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  1. Software

    ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data

    Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to re...

    Giorgos Minas, Hiroshi Momiji, Dafyd J. Jenkins, Maria J. Costa, David A. Rand and Bärbel Finkenstädt

    BMC Bioinformatics 2017 18:316

    Published on: 26 June 2017

  2. Methodology Article

    Early response index: a statistic to discover potential early stage disease biomarkers

    Identifying disease correlated features early before large number of molecules are impacted by disease progression with significant abundance change is very advantageous to biologists for developing early dise...

    Sirajul Salekin, Mehrab Ghanat Bari, Itay Raphael, Thomas G. Forsthuber and Jianqiu (Michelle) Zhang

    BMC Bioinformatics 2017 18:313

    Published on: 23 June 2017

  3. Correspondence

    Bioinformatics: indispensable, yet hidden in plain sight?

    Bioinformatics has multitudinous identities, organisational alignments and disciplinary links. This variety allows bioinformaticians and bioinformatic work to contribute to much (if not most) of life science r...

    Andrew Bartlett, Bart Penders and Jamie Lewis

    BMC Bioinformatics 2017 18:311

    Published on: 21 June 2017

  4. Methodology Article

    Quasi-linear score for capturing heterogeneous structure in biomarkers

    Linear scores are widely used to predict dichotomous outcomes in biomedical studies because of their learnability and understandability. Such approaches, however, cannot be used to elucidate biodiversity when ...

    Katsuhiro Omae, Osamu Komori and Shinto Eguchi

    BMC Bioinformatics 2017 18:308

    Published on: 19 June 2017

  5. Research Article

    Biomarker correlation network in colorectal carcinoma by tumor anatomic location

    Colorectal carcinoma evolves through a multitude of molecular events including somatic mutations, epigenetic alterations, and aberrant protein expression, influenced by host immune reactions. One way to interr...

    Reiko Nishihara, Kimberly Glass, Kosuke Mima, Tsuyoshi Hamada, Jonathan A. Nowak, Zhi Rong Qian, Peter Kraft, Edward L. Giovannucci, Charles S. Fuchs, Andrew T. Chan, John Quackenbush, Shuji Ogino and Jukka-Pekka Onnela

    BMC Bioinformatics 2017 18:304

    Published on: 17 June 2017

  6. Software

    Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data

    The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration...

    Atul Kamboj, Claus V. Hallwirth, Ian E. Alexander, Geoffrey B. McCowage and Belinda Kramer

    BMC Bioinformatics 2017 18:305

    Published on: 17 June 2017

  7. Research article

    Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences

    DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA), and DNA-binding p...

    Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu and Keliang Li

    BMC Bioinformatics 2017 18:300

    Published on: 12 June 2017

  8. Research

    Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire

    For fighting cancer, earlier detection is crucial. Circulating auto-antibodies produced by the patient’s own immune system after exposure to cancer proteins are promising bio-markers for the early detection of...

    Ekaterina Gerasimov, Alex Zelikovsky, Ion Măndoiu and Yurij Ionov

    BMC Bioinformatics 2017 18(Suppl 8):244

    Published on: 7 June 2017

    This article is part of a Supplement: Volume 18 Supplement 8

  9. Research

    A greedy alignment-free distance estimator for phylogenetic inference

    Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k-mer base...

    Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan and Srinivas Aluru

    BMC Bioinformatics 2017 18(Suppl 8):238

    Published on: 7 June 2017

    This article is part of a Supplement: Volume 18 Supplement 8

  10. Methodology

    ATria: a novel centrality algorithm applied to biological networks

    The notion of centrality is used to identify “important” nodes in social networks. Importance of nodes is not well-defined, and many different notions exist in the literature. The challenge of defining centrality...

    Trevor Cickovski, Eli Peake, Vanessa Aguiar-Pulido and Giri Narasimhan

    BMC Bioinformatics 2017 18(Suppl 8):239

    Published on: 7 June 2017

    This article is part of a Supplement: Volume 18 Supplement 8

  11. Research

    A theorem proving approach for automatically synthesizing visualizations of flow cytometry data

    Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytome...

    Sunny Raj, Faraz Hussain, Zubir Husein, Neslisah Torosdagli, Damla Turgut, Narsingh Deo, Sumanta Pattanaik, Chung-Che (Jeff) Chang and Sumit Kumar Jha

    BMC Bioinformatics 2017 18(Suppl 8):245

    Published on: 7 June 2017

    This article is part of a Supplement: Volume 18 Supplement 8

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