Results and data

This section incorporates novel results, useful tools, and methods using bioinformatics in new ways, including but not limited to: biological conclusions that are only supported by bioinformatics analyses.

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  1. Software

    chngpt: threshold regression model estimation and inference

    Threshold regression models are a diverse set of non-regular regression models that all depend on change points or thresholds. They provide a simple but elegant and interpretable way to model certain kinds of ...

    Youyi Fong, Ying Huang, Peter B. Gilbert and Sallie R. Permar

    BMC Bioinformatics 2017 18:454

    Published on: 16 October 2017

  2. Database

    LiverWiki: a wiki-based database for human liver

    Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. Howe...

    Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao and Yunping Zhu

    BMC Bioinformatics 2017 18:452

    Published on: 13 October 2017

  3. Research Article

    An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome

    Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of ...

    Michael Ferlaino, Mark F. Rogers, Hashem A. Shihab, Matthew Mort, David N. Cooper, Tom R. Gaunt and Colin Campbell

    BMC Bioinformatics 2017 18:442

    Published on: 6 October 2017

  4. Database

    RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement

    Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to de...

    Maninder Sandhu, V. Sureshkumar, Chandra Prakash, Rekha Dixit, Amolkumar U. Solanke, Tilak Raj Sharma, Trilochan Mohapatra and Amitha Mithra S. V.

    BMC Bioinformatics 2017 18:432

    Published on: 30 September 2017

  5. Software

    pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms

    Genome-wide association studies allow us to understand the genetics of complex diseases. Human metabolism provides information about the disease-causing mechanisms, so it is usual to investigate the associatio...

    Sophie Molnos, Clemens Baumbach, Simone Wahl, Martina Müller-Nurasyid, Konstantin Strauch, Rui Wang-Sattler, Melanie Waldenberger, Thomas Meitinger, Jerzy Adamski, Gabi Kastenmüller, Karsten Suhre, Annette Peters, Harald Grallert, Fabian J. Theis and Christian Gieger

    BMC Bioinformatics 2017 18:429

    Published on: 29 September 2017

  6. Software

    High-throughput PCR assay design for targeted resequencing using primerXL

    Although the sequencing landscape is rapidly evolving and sequencing costs are continuously decreasing, whole genome sequencing is still too expensive for use on a routine basis. Targeted resequencing of only ...

    Steve Lefever, Filip Pattyn, Bram De Wilde, Frauke Coppieters, Sarah De Keulenaer, Jan Hellemans and Jo Vandesompele

    BMC Bioinformatics 2017 18:400

    Published on: 6 September 2017

  7. Methodology Article

    A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support

    Probabilistic assessments of clinical care are essential for quality care. Yet, machine learning, which supports this care process has been limited to categorical results. To maximize its usefulness, it is imp...

    Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram and John Pestian

    BMC Bioinformatics 2017 18:361

    Published on: 7 August 2017

  8. 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

  9. Research Article

    Learning rule sets from survival data

    Survival analysis is an important element of reasoning from data. Applied in a number of fields, it has become particularly useful in medicine to estimate the survival rate of patients on the basis of their co...

    Łukasz Wróbel, Adam Gudyś and Marek Sikora

    BMC Bioinformatics 2017 18:285

    Published on: 30 May 2017

  10. Research Article

    On the association analysis of CNV data: a fast and robust family-based association method

    Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical m...

    Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C. Elston, Bong-Jo Kim and Sungho Won

    BMC Bioinformatics 2017 18:217

    Published on: 18 April 2017

  11. Research article

    Comparison of different cell type correction methods for genome-scale epigenetics studies

    Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular h...

    Akhilesh Kaushal, Hongmei Zhang, Wilfried J. J. Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith and Shu-Li Wang

    BMC Bioinformatics 2017 18:216

    Published on: 14 April 2017

  12. Database

    DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins

    Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding ...

    Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou and Ji-Hua Wang

    BMC Bioinformatics 2017 18:206

    Published on: 5 April 2017

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