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  1. Targeted next-generation sequencing is playing an increasingly important role in biological research and clinical diagnosis by allowing researchers to sequence high priority genes at much higher depths and at ...

    Authors: Likun Wang, Cong Zhang, Johnathan Watkins, Yan Jin, Michael McNutt and Yuxin Yin
    Citation: BMC Bioinformatics 2016 17:153
    Content type: Software Published on:

  3. Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and ...

    Authors: Joost B. Beltman, Jos Urbanus, Arno Velds, Nienke van Rooij, Jan C. Rohr, Shalin H. Naik and Ton N. Schumacher
    Citation: BMC Bioinformatics 2016 17:151
    Content type: Methodology article Published on:

  4. The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial fir...

    Authors: Jouhyun Jeon, Roland Arnold, Fateh Singh, Joan Teyra, Tatjana Braun and Philip M. Kim
    Citation: BMC Bioinformatics 2016 17:150
    Content type: Software Published on:

  6. Massive parallel sequencing of transcriptomes, revealed the presence of many miRNAs and miRNAs variants named isomiRs with a potential role in several cellular processes through their interaction with a target...

    Authors: Gianvito Urgese, Giulia Paciello, Andrea Acquaviva and Elisa Ficarra
    Citation: BMC Bioinformatics 2016 17:148
    Content type: Software Published on:

  8. RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small nu...

    Authors: Ran Bi and Peng Liu
    Citation: BMC Bioinformatics 2016 17:146
    Content type: Methodology Article Published on:

  9. Random forests have often been claimed to uncover interaction effects. However, if and how interaction effects can be differentiated from marginal effects remains unclear. In extensive simulation studies, we i...

    Authors: Marvin N. Wright, Andreas Ziegler and Inke R. König
    Citation: BMC Bioinformatics 2016 17:145
    Content type: Research Article Published on:

  11. In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all 203 possi...

    Authors: Michael Hoff, Stefan Orf, Benedikt Riehm, Diego Darriba and Alexandros Stamatakis
    Citation: BMC Bioinformatics 2016 17:143
    Content type: Research Article Published on:

  12. High-throughput bio-OMIC technologies are producing high-dimension data from bio-samples at an ever increasing rate, whereas the training sample number in a traditional experiment remains small due to various ...

    Authors: Ruiquan Ge, Manli Zhou, Youxi Luo, Qinghan Meng, Guoqin Mai, Dongli Ma, Guoqing Wang and Fengfeng Zhou
    Citation: BMC Bioinformatics 2016 17:142
    Content type: Methodology article Published on:

  15. The pathophysiological overlapping between Sjorgen’s Syndrome (SS) and HCV, presence of anti- muscarinic receptor type 3 (M3R) antibodies in SS, the role that M3R plays in the regulation of the heart rate, has...

    Authors: Sanja Glišić, David P. Cavanaugh, Krishnan K. Chittur, Milan Sencanski, Vladimir Perovic and Tijana Bojić
    Citation: BMC Bioinformatics 2016 17:139
    Content type: Research article Published on:

  16. Several techniques have been tailored to the quantification of microRNA expression, including hybridization arrays, quantitative PCR (qPCR), and high-throughput sequencing. Each of these has certain strengths ...

    Authors: Matthew N. McCall, Alexander S. Baras, Alexander Crits-Christoph, Roxann Ingersoll, Melissa A. McAlexander, Kenneth W. Witwer and Marc K. Halushka
    Citation: BMC Bioinformatics 2016 17:138
    Content type: Research Article Published on:

  22. Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available...

    Authors: Sapna Kumari, Wenping Deng, Chathura Gunasekara, Vincent Chiang, Huann-sheng Chen, Hao Ma, Xin Davis and Hairong Wei
    Citation: BMC Bioinformatics 2016 17:132
    Content type: Methodology article Published on:

  25. It is generally acknowledged that a functional understanding of a biological system can only be obtained by an understanding of the collective of molecular interactions in form of biological networks. Protein ...

    Authors: Shailesh Tripathi, Salissou Moutari, Matthias Dehmer and Frank Emmert-Streib
    Citation: BMC Bioinformatics 2016 17:129
    Content type: Research Article Published on:

  26. Molecular structures can be represented as strings of special characters using SMILES. Since each molecule is represented as a string, the similarity between compounds can be computed using SMILES-based string...

    Authors: Hakime Öztürk, Elif Ozkirimli and Arzucan Özgür
    Citation: BMC Bioinformatics 2016 17:128
    Content type: Research Article Published on:

  27. Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end...

    Authors: Luis de la Garza, Johannes Veit, Andras Szolek, Marc Röttig, Stephan Aiche, Sandra Gesing, Knut Reinert and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2016 17:127
    Content type: Software Published on:

  28. Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biom...

    Authors: Kévin Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew C. Parnell, Stephen V. Gordon and David E. MacHugh
    Citation: BMC Bioinformatics 2016 17:126
    Content type: Software Published on:

  29. Illumina’s sequencing platforms are currently the most utilised sequencing systems worldwide. The technology has rapidly evolved over recent years and provides high throughput at low costs with increasing read...

    Authors: Melanie Schirmer, Rosalinda D’Amore, Umer Z. Ijaz, Neil Hall and Christopher Quince
    Citation: BMC Bioinformatics 2016 17:125
    Content type: Research Article Published on:

  31. We examine several of the choices that went into the design of tDRmapper, a recently reported tool for identifying transfer RNA (tRNA) fragments in deep sequencing data, evaluate them in the context of current...

    Authors: Aristeidis G. Telonis, Phillipe Loher, Yohei Kirino and Isidore Rigoutsos
    Citation: BMC Bioinformatics 2016 17:123
    Content type: Correspondence Published on:

  32. Identifying subpopulations within a study and inferring intercontinental ancestry of the samples are important steps in genome wide association studies. Two software packages are widely used in analysis of sub...

    Authors: Yafang Li, Jinyoung Byun, Guoshuai Cai, Xiangjun Xiao, Younghun Han, Olivier Cornelis, James E. Dinulos, Joe Dennis, Douglas Easton, Ivan Gorlov, Michael F. Seldin and Christopher I. Amos
    Citation: BMC Bioinformatics 2016 17:122
    Content type: Software Published on:

  34. Confounding due to cellular heterogeneity represents one of the foremost challenges currently facing Epigenome-Wide Association Studies (EWAS). Statistical methods leveraging the tissue-specificity of DNA meth...

    Authors: Devin C. Koestler, Meaghan J. Jones, Joseph Usset, Brock C. Christensen, Rondi A. Butler, Michael S. Kobor, John K. Wiencke and Karl T. Kelsey
    Citation: BMC Bioinformatics 2016 17:120
    Content type: Methodology Article Published on:

  39. Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive ...

    Authors: Mohammed-Amin Madoui, Carole Dossat, Léo d’Agata, Jan van Oeveren, Edwin van der Vossen and Jean-Marc Aury
    Citation: BMC Bioinformatics 2016 17:115
    Content type: Methodology article Published on:

  40. Interpreting non-targeted metabolomics data remains a challenging task. Signals from non-targeted metabolomics studies stem from a combination of biological causes, complex interactions between them and experi...

    Authors: Youzhong Liu, Kirill Smirnov, Marianna Lucio, Régis D. Gougeon, Hervé Alexandre and Philippe Schmitt-Kopplin
    Citation: BMC Bioinformatics 2016 17:114
    Content type: Methodology article Published on:

  41. Genomic, transcriptomic, and metabolic variations shape the complex adaptation landscape of bacteria to varying environmental conditions. Elucidating the genotype-phenotype relation paves the way for the predi...

    Authors: Claudio Angione, Max Conway and Pietro Lió
    Citation: BMC Bioinformatics 2016 17(Suppl 4):83
    Content type: Research Article Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  42. Bisulfite treatment of DNA followed by sequencing (BS-seq) has become a standard technique in epigenetic studies, providing researchers with tools for generating single-base resolution maps of whole methylomes...

    Authors: Nicola Prezza, Francesco Vezzi, Max Käller and Alberto Policriti
    Citation: BMC Bioinformatics 2016 17(Suppl 4):69
    Content type: Research Article Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  43. The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology. The topics of the workshop were centre...

    Authors: Paolo Romano and Francesca Cordero
    Citation: BMC Bioinformatics 2016 17(Suppl 4):62
    Content type: Editorial Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:293

  44. Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at d...

    Authors: Paolo Romano, Aldo Profumo, Mattia Rocco, Rosa Mangerini, Fabio Ferri and Angelo Facchiano
    Citation: BMC Bioinformatics 2016 17(Suppl 4):61
    Content type: Research article Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  45. Phosphorylation is one of the most important post-translational modifications (PTM) employed by cells to regulate several cellular processes. Studying the effects of phosphorylations on protein structures allo...

    Authors: Federica Chiappori, Luca Mattiazzi, Luciano Milanesi and Ivan Merelli
    Citation: BMC Bioinformatics 2016 17(Suppl 4):57
    Content type: Research article Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  46. Biologists generally interrogate genomics data using web-based genome browsers that have limited analytical potential. New generation genome browsers such as the Integrated Genome Browser (IGB) have largely ov...

    Authors: Arnaud Céol, Lisette G. G. C. Verhoef, Mark Wade and Heiko Muller
    Citation: BMC Bioinformatics 2016 17(Suppl 4):54
    Content type: Research article Published on:

    This article is part of a Supplement: Volume 17 Supplement 4

  47. Drug discovery and design are important research fields in bioinformatics. Enumeration of chemical compounds is essential not only for the purpose, but also for analysis of chemical space and structure elucida...

    Authors: Jira Jindalertudomdee, Morihiro Hayashida, Yang Zhao and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2016 17:113
    Content type: Research Article Published on:

  48. MicroRNAs (miRNAs) regulate gene expression by targeting complementary mRNAs for destruction or translational repression. Aberrant expression of miRNAs has been associated with various diseases including cance...

    Authors: Biao Liu, Jessica L. Childs-Disney, Brent M. Znosko, Dan Wang, Mohammad Fallahi, Steven M. Gallo and Matthew D. Disney
    Citation: BMC Bioinformatics 2016 17:112
    Content type: Research article Published on:

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