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  1. Methodology article

    MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes

    Tracing stable isotopes, such as 13C using various mass spectrometry (MS) methods provides a valuable information necessary for the study of biochemical processes in cells. However, extracting such information re...

    Vitaly A. Selivanov, Adrián Benito, Anibal Miranda, Esther Aguilar, Ibrahim Halil Polat, Josep J. Centelles, Anusha Jayaraman, Paul W. N. Lee, Silvia Marin and Marta Cascante

    BMC Bioinformatics 2017 18:88

    Published on: 3 February 2017

  2. Methodology article

    Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data

    Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based o...

    Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert D. Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe and Denise M. Scholtens

    BMC Bioinformatics 2017 18:84

    Published on: 2 February 2017

  3. Methodology article

    Metabolomics variable selection and classification in the presence of observations below the detection limit using an extension of ERp

    ERp is a variable selection and classification method for metabolomics data. ERp uses minimized classification error rates, based on data from a control and experimental group, to test the null hypothesis of n...

    Mari van Reenen, Johan A. Westerhuis, Carolus J. Reinecke and J Hendrik Venter

    BMC Bioinformatics 2017 18:83

    Published on: 2 February 2017

  4. Methodology article

    Visualizing phylogenetic tree landscapes

    Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes...

    James C. Wilgenbusch, Wen Huang and Kyle A. Gallivan

    BMC Bioinformatics 2017 18:85

    Published on: 2 February 2017

  5. Research article

    Classifying kinase conformations using a machine learning approach

    Signaling proteins such as protein kinases adopt a diverse array of conformations to respond to regulatory signals in signaling pathways. Perhaps the most fundamental conformational change of a kinase is the t...

    Daniel Ian McSkimming, Khaled Rasheed and Natarajan Kannan

    BMC Bioinformatics 2017 18:86

    Published on: 2 February 2017

  6. Methodology article

    Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

    Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic p...

    O. Pipek, D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai and D. Szüts

    BMC Bioinformatics 2017 18:73

    Published on: 31 January 2017

  7. Methodology Article

    Disorder recognition in clinical texts using multi-label structured SVM

    Information extraction in clinical texts enables medical workers to find out problems of patients faster as well as makes intelligent diagnosis possible in the future. There has been a lot of work about disord...

    Wutao Lin, Donghong Ji and Yanan Lu

    BMC Bioinformatics 2017 18:75

    Published on: 31 January 2017

  8. Methodology Article

    Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data

    With the increase in the amount of DNA methylation and gene expression data, the epigenetic mechanisms of cancers can be extensively investigate. Available methods integrate the DNA methylation and gene expres...

    Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiaotai Huang and Wanxin Tang

    BMC Bioinformatics 2017 18:72

    Published on: 31 January 2017

  9. Software

    GSAR: Bioconductor package for Gene Set analysis in R

    Gene set analysis (in a form of functionally related genes or pathways) has become the method of choice for analyzing omics data in general and gene expression data in particular. There are many statistical me...

    Yasir Rahmatallah, Boris Zybailov, Frank Emmert-Streib and Galina Glazko

    BMC Bioinformatics 2017 18:61

    Published on: 24 January 2017

  10. Research Article

    A systematic comparative evaluation of biclustering techniques

    Biclustering techniques are capable of simultaneously clustering rows and columns of a data matrix. These techniques became very popular for the analysis of gene expression data, since a gene can take part of ...

    Victor A. Padilha and Ricardo J. G. B. Campello

    BMC Bioinformatics 2017 18:55

    Published on: 23 January 2017

  11. Research article

    Dynamic substrate preferences predict metabolic properties of a simple microbial consortium

    Mixed cultures of different microbial species are increasingly being used to carry out a specific biochemical function in lieu of engineering a single microbe to do the same task. However, knowing how differen...

    Onur Erbilgin, Benjamin P. Bowen, Suzanne M. Kosina, Stefan Jenkins, Rebecca K. Lau and Trent R. Northen

    BMC Bioinformatics 2017 18:57

    Published on: 23 January 2017

  12. Methodology Article

    Eigen-Epistasis for detecting gene-gene interactions

    A large amount of research has been devoted to the detection and investigation of epistatic interactions in genome-wide association studies (GWASs). Most of the literature focuses on low-order interactions bet...

    Virginie Stanislas, Cyril Dalmasso and Christophe Ambroise

    BMC Bioinformatics 2017 18:54

    Published on: 23 January 2017

  13. Software

    RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation

    RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of...

    Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang and Qin Ma

    BMC Bioinformatics 2017 18:51

    Published on: 21 January 2017

  14. Methodology Article

    Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy

    The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic mod...

    David R. Penas, Patricia González, Jose A. Egea, Ramón Doallo and Julio R. Banga

    BMC Bioinformatics 2017 18:52

    Published on: 21 January 2017

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