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  1. Commentary

    Solving the master equation for Indels

    Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that a...

    Ian H. Holmes

    BMC Bioinformatics 2017 18:255

    Published on: 12 May 2017

  2. Research Article

    LASSIE: simulating large-scale models of biochemical systems on GPUs

    Mathematical modeling and in silico analysis are widely acknowledged as complementary tools to biological laboratory methods, to achieve a thorough understanding of emergent behaviors of cellular processes in ...

    Andrea Tangherloni, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri and Paolo Cazzaniga

    BMC Bioinformatics 2017 18:246

    Published on: 10 May 2017

  3. Software

    ImmunoNodes – graphical development of complex immunoinformatics workflows

    Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based immunoinformatics tools, on the...

    Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer and Oliver Kohlbacher

    BMC Bioinformatics 2017 18:242

    Published on: 8 May 2017

  4. Research Article

    A time series driven decomposed evolutionary optimization approach for reconstructing large-scale gene regulatory networks based on fuzzy cognitive maps

    Reconstructing gene regulatory networks (GRNs) from expression data plays an important role in understanding the fundamental cellular processes and revealing the underlying relations among genes. Although many...

    Jing Liu, Yaxiong Chi, Chen Zhu and Yaochu Jin

    BMC Bioinformatics 2017 18:241

    Published on: 8 May 2017

  5. Database

    Geminivirus data warehouse: a database enriched with machine learning approaches

    The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible fo...

    Jose Cleydson F. Silva, Thales F. M. Carvalho, Marcos F. Basso, Michihito Deguchi, Welison A. Pereira, Roberto R. Sobrinho, Pedro M. P. Vidigal, Otávio J. B. Brustolini, Fabyano F. Silva, Maximiller Dal-Bianco, Renildes L. F. Fontes, Anésia A. Santos, Francisco Murilo Zerbini, Fabio R. Cerqueira and Elizabeth P. B. Fontes

    BMC Bioinformatics 2017 18:240

    Published on: 5 May 2017

  6. Software

    WebGIVI: a web-based gene enrichment analysis and visualization tool

    A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined fo...

    Liang Sun, Yongnan Zhu, A. S. M. Ashique Mahmood, Catalina O. Tudor, Jia Ren, K. Vijay-Shanker, Jian Chen and Carl J. Schmidt

    BMC Bioinformatics 2017 18:237

    Published on: 4 May 2017

  7. Methodology Article

    Power analysis for RNA-Seq differential expression studies

    Sample size calculation and power estimation are essential components of experimental designs in biomedical research. It is very challenging to estimate power for RNA-Seq differential expression under complex ...

    Lianbo Yu, Soledad Fernandez and Guy Brock

    BMC Bioinformatics 2017 18:234

    Published on: 3 May 2017

  8. Software

    microTaboo: a general and practical solution to the k-disjoint problem

    A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting....

    Mohammed Al-Jaff, Eric Sandström and Manfred Grabherr

    BMC Bioinformatics 2017 18:228

    Published on: 2 May 2017

  9. Methodology Article

    Zipper plot: visualizing transcriptional activity of genomic regions

    Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA...

    Francisco Avila Cobos, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter and Pieter Mestdagh

    BMC Bioinformatics 2017 18:231

    Published on: 2 May 2017

  10. Software

    ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins

    Recent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called “microbial dark matter” (microbes that until now have ...

    Bertjan Broeksema, Magdalena Calusinska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse and Mohammad Ghoniem

    BMC Bioinformatics 2017 18:233

    Published on: 2 May 2017

  11. Research Article

    A vascular image registration method based on network structure and circuit simulation

    Image registration is an important research topic in the field of image processing. Applying image registration to vascular image allows multiple images to be strengthened and fused, which has practical value ...

    Li Chen, Yuxi Lian, Yi Guo, Yuanyuan Wang, Thomas S. Hatsukami, Kristi Pimentel, Niranjan Balu and Chun Yuan

    BMC Bioinformatics 2017 18:229

    Published on: 2 May 2017

  12. Software

    QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

    Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to f...

    Loris Bertoldi, Claudio Forcato, Nicola Vitulo, Giovanni Birolo, Fabio De Pascale, Erika Feltrin, Riccardo Schiavon, Franca Anglani, Susanna Negrisolo, Alessandra Zanetti, Francesca D’Avanzo, Rosella Tomanin, Georgine Faulkner, Alessandro Vezzi and Giorgio Valle

    BMC Bioinformatics 2017 18:225

    Published on: 28 April 2017

  13. Database

    MYCbase: a database of functional sites and biochemical properties of Myc in both normal and cancer cells

    Myc is an essential gene having multiple functions such as in cell growth, differentiation, apoptosis, genomic stability, angiogenesis, and disease biology. A large number of researchers dedicated to Myc biolo...

    Debangana Chakravorty, Tanmoy Jana, Sukhen Das Mandal, Anuradha Seth, Anubrata Bhattacharya and Sudipto Saha

    BMC Bioinformatics 2017 18:224

    Published on: 28 April 2017

  14. Methodology Article

    De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline

    The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together...

    You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen and Hurng-Yi Wang

    BMC Bioinformatics 2017 18:223

    Published on: 26 April 2017

  15. Software

    An auditory display tool for DNA sequence analysis

    DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorith...

    Mark D. Temple

    BMC Bioinformatics 2017 18:221

    Published on: 24 April 2017

  16. Research Article

    AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

    Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the...

    Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee and Chatchai Tayapiwatana

    BMC Bioinformatics 2017 18:220

    Published on: 19 April 2017

  17. Research Article

    On the association analysis of CNV data: a fast and robust family-based association method

    Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical m...

    Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C. Elston, Bong-Jo Kim and Sungho Won

    BMC Bioinformatics 2017 18:217

    Published on: 18 April 2017

  18. Research article

    Comparison of different cell type correction methods for genome-scale epigenetics studies

    Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular h...

    Akhilesh Kaushal, Hongmei Zhang, Wilfried J. J. Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith and Shu-Li Wang

    BMC Bioinformatics 2017 18:216

    Published on: 14 April 2017

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