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  1. Software

    LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data

    Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Me...

    Jeremy P. Koelmel, Nicholas M. Kroeger, Candice Z. Ulmer, John A. Bowden, Rainey E. Patterson, Jason A. Cochran, Christopher W. W. Beecher, Timothy J. Garrett and Richard A. Yost

    BMC Bioinformatics 2017 18:331

    Published on: 10 July 2017

  2. Research Article

    Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm

    Biomarker detection presents itself as a major means of translating biological data into clinical applications. Due to the recent advances in high throughput sequencing technologies, an increased number of met...

    Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin and Jan Suchodolski

    BMC Bioinformatics 2017 18:328

    Published on: 10 July 2017

  3. Software

    sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

    sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA)....

    Shailesh Tripathi, Jason Lloyd-Price, Andre Ribeiro, Olli Yli-Harja, Matthias Dehmer and Frank Emmert-Streib

    BMC Bioinformatics 2017 18:325

    Published on: 4 July 2017

  4. Methodology Article

    An improved filtering algorithm for big read datasets and its application to single-cell assembly

    For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This lea...

    Axel Wedemeyer, Lasse Kliemann, Anand Srivastav, Christian Schielke, Thorsten B. Reusch and Philip Rosenstiel

    BMC Bioinformatics 2017 18:324

    Published on: 3 July 2017

  5. Software

    SLMSuite: a suite of algorithms for segmenting genomic profiles

    The identification of copy number variants (CNVs) is essential to study human genetic variation and to understand the genetic basis of mendelian disorders and cancers. At present, genome-wide detection of CNVs...

    Valerio Orlandini, Aldesia Provenzano, Sabrina Giglio and Alberto Magi

    BMC Bioinformatics 2017 18:321

    Published on: 28 June 2017

  6. Software

    Semi-automated quantitative Drosophila wings measurements

    Drosophila melanogaster is an important organism used in many fields of biological research such as genetics and developmental biology. Drosophila wings have been widely used to study ...

    Sheng Yang Michael Loh, Yoshitaka Ogawa, Sara Kawana, Koichiro Tamura and Hwee Kuan Lee

    BMC Bioinformatics 2017 18:319

    Published on: 28 June 2017

  7. Software

    SparkBLAST: scalable BLAST processing using in-memory operations

    The demand for processing ever increasing amounts of genomic data has raised new challenges for the implementation of highly scalable and efficient computational systems. In this paper we propose SparkBLAST, a...

    Marcelo Rodrigo de Castro, Catherine dos Santos Tostes, Alberto M. R. Dávila, Hermes Senger and Fabricio A. B. da Silva

    BMC Bioinformatics 2017 18:318

    Published on: 27 June 2017

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

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