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  1. Methodology Article

    DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

    The development of single-cell RNA sequencing has enabled profound discoveries in biology, ranging from the dissection of the composition of complex tissues to the identification of novel cell types and dynami...

    Zhuo Wang, Shuilin Jin, Guiyou Liu, Xiurui Zhang, Nan Wang, Deliang Wu, Yang Hu, Chiping Zhang, Qinghua Jiang, Li Xu and Yadong Wang

    BMC Bioinformatics 2017 18:270

    Published on: 23 May 2017

  2. Software

    CircularLogo: A lightweight web application to visualize intra-motif dependencies

    The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-mo...

    Zhenqing Ye, Tao Ma, Michael T. Kalmbach, Surendra Dasari, Jean-Pierre A. Kocher and Liguo Wang

    BMC Bioinformatics 2017 18:269

    Published on: 22 May 2017

  3. Research Article

    Coordinates and intervals in graph-based reference genomes

    It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represe...

    Knut D. Rand, Ivar Grytten, Alexander J. Nederbragt, Geir O. Storvik, Ingrid K. Glad and Geir K. Sandve

    BMC Bioinformatics 2017 18:263

    Published on: 18 May 2017

  4. Software

    NFPscanner: a webtool for knowledge-based deciphering of biomedical networks

    Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are u...

    Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo and Fei Li

    BMC Bioinformatics 2017 18:262

    Published on: 18 May 2017

  5. Research Article

    The rainfall plot: its motivation, characteristics and pitfalls

    A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference geno...

    Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig and Geir Kjetil Sandve

    BMC Bioinformatics 2017 18:264

    Published on: 18 May 2017

  6. Software

    Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order

    Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually ch...

    Miles Aron, Richard Browning, Dario Carugo, Erdinc Sezgin, Jorge Bernardino de la Serna, Christian Eggeling and Eleanor Stride

    BMC Bioinformatics 2017 18:254

    Published on: 12 May 2017

  7. Methodology Article

    HLAscan: genotyping of the HLA region using next-generation sequencing data

    Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, ...

    Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim and Jongsun Jung

    BMC Bioinformatics 2017 18:258

    Published on: 12 May 2017

  8. Methodology Article

    Epimetheus - a multi-profile normalizer for epigenomic sequencing data

    Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene...

    Mohamed-Ashick M. Saleem, Marco-Antonio Mendoza-Parra, Pierre-Etienne Cholley, Matthias Blum and Hinrich Gronemeyer

    BMC Bioinformatics 2017 18:259

    Published on: 12 May 2017

  9. Research Article

    Ranking metrics in gene set enrichment analysis: do they matter?

    There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment...

    Joanna Zyla, Michal Marczyk, January Weiner and Joanna Polanska

    BMC Bioinformatics 2017 18:256

    Published on: 12 May 2017

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

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