange and Domenica D’Elia

    BMC Bioinformatics 2017 18(Suppl 5):101

    Published on: 23 March 2017

    This article is part of a Supplement: Volume 18 Supplement 5

  7. 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

  8. Research

    Network-based analysis of transcriptional profiles from chemical perturbations experiments

    Methods for inference and comparison of biological networks are emerging as powerful tools for the identification of groups of tightly connected genes whose activity may be altered during disease progression o...

    Francesca Mulas, Amy Li, David H. Sherr and Stefano Monti

    BMC Bioinformatics 2017 18(Suppl 5):130

    Published on: 23 March 2017

    This article is part of a Supplement: Volume 18 Supplement 5

  9. Research

    In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression

    In recent years long non coding RNAs (lncRNAs) have been the subject of increasing interest. Thanks to many recent functional studies, the existence of a large class of lncRNAs with potential regulatory functi...

    Umberto Perron, Paolo Provero and Ivan Molineris

    BMC Bioinformatics 2017 18(Suppl 5):144

    Published on: 23 March 2017

    This article is part of a Supplement: Volume 18 Supplement 5

  10. 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

  11. Research

    Improving the accuracy of high-throughput protein-protein affinity prediction may require better training data

    One goal of structural biology is to understand how a protein’s 3-dimensional conformation determines its capacity to interact with potential ligands. In the case of small chemical ligands, deconstructing a st...

    Raquel Dias and Bryan Kolaczkowski

    BMC Bioinformatics 2017 18(Suppl 5):102

    Published on: 23 March 2017

    This article is part of a Supplement: Volume 18 Supplement 5

  12. Research

    GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data

    NGS technology represents a powerful alternative to the standard Sanger sequencing in the context of clinical setting. The proprietary software that are generally used for variant calling often depend on prese...

    Simona De Summa, Giovanni Malerba, Rosamaria Pinto, Antonio Mori, Vladan Mijatovic and Stefania Tommasi

    BMC Bioinformatics 2017 18(Suppl 5):119

    Published on: 23 March 2017

    This article is part of a Supplement: Volume 18 Supplement 5

  13. 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

  14. Research

    NEArender: an R package for functional interpretation of ‘omics’ data via network enrichment analysis

    The statistical evaluation of pathway enrichment, i.e. of gene profiles' confluence to the pathway level, allows exploring molecular landscapes using functionally annotated gene sets. However, pathway scores c...

    Ashwini Jeggari and Andrey Alexeyenko

    BMC Bioinformatics 2017 18(Suppl 5):118

    Published on: 23 March 2017

    This article is part of a Supplement: Volume 18 Supplement 5

  15. 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

  16. 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

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